SARS-CoV-2 and COVID-19 (27...)

Santa gifted us with Aranet CO2 monitor, which we're finding most useful to control air quality, hopefully minimizing virus, on a car trip (vehicle interior, motel, rented house, etc.) Others post CO2 results for museums, arenas, gyms, schools, etc. on Twitter. Below Aranet offers a way for public and commercial establishments to reassure patrons that one is managing air quality to be topnotch.

Aranet Public CO2 Monitor for Indoor Spaces
11 Jan, 2022

Want to reassure your clients that your indoor venue is safe to visit?

Introducing Aranet Public CO2 Monitor – a public URL that lets you share air quality information directly with anyone interested in visiting your premises. Whether it’s a café, restaurant, supermarket, gym, or some other indoor space, Aranet Public CO2 Monitor allows you to show that the air quality inside your venue is optimal and the risk of COVID-19 is reduced.

How does it work? Once you’ve set up your Aranet ecosystem, simply create an Aranet Public CO2 Monitor link. Through this URL, clients can check the real-time CO2 levels in your venue and view data from the past 24 hours...

You can also use this link to display real-time CO2 level on your monitors so that your customers can see it when entering the place or while spending time there...

https://aranet.com/aranet-public-co2-monitor-for-indoor-spaces/

Omicron: sore throats!

Eric Topol (Scripps) @EricTopol | 11:38 AM · Jan 14, 2022
Much less loss of smell and taste with Omicron, but more sore throat than with Delta
https://assets.publishing.service.gov.uk/government/uploads/system/uploads/attac...
@UKHSA symptom data from ~175,000 Omicron and ~88,000 Delta cases

https://twitter.com/EricTopol/status/1482029245580808192/photo/1

CDC on masks + Topol edit:

Eric Topol @EricTopol | 9:36 AM · Jan 15, 2022:
Needed a little editing @CDCgov
Image ( https://twitter.com/EricTopol/status/1482360950887911424/photo/1 )

Eric (Scripps) Topol: Omicron is not "milder" for so many people—the unvaccinated, the vaccinated but waned, and especially the immunocompromised, more than 7 million Americans who get left out and lack of respect

Omicron Isn’t Milder for Everyone, Like Our Patients
Jan. 13, 2022 | Dorry Segev and William Werbel

Dr. Segev and Dr. Werbel are researchers who treat transplant recipients at Johns Hopkins University School of Medicine. They are studying Covid-19 vaccine responses in immunocompromised people.

https://www.nytimes.com/2022/01/13/opinion/omicron-immunocompromised.html

Eric Topol (Scripps) @EricTopol
Just published @NatureMedicine
Extraordinary protection of pregnant mothers and their babies with vaccination.
91% of hospital admissions,
98% ICUs,
77% of infections among unvaccinated in Scotland

Fig 4.d. ( https://twitter.com/EricTopol/status/1481661789943177216/photo/1 )
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Sarah J. Stock et al. 2021. SARS-CoV-2 infection and COVID-19 vaccination rates in pregnant women in Scotland.
Nature Medicine (13 Jan 2022) https://nature.com/articles/s41591-021-01666-2

Abstract
Population-level data on COVID-19 vaccine uptake in pregnancy and SARS-CoV-2 infection outcomes are lacking. We describe COVID-19 vaccine uptake and SARS-CoV-2 infection in pregnant women in Scotland, using whole-population data from a national, prospective cohort. Between the start of a COVID-19 vaccine program in Scotland, on 8 December 2020 and 31 October 2021, 25,917 COVID-19 vaccinations were given to 18,457 pregnant women. Vaccine coverage was substantially lower in pregnant women than in the general female population of 18−44 years; 32.3% of women giving birth in October 2021 had two doses of vaccine compared to 77.4% in all women. The extended perinatal mortality rate for women who gave birth within 28 d of a COVID-19 diagnosis was 22.6 per 1,000 births ...; pandemic background rate 5.6 per 1,000 births; 452 out of 80,456;...). Overall, 77.4% (3,833 out of 4,950; ...) of SARS-CoV-2 infections, 90.9% (748 out of 823; ...) of SARS-CoV-2 associated with hospital admission and 98% (102 out of 104; ...7) of SARS-CoV-2 associated with critical care admission, as well as all baby deaths, occurred in pregnant women who were unvaccinated at the time of COVID-19 diagnosis. Addressing low vaccine uptake rates in pregnant women is imperative to protect the health of women and babies in the ongoing pandemic.

...Of the 2,364 total births, 11 were stillbirths (deaths in utero  24 weeks or more gestation) and eight live births resulted in neonatal deaths (death within 28 d of birth), giving an extended perinatal mortality rate of 8.0 per 1,000 births following SARS-CoV-2 infection at any point in pregnancy (19 out of 2,364; 95% CI 5.0−12.8). Ten of the stillbirths and four neonatal deaths occurred in babies born within 28 d of the onset of maternal infection, giving an extended perinatal mortality rate of 22.6 per 1,000 births (14 out of 620, 95% 12.9−38.5) in this population. All perinatal deaths following SARS-CoV-2 infection in pregnancy occurred in women who were unvaccinated at the time of SARS-CoV-2 infection. We do not have access to detailed clinical records to assess whether COVID-19 directly or indirectly contributed to the preterm births and deaths seen following maternal infection...

Could COVID be like measles--disrupting subsequent immunity?

Anthony J Leonardi, PhD, MS (T cell immunologist) @fitterhappierAJ | 7:20 PM · Jan 15, 2022:
https://twitter.com/fitterhappierAJ/status/1482508126138032129

hey guys, don't get covid or long covid, with it's missing t cell subset.
And for christssake, dont give this to kids to build their immunity, you idiots…

------------------------------------------------------
Above is further to inadvertent post in COVID-19 thread:

"These observations describe an abnormal immune profile in patients with COVID-19 at extended time points after infection and provide clear support for the existence of a syndrome of Long Covid (LC)."

"Patients with Long Covid...lacked naive T and B cells"
Implications for reinfection etc. informally discussed at https://twitter.com/fitterhappierAJ/status/1481721174921039880
---------------------------------------

Chansavath Phetsouphanh et al. 2021. Immunological dysfunction persists for 8 months following initial mild-to-moderate SARS-CoV-2 infection (Letter). Nature Immunology (13 Jan 2022) https://www.nature.com/articles/s41590-021-01113-x?s=09

Abstract
A proportion of patients surviving acute coronavirus disease 2019 (COVID-19) infection develop post-acute COVID syndrome (long COVID (LC)) lasting longer than 12 weeks. Here, we studied individuals with LC compared to age- and gender-matched recovered individuals without LC, unexposed donors and individuals infected with other coronaviruses. Patients with LC had highly activated innate immune cells, lacked naive T and B cells and showed elevated expression of type I IFN (IFN-β) and type III IFN (IFN-λ1) that remained persistently high at 8 months after infection. Using a log-linear classification model, we defined an optimal set of analytes that had the strongest association with LC among the 28 analytes measured. Combinations of the inflammatory mediators IFN-β, PTX3, IFN-γ, IFN-λ2/3 and IL-6 associated with LC with 78.5–81.6% accuracy. This work defines immunological parameters associated with LC and suggests future opportunities for prevention and treatment.

...In summary, our data indicate an ongoing, sustained inflammatory response following even mild-to-moderate acute COVID-19, which is not found following prevalent coronavirus infection. The drivers of this activation require further investigation, but possibilities include persistence of antigen, autoimmunity driven by antigenic cross-reactivity or a reflection of damage repair. These observations describe an abnormal immune profile in patients with COVID-19 at extended time points after infection and provide clear support for the existence of a syndrome of LC. Our observations provide an important foundation for understanding the pathophysiology of this syndrome and potential therapeutic avenues for intervention.

The Omicron Whirlwind: A Conversation with Eric Topol - The Current and Future State of the Pandemic
(59:35--intros thru 7:00)
UCSF Department of Medicine | Jan 13, 2022

Eric Topol is a world-renowned cardiologist and geneticist, bestselling author, editor-in-chief of Medscape (and a graduate of the UCSF Medicine residency program). Since the Covid pandemic began, his Twitter feed has been an essential resource for his nearly 600,000 followers to watch and understand the emerging literature. In this session, Topol and Bob Wachter will discuss the implications of the current surge, what we can learn from other countries, the efficacy of vaccines and medications, isolation policies, and the prospects for the future...

https://www.youtube.com/watch?v=lCAvFHd3B38

zeynep tufekci (UNC) zeynep | 6:56 PM · Jan 15, 2022:
*Amazing* detailed data on 3rd shots and vaccines from Alberta. Essentially:
“The hospitalization rate among 3x-vaccinated 80+ year olds is lower than the hospitalization rate among unvaccinated 12-29-year-olds.” Incredible. Wow...

Table: https://twitter.com/zeynep/status/1482501951065661440/photo/1

COVID-19 Alberta statistics
Interactive aggregate data on COVID-19 cases in Alberta
https://alberta.ca/stats/covid-19-alberta-statistics.htm#vaccine-outcomes
--------------------------------------------

Dina D. Pomeranz (Econ Harvard) @DinaPomeranz | 8:35 PM · Jan 15, 2022:
Data from Alberta, Canada:
Hospitalization rate among 3x-vaccinated 80+ year olds is lower than the hospitalization rate among unvaccinated 12-29 year olds.

Hospitalization rate of unvaccinated 80+ year olds is 175 times higher!

Kashif Pirzada, MD, (emergency physician in Toronto) liked following tweet...
Pediatric Nursey @pediatricnursey | 6:38 PM · Jan 16, 2022:
https://twitter.com/pediatricnursey/status/1482859953979367427

COVID is EVERYWHERE in our children’s hospital. These kids are SICK.
Also fun fact: we’re seeing a lot of young kids with bradycardia, junction(al) rhythms and heart blocks.
Like 0-6 month olds with heart rates in the 50-60s.

How to set up an emergency isolation room inside a home or apartment for a suspected infected occupant.
Robert Bean, ASHRAE Fellow & Distinguished Lecturer | 2021

Figure 1. Home-based isolation bedroom with attached bathroom.
Figure 2. Home-based isolation bedroom with attached bathroom.
Figure 3. Home-based isolation bedroom with attached bathroom.
Figure 4. Home-based isolation bedroom with attached bathroom.
Figure 5. Home-based isolation bedroom WITHOUT attached bathroom.
Figure 6. Home-based isolation bedroom sharing a common bathroom with a non-isolated bedroom.
Figure 7. As above in Figure 6 but shown set up for bathroom access to non quarantined person.
Figure 8. Examples from the authors inventory of DIY filter/fan assemblies, instruments and humidifiers. All the components are available online.

http://www.healthyheating.com/2021.COVID.Residential.Isolation.Rooms/2021.Reside...

Merlin Davies et al. 2021. Persistence of clinically relevant levels of SARS-CoV2 envelope gene subgenomic RNAs in non-immunocompromised individuals. International Journal of Infectious Diseases, Available online 7 December 2021. In Press, Corrected Proof. https://doi.org/10.1016/j.ijid.2021.12.312 https://www.sciencedirect.com/science/article/pii/S1201971221012066

Highlights
• SARS-CoV-2 activity is difficult to assess with conventional PCR assays.
• Subgenomic RNA (sgRNA) may be a better proxy for infectivity.
• Over 10% of COVID-19 patients were sgRNA positive beyond a 10-day period.
• Long-duration sgRNA-positive patients were clinically unremarkable.
• Vulnerable settings may require additional measures to minimize transmission.

Abstract
...Conclusions
Our results suggest that potentially active virus can sometimes persist beyond a 10-day period, and could pose a potential risk of onward transmission. Where this would pose a serious public health threat, additional mitigation strategies may be necessary to reduce the risk of secondary cases in vulnerable settings.

A genetic analysis hints at why COVID-19 can mess with smell
People with variants near smell-related genes may have a higher risk of losing smell or taste
Erin Garcia de Jesús | Jan 17, 2022

...A study of nearly 70,000 adults with COVID-19 found that individuals with certain genetic tweaks on chromosome 4 were 11 percent more likely to lose the ability to smell or taste than people without the changes, researchers report January 17 in Nature Genetics. The data come from people who’d had their DNA analyzed by genetic testing company 23andMe and self-reported a case of COVID-19...

https://www.sciencenews.org/article/covid-coronavirus-smell-taste-gene-genetic
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J.F. Shelton et al. The UGT2A1/UGT2A2 locus is associated with COVID-19-related loss of smell or taste. Nature Genetics. Published online January 17, 2022. doi: 10.1038/s41588-021-00986-w https://www.nature.com/articles/s41588-021-00986-w

Abstract
Using online surveys, we collected data regarding COVID-19-related loss of smell or taste from 69,841 individuals. We performed a multi-ancestry genome-wide association study and identified a genome-wide significant locus in the vicinity of the UGT2A1 and UGT2A2 genes. Both genes are expressed in the olfactory epithelium and play a role in metabolizing odorants. These findings provide a genetic link to the biological mechanisms underlying COVID-19-related loss of smell or taste.

US:
Free at-⁠home COVID-⁠19 tests

Every home in the U.S. can soon order #44 free at-⁠home COVID-⁠19 tests. The tests will be completely free—there are no shipping costs and you don’t need to enter a credit card number.

Ordering begins January 19.

https://www.covidtests.gov/

Fourth vaccine dose boosts antibodies, researchers say, but likely not enough to prevent Omicron breakthrough infections
Jacqueline Howard | January 18, 2022

...preliminary... (Dr. Gili Regev-Yochay, director of the Infection Prevention and Control Unit at Sheba Medical Center) said that although the researchers saw an increase in antibodies among those who got fourth doses, the level of antibodies needed to protect against infection from Omicron "is probably too high for the vaccine, even if it's a good vaccine." Still, she said that slightly fewer infections were observed among those who got the vaccine, compared with the control group.

There was no significant difference among those who received the Pfizer/BioNTech dose versus Moderna, Regev-Yochay added...

https://www.cnn.com/2022/01/17/health/israel-fourth-dose-early-data/index.html

Le Guide pour la priorisation et la gestion des hospitalisations en courte durée en contexte de pandémie de COVID-19, daté du 12 janvier, prévoit quatre axes d'actions.

Ne plus mettre tous les efforts pour empêcher l'intrusion du virus à l'hôpital et accepter les risques.
Freiner les entrées de patients et accélérer les sorties de l'hôpital.
Les familles appelées à contribuer aux soins à l'hôpital ou en dehors.
Redéfinir la qualité minimale des soins.

(Google translate)

The Guide for the prioritization and management of short-term hospitalizations in the context of the COVID-19 pandemic, dated January 12, provides for four areas of action.

No longer make every effort to prevent the intrusion of the virus into the hospital and accept the risks.
Slowing down patient entries and accelerating hospital discharges.
Families called upon to contribute to care in or outside the hospital.
Redefining the minimum quality of care.
------------------------------------------------------------

https://ici.radio-canada.ca/nouvelle/1854928/delestage-guide-priorisation-hospit...

Eric Topol (Scripps) @EricTopol | 10:06 AM · Jan 18, 2022:
Omicron cases turnaround in some US states with low vaccination rates (52-55%) is a good sign
Graphs, # cases July-Jan 17, 2022, KY MS GA ( https://twitter.com/EricTopol/status/1483455755051315205/photo/1 )

Eric Topol. 2021. It’s not too late (editorial). Science • 18 Jan 2022 • First Release • DOI: 10.1126/science.abo1074 https://www.science.org/doi/10.1126/science.abo1074

... Department of Health and Human Services (HHS), led by Secretary Xavier Becerra...should be mediating (FDA, NIH, CDC, WH) conflicts, with the goal of a single, consistent, and unified public message. That, along with data that justify government decisions, would promote clarity and trust...

(highlighted editorial) https://twitter.com/EricTopol/status/1483461129867255818/photo/1

Bet years from now, the Chinese Communists' worst headaches will be people who had their hamsters torn away from them in 2022?

Hong Kong will cull thousands of hamsters after Covid cases in a pet shop.
Austin Ramzy | Jan. 18, 2022,

Two people and at least 11 hamsters connected to the Little Boss pet shop in Hong Kong tested positive for Covid...

...two shipments of hamsters from the Netherlands were particularly worrying...

...All hamsters at the city’s 34 licensed shops will be seized for testing and then culled, officials said. Anyone who bought a hamster after Dec. 22 is asked to surrender the animal to be tested and euthanized...

https://www.nytimes.com/2022/01/18/world/asia/covid-hong-kong-hamsters.html

Eric Topol (Scripps) @EricTopol | 12:34 PM · Jan 17, 2022:
Canada's Omicron wave U-turn
Graph # cases US and Canada Mar 2020-Jan 2022
( https://twitter.com/EricTopol/status/1483130728665677825/photo/1 )

Discussion (age groups, testing) at https://twitter.com/DFisman/status/1483132461441761283

Possible Achilles’ Heel Discovered for Respiratory Viruses – Like COVID-19 – That Hijack Immune Mechanisms

...Like other respiratory viruses, including the COVID-19-causing SARS-CoV-2 virus, RSV infects the lung cells responsible for exchanging gases and uses them as factories to make more viruses. Uncontrollable virus multiplication in these cells leads to their destruction and manifestation of severe inflammation; lung diseases like pneumonia; and sometimes death.

...viral NS2 protein as a key regulator of autophagy, a cellular process that modulates immune defense during virus infection. Autophagy is mediated by a cellular protein known as Beclin1.

When (RSV) virus enters the cell, Beclin1 can recognize and clear the threat from the cell. It does this by attaching to certain smaller gene proteins through a process known as ISGylation. It is almost like Beclin1 is putting on a suit of armor, (Kim Chiok, a WSU post-doctoral researcher who led the study) said.

The study showed that RSV’s NS2 protein removes this “armor” from Beclin1 which allows the virus to persist and replicate within the cell, spreading to other cells and causing damage that initiates an exaggerated inflammatory response from the body that culminates in airway diseases like pneumonia. Without the NS2 protein, the virus is routinely destroyed by Beclin1.

“In a way you are disabling NS2’s ability to modulate the cell’s immune defense mechanism,” Chiok said. “You can use therapeutics to target that protein, and potentially transfer this concept to other respiratory viruses like influenza A virus and SARS-CoV-2.”

https://scitechdaily.com/possible-achilles-heel-discovered-for-respiratory-virus...
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Kim Chiok et al. 2022. Human respiratory syncytial virus NS2 protein induces autophagy by modulating Beclin1 protein stabilization and ISGylation. 18 January 2022, mBio. DOI: 10.1128/mbio.03528-21 https://journals.asm.org/doi/full/10.1128/mbio.03528-21

Eric Topol @EricTopol | 9:34 AM · Jan 18, 2022
"Omicron infection enhances preexisting immunity elicited by vaccines, but on its own may not induce broad, cross-neutralizing humoral immunity in unvaccinated individuals."

Implications re: immunity wall built from Omicron infections alone
Image ( https://twitter.com/EricTopol/status/1483447774293237761/photo/1 )
-----------------------------------------------
Rahul K Suryawanshi et al. 2022. Limited cross-variant immunity after infection with the SARS-CoV-2 Omicron variant without vaccination. MedRxiv Jan 17, 2022. doi: https://doi.org/10.1101/2022.01.13.22269243 https://medrxiv.org/content/10.1101/2022.01.13.22269243v1

This article is a preprint and has not been certified by peer review.

Abstract
SARS-CoV-2 Delta and Omicron strains are the most globally relevant variants of concern (VOCs). While individuals infected with Delta are at risk to develop severe lung disease, Omicron infection causes less severe disease, mostly upper respiratory symptoms. The question arises whether rampant spread of Omicron could lead to mass immunization, accelerating the end of the pandemic. Here we show that infection with Delta, but not Omicron, induces broad immunity in mice. While sera from Omicron-infected mice only neutralize Omicron, sera from Delta-infected mice are broadly effective against Delta and other VOCs, including Omicron. This is not observed with the WA1 ancestral strain, although both WA1 and Delta elicited a highly pro-inflammatory cytokine response and replicated to similar titers in the respiratory tracts and lungs of infected mice as well as in human airway organoids. Pulmonary viral replication, pro-inflammatory cytokine expression, and overall disease progression are markedly reduced with Omicron infection. Analysis of human sera from Omicron and Delta breakthrough cases reveals effective cross-variant neutralization induced by both viruses in vaccinated individuals. Together, our results indicate that Omicron infection enhances preexisting immunity elicited by vaccines, but on its own may not induce broad, cross-neutralizing humoral immunity in unvaccinated individuals.

>21 margd: Universal vaxx imp. to stop the variant roller coaster...

Khadija Khan...Alex Sigal. 2022. Omicron infection of vaccinated individuals enhances neutralizing immunity
against the Delta variant. Ms being submitted to MedRxiv. 14 p. https://secureservercdn.net/50.62.198.70/1mx.c5c.myftpupload.com/wp-content/uplo...

...In vaccinated participants (recovering from Omicron), neutralization of Omicron increased 13.7-fold over baseline. This compared to a 4.4-fold increase in unvaccinated individuals. Over the same period, Delta virus neutralization was enhanced 6.6-fold in vaccinated but only 2.5-fold in unvaccinated participants. Moreover, vaccinated participants were able to mount a stronger neutralization response against Delta relative to Omicron virus. This was not the case in unvaccinated individuals, some of whom continued to show low Delta neutralization, and contrasted sharply with poor cross-neutralization of Omicron in Delta infected persons. Higher Omicron neutralization in vaccinated individuals may enable a more effective immune response to Omicron, while enhancement of Delta neutralization should lead to lower Delta re-infections. Given emerging data indicating Omicron is less pathogenic than Delta, such an outcome may have implications in terms of decreasing Covid-19 severe disease.

>22 margd: Universal vaxx imp. to stop the variant roller coaster...

Prof Peter Hotez MD PhD (U TX) @PeterHotez | 8:38 PM · Jan 18, 2022:
Our post omicron world:
1. Omicron goes down
2. It fails to produce herd immunity, durable protection
3. We’ll have 6 mo to vaccinate the world & prevent a new variant from emerging this summer
4. It may not resemble omicron
5. Vaccinating world in next 6 months = our best path

3M says its masks (elastics, nose foam, etc.) "expire" after 5 years. No sense leaving them to expire (as happened last year with ventilators in national stockpile) when they can be doing some good now...

Biden plans giveaway of 400M masks as Omicron surges
DAVID LIM and ADAM CANCRYN | 01/18/2022

The federal government has 737 million N95 masks in the Strategic National Stockpile sourced from 12 domestic manufacturers.

...The administration plans to make the masks available at tens of thousands of pharmacies and health centers by early February, the White House official said, which people will then be able to pick up for free.

...The supply will not include child-sized masks, though two people with knowledge of the matter said the government is working to procure them...

https://www.politico.com/news/2022/01/18/biden-free-masks-omicron-surge-527335

After Omicron, This Pandemic Will Be Different
William Hanage (researcher, evolution and epidemiology of infectious diseases, Harvard T.H. Chan School of Public Health.) | Jan. 19, 2022

...No one should confidently assert that Omicron signals the end of the pandemic, but we should be confident that future surges of infections, whether with Omicron or whatever variant comes next, will make fewer of us seriously ill than they would have before. That’s not to say that the rate of serious illness is the only measure that matters. There hasn’t been enough time to determine Omicron’s contribution to long Covid, for example. And the havoc that Omicron has sown is not trivial — we are seeing the effects in overwhelmed hospitals and closed schools.

Much better days may be ahead. But as the world has learned over the past two years, only fools with short memories make promises in a pandemic.

https://www.nytimes.com/2022/01/19/opinion/omicron-covid-surge.html

Study reports of receptor-binding domain (RBD) multimer capable of enhancing the immune response against SARS-CoV-2
Sam Hancock | Jan 19 2022

...The conclusion
The authors highlight that they successfully combined the RBD antigen produced in a eukaryote (cell w nucleus) with the BLS (Brucella abortus) carrier expressed from E. coli. As well as this, the pseudovirus neutralization assay and immunization results suggest that RBD-BLS HM (higher multiplicities) could be a very strong candidate for inducing neutralizing antibodies and could potentially be used in vaccine research in future.

https://www.news-medical.net/news/20220119/Study-reports-of-receptor-binding-dom...
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Berguer, P. et al. (2022) "Covalent coupling of Spike’s receptor binding domain to a multimeric carrier produces a high immune response against SARS-CoV-2", Scientific Reports, 12(1). doi: 10.1038/s41598-021-03675-0. https://www.nature.com/articles/s41598-021-03675-0

Abstract
The receptor binding domain (RBD) of the Spike protein from SARS-CoV-2 is a promising candidate to develop effective COVID-19 vaccines since it can induce potent neutralizing antibodies. We have previously reported the highly efficient production of RBD in Pichia pastoris, which is structurally similar to the same protein produced in mammalian HEK-293T cells. In this work we designed an RBD multimer with the purpose of increasing its immunogenicity. We produced multimeric particles by a transpeptidation reaction between RBD expressed in P. pastoris and Lumazine Synthase from Brucella abortus (BLS), which is a highly immunogenic and very stable decameric 170 kDa protein. Such particles were used to vaccinate mice with two doses 30 days apart. When the particles ratio of RBD to BLS units was high (6–7 RBD molecules per BLS decamer in average), the humoral immune response was significantly higher than that elicited by RBD alone or by RBD-BLS particles with a lower RBD to BLS ratio (1–2 RBD molecules per BLS decamer). Remarkably, multimeric particles with a high number of RBD copies elicited a high titer of neutralizing IgGs. These results indicate that multimeric particles composed of RBD covalent coupled to BLS possess an advantageous architecture for antigen presentation to the immune system, and therefore enhancing RBD immunogenicity. Thus, multimeric RBD-BLS particles are promising candidates for a protein-based vaccine.

Constanze Kuhlmann et al. 2022. Breakthrough infections with SARS-CoV-2 omicron despite mRNA vaccine booster dose (Correspondence). The Lancet Published:January 18, 2022. DOI:https://doi.org/10.1016/S0140-6736(22)00090-3 https://www.thelancet.com/journals/lancet/article/PIIS0140-6736(22)00090-3/fullt...

...In-vitro data suggest lower titres of neutralising antibodies against omicron compared to other SARS-CoV-2 lineages following BNT162b2 vaccination but increased titres after a third dose...supporting calls for booster doses while the omicron variant appears to be spreading globally. Our study, however, demonstrates insufficient prevention of symptomatic infection in otherwise healthy individuals who had received three doses of COVID-19 mRNA vaccines.

These findings support the need for updated vaccines to provide better protection against symptomatic infection with omicron...and emphasise that non-pharmaceutical measures should be maintained. Encouragingly, early data from South Africa suggest maintained if reduced effectiveness of the BNT162b2 vaccine against hospital admission.1

Eric Topol (Scripps) @EricTopol | 9:55 AM · Jan 19, 2022
Parents, please take note of this important finding on 90% vaccine protection vs MIS-C below.
And good to see new data that the recovery of heart function for MIS-C is fairly rapid in most children when this dreaded outcome occurs *
Graphs--cardiac outcomes MIS-C (https://twitter.com/EricTopol/status/1483815319869145089/photo/1)

Quote Tweet
David Fisman (U Toronto) @DFisman· 14h
A single dose of covid vaccine reduces risk of multisystem inflammatory syndrome by more than 90%. No kids with two doses of vaccine had MIS-C. Please vaccinate your children. **

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* Daisuke Matsubara et al. 2022. Longitudinal Assessment of Cardiac Outcomes of Multisystem Inflammatory Syndrome in Children Associated With COVID‐19 Infections. Journal of the American Heart Association. https://doi.org/10.1161/JAHA.121.023251 https://ahajournals.org/doi/epub/10.1161/JAHA.121.023251

Preprint

ABSTRACT
...Conclusions
Our short‐term study suggests that functional recovery and coronary outcomes are good in multisystem inflammatory syndrome in children. Use of sensitive deformation parameters provides further reassurance that there is no persistent subclinical dysfunction after 3 months...

----------------------------------------------------
** Michael Levy et al. 2022. Multisystem Inflammatory Syndrome in Children by COVID-19 Vaccination Status of Adolescents in France. JAMA. 2022;327(3):281-283. doi:10.1001/jama.2021.23262 https://jamanetwork.com/journals/jama/fullarticle/2787495

...Discussion
Most adolescents with MIS-C for whom vaccination was indicated in France had not been vaccinated. These results suggest that COVID-19 mRNA vaccination was associated with a lower incidence of MIS-C in adolescents. The median of 25 days between single vaccine injection and MIS-C onset compared with a mean 28-day delay between SARS-CoV-2 infection and MIS-C onset...suggests that, in most cases, SARS-CoV-2 infection occurred before or shortly after the vaccine injection, when immune response was incomplete. The absence of MIS-C cases in fully vaccinated children prevented calculation of an HR for this group but suggests that 2 doses are warranted for efficient protection. The study had limitations, including the low number of patients, use of national data to calculate HRs without considering regional variations, and inability to control for individual risks of MIS-C, such as sex, race and ethnicity, and comorbidities...

The association between mRNA vaccination with MIS-C in younger children should be evaluated as vaccines are approved for use in children aged 5 to 11 years. Close monitoring is required given the alert on myocarditis occurring in adolescents after COVID-19 mRNA vaccine...

>23 margd: Strongly agree and given the past 2 years, that we suddenly wake up and do this in a serious fashion seems sadly unlikely

>25 margd: When I read this earlier, I had that validating feeling that someone else sees this in a way similar to mine. Then I reminded myself of how unpredictable the pandemic as been both in viral mutation and human response. And I felt the need to say something like he did: “only fools with short memories make promises in a pandemic.”

Which makes one wonder how seriously to take the whole optimistic attitude. But life hasn’t yet beat it out of me, so I keep hoping. And I repeat my mantra: “There have been many pandemics in history, and they all end eventually”

>30 stellarexplorer: So-o hopeful that THIS time, Lucy (COVID) won't take the football away when we're about to kick it out of the park! Of course, our vaccine game needs contd. attention: R&D, global programs...

Eric Topol (Scripps)@EricTopol | 7:21 PM · Jan 19, 2022
Omicron posed no match to Paxlovid
A new lab study report of the anti-Covid pill, woefully in less than scarce availability
Graphic, diagram--Paxlovid v. wild type, omicron
( https://twitter.com/EricTopol/status/1483957872551620610/photo/1 )
-------------------------------------------

Samantha E Greasley et al. 2022. Structural basis for Nirmatrelvir in vitro efficacy against the Omicron variant of SARS-CoV-2. BioRxiv Jan 19, 2022. doi: https://doi.org/10.1101/2022.01.17.476556 https://www.biorxiv.org/content/10.1101/2022.01.17.476556v1

This article is a preprint and has not been certified by peer review

Abstract
The COVID-19 pandemic continues to be a public health threat with emerging variants of SARS-CoV-2. Nirmatrelvir (PF-07321332) is a reversible, covalent inhibitor targeting the main protease (Mpro) of SARS-CoV-2 and the active protease inhibitor in PAXLOVID (nirmatrelvir tablets and ritonavir tablets). One of the predominant SARS-CoV-2 variants emerging is the B.1.1.529 Omicron harboring a mutation at amino acid position 132 in the Mpro changing a proline to a histidine (P132H). In vitro biochemical enzymatic assay characterization of the enzyme kinetics of the Omicron Mpro (P132H) demonstrate that it is catalytically comparable to wildtype and that nirmatrelvir has similar potency against both wildtype and Omicron (P132H) Mpro with Ki of 0.933nM (wildtype) and 0.635nM (P132H) each, respectively. This observation is reinforced by our structural determination of nirmatrelvir bound to the omicron Mpro at 1.63Å resolution. These in vitro data suggest that PAXLOVID has the potential to maintain plasma concentrations of nirmatrelvir many-fold times higher than the amount required to stop the SARS-CoV-2 variant Omicron from replicating in cells.

Eric Topol @EricTopol | 5:08 PM · Jan 19, 2022:
The Qatar comparison of 2-shot mRNA vaccines (matched more than 192,000 people) shows superiority of Moderna over Pfizer for less breakthrough infections over time (pre-Omicron). No significant difference in hospitalizations or deaths...
Graph, table--breakthrough pre-omicron infections, Pfizer v Moderna
https://twitter.com/EricTopol/status/1483924381436833793/photo/1

Laith J. Abu-Raddad et al. 2022. Effectiveness of mRNA-1273 and BNT162b2 Vaccines in Qatar (Correspondence). NEJM January 19, 2022. DOI: 10.1056/NEJMc2117933 http://nejm.org/doi/full/10.1056/NEJMc2117933

Strange that Denmark not leading way out of omicron(?)

Eric Topol @EricTopol | 6:26 PM · Jan 19, 2022:
After South Africa, Denmark was one of the first countries hit by Omicron.
There's little sign of any let up, except in ICU patients
Graphs-Cases, hospitalization, ICU, deaths in Denmark Feb 2020-Jan 18, 2022

>34 margd: Yes. But we still have an large supply of people who haven't had Omicron yet and as the number of patients and especially ICU patients doesn't seem to rise much, so we keep schools etc open. At the current rate we _will_ run out of Danes to feed to Omicron, but it'll take a few months.

And meanwhile BA.2 is taking over here:
https://en.ssi.dk/news/news/2022/omicron-variant-ba2-accounts-for-almost-half-of...

so maybe the next variants are coming before Omicron has burned out here.

>35 bnielsen: Uh oh? Thought BA.2 was some minor variant in s France?
_________________________________

Would be good news if Sputnik V outperformed Pfizer against omicron, but given Russia's dis & mis information campaigns, I'll wait for peer review and publication on this one... (Actually maybe bad news? Wouldn't hurt right now for COVID to disable the 100,000 Russian troops on Ukraine border? Not kill them, just render them unable to invade?)

Sputnik V @sputnikvaccine | 6:00 AM · Jan 20, 2022:
2/5 Study, conducted in equal lab conditions in Spallanzani Inst in Italy on comparable sera samples, shows Sputnik V induces 2.1x higher virus neutralizing antibodies titers than 2 doses of #Pfizer jab in total, 2.6x higher 3 months after vaccination
https://medrxiv.org/content/10.1101/2022.01.15.22269335v1*

InViennaVeritas@yousitonmyspot | 7:25 AM · Jan 20, 2022:
Seems in contradiction to
https://biorxiv.org/content/10.1101/2021.12.12.472269v1.full.pdf **
-------------------------------------------

* Daniele Lapa et al. 2022. Retention of Neutralizing response against SARS-CoV-2 Omicron variant in Sputnik V vaccinated individuals. Med Rxiv Jan 19, 2022. doi: https://doi.org/10.1101/2022.01.15.22269335 https://medrxiv.org/content/10.1101/2022.01.15.22269335v1

This article is a preprint and has not been certified by peer review

Abstract
The new variant Omicron (B.1.1.529) of SARS-CoV-2, first identified in November 2021, is rapidly spreading all around the world. The Omicron becomes the dominant variant of SARS-CoV-2. There are many ongoing studies evaluating the effectiveness of existing vaccines. Studies on neutralizing activity of vaccinated sera against Omicron variant are currently being carried out in many laboratories. In this study, we have shown the neutralizing activity of sera against SARS-CoV-2 Omicron (B.1.1.529) variant compared to the reference Wuhan D614G (B.1) variant in individuals vaccinated with 2 doses of Sputnik V or BNT162b2 in different time points up to 6 months after vaccination. We performed analysis on sample pools with comparable NtAb to Wuhan D614G variant. The decrease in neutralizing antibody (NtAb) to the Omicron variant was 8.1 folds for group of Sputnik V-vaccinated and 21.4 folds for group of BNT162b2-vaccinated. Analysis showed that 74.2% of Sputnik V- and 56.9% of BNT162b2-vaccinated sera had detectable NtAb to SARS-CoV-2 Omicron variant. The decrease in NtAb to SARS-CoV-2 Omicron variant compared to Wuhan variant has been shown for many COVID-19 vaccines in use, with some showing no neutralization at all. Today the necessity of third booster vaccination is obvious. And the most effective approach, already shown in several studies, is the use of heterologous booster vaccination pioneered in COVID-19 vaccines by Sputnik V.
------------------------------------------------

** Elisabetta Cameron et al. 2022. Broadly neutralizing antibodies overcome SARS-CoV-2 Omicron
antigenic shift. BioRxiv December 14, 2021. https://doi.org/10.1101/2021.12.12.472269doi:b https://biorxiv.org/content/10.1101/2021.12.12.472269v1.full.pdf . 37 p.

SUMMARY:
The recently emerged SARS-CoV-2 Omicron variant harbors 37 amino acid substitutions in the spike (S) protein, 15 of which are in the receptor-binding domain (RBD), thereby raising concerns about the effectiveness of available vaccines and antibody therapeutics. Here, we show that the Omicron RBD binds to human ACE2 with enhanced affinity relative to the Wuhan-Hu-1 RBD and acquires binding to mouse ACE2. Severe reductions of plasma neutralizing activity were observed against Omicron compared to the ancestral pseudovirus for vaccinated and convalescent individuals. Most (26 out of 29) receptor-binding motif (RBM)-directed monoclonal antibodies (mAbs) lost in vitro neutralizing activity against
Omicron, with only three mAbs, including the ACE2-mimicking S2K146 mAb1, retaining unaltered potency. Furthermore, a fraction of broadly neutralizing sarbecovirus mAbs recognizing antigenic sites outside the RBM, including sotrovimab2, S2X2593 and S2H974, neutralized Omicron. The magnitude of Omicron-mediated immune evasion and the acquisition of binding to mouse ACE2 mark a major SARS-CoV-2 mutational shift. Broadly neutralizing sarbecovirus mAbs recognizing epitopes conserved among SARS-CoV-2 variants and other sarbecoviruses may prove key to controlling the ongoing pandemic and future zoonotic spillovers.

Vincent Rajkumar (Mayo) @VincentRK | 8:28 AM · Jan 20, 2022:
It's a medical miracle how vaccines developed within one year against the wild strain of COVID have maintained 90% efficacy against hospitalizations against an onslaught of variants. https://coronavirus.health.ny.gov/covid-19-breakthrough-data
Graph-hospitalization by vaxx status, omicron, NY https://twitter.com/VincentRK/status/1484155781004070920/photo/1

Risk reduction is how most of medicine works. Few things in medicine work 100%.
Few things work 90%.

You see the same effect in other places as well.
deaths by vaccination status Switzerland ( https://twitter.com/VincentRK/status/1484160254300536837/photo/1 )

Chile has similar data showing the high efficacy of vaccines in preventing deaths in both delta and omicron waves.
( https://twitter.com/VincentRK/status/1484161726723641350/photo/1 )

>35 bnielsen: BA.2 ...
Tom Peacock (virologist, Imperial College) @PeacockFlu | 6:49 AM · Jan 19, 2022:
https://twitter.com/PeacockFlu/status/1483768659420094464
As its been getting increasing attention recently, I'm going to write a short thread on what we currently know about BA.2.
-what is BA.2?
-what is BA.2 doing currently?
-Should we be concerned about it?

First off - what is BA.2?
BA.2 is a sister lineage to BA.1. Currently both lineages are defined as the Omicron variant.
As @shay_fleishon shows - BA.2 shares a lot of mutations with BA.1, but it also has many differences
( https://twitter.com/shay_fleishon/status/1480934070012059649 )

BA.2 also lacks the Spike Δ69-70 mutations that means it does not cause S gene target failure in the taqman qPCR assay. This assay was used early on in the Omicron wave to estimate how rapidly BA.1 spread. This is why BA.2 was misdescribed as a 'stealth variant' early on.

Next what is BA.2 currently doing?
BA.2 appears to be the major Omicron lineage in (part of) India and the Philippines and there is evidence it is growing compared to BA.1 in Denmark, the UK and Germany as shown nicely by @CorneliusRoemer below
( https://twitter.com/CorneliusRoemer/status/1482833651276697612 )

Consist(e)nt growth across multiple countries is evidence BA.2 may be some degree more transmissible than BA.1. This is the main reason BA.2 is currently in the news.

Unfortunately this is really where the evidence mostly ends - we do not currently have a strong handle on antigenicity, severity or a much evidence for how much more transmissibility BA.2 might have over BA.1 - however we can make some guesses/early observations

*Very* early observations from India and Denmark suggest there is no dramatic difference in severity compared to BA.1. This data should become more solid (one way or another) in the coming weeks.

Some predictions by @jbloom_lab suggest the Spike RBD mutations are likely to have a fairly minimal impact on antigenicity compared to BA.1. ( https://twitter.com/jbloom_lab/status/1470442877494824961 )

I would also agree with this that there is likely to be minimal differences in vaccine effectiveness against BA.1 and BA.2 and, its also highly likely BA.1 infection will give decent cross-reactivity against BA.2 infection.

So how worried should we be? Those working in sequencing/surveillence should definitley be keeping a close eye on BA.2 (and very likely already are!). Personally, I'm not sure BA.2 is going to have a substancial impact on the current Omicron wave of the pandemic...

Several countries are near, or even past the peak of BA.1 waves. I would be very surprised if BA.2 caused a second wave at this point. Even with slightly higher transmissibility this absolutely is not a Delta -> Omicron change and instead is likely to be slower and more subtle.

That said I wouldnt be that surprised if BA.2 slowly replaces BA.1 over the coming months with a slightly 'optimised' mutational profile (think a more extreme version of AY.4.2 vs Delta in the UK). That said this is just a prediction and could be quite wrong...

Several folks are closely monitoring the BA.2 situation - for more updates/info, and a range of opinions would recommend following @JosetteSchoenma @shay_fleishon and @CorneliusRoemer who are putting in great work monitoring this variant.

One final post I forgot to add - nearly all literature on Omicron is done using BA.1. Virology labs worldwide are currently scrambling to assess BA.2 (and see if it does the same as BA.1) - I suspect lab data will start appearing in next couple of weeks.

One final TL;DR on BA.2 - mostly we just don't have solid data yet - we can make some educated guesses which *may* turn out to be correct but the coming weeks should make everything a lot clearer.

The numbers from today are 40626 new infections ... 2639 of them had tested positive sometime earlier in the pandemic, but they still count :-)

And +40K on one day is a first. But our hospitals are still okay and all schools, high schools etc are open. If possible, we should work from home, wear masks when in shops etc. But we are kind of used to that by now :-)

17.6% of the tests (PCR-only) were positive, so 40626 is probably way too low.

Nocebo responses explain up to 76% of COVID vaccine side effects
Some vaccine side effects are very real, but many may be anxiety and misattribution.
Beth Mole | 1/19/2022
https://arstechnica.com/science/2022/01/up-to-76-of-covid-vaccine-side-effects-a...
-------------------------------------------

Julia W. Haaset al. 2022. Frequency of Adverse Events in the Placebo Arms of COVID-19 Vaccine TrialsA Systematic Review and Meta-analysis. JAMA Netw Open. Jan 18, 2022;5(1):e2143955. doi:10.1001/jamanetworkopen.2021.43955
https://jamanetwork.com/journals/jamanetworkopen/fullarticle/2788172

Key Points
Question What was the frequency of adverse events (AEs) in the placebo groups of COVID-19 vaccine trials?

Findings In this systematic review and meta-analysis of 12 articles including AE reports for 45 380 trial participants, systemic AEs were experienced by 35% of placebo recipients after the first dose and 32% after the second. Significantly more AEs were reported in the vaccine groups, but AEs in placebo arms (“nocebo responses”) accounted for 76% of systemic AEs after the first COVID-19 vaccine dose and 52% after the second dose.

Meaning This study found that the rate of nocebo responses in placebo arms of COVID-19 vaccine trials was substantial; this finding should be considered in public vaccination programs.

ABSTRACT
...Conclusions and Relevance In this systematic review and meta-analysis, significantly more AEs were reported in vaccine groups compared with placebo groups, but the rates of reported AEs in the placebo arms were still substantial. Public vaccination programs should consider these high rates of AEs in placebo arms.

Patients with and without COVID can share hospital rooms, say new Fraser Health recommendations
Simon Little | January 20, 2022

...The (BC Centre for Disease Control) guidelines go on to say that it is preferable to keep COVID-positive patients in single-occupancy rooms, but that if one is not available they can be placed in a multi-bed room “ensuring at least two metres of space from other beds.”

“Patients on droplet precautions should not share a room with high-risk patients including immunocompromised patients, patients with chronic cardiac or respiratory disease, neonates, and patients with other respiratory illnesses,” the guidelines state.

COVID-19-positive patients are only to be placed with fully-vaccinated roommates, and should have dedicated toileting, the guidelines add...

https://globalnews.ca/news/8527928/covid-positive-negative-patients-shared-hospi...

https://www.mediaite.com/tv/tucker-carlson-excoriates-howard-stern-as-a-covid-co...
Tucker Carlson Excoriates Howard Stern as a Covid ‘Coward’: ‘He’s Declined in this Quivering Mass of Neuroses and Hatred’

***
Dudes and gals who play Russian roulette with their lives and the lives of people in their orbits deserve minimal care. In the post Trump era, anti-government people taking responsibility for their unfortunate actions is no longer a GOP rant theme. All anti-government actions carried out by white people are A-OK.

Tucker unintentionally used words that describe himself perfectly! One can just imagine the type of appalling ideas TC, and his ilk, spoon-fed their children at the dinner table during their formative years.

Natural immunity was more potent than vaccines during US Delta wave — study
But authors of paper warn against depending on infection, given the higher risks of hospitalization, long-term impacts and death
AFP and TOI staff | Jan 21,2022

Prior to Delta becoming dominant, vaccination conferred greater immunity than infection. But the relationship shifted when the variant became predominant in late June and July.

By the week of October 3, vaccinated people who did not have prior COVID were three to four times (in California and New York, respectively) more likely to be infected than unvaccinated people with prior COVID.

In the weeks of October 13 to November 14, vaccinated people who did not have prior COVID in California, were around three times more likely to be hospitalized than unvaccinated people with prior COVID.

Protection was highest among those who had both vaccination and prior COVID.

The study could however be impacted by an effect known as “selection bias,” since it excluded people who died, who were overwhelmingly unvaccinated...

https://www.timesofisrael.com/natural-immunity-was-more-potent-than-vaccines-dur...
--------------------------------
(margd: Following MIGHT be the CDC study (?). I'll post again if better one posted. References to benefits of previous infection in one below is between-the-lines, at best(?))

Johnson AG, Amin AB, Ali AR, et al. COVID-19 Incidence and Death Rates Among Unvaccinated and Fully Vaccinated Adults with and Without Booster Doses During Periods of Delta and Omicron Variant Emergence — 25 U.S. Jurisdictions, April 4–December 25, 2021. MMWR Morb Mortal Wkly Rep. ePub: 21 January 2022. DOI: http://dx.doi.org/10.15585/mmwr.mm7104e2 https://www.cdc.gov/mmwr/volumes/71/wr/mm7104e2.htm?s_cid=mm7104e2_w
_________________________

Herd Immunity a Mirage? High Protection Didn't Stop Surges
Randy Dotinga | January 21, 2022

...72% (69.8% – 74.4%) of the population had antibodies or at least one vaccine dose

Despite these high levels of apparent protection, the Delta surge hit Los Angeles hard starting in July 2021, just 2 months after the study was conducted. "The early notion was that herd immunity was around 70%," (lead author Neeraj Sood, PhD, a professor with the University of Southern California Price School of Public Policy) said. "This is telling us that original estimate was wrong, and herd immunity is probably not achievable."

The Omicron surge has been even more devastating in terms of infection numbers. "This lays to rest the idea that we've got to have herd immunity, and then we're not going to experience future surges," Sood said.

Thomas McDade, PhD, a biological anthropologist at Northwestern University who studies disease, said the study is useful and suggests a high level of community transmission in poorer communities. "Los Angeles County is big and densely packed with a lot of poverty and concentrated disadvantage," he said. "This, in combination with new variants and waning immunity following vaccination and prior infection, laid the groundwork for additional waves of infection."

Still, the high level of protection via antibodies "should afford some level of protection, particularly against severe disease," he said. "However, we know that one vaccine dose does not provide a high level of protection, and prior infection is not a guarantee of protection against future infection, particularly against viral variants like Delta and Omicron. It remains important for people to be up to date with their vaccinations if we want to effectively reduce community spread through population immunity."

https://www.medscape.com/viewarticle/966991
----------------------------------

Neeraj Sood et al. 2022. Seroprevalence of Antibodies Specific to Receptor Binding Domain of SARS-CoV-2 and Vaccination Coverage Among Adults in Los Angeles County, April 2021: The LA Pandemic Surveillance Cohort Study (Research Letter). JAMA Netw Open. Jan 20 2022;5(1):e2144258. doi:10.1001/jamanetworkopen.2021.44258 https://jamanetwork.com/journals/jamanetworkopen/fullarticle/2788249

...Discussion
This study found that in April 2021 approximately 72% of LAC adults had potential protective immunity against SARS-CoV-2. Despite this high level of population immunity and continuing vaccination efforts, LAC experienced a surge in COVID-19 cases in July 2021 suggesting that reaching herd immunity might be more difficult than anticipated,

...Almost all of the unvaccinated individuals with prior infection had RBD antibodies, even though many participants had infections several months prior to antibody testing. This suggests that RBD antibodies were not waning...

Craig Spencer MD MPH (NYC emerg, Columbia Med School, Ebola survivor) @Craig_A_Spencer | 0:56 AM · Jan 21, 2022:

Updated data from NYC’s Omicron surge.
The graphs speak for themselves.
Absolutely stunning.

Cases showing dramatic difference between vaccinated and unvaccinated. https://twitter.com/Craig_A_Spencer/status/1484555496837333002/photo/1
Hospitalizations showing dramatic difference between vaccinated and unvaccinated. https://twitter.com/Craig_A_Spencer/status/1484555496837333002/photo/2
Deaths showing dramatic difference between vaccinated and unvaccinated. https://twitter.com/Craig_A_Spencer/status/1484555496837333002/photo/3

Why most of us should be wearing N95 masks
The short answer: Because they’re the most protective, and they’re finally widely available.
Aaron Steckelberg and Bonnie Berkowitz | 1/20/2022

How N95 masks work
Who should not wear an N95?

https://www.washingtonpost.com/health/2022/01/20/n95-mask-effectiveness/

Eric Topol (Scripps) @EricTopol | 11:59 AM · Jan 21, 2022:
Now there are 3 reports for vaccine effectiveness vs Omicron hospitalization, @UKHSA , @KPSCalResearch and today's @CDCMMWR. They are quite consistent for marked protection of the 3rd shot (booster).

My summary table here
https://twitter.com/EricTopol/status/1484571282393866244/photo/1

Dr. Tom Frieden (frmr CDC director) @DrTomFrieden | 4:21 PM · Jan 21, 2022:
A new CDC study found that a booster dose increases your protection against hospitalization from Covid.
To maintain the highest protection, including against Omicron, stay up-to-date on vaccination.

During Omicron predominance, vaccine efficacy against Covid hospitalization was 81% among adults who had received their second dose less than six months earlier, 57% among those who had received it more than six months earlier, and 90% after a third dose.

TABLE 1. Characteristics of emergency department and urgent care encounters among adults with COVID-19–like illness,* by mRNA COVID-19 vaccination status† and SARS-CoV-2 test result — 10 states, August 2021–January 2022§
https://www.cdc.gov/mmwr/volumes/71/wr/mm7104e3.htm

...

Whew!

BNO Newsroom @BNODesk | 12:26 PM · Jan 21, 2022:
Denmark health institute says no increase in hospitalizations seen for Omicron sub-variant BA.2

How to get your At-Home Over-The-Counter COVID-19 Test for Free
Center for Medicare and Medicaid Services
https://www.cms.gov/how-to-get-your-at-home-OTC-COVID-19-test-for-free

BREAKING: It’s Official!
CDC Director Walensky Says Definition of Fully Vaccinated is Being Changed to Include Covid Booster!
0:29 ( https://twitter.com/nick_moseder/status/1484621251146665991 )

- nick moseder @nick_moseder | 3:17 PM · Jan 21, 2022
---------------------------------------------------------

Based on new CDC data showing if you don't get boosted (after 6 months) the 2 dose mRNA is only 57% protective vs hospitalization, 38% vs ER visits vs omicron, but goes to 90% and 82% respectively post-boost.

Or as I've said for the last yr: it's a 3 dose vaccine, always was.

- Prof Peter Hotez MD PhD @PeterHotez | 4:47 PM · Jan 21, 2022

>48 margd: With the current number of new cases in Denmark I think it should be renamed to omnicron. (Yesterday +46.000 cases, today +36.000 cases.)

>51 bnielsen: Fingers crossed, that's the case... No worse than original omicron sub-variant...
_____________________________________
CDC and twitter MDs flustered by finding yesterday that natural infection provided better protection against infection than vaxx alone against some variants--judging by flurry of graphs, etc. on vaxx v. deaths and serious disease?

Vincent Rajkumar (Mayo) @VincentRK | 2:17 PM · Jan 21, 2022
For the skeptics: Vaccines work all right.
Deaths per 100,000. The top curve is unvaccinated. Bottom lines are vaccinated. @CDCgov

Graph--deaths, vaxx v unvaxxed ( https://twitter.com/VincentRK/status/1484606177103200259/photo/1 )

Johnson AG, Amin AB, Ali AR, et al. COVID-19 Incidence and Death Rates Among Unvaccinated and Fully Vaccinated Adults with and Without Booster Doses During Periods of Delta and Omicron Variant Emergence — 25 U.S. Jurisdictions, April 4–December 25, 2021. MMWR Morb Mortal Wkly Rep. ePub: 21 January 2022. DOI: http://dx.doi.org/10.15585/mmwr.mm7104e2 https://cdc.gov/mmwr/volumes/71/wr/mm7104e2.htm?s_cid=mm7104e2_w#F1_down
-----------------------------------------------------

Vincent Rajkumar @VincentRK | 2:21 PM · Jan 21, 2022
90% efficacy against hospitalizations following booster dose in another study released today.

Thompson MG, Natarajan K, Irving SA, et al. Effectiveness of a Third Dose of mRNA Vaccines Against COVID-19–Associated Emergency Department and Urgent Care Encounters and Hospitalizations Among Adults During Periods of Delta and Omicron Variant Predominance — VISION Network, 10 States, August 2021–January 2022. MMWR Morb Mortal Wkly Rep. ePub: 21 January 2022. DOI: http://dx.doi.org/10.15585/mmwr.mm7104e3external icon
https://www.cdc.gov/mmwr/volumes/71/wr/mm7104e3.htm?s_cid=mm7104e3_w
-------------------------------------------------------

Vincent Rajkumar @VincentRK | 3:08 PM · Jan 21, 2022:
Adds to these data.

Quote Tweet
Vincent Rajkumar @VincentRK · Jan 5
If omicron appears milder, you can thank vaccines for that to a large part. Data from Switzerland. https://ourworldindata.org/covid-deaths-by-vaccination
Graph--deaths by vaxx status, Switzerland ( https://twitter.com/VincentRK/status/1478944588513611777/photo/1 )

Ontario

Clinical Practice Guideline Summary: Recommended Drugs and Biologics in Adult Patients with COVID-19
Ontario COVID-19 Drugs and Biologics Clinical Practice Guidelines Working Group on behalf of the Ontario COVID-19 Science Advisory Table
Version 9.0 | https://doi.org/10.47326/ocsat.cpg.2022.9.0
Published: January 21, 2022

https://covid19-sciencetable.ca/sciencebrief/clinical-practice-guideline-summary...
----------------------------------------------------

A Thread on why Paxlovid is NOT first-line...-
- Andrew Morris (infectious disease MD) @ASPphysician | 8:04 AM · Jan 22, 2022
https://twitter.com/ASPphysician/status/1484874519252721664

(No published paper to review, etc.)

>51 bnielsen: The Groundhog will see his shadow, and our long winter will drag on some more? :(

Brian Hjelle, virologist @hjelle_brian | 3:10 PM · Jan 21, 2022:
Denmark and France both experiencing resurgence of Omicron, presumably BA.2. This will extend epidemic in Europe and soon N America.

Mark Austin @mraustin | 3:40 PM · Jan 21, 2022:
It's interesting to look at
Overview of Variants in Countries
https://covariants.org/per-country .
Denmark V good at sequencing & you can see BA.2 (21L) gaining, not seeing that in France yet.
Growth in Sweden South Africa India some signs in other countries but too few samples.
Just beginning in United Kingdom. Still impressive the numbers that United Kingdom is sequencing.

>54 margd: contd.?
>51 bnielsen: Is Danish translated correctly in second tweet?

Yaneer Bar-Yam (physicist) @yaneerbaryam | 8:55 AM · Jan 22, 2022:
Norway: Omicron sub-variant BA.2, increasing rapidly relative to Omicron BA.1.

Jan 4: 7 cases
Jan 19: 611 cases (mainly in Oslo)

properties unknown other than more contagious than BA.1. Also increasing in Denmark, Sweden.

https://fhi.no/en/publ/2020/weekly-reports-for-coronavirus-og-covid-19/
---------------------------------------------

Yaneer Bar-Yam @yaneerbaryam | 9:00 AM · Jan 22, 2022:
People being reinfected with BA.2 right after having had BA.1

Danish researcher (Infectious Disease Institute SSI) spoke yesterday of reports from Norway’s Institute of Public Health.
https://nyheder.tv2.dk/2022-01-21-ny-omikron-variant-spreder-sig-du-kan-muligvis...

This is the translation of the text which is clear: "- It is possible that you can be infected with BA.1 Omikron first, and then shortly after with BA.2, he says in ‘Go morgen Danmark’.
In Norway, where BA.2 is also spreading, a few cases have been seen where this has happened."
----------------------------------------------

Mind you, it's been estimated that hundreds of COVID particles ("virules") are needed to infect one?

Omicron found to have higher environmental stability among SARS-CoV-2 variants
Ramya Dwivedi | Jan 21 2022

...On the plastic surface, the researchers analyzed the survival times of the Wuhan strain, Alpha variant, Beta variant, Gamma variant, Delta variant, and Omicron variant to be 56.0 h, 191.3 h, 156.6 h, 59.3 h, 114.0 h, and 193.5 h, respectively.

While on the human skin surface, they analyzed the survival times of the Wuhan strain, Alpha variant, Beta variant, Gamma variant, Delta variant, and Omicron variant to be 8.6 h, 19.6 h, 19.1 h, 11.0 h, 16.8 h, and 21.1 h, respectively; with the Omicron variant having the longest survival time. The researchers reported that the half-life values had the same tendency as the survival time.

The disinfectants were effective against all the viruses within 15s. However, the VOCs were slightly more resistant than the Wuhan strain. On human skin, an ex vivo evaluation showed complete inactivation of all the viruses with exposure to 35% ethanol within 15s. Therefore, the researchers highly recommend the current protocol of hand hygiene practices to continue for infection control as advised by the World Health Organization.

Thus, this study showed that on plastic and skin surfaces, the VOCs exhibited more than two-fold longer survival times than those of the Wuhan strain and remained infective on the skin surfaces for more than 16h...

https://www.news-medical.net/news/20220121/Omicron-found-to-have-higher-environm...
-------------------------------------------------------

Ryohei Hirose, Yoshito Itoh, Hiroshi Ikegaya, Hajime Miyazaki, Naoto Watanabe, Takuma Yoshida, Risa Bandou, Tomo Daidoji, Takaaki Nakaya. (2022). Differences in environmental stability among SARS-CoV-2 variants of concern: Omicron has higher stability. bioRxiv. doi: https://doi.org/10.1101/2022.01.18.476607 https://www.biorxiv.org/content/10.1101/2022.01.18.476607v1

Abstract
We analyzed the differences in viral environmental stability between the SARS-CoV-2 Wuhan strain and all variants of concern (VOCs). On plastic and skin surfaces, Alpha, Beta, Delta, and Omicron variants exhibited more than two-fold longer survival than the Wuhan strain and maintained infectivity for more than 16 h on skin surfaces. The high environmental stability of these VOCs could increase the risk of contact transmission and contribute to their spread.

>55 margd: Yes, quite correct translation of what Anders Fomsgaard is saying. It seems like a few cases of first getting BA.1 and then BA.2 have been seen in Norway.

BTW Anders Fomsgaard's been at the game for quite a while:
https://research.regionh.dk/da/publications/id(6ac7348b-6ad4-4290-b8c2-ae81a37c8...

And he was married to Sylvie Corbet (french virus researcher). Alas she died in 2008.

So I listen carefully, when he speaks :-)

>57 bnielsen: Tx! Someone challenged the translation. Not someone on my twitter "credibility chain", but thought I'd better check. ;)

>52 margd: Let’s see whether this holds up after replication. But I agree with the flustered part. Most people in the field are somewhat nonplussed by this result. Time will tell.

>59 stellarexplorer: I'd never choose even mild COVID over jab--whatever I had made for miserable experience! And if ever I catch it, I want to be up to date on my vaxx, so that I am best placed to avoid the worst outcomes. I do worry that my anti-vaxxing loved ones will no longer be merely blase about the virus, but seek it out, cheered on by idiots in social media...

>60 margd: Many people hold their own judgment in undue esteem

Nazrul Islam et al. 2021. Effects of covid-19 pandemic on life expectancy and premature mortality in 2020: time series analysis in 37 countries. BMJ 2021; 375:e066768 . (Published 03 November 2021) doi: https://doi.org/10.1136/bmj-2021-066768 https://www.bmj.com/content/375/bmj-2021-066768

ABSTRACT
...Results Reduction in life expectancy in men and women was observed in all the countries studied except New Zealand, Taiwan, and Norway, where there was a gain in life expectancy in 2020. No evidence was found of a change in life expectancy in Denmark, Iceland, and South Korea. The highest reduction in life expectancy was observed in
Russia (men: −2.33...; women: −2.14 ...), the
United States (men: −2.27 ...; women: −1.61 ...),
Bulgaria (men: −1.96 ...; women: −1.37 ...),
Lithuania (men: −1.83 ...; women: −1.21 ...),
Chile (men: −1.64 ...; women: −0.88 ...), and
Spain (men: −1.35 ...; women: −1.13 ...).

Years of life lost in 2020 were higher than expected in all countries except Taiwan, New Zealand, Norway, Iceland, Denmark, and South Korea. In the remaining 31 countries, more than 222 million years of life were lost in 2020, which is 28.1 million ... years of life lost more than expected (17.3 million ... in men and 10.8 million ... in women).

The highest excess years of life lost per 100 000 population were observed in
Bulgaria (men: 7260...; women: 3730...),
Russia (men: 7020...; women: 4760...),
Lithuania (men: 5430...; women: 2640...),
the US (men: 4350...; women: 2430...),
Poland (men: 3830...; women: 1830...), and
Hungary (men: 2770; women: 1920...).

The excess years of life lost were relatively low in people younger than 65 years, except in Russia, Bulgaria, Lithuania, and the US where the excess years of life lost was more than 2000 per 100 000.

Conclusion More than 28 million excess years of life were lost in 2020 in 31 countries, with a higher rate in men than women. Excess years of life lost associated with the covid-19 pandemic in 2020 were more than five times higher than those associated with the seasonal influenza epidemic in 2015...
____________________________________________
Because earlier deaths are no longer part of one's life expectancy calculation...

A shocking number of people don't seem to understand that an avg. national life expectancy of 82 emphatically does not mean the nation's 80 & 90-somethings are liable to drop dead at any time, for no reason. An average 80-year-old Canadian can expect to live another 9 years.
- Ed Tubb (Toronto Star) @EdTubb | 11:38 AM · Jan 23, 2022

Bob Wachter (Chr, UCSF Med Dept) @Bob_Wachter | 3:21 PM · Jan 23, 2022:
Reminder that, despite its infectivity, Omicron's household attack rate is ~1-in-3 (less in fully vaxxed). People often assume that, if one person in household is infected, it's inevitable everybody'll get it. Ain't so; worth trying to isolate if feasible.
---------------------------------------------------
Danish researchers investigate Omicron transmission in Danish households
The study found an increased transmission for unvaccinated individuals and a reduced transmission for booster-vaccinated individuals, compared to fully vaccinated individuals.
Updated 3 January 2022

The study included 11.937 Danish households (2.225 Omicron-infected households) and 27.874 household members in December 2021. A total of 6.397 household members tested positive 1-7 days after the primary case. The estimated secondary attack rate (SAR) was 31% and 21% in Omicron- and Deltavariant-infected households respectively.

https://en.ssi.dk/news/news/2022/danish-researcher-investigate-omicron-transmiss...
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Frederik Plesner Lyngse et al. 2021. SARS-CoV-2 Omicron VOC Transmission in Danish Households. MedRxiv Dec 21, 2021. doi: https://doi.org/10.1101/2021.12.27.21268278 https://www.medrxiv.org/content/10.1101/2021.12.27.21268278v1

This article is a preprint and has not been peer-reviewed

Abstract
The Omicron variant of concern (VOC) is a rapidly spreading variant of SARS-CoV-2 that is likely to overtake the previously dominant Delta VOC in many countries by the end of 2021.

We estimated the transmission dynamics following the spread of Omicron VOC within Danish households during December 2021. We used data from Danish registers to estimate the household secondary attack rate (SAR).

Among 11,937 households (2,225 with the Omicron VOC), we identified 6,397 secondary infections during a 1-7 day follow-up period. The SAR was 31% and 21% in households with the Omicron and Delta VOC, respectively. We found an increased transmission for unvaccinated individuals, and a reduced transmission for booster-vaccinated individuals, compared to fully vaccinated individuals. Comparing households infected with the Omicron to Delta VOC, we found an 1.17 (95%-CI: 0.99-1.38) times higher SAR for unvaccinated, 2.61 times (95%-CI: 2.34-2.90) higher for fully vaccinated and 3.66 (95%-CI: 2.65-5.05) times higher for booster-vaccinated individuals, demonstrating strong evidence of immune evasiveness of the Omicron VOC.

Our findings confirm that the rapid spread of the Omicron VOC primarily can be ascribed to the immune evasiveness rather than an inherent increase in the basic transmissibility.

US Vaccine Breakthrough Data Reporting Scorecard (map of states as of 13 Jan 2022)
Pandemic Tracking Collective is working with The Rockefeller Foundation’s Pandemic Prevention Institute

Grades reflect the completeness of each state's publicly available vaccine breakthrough data reporting and presentation, with a focus on both data transparency and data interpretability.

https://www.rockefellerfoundation.org/pandemicpreventioninstitute/%20u-s-vaccine...

COVID-19: Vaccine boosters
NZ Ministry of Health | Last updated: 23 January 2022

...The Government announced on 21 December 2021 that COVID-19 booster vaccinations would be mandated for workforces covered by the COVID-19 Public Health Response (Vaccinations) Order 2021 (Vaccinations Order). This has come into effect as of the 23 January 2022.

There are different mandated dates for when booster vaccinations are required for the workforces covered by the Vaccinations Order. These are:

Border and MIQ workforces, if eligible for a booster, are required to have this by 15 February 2022
Health and Disability workforces, if eligible for a booster, are required to have this by 15 February 2022
Education, Corrections, Police, Defence, and Fire and Emergency workforces, if eligible for a booster, are required to have this by 1 March 2022...

https://www.health.govt.nz/our-work/diseases-and-conditions/covid-19-novel-coron...

Where do we stand with Omicron?
The data, the math, the patterns, and the exit
Eric Topol | Jan 22, 2022

...Now is not the time to rely on sharp descents and that somehow “it’s over". If that happens, and we quickly get to containment and low levels of circulating virus that are no more threatening than annual flu, terrific. It seems quite unlikely with so much of the world’s population, especially in low and middle income countries, have yet to be vaccinated. If there's one thing we learned about predicting the path of SARS-CoV-2, it’s that it’s unpredictable. So we shouldn’t plan on a rosy picture. There’s too much we can do right now to seize control in case the most optimistic scenarios don’t play out.

https://erictopol.substack.com/p/where-do-we-stand-with-omicron

Brain damage markers greater in people with severe COVID-19 than those with Alzheimer's
Lori Uildriks on January 21, 2022

A study demonstrated that participants hospitalized with COVID-19 experiencing neurological complications had higher levels of blood proteins or biomarkers associated with neurological damage than people with Alzheimer’s.

Increased biomarker levels correlated with COVID-19 severity, mortality risk, and the presence of neurological disorder

Long-term follow-up is necessary to determine if biomarker elevation is associated with an increased risk of developing subsequent neurodegenerative disorders...

https://www.medicalnewstoday.com/articles/brain-damage-markers-greater-in-people...
----------------------------------------------------

Jennifer A. Frontera et al.Comparison of serum neurodegenerative biomarkers among hospitalized COVID-19 patients versus non-COVID subjects with normal cognition, mild cognitive impairment, or Alzheimer's dementia. Alzheimer's Dementia 13 January 2022. https://doi.org/10.1002/alz.12556 https://alz-journals.onlinelibrary.wiley.com/doi/10.1002/alz.12556

Abstract
...Results
Admission t-tau, p-tau181, GFAP (glial fibrillary acidic protein), and NfL (neurofilament light chain) were significantly elevated in patients with encephalopathy and in those who died in-hospital, while t-tau, GFAP, and NfL were significantly lower in those discharged home. These markers correlated with severity of COVID illness. NfL, GFAP, and UCHL1 (ubiquitin carboxy-terminal hydrolase L1) were higher in COVID patients than in non-COVID controls with MCI (mild cognitive impairment) or AD (Alzheimer's disease).

Discussion
Neurodegenerative biomarkers were elevated to levels observed in AD dementia and associated with encephalopathy and worse outcomes among hospitalized COVID-19 patients...

COVID-19: Alpha’s (B.1.1.7)mutations provide insight into Omicron
Deep Shukla | January 20, 2022

Scientists do not yet fully understand how individual mutations in SARS-CoV-2 variants influence contagiousness or disease severity.

To enter a human cell, the SARS-CoV-2’s spike protein must be activated. This happens following cleavage by an enzyme called furin.

Scientists have theorized that mutations at the furin cleavage site might play an important role in a variant’s ability to infect or replicate in human cells.

Contrary to expectations, the authors of a new study found that this mutation did not influence the ability of the virus to enter or spread between cells.

Some variants of concern, such as Delta and Omicron, also have mutations at the same furin cleavage site, and this study may help understand the changes in their contagiousness and ability to produce disease...

https://www.medicalnewstoday.com/articles/covid-19-alphas-mutations-provide-insi...
-----------------------------------------------

G.Diel et al. 2022. Functional evaluation of the P681H mutation on the proteolytic activation of the SARS-CoV-2 variant B.1.1.7 (Alpha) spike. iScience Volume 25, Issue 1, 21 January 2022, 103589. https://doi.org/10.1016/j.isci.2021.103589 https://www.sciencedirect.com/science/article/pii/S2589004221015595

Highlights
• SARS-CoV-2 B.1.1.7 P681H mutation in the spike is predicted to enhance viral infection
• P681H does not significantly impact furin cleavage, viral entry, or cell-cell spread
• Other mutations in the SARS-CoV-2 B.1.1.7 VOC may account for increased infection rates

Summary
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the agent causing the COVID-19 pandemic. SARS-CoV-2 B.1.1.7 (Alpha), a WHO variant of concern first identified in the United Kingdom in late 2020, contains several mutations including P681H in the spike S1/S2 cleavage site, which is predicted to increase cleavage by furin, potentially impacting the viral cell entry. Here, we studied the role of the P681H mutation in B.1.1.7 cell entry. We performed assays using fluorogenic peptides mimicking the Wuhan-Hu-1 and B.1.1.7 S1/S2 sequence and observed no significant difference in furin cleavage. Functional assays using pseudoparticles harboring SARS-CoV-2 spikes and cell-to-cell fusion assays demonstrated no differences between Wuhan-Hu-1, B.1.1.7, or a P681H point mutant. Likewise, we observed no differences in viral growth between USA-WA1/2020 and a B.1.1.7 isolate in cell culture. Our findings suggest that, although the B.1.1.7 P681H mutation may slightly increase S1/S2 cleavage, this does not significantly impact viral entry or cell-cell spread...

Fact-check: Is Omicron 'the fastest-spreading virus known to humankind'?
Monique Caret | Jan 24, 2022

...Our ruling

A Facebook video said, "Omicron is now the fastest-spreading virus known to humankind."

When it comes to how quickly viruses spread across the world, omicron is the fastest, experts say.

When it comes to how viruses are transmitted from person to person, measles is the most contagious. Each person who has measles can infect 12 to 18 other people, in a population not protected by vaccines and other preventative measures, according to the CDC.

But the omicron variant of SARS-CoV-2 is a close second. Estimates put it at 1.5 to 2 times more transmissible than the delta variant, which saw each sick person infecting between five and seven others. So each person who contracts the omicron variant can infect between 7 and 14 people in an unvaccinated, unprotected population.

We rate this claim Mostly True.

https://www.statesman.com/story/news/politics/politifact/2022/01/24/fact-check-o...

The kids are not alright: Data suggests 10% of children with COVID-19 become "long-haulers"
Kari Dequine Harden | January 22, 2022

...there is now growing consensus that somewhere around 10 percent of COVID-19 cases in kids turn into long Covid — at least according to the data collected for primarily pre-omicron and pre-vaccine cases.

...On Jan. 18, the American Academy of Pediatrics reported more than 981,000 new COVID cases confirmed in children in the United States during the week ending on Jan. 13, representing a 69% increase from the previous week, according to the Academy.

...older children and adolescents appear more at risk of long Covid than babies and young children...girls ...The majority of children developing long Covid had only mild cases of the initial SARS-CoV2 infection, and were healthy pre-COVID with no underlying conditions. A significant portion had asymptomatic cases.

...most common symptoms of long Covid in kids:
Fatigue or decreased physical performance, difficulty thinking or concentrating and memory loss (known as brain fog), headaches, dizziness, trouble breathing, loss of taste and smell, sleep disturbance, chest tightness or pain, abdominal pain, fever, mood changes, muscle and joint pain, congested or runny nose, cough, heart palpitations, loss of appetite or weight, and rash.

... most cases resolve within about six months

...diabetes

...ruling out every other medical explanation takes time and evaluations from different specialists

https://www.salon.com/2022/01/22/the-kids-are-not-alright-data-suggests-10-of-ch...

Study highlights the neurologic manifestations linked with COVID-19 in hospitalized children
Reviewed by Emily Henderson, B.Sc. | Jan 22 2022

Of hospitalized children who tested or were presumed positive for SARS-CoV-2, 44% developed neurological symptoms, and these kids were more likely to require intensive care than their peers who didn't experience such symptoms..

The most common neurologic symptoms were headache and altered mental status, known as acute encephalopathy.

...Journal reference:
Fink, E.L., et al. (2021) Prevalence and Risk Factors of Neurologic Manifestations in Hospitalized Children Diagnosed with Acute SARS-CoV-2 or MIS-C. Pediatric Neurology. doi.org/10.1016/j.pediatrneurol.2021.12.010.

https://www.news-medical.net/news/20220122/Study-highlights-the-neurologic-manif...

Omicron’s Radical Evolution
Carl Zimmer | Jan. 24, 2022

Thirteen of Omicron’s mutations should have hurt the variant’s chances of survival. Instead, they worked together to make it thrive...

https://www.nytimes.com/2022/01/24/science/omicron-mutations-evolution.html
-------------------------------------------------

Darren P Martin et al. 2022. Selection analysis identifies unusual clustered mutational changes in Omicron lineage BA.1 that likely impact Spike function. BioRxiv Jan 18, 2022. doi: https://doi.org/10.1101/2022.01.14.476382 https://www.biorxiv.org/content/10.1101/2022.01.14.476382v1

Preprint

Abstract
Among the 30 non-synonymous nucleotide substitutions in the Omicron S-gene are 13 that have only rarely been seen in other SARS-CoV-2 sequences. These mutations cluster within three functionally important regions of the S-gene at sites that will likely impact (i) interactions between subunits of the Spike trimer and the predisposition of subunits to shift from down to up configurations, (ii) interactions of Spike with ACE2 receptors, and (iii) the priming of Spike for membrane fusion. We show here that, based on both the rarity of these 13 mutations in intrapatient sequencing reads and patterns of selection at the codon sites where the mutations occur in SARS-CoV-2 and related sarbecoviruses, prior to the emergence of Omicron the mutations would have been predicted to decrease the fitness of any genomes within which they occurred. We further propose that the mutations in each of the three clusters therefore cooperatively interact to both mitigate their individual fitness costs, and adaptively alter the function of Spike. Given the evident epidemic growth advantages of Omicron over all previously known SARS-CoV-2 lineages, it is crucial to determine both how such complex and highly adaptive mutation constellations were assembled within the Omicron S-gene, and why, despite unprecedented global genomic surveillance efforts, the early stages of this assembly process went completely undetected.

Worrisome that parallels seen between symptoms of Long CoVID, post-Lyme, chronic fatigue syndrome (Epstein Barr Virus, recently associated with MS), etc.

Serena Spudich and Avindra Nath. 2022. Nervous system consequences of COVID-19 (Perspective). Science • 20 Jan 2022 • Vol 375, Issue 6578 • pp. 267-269 • DOI: 10.1126/science.abm2052 https://www.science.org/doi/10.1126/science.abm2052

...the preponderance of evidence from CSF (cerebrospinal fluid) and brain tissue suggests that immune activation and inflammation within the CNS (central nervous system) is the primary driver of neurologic disease in acute COVID-19.

...It is plausible that subtle forms of generalized vascular dysfunction, including thrombotic microangiopathy (microscopic blood clots) in the brain, may lead to neurological symptoms even in the absence of clinically apparent stroke.

...Long Covid...often include(s) predominant neurologic and psychiatric symptoms, such as difficulty with memory, concentration, and ability to accomplish everyday tasks, frequent headaches, alterations in skin sensation, autonomic dysfunction, intractable fatigue, and in severe cases, delusions and paranoia.

...Long Covid (symptoms) are similar to those of myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS), which is also considered to be a postinfectious syndrome caused by a variety of infectious agents...poorly understood and there are no effective disease-modifying therapies...There is also overlap in symptoms of post–Lyme disease, suggesting that there may be common host susceptibility factors that underlie these illnesses.

...possibility that infection may accelerate or trigger future development of neurodegenerative diseases such as Alzheimer’s or Parkinson’s diseases.

No information is yet available regarding neurodevelopmental trajectories in children, who usually experience mild COVID-19 and manifest few neurologic or psychiatric symptoms during or after acute illness. Those who experience the rare multisystem-inflammatory syndrome in children (MIS-C) may be at particular risk for neurological sequelae owing to widespread endothelial activation, often involving the brain.

... It will be critical to characterize the pattern(s) of immune dysregulation in Long Covid patients. Is it possible that persistent immune dysregulation underlies ongoing symptoms? If so, this may be driven by host antigens with autoimmune responses, or a persistent viral infection with restricted viral replication in tissue reservoirs. Whether antiviral or immunetargeted interventions early in the disease course or prophylactic vaccination against COVID-19 will alter the trajectory of neurologic complications of COVID-19 is also unknown...

Diagram ( https://twitter.com/ScienceMagazine/status/1485915368539496448/photo/1 )

What to do if family member brings home COVID?

Kimberly Prather, Ph.D. (atmospheric chemist UCSF) @kprather88 | 7:45 PM · Jan 24, 2022:
https://twitter.com/kprather88/status/1485775886091571203

My top advice (for families with a member positive for COVID)....add a CR (Corsi Rosenthal) box ASAP. Simple as taping together a box yet life saving. Every family I know who has added this layer of filtration has stopped the spread through the family. @CleanAirCrewOrg https://cleanaircrew.org/box-fan-filters/

Quote Tweet
Olimpia Justice @OlimpiaJustice · 11h
My 11 year old is isolated in the guest room. She tested + today. 3 years we avoided this. So far the rest of us tested - and no symptoms. She is symptomatic and now I'm freaking out re air quality in the home. I placed a HUGE Potted plant in the room with her, at least she has a friend

Kimberly Prather, Ph.D. @kprather88 | 5:49 PM · Jan 24, 2022:
Warning: SARS-2 is airborne. Watch those poorly ventilated indoor corridors which can fill with air from surrounding rooms. Even if you don't see anyone else, wear a mask at all times indoors.
-------------------------------------------------
margd: On recent road trip, we chose motel room with outside access and window AC, and no indoor corridor. Upon arrival, CO2 monitor read 1800 ppm IN the room! Opened the door and ran the air exchange before we settled in. | Watch out for elevators also. CO2 in local U hospital approached that of outdoors (500 ppm) --except in the elevator...

There’s a new version of omicron but so far it doesn’t appear to be more dangerous
Lenny Bernstein | 1/24/2022

...Anders Fomsgaard a virologist at the State Serum Institute in Denmark, said in an email Monday that BA. 2 has become the dominant form of the virus in his nation of nearly 6 million people, where it now accounts for about 65 percent of new cases as BA. 1 is on the decline.

At the same time, Fomsgaard said, “we are not so concerned, since we so far do not see major differences in age distribution, vaccination status, breakthrough infections and risk of hospitalization. Also, despite the high infection rate of BA. 2, the numbers of hospitalizations in ICUs are decreasing.”

The United Kingdom Health Security Agency identified more than 400 cases of BA. 2 in the first 10 days of January and on Friday designated BA. 2 a “virus under investigation,” according to Al Jazeera. The agency said BA. 2 has been identified in 40 countries and “there is still uncertainty around the significance of the changes to the viral genome.”

...Some scientists have dubbed BA. 2 the “stealth omicron” because it has genetic traits that make it more difficult to identify the omicron form of the virus on PCR tests.

A French epidemiologist told Agence France-Presse that “what surprised us is the rapidity with which this sub-variant, which has been circulating to a great extent in Asia, has taken hold in Denmark.”

https://www.washingtonpost.com/health/2022/01/24/covid-omicron-ba2/

UP Open University @UPOpenU | 11:48 PM · Jan 24, 2022:
Everyone is invited to join the first part of the

“#COVIDisAirborne: Understanding and Implementing the Paradigm Shift”
on 3 February 2022, 8:00 AM (PST).
Visit https://tinyurl.com/airbornepart1 to register.
Read more: https://upou.edu.ph/announcement/covidisairborne/

Pfizer and BioNTech Initiate Study to Evaluate Omicron-Based COVID-19 Vaccine in Adults 18 to 55 Years of Age
Pfizer | Tuesday, January 25, 2022

...(Pfizer Inc. and BioNTech) today announced the initiation of a clinical study to evaluate the safety, tolerability and immunogenicity of an Omicron-based vaccine candidate in healthy adults 18 through 55 years of age. The study will have three cohorts examining different regimens of the current Pfizer-BioNTech COVID-19 vaccine or an Omicron-based vaccine. The study will draw upon some participants from the companies’ Phase 3 COVID-19 booster study and is part of their ongoing efforts to address Omicron and determine the potential need for variant-based vaccines.

“While current research and real-world data show that boosters continue to provide a high level of protection against severe disease and hospitalization with Omicron, we recognize the need to be prepared in the event this protection wanes over time and to potentially help address Omicron and new variants in the future,” said Kathrin U. Jansen, Ph.D., Senior Vice President and Head of Vaccine Research & Development at Pfizer. “Staying vigilant against the virus requires us to identify new approaches for people to maintain a high level of protection, and we believe developing and investigating variant-based vaccines, like this one, are essential in our efforts towards this goal.”...

https://www.pfizer.com/news/press-release/press-release-detail/pfizer-and-bionte...

After Omicron, some scientists foresee ‘a period of quiet’
The variant’s modest toll in many countries has led to a sense of optimism. But new surprises are likely
Kai Kupferschmidt | 25 Jan 2022

...“We anticipate that there will be a period of quiet before COVID-19 may come back towards the end of the year, but not necessarily the pandemic coming back,” Hans Kluge, director of the European Region of the World Health Organization (WHO), recently said in an interview. In the United Kingdom, where the Omicron wave crested early, many restrictions were scheduled to be dropped this week, including mandatory masks in public indoor spaces and COVID-19 vaccination passes.

The optimism is shared—although couched in caveats—even by some scientists and public health experts who have stressed the risks of the pandemic from the start and implored politicians to take stricter action. “We have reached a bit of a turning point,” says Devi Sridhar, a global health expert at the University of Edinburgh and an outspoken critic of the U.K. government’s past COVID-19 policies. Not only has the Omicron wave crested in several countries, but its toll has been smaller than feared. And the wave of infections has likely boosted immunity at the population level, which means future waves may wreak even less havoc.

Still, researchers urge caution. Omicron has shown that even a relatively mild wave can put a tremendous burden on health systems and societies as a whole, and it’s unclear how long Omicron immunity will last, how the virus will evolve from here on, and how often breakthrough infections will lead to long-term health problems. “I remain firmly in the camp of: We’ve made great progress but we still have a ways to go before this is truly over,” says Boghuma Titanji, a virologist at Emory University School of Medicine. Besides, “Wealthy countries moving on I fear will push the issues of access to vaccines and therapeutics access down the global priority list,” she says...

https://www.science.org/content/article/after-omicron-some-scientists-foresee-pe...

ETA
...Research has found that there is a connection between the factors and long COVID, even if the infection was mild...

The top four factors are:

The viral load in one’s blood
The presence of certain autoantibodies, which are often used to combat the virus and its symptoms
The reactivation of the Epstein-Barr virus, which has been known to infect people at a young age
The patient has Type 2 diabetes

Dr. Onur Boyman, a researcher in the department of immunology at University Hospital Zurich made a comment on the four factors. “These individuals might have a disadvantage from the start…they might also react slightly differently to viruses, which then leads to a misguided immune response.”

Identifying these factors is important because “if these pathways get confirmed, we as clinicians can actually design interventions to make people better.”...

https://www.fingerlakes1.com/2022/01/28/four-factors-that-effect-your-likelihood...

-------------------------------------------------

Who will get long COVID? Study may offer clues
Erika Edwards | Jan 25, 2022

A blood test may someday help determine a person’s risk for long COVID, new research suggests.

The study, published Tuesday in the journal Nature Communications*, found that people who go on to develop long Covid have lower levels of certain antibodies in their blood soon after they are infected with the coronavirus.

If confirmed through larger studies, the findings could help scientists develop a test to predict who may continue to suffer from symptoms weeks, months and even years following infection...

https://www.msn.com/en-us/health/medical/who-will-get-long-covid-study-may-offer...
-----------------------------------------------------

Carlo Cervia et al. 2022. Immunoglobulin signature predicts risk of post-acute COVID-19 syndrome. Nature Communications volume 13, Article number: 446 (25 Jan 2022). https://www.nature.com/articles/s41467-021-27797-1

Abstract
Following acute infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) a significant proportion of individuals develop prolonged symptoms, a serious condition termed post-acute coronavirus disease 2019 (COVID-19) syndrome (PACS) or long COVID. Predictors of PACS are needed. In a prospective multicentric cohort study of 215 individuals, we study COVID-19 patients during primary infection and up to one year later, compared to healthy subjects. We discover an immunoglobulin (Ig) signature, based on total IgM and IgG3 levels, which – combined with age, history of asthma bronchiale, and five symptoms during primary infection (fever, fatigue, cough, shortness of breath (dyspnea), and gastrointestinal symptoms) – is able to predict the risk of PACS independently of timepoint of blood sampling. We validate the score in an independent cohort of 395 individuals with COVID-19. Our results highlight the benefit of measuring Igs for the early identification of patients at high risk for PACS, which facilitates the study of targeted treatment and pathomechanisms of PACS.

COVID-19 infection before or after vaccination could create ‘super immunity’, OHSU researchers find
Fedor Zarkhin | Jan. 25, 2022

Getting a COVID-19 infection before or after the COVID-19 vaccine can create “super immunity,” researchers in Oregon found, complementing previous research that could point to an eventual path to co-existence with the virus.

...The OHSU (Oregon Health & Science University) research team previously found that the blood of those who had an infection after being vaccinated — called a breakthrough infection — produced a dramatic antibody response when exposed to the virus, as compared to blood from people who were vaccinated but didn’t get sick.

Now, the research shows that getting a shot after recovering from COVID-19 provides similarly strong protections, dubbed “super immunity.” In both cases, antibodies in the blood were found to be 10 times or more as potent as the antibodies in people who have been vaccinated but never had the disease, the researchers found.

People with this “super immunity” should be better protected from both infection and severe illness, the researchers said.

(Senior co-author Fikadu Tafesse )...the research indicates people who have had COVID-19 should get vaccinated...warning that it is not worth intentionally getting a COVID-19 infection, especially with the risk of long-term consequences.

But the question could be moot because the omicron variant is so incredibly transmissible that health officials have said they believe most Oregonians will come in contact with it.

The “end game” could be that a combination of vaccinations, booster shots and infection-derived immunity make infections from the virus less and less severe, Tafesse said.

https://www.oregonlive.com/coronavirus/2022/01/covid-19-infection-before-or-afte...
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Timothy A. Bates et al. 2022. Vaccination before or after SARS-CoV-2 infection leads to robust humoral response and antibodies that effectively neutralize variants. Science Immunology • 25 Jan 2022 • First Release • DOI: 10.1126/sciimmunol.abn8014 https://www.science.org/doi/10.1126/sciimmunol.abn8014

Abstract
...Here, we measure neutralizing antibody responses from 104 vaccinated individuals, including those with breakthrough infections, hybrid immunity, and no infection history. We find that human immune sera following breakthrough infection and vaccination following natural infection, broadly neutralize SARS-CoV-2 variants to a similar degree. While age negatively correlates with antibody response after vaccination alone, no correlation with age was found in breakthrough or hybrid immune groups. Together, our data suggest that the additional antigen exposure from natural infection substantially boosts the quantity, quality, and breadth of humoral immune response regardless of whether it occurs before or after vaccination.

Freda Kreier. 2022. Long-COVID symptoms less likely in vaccinated people, Israeli data say (News). Nature 25 January 2022 doi: https://doi.org/10.1038/d41586-022-00177-5 https://www.nature.com/articles/d41586-022-00177-5

...Researchers in Israel report that people who have had both SARS-CoV-2 infection and doses of Pfizer–BioNTech vaccine were much less likely to report any of a range of common long-COVID symptoms than were people who were unvaccinated when infected. In fact, vaccinated people were no more likely to report symptoms than people who’d never caught SARS-CoV-2.

...Some estimate that up to 30% of infected people, including many who were never hospitalized, have persistent symptoms.

...Claire Steves, a geriatrician at King’s College London who led the UK study (Antonelli, M. et al. Lancet Infect. Dis. 22, 43–55 (2022)), agrees that the Israeli data support earlier findings. “It’s really good to see different study designs correlating, with the same results,” she says.

Although the results of both the UK and Israel studies show that vaccination reduces the risk of long COVID, she says, even fully vaccinated people are still at risk of developing the condition. And whether vaccination protects people from Omicron-induced long COVID is still unclear.

Regardless, (Akiko Iwasaki, a viral immunologist at the Yale School of Medicine in New Haven, Connecticut) says these findings are encouraging. “Long COVID is a terrible and debilitating disease. Any measures we can take to prevent long COVID are key to limiting more suffering in the future,” she says. “One more reason to get vaccinated.”
--------------------------------------------------------------

Paul Kuodi et al, 2022. Association between vaccination status and reported incidence of post-acute COVID-19 symptoms in Israel: a cross-sectional study of patients tested between March 2020 and November 2021. MedRxiv Jan 17, 2022. doi: https://doi.org/10.1101/2022.01.05.22268800 https://www.medrxiv.org/content/10.1101/2022.01.05.22268800v2

This article is a preprint and has not been peer-reviewed

Abstract
...Results We included 951 infected and 2437 uninfected individuals. Of the infected, 637(67%) were vaccinated. The most commonly reported symptoms were; fatigue (22%), headache (20%), weakness (13%), and persistent muscle pain (10%). After adjusting for follow-up time and baseline symptoms, those who received two doses less likely than unvaccinated individuals to report any of these symptoms by 64%, 54%, 57%, and 68% respectively, (Risk ratios 0.36, 0.46, 0.43, 0.32,...in the listed sequence). Those who received two doses were no more likely to report any of these symptoms than individuals reporting no previous SARS-CoV-2 infection.

Conclusions Vaccination with at least two doses of COVID-19 vaccine was associated with a substantial decrease in reporting the most common post-acute COVID-19 symptoms, bringing it back to baseline. Our results suggest that, in addition to reducing the risk of acute illness, COVID-19 vaccination may have a protective effect against long COVID.

Less risk of myocarditis with vaxx than COVID, but still... young men should know risk. Good news is that 96% of those hospitalized as a result of vaxx-induced myocarditis were resolved by discharge. The most common treatment was nonsteroidal anti-inflammatory drugs (87%).

Matthew E. Oster et al. 2022. Myocarditis Cases Reported After mRNA-Based COVID-19 Vaccination in the US From December 2020 to August 2021. JAMA. Jan 25, 2022;327(4):331-340. doi:10.1001/jama.2021.24110. https://jamanetwork.com/journals/jama/fullarticle/2788346

Key Points
Question What is the risk of myocarditis after mRNA-based COVID-19 vaccination in the US?

Findings In this descriptive study of 1626 cases of myocarditis in a national passive reporting system, the crude reporting rates within 7 days after vaccination exceeded the expected rates across multiple age and sex strata. The rates of myocarditis cases were highest after the second vaccination dose in adolescent males aged 12 to 15 years (70.7 per million doses of the BNT162b2 vaccine), in adolescent males aged 16 to 17 years (105.9 per million doses of the BNT162b2 vaccine), and in young men aged 18 to 24 years (52.4 and 56.3 per million doses of the BNT162b2 vaccine and the mRNA-1273 vaccine, respectively).

Meaning Based on passive surveillance reporting in the US, the risk of myocarditis after receiving mRNA-based COVID-19 vaccines was increased across multiple age and sex strata and was highest after the second vaccination dose in adolescent males and young men.

Abstract
Importance Vaccination against COVID-19 provides clear public health benefits, but vaccination also carries potential risks. The risks and outcomes of myocarditis after COVID-19 vaccination are unclear.

Objective To describe reports of myocarditis and the reporting rates after mRNA-based COVID-19 vaccination in the US.

Design, Setting, and Participants Descriptive study of reports of myocarditis to the Vaccine Adverse Event Reporting System (VAERS) that occurred after mRNA-based COVID-19 vaccine administration between December 2020 and August 2021 in 192 405 448 individuals older than 12 years of age in the US; data were processed by VAERS as of September 30, 2021.

Exposures Vaccination with BNT162b2 (Pfizer-BioNTech) or mRNA-1273 (Moderna).

Main Outcomes and Measures Reports of myocarditis to VAERS were adjudicated and summarized for all age groups. Crude reporting rates were calculated across age and sex strata. Expected rates of myocarditis by age and sex were calculated using 2017-2019 claims data. For persons younger than 30 years of age, medical record reviews and clinician interviews were conducted to describe clinical presentation, diagnostic test results, treatment, and early outcomes.

Results Among 192 405 448 persons receiving a total of 354 100 845 mRNA-based COVID-19 vaccines during the study period, there were 1991 reports of myocarditis to VAERS and 1626 of these reports met the case definition of myocarditis. Of those with myocarditis, the median age was 21 years (IQR, 16-31 years) and the median time to symptom onset was 2 days (IQR, 1-3 days). Males comprised 82% of the myocarditis cases for whom sex was reported. The crude reporting rates for cases of myocarditis within 7 days after COVID-19 vaccination exceeded the expected rates of myocarditis across multiple age and sex strata. The rates of myocarditis were highest after the second vaccination dose in adolescent males aged 12 to 15 years (70.7 per million doses of the BNT162b2 vaccine), in adolescent males aged 16 to 17 years (105.9 per million doses of the BNT162b2 vaccine), and in young men aged 18 to 24 years (52.4 and 56.3 per million doses of the BNT162b2 vaccine and the mRNA-1273 vaccine, respectively). There were 826 cases of myocarditis among those younger than 30 years of age who had detailed clinical information available; of these cases, 792 of 809 (98%) had elevated troponin levels, 569 of 794 (72%) had abnormal electrocardiogram results, and 223 of 312 (72%) had abnormal cardiac magnetic resonance imaging results. Approximately 96% of persons (784/813) were hospitalized and 87% (577/661) of these had resolution of presenting symptoms by hospital discharge. The most common treatment was nonsteroidal anti-inflammatory drugs (589/676; 87%).

Conclusions and Relevance Based on passive surveillance reporting in the US, the risk of myocarditis after receiving mRNA-based COVID-19 vaccines was increased across multiple age and sex strata and was highest after the second vaccination dose in adolescent males and young men. This risk should be considered in the context of the benefits of COVID-19 vaccination.

The percentage of people with COVID-19 being admitted to intensive care units or needing mechanical ventilation is lower than ever

Iuliano AD, Brunkard JM, Boehmer TK, et al. Trends in Disease Severity and Health Care Utilization During the Early Omicron Variant Period Compared with Previous SARS-CoV-2 High Transmission Periods — United States, December 2020–January 2022. MMWR Morb Mortal Wkly Rep. ePub: 25 January 2022. DOI: http://dx.doi.org/10.15585/mmwr.mm7104e4 https://www.cdc.gov/mmwr/volumes/71/wr/mm7104e4.htm

Summary
What is already known about this topic?
The SARS-CoV-2 B.1.1.529 (Omicron) variant became predominant in the United States by late December 2021, leading to a surge in COVID-19 cases and associated ED visits and hospitalizations.

What is added by this report?
Despite Omicron seeing the highest reported numbers of COVID-19 cases and hospitalizations during the pandemic, disease severity indicators, including length of stay, ICU admission, and death, were lower than during previous pandemic peaks.

What are the implications for public health practice?
Although disease severity appears lower with the Omicron variant, the high volume of hospitalizations can strain local health care systems and the average daily number of deaths remains substantial. This underscores the importance of national emergency preparedness, specifically, hospital surge capacity and the ability to adequately staff local health care systems. In addition, being up to date on vaccinations and following other recommended prevention strategies are critical to preventing infections, severe illness, or death from COVID-19...

About two-thirds of the symptoms people experience after having a COVID-19 vaccine can be due to a negative placebo effect, rather than the shot itself.

Julia W. Haas et al. 2022. Frequency of Adverse Events in the Placebo Arms of COVID-19 Vaccine TrialsA Systematic Review and Meta-analysis. JAMA Netw Open. 18 Jan 2022;5(1):e2143955. doi:10.1001/jamanetworkopen.2021.43955

Key Points
Question What was the frequency of adverse events (AEs) in the placebo groups of COVID-19 vaccine trials?

Findings In this systematic review and meta-analysis of 12 articles including AE (adverse events) reports for 45 380 trial participants, systemic AEs were experienced by 35% of placebo recipients after the first dose and 32% after the second. Significantly more AEs were reported in the vaccine groups, but AEs in placebo arms (“nocebo responses”) accounted for 76% of systemic AEs after the first COVID-19 vaccine dose and 52% after the second dose.

Meaning This study found that the rate of nocebo responses in placebo arms of COVID-19 vaccine trials was substantial; this finding should be considered in public vaccination programs.

Abstract
...Results Twelve articles with AE reports for 45 380 participants (22 578 placebo recipients and 22 802 vaccine recipients) were analyzed. After the first dose, 35.2%...of placebo recipients experienced systemic AEs, with headache (19.3%...) and fatigue (16.7%...) being most common. After the second dose, 31.8%... of placebo recipients reported systemic AEs. The ratio between placebo and vaccine arms showed that nocebo responses accounted for 76.0% of systemic AEs after the first COVID-19 vaccine dose and for 51.8% after the second dose. Significantly more vaccine recipients reported AEs, but the group difference for systemic AEs was small after the first dose (OR, −0.47...; standardized mean difference, −0.26; ...) and large after the second dose (OR, −1.36; ...; standardized mean difference, −0.75...).

Conclusions and Relevance In this systematic review and meta-analysis, significantly more AEs were reported in vaccine groups compared with placebo groups, but the rates of reported AEs in the placebo arms were still substantial. Public vaccination programs should consider these high rates of AEs in placebo arms.

Omicron: the percentage of people with COVID-19 being admitted to intensive care units or needing mechanical ventilation was lower than ever.

Iuliano AD, Brunkard JM, Boehmer TK, et al. Trends in Disease Severity and Health Care Utilization During the Early Omicron Variant Period Compared with Previous SARS-CoV-2 High Transmission Periods — United States, December 2020–January 2022. MMWR Morb Mortal Wkly Rep. ePub: 25 January 2022. DOI: http://dx.doi.org/10.15585/mmwr.mm7104e4 https://www.cdc.gov/mmwr/volumes/71/wr/mm7104e4.htm

Summary
What is already known about this topic?
The SARS-CoV-2 B.1.1.529 (Omicron) variant became predominant in the United States by late December 2021, leading to a surge in COVID-19 cases and associated ED visits and hospitalizations.

What is added by this report?
Despite Omicron seeing the highest reported numbers of COVID-19 cases and hospitalizations during the pandemic, disease severity indicators, including length of stay, ICU admission, and death, were lower than during previous pandemic peaks.

What are the implications for public health practice?
Although disease severity appears lower with the Omicron variant, the high volume of hospitalizations can strain local health care systems and the average daily number of deaths remains substantial. This underscores the importance of national emergency preparedness, specifically, hospital surge capacity and the ability to adequately staff local health care systems. In addition, being up to date on vaccinations and following other recommended prevention strategies are critical to preventing infections, severe illness, or death from COVID-19.

From Dec 2020. Wonder if children at least, infected by SARS-CoV-19 will be protected against colds caused by human coronaviruses(?)

Jenna J. Guthmiller and Patrick C. Wilson 2020. Remembering seasonal coronaviruses (Perspective). Science • 11 Dec 2020 • Vol 370, Issue 6522 • pp. 1272-1273 • DOI: 10.1126/science.abf4860

...Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has differential effects according to age, with symptomatic and severe infections mostly occurring in older adults. One possible explanation for this variation is that children and younger adults have more preexisting immunity against seasonal human coronaviruses (HCoVs) that cross-react with SARS-CoV-2, providing protection from severe and even symptomatic SARS-CoV-2 infection.

...Upon repeated exposure to seasonal human coronaviruses (HCoVs), strain-specific and cross-reactive antibodies are generated. Upon subsequent exposure to SARS-CoV-2, cross-reactive antibodies are produced (back-boosted) to mitigate infection.

Eric Topol @EricTopol | 5:01 PM · Jan 26, 2022:
...The Moderna vaccine booster vs Omicron: neutralization antibody titer 20-fold higher than the 2nd dose
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Rolando Pajon et al. 2022. Omicron Variant Neutralization after mRNA-1273 Booster Vaccination. NEJM January 26, 2022
DOI: 10.1056/NEJMc2119912 https://www.nejm.org/doi/full/10.1056/NEJMc2119912

>79 margd: I see it this way too, but I always remind myself never to underestimate a virus. But I can’t help that a ray of optimism is sneaking through anyway…

Here our infection numbers are at a record high (53.655 new since yesterday) and everything is going back to (mostly) normal on Tuesday :-)
Which is probably a good decision.

Eric Topol (Scripps) @EricTopol | 9:17 AM · Jan 28, 2022:
https://twitter.com/EricTopol/status/1487067427875680262
How to reduce Covid hospitalizations by 97%?
Get vaccinated and boosted.

Rates of laboratory-confirmed COVID-19 hospitalizations by vaccination status
CDC: " posted on January 27, 2022 and reflect hospitalizations through December 25, 2021"
https://covid.cdc.gov/covid-data-tracker/#covidnet-hospitalizations-vaccination

Age 65+ 98% reduction
Graph--hospitalization rate Nov-Dec 2021 vaxxed and unvaxxed 65+ ( https://twitter.com/EricTopol/status/1487067427875680262/photo/1 )

Age 50-64 97% reduction
Graph--hospitalization rate Nov-Dec 2021 vaxxed and unvaxxed 50-64 ( https://twitter.com/EricTopol/status/1487067433143705600/photo/1 )

Eric Topol (Scripps) @EricTopol | 8:18 PM · Jan 27, 2022:
More than 3,000 American Covid deaths reported today, 7-day average > 2,500, and
the sharp continued rise indicates this peak may exceed that before there were vaccines. Which is unfathomable.

Graph--7-day moving average US deaths March 2020-Jan 27, 2022
( https://twitter.com/EricTopol/status/1486871381279006722/photo/1 )

Eric Topol (Scripps) @EricTopol | 9:00 AM · Jan 28, 2022

New @CDCMMWR data for 2 and 3 dose mRNA vaccine effectiveness (VE) vs hospitalization,
for both immunocompetent and immuncocompromised, all ages

Tenforde MW, Patel MM, Gaglani M, et al. Effectiveness of a Third Dose of Pfizer-BioNTech and Moderna Vaccines in Preventing COVID-19 Hospitalization Among Immunocompetent and Immunocompromised Adults — United States, August–December 2021. MMWR Morb Mortal Wkly Rep 2022;71:118–124. DOI: http://dx.doi.org/10.15585/mmwr.mm7104a2 https://cdc.gov/mmwr/volumes/71/wr/mm7104a2.htm?s_cid=mm7104a2_w

The VE increase from 2-shot 82% to 3-shot (booster) 97% in people without immuncompromised status is striking
Table 3--effectivesness of 2 and 3 dose vax in immuno-competent and -compromised, Aug-Dec 2021
https://twitter.com/EricTopol/status/1487062908118970368/photo/1

Smriti Mallapaty. 2022. Where did Omicron come from? Three key theories. Nature 602, 26-28 (28 January 2022). doi: https://doi.org/10.1038/d41586-022-00215-2 https://www.nature.com/articles/d41586-022-00215-2

The highly transmissible variant emerged with a host of unusual mutations. Now scientists are trying to work out how it evolved...series of mutations...mutations in one person, as part of a long-term infection...or other animal hosts, such as mice or rats...a combination of the three scenarios...

COVID-19: Moderna vaccine may reduce infection risk more than Pfizer
Timothy Huzar | January 27, 2022

...The researchers found that in November 2021, there were 2.8 breakthrough cases of COVID-19 in people fully vaccinated with the Pfizer vaccine per 1,000 people. They included breakthrough cases if the people had not received the booster vaccination or had not had a prior recorded infection with SARS-CoV-2.

For the Moderna vaccine, the monthly figure was significantly lower, at 1.6 breakthrough cases per 1,000 people who received these shots.

The risk of hospitalization in the 60 days after infection was also lower for people fully vaccinated with the Moderna vaccine: 12.7% for Moderna versus 13.3% for Pfizer.

The researchers did not see a significant difference in mortality rates between the two vaccine groups...

https://www.medicalnewstoday.com/articles/covid-19-moderna-vaccine-may-reduce-in...
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Lindsey Wang et al. 2022. Comparison of mRNA-1273 and BNT162b2 Vaccines on Breakthrough SARS-CoV-2 Infections, Hospitalizations, and Death During the Delta-Predominant Period (Research Letter). JAMA. Published online January 20, 2022. doi:10.1001/jama.2022.0210 https://jamanetwork.com/journals/jama/fullarticle/2788408

Trevor Bedford (scientist, Fred Hutch) @trvrb | 11:48 AM · Jan 28, 2022
https://twitter.com/trvrb/status/1487105396879679488
https://threadreaderapp.com/thread/1487105396879679488.html

Omicron viruses can be divided into two major groups, referred to as PANGO lineages BA.1 and BA.2 or @nextstrain
clades 21K and 21L. The vast majority of globally sequenced Omicron have been 21K (~630k) compared a small minority of 21L (~18k), but 21L is gaining ground. 1/15

...For comparison Alpha, Beta and Gamma are each about as divergent from each other in terms of amino acid changes across the genome as Omicron 21K and 21L are from each other. Figure from @nextstrain
(https://nextstrain.org/ncov/gisaid/global?l=unrooted&m=div). 3/15

...Given that Omicron 21K viruses spread easily in populations with prior immunity and given that @UKHSA
reports similar VE for 21K and 21L (https://assets.publishing.service.gov.uk/government/uploads/system/uploads/attachment_data/file/1050721/Vaccine-surveillance-report-week-4.pdf), I'd suspect that 21L's advantage derives from intrinsic transmission rather than greater immune escape. 11/15

The extensive wave of Omicron 21K in the US and elsewhere has created a large degree of immunity to Omicron 21K and very likely to 21L. 12/15

Given differences in NTD between Omicron 21K and 21L, it may be possible to see some re-infections of individuals recovered from 21K by 21L. 13/15

But given that we'll still have ~60% of the US that weren't infected in the January Omicron 21K wave, this leaves the potential for a more transmissible Omicron virus to spread further in this fraction of the population. 14/15

This said, I would guess we'll see 21L create a substantially longer tail of circulation of Omicron than would have existed with just 21K, but that it won't drive the scale of epidemics we've experienced with Omicron in January. 15/15

Francisco de Asis @franciscodeasis
what is the tMRCA of BA.1 and BA.2?

Trevor Bedford @trvrb
Nextstrain clock via TreeTime places the common ancestor of BA.1 (21K) and BA.2 (21L) at Feb 2021 but with wide 95% CI of Nov 2020 to Jun 2021 (https://nextstrain.org/ncov/gisaid/global?label=clade:21M%20%28Omicron%29
). However, this is effectively just counting total mutations and selection is likely to throw this off.

Proof of concept (in mice) for a vaccine that prevents pathogen from establishing in mucosa, thereby preventing infection as well as disease.

Prof. Akiko Iwasaki (Yale) @VirusesImmunity | 8:25 PM · Jan 26, 2022:
https://twitter.com/VirusesImmunity/status/1486510697332842498
Vaccines that reduce infection & disease are needed to combat the pandemic.
Here, @tianyangmao @BenIsraelow et al. describe our new mucosal booster strategy, Prime and Spike,
to induce such immunity via nasal delivery of unadjuvanted spike vaccine Thread (1/)
Infographic ( https://twitter.com/VirusesImmunity/status/1486510697332842498/photo/1 )

...17/

This is the first step in making this a reality. After this proof of concept in mice, this strategy needs to be tested for safety and efficacy in larger animals and in clinical trials. Similar strategies can be used to combat other mucosal viral pathogens in the future. (End)
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Tianyang Mao...Akiko Iwasaki. 2022. Unadjuvanted intranasal spike vaccine booster elicits robust protective mucosal immunity against sarbecoviruses. BioRxiv Jan 26, 2022. doi: https://doi.org/10.1101/2022.01.24.477597 https://biorxiv.org/content/10.1101/2022.01.24.477597v1

This article is a preprint and has not been certified by peer review

Abstract

As the SARS-CoV-2 pandemic enters its third year, vaccines that not only prevent disease, but also prevent transmission are needed to help reduce global disease burden. Currently approved parenteral vaccines induce robust systemic immunity, but poor immunity at the respiratory mucosa. Here we describe the development of a novel vaccine strategy, Prime and Spike, based on unadjuvanted intranasal spike boosting that leverages existing immunity generated by primary vaccination to elicit mucosal immune memory within the respiratory tract. We show that Prime and Spike induces robust T resident memory cells, B resident memory cells and IgA at the respiratory mucosa, boosts systemic immunity, and completely protects mice with partial immunity from lethal SARS-CoV-2 infection. Using divergent spike proteins, Prime and Spike enables induction of cross-reactive immunity against sarbecoviruses without invoking original antigenic sin.*

* Original antigenic sin (OAS) describes the phenomenon whereby the development of immunity against pathogens/Ags is shaped by the first exposure to a related pathogen/Ag. https://www.jimmunol.org/content/202/2/335

Some contest conclusions?

"Long COVID in children is rare and mainly of short duration."

Luise Borch et al. 2022. Long COVID symptoms and duration in SARS-CoV-2 positive children — a nationwide cohort study. European Journal of Pediatrics (9 Jan 2022) https://link.springer.com/article/10.1007/s00431-021-04345-z

Abstract
Most children have a mild course of acute COVID-19. Only few mainly non-controlled studies with small sample size have evaluated long-term recovery from SARS-CoV-2 infection in children. The aim of this study was to evaluate symptoms and duration of ‘long COVID’ in children. A nationwide cohort study of 37,522 children aged 0–17 years with RT-PCR verified SARS-CoV-2 infection (response rate 44.9%) and a control group of 78,037 children (response rate 21.3%). An electronic questionnaire was sent to all children from March 24th until May 9th, 2021. Symptoms lasting more than 4 weeks were common among both SARS-CoV-2 children and controls. However, SARS-CoV-2 children aged 6–17 years reported symptoms more frequently than the control group (percent difference 0.8%). The most reported symptoms among pre-school children were fatigue Risk Difference (RD) 0.05..., loss of smell RD 0.01 ...), loss of taste RD 0.01... and muscle weakness RD 0.01... Among school children the most significant symptoms were loss of smell RD 0.12 ..., loss of taste RD 0.10 ..., fatigue RD 0.05 ..., respiratory problems RD 0.03 ..., dizziness RD 0.02 ..., muscle weakness RD 0.02 ... and chest pain RD 0.01... Children in the control group experienced significantly more concentration difficulties, headache, muscle and joint pain, cough, nausea, diarrhea and fever than SARS-CoV-2 infected. In most children ‘long COVID’ symptoms resolved within 1–5 months.

Conclusions: Long COVID in children is rare and mainly of short duration.

Hong Kong Study Shows Hamster-to-Human Covid Spread: Lancet
Zheping Huang | January 29, 2022

Hong Kong researchers have found evidence that pet hamsters can spread Covid-19 to people, and linked the animals to human infections in the city.

The study, published Saturday in The Lancet as a preprint and not yet peer-reviewed, provided the first documented evidence of hamster-to-human transmission of the Delta variant. Researchers from the University of Hong Kong and the city’s government found two independent cases of such transmission, after testing viral swabs and blood samples from animals collected from local pet shops.

The hamsters in question were infected around Nov. 21, before they were imported to Hong Kong, suggesting pet animal trade may be a pathway that facilitates Covid to spread across borders, according to the study.

“This study reveals that pet hamsters can acquire SARS-CoV-2 infection in real-life settings and can transmit the virus back to humans”’ the researchers said in the study. “The SARS-CoV-2 circulating in hamsters can allow sustainable virus transmission in humans.”

The Hong Kong government ordered the culling of thousands of hamsters after the infections at pet shops. It advised members of the public earlier this month to surrender hamsters purchased on or after Dec. 22 for “humane dispatch,” after some pet store workers and customers tested positive for the virus, and some of the animals imported from the Netherlands at the store tested preliminary positive.

https://www.bloomberg.com/news/articles/2022-01-29/hong-kong-study-shows-hamster...
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Yen, Hui-Ling and Sit, Thomas HC and Brackman, Christopher J. and Chuk, Shirley SY and Cheng, Samuel M.S. and Gu, Haogao and Chang, Lydia DJ and Krishnan, Pavithra and Ng, Daisy YM and Liu, Gigi YZ and Hui, Mani MY and Ho, Sin Ying and Tam, Karina WS and Law, Pierra YT and Su, Wen and Sia, Sin Fun and Choy, Ka-Tim and Cheuk, Sammi SY and Lau, Sylvia PN and Tang, Amy WY and Koo, Joe CT and Yung, Louise and Leung, Gabriel and Peiris, J.S. Malik and Poon, Leo LM, Transmission of SARS-CoV-2 (Variant Delta) from Pet Hamsters to Humans and Onward Human Propagation of the Adapted Strain: A Case Study. Available at SSRN: https://ssrn.com/abstract=4017393 https://papers.ssrn.com/sol3/papers.cfm?abstract_id=4017393

Preprints with The Lancet. Not yet peer-reviewed.

Abstract

Background: Transmission of SARS-CoV-2 from humans to other mammals, including pet animals, has been reported. However, with the exception of farmed mink, there is no previous documentation that these infected animals can infect humans, nor of further onward spread among humans. Following a confirmed SARS-CoV-2 infection of a pet store worker, animals in the store and the warehouse supplying it were tested for evidence of SARS-CoV-2 infection.

Methods: Viral swabs and blood samples from pet animals were collected in a pet shop and the warehouse supplying it and tested by SARS-CoV-2 RT-PCR and serological assays, respectively. SARS-CoV-2 RT-PCR positive samples were studied by full genome sequencing analysis.

Findings: Over 50% of individually tested Syrian hamsters in the pet shop (8/16) and warehouse (7/12) were positive for SARS-CoV-2 infection in RT-PCR or serological tests. None of dwarf hamsters (n=77), rabbits (n=246), Guinea pigs (n=66), chinchilla (n=116) and mice (n=2) were confirmed positive in RT-PCR tests. SARS-CoV-2 viral genomes deduced from human and hamster cases in this incident all belong to Delta variant of concern (AY.127) that had not been circulating locally prior. These sequences are highly similar, but distinct. The viral genomes obtained from hamsters are phylogenetically related with some sequence heterogeneity and phylogenetic dating suggest infection in these hamsters occurred around 21 November 2021. Two separate transmission events to humans are documented, one leading to onward household spread.

Interpretation: Pet hamsters can be naturally infected in “real-life” settings. The virus can circulate within hamsters and lead to human infections. Both genetic and epidemiological results strongly suggest that there were two independent hamster-to-human transmission and that such events can lead to onward human transmission. Importation of infected hamsters was the most likely source of virus infection.

Denmark: take care, bnielsen!
Looks like all our powers-that-be are deciding just to live with it?
Deaths may be down but could change if # hospitalized exceed hospital capacities...

Eric Topol (Scripps) @EricTopol | 10:22 PM · Jan 28, 2022:
That's quite a graph
https://ft.com/content/037a3ac9-830b-4592-9ff3-feed2008bdb7 ...

Denmark lifting all restrictions as hospitalizations and deaths are cases (BA.2, Omicron) still increasing

Graph--cases, hospitalizations, ICU, deaths Denmark, Oct 2020-Jan 2022
https://twitter.com/EricTopol/status/1487264933993615362/photo/1

Lung abnormalities found in long COVID patients with breathlessness
National Institute of health Research | 29/01/2022

Researchers have identified abnormalities in the lungs of long COVID patients with breathlessness but whose other tests are normal.

The EXPLAIN study is using hyperpolarised xenon MRI scans to investigate possible lung damage in long COVID patients who experience breathlessness and were not hospitalised when they had COVID-19.

These early results suggest that COVID-19 may result in persistent impairment in gas transfer and underlying lung abnormalities. However, the extent to which these abnormalities contribute to breathlessness is currently unclear.

Hyperpolarised xenon MRI requires the patient to lie in an MRI scanner and breathe in one litre of xenon gas that has had its atomic structure altered so it can be seen using MRI. Xenon is an inert gas that behaves in a very similar way to oxygen, so radiologists then can observe how the gas moves from the lungs into the bloodstream...

https://www.nihr.ac.uk/news/lung-abnormalities-found-in-long-covid-patients-with...
-------------------------------------------------------

James T. Grist et al. 2022. The Investigation of Pulmonary Abnormalities using Hyperpolarised Xenon Magnetic Resonance Imaging in Patients with Long-COVID. https://oxfordbrc.nihr.ac.uk/preprint_explain_study/

PREPRINT

Abstract
...Conclusion
There are RBC:TP abnormalities in NHLC and PHC patients, with NHLC patients also demonstrating lower TLco than PHC patients despite their having normal CT scans. These abnormalities are present many months after the initial infection.

Summary statement
Hyperpolarized Xenon MRI and TLco demonstrate significantly impaired gas transfer in nonhospitalised long-COVID patients when all other investigations are normal. These abnormalities are present many months after the initial infection.

>100 margd: Since Omicron took over here in late December / early January the numbers for hospitalized and deaths went up simply because a lot of hospitalized and dead got Omicron on top of whatever was bugging them. For the first time in the pandemic I had several of my friends and job colleagues testing positive at the same time but almost all of them with no or very few symptoms. But yes, still a strain on the hospitals, since they have to isolate patients with a positive test.
I think it is the booster shot which enables us to open up now without too severe problems.

BTW one of the nearby towns (Søften) had an incidence of 10% recently, i.e. 10% of everybody got infected in just one week. But it doesn't scare people anymore, since it doesn't seem to send you to the hospital. Some have no symptoms at all, some have some very mild symptoms, and some have a sort of three-day flu.

"Atomic structures of the Omicron Spike in complex with three types of all five VOC-reactive antibodies ... revealed a key antibody escape site, G446S... . Our results rationalize the use of 3-dose immunization regimens and suggest...a rational target for a universal sarbecovirus vaccine."

Kang Wang et al. 2022. Memory B cell repertoire from triple vaccinees against diverse SARS-CoV-2 variants. Nature (28 Jan 2022). https://www.nature.com/articles/s41586-022-04466-x

Accepted, unedited ms.

Abstract
Omicron, the most heavily mutated SARS-CoV-2 variant so far, is highly resistant to neutralizing antibodies, raising unprecedented concerns about the effectiveness of antibody therapies and vaccines.... We examined whether sera from individuals who received two or three doses of inactivated vaccine, could neutralize authentic Omicron. The seroconversion rates of neutralizing antibodies were 3.3% (2/60) and 95% (57/60) for 2- and 3-dose vaccinees, respectively. For three-dose recipients, the geometric mean neutralization antibody titre (GMT) of Omicron was 16.5-fold lower than that of the ancestral virus... We isolated 323 human monoclonal antibodies (mAbs) derived from memory B cells in 3-dose vaccinees, half of which recognize the receptor binding domain (RBD) and show that a subset of them (24/163) neutralize all SARS-CoV-2 variants of concern (VOCs), including Omicron, potently. Therapeutic treatments with representative broadly neutralizing mAbs were highly protective against SARS-CoV-2 Beta and Omicron infections in mice. Atomic structures of the Omicron Spike in complex with three types of all five VOC-reactive antibodies defined the binding and neutralizing determinants and revealed a key antibody escape site, G446S, that confers greater resistance to one major class of antibodies bound at the right shoulder of RBD through altering local conformation at the binding interface. Our results rationalize the use of 3-dose immunization regimens and suggest that the fundamental epitopes revealed by these broadly ultrapotent antibodies are a rational target for a universal sarbecovirus vaccine.

>103 margd: "Our results rationalize the use of 3-dose immunization regimens and suggest that the fundamental epitopes revealed by these broadly ultrapotent antibodies are a rational target for a universal sarbecovirus vaccine."

So this is interesting. I've been trying to follow the work (which seems very promising except that half of all people in my country will probably not take it ) on a pancoronavirus vaccine. I think this would be our best protection against future coronavirus infections, and one of these days we may see one that kills 50% of people instead of 1-2%. MERS kills 33% for example.
Anyway, most of these efforts are working on places in the virus less prone to mutation, or whee mutation is unlikely to retain a viable virus. The interesting thing is that as I understand it, that work is generally not focused on the highly mutable spike protein, but on the rest of the viral structure. So it's interesting that this paper argues for a vaccine still based on the spike. I wonder about the capacity for future variants or coronaviruses to mutate in ways we have not yet seen, making this a less effective strategy, or whether there's reason to doubt that. I'd love to get the thoughts of those doing the vaccine work itself.

John Burn-Murdoch (Financial Times) @jburnmurdoch | 4:39 AM · Jan 31, 2022
NEW: our big story as trailed on Friday is a detailed analysis of the critical importance of vaccination in beating Covid

Top-line: if US had matched vaccination coverage of leading European countries, it would have *halved* its Covid hospitalisations
https://ft.com/content/03aa46e2-ac3a-4c16-82be-431ea4c43e58

Graph-US hospitalizations, actual v. Denmark vaxx rate, July 2021-Jan 2022
https://twitter.com/jburnmurdoch/status/1488084513829924867/photo/1

Frederik Plesner Lyngse (U Copengagen) @LyngseF | 2:44 AM · Jan 31, 2022:
Thread on omicron subvariant transmission is worth the read:
https://twitter.com/LyngseF/status/1488055617864536066

We conclude that Omicron BA.2 is inherently substantially more transmissible than BA.1. It also possesses immune-evasive properties that reduce the protective effect of vac. against infection, but do not increase its transmissibility from vac. persons with breakthrough infect. 2/ ... 13/
-----------------------------------------------------
Frederik Plesner Lyngse et al. 2022. Transmission of SARS-CoV-2 Omicron VOC subvariants BA.1 and BA.2: Evidence from Danish Households. MedRXiv Jan 30 2022. doi: https://doi.org/10.1101/2022.01.28.22270044 https://www.medrxiv.org/content/10.1101/2022.01.28.22270044v1

This article is a preprint and has not been certified by peer review

Abstract
...The secondary attack rate (SAR) was estimated as 29% and 39% in households infected with Omicron BA.1 and BA.2, respectively.

We found BA.2 to be associated with an increased susceptibility of infection for unvaccinated individuals (Odds Ratio (OR) 2.19...), fully vaccinated individuals (OR 2.45... ) and booster-vaccinated individuals (OR 2.99...), compared to BA.1.

We also found an increased transmissibility from unvaccinated primary cases in BA.2 households when compared to BA.1 households, with an OR of 2.62... The pattern of increased transmissibility in BA.2 households was not observed for fully vaccinated and booster-vaccinated primary cases, where the OR of transmission was below 1 for BA.2 compared to BA.1.

We conclude that Omicron BA.2 is inherently substantially more transmissible than BA.1, and that it also possesses immune-evasive properties that further reduce the protective effect of vaccination against infection, but do not increase its transmissibility from vaccinated individuals with breakthrough infections.

97% of children aged between 2 and 18 have been vaccinated against Covid-19 in Cuba
- Prof. Gavin Yamey MD MPH (Duke U) @GYamey | 6:18 PM · Jan 30, 2022

Quote Tweet
Instituto Finlay de Vacunas @FinlayInstituto · 14h
La campaña masiva de vacunación pediátrica con las vacunas #Soberana02 alcanzó 1.7 millones de niños entre 2-18 años, lo que representa el 96.6% de ese grupo poblacional.
Se han aplicado 5.1 millones de dosis de #Soberana02 y #SoberanaPlus a los niños cubanos
#CubaPorLaVida
Image ( 5:12 PM · Jan 30, 2022 )

Translated from Spanish by google
The massive pediatric vaccination campaign with the vaccines #Soberana02 reached 1.7 million children between 2-18 years of age, which represents 96.6% of this population group.
5.1 million doses of #Soberana02 and #SoberanaPlus have been applied to Cuban children
#CubaPorLaVida

Gut bacteria may play a role in the development of long COVID
James Kingsland | February 1, 2022

Many people who recover from COVID-19 report lingering symptoms such as fatigue, muscle weakness, and insomnia, known collectively as post-acute COVID syndrome (PACS) or long COVID.
Previous research has found that individuals who experience severe COVID-19 tend to have gut dysbiosis, a disruption in the community of microorganisms living in the gut.
A new study has found the first evidence that there may also be a connection between gut dysbiosis and long COVID.
Future clinical trials could therefore investigate probiotics, dietary changes, or fecal transplants as potential treatments for long COVID.

As many as three-quarters of people who recover from COVID-19 report experiencing at least one lingering symptom 6 months later...

https://www.medicalnewstoday.com/articles/gut-bacteria-may-play-a-role-in-the-de...

------------------------------------------------------------------

Qin Liu rt al. 2021 Gut microbiota dynamics in a prospective cohort of patients with post-acute COVID-19 syndrome. BMJ Gut http://dx.doi.org/10.1136/gutjnl-2021-325989 https://gut.bmj.com/content/gutjnl/early/2022/01/05/gutjnl-2021-325989.full.pdf

Abstract

Background Long-term complications after COVID-19 are common, but the potential cause for persistent symptoms after viral clearance remains unclear.

Objective To investigate whether gut microbiome composition is linked to post-acute COVID-19 syndrome (PACS), defined as at least one persistent symptom 4 weeks after clearance of the SARS-CoV-2 virus.

Methods We conducted a prospective study of 106 patients with a spectrum of COVID-19 severity followed up from admission to 6 months and 68 non-COVID-19 controls. We analysed serial faecal microbiome of 258 samples using shotgun metagenomic sequencing, and correlated the results with persistent symptoms at 6 months.

Results At 6 months, 76% of patients had PACS and the most common symptoms were fatigue, poor memory and hair loss. Gut microbiota composition at admission was associated with occurrence of PACS. Patients without PACS showed recovered gut microbiome profile at 6 months comparable to that of non-COVID-19 controls. Gut microbiome of patients with PACS were characterised by higher levels of Ruminococcus gnavus, Bacteroides vulgatus and lower levels of Faecalibacterium prausnitzii. Persistent respiratory symptoms were correlated with opportunistic gut pathogens, and neuropsychiatric symptoms and fatigue were correlated with nosocomial gut pathogens, including Clostridium innocuum and Actinomyces naeslundii (all p

"Being exposed to a single nasal droplet is enough to cause a person to develop COVID-19, according to a landmark trial. The study, in which researchers deliberately exposed 36 healthy volunteers to SARS-CoV-2, also showed that people developed symptoms rather quickly, in as little as 42 hours." (Medical News Today)

Ben Killingley et al. 2022. Safety, tolerability and viral kinetics during SARS-CoV-2 human challenge. Nature Portfolio Version 1 Posted 01 Feb, 2022 DOI:10.21203/rs.3.rs-1121993/v1 https://www.researchsquare.com/article/rs-1121993/v1

Preprint under review.

To establish a novel SARS-CoV-2 human challenge model, 36 volunteers aged 18-29 years without evidence of previous infection or vaccination were inoculated with 10 TCID50 of a wild-type virus (SARS-CoV-2/human/GBR/484861/2020) intranasally. Two participants were excluded from per protocol analysis due to seroconversion between screening and inoculation. Eighteen (~53%) became infected, with viral load (VL) rising steeply and peaking at ~5 days post-inoculation. Virus was first detected in the throat but rose to significantly higher levels in the nose, peaking at ~8.87 log10 copies/ml ... Viable virus was recoverable from the nose up to ~10 days post-inoculation, on average. There were no serious adverse events. Mild-to-moderate symptoms were reported by 16 (89%) infected individuals, beginning 2-4 days post-inoculation. Anosmia/dysosmia developed more gradually in 12 (67%) participants. No quantitative correlation was noted between VL and symptoms, with high VLs even in asymptomatic infection, followed by the development of serum spike-specific and neutralising antibodies. However, lateral flow results were strongly associated with viable virus and modelling showed that twice-weekly rapid tests could diagnose infection before 70-80% of viable virus had been generated. Thus, in this first SARS-CoV-2 human challenge study, no serious safety signals were detected and the detailed characteristics of early infection and their public health implications were shown. ClinicalTrials.gov identifier: NCT04865237.

Eric Topol (Scripps) @EricTopol | 5:16 PM · Feb 1, 2022:

Not a very encouraging title or report...*
(based on 5 cases; whether and how often the virus directly infects neurons is a controversy)
Photos-infected brain cells ( https://twitter.com/EricTopol/status/1488637332689342468/photo/1 )

Wei-Bin Shen et al. 2022. SARS-CoV-2 invades cognitive centers of the brain and induces Alzheimer's-like neuropathology. BioRxiv Feb 1, 2022. doi: https://doi.org/10.1101/2022.01.31.478476 https://biorxiv.org/content/10.1101/2022.01.31.478476v1

Preprint. Not yet reviewed.

Abstract
Major cell entry factors of SARS-CoV-2 are present in neurons; however, the neurotropism of SARS-CoV-2 and the phenotypes of infected neurons are still unclear. Acute neurological disorders occur in many patients, and one-third of COVID-19 survivors suffer from brain diseases. Here, we show that SARS-CoV-2 invades the brains of five patients with COVID-19 and Alzheimers, autism, frontotemporal dementia or no underlying condition by infecting neurons and other cells in the cortex. SARS-CoV-2 induces or enhances Alzheimers-like neuropathology with manifestations of beta-amyloid aggregation and plaque formation, tauopathy, neuroinflammation and cell death. SARS-CoV-2 infects mature but not immature neurons derived from inducible pluripotent stem cells from healthy and Alzheimers individuals through its receptor ACE2 and facilitator neuropilin-1. SARS-CoV-2 triggers Alzheimers-like gene programs in healthy neurons and exacerbates Alzheimers neuropathology. A gene signature defined as an Alzheimers infectious etiology is identified through SARS-CoV-2 infection, and silencing the top three downregulated genes in human primary neurons recapitulates the neurodegenerative phenotypes of SARS-CoV-2. Thus, SARS-CoV-2 invades the brain and activates an Alzheimers-like program.

U.S. Has Far Higher Covid Death Rate Than Other Wealthy Countries
Benjamin Mueller and Eleanor Lutz | Feb. 1, 2022

Two years into the pandemic, the coronavirus is killing Americans at far higher rates than people in other wealthy nations, a sobering distinction to bear as the country charts a course through the next stages of the pandemic.

Cumulative U.S. Covid-19 deaths per capita are highest among other large, high-income countries
Several countries had higher per capita Covid-19 deaths earlier in the pandemic, but the U.S. death toll now exceeds that of peer nations...

https://www.nytimes.com/interactive/2022/02/01/science/covid-deaths-united-state...
---------------------------------------------------

Mark Miller @RetireRevised | 9:20 PM · Feb 1, 2022
43% of Americans over age 65 have not had a booster shot, compared with 9% in Great Britain.

Eric Topol (Scripps) @EricTopol | 2:21 PM · Feb 1, 2022·Twitter Web App
discussion at https://twitter.com/EricTopol/status/1488593248838840320

Prior to Omicron's emergence reinfections were rare, less than 1% During the Omicron wave in the UK, they have gone up to 10-11% of cases, approximately a 16-fold risk compared with prior variants by @UKHSA, reflecting its immune evasion (and less protection afforded by Prior Covid)

Quote Tweet
Colin Angus (policy modeller) @VictimOfMaths · Feb 1
The UK dashboard now includes data on COVID reinfections for the first time (which were previously excluded from the totals).
It doesn't really change anything, just makes the Omicron peak even higher.
Graph-daily cases July 2020-Jan 2022 ( https://twitter.com/VictimOfMaths/status/1488501500691337216/photo/1 )
---------------------------------------------

JusDayDa @JusDayDa 2:20 PM · Feb 1, 2022

#Reinfection Update
1 - UK ~10% (flat)
2 - Minnesota ~11% (flattening)
3 - Missouri ~8% (rising)
4 - Denmark ~6% (dropping)

Minnesota cleared its data backlog
Omicron rate ~10%-11%

Similarity of curves with an Ocean in-between
England v MN
Graph- England reinfections ( https://twitter.com/JusDayDa/status/1488593047868743683/photo/1 )
Graph- Minnesota reinfections ( https://twitter.com/JusDayDa/status/1488593047868743683/photo/2 )

Eric Topol @EricTopol | 8:37 AM · Jan 25, 2021:
Just published nature*
Understanding why some people develop severe covid while others have mild disease with extensive single-cell RNA-seq of immune cell response

Mild: good interferon (IFN) response
Severe: block IFN, "overzealous" antibody response
-----------------------------------------------------

*Alexis J. Combes etal. 2022. Global absence and targeting of protective immune states in severe COVID-19. Nature volume 591, pages 124–130 (25 Jan 2021)

Abstract
Although infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has pleiotropic and systemic effects in some individuals..., many others experience milder symptoms. Here, to gain a more comprehensive understanding of the distinction between severe and mild phenotypes in the pathology of coronavirus disease 2019 (COVID-19) and its origins, we performed a whole-blood-preserving single-cell analysis protocol to integrate contributions from all major immune cell types of the blood—including neutrophils, monocytes, platelets, lymphocytes and the contents of the serum. Patients with mild COVID-19 exhibit a coordinated pattern of expression of interferon-stimulated genes (ISGs)... across every cell population, whereas these ISG-expressing cells are systemically absent in patients with severe disease. Paradoxically, individuals with severe COVID-19 produce very high titres of anti-SARS-CoV-2 antibodies and have a lower viral load compared to individuals with mild disease. Examination of the serum from patients with severe COVID-19 shows that these patients uniquely produce antibodies that functionally block the production of the ISG-expressing cells associated with mild disease, by activating conserved signalling circuits that dampen cellular responses to interferons. Overzealous antibody responses pit the immune system against itself in many patients with COVID-19, and perhaps also in individuals with other viral infections. Our findings reveal potential targets for immunotherapies in patients with severe COVID-19 to re-engage viral defence.

Prevent airborne diseases (infographic)
https://twitter.com/MarieTattersall/status/1488355830223282176/photo/1

Available in English | Spanish | French | Italian | German | Turkish |
https://www.covidisairborne.org/resources/ventilate

South African scientists copy Moderna’s COVID vaccine
Amy Maxmen | 03 February 2022

Researchers at a South African biotechnology company say they have nearly created a copy of Moderna’s messenger-RNA-based vaccine against COVID-19, without Moderna’s involvement.

The company, Afrigen Biologics and Vaccines, in Cape Town, has made only microlitres of the vaccine, based on data that Moderna used to make its shot. But the achievement is a milestone for a major initiative launched by the World Health Organization (WHO) — a technology transfer hub meant to build capacity for vaccine manufacturing in low- and middle-income countries.

During the COVID-19 pandemic, the developers of mRNA vaccines — Moderna and Pfizer, based in the United States, and Germany’s BioNTech — have sent more than 70% of their doses to wealthy nations, according to vaccine-tracking analyses. Meanwhile, millions of vaccine orders purchased by or promised to countries in the global south for these vaccines have been delayed . “Moderna and Pfizer-BioNTech’s vaccines are mainly still going to just the richest countries,” says Martin Friede, the WHO official coordinating the hub. “Our objective is to empower other countries to make their own.”

Many steps remain before Afrigen’s mRNA vaccine mimic could be distributed to people in Africa and beyond, and it definitely won’t help curb the pandemic this year. But the WHO hopes that the process of creating it will lay the foundation for a more globally distributed mRNA vaccine industry in the future...

https://www.nature.com/articles/d41586-022-00293-2

"male SARS-CoV-2 infection may be associated with a short-term decline in fertility and that COVID-19 vaccination does not impair fertility in either partner"

Study finds 'no adverse association between COVID-19 vaccination and fertility'
Leigh Ann Green | February 2, 2022

Some reproductive-aged individuals are concerned about the potential adverse effects of COVID-19 vaccination on their ability to conceive.

Some earlier research has concluded that COVID-19 vaccinations do not appear to reduce fertility.

A new study adds to this evidence, finding that the vaccines do not affect fertility in males or females.

However, SARS-CoV-2 infection in males does seem to have short-term effects on fertility....

https://www.medicalnewstoday.com/articles/study-finds-no-adverse-association-bet...
-------------------------------------------------

Amelia K Wesselink et al. 2022. A prospective cohort study of COVID-19 vaccination, SARS-CoV-2 infection, and fertility.
American Journal of Epidemiology, Published: 20 January 2022, https://doi.org/10.1093/aje/kwac011 https://academic.oup.com/aje/advance-article/doi/10.1093/aje/kwac011/6511811

Accepted manuscript.

Abstract
Some reproductive-aged individuals remain unvaccinated against COVID-19 due to concerns about potential adverse effects on fertility. We examined the associations of COVID-19 vaccination and SARS-CoV-2 infection with fertility among couples trying to conceive spontaneously using data from an internet-based preconception cohort study. We enrolled 2,126 self-identified females residing in the U.S. or Canada during December 2020-September 2021 and followed them through November 2021. Participants completed questionnaires every 8 weeks on sociodemographics, lifestyle, medical factors, and partner information. We fit proportional probabilities regression models to estimate associations between self-reported COVID-19 vaccination and SARS-CoV-2 infection in both partners with fecundability, the per-cycle probability of conception, adjusting for potential confounders. COVID-19 vaccination was not appreciably associated with fecundability in either partner (female FR=1.08...; male FR=0.95...). Female SARS-CoV-2 infection was not strongly associated with fecundability (FR=1.07...). Male infection was associated with a transient reduction in fecundability (FR=0.82...for infection within 60 days; FR=1.16...for infection greater than 60 days). These findings indicate that male SARS-CoV-2 infection may be associated with a short-term decline in fertility and that COVID-19 vaccination does not impair fertility in either partner.

Here in MI, USPS e-mailed that tests were to be delivered imminently, but then "Delivery Attempted - No Access to Delivery Location". Other locations on our route may have been snowed in, but our roadside mailbox, private road, driveway and porch were all clear... Hope tests didn't spend night in a frozen truck... However, single (as opposed to multiple) freeze-thaws shouldn't destroy the test:

Michael Mina (frmr Harvard, proponent rapid tests) @michaelmina_lab | 11:13 PM · Feb 3, 2022:
Important: A common ?
- Your Rapid Test was delivered to you in the middle of the winter
- It froze in your mailbox
Is it still OK?

YES. a single freeze-thaw isn’t going to destroy the rapid antigen test. May reduce sensitivity a Little bit, but not much.

and Heat?… 1/
Very high heat can cause a lot of damage to a rapid antigen test… don’t let your test boil in the sun in the summer… the proteins can fall apart and the test can be irreparably harmed. 2/

>73 margd: contd. A Med Page article on Spudich and Nath (2022):

The neurological impact of COVID-19: What we know so far
Mary McGorray, M.D. | February 3, 2022
https://www.medicalnewstoday.com/articles/the-neurological-impact-of-covid-19-wh...
-------------------------------------------------------------

Serena Spudich and Avindra Nath. 2022. Nervous system consequences of COVID-19 (Perspective). Science • 20 Jan 2022 • Vol 375, Issue 6578 • pp. 267-269 • DOI: 10.1126/science.abm2052 https://www.science.org/doi/10.1126/science.abm2052

Unpublished, preliminary research presented at conference:

Stroke risk among older adults highest in first 3 days after COVID-19 diagnosis
American Stroke Association International Stroke Conference, Presentation TMP16
(News Release) NEW ORLEANS, Feb. 3, 2022

...The analysis found:
The greatest risk of stroke occurred during the first three days after COVID-19 diagnosis - 10 times higher than during the control period.

Following the first three days after COVID-19 diagnosis, the stroke risk quickly declined yet remained higher compared to the control period. Specifically, between days 4-7 the stroke risk was 60% higher, and between days 8-14, the stroke risk was 44% higher compared to the control period. The lowest stroke risk occurred after 15-28 days when the risk of stroke was 9% higher than during the control period.

A younger subset of participants, those ages 65-74 years old, had a greater risk of stroke after COVID-19 diagnosis, compared to those ages 85 and older, and among those without a history of stroke.

There were no differences in stroke risk related to sex, or race and ethnicity...

https://newsroom.heart.org/news/stroke-risk-among-older-adults-highest-in-first-...

Younger Americans Benefited Less From Booster Shots Than Older People
Apoorva Mandavilli | Feb. 4, 2022

Among those under age 50, vaccination even without a booster protected strongly against hospitalization and death, according to ...new C.D.C. data (through the end of December, when the Omicron surge had just begun)*...booster doses are most beneficial to older adults

As of Dec. 25, the rate of hospitalization among unvaccinated adults older than age 65 was 246 per 100,000 people. That rate dropped to 27.4 per 100,000 among people who were vaccinated without a booster dose, and to 4.9 among those who were vaccinated and received a booster.

There were roughly 44 deaths per 100,000 unvaccinated adults 65 and older. Vaccinations dropped that number to about 3.6 deaths per 100,000, one-twelfth as much. Booster shots reduced the rate further, to about 0.5 deaths per 100,000, a figure 90 times as small.

Among adults 50 to 64, 73 unvaccinated adults per 100,000 were hospitalized, compared with nine per 100,000 among those who were vaccinated and just two per 100,000 among those who had also received a booster shot.

...The agency did not provide hospitalization numbers for adults 18 through 49, perhaps because the numbers were too small.

Boosters made less of a difference in the number of Covid deaths in this age group. Vaccinations decreased the rate to 0.4 deaths per 100,000 from 8.26 per 100,000. With boosters, that number fell to 0.1 deaths per 100,000 people...

https://www.nytimes.com/2022/02/04/health/covid-boosters-older-younger.html

* https://covid.cdc.gov/covid-data-tracker/#covidnet-hospitalizations-vaccination
https://covid.cdc.gov/covid-data-tracker/#rates-by-vaccine-status

Brian Hjelle, virologist* @hjelle_brian | 6:15 PM · Feb 4, 2022:
I actually don't know for sure that a SARS2 infection is persistent in wt (white tail) deer, but it sure smells like it.
We find huge fractions positive for virus, sampling anatomic sites generally unavailable for sampling in humans.
Who wants to bet we aren't the same?

* Brian Hjelle, virologist @hjelle_brian--Scientist (ret). Virologist. Pathologist. MD, Johns Hopkins.

Shelly Miller, PhD (env engr U CO) @ShellyMBoulder | 6:08 PM · Feb 4, 2022:
Recent pilot data from my lab shows higher particle # concentration and CO2 released during whispering compared to loud talking. (Used an AMS). Surprise. We repeated this measure 2x. Same result. Anyone else see this? @Smogdr

Daniel A. Walker @danwalker9999 | 6:36 PM · Feb 4, 2022
Hold your hand 5 cm in front of your mouth and whisper the word “whisper”. Then speak the word “whisper” normally.

Allison I Hilger (speech sci U CO) @drahilger | 9:49 PM · Feb 4, 2022:
The vocal folds are partially adducted but not vibrating so are likely
causing turbulent airflow and greater friction along the mucosal layer of the glottis and vocal tract.

Translated from German by google:
Corona in 5 to 14 year olds: Every tenth child has been infected since the beginning of the year

ZDFheute @ZDFheute | 11:10 AM · Feb 4, 2022
Corona bei 5- bis 14-Jährigen: Jedes zehnte Kind seit Jahresbeginn infiziert

Corona bei 5- bis 14-Jährigen - Jedes zehnte Kind seit Jahresbeginn infiziert
von Kathrin Wolff | 04.02.2022
https://www.zdf.de/nachrichten/panorama/corona-infektionen-kinder-100.html#xtor=...

Trisha Greenhalgh @trishgreenhalgh | 3:12 PM · Feb 4, 2022:
NEW study showing lay people are better protected by respirators (83% lower odds testing pos than with no mask) than standard medical (66%) or cloth face masks (56%).

Andrejko KL, Pry JM, Myers JF, et al. Effectiveness of Face Mask or Respirator Use in Indoor Public Settings for Prevention of SARS-CoV-2 Infection — California, February–December 2021. MMWR Morb Mortal Wkly Rep. ePub: 4 February 2022. DOI: http://dx.doi.org/10.15585/mmwr.mm7106e1 https://www.cdc.gov/mmwr/volumes/71/wr/mm7106e1.htm?s_cid=mm7106e1_w%20%5bcdc.go...

Ashish K. Jha, MD, MPH (Brown SPH) @ashishkjha | 11:06 PM · Feb 4, 2022:

900,000 of our fellow Americans have died of COVID
And we'll likely have 1 million deaths by April
If everyone had gotten vaccinated and boosted as vaccines became available
300,000 Americans would likely still be with us
The loss is staggering. And so much of it, preventable

Molly Jong-Fast (The Atlantic) @MollyJongFast | 8:25 AM · Feb 6, 2022
Pretty good case for moving out of New York City right here

In New York City Sewage, a Mysterious Coronavirus Signal
For the past year, scientists have been looking for the source of strange coronavirus sequences that have appeared in the city’s wastewater.
Emily Anthes | Feb. 3, 2022

Last January, a team of researchers searching for the coronavirus in New York City’s wastewater spotted something strange in their samples. The viral fragments they found had a unique constellation of mutations that had never been reported before in human patients — a potential sign of a new, previously undetected variant.

For the past year, these oddball sequences, or what the scientists call “cryptic lineages,” have continued to pop up in the city’s wastewater.

There is no evidence that the lineages, which have been circulating for at least a year without overtaking Delta or Omicron, pose an elevated health risk to humans...

https://www.nytimes.com/2022/02/03/health/coronavirus-wastewater-new-york.html
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Davida S. Smyth et al. 2022. Tracking cryptic SARS-CoV-2 lineages detected in NYC wastewater. Nature Communications volume 13, Article number: 635 (03 February 2022) https://www.nature.com/articles/s41467-022-28246-3

Abstract
Tracking SARS-CoV-2 genetic diversity is strongly indicated because diversifying selection may lead to the emergence of novel variants resistant to naturally acquired or vaccine-induced immunity. To monitor New York City (NYC) for the presence of novel variants, we deep sequence most of the receptor binding domain coding sequence of the S protein of SARS-CoV-2 isolated from the New York City wastewater. Here we report detecting increasing frequencies of novel cryptic SARS-CoV-2 lineages not recognized in GISAID’s EpiCoV database. These lineages contain mutations that had been rarely observed in clinical samples, including Q493K, Q498Y, E484A, and T572N and share many mutations with the Omicron variant of concern. Some of these mutations expand the tropism of SARS-CoV-2 pseudoviruses by allowing infection of cells expressing the human, mouse, or rat ACE2 receptor. Finally, pseudoviruses containing the spike amino acid sequence of these lineages were resistant to different classes of receptor binding domain neutralizing monoclonal antibodies. We offer several hypotheses for the anomalous presence of these lineages, including the possibility that these lineages are derived from unsampled human COVID-19 infections or that they indicate the presence of a non-human animal reservoir.
_________________________________________________

Molly Jong-Fast (The Atlantic) @MollyJongFast:
Never mind, might as well stay in New York City
Text re similar findings in CA (https://twitter.com/MollyJongFast/status/1490316124977782792/photo/1)

Rachel Thomas Data sci prof) @math_rachel | 5:15 PM · Feb 4, 2022:
https://twitter.com/math_rachel/status/1489724443329204224

“They offered people vaccines. There’s nothing more our leaders can do"
There’s actually a lot more, including: 1/

Quote Tweet
wsbgnl @wsbgnl · Jan 24
Some tools we do not have: adequate availability of free high quality masks and testing, paid sick and family leave, hazard pay, free isolation options for people in crowded housing, public indoor air quality standards, affordable health care, short-term disability benefits

Dr. Lisa Iannattone (dermatology U Montreal) @lisa_iannattone | 12:00 AM · Feb 5, 2022
“The flu is more dangerous for kids.”
Then why have more kids died of covid in the US in 2 years than died of influenza in the last 11 years?
Because the likelihood of catching a virus factors into the likelihood of having a bad outcome and covid is far more contagious.

Quote Tweet
Ben Weston MD MPH · Feb 3
Replying to @VPrasadMDMPH
Fatality rates can't stand alone.
Transmissibility needs to be considered (as pointed out as important context in original figure by @jburnmurdoch).
That is how you end up getting a figure like the one below to balance out the understanding of COVID impact on kids.
Graph- deaths flu v COVID, 0-17y ( https://twitter.com/BenWWeston/status/1489263095990026248/photo/1 )

Michael Lin, MD PhD (Stanford) @michaelzlin | 1:30 PM · Feb 6, 2022:

Just out: a new study of immunity against Omicron after vaccines or infection + vaccines.
Simple takeaway: you need 3 hits, whether vaccine or infection, for high antibodies
Interesting nuance: infection has a head start over vax but dose #3 closes it

Wratil, P.R., Stern, M., Priller, A. et al. Three exposures to the spike protein of SARS-CoV-2 by either infection or vaccination elicit superior neutralizing immunity to all variants of concern. Nat Med (2022). https://doi.org/10.1038/s41591-022-01715-4 https://www.nature.com/articles/s41591-022-01715-4#Sec15

Accepted, unedited ms.

Abstract
Infection-neutralizing antibody responses after SARS-CoV-2 infection or COVID-19 vaccination are an essential component of antiviral immunity. Antibody-mediated protection is challenged by the emergence of SARS-CoV-2 variants of concern (VoCs) with immune escape properties, such as omicron (B.1.1.529) that is rapidly spreading worldwide. Here, we report neutralizing antibody dynamics in a longitudinal cohort of COVID-19 convalescent and infection-naive individuals vaccinated with mRNA BNT162b2 by quantifying anti-SARS-CoV-2-spike antibodies and determining their avidity and neutralization capacity in serum. Using live-virus neutralization assays, we show that a superior infection-neutralizing capacity against all VoCs, including omicron, developed after either two vaccinations in convalescents or after a third vaccination or breakthrough infection of twice-vaccinated, naive individuals. These three consecutive spike antigen exposures resulted in an increasing neutralization capacity per anti-spike antibody unit and were paralleled by stepwise increases in antibody avidity. We conclude that an infection-plus-vaccination-induced hybrid immunity or a triple immunization can induce high-quality antibodies with superior neutralization capacity against VoCs, including omicron.

>126 margd: Always wear a mask, and spray w disinfectant when cleaning up rodent droppings and bat guano. Aerosolized feces can spread pathogens such as Hantah virus and histoplasmosis fungus--and maybe new strains of SARS-CoV-19 as suspected with omicron and now NYC and LA wastewater.

Michael Mina @michaelmina_lab | Feb 2, 2022:
https://twitter.com/michaelmina_lab/status/1488988413948829696
@CDCgov exit isolation at day 5 w/out Neg Rapid Ag Test = dangerous policy

To clarify our new research
It does NOT show boosters are causing people to be more infectious longer

It DOES suggest Boosted ppl enter isolation sooner after exposure, and are thus much more likely to be at peak virus load at Day 5 h
--------------------------------------------

Emily Landon...Michael J. Mina. 2022. High Rates of Rapid Antigen Test Positivity After 5 days of Isolation for COVID-19. MedRxiv Feb 2, 2022. doi: https://doi.org/10.1101/2022.02.01.22269931

This article is a preprint and has not been peer-reviewed

Abstract
...Discussion More than 40% of vaccinated HCW who felt well enough to work still had positive RAT (Rapid Antigen) tests when presenting for a first test between days 5 and 10. Boosted individuals were nearly 3x as likely to result positive on day 5, their first day eligible for return, and ∼2x as likely to result positive on first RAT overall. New guidance provides clearance to exit isolation after 5 days from symptom onset, without the need for a negative rapid antigen test to exit, as long as symptoms are beginning to resolve. Per CDC, the guidance was driven by prior studies, mostly collected before Omicron and before most people were vaccinated or infected, that reported on symptom onset beginning one or more days after peak virus loads. In such an instance, where isolation based on symptom onset often did not begin until peak virus load was already attained, then release from isolation at 5 days would be appropriate. However, reports showing much earlier onset of symptoms, coupled with our own results here demonstrate that the relationship between symptom onset and peak virus load has changed, and 5 days from symptom onset may no longer be an appropriate window to end isolation without a negative rapid antigen test to support safe exit.

Conclusion These results indicate that a substantial proportion of individuals with COVID-19 are likely still contagious after day 5 of illness regardless of symptom status. Early liberation from isolation should be undertaken only with the understanding that inclusion of individuals on day 6-10 of illness in community or work settings may increase the risk of COVID-19 spread to others which, in turn, may undermine the intended benefits to staffing by resulting in more sick workers.

Ohio data well-represented:

SARS-CoV-2 RNA Levels in Wastewater in the United States

Maps, charts, and data provided by CDC, updated by 8pm ET. Represents all wastewater data submitted directly to CDC’s National Wastewater Surveillance System's DCIPHER platform, subject to suppression criteria described in Footnotes.

For more information on wastewater surveillance, please visit the National Wastewater Surveillance System page...

https://covid.cdc.gov/covid-data-tracker/#wastewater-surveillance

Eric Topol (Scripps) @EricTopol | 10:05 AM · Feb 7, 2022
The first comprehensive assessment of the cardiovascular complications of #LongCovid at 1 year, just published @NatureMedicine

Yan Xie et al. 2022. Long-term cardiovascular outcomes of COVID-19. Nature Medicine (Feb 7, 2022) https://www.nature.com/articles/s41591-022-01689-3

Fig. 6: Risks and 12-month burdens of incident post-acute COVID-19 composite cardiovascular outcomes compared with the contemporary control cohort by care setting of the acute infection. ( https://twitter.com/EricTopol/status/1490703191712825345/photo/2 )

Abstract
The cardiovascular complications of acute coronavirus disease 2019 (COVID-19) are well described, but the post-acute cardiovascular manifestations of COVID-19 have not yet been comprehensively characterized. Here we used national healthcare databases from the US Department of Veterans Affairs to build a cohort of 153,760 individuals with COVID-19, as well as two sets of control cohorts with 5,637,647 (contemporary controls) and 5,859,411 (historical controls) individuals, to estimate risks and 1-year burdens of a set of pre-specified incident cardiovascular outcomes. We show that, beyond the first 30 d after infection, individuals with COVID-19 are at increased risk of incident cardiovascular disease spanning several categories, including cerebrovascular disorders, dysrhythmias, ischemic and non-ischemic heart disease, pericarditis, myocarditis, heart failure and thromboembolic disease. These risks and burdens were evident even among individuals who were not hospitalized during the acute phase of the infection and increased in a graded fashion according to the care setting during the acute phase (non-hospitalized, hospitalized and admitted to intensive care). Our results provide evidence that the risk and 1-year burden of cardiovascular disease in survivors of acute COVID-19 are substantial. Care pathways of those surviving the acute episode of COVID-19 should include attention to cardiovascular health and disease.

Discussion
...Governments and health systems around the world should be prepared to deal with the likely significant contribution of the COVID-19 pandemic to a rise in the burden of cardiovascular diseases. Because of the chronic nature of these conditions, they will likely have long-lasting consequences for patients and health systems and also have broad implications on economic productivity and life expectancy. Addressing the challenges posed by Long COVID will require a much-needed, but so far lacking, urgent and coordinated long-term global response strategy...

Moderna’s omicron booster was only as good as current vaccine in monkey study
Boosting with an omicron-specific vaccine didn't offer more protection against omicron.
Beth Mole - 2/7/2022
https://arstechnica.com/science/2022/02/monkey-study-casts-doubt-on-need-for-an-...
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Matthew Gagne et al. 2022. mRNA-1273 or mRNA-Omicron boost in vaccinated macaques elicits comparable B cell expansion, neutralizing antibodies and protection against Omicron. BioRxiv Feb 4, 2022. doi: https://doi.org/10.1101/2022.02.03.479037 https://www.biorxiv.org/content/10.1101/2022.02.03.479037v1

This article is a preprint and has not been certified by peer review

Summary
SARS-CoV-2 Omicron is highly transmissible and has substantial resistance to antibody neutralization following immunization with ancestral spike-matched vaccines. It is unclear whether boosting with Omicron-specific vaccines would enhance immunity and protection. Here, nonhuman primates that received mRNA-1273 at weeks 0 and 4 were boosted at week 41 with mRNA-1273 or mRNA-Omicron. Neutralizing antibody titers against D614G* were 4760 and 270 reciprocal ID50 at week 6 (peak) and week 41 (pre-boost), respectively, and 320 and 110 for Omicron. Two weeks after boost, titers against D614G and Omicron increased to 5360 and 2980, respectively, for mRNA-1273 and 2670 and 1930 for mRNA-Omicron. Following either boost, 70-80% of spike-specific B cells were cross-reactive against both WA1 and Omicron. Significant and equivalent control of virus replication in lower airways was observed following either boost. Therefore, an Omicron boost may not provide greater immunity or protection compared to a boost with the current mRNA-1273 vaccine.

* Mansbach et al. (Apr 2021): "A viral variant has recently emerged, carrying a single amino acid substitution in Spike at residue 614 from an aspartic acid (D) to a glycine (G) (D614G). This G-form (also referred to as G614) is now the globally prevalent form and is potentially more transmissible than the originally observed D-form (also referred to as D614)"
https://www.science.org/doi/10.1126/sciadv.abf3671

margd: this was first seen in Seattle, WA mutation of the Wuhan strain, i.e., SARS-CoV-2 USA-WA1/2020 strain (?)

Eric Topol @EricTopol | 9:58 AM · Feb 8, 2022:
https://twitter.com/EricTopol/status/1491063815727108097
There is zero evidence that vaccines cause infertility in men (or women) but a new report about Covid and live virus found in testicles:

Guilherme M J Costa et al. 2022. SARS-CoV-2 infects, replicates, elevates angiotensin II and activates immune cells in human testes
MedRXiv Feb 8, 2022. doi: https://doi.org/10.1101/2022.02.05.22270327 https://medrxiv.org/content/10.1101/2022.02.05.22270327v1

This article is a preprint and has not been certified by peer review

Abstract
Although much has been published since the first cases of COVID-19, there remain unanswered questions regarding SARS-CoV-2 impact on testes and the potential consequences for reproductive health. We investigated testicular alterations in deceased COVID-19-patients, the precise location of the virus, its replicative activity, and the molecules involved in the pathogenesis. We found that SARS-CoV-2 testicular tropism is higher than previously thought and that reliable viral detection in the testis requires sensitive nanosensoring or RT-qPCR using a specific methodology. Macrophages and spermatogonial cells are the main SARS-CoV-2 lodging sites and where new virions form inside the Endoplasmic Reticulum Golgi Intermediate Complex. Moreover, we showed infiltrative infected monocytes migrating into the testicular parenchyma. SARS-CoV-2 maintains its replicative and infective abilities long after the patient infection, suggesting that the testes may serve as a viral sanctuary. Further, infected testes show thickening of the tunica propria, germ cell apoptosis, Sertoli cell barrier loss, evident hemorrhage, angiogenesis, Leydig cell inhibition, inflammation, and fibrosis. Finally, our findings indicate that high angiotensin II levels and activation of mast cells and macrophages may be critical for testicular pathogenesis. Importantly, our data suggest that patients who become critically ill exhibit severe damages and may harbor the active virus in testes.

Eric Topol (Scripps) @EricTopol | 8:29 PM · Feb 7, 2022
The accompanying editorial reviews ... 2 new reports and the previous studies about #LongCovid in teens and is reassuring

Text, highlighted:
https://twitter.com/EricTopol/status/1490860416976953344/photo/1
https://twitter.com/EricTopol/status/1490860416976953344/photo/2

Erika Molteni et al. 2022. Assessing the impact of the pandemic in children and adolescents: SARS-CoV-2 infection and beyond. The Lancet Child and Adolescent Health. Published:February 07, 2022 DOI:https://doi.org/10.1016/S2352-4642(22)00035-9
https://thelancet.com/journals/lanchi/article/PIIS2352-4642(22)00035-9/fulltext

Health & Veritas: Is Long COVID One Disease or Many? (Ep. 19) (33:42)

On the Health & Veritas podcast, Yale physician-professors Howard Forman and Harlan Krumholz talk about the latest news and ideas in healthcare and seek out the truth amid the noise. In the latest episode, they talk with Dr. Akiko Iwasaki about her research trying to understand the cause or causes of long COVID, which has more than 200 reported symptoms.

https://insights.som.yale.edu/insights/health-veritas-is-long-covid-one-disease-...

Dr. Vin Gupta ( Lung MD | Faculty @IHME_UW ) @VinGuptaMD | 8:51 PM · Feb 7, 2022
Since some like to talk about “pandemic restrictions” like we are back in March 2020, here’s the *actual* reality below Downwards arrow⁩
Orange means no restrictions. Lots of orange below.
People are not being restricted.
Ignore those who want to convince you otherwise.
Table ( https://twitter.com/VinGuptaMD/status/1490865865054556160/photo/1 )

COVID-19: Loss of smell gives clues about long COVID
James Kingsland | February 9, 2022

Scientists are unsure why COVID-19 causes smell loss in so many people because the virus that causes the disease, SARS-CoV-2, cannot infect olfactory sensory neurons.

A new study in hamsters suggests that the infection of neighboring cells may trigger a reorganization in the nuclei of these sensory neurons.

This reorganization appears to disrupt the production of odor receptors in the cells.

The findings may shed light on the causes of other lingering neurological effects of COVID-19, such as “brain fog,” headaches, and depression...

https://www.medicalnewstoday.com/articles/covid-19-loss-of-smell-gives-clues-abo...
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Marianna Zazhytska et al. 2022. Non-cell autonomous disruption of nuclear architecture as a potential cause of COVID-19 induced anosmia. Cell. Available online 2 February 2022. https://doi.org/10.1016/j.cell.2022.01.024 https://www.sciencedirect.com/science/article/pii/S0092867422001350

In Press, Journal Pre-proof

Highlights
• Downregulation of odor detection pathways may explain COVID-19 induced anosmia.
• SARS-CoV-2 mediated disruption of nuclear architecture may impair odor detection.
• SARS-CoV-2 mediated nuclear reorganization is non-cell autonomous.

Abstract:
SARS-CoV-2 infects less than 1% of cells in the human body, yet it can cause severe damage in a variety of organs. Thus, deciphering the non-cell autonomous effects of SARS-CoV-2 infection is imperative for understanding the cellular and molecular disruption it elicits. Neurological and cognitive defects are among the least understood symptoms of COVID-19 patients, with olfactory dysfunction being their most common sensory deficit. Here, we show that both in humans and hamsters SARS-CoV-2 infection causes widespread downregulation of olfactory receptors (OR) and of their signaling components. This non-cell autonomous effect is preceded by a dramatic reorganization of the neuronal nuclear architecture, which results in dissipation of genomic compartments harboring OR genes. Our data provide a potential mechanism by which SARS-CoV-2 infection alters the cellular morphology and the transcriptome of cells it cannot infect, offering insight to its systemic effects in olfaction and beyond.

>133 margd: contd.

COVID-19 takes serious toll on heart health—a full year after recovery
Giant study shows striking rise in long-term heart and vessel disease
Meredith Wadman | 9 Feb 2022

"One limitation of the study* is that the veteran population skews older, white, and male: In all three groups, about 90% of patients were men and 71% to 76% were white. Patients were in their early 60s, on average.

The researchers controlled for the possibility that the people who contracted COVID-19 were already more prone to developing cardiovascular disease. They found that “COVID is an equal opportunity offender,” (senior author Ziyad Al-Aly, a clinical epidemiologist at Washington University in St. Louis and chief of research at the VA St Louis Health Care system.) says. “We found an increased risk of cardiovascular problems in old people and in young people, in people with diabetes and without diabetes, in people with obesity and people without obesity, in people who smoked and who never smoked.”

COVID-19 boosted the risk of all 20 cardiovascular ailments studied, including heart attacks, arrhythmias, strokes, transient ischemic attacks, heart failure, inflammatory heart disease, cardiac arrest, pulmonary embolism, and deep vein thrombosis...

https://www.science.org/content/article/covid-19-takes-serious-toll-heart-health...
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* Yan Xie et al. 2022. Long-term cardiovascular outcomes of COVID-19. Nature Medicine (Feb 7, 2022) https://www.nature.com/articles/s41591-022-01689-3

"no presently approved or authorized monoclonal antibody therapy could adequately cover all sublineages of the Omicron variant."

ChristosArgyropoulos MD, PhD FlozinatorInChief @ChristosArgyrop | 10:38 PM · Feb 9, 2022:
I hate to break the bad news to you, but we just lost sotrovimab (27 fold less activity again BA.2).
(Also "natural boosting" less Ab (antibodies) than vaxx, which overwhelmingly sucked against the Cron esp in the absence of #Gigavaxx ...

While acknowledging this data, the company says their own data suggests that Sotrovimab retain activity and promise to release their own data (on pseudoviral neutralization assays) in the next few days, with live virus data to follow: https://www.globenewswire.com/news-release/2022/02/10/2382435/0/en/Data-Suggest-...
-----------------------------------------------------------------------

Sho Iketani (Columbia U Irving Medical Center) et al. 20220. Antibody Evasion Properties of SARS-CoV-2 Omicron Sublineages.BioRxiv Feb 9, 2022.
doi: https://doi.org/10.1101/2022.02.07.479306 https://www.biorxiv.org/content/10.1101/2022.02.07.479306v1

This article is a preprint and has not been certified by peer review

Abstract
The identification of the Omicron variant (B.1.1.529.1 or BA.1) of SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) in Botswana in November 20211 immediately raised alarms due to the sheer number of mutations in the spike glycoprotein that could lead to striking antibody evasion. We... and others... recently reported results in this Journal confirming such a concern. Continuing surveillance of Omicron evolution has since revealed the rise in prevalence of two sublineages, BA.1 with an R346K mutation (BA.1+R346K) and B.1.1.529.2 (BA.2), with the latter containing 8 unique spike mutations while lacking 13 spike mutations found in BA.1. We therefore extended our studies to include antigenic characterization of these new sublineages. Polyclonal sera from patients infected by wild-type SARS-CoV-2 or recipients of current mRNA vaccines showed a substantial loss in neutralizing activity against both BA.1+R346K and BA.2, with drops comparable to that already reported for BA.12,3,5,6. These findings indicate that these three sublineages of Omicron are antigenically equidistant from the wild-type SARS-CoV-2 and thus similarly threaten the efficacies of current vaccines. BA.2 also exhibited marked resistance to 17 of 19 neutralizing monoclonal antibodies tested, including S309 (sotrovimab)..., which had retained appreciable activity against BA.1 and BA.1+R346K... This new finding shows that no presently approved or authorized monoclonal antibody therapy could adequately cover all sublineages of the Omicron variant.

White, Laura F., Eleanor J. Murray, and Arijit Chakravarty. 2022. “The Role of Schools in Driving Sars-cov-2 Transmission: Not Just an Open-and-shut Case.” OSF Preprints. February 8. osf.io/2eh5m. https://osf.io/2eh5m/

Summary
Keeping schools open without permitting COVID-19 spread has been complicated by conflicting messages around the role of children and schools in fueling the pandemic. Here, we describe methodological limitations of research minimizing SARS-CoV-2 transmission in schools, and we review evidence for safely operating schools while reducing overall SARS-CoV-2 transmission

Table summarizing biases and impacts on conclusions ( https://twitter.com/EpiEllie/status/1491132722752135168/photo/1 )

Eric Feigl-Ding @DrEricDing | 1:10 PM · Feb 9, 2022:
18) Further—“results indicate that Omicron infection enhances preexisting immunity elicited by vaccines,
but on its own **may NOT induce broad, cross-neutralizing humoral immunity in unvaccinated** individuals.”
Warning... Don’t risk #Omicron BA2 if unvaxxed!

Rahul K. Suryawanshi et al. 2022. Limited cross-variant immunity after infection with the SARS-CoV-2 Omicron variant without vaccination. MedRxiv Feb 9, 2022. doi: https://doi.org/10.1101/2022.01.13.22269243 https://www.medrxiv.org/content/10.1101/2022.01.13.22269243v3

This article is a preprint and has not been certified by peer review

Abstract
SARS-CoV-2 Delta and Omicron strains are the most globally relevant variants of concern (VOCs). While individuals infected with Delta are at risk to develop severe lung disease..., Omicron infection causes less severe disease, mostly upper respiratory symptoms... The question arises whether rampant spread of Omicron could lead to mass immunization, accelerating the end of the pandemic. Here we show that infection with Delta, but not Omicron, induces broad immunity in mice. While sera from Omicron-infected mice only neutralize Omicron, sera from Delta-infected mice are broadly effective against Delta and other VOCs, including Omicron. This is not observed with the WA1 ancestral strain, although both WA1 and Delta elicited a highly pro-inflammatory cytokine response and replicated to similar titers in the respiratory tracts and lungs of infected mice as well as in human airway organoids. Pulmonary viral replication, pro-inflammatory cytokine expression, and overall disease progression are markedly reduced with Omicron infection. Analysis of human sera from Omicron and Delta breakthrough cases reveals effective cross-variant neutralization induced by both viruses in vaccinated individuals. Together, our results indicate that Omicron infection enhances preexisting immunity elicited by vaccines, but on its own may not induce broad, cross-neutralizing humoral immunity in unvaccinated individuals.

Dr. Tom Frieden (former director CDC) @DrTomFrieden | 10:38 AM · Feb 9, 2022:
These findings are another reason for expecting moms to get vaccinated and boosted if they haven't been already.

Lydia L. Shook et al. 2022. Durability of Anti-Spike Antibodies in Infants After Maternal COVID-19 Vaccination or Natural Infection (Research letter). JAMA. Published online February 7, 2022. doi:10.1001/jama.2022.1206 https://jamanetwork.com/journals/jama/fullarticle/2788986

Discussion
This study found that the majority of infants born to COVID-vaccinated mothers had persistent anti-S antibodies at 6 months, compared with infants born to mothers with SARS-CoV-2 infection. Understanding the persistence of maternal antibody levels in infants is important because COVID-19 infections in this age group account for a disproportionate burden of pediatric SARS-CoV-2–associated morbidity... and because COVID-19 vaccines are not currently planned for administration to infants younger than 6 months. Study limitations include the small number of infants, the longer mean time to follow-up in the infected group (due to pragmatic constraints related to timing of COVID-19 surges in Boston and the availability of participants for timely follow-up), and the reporting of antibody titers rather than clinical outcomes. Although the antibody titer known to be protective against COVID-19 in infants is unknown, these findings provide further incentive for pregnant individuals to pursue COVID-19 vaccination.

Could this bat-crazy, Halloweenie virus get any weirder? Apparently it resurrects remnants of zombie viruses... :(

Yaneer Bar-Yam @yaneerbaryam | 4:57 PM · Feb 8, 2022:
Human DNA has remnants of ancient viral infections called Human Endogenous Retroviruses(HERV)
Infographic ( https://twitter.com/yaneerbaryam/status/1491169257639788546/photo/1 )

Benjamin Charvet, et al. 2022. SARS-CoV-2 induces human endogenous retrovirus type W envelope protein expression in blood lymphocytes and in tissues of COVID-19 patients. MedRxiv January 21, 2022. doi: https://doi.org/10.1101/2022.01.18.21266111 https://www.medrxiv.org/content/10.1101/2022.01.18.21266111v2

This article is a preprint and has not been peer-reviewed

Abstract
Patients with COVID-19 may develop abnormal inflammatory response and lymphopenia, followed in some cases by delayed-onset syndromes, often long-lasting after the initial SARS-CoV-2 infection. As viral infections may activate human endogenous retroviral elements (HERV), we studied the effect of SARS-CoV-2 on HERV-W and HERV-K envelope (ENV) expression, known to be involved in immunological and neurological pathogenesis of human diseases. Our results have showed that the exposure to SARS-CoV-2 virus activates early HERV-W and K transcription but only HERV-W ENV protein expression, in an infection- and ACE2-independent way within peripheral blood mononuclear cell cultures from one-third of healthy donors. Moreover, HERV-W ENV protein was significantly increased in serum and plasma of COVID-19 patients, correlating with its expression in CD3+ lymphocytes and with disease severity. Finally, HERV-W ENV was found expressed in post-mortem tissues of lungs, heart, brain olfactory bulb and nasal mucosa from acute COVID-19 patients in cell-types relevant for COVID-19-associated pathogenesis within affected organs, but different from those expressing of SARS-CoV-2 antigens. Altogether, the present study revealed that SARS-CoV-2 can induce HERV-W ENV expression in cells from individuals with symptomatic and severe COVID-19. Our data suggest that HERV-W ENV is likely to be involved in pathogenic features underlying symptoms of acute and post-acute COVID. It highlights the importance to further understand patients’ genetic susceptibility to HERV-W activation and the relevance of this pathogenic element as a prognostic marker and a therapeutic target in COVID-19 associated syndromes.

In Canada, at least

... Border PCR testing is well past its usefulness, and can be relaxed.
Even vaccine passports have served their purpose, (more than) 90% of adults are vaccinated.
But removing masks, and letting the virus rip through the public over and over again is a terrible idea at this time.

- Kashif Pirzada (emergency MD Toronto), MD@KashPrime | 12:24 AM · Feb 12, 2022

COVID-19 and Improving Indoor Air Quality in Schools
CA DPH | February 10, 2022

Optimize or Upgrade Your Mechanical Ventilation (HVAC) System
Open Doors and Windows (Natural Ventilation)
Add Portable Air Cleaning Devices (PACs)

RESOURCES

https://www.cdph.ca.gov/Programs/CID/DCDC/Pages/COVID-19/COVID-19-and-Improving-...

Eric Topol @EricTopol | Feb 11, 2022 3:08 am
A new review of effective anti-#SARSCoV2 treatments to prevent hospitalizations and deaths
only 1 in pill form with high efficacy ~90% (Paxlovid)
https://twitter.com/EricTopol/status/1492229128493223936/photo/1
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Manmeet Singh and Emmie de Witt. 2022. Antiviral agents for the treatment of COVID-19: progress and challenges. Cell Reports Medicine. Open AccessPublished:February 10, 2022. DOI:https://doi.org/10.1016/j.xcrm.2022.100549 https://www.cell.com/cell-reports-medicine/fulltext/S2666-3791(22)00055-6#relate...
Summary
The COVID-19 pandemic has seen clinical development and use of antiviral therapies at an unprecedented speed. Antiviral therapies have greatly improved the clinical outcome in COVID-19 patients, especially when administered early after diagnosis. Here, we discuss the successes and challenges of COVID-19 antiviral therapies, and lessons for future pandemics.

COVID infection of placenta, but not fetus, responsible for fetus's (rare) death:

In unvaccinated pregnant women, Covid can cause deadly harm to babies
Though rare, Covid during pregnancy can increase a woman's risk of stillbirth.
Kaitlin Sullivan | Feb. 10, 2022 / Updated Feb. 11, 2022

Research published Thursday paints a startling picture of the destructive toll Covid-19 can take on pregnant women and their growing fetuses.

The virus can attack and destroy the placenta, a vascular organ that serves as a fetus’s lifeline, leading to asphyxiation and stillbirth, according to the study in the journal Archives of Pathology & Laboratory Medicine.

“We have never seen this level of destruction from an infectious illness before. It rendered the placenta unfit to carry out its duties,” said Dr. David Schwartz, a perinatal pathologist in private practice in Atlanta, who led the study. “These fetuses and newborns died from asphyxiation due to lack of oxygen.” ...

https://www.nbcnews.com/health/health-news/covid-stillbirths-coronavirus-can-sev...
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David A. Schwartz et al. 2022. Placental Tissue Destruction and Insufficiency from COVID-19 Causes Stillbirth and Neonatal Death from Hypoxic-Ischemic Injury: A Study of 68 Cases with SARS-CoV-2 Placentitis from 12 Countries. Arch Pathol Lab Med (Feb 10, 2022) https://doi.org/10.5858/arpa.2022-0029-SA https://meridian.allenpress.com/aplm/article/doi/10.5858/arpa.2022-0029-SA/47769...

ABSTRACT
Context.—
Perinatal death is an increasingly important problem as the COVID-19 pandemic continues, but the mechanism of death has been unclear.

Objective.—
To evaluate the role of the placenta in causing stillbirth and neonatal death following maternal infection with COVID-19 and confirmed placental positivity for SARS-CoV-2.

Design.—
Case-based retrospective clinico-pathological analysis by a multinational group of 44 perinatal specialists from 12 countries of placental and autopsy pathology findings from 64 stillborns and 4 neonatal deaths having placentas testing positive for SARS-CoV-2 following delivery to mothers with COVID-19.

Results.—
All 68 placentas had increased fibrin deposition and villous trophoblast necrosis and 66 had chronic histiocytic intervillositis, the three findings constituting SARS-CoV-2 placentitis. Sixty-three placentas had massive perivillous fibrin deposition. Severe destructive placental disease from SARS-CoV-2 placentitis averaged 77.7% tissue involvement. Other findings included multiple intervillous thrombi (37%; 25/68) and chronic villitis (32%; 22/68). The majority (19, 63%) of the 30 autopsies revealed no significant fetal abnormalities except for intrauterine hypoxia and asphyxia. Among all 68 cases, SARS-CoV-2 was detected from a body specimen in 16 of 28 cases tested, most frequently from nasopharyngeal swabs. Four autopsied stillborns had SARS-CoV-2 identified in internal organs.

Conclusions.—
The pathology abnormalities composing SARS-CoV-2 placentitis cause widespread and severe placental destruction resulting in placental malperfusion and insufficiency. In these cases, intrauterine and perinatal death likely results directly from placental insufficiency and fetal hypoxic-ischemic injury. There was no evidence that SARS-CoV-2 involvement of the fetus had a role in causing these deaths.

Ferdinands JM, Rao S, Dixon BE, et al. Waning 2-Dose and 3-Dose Effectiveness of mRNA Vaccines Against COVID-19–Associated Emergency Department and Urgent Care Encounters and Hospitalizations Among Adults During Periods of Delta and Omicron Variant Predominance — VISION Network, 10 States, August 2021–January 2022. MMWR Morb Mortal Wkly Rep. ePub: 11 February 2022. DOI: http://dx.doi.org/10.15585/mmwr.mm7107e2 https://www.cdc.gov/mmwr/volumes/71/wr/mm7107e2.htm?s_cid=mm7107e2_x

...Discussion
In a multistate analysis of 241,204 ED/UC ( emergency department/urgent car) encounters and 93,408 hospitalizations among adults with COVID-19–like illness during August 26, 2021–January 22, 2022, estimates of VE (vaccine effectiveness) against laboratory-confirmed COVID-19 were lower during the Omicron-predominant than during the Delta-predominant period, after accounting for both number of vaccine doses received and time since vaccination. During both periods, VE after receipt of a third dose was always higher than VE following a second dose; however, VE waned with increasing time since vaccination. During the Omicron-predominant period, mRNA vaccination was highly effective against both COVID-19–associated ED/UC encounters (VE = 87%) and COVID-19 hospitalizations (VE = 91%) within 2 months after a third dose, but effectiveness waned, declining to 66% for prevention of COVID-19–associated ED/UC encounters by the fourth month after receipt of a third dose and to 78% for hospitalizations by the fourth month after receipt of a third dose. The finding of lower VE for 2 or 3 doses during the Omicron-predominant period is consistent with previous reports from the VISION network and others... Waning of VE after receipt of a third dose of mRNA vaccine has also been observed in Israel... and in preliminary reports from the VISION Network...

...limitations...

These findings underscore the importance of receiving a third dose of mRNA COVID-19 vaccine to prevent both COVID-19–associated ED/UC encounters and COVID-19 hospitalizations among adults. The finding that protection conferred by mRNA vaccines waned in the months after receipt of a third vaccine dose reinforces the importance of further consideration of additional doses to sustain or improve protection against COVID-19–associated ED/UC encounters and COVID-19 hospitalizations. All eligible persons should remain up to date with recommended COVID-19 vaccinations to best protect against COVID-19–associated hospitalizations and ED/UC visits.

Common Over-the-Counter Medication May Provide Relief for People With Long COVID-19 Symptoms
University of California - Irvine February 12, 2022

Antihistamines may provide relief for the millions of people suffering from the painful, debilitating symptoms of long COVID-19 that impair daily functioning. That’s the conclusion of a case report on the experiences of two such patients co-authored by nursing scholars at the University of California, Irvine...

https://scitechdaily.com/common-over-the-counter-medication-may-provide-relief-f...
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“Antihistamines for Postacute Sequelae of SARS-CoV-2 Infection” by Melissa D. Pinto, Natalie Lambert, Charles A. Downs, Heather Abrahim, Thomas D. Hughes, Amir M. Rahmani, Candace W. Burton and Rana Chakraborty, 7 February 2022, The Journal for Nurse Practitioners. DOI: 10.1016/j.nurpra.2021.12.016 https://www.npjournal.org/article/S1555-4155(21)00547-X/fulltext

Abstract
Postacute sequelae of SARS-CoV2 (PASC) infection is an emerging global health crisis, variably affecting millions worldwide. PASC has no established treatment. We describe 2 cases of PASC in response to opportune administration of over-the-counter antihistamines*, with significant improvement in symptoms and ability to perform activities of daily living. Future studies are warranted to understand the potential role of histamine in the pathogenesis of PASC and explore the clinical benefits of antihistamines in the treatment of PASC.

* diphenhydramine HCl (Benadryl)

>149 margd: Awful! Full term delivery and neonatal death - ugh!

>145 margd:

Prof Peter Hotez MD PhD (TX Tropical Pediatrics0 | 4:25 PM · Feb 12, 2022:
https://twitter.com/PeterHotez/status/1492610767346089990

Also the underlying molecular and immunological mechanisms for longCovid are fascinating but chilling. Some really interesting things, autoantibodies, microglial activation, some of this work by @VirusesImmunity (Akiko Iwasaki, Yale)

If I were starting over in science I would give serious thought to working on this infection-neuroscience axis through systems biology and other approaches. It would teach us not only about longCovid but things like CFS, fibromyalgia, other post-infectious sequelae

It’s also another reason I bristle at antivaccine activists who show no compassion for longCovid sufferers or who focus on ways to deflate the death stats among young and middle age adults or kids

This is why I'm particularly disgusted at the 'COVID' is just a mild infection in children so let them catch it. I am very concerned about what we don't know about long term complications.