COVID-19 day 336: 📈 UK variant of SARS-CoV-2 appears more transmissible, one-third of the country under new restrictions : 20 December 2020

US vaccination priority list changed Sunday, shipments cut for this week; no ICU beds in main public hospital in LA County, the largest in the country; more US adults report wearing masks

Sunday was day 336 since the first case of coronavirus disease was announced in the United States. The US will probably report 18 million cases on Monday. In the UK, we have news of a variant that appears to accelerate transmission.

The first doses of the Moderna vaccine began shipping Sunday. In the past week, Americans began receiving the first of two doses of the Pfizer-BioNTech vaccine. The second dose is scheduled 21 days after the first; immunity begins seven days after the second injection for P-B and 14 days for Moderna.

Thus it will be mid-January 2021 before vaccine recipients begin to experience immunity. It is unknown how long immunity will last, but news from the UK this weekend casts doubt on immunity being a once-and-done vaccine.

As of Friday, more than 128,000 Americans had been vaccinated, according to a New York Times database tracking vaccinations. For context, on Friday Johns Hopkins reported almost twice as many new cases (252,649). On Sunday, the CDC reported 556,208 vaccinations or about one-quarter of the initial vaccine disbursement.

Also, according to the NYTimes, officials in California, Connecticut, IdahoIowa, Massachusetts, Michigan, MinnesotaNew Jersey, Nevada, Oregon, Vermont, Virginia, Washington, Wisconsin found out that this week’s shipment of the vaccine will contain fewer doses than promised. Of these 14 states, 12 voted Democratic in November. (Idaho and Iowa are the exceptions.)

Army Gen. Gustave Perna, responsible for distribution of COVID-19 vaccines, apologized for the miscommunication.

On Sunday, the CDC Advisory Committee on Immunization Practices pivoted on its recommendation for who should receive vaccines after health care workers and nursing homes. Adults 75 and older — about 19 million people — have been added to Phase 1B. This brings US policy closer in line to other nations such as Canada, Germany and the UK, where the elderly, who account for most deaths.

Good news: a Pfizer-BioNTech vial is supposed to contain five doses. Pharmacists have reported six doses in some vials. The FDA scrambled this week to allow that extra dose to be used. Pharmacists cannot mix leftovers from multiple vials, however.

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Sections (no jump links, sorry!)
1, One big thing; 2, Recommendations; 3, Politics, economics & COVID; 4, Key metrics;
5, Resources

⓵ One big thing - a new mutation

It’s been about a year since a new and unnamed virus began spreading through Wuhan, China. Its D614G mutation emerged in Europe in February 2020. Another mutation, A222V, was linked to summer holidays in Spain.

This weekend, COVID-19 news has been driven by B.1.1.7 (earlier dubbed VUI-202012/01, the first “Variant Under Investigation” in December 2020). According to the BCC, it is “unusually highly mutated.” There’s a significant N501Y mutation in the protein that allows the virus to attach to our ACE2 receptor. And this version of SARS-CoV-2 is spreading fast.

On Saturday, UK Prime Minister Boris Johnson “placed a third of England’s population under new tier 4 restrictions” because this new strain is “believed to be up to 70% more transmissible than previous variants.” Travel into and out of Tier 4 areas, London and southeast England, is prohibited.

These 16 million will not be able to gather with other households over Christmas. Non-essential shops, closed. A stay-at-home order. Officials will review the lockdown in two weeks, and “significant policing is being planned for New Year’s Eve.”

Researchers first detected the variant in September. The mutation could increase the R number by 0.4. By mid-December, nearly two-thirds of cases in London carried this version of SARS-CoV-2.

This mutation has been detected in Australia, Denmark and the Netherlands.

European nations including Belgium, France, Germany, Ireland, Italy, and the Netherlands have halted flights to and from the UK. 

South Africa is also reporting a new strain (501.V2), similar to the UK one with one exception. It seems “to affect young people more than [prior] strains.”

Trevor Bedford, researcher at Fred Hutch in the Vaccine and Infectious Disease Division and Affiliate Associate Professor in the Department of Genome Sciences and the Department of Epidemiology at the University of Washington, has a long thread on Twitter about the UK mutation. Its possible impact: that vaccines will need to be updated periodically, like the annual influenza vaccine.

Emma Hodcroft, a viral geneticist at the University of Bern in Switzerland:

“The UK and Denmark are the [world’s] most regular and prolific sequencers. So the variant could be elsewhere and not detected yet. More co-ordinated sequencing efforts regionally and globally would help us monitor variants.”

⓶ Recommendations

🤓 Recommended reading

▪️A primer on proteins, amino acids and DNA and viral mutation. Its conclusion about the mutant’s transmissibility appears to have been premature, however.

Should we be worried about coronavirus mutations? An expert explains. World Economic Forum, 18 December 2020.

🔬 Research and medical news

▪️FDA has provided emergency use authorization for two vaccines, the Pfizer-BioNTech vaccine and the Moderna vaccine. It is unlikely that anyone will be given a choice; due to the need for special handling (ultra-cold freezer between -80⁰C/-112⁰F and -60⁰C/-76⁰F), the Pfizer-BioNTech vaccine will probably be limited to metro areas.

A side-by-side comparison of the Pfizer/BioNTech and Moderna vaccines. STAT News, 19 December 2020.

As COVID patients have flooded into [Los Angeles County+USC Medical Center, a 600-bed public hospital] in recent weeks, they’ve put an immense strain on its ICU capacity and staff — especially since non-COVID patients, with gunshot wounds, drug overdoses, heart attacks and strokes, also need intensive care. No more ICU beds were available, said Dr. Brad Spellberg, the hospital’s chief medical officer…

In California, only 3% of ICU beds were available as of Thursday. In the 11-county Southern California region, no ICU beds were open, and in the San Joaquin Valley, just 0.7% were.

No More ICU Beds at the Main Public Hospital in the Nation’s Largest County. KHN, 18 December 2020.

🛠 Tools

⓷ Politics, economics and COVID-19

🏥 French President Emmanuel Macron is in a “stable” condition after testing positive for coronavirus. Slovakia's Prime Minister Igor Matovic, who attended an EU summit with President Macron last week, has also tested positive.

📣 Australia's most populous state, New South Wales, has announced new restrictions for the Greater Sydney area. Germany and the Netherlands have imposed lockdowns until January. Italy has ordered a nationwide lockdown over much of the Christmas and New Year period. (BBC)

✅ A new Kaiser Family Foundation poll of US adults reported Friday that about 3-in-4 Americans report wearing a mask every time they leave home. Half believe the worst is yet to come, an increase from September and October (4-in-10).

⓸ Key metrics

🦠 Friday, Johns Hopkins reported 17,459,296 (252,649 new) cases and 313,588 (2,889 new) deaths, an increase of 1.47% and 0.93%, respectively, since Thursday. A week ago, the daily numbers increased by 1.48 % and 1.13%, respectively.

  • Friday
    - 🔺230,930 cases and 🔺2,591 deaths (seven-day average)
    - 🔺1,513,120 cases last seven days (CDC)
    - 🔺66.1 cases/100K (CDC, today)
    - 🔺114,751 hospitalizations (CTP, today)
    - 1.80% cases leading to death (today)
    - total cases and deaths per 100K: 5,275 and 95

  • One week ago
    - 🔺210,761 cases and 🔺2,360 deaths (seven-day average)
    🔺1,433,460 cases last seven days (CDC)
    🔺62.6 cases/100K (CDC, today)
    🔺108,044 hospitalizations (CTP, today)
    - 1.86 % cases leading to death (today)
    - total cases and deaths per 100K: 4,786 and 89

Note: the seven-day average is important because dailies vary due to factors other than actual case numbers, particularly over a weekend.

🇺🇸 18 December 

  • CDC: 16,987,911 (231,330 new) cases & 309,880 (3,453 new) deaths
    One week ago: 15,474,800 (203,229 new) cases & 291,522 (2,760 new) deaths

  • State data*:  xxx (xxx new) cases & xxx (xxx new) deaths
    One week ago: 15,598,772 (231,706 new) cases & 287,116 (3,659 new) deaths
    KS reports only M-W-F; CT and RI report only M-F

  • WHO: 16,682,649 (235,805 new) cases & 304,960 (3,424 new) deaths
    One week ago: 15,203,208 (230,852 new) cases & 287,384 (3,390 new) deaths

Note: Covid Tracking Project is now including probable cases from the Texas dashboard as well as Washington. I am using those data.

🌎 18 December 

Johns Hopkins interactive dashboard (11.00 pm Pacific)

  • Global: 75,672,782 (720,593 new) cases & 1,674,840 (12,713 new) deaths
    One week ago: 71,081,571 (1,489,020 new) cases & 1,594,777 (12,921 new) deaths

* Johns Hopkins data, ~11.00 pm Pacific.
State data include DC, Guam, the Northern Mariana Islands, Puerto Rico and the US Virgin Islands

The virus was not created in a lab and the weight of evidence is that it was not released intentionallyAlthough early reports tied the outbreak to a market in Wuhan, China, analyses of genomic data have suggested that the virusdeveloped elsewhere.

⓹ Resources

👓 See COVID-19 resource collection at WiredPen.
📝 Subscribe to Kathy’s COVID-19 Memo :: COVID-19 Memo archives
🦠 COVID-19 @ WiredPen.com
📊 Visualizations: USWorld
🌐 Global news(at WiredPen)

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