Coronavirus Tidbits #112 1/14/20

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First, there is now a Resources Page here for the most commonly asked questions I’m getting.

Happy to continue to answer your questions/concerns as best I can, so don’t be shy about that.


Mutations and vaccine efficacy

“The mutation, identified in a variant first seen in South Africa and separately seen in another variant in Brazil, changes a part of the virus that your immune system’s antibodies get trained to recognize after you’ve been infected or vaccinated. Lab studies show that the change could make people’s antibodies less effective at neutralizing the virus. The mutation seems to help the virus disguise part of its signature appearance, so the pathogen might have an easier time slipping past immune protection.

It’s not that the mutation (E484K change) will render existing vaccines useless…raise the possibility that the vaccines would be less effective, not that they won’t work at all.”

The UK variant, “B.1.1.7, is not thought to have mutations that will greatly affect vaccines, the evidence so far indicates.”

B.1.1.7, which has since spread to other parts of the world, appears to be even more infectious, with some estimates saying it’s 50% more transmissible. One of its mutations, called N501Y, improves how well the virus’ spike protein can attach to a receptor called ACE2 on human cells, making it more likely for the virus to successfully infect cells and for the virus to pass from person to person.

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Could new COVID variants undermine vaccines? Labs scramble to find out

A preprint published on 8 January1 found that a mutation shared by both variants did not alter the activity of antibodies produced by people who received a vaccine developed by Pfizer and BioNTech.

“Much of the effort is focused on a change to the spike protein that is shared by both lineages, called N501Y. This mutation alters a portion of the spike, called the receptor binding domain, that locks onto a human protein to allow infection. One hypothesis that previous studies have hinted at is that the N501Y change allows the virus to attach to cells more strongly, making infection easier, says Barclay.”

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B117 has been found in California, Florida, Colorado, Texas, New York, Georgia, Connecticut and Pennsylvania. Besides its infectiousness, most states aren’t doing the genomic testing needed to detect its spread.


still an incredible, negligent lack of testing.

Variant B.1.1.7 and other genetic variants may impact the performance of certain diagnostic tests, and the agency emphasized false-negative results can occur

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Drugs and Vaccines:

Increased evidence for value of Vit D in Covid treatment

Also, “Toxicity was not seen in people who reported taking doses as high as 20,000 IU per day, an amount roughly equivalent to what’s generated by an afternoon of summer sun on the skin. (Various medical societies state that doses only up to 4,000 IU of vitamin D per day are safe without medical supervision, and that up to 10,000 IU per day showed no observed adverse effects.)”

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Administrators and young graduate students have been inoculated at leading research hospitals, contrary to state and federal guidelines.

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In contrast, Moderna doses were tossed at some centers who were strictly following guidance, rather than give them to non-HCWs. (via Ashish Jha)

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Undocumented immigrant workers in the U.S. have a right to get vaccinated against SARS-CoV-2 — and Mexico will pay for it, said the country’s president, following arguments to the contrary by Nebraska’s governor. (Reuters)

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CDC: Anaphylaxis Rate With COVID Vax 10 Times Greater Than for Flu Shots

Overall, 21 cases of anaphylaxis following COVID vaccination were reported out of about 1.9 million doses given as of Dec. 23, according to an early Morbidity and Mortality Weekly Report release. [no fatalities] ~ ~ ~

How can countries stretch COVID vaccine supplies? Scientists are divided over dosing strategies

Researchers worry that efforts to free up limited vaccine doses are driven by desperation rather than data…proposals include stretching out the period between first and 2nd doses or giving 1/2 dose (Moncef Slaoui, Moderna). FDA’s Steve Hahn notes, “changes to the FDA-authorized dosing or schedules of these vaccines is premature and not rooted solidly in the available evidence.”

“It is normal for viruses to mutate, but the more the SARS-CoV-2 virus spreads, the more opportunities it has to change. High levels of transmission mean that we should expect more variants to emerge.

Of the significant variants reported so far, some are associated with increases in transmissibility but not disease severity.”

Others are concerned that “partial immunity” from just 1 dose of vaccine will encourage mutations and resistance to vaccines.

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“The Pfizer–BioNTech vaccine was 52.4% effective during the three-week period between the two doses. It adds that most vaccine failures recorded during this period occurred shortly after vaccination, and that the short-term protection provided by the first dose seems to be very high from day ten after vaccination. For the AstraZeneca vaccine, it says that vaccine efficacy from 22 days after the first dose was 73%.

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US plan to expand access to Covid-19 vaccine likely sets up new debacles

But it will be several months before there is enough vaccine available to meet that kind of demand. The move all but ensures the current narrative around the vaccine rollout — it’s too slow — will shift, but not in a positive direction: The incoming Biden administration will likely face a groundswell of complaints about long lines, failed efforts to find vaccine supplies, and an inequitable distribution system as it tries to live up to its promise of seeing 100 million vaccine doses administered in the new president’s first 100 days in office.

new prioritization scheme pushes everyone 65 and older, as well as people 16 and older with one high-risk medical condition, to the front of the vaccine line.

If states follow Azar’s instructions, a 24-year-old smoker who works from home would have the same vaccine priority status as a frail 85-year-old — and would be ahead of non-smoking teachers, municipal bus drivers, meat packing plant employees, and other front-line essential workers whom the CDC had previously recommended should be vaccinated in Phase 1b.”

If states follow Azar’s instructions, efforts to protect front-line essential workers — people who cannot work from home and whose work puts them at greater risk of contracting Covid — will tumble further back in the prioritization scheme.”


Epidemiology/Infection control:

Do our same defenses work against the mutation as effectively?

Two newly identified variants of Covid-19 first identified in the U.K. and South Africa —  known as B.1.1.7 and 501Y.V2, respectively— do indeed seem to be more transmissible and are spreading rapidly around the world. “The same defenses from before — masking, hand washing, distancing — all work but are even more important now,”

Previous studies have clearly shown that efforts including masking and social distancing help tamp down spread of the virus. One study published in September, for example, found that in a survey of more than 1,000 Maryland residents, people who frequently used public transportation were more than four times as likely to have had Covid-19 than those who didn’t. Those who reported practicing strict social distancing were just one-tenth as likely to report ever being SARS-CoV-2-positive.

Hidalgo said that, unfortunately, there isn’t yet much data about how those mitigation strategies might be affected by the new variant. So it’s best not to let our guard down.

“We need to be even more vigilant about ventilation indoors and masking at all times in and outdoors,” she said. “The advice is generally to be more adherent to public health recommendations than ever.”

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Rep. Susan Wild (D-Pa.) told CBS News that 300-400 lawmakers hid in a secure room during the violence and some refused to wear masks even when offered them. “It’s what I would call a COVID super-spreader event,” she said.

As if to confirm her fear, Rep. Jake LaTurner (R-Kan.) tested positivehours after casting votes Wednesday in the House. (CNN)

And now Rep. Bonnie Watson Coleman, a 75-year-old cancer survivor, has tested COVID19 positive after taking shelter in a room,

Rep. Watson Coleman: I’m 75. I had cancer. I got Covid-19 because my GOP colleagues dismiss facts. Powerful op-ed:

Reps. Pramila Jayapal (D-Wash.) and Brad Schneider (D-Ill.), have also tested positive

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California coronavirus deaths hit 30,000 after 10,000 fatalities in a month

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Unknowingly infected individuals may be spreading COVID as widely as those who’ve tested positive

asymptomatic COVID-19 carriers account for at least half of all community transmissions. This includes carriers who never develop symptoms as well as those who later do.

JAMA Network Open has posted the team’s report.

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Three western lowland gorillas at the San Diego Zoo Safari Park have tested positive for the coronavirus, the U.S. Department of Agriculture announced this afternoon, making them the world’s first-known great apes to contract the virus.

The gorillas, who live in a troop of eight, are expected to recover.

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Broken promises: How Singapore lost trust on contact tracing privacy

Guarantees that Singaporean phone data would only be used to fight covid-19 were hollow. The implications could stretch beyond the country’s borders.

For Singaporeans, the covid-19 pandemic has been closely intertwined with technology: two technologies, to be specific. The first is the QR code, whose little black-and-white squares have been ubiquitous all over the country as part of the SafeEntry contact tracing system rolled out in April and May.

Under SafeEntry, anyone entering a public venue—restaurants, stores, malls—must scan a code and register with a name, ID or passport number, and phone number. If somebody tests positive for covid-19, contact tracers use it to track down those who got close enough to be potentially infected.

There’s also TraceTogether, an app that launched in March 2020. It uses Bluetooth to ping close contacts; if two users are in proximity, their devices trade anonymized and encrypted user IDs that can be decrypted by the Ministry of Health should one person test positive for covid-19.

For those who can’t or don’t want to use a smartphone app, the government also offers TraceTogether tokens, small digital fobs that serve the same purpose. And while TraceTogether is currently voluntary, the government has announced that it is going to merge the two systems, which would make it mandatory to either download the app or collect a token.

When the two systems were launched, there wasn’t much space for the public to discuss apprehensions: they were seen as necessary to fight the pandemic, and the Singaporean government acted in typical top-down fashion. It did seek to assuage fears, however, by repeatedly assuring Singaporeans that the data collected with such technology would be used only for contact tracing during the pandemic.

And that’s where things went wrong.

Private data being used by police

Earlier this month, it emerged that the government’s claim was false. The Ministry of Home Affairs confirmed that data could actually be accessed by the police for criminal investigations; the day after this admission, a minister revealed that such data had, in fact, already been used in a murder investigation. It rapidly became clear that despite what ministers had previously said, Singaporean law meant it had been possible for law enforcement to use TraceTogether data all along.

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How COVID-19 Hollowed Out a Generation of Young Black Men

To understand why COVID-19 killed so many young Black men, you need to know the legend of John Henry.

While COVID-19 has killed 1 out of every 800 African Americans, a toll that overwhelms the imagination, even more stunning is the deadly efficiency with which it has targeted young Black men like Bates. One study using data through July found that Black people ages 35 to 44 were dying at nine times the rate of white people the same age, though the gap slightly narrowed later in the year.

Tips, general reading for public:


Wash your hands.

Rinse and repeat.

Want to know how your hospital is regarding bed availability?

This obscure site is what you want:


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Amy Coney Barrett’s gift

Feel good du jour:

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Most impressive is his calmness and quick thinking to lure the mob all the wrong way, away from the senate. When I saw him alone, I was afraid he had been set up/abandoned by other police and would be killed. Now I am afraid he will be targeted for his heroism.

Comic relief:


Fiona Hill on Trump’s attempted coup:

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Bits of beauty:

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And from my own little sanity break, a walk by the canal. Not a great pic, but good to get out. “Speck-tacular” hooded mergansers.

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