Coronavirus Tidbits #174 1/9/22

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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.

Recent articles:

Freshwater Aquarium Provides Source for Melioidosis Infection  —

a fascinating CDC sleuthing case discovering how a Maryland woman got a life-threatening infection from a bacteria mostly found in SE Asia.

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While Covid-19 Skyrockets, Florida’s Gov. DeSantis And Surgeon General Ladapo Are Still Spreading Misinformation

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CDC’s Isolation Guidelines Are Inadequate



See What to do if newly infected, under Tips, below:



US hits 1m Covid infections in one day (and 2 mill/d globally)

Covid-19 infections in the US surpassed one million cases in one day for the first time on Monday, The Guardian reported. In total, 1.06 million new positive tests were recorded, according to the Johns Hopkins University database. The figure is almost double the previous record of about 590,000 set just four days ago in the US – itself a doubling from the week before.

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Omicron’s feeble attack on the lungs could make it less dangerous

Mounting evidence from animal studies suggests that Omicron does not multiply readily in lung tissue, which can be badly damaged in people infected with other variants.

Nature Max Kozlov

But Omicron’s hyper-transmissibility means that hospitals are filling quickly – despite any decrease in the severity of the disease it causes.

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Military deployed at London hospitals over Omicron

Some 200 military personnel, including 40 army doctors, have been drafted in to London hospitals to help with the Omicron Covid surge, the Guardian reports. The extra support follows huge hospital staff absences due to the disease. The other 160 personnel, who have no medical training, will check in patients, ensure stocks are maintained and would also be “conducting basic checks”, the Ministry of Defence said.


Other Covid news:

Members of Biden’s transition team call for new COVID plan

Former members of President Joe Biden’s transition team are calling for a new long-term strategy that envisions a world in which humans learn to live with the new coronavirus.

Six former advisers published three opinion articles Thursday in the Journal of the American Medical Association detailing what needs to be done now to make that happen.

Dr. Ezekiel Emanuel, an oncologist, medical ethicist and University of Pennsylvania professor who advised former President Barack Obama, is the driving force behind the effort.

The experts suggest that the Biden administration take a broader view of the pandemic and acknowledge the virus won’t be going away. They expressed concern about a “perpetual state of emergency” in response to new surges, such as the highly contagious Omicron variant.

“From a macro perspective, it feels like we are always fighting yesterday’s crisis and not necessarily thinking what needs to be done today to prepare us for what comes next,” one author, Dr. Luciana Borio, told The New York Times. She’s a former acting chief scientist at the U.S. Food and Drug Administration.

The authors called for a “new normal” of living with the virus indefinitely. They suggested preparing for future outbreaks by creating goals and benchmarks for what metrics would set emergency measures in motion. These might include specific numbers for hospitalizations and deaths from respiratory viruses.

One of the pieces called for a new national plan. The other two suggest improvements in testing, surveillance, vaccines and therapeutics.

They also called for broader vaccine mandates, including for children, and recommended that oral treatments and N95 masks be free and readily available. on vaccines on testing, mitigation on the new normal

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China steps up checks after coronavirus fruit findings

China has tightened import rules after finding the virus that causes COVID-19 on packaging of fruit from Vietnam and Thailand.

At least nine Chinese cities have recorded positive coronavirus tests in relation to dragon fruit from Vietnam and longan fruit from Thailand, according to media reports.

China had already stopped at least some dragon fruit imports from Vietnam until the end of January because of coronavirus findings in late December.

Authorities have now started screening of imported food products, temporarily shut food stores and ordered people who bought the implicated fruit to quarantine.

In September this past year, China detected the SARS-CoV-2 virus on the packaging and boxes containing dragon fruits imported from Vietnam and suspended imports for a week.

These measures are despite organizations such as the Food and Agriculture Organization of the United Nations (FAO) saying the virus that causes COVID-19 is not a direct food safety concern.

Current data indicates that neither food nor food packaging is a pathway for the spread of viruses such as SARS-CoV-2. Coronaviruses cannot multiply in food or on surfaces. Once in the environment, viruses degrade and become less infectious, according to guidance.

Detection of virus or viral ribonucleic acid (RNA) remnants on foods and packaging shows evidence of previous contamination but there is no confirmation of SARS-CoV-2 being transmitted by food or packaging and causing illness in people who touch them.

China has reportedly found the COVID-19 virus in food imports from India, the United States and Canada following nucleic acid tests on imported food and packaging. As of June 2021, customs had detected 26 positive COVID-19 virus samples related to exports of packaged products such as chicken wings, seafood and fish.

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IHU variant:

WHO not concerned about new variant in France

Researchers at IHU Mediterranee Infection in France have detected a new variant of the coronavirus, according to early research published Dec. 29 on MedRxiv.

The variant, B.1.640.2, is dubbed IHU after the facility where it was discovered on Dec. 10.

Researchers say it contains 46 mutations, even more than omicron. The variant carries the N501Y mutation, seen in the alpha variant, which experts believe can make it more transmissible. Research has also shown the variant carries the E484K mutation, which could mean it may be more resistant to vaccines.

Experts were quick to clarify the discovery of a new variant does not necessarily indicate IHU will be as infectious as other variants, including omicron, The Independent reported.

The variant has been identified in 12 individuals thus far near Marseille, France, according to The Independent. The first case was linked to a fully vaccinated individual returning from a three-day trip to the African country of Cameroon.

It has not been spotted in any other countries. An official from the World Health Organization said the variant has been on the agency’s radar since November, but has not been a cause for concern given its spread over the last two months, The New York Times reported Jan. 5

The research has not yet been peer reviewed.

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Do rapid tests work with omicron? Should I swab my throat? Covid test questions, answered.

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Scientists try to pinpoint why rapid Covid tests are missing some cases

Growing evidence indicates Omicron collects in the throat, not in the nose, which could be why the nasal swabs used in rapid testing kits often aren’t detecting the variant.

“One of the things that we’re worried about is with all of this rapid antigen testing with nasal swabs, are we missing a lot of early infection?” said Donald Milton, a co-author of a December study showing that saliva tests may work better. “We know that people are transmitting during that period – minus three to plus two days of symptom onset. It’s when transmission happens.”

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Opinion: Containing Covid-19 requires rapid tests that are highly sensitive to infections. Why is the FDA asking for something different

The key marker of effectiveness for home Covid-19 tests should be few false negatives, rather than the fewest false positives.

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Free rapid antigen tests makes economic sense for governments

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Drugs and Vaccines:

64,970 Pfizer COVID-19 Pills (Paxlovid) Ship Throughout the U.S.

The actual distribution list is published on this webpageAllocation will be through state health department.

To meet future patient demands, the U.S. Government had ordered 20 million treatments as of January 4, 2022.

Approximately 10 million Paxlovid treatment courses have been accelerated for delivery by the end of June 2022, with the remaining 10 million to follow by the end of September 2022.

  is co-administered with a low dose of ritonavir that helps slow the metabolism, or breakdown, of the antiviral, allowing it to remain active in the body longer.

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Monoclonal Antibody distribution:

is through the state health departments. Here’s the original allocation, although Florida’s DeSantis successfully pushed for more. Since they refuse mask mandates and do not encourage (actually discourage) vaccinations, I wouldn’t have given more.

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COVID-19 vaccine does not increase risk of preterm birth, says study

Pregnant people who contract COVID-19 have an increased risk of disease severity and death, yet only 31% of pregnant people in the United States had received vaccines as of September 2021. One barrier to vaccine acceptance is the concern that vaccination might disrupt pregnancy.

A Yale co-led study, which looked at more than 40,000 pregnant individuals, adds new evidence supporting the safety of COVID-19 vaccination during pregnancy.

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Vaccinated women pass COVID-19 antibodies to breastfeeding babies

Women vaccinated against COVID-19 transfer SARS-CoV-2 antibodies to their breastfed infants, potentially giving their babies passive immunity against the coronavirus, according to University of Massachusetts Amherst research.

The study, published in the journal Obstetrics & Gynecology, measured the immune response to the COVID-19 mRNA vaccine in both breast milk and the stools of breastfed infants.

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Preprint study shows significant vaccine efficacy waning in adolescents

Yesterday a new preprint study out of Israel showed the efficacy of the Pfizer-BioNTech vaccine waned in 12- to 17-year-olds in a similar pattern seen in adult recipients. Within 5 month after completing the initial two-dose vaccinations series, protection against infection with SARS-CoV-2 dropped to 58%. The study was published on the preprint server medRxiv.

The peak protection provided by the vaccine was between 2 weeks and 3 months after the second dose, and the effectiveness of the vaccine against infection was subsequently reduced to 75% (95% confidence interval [CI]: 71% to 79%) and 58% (95% CI: 52% to 64%) 90 to149 days and 150 to180 days following receipt of the second dose, respectively.

“Long-term protection conferred by the vaccine was reduced to 75-78% against infection and symptomatic infection, respectively, 3 to 5 months after the second dose, and waned to 58% against infection and 65% against COVID-19 after 5 months,” the authors said.
Jan 5 medRxiv study

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Study finds no link between flu vaccination and COVID-19 risk

A large Danish study of more than 46,000 health workers found that flu vaccination didn’t affect COVID-19 hospitalization or influence the development of SARS-CoV-2 antibodies. A team based at the University of Copenhagen detailed their findings today in the Journal of Infection.

Researchers said they explored the links, due to speculation that flu vaccination might afford some protection against COVID-19, given that the two viruses produce similar host immune response. Also, some wondered whether flu vaccination might influence the risk of COVID-19 infection.

For the study, a cohort of 46,112 health workers were tested for SARS-CoV-2 antibodies and completed surveys on COVID-19 symptoms, hospitalization, and flu vaccination.

When they compared vaccinated to unvaccinated health workers, they found no difference in COVID-19 hospitalization or symptoms and no clinical difference in contracting COVID-19, as measured by the development of antibodies against SARS-CoV-2.
Jan 5 J Infect abstract

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What Happened to the Novavax Vaccine?

– As mRNA vaccines saturate the U.S. market, is there room for another, made w older technology (protein subunit)

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People are receiving unapproved extra COVID-19 vaccine doses. Is it a problem?

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Booster dose of mRNA COVID-19 vaccine required for immune protection against Omicron variant of SARS-CoV-2, says study

An additional “booster” dose of Moderna or Pfizer mRNA-based vaccine is needed to provide immunity against the Omicron variant of SARS-CoV-2, the virus that causes COVID-19, according to a study by researchers at the Ragon Institute of MGH, MIT and Harvard. The results of this study, reported in the journal Cell, indicate that traditional dosing regimens of COVID-19 vaccines available in the United States do not produce antibodies capable of recognizing and neutralizing the Omicron variant.

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Dry heat disinfecting of N95 mask works, preserves fit

[Masks were heated to 212 F]

A study led by Stony Brook University researchers discovered that a readily available method using dry ovens can be used to disinfect N95s for reuse, in settings where new masks may not be available. Their findings are published in PLOS ONE.

 PLOS ONE (2022). DOI: 10.1371/journal.pone.0257963

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Wondering if your mask is legit or a counterfeit?

Check the numbers

To be sure that any masks you buy are authentic, Miller advises consumers to look for the TC number on N95 masks. “It says TC-and then three more digits and then two digits and also a lot number,” she said. Real N95 masks also come with a head strap.

For KN95 masks, Miller said the mask should say: “GB 2626-2019 then a space and then KN95. If it does not have that printed on the face of the mask, it is not made to the standard.”

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Epidemiology/Infection control:

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Which Fully Vaccinated Adults Are Most at Risk of Severe COVID?

A significant proportion of all fully vaccinated adults who died of COVID-19 had at least four risk factors associated with severe outcomes, researchers found.

In addition to older age (65 and up) and being immunosuppressed, having chronic kidney, cardiac, pulmonary, neurologic, or liver diseases, as well as diabetes, were all associated with higher odds of severe COVID outcomes, and 77.8% of fully vaccinated adults who died had at least four of these risk factors, reported Sameer Kadri, MD, of the NIH Clinical Center in Bethesda, Maryland, and colleagues in the Morbidity and Mortality Weekly Report.

However, there were no increased odds of severe outcomes associated with sex, race/ethnicity, time since primary vaccination, or whether the infection occurred during the Delta variant wave.

Interestingly, Pfizer vaccine recipients had comparable risks of severe outcomes to those who received the Johnson & Johnson vaccine (aOR 0.70, 95% CI 0.39-1.26), while these risks were lower for those who received Moderna (aOR 0.56, 95% CI 0.32-0.98).

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COVID-19 vaccines significantly cut MIS-C risk in teens (and kids, probably)

multisystem inflammatory syndrome in children = (MIS-C)

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Tips, general reading for public:

Tatiana Prowell (@tmprowell) and others have tips for newly infected and/or exposed, below. See also

1/ The first thing to say is that if someone has #COVID19 symptoms (#Omicron most common: nasal congestion/runny nose, scratchy sore throat, fever, & aches), you have to assume they have it. You may not have a test (urgent cares are still open & do) or they may still be neg.

2/ You, as the person exposed to the one with symptoms, have to assume that you both do & don’t have #Omicron too. Wait, what?  I mean: assume you could infect others now & take care to avoid exposing them, BUT don’t assume it’s too late for you to avoid getting it.

3/ Especially in households with #vaccinated (& #boosted) family members, I have seen people manage to limit #Omicron to the first person who was infected. This #CovidVariant is incredibly contagious, but It CAN be done. Don’t give up on the idea!

4/ If you have N95/KN95/KF94 masks, get in them immediately. If you have only 1, put the sick person in it for source control. If you have >1 but not enough for all put the sick one & the highest risk (older, #immunocompromised) people in them. Then get outside, & leave door open.

5/ Fresh air is a friend & shared air is an enemy. The more you can ventilate your , now & until this is over, the better. You want the concentration of #omicron in air as low as possible. This decreases odds of infection & may make you less sick if you do get infected.

6/ Plan to bundle up if you’re in a  climate, because you’re going to need to leave doors & windows open enough for air exchange, esp for next 5d or so, & a cross draft. If you have a fresh HVAC filter, change it. If a hardware place is open, get a MERV13 HVAC filter. (Amazon has too.)

7/ Run the fan on your thermostat on high. Filter that #Omicron ! If you need supplies of any kind, please do curbside pickup or same-day delivery or drive-thru. No one exposed should be indoors in public, & def not the one with symptoms, to prevent further spread.

8/ If you don’t have any N95/KN95/KN94 masks, please see if a nearby friend or neighbor has unused ones you can have & order them replacements. The nonprofit @projectn95  ( is a great place to get them. Your backup plan for right now is a surgical mask.

9/ A surgical mask (ASTM level 3, 3-ply is best) has good filtration but usually not good fit. There are often gaps. Knot ear loops where they join the mask & then tuck to improve the mask fit. Here’s a short video demo: Put a cloth mask over the surg mask.

10/ Now it’s time to create the space where the infected person or people will isolate for 10d to let #Omicron run its course. This prior  of mine covers what is helpful to have in there & other things to consider.

11/ This whole scenario assumes that things are going ok with the person who has #Omicron. How do you know if they are ok? As I mentioned before, if you have a pulse oximeter (O2 sat monitor)-the thing drs put on your fingertip to measure O2-use it. See guide in .

12/ If you don’t have a pulse oximeter, many pharmacies carry them. They are over the counter. Ask the pharmacist if you don’t see them. You can order them online from many places too. Get one highly rated by many people. They need not be expensive. $15 gets a very good one.

13/ Some of your devices (smart watches, fitness trackers) can detect heart rate (60-100 normal for adults) & less reliably O2 levels. If you have them & they read low O2 levels, def do call a dr or seek care. Video calls are helpful to check on the sick as well.

14/ If the person w/ #Omicron is high-risk (especially #immunocompromised, organ or bone marrow transplant, active #cancer#pregnant#diabetes, older, etc), they should contact a dr even if they seem ok. There are outpatient treatments that sig risk of being hospitalized.

15/ These include monoclonal antibodies (some brands no longer work vs #Omicron, but 1 called sotrovimab remains effective). It is given IV as a single dose. There are also two types of pills taken for 5d at home. All are in short supply at the moment.….

16/ All of these things to treat outpatients w/ #Omicron, the monoclonal antibody sotrovimab, as well as the pills (Paxlovid:…) & (molnupiravir:…) are new, so they are being reserved for higher-risk folks while supply increases. [Paxlovid is better imho] 17/ If you are not the sick person, but one of the exposed, & you can walk-up/drive-up (NOT indoors & ONLY in a !) to #GetVaccinated, do it. If age 16+ & 6+ mos post dose 2 of vaccine (or 2+ post J&J), go #GetBoosted now! The booster protects w/in a wk! 19/ If you are high-risk #immunocompromised or #immunosuppressed, we know that #vaccineswork less well in many of you. While you should still #GetVaccinated & #GetBoostedan injection (Evusheld) can decrease your risk of #COVID19. It’s given every 6 mos. ~ ~ ~ Also #Remdesivir might be available as an outpatient for high-risk- (1.6%) in the remdesivir group and 21 of 252 (8.3%) hosp or death in placebo I suggest contacting the local health department +/- hospital to see where any of these drugs might be available. There are very limited supplies.


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Feel good du jour:

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Comic relief:

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Bits of beauty:

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