Coronavirus Tidbits #168 11/28/21

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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.

New Post:

Surveillance for Measles Is a Victim of the COVID Pandemic

A drop in surveillance and missed vaccine schedules due to the pandemic means potential new outbreaks of measles and other infectious diseases.


New COVID variant alarms researchers, triggers travel bans

South Africa’s health ministry, in an urgent media briefing yesterday, announced the detection of a new SARS-CoV-2 variant, B.1.1.529, that has quickly outpaced the Delta (B1617.2) variant and has a host of mutations that might change how the virus behaves.

The new findings triggered an unprecedented and fast response in science and government ranks yesterday, with experts raising deep concerns about the new variant’s mutation profile and the World Health Organization (WHO) today convening its technical advisory group (TAG), with speculation swirling that it would designate B.1.1.529 as the fifth variant of concern and name it Nu.

Also yesterday, countries-including Israel and the United Kingdom-began barring flights from South Africa and other countries where the virus has been detected.

The new development is buffeting stock markets and oil prices and comes at a time when the world, weary of COVID-19, will soon enter the third year of the pandemic.

South Africa sees virus outcompete Delta

At South Africa’s media briefing, officials said the variant was detected in Gauteng province, where positivity rates in the area around Pretoria jumped from 1% to more than 30% in less than 2 weeks. Sequencing of the recent Gauteng samples found that nearly all were the new variant. South Africa is known for its strong genetic sequencing capacity.

Prior to South Africa’s announcement, scientists from Botswana, Hong Kong, and South Africa had uploaded B.1.1.529 variant sequences to sharing databases.

Tulio de Oliveira, PhD, who directs South Africa’s Centre for Epidemic Response and Innovation, said yesterday on Twitter that the country’s scientists made the data public and raised the alarms to protect the country and the world, despite the harm that steps like a lockdown and travel bans would have on South Africa’s people and its economy.

“This new variant is really worrisome at the mutational level. South Africa and Africa will need support (financially, public health, scientific) to control it so it does not spread in the world,” he wrote. “Our poor and deprived population cannot be in lockdown without financial support.”

Yesterday during an online WHO question and answer session, Maria Van Kerkhove, PhD, the WHO’s technical lead for COVID-19, said the variant has a large number of mutations, and that while it’s not clear what their impact will be on how the virus behaves, the findings are concerning. So far there are less than 100 full genome sequences for scientists to review and it will take a few weeks to assess how tests, treatments, and vaccines will hold up against the new variant.

She said continuing COVID-19 circulation gives the virus more opportunities to change and that everyone has a role to play in decreasing exposure and taking precautions.

In a variant update today, the UK’s Health Security Agency said B.1.1.529 contains multiple spike mutations, plus others outside the spike with unknown significance. Based on what’s know about other variants, it said the mutations may have implications for immune escape, transmissibility, and response to treatments, especially regarding monoclonal antibodies.

Quick global response

The new variant developments immediately prompted new risk assessments and intensive efforts to identify cases in other countries. Also, more countries have now announced bans on travelers from South Africa, with some including other African nations where variant cases have already been detected.

Anthony Fauci, MD, White House chief medical adviser, told CNN today that so far, there’s no sign that the variant is in the United States and that US experts are working with their counterparts in South Africa to learn more.

The European Centre for Disease Prevention and Control (ECDC) said it is monitoring the situation closely and will issue a threat assessment later today.

Two more countries outside of Africa today announced their first B11 detections. Belgian officials said the new variant was identified in a traveler who returned from Egypt on Nov 11, and Israel announced its first detection, which involves a traveler who had returned from Malawi.

Unsettling possibilities, but too soon to tell

Michael Osterholm, PhD, MPH, who directs the University of Minnesota’s Center for Infectious Disease Research and Policy (CIDRAP), publisher of CIDRAP News, said it’s important to be careful in interpreting early data, but said the signals are extremely concerning. The uncertainties surrounding the impact of new SARS-CoV-2 variants, compared to what we expect a pandemic influenza virus to do over time, is what makes responding to evolving threats from the virus so hard. “This situation is a reminder that the future course of this pandemic as it relates to evolving variants is not settled,” he said.

For example, he said a more transmissible variant could accelerate what would already happen with community spread without changing the overall long-term impact of the pandemic. But if a new variant evades immunity, it would be a whole new ballgame and change the epidemiology of the disease. “It’s too early to say,” Osterholm said, pointing out that another variant of concern from South Africa- Beta (B1.350)-spread globally, but never became dominant.

The recent focus on surges in Europe and North America belies the fact that many countries are still vulnerable, with low levels of vaccination and immunity, he said.

The first more transmissible variant-Alpha (B117), first detected in the UK-arrived on the scene nearly a year ago, and scientists had no idea about what would follow in its wake, Osterholm said. “We know enough now about variants to be certain that the world doesn’t want this one.”

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Increasing Seasonal Influenza A (H3N2) Activity, Especially Among Young Adults and in College and University Settings, During SARS-CoV-2 Co-Circulation

Distributed via the CDC Health Alert Network
November 24, 2021, 11:00 AM ET Summary
Health Advisory about increased influenza A(H3N2) activity that could mark the beginning of the 2021-2022 influenza season. The purpose of this:

  1. Remind…to recommend and offer the current seasonal influenza vaccine to all eligible persons aged six months and older (Flu vaccine and COVID-19 vaccine can be given at the same visit).
  2. Remind clinicians to consider testing for both influenza virus and SARS-CoV-2 in patients with influenza-like illness (ILI).
  3. Advise clinicians that antiviral treatment is recommended as early as possible for any patient with confirmed or suspected influenza who is: a) hospitalized; b) at higher risk for influenza complications; or c) developing progressive illness. In patients with suspected influenza, decisions about starting antiviral treatment should not wait for laboratory confirmation of influenza, however COVID-19 should be excluded if a rapid assay is available.
  4. Remind the public to stay home when sick, covering coughs and sneezes, and washing hands often.


most of these increased flu infections are occurring in young adults. CDC also is aware of influenza outbreaks in colleges and universities in several states. Influenza vaccination coverage is still low and there is still time this season to benefit from getting an annual influenza vaccine.

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still an incredible, negligent last of testing.

Drugs and Vaccines:

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COVID-19 Vaccine: More Antibodies Means More Protection

COVID-19 vaccine boosters are likely to be a hot topic of conversation around many Thanksgiving gatherings this week. The idea of a booster is, in part, to increase the number of circulating antibodies being made against SARS-CoV-2. But, it has remained unknown how correlated the level of antibodies is to the level of protection against infection. Now, by measuring antibodies against the SARS-CoV-2 spike protein in participants in a Phase III trial of the Moderna COVID-19 vaccine, researchers found that the higher the antibody level, the greater the vaccine protection against COVID-19.

This work is published in Science, in the paper, “Immune correlates analysis of the mRNA-1273 COVID-19 vaccine efficacy clinical trial.”

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Swiss strike deal to get 1 mln Moderna doses to COVAX quickly

GENEVA, Nov 24 (Reuters) – Switzerland has become the first country to swap places in the supply queue for COVID-19 vaccines, allowing 1 million doses of the Moderna (MRNA.O) shot to go first to the COVAX dose-sharing programme, the GAVI vaccine alliance said on Wednesday.

GAVI, which leads COVAX’s procurement and delivery of supplies to low and middle income countries, other governments to “slot-swap” and work with manufacturers to ensure COVAX purchase

“Through this collaboration, 1 million doses of the Moderna vaccine originally planned to be delivered to Switzerland will instead be made available to COVAX in Q4 2021. Switzerland will then take COVAX’s place in the queue, and receive these doses later in 2022,” the Geneva-based GAVI said in a statement.

Switzerland’s voluntary vaccination campaign has stalled, with just over 65% of the population fully vaccinated.

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Cuba’s bet on home-grown COVID vaccines is paying off

Preprint data show that a three-dose combo of Soberana jabs has 92.4% efficacy in clinical trials.

Nature Sara Reardon 22 November 2021

When the COVID-19 pandemic began, Cuba decided not to wait on the rest of the world to develop vaccines. The United States’ 60-year-old economic embargo against the country, which prevents US-made products from being exported there, would make it difficult for Cuba to acquire vaccines and therapies, researchers and officials knew. “It was best, for protecting our population, to be independent,” says Vicente Vérez Bencomo, director-general of the Finlay Institute of Vaccines in Havana.

So the Finlay Institute and Cuba’s other state-run biotechnology centres started developing their own COVID-19 vaccines in the hope that at least one of them would be effective. Their bet seems to be paying off: in a 6 November preprint published on medRxiv1, Vérez Bencomo and his colleagues report that one of the institute’s vaccines, Soberana 02, is more than 90% effective in protecting against symptomatic COVID-19 infection when used in combination with a related vaccine. Importantly, the combination seems to be effective against the highly transmissible Delta variant of the coronavirus SARS-CoV-2, which has caused surges in hospitalizations and death across the world and now accounts for nearly all COVID-19 cases in Cuba.

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Covid antivirals could be pandemic game-changers. But Americans might struggle to access them

By Lev Facher  Nov. 23, 2021  STAT

Antiviral drugs for treating Covid-19 have been hailed as a pandemic “game-changer” – a tool that could, perhaps, finally help life return to normal. But basic gaps in the U.S. health system could mean that two new treatments from Pfizer and Merck won’t make much of a difference after all.

The companies’ treatments, which haven’t yet received emergency authorization, could make a Covid diagnosis dramatically less threatening. But in practice, before receiving the pills, patients may need to jump through a series of hoops that often prevent Americans from accessing care: Recognizing their symptoms, taking a test, getting a prescription from a clinician, and filling the prescription at a pharmacy.

“Our routine medical systems are not really set up for this,” said Céline Gounder, a physician and NYU professor who served on President Biden’s Covid advisory board in the months before his inauguration. “These are medications that need to be started within three days of developing symptoms. It can take you longer than three days to get an appointment.”

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WHO: Vaccine hesitancy persists among Africa health workers

Africa is seeing a rise in deliveries of vaccine doses to the continent, but only one in four of its health workers has been fully vaccinated against COVID-19, the World Health Organization regional office said on Thursday.

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Why Are So Few Sick From COVID in Sub-Saharan Africa?

Both rural and urban areas of Mali experienced high seroprevalence of COVID-19, but a low burden of symptomatic disease, a researcher said.

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Does Meta-Analysis Slam the Door on Colchicine for COVID-19?

– Pooled data showed no mortality benefit and higher risk of adverse events



Epidemiology/Infection control:

What makes the delta variant of COVID-19 so contagious?

The delta variant of SARS-CoV-2 has swept the planet, becoming the dominant variant within just a few months. A new study from Boston Children’s Hospital, published in Science, explains why delta spreads so easily and infects people so quickly. It also suggests a more targeted strategy for developing next-generation COVID-19 vaccines and treatments.

Chen and colleagues demonstrated that delta’s  protein is especially adept at membrane fusion. This allowed a simulated delta virus to infect  much more quickly and efficiently than the other five SARS-CoV-2 variants. Delta had the advantage especially when cells had relatively low amounts of the ACE2 receptor.

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COVID-19 : Measuring viral RNA to predict which patients will die

The amount of a SARS-CoV-2 genetic material-viral RNA-in the blood is a reliable indicator in detecting which patients will die of the disease, a team led by Université de Montréal medical professor Dr. Daniel Kaufmann has found.

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Cases rising, especially in Europe

upward trends are already being seen in the Americas, which saw cases rise 23% last week, especially in the United States and Canada, along with some locations in the Caribbean and South America.

“Throughout this pandemic, Europe has been a window into the future for the Americas,” the PAHO Director warned. “The future is unfolding before us, and it must be a wakeup call for our region.”

Globally, cases rose 6% last week, marking a month-long climb, the WHO said yesterday in its weekly pandemic update. Deaths also rose by 6% compared to the previous week, with the Western Pacific and Americas regions reporting sharp increases in fatalities.

The five countries that reported the most cases include the United States, Germany, United Kingdom, Russia, and Turkey.

Deaths on track to pass 2 million by spring

COVID-19 deaths in the WHO European region have doubled since late September, and they recently passed the grim milestone of 1.5 million since the start of the pandemic-and could reach 2.2 million by next spring, the WHO said.

Currently, COVID-19 is the leading cause of death across Europe and Central Asia, based on modeling estimates from the Institute for Health Metrics and Evaluation.

What’s driving Europe’s surge?

Three main factors are driving Europe’s ongoing COVID-19 surge, the WHO said. One is the more transmissible Delta (B1617.2) variant. Second, many countries have eased their COVID-19 measures, and cooler temperatures are bringing people indoors to gather in groups.

Also, the WHO said many people are vulnerable to the disease due to large numbers of unvaccinated people and waning vaccine-induced protection against infection and mild disease. The region’s 53.5% level of people who received their primary vaccination series hides a wide difference in coverage between countries, which ranges from less than 10% to over 80%.

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Vaccines and long Covid

Vaccines reduce the risk of long COVID by lowering the chances of contracting COVID-19 in the first place. But for those who do experience a breakthrough infection, studies suggest that vaccination might only halve the risk of long COVID – or have no effect on it at all1,2. Understanding the prevalence of long COVID among vaccinated people has urgent public-health implications as restrictions that limited viral spread are eased in some countries. It could also offer clues about what causes lingering COVID-19 symptoms long after the acute infection has cleared.

At present, public-health officials are flying blind when it comes to long COVID and vaccination. Although vaccines greatly reduce the rates of serious illness and death caused by COVID-19, they are not as effective at completely preventing the disease, and long COVID can arise even after a mild or asymptomatic coronavirus infection. Countries with high infection rates could still end up with many cases of long COVID, even if nations have high rates of vaccination. “That is hard to predict,” says Nisreen Alwan, an epidemiologist at the University of Southampton, UK, who has had long COVID. “We still need to see how much long COVID there is and how long it lasts after vaccination.”

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Portugal returns to COVID restrictions despite high jab rate

Portugal is bringing back some tight pandemic restrictions, less than two months after scrapping most of them when the goal of vaccinating 86% of the population against COVID-19 was reached.

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Tips, general reading for public:


Wash your hands.

Rinse and repeat.


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Califf, Biden’s pick to lead FDA, has millions invested in pharma and tech companies

STAT By Nicholas Florko  Nov. 23, 2021

WASHINGTON – Robert Califf, President Biden’s choice to lead the Food and Drug Administration, earned $2.7 million as an executive at Google’s life science arm Verily, and he holds between $1 million and $5 million in equity in the company, according to a recent financial statement filed with the White House.

Califf is also coming into the FDA’s top job with a massive stock portfolio. His financial statement lists roughly 30 companies in which he owns more than $100,000 worth of stock as part of a retirement account. His holdings include between $250,000 and $500,000 worth of stock in the pharmaceutical giants Bristol Myers Squibb and Amgen and between $100,000 and $250,000 in Gilead…BUT

Califf will divest all of his holdings in Verily, Centessa, and Cytokinetics within 90 days of being confirmed and he will recuse himself from all FDA matters involving those companies for at least one year, the disclosure states. Califf will also recuse himself for a year from matters involving Clintec, a research organization where he sits on the board. Califf will also forfeit a small amount of stock options in the company.

Califf has also agreed to divest his stock portfolio, including companies like MasterCard and Carrier Global Corporation, which typically have no financial stake in FDA decisions. He has agreed to divest in those companies within 90 days of being confirmed, the form states.

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Five Democratic senators have told the White House they won’t support Saule Omarova to head the Office of the Comptroller of the Currency, effectively killing her nomination for the powerful bank-regulator position: Sens. Jon Tester (D-Mont.) Mark Warner (D-Va.) and Kyrsten Sinema (D-Ariz.), Sens. John Hickenlooper (D-Colo.) and Mark Kelly (D-Ariz.).

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Feel good du jour:

Nice that the boy did this, but what an indictment of our society that he felt he had to…

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Comic relief:

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Bits of beauty:

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One Comment

  • Diane S McMahon

    Hi Judy –

    I hope you and your family are well.

    Thanks for this update – I was checking daily for it.

    It is comforting to know that I can read the “rea deal” about new developments around COVID from this blog.

    I was hoping you would publish something soon about the new variant.

    Thanks for taking the time out of your busy life to do this!

    Take care,