The @CovidGenomicsUK Mutation Explorer http://sars2.cvr.gla.ac.uk/cog-uk/ is now tracking the combinations of spike substitutions known to reduce binding by either casirivimab or imdevimab, the constituents of the therapeutic antibody cocktail Ronapreve

In June, Taco Bell locations in California offered "a free seasoned beef Nacho Cheese Doritos® Locos Tacos" to anyone who provided proof of vaccination. The company said it was offering the promotion because there are "still plenty of young people who need to get vaccinated." The company said that it was important to "increase vaccinations" to keep everyone safe. But if you stop in for a Chalupa today, the odds are that your cashier still won't be vaccinated. A new study found that, as of November 2021, just 46% of Taco Bell workers have received a vaccine. The same study found low vaccination rates at many of the nation's most popular casual restaurants — including Subway (43%), IHOP (47%), Waffle House (50%), Burger King (51%), Domino's (51%), Chick-fil-A (53%), and Wendy's (54%). Frontline employees at these establishments are at high risk because they are exposed to large numbers of people in enclosed spaces. Yet their vaccination rates lag well behind the overall adult population (72%). 

Why more than half of Taco Bell workers are unvaccinated

South Africa: Christmas update Hospitalizations15% week over week, 0.4% from yesterday. Gauteng Province 1.8% week over week0.1% from yesterday We are 2+ weeks from peak in cases and plateauing is not complete. Longer tail to this than usual.

DOI: 10.1126/science.abc8511

Coronavirus disease 2019 (COVID-19) has affected millions of people globally, yet how the human immune system responds to and influences COVID-19 severity remains unclear. Mathew et al. present a comprehensive atlas of immune modulation associated with COVID-19. They performed high-dimensional flow cytometry of hospitalized COVID-19 patients and found three prominent and distinct immunotypes that are related to disease severity and clinical parameters. Arunachalam et al. report a systems biology approach to assess the immune system of COVID-19 patients with mild-to-severe disease. These studies provide a compendium of immune cell information and roadmaps for potential therapeutic interventions.

Deep immune profiling of COVID-19 patients reveals distinct immunotypes with therapeutic implications

NEW: @UKHSA Variant Technical Briefing Technical Briefing 34 https://gov.uk/government/publications/investigation-of-sars-cov-2-variants-technical-briefings… Updated Omicron Risk Assessment https://assets.publishing.service.gov.uk/government/uploads/system/uploads/attachment_data/file/1046614/12-january-2022-risk-assessment-SARS-Omicron_VOC-21NOV-01_B.1.1.529.pdf… A

RT with a better screenshot.

BEST. VIDEO. ALL. YEAR. Please share with friends how the mRNA vaccine works to fight the coronavirus. NOTA BENE—The mRNA never interacts with your DNA . #vaccinate (Special thanks to the Vaccine Makers Project @vaccinemakers of @ChildrensPhila). #COVID19

Americans who believe COVID vaccine misinformation tend to be more vaccine-resistant. They are also more likely to distrust the government, media, science, and medicine. That pattern is reversed with regard to trust in Fox News and Donald Trump. https://osf.io/9ua2x/ (5/7)

Misinfo beliefs improve over time, but in strikingly different ways based on socioeconomic status. Ppl with high income and graduate degrees see huge drops in believing false claims, those in the lowest income and education categories see no change. https://osf.io/9ua2x/ (3/7)

Our new report on #COVID vaccine misinformation trends is out. We look at shifts in beliefs across demographics and find links to trust in science, government, and media. Many who believe false claims are aware they contradict science. http://covidstates.org #fakenews (1/7)

After a year, we see 16% of Americans still hold vaccine misperceptions, 46% are uncertain about false vaccine claims. Misperceptions are most prevalent among age 25-44, parents, those who didn’t go to college, and Republicans. https://osf.io/9ua2x/ (2/7)

A third of the people who believe vaccine misinformation do know that it has been rejected by scientists and medical experts. And, over 20% of Americans know scientists reject some claims, but are still not sure whether to believe them. https://osf.io/9ua2x/ (4/7)

This is report #82 by our great COVID States team (http://covidstates.org): @davidlazer, @matthewabaum, @royperlis, @MauSantillana, @_Jon_Green, @klunztrujillo, @safar_a_c, @hqu, @Atauslu, @CarolinePippert, and others including off-Twitter members Jamie Druckman & Alexi Quintana

We also find the more people think they know about #COVID vaccines, the more likely they are to believe misinformation. Yes, you read that one right. People who say they are vaccine experts are overwhelmingly more likely to hold misperceptions. https://osf.io/9ua2x/ (6/7)

UKHSA tech report out - TL;DR: -BA.2 now represents >80% of omicron in England -Growth rate 80% greater relative to BA.1 per wk - regional growth seems to correlate with BA.2 frequency -?lab reports indicating that BA.1 infection may lead to lower neutralisation against BA.2

Unvaccinated people in Austria have been locked down for two-and-a-half months. I wonder if people will stop pretending they are to blame for infection rates.

A multimodal #AI study of ~54 million blood cells from Covid patients @YaleMedicine for predicting mortality risk highlights protective T cell role (not TH17), poor outcomes of granulocytes, monocytes, and has 83% accuracy https://nature.com/articles/s41587-021-01186-x… @NatureBiotech @KrishnaswamyLab

1. A thread on the CDC’s recommendation to de-isolate five days after the onset of symptoms or positive test. First, a disclosure: I was paid as a consultant for this work, done in collaboration with @Color Health, which provides COVID testing services and vaccination logistics.

Genomic epidemiology of SARS-CoV-2 in Africa focused on different regions @AfricaCDC https://bit.ly/3tcDuJl . Using Africa Pathogen Genomics Initiative (Africa PGI) data @GISAID & @Nextstrain to visualize the emergency & spread of the new COVID-19 variant Omicron in Africa.

1. #ACIP is meeting this afternoon to discuss the recently @US_FDA authorization of Covid boosters for youths aged 12 to 15. I'll be live tweeting. The agenda is here https://cdc.gov/vaccines/acip/meetings/downloads/agenda-archive/agenda-2022-01-05-508.pdf… and the meeting can be monitored here:

Bleibt allergrößtes menschliches Rätsel für mich. Das zu wissen, und sich "aus Überzeugung", "trotzdem" nicht impfen zu lassen.

Gesundheitsämter stellen Kontaktverfolgung wegen Personalmangel ein

Landeschefs fordern Feststellung einer epidemischen Notlage +++ Amt für Katastrophenschutz: Kritische Infrastruktur nicht in Gefahr +++ Entwicklungen zur Pandemie im Corona-Liveblog.

Coronavirus disease (COVID-19): How is it transmitted?

Schools: still a gaping hole in the English covid strategy

In August, one of us (CP) wrote about schools being the gaping hole in the English covid strategy. This was written in the face of the highly transmissible delta covid-19 variant.1 Three failings were identified: delayed vaccination of 12-15 year olds; lack of public health measures in schools such as masks and ventilation; and continued high community transmission leaving schools vulnerable. So what happened? And what needs to happen next?

Covid admissions have already surpassed the peak of last winter’s wave in hospitals in Greater Manchester, north-west England, with health chiefs warning patient care is under threat as they struggle to cope with “severe” staff shortages.

Covid hospital admissions in Greater Manchester surpass last winter’s peak

Last summer, I pulled together the occasional vaccination rate scatter plot graphs I'd been compiling for months into a single animated GIF image to show how both the correlation (R^2) and steepness (slope) of the partisan COVID vaccination divide grew from almost nothing at all to a gaping chasm over a six month period, from February 2021 through August 2021. Today, I'm presenting an updated version of this animation which not only includes the following six months as well (September 2021 - February 2022), but also cleans up & standardizes the layout of each graph as much as possible. This includes making sure the thru date is in the upper right-hand corner on all of them, moving the population key to the lower-right corner, removing the (naive in retrospect) "herd immunity target" line, and moving the R^2 stamp immediately below the thru date to make the graph itself as clean as possible.

Updated: A Full Year of U.S. COVID Vaccinations by Partisan Lean...Animated

This time last week, nearly all Americans were still being urged by the nation’s leadership to please, keep those darn masks on. Then the Great American Unmasking Part Deux began. On Friday, the CDC debuted a new set of COVID-19 guidelines that green-lit roughly 70 percent of us—effectively, anyone living in a place where hospitals are not being actively overrun by the coronavirus—to doff our masks in most indoor public settings. The stamina of mask policy had been flagging for quite some time: Governors and mayors had already been weeks deep into vanishing their own mask mandates (and other pandemic precautions), including in schools. But the CDC’s decision still marks a substantial cross-continental change, delivering a final blow to what little remained of the country’s collective approach to quashing the pandemic.

The Biden Administration Killed America’s Collective Pandemic Approach

BA.2 & BA.1.1 (Omicron variants) are growing in many countries . Quite what this means in terms of cases, hospitalisation, deaths & long covid is unknown but - once again - Omicron from Dec (BA.1) is not the last variant. Also @Unusual_Times highlighted BA.1.1 in UK weeks ago.

NYC update Cases down 40%; positive rate 4.0% Hospital census back to levels of December 27 and declining. New hospitalizations back to levels of 12/19 and declining. BA.2 may well be of concern, but not meaningful impact... yet.

Speaking of which, latest COG UK data shows that BA.2 is dominant already in NI & likely dominant within Scotland & Eng within 2 weeks. It doesn't seem more severe, but some (v early) sign that kids get reinfected with BA.2 faster than adults https://twitter.com/kallmemeg/status/1494100192873885698?s=20&t=RgXoqBNEVDl_Tf-rv78QOQ… 5/7

Addendum: please see Dr McCafferty's wonderful tweetorial on milestone surveillance & screening for more info.

You could also just read the paper that clearly outlines this thinking rather relying on bad journalism and misinformation from contrarian doctors. End/

A higher 75% threshold or identifying the 25% of kids not reaching that milestone (30 words by age 2) will mean more referrals for these at risk kids & less "wait & see." All of this is clear to anyone with knowledge of child development. But isn't clear to an adult oncologist.3/

The prior developmental milestone screening tools hinged on 50% of children not reaching that goal (e.g. 50 words by age 2) to identify delays. The unintended result is that many times parents, providers, etc adopted a "wait & see" approach rather than referring to therapy. 2/

No, the CDC did not quietly revise language development guidelines to hide mask induced delays. This is misinformation. The change is based on a 15 year update on the 2004 recs & a lit review performed in *2019* with the explicit goal of identifying higher risk kids. 1/

Effectiveness of mRNA-1273 against-Omicron and Delta variants The 3dose VE was 71.6% and 47.4% against Omicron infection (14-60 days) The 3dose VE was 29.4% against Omicron infection in immunocompromised individuals H/T ⁦⁦@michaelgcollett

Today on #TheDoseCBC: a frank discussion about the new #Omicron sub-variant with virologist @angie_rasmussen, who says BA.2 isn't necessarily more pathogenic — but we need to proceed with caution. Learn more: http://bit.ly/3gnlPak

Comirnaty (Pfizer) was registered by the TGA on 28 January 2022 for use as a booster in the 16–17 year age group. ATAGI now extends the recommendation of a booster dose to include all individuals aged 16-17 years. This clinical recommendation aims to maximise protection for this age group who are at a critical point in their secondary education and early working lives. People in this age group are also very mobile and may engage in increased social mixing. Comirnaty (Pfizer) is the only vaccine registered for use as a booster for people aged 16–17 years at present. Evidence demonstrates that waning of protection against the Omicron variant occurs after a two-dose primary vaccination schedule and a booster dose is required to increase protection against infection and severe disease. For more information see: ATAGI advice on the omicron variant and the timing of COVID-19 booster vaccination.

ATAGI recommendations for use of Pfizer COVID-19 vaccine as a booster dose in adolescents aged 16-17 years

Hope springs eternal.

I took a look at all these NY sequences. I don't think these point mutations S:681H are real. Why? Because they appear all over the Omicron diversity. Some sequences have S:346K, some S:701V, most miss S679K, a few have it. That's the signature of contamination/co-infection.

After two years of an exhausting global pandemic, people are naturally a bit fed up. As time has progressed, we’ve all generally gone from willing engagement and reasonable debate to shouting matches where the real question is who can get their point across with more vigor.Nowhere is this more true than in debates about vaccinations. On the one hand, there is strong scientific evidence that vaccines are safe, effective, and can largely prevent the severe disease that has caused COVID-19 to be such a scourge. On the other, there are sometimes reasonable concerns and misunderstandings about immunization, which are amplified by a group of anti-vaccination advocates into a storm of scientific misinformation. This, understandably, leads to some quite fractious debates.Pictured: Civil vaccine discussion. They don’t even have knives out. Source: PexelsAmid these discussions, a common theme has been cropping up again and again — the idea that people who are unvaccinated are immoral, and thus they do not deserve healthcare if they get sick. The idea is that being unvaccinated is, at this point, an ignorant personal choice, and thus we should leave these people to fend for themselves if they do get sick from COVID-19.This is, in a word, ridiculous. Unvaccinated people are still people, and we should always provide them with the medical care they require.

Of Course Unvaccinated People Should Get Medical Care

I think when we're okay with 1000 people dying each week from a preventable illness, and say this is good news, maybe we need to recalibrate where we've gotten to. When we say, a crisis leading to 100K cases is ok, because it may not get us to Jan '21, maybe it's time to reflect.

In effect govt, media, and sadly even some scientists have moved the target to it's ok as long as it's not like the catastrophe it was at x point in time - which means we just tolerate more infection, rather than consider that perhaps we should do better.

Now we're happy to accept 30-50,000 deaths/year, despite all the research on COVID-19, all the technological advancements. It hasn't meant we accept less suffering as a society, it's bizarrely just meant we tolerate more infection as long as deaths are *less than* before.

The reason this worries me - is that I think two years ago, the idea of 170,000 deaths happening over 4 months (many avoidable), and 1.2 million people, including 77000 children getting chronic illness would've been far more shocking than it is now.

We've had 20 months of learning. So why are we still ready to accept things getting as bad as Jan '21 or March '20 before we act. Surely, with all we've gained in 20 months we should be less accepting of people getting ill & dying, rather than comparing with Jan.

And of course we have 1.2 million with long COVID with children seeing a doubling in 4 months. But all this is okay, because it's not as bad as Jan, or March last year. When the pandemic hit in March, we were thoroughly unprepared.

Many pointed to summer in the UK saying it was a success because 'freedom day' didn't translate to anything like Jan 21 or March '20. No it didn't, but >18000 people died since (many deaths may have been avoided with simple measures like mask mandates, mitigations in schools)

Some brief thoughts on the concerning relativism I've seen creeping into media, and scientific rhetoric over the past 20 months or so - the idea that things are ok because they're better *relative to* a point where things got really really bad.

10.1136/bmj.n3149