Weekly coronavirus-related chat, questions, and minor updates - week of January 17

Back on December 27, @xnaas posted this in the weekly thread:

Anecdotally, this is the first time I've seen multiple simultaneous cases in my social circles (family, coworkers, etc.) Prior to this last week, I never knew more than 1 case at a time in very, very extended circles of people I know. I'm sure that's not a good sign. 😬

I'm following up to say this remains true for me. In the past weeks the number of cases in my social and familial circles have gone up so much that they are no longer distinctly countable. The numbers in my area have rocketed up well past our previous peak -- we are seeing far more positives for COVID than ever before. I now know of too many people who've had it to mentally "keep track", like I had been doing for nearly two years now.

Anecdotally, I also have a lot of people in my circles who suspect they've had it but weren't able to get PCR tests due to demand and who continued to test negative on rapid tests.

Staffing and student attendance remain an issue at my school. We came close to closing down but were able to weather it by pooling kids in common areas when we were down staff. It's a lot easier to have one/two adults watch a large group of kids in the auditorium instead of having them all spread out between multiple classes, for example.

My husband (who also works a high-exposure job) and I have moved our goalposts from "we hope we don't get it" to "when we do get it we hope it's mild". It feels inescapable at this point.

McSweeney's: The safest place for your kids right now is inside the scorpion pit

Americans are locked in a heated debate: Should we close public schools due to this new wave of deadly scorpions? And while some might beg to differ, the experts all agree: there is no safer place for your kids to be than trapped inside a scorpion pit.

I get it. That sounds insane. But you have to look at the numbers. Only a few varieties of scorpions can actually kill you. Most scorpion stings will only maim the victim, with symptoms ranging from brief bouts of unbearable pain, mild convulsing, and some slight difficulty breathing. Are we supposed to disrupt our children’s education just because a handful of teachers don’t feel comfortable teaching in a dank pit with a bed of scorpions crawling all over everyone?

For those in the US, order your test kits now (@kfwyre - looking at you)

https://special.usps.com/testkits

I don't know if anyone here needs to hear this, but I've seen this bad argument elsewhere so apparently this needed to be written:

It’s a Terrible Idea to Deny Medical Care to Unvaccinated People (Ed Yong, The Atlantic)

COVID-19: mRNA booster vaccine offers best protection against Omicron

The study stratified participants into five groups:

• people who received the primary vaccination series in the past 3 months and never developed COVID-19 —recently vaccinated
• people who received the primary vaccination series in the past 6–12 months and never developed COVID-19 —distantly vaccinated
• people who received the primary vaccination series in the past 6–12 months and developed COVID-19 — distantly vaccinated with infection
• people who received a booster dose of the Pfizer or Moderna vaccine in the past 3 months and never developed COVID-19 — booster

The researchers measured the neutralizing antibody response of the blood samples from the four participant groups against the wild-type, Delta, and Omicron pseudoviruses. Researchers found a decreased neutralizing antibody response to the Delta and Omicron pseudovirus versus the original variant.

With the Delta pseudovirus, neutralization was slightly reduced in the recently vaccinated, distantly vaccinated with infection, and booster groups, but undetectable in the distantly vaccinated group.

Booster provided best protection

However, only the participants receiving the booster vaccination demonstrated robust Omicron pseudovirus neutralization, while the other groups showed substantial decreases in neutralization capability.

When researchers compared blood samples from the group recently receiving the primary series of the COVID-19 vaccines to those receiving a booster vaccine within the last 3 months, they found that those receiving boosters had a greater scope and cross-reactivity of neutralizing antibody response to the Omicron pseudovirus.

Discussion on /r/science:
https://old.reddit.com/r/science/comments/s6ew6s/two_doses_of_an_mrna_pfizerbiontech_or_moderna/

Thanks to Omicron, My school posted that they will only say whether classes will be presential 3 days before classes begin. Given cases on Brazil have gone from 3 thousand a day to 100 thousand, I'm not bullish on in-person classes.

Your Local Epidemiologist has a good overview of recent studies comparing Antigen to PCR tests.

Bottom line: Use antigen tests. Use antigen tests. Use antigen tests. Do so wisely.

Be aware of false negatives in the early stages of infection, and know that it can take several days after symptoms for the virus to take hold in your nose. Once you reach the tipping point, rapid tests are a reliable way to detect and monitor your infection.

Trust your positive test during the Omicron wave.

If at all possible, do not leave isolation without testing (I don’t care what the CDC says). If you can’t access tests, assume you are contagious for 10 days, and act accordingly.

What is Biological E, the Indian company producing Corbevax? (The Guardian)

The Indian biotechnology and biopharmaceutical company Biological E has produced the country’s first locally developed Covid-19 vaccine in partnership with the Texas Children’s Hospital Center for Vaccine Development at Baylor College of Medicine.

The Hyderabad-based company has already produced 150m doses of the vaccine, called Corbevax, and will produce 100m doses each month beginning in February. It is expected that 1bn doses will be produced by the end of 2022 – just shy of India’s nearly 1.4-billion population.

[...]

The development of Corbevax, a recombinant protein sub-unit vaccine made by a process involving yeast and the coronavirus spike protein, was made possible because of a patentless formula shared by Texas Children’s Hospital scientists Drs Peter Hotez and Maria Bottazzi.

[...]

Biological E has also developed vaccines for tetanus, Japanese encephalitis and measles and rubella. Corbevax has been approved by the ministry of health and family welfare’s drugs controller general of India, the nation’s authority on drugs and vaccines licenses.

I got the 'rona. I feel better now - no more chills, no more fever, no more fatigue, no more headache, no more cough, no more runny nose. Just that crusty, post-flu or post-cold feeling. The worst symptoms lasted about a day each: a day of nasty chills, and a day-long horrible sinus headache. The coughing lasted probably 4 or 5 days but wasn't too bad compared to a flu I had once.

I am vaccinated and had the booster shot the month before. I mask up and use alcohol hand sanitizer every time I enter a building.

Direct Comparison of SARS-CoV-2 Nasal RT- PCR and Rapid Antigen Test (BinaxNOW(TM)) at a Community Testing Site During an Omicron Surge (Preprint)

Here is the abstract:

In 731 persons seeking COVID-19 testing at a walk-up San Francisco community site in January 2022, simultaneous nasal rapid antigen testing (BinaxNOW(TM)) and RT-PCR testing was performed. There were 296 (40.5%) positive tests by RT-PCR; 98.5% of a random sample (N=67) were the omicron variant. Sensitivity of a single antigen test was 95.2% (95% CI 92-98%); 82.1% (95% CI 77-87%) and 65.2% (95% CI 60-71%) for Ct threshold of < 30, < 35 and no threshold, respectively. We also compared BinaxNOW(TM) to RT-PCR from oral cheek swabs to nasal swabs (N=75); oral cheek specimen was significantly less sensitive than nasal swab. A single BinaxNOW(TM) oral cheek rapid antigen test failed to detect 91% (20 of 22) of specimens that were BinaxNOW(TM) positive from the standard nasal sampling. In a separate direct comparison of BinaxNOW(TM) between specimens collected from nasal or throat (tonsillar) swab (N=115), sensitivity was 97.7% for nasal and 48.8% for throat swabs that were PCR-positive on nasal swab with a Ct threshold < 30. Among persons with either a nasal or throat RT-PCR positive swab with Ct<30, BinaxNOW(TM) sensitivity was 85.7% for nasal and 89.8% for nasal plus throat swabs. BinaxNOW continues to be a very useful diagnostic during the omicron surge; oral (throat or cheek swab) should not replace nasal swabs due to significantly reduced sensitivity compared to nasal. As currently recommended, repeat testing should be done for high-risk persons with an initial negative antigen test result.

For that last part, the absolute numbers are 42/49 for Nasal alone and 44/49 for Nasal and Throat.

An important limitation:

Importantly, our data are cross sectional and cannot inform questions on natural history of infection.
Omicron putatively has a shorter incubation period than prior variants. Symptoms are more intense in the upper respiratory track, and the virus appears to be less pathogenic in the lower airway compared to prior variants. One small study with five positive health care workers suggested detection is faster from oral versus nasal swabs.