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USA Facts: Learn more about who is getting vaccinated by parsing the data by age, sex and race.


2021/12/02   DIY Protein Engineering for Education, Rationality, and Immigrant Hating Antivaxxers

Good luck, homeschoolers.  Really.

2021/11/01   Here’s how many NYPD cops are on unpaid leave over vax mandate, By Craig McCarthy and Tina Moore, New York Post

New York Police Commissioner Dermot Shea said that 34 cops and 40 civilian civilian members of the force, less than 0.15% of the force, did not comply with Mayor de Blasio's mandate requiring that first jabs by Monday.


The NYPD’s current vaccination rate was 85 percent Monday morning, which reflects a nearly 15-point jump from the start of last week, leaving just under 8,000 uniformed and civilian members without the jab.  NYPD’s Equal Employment Opportunity Division, which will review the applications for exemption, is expected to shoot down any religious exemption requests from cops who have nothing on file previously, such as requesting special accommodations for religious holidays. One source mocked the religious reasoning on some cops’ applications.


“All these guys are now giving passages from the Bible, it’s bulls–t,” the source grumbled. “We have one female who has lupus. Now that’s different. Lupus and the shot don’t mix.”



2021/10/28   Is Moderna Really Better Than Pfizer—Or Is It Just a Higher Dose? By Rachel Gutman, The Atlantic

It’s possible that a good deal of the difference in the shots’ performance can be summed up with a simple phrase: More is better.


J&J, the least effective in the studies, has only one shot in its primary series; the mRNA vaccines have two. So anyone who got J&J (and hasn’t yet gotten a booster) received half as many doses total. Comparing Pfizer with Moderna, you see another dose difference: Each shot of Pfizer contains 30 micrograms of mRNA, while each one of Moderna contains 100. (Doses for children could also differ in size: Pfizer has proposed 10-microgram shots, while Moderna is going with 50.) Just how much of the difference in the shots’ performance can be summed up by saying “More vaccine is better”?


“More vaccine” is not a simple proposition. For one thing, doses of Pfizer and Moderna are measured in mass of mRNA lipid nanoparticles; J&J doses are measured by counting the number of harmless adenovirus particles that each one contains (about 50 billion). You can’t really compare lipid nanoparticles with viral particles, several experts told me. According to Michael Arand of the University of Zurich’s Institute of Pharmacology and Toxicology, you shouldn’t even assume that each 50-billion-particle dose of J&J will be equivalent in size to the next one, since, depending on the details of production, some particles can be more infectious than others. A better dosage measure for adenovirus-based vaccines, he argued in a recent opinion paper, would be “infectious units.” When I asked him via email whether developing a standard measure that works across different vaccine platforms might be possible, he said, “I do not think so.”

10/27/2021   Five Big Questions About COVID Vaccines for Kids, by Katherine J. Wu, The Atlantic

Some good news finally—finally—appears to be on the horizon for roughly 28 million of the United States’ youngest residents. On the heels of an advisory meeting convened yesterday, the FDA is likely on the cusp of green-lighting a kid-size dose of Pfizer’s COVID-19 vaccine for Americans ages 5 to 11, a move that’s been months in the making.

2015/05/08   How World War II spurred vaccine innovation, by Kendall Hoyt, The Conversation

Before World War II, soldiers died more often of disease than of battle injuries. The ratio of disease-to-battle casualties was approximately 5-to-1 in the Spanish-American War and 2-to-1 in the Civil War. Improved sanitation reduced disease casualties in World War I, but it could not protect troops from the 1918 influenza pandemic. During the outbreak, flu accounted for roughly half of US military casualties in Europe.

 2021/10/14   FDA vaccine advisers recommend emergency use authorization for booster dose of Moderna's Covid-19 vaccine, by Maggie Fox and Jamie Gumbrecht, CNN

All 19 members of the FDA's Vaccines and Related Biological Products Advisory Committee supported authorizing a 50-microgram booster dose -- half the size of the 100-microgram doses used in the primary series of the two-dose vaccine -- at least six months after the second dose, and only for certain groups: people age 65 and older; people ages 18 to 64 who are at high risk of severe Covid-19; and people ages 18 to 64 whose exposure to the coronavirus in their settings or jobs put them at risk for Covid-19 complications or severe illness.

2021/10/13   How mRNA is transforming the way we treat illnesses from flu to cancer, by Michael Le Page, NewScientist

The mRNA technique used in covid-19 vaccines recruits our bodies to make their own medicines. That could revolutionise treatments for all manner of conditions – and make personalised therapies cheaper and easier


TweetOfCovid 2021 10 14 UnitedAirlinesVaccinations 

10/29/2021   Conservatives Are Giving Ron DeSantis the Trump Treatment Defend the imaginary version, ignore the real thing. By Jonathan Chait, Intelligencer / New York Magazine

On the whole, Florida’s per-capita death rate from COVID ranks seventh highest of any state. That is a raw figure that doesn’t account for factors like age. But finer-grained analyses don’t necessarily paint a more flattering picture.


Florida has had the highest per-capita death rate among the elderly of any state during the COVID surge:


In the zipcode containing Miami airport, a vaccination hub, the number of first doses given to adults is more than 35x the adult population, yet in official statistics all of these doses count towards Miami's vaccine coverage.


Calculating coverage based on residents only finds three times more unvaccinated elderly people in Florida than according to official CDC statistics.

2021/10/08   Scientists hail historic malaria vaccine approval — but point to challenges ahead, by Amy Maxmen, Nature

Compared with other childhood vaccinations, RTS,S has only modest efficacy, preventing about 30% of severe malaria cases after a series of four injections in children under the age of five.    Nevertheless, one modelling study suggests that it could prevent the deaths of 23,000 children a year, if the full series of doses were given to all kids in countries with a high incidence of malaria2 — making a significant dent in the tremendous toll of the disease, which killed 411,000 people in 2018.

10/8/2021   Heart-inflammation risk from Pfizer COVID vaccine is very low, by Smriti Mallapaty, Nature

Two studies from Israel quantify the risk of myocarditis following the Pfizer–BioNTech shot, with one suggesting the chance of developing the condition is about one in 50,000.


In one study1 of more than 5 million people who had received the Pfizer–BioNTech COVID-19 vaccine, 136 developed myocarditis reported within one month of having a Pfizer shot. Of these, 95% were mild, but one person died.. 


The researchers found that up to 4 in 100,000 men developed myocarditis after receiving their second dose of the Pfizer–BioNTech vaccine, but the incidence for women was fewer than one in 100,000. Overall, fully vaccinated individuals were about twice as likely to be diagnosed with myocarditis as were unvaccinated individuals.


But young men aged 16–19 had a 15 in 100,000 chance of developing myocarditis after their second shot. The vast majority of these cases were mild and eventually resolved. The researchers also found that myocarditis was more likely to develop after the second vaccine dose than the first.


The other study2, of more than 2.5 million people who received the shot, identified just 54 cases of myocarditis.  Balicer and his co-authors analysed data from some 2.5 million people insured by Clalit Health Services, and asked cardiologists to review hospital records. They found that 2 out of every 100,000 people who received at least one Pfizer shot developed myocarditis, and that the incidence increased to almost 11 out of 100,000 among men aged 16–29. Overall, 76% of the cases involved mild symptoms and 22% involved intermediate symptoms.


A study of US military personnel by Leslie Cooper, a cardiologist at Mayo Clinic in Jacksonville, Florida, and his colleagues, published in June, identified 23 cases of myocarditis in men aged 20–51 who had received an mRNA vaccine, working out to 8 cases per 100,000. All of the men recovered. The same month, the US Centers for Disease Control and Prevention (CDC) reported that it had identified 5 cases out of 100,000 in men aged 18–24, rising to 6 cases per 100,000 in male adolescents aged 12–17. Most people who developed myocarditis recovered quickly, according to the CDC.


He says the new studies clearly show that the benefits of vaccination against COVID-19 outweigh the risks of people aged 16 and older developing myocarditis. Previous research4 co-authored by Balicer found that in this age group, becoming infected with SARS-CoV-2 made a person 18 times more likely to develop myocarditis — a much more significant risk than is observed following vaccination.

10/7/2021    Anti-SARS-CoV-2 receptor binding domain antibody evolution after mRNA vaccination, by Alice Cho, Frauke Muecksch, […]Michel C. Nussenzweig, Nature

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection produces B cell responses that continue to evolve for at least one year. During that time, memory B cells express increasingly broad and potent antibodies that are resistant to mutations found in variants of concern1. As a result, vaccination of coronavirus disease 2019 (COVID-19) convalescent individuals with currently available mRNA vaccines produces high levels of plasma neutralizing activity against all variants tested1,2. Here we examine memory B cell evolution 5 months after vaccination with either Moderna (mRNA-1273) or Pfizer-BioNTech (BNT162b2) mRNA vaccines in a cohort of SARS-CoV-2 naive individuals. Between prime and boost, memory B cells produce antibodies that evolve increased neutralizing activity, but there is no further increase in potency or breadth thereafter. Instead, memory B cells that emerge 5 months after vaccination of naive individuals express antibodies that are similar to those that dominate the initial response. While individual memory antibodies selected over time by natural infection have greater potency and breadth than antibodies elicited by vaccination, the overall neutralizing potency of plasma is greater following vaccination. These results suggest that boosting vaccinated individuals with currently available mRNA vaccines will increase plasma neutralizing activity but may not produce antibodies with equivalent breadth to those obtained by vaccinating convalescent individuals.

2021/10/06   A ‘Historic Event’: First Malaria Vaccine Approved by W.H.O., by Apoorva Mandavilli, The New York Times

Malaria kills about 500,000 people each year, about half of them children in Africa. 


The vaccine, called Mosquirix, is not just a first for malaria — it is the first developed for any parasitic disease. Parasites are much more complex than viruses or bacteria, and the quest for a malaria vaccine has been underway for a hundred years.

10/5/2021   COVID-19 shots helped prevent thousands of senior deaths in Mich., report finds, by Karen Bouffard, The Detroit News

The studyfound that seniors were better protected from the virus when vaccination rates were high among all adults in a community.

10/1/2021    Why it’s not possible for the Covid vaccines to contain a magnetic tracking chip that connects to 5G, by Katie Schoolov, CNBC

The Covid vaccines are administered with 25- to 22-gauge needles, which have internal diameters between about 0.26 and 0.41 millimeters. Meanwhile, a chip with 5G functionality is a little smaller than a penny. The smallest radio-frequency identification, or RFID chip, is indeed small enough at 0.125 millimeters. But they only function when attached to a coil antenna that makes the single-chip system about the size of a grain of rice, which would require a syringe about 13 times larger than the one used to inject the vaccines.

9/30/2021   New York Covid shot mandate boosts vaccination rates, AFP

The percentage of nursing home staffers that have received at least one vaccine dose has gone up from 71 percent on August 24 to 92 percent as of Monday.

9/30/2021   Turns out a lot of those never-vaxxers were really ‘I’ll get it if required’, by Philip Bump, The Washington Post

9/30/2021   KFF COVID-19 Vaccine Monitor Dashboard, Kaiser Family Foundation

9/30/2021   About a third of parents say they will vaccinate 5-to-11-year-olds ‘right away’ when eligible, report finds, by Paulina Firozi, The Washington Post

The Kaiser Family Foundation polling report

9/30/2021   AstraZeneca vaccine shows 74 percent efficacy in U.S. trial, by Adela Suliman, The Washington Post

9/30/2021 - Vaccine related articles from Chemical & Engineering News.  Read 3 for free.

9/29/2021   A man awoke to a bat on his neck and declined a vaccine. Weeks later, he died of rabies. By Caroline Anders, The Washington Post

The disease is more than 99 percent fatal once contracted.  Although few people actually contract the disease, about 60,000 Americans receive the post-exposure vaccine series each year.

9/29/2021   The evidence is building: Vaccine mandates work — and well, by Aaron Blake, The Washington Post

United Airlines was one of the first big companies to adopt a mandate, and it announced this week that 98.5 percent of employees have been vaccinated. Just 593 out of 67,000 employees face being fired for refusing the vaccine.

9/29/2021   Phase 3 Safety and Efficacy of AZD1222 (ChAdOx1 nCoV-19) Covid-19 Vaccine,  by Ann R. Falsey, M.D., Magdalena E. Sobieszczyk, M.D., M.P.H., Ian Hirsch, Ph.D., Stephanie Sproule, M.Math., Merlin L. Robb, M.D., Lawrence Corey, M.D., Kathleen M. Neuzil, M.D., William Hahn, M.D., Julie Hunt, Ph.D., Mark J. Mulligan, M.D., Charlene McEvoy, M.D., M.P.H., Edwin DeJesus, M.D., et al., for the AstraZeneca AZD1222 Clinical Study Group*, The New England Journal of Medicine

Overall estimated vaccine efficacy was 74.0% (95% confidence interval [CI], 65.3 to 80.5; P<0.001) and estimated vaccine efficacy was 83.5% (95% CI, 54.2 to 94.1) in participants 65 years of age or older. High vaccine efficacy was consistent across a range of demographic subgroups. In the fully vaccinated analysis subgroup, no severe or critical symptomatic Covid-19 cases were observed among the 17,662 participants in the AZD1222 group; 8 cases were noted among the 8550 participants in the placebo group (<0.1%). The estimated vaccine efficacy for preventing SARS-CoV-2 infection (nucleocapsid antibody seroconversion) was 64.3% (95% CI, 56.1 to 71.0; P<0.001). SARS-CoV-2 spike protein binding and neutralizing antibodies increased after the first dose and increased further when measured 28 days after the second dose.

9/28/2021   Vaccine Data for Kids Under 5 Are Coming ‘Before the End of the Year’, by Sarah Zhang, The Atlantic

Once the results for each age cohort are collected, Pfizer will submit them to the FDA to review for safety and efficacy. The agency doesn’t work on a set timeline, but for context, emergency use of Pfizer’s vaccine took 21 days from filing to authorization for adults and 31 days for teens age 12 to 15. If that precedence holds, then kids 5 to 11 will likely be able to get shots around Halloween and those 2 to 4 will be eligible by early next year.

9/26/2021   Key Stages of the SARS-CoV-2 Life Cycle, Pfizer   [more marketing than anything else]

SARS-CoV-2 proteolysis is driven by two virally encoded proteases, the 3C-like protease, 3CL (known as the main protease); and the papain-like protease.2,4 The 3CL protease cleaves the viral pp1ab polyprotein at 11 sites, while the papain-like protease cleaves at 3 sites, generating proteins critical for viral replication.2,4   Despite coronaviruses being subject to extensive mutagenesis, proteases are highly conserved among coronaviruses. SARS-CoV-2 proteases are potential targets for stopping replication.2,3,6,7

9/23/2021   Quebec swiftly passes new bill to prohibit anti-vaccine protests near schools, hospitals, by Selena Ross and Joe Lofaro, CTV News Montreal

MONTREAL -- After just a few hours of debate, Quebec's National Assembly voted unanimously Thursday evening to pass a new bill that would prohibit anti-vaccine protesters from demonstrating near schools, daycares, hospitals, as well as COVID-19 testing and vaccine sites -- an offence punishable by a fine of up to $12,000.

9/22/2021   Who Remains Unvaccinated? Unvaccinated Adults Are Younger, Less Educated, And More Republican Than Those Who Are Vaccinated, Kaiser Family Foundation COVID-19 Vaccine Monitor Dashboard

Two-thirds of adults who have not gotten a COVID-19 vaccine are under age 50, six in ten identify as Republicans or lean Republican, almost half have a high school education or less, and over a third have household incomes under $40,000. By contrast, adults who have gotten at least one dose of a COVID-19 vaccine are somewhat older, more educated, have higher incomes, and are more likely to identify as Democrats or lean Democrat.

9/20/2021   India to resume exporting COVID-19 vaccines next month, by Monique Beals, The Hill

9/20/2021   Pfizer says its vaccine is safe for kids aged five to eleven, requests authorisation for use, by Michael Erman, 7 News - Australia

9/14/2021   The tangled history of mRNA vaccines, by Elie Dolgin, Nature

Hundreds of scientists had worked on mRNA vaccines for decades before the coronavirus pandemic brought a breakthrough.

Although some involved in mRNA’s development, including Malone, think they deserve more recognition, others are more willing to share the limelight. “You really can’t claim credit,” says Cullis. When it comes to his lipid delivery system, for instance, “we’re talking hundreds, probably thousands of people who have been working together to make these LNP systems so that they’re actually ready for prime time.”


“Everyone just incrementally added something — including me,” says Karikó.


Looking back, many say they’re just delighted that mRNA vaccines are making a difference to humanity, and that they might have made a valuable contribution along the road. “It’s thrilling for me to see this,” says Felgner. “All of the things that we were thinking would happen back then — it’s happening now.”

9/14/2021   Howard Stern slams Joe Rogan, tells skeptics to get vaccinated or leave the country, by Christie D'Zurilla, Los Angeles Times, (via The Detroit News)

9/13/2021   Two departing FDA leaders among scientists who say Covid-19 vaccines do not currently 'show a need for boosting', by Jacqueline Howard, CNN

The scientist argue in their paper that the current Covid-19 vaccine supply could "save more lives" if used in people who are not yet vaccinated than if used as boosters. In early August, the World Health Organization called for a moratorium on booster shots until at least the end of September.

9/13/2021   Considerations in boosting COVID-19 vaccine immune responses, by Philip R Krause, MD, Prof Thomas R Fleming, PhD, Prof Richard Peto, FRS, Prof Ira M Longini, PhD, Prof J Peter Figueroa, PhD, Prof Jonathan A C Sterne, PhD, et al., The Lancet

9/10/2021   Biden Pushes Companies on Vaccine Mandates, The White House’s latest effort to tackle Covid-19 includes a mandate for businesses with over 100 employees, by Andrew Ross Sorkin, Jason Karaian, Sarah Kessler, Stephen Gandel, Lauren Hirsch, Ephrat Livni and Anna Schaverien, The New York Times


8/3/2021   COVID Anti-Vaxxers Aren’t a MAGA Death Cult — It’s Worse Than That, by Tim Wise, Medium

Deathbed regrets from vaccine resisters speak volumes about the brokenness of conservatism


To them, COVID was a virus of the big city and those who live there, of old people, or persons with multiple pre-existing conditions (of which they didn’t believe their cholesterol-lined arteries and COPD qualified as examples).

It was only killing the weak.

And they were strong — cowboy strong, to be precise, or at least Sturgis motorcycle ridin’ strong.

High on a delusional mix of rugged individualism, toxic masculine bravado, pseudoscientific faith in vitamin supplements, and a belief that God would pull them through, they were convinced they were safe.

Only others were at risk — the less good people.


It’s a Mass Murder Movement


9/16/2021   Uncoupling vaccination from politics: a call to action, by Sharfstein, Callaghan, Carpiano, Sgaier, Brewer, Galvani, et al, The Lancet

9/16/2021   GOP Group That Fights Against Vaccine Mandates And For Election Integrity Might Miss Campaign Filing Deadline After Bookkeeper Dies From Covid, by Zach Everson, Forbes

9/15/2021   A Michigan doctor goes to Facebook over dying, unvaccinated COVID patients, by Robin Erb, BridgeMI

And with a click of a button, Trunsky — a specialist in pulmonology, critical care and hospice and palliative care — joined the growing ranks of U.S. health care workers who are publicly venting their exasperation with the unvaccinated, who comprise the vast majority of COVID patients in hospital emergency rooms and ICU’s.


“They’ve screwed up. They didn’t get vaccinated,” Trunsky told Bridge Michigan in an interview about his Facebook post. “And now they’re begging for care.”

9/8/2021   Vermont State troopers accused of making fake vaccination cards resign after colleagues turn them in, by Timothy Bella and Andrew Jeong, The Washington Post

Arrests have been made in recent months of homeopathic doctors, bar owners, pharmacists and others accused of selling fake cards. The Manhattan district attorney announced last week that the person behind the “AntiVaxMomma” Instagram account — Jasmine Clifford, 31, of Lyndhurst, N.J. — has been charged with selling hundreds of fake vaccination cards. Clifford advertised fake cards on social media for $200 apiece featuring “real serial [numbers]” and available to “be mailed to any state” — some of which allegedly went to front-line workers.


“Some people, rather than get the vaccine, which is free, are paying money for a fake card and risking prosecution because it’s against the law,” he said at an August news conference. “Who could be that dumb?” - Senator Chuck Shumar

9/3/2021   CDC: US states with high vaccination rates protecting children from hospitalization, Associated Press

Cases, emergency room visits and hospitalizations are much lower among children in communities with higher vaccination rates," CDC Director Dr. Rochelle Walensky said Thursday at a White House briefing.  In August, the hospitalization rate among children was nearly four times higher in states with the lowest vaccine coverage compared to states with high coverage.  Citing a second study, Walensky said the hospitalization rate in unvaccinated adolescents was nearly 10 times higher in July than among fully vaccinated adolescents.

9/2/2021   India’s DNA COVID vaccine is a world first – more are coming, by Smriti Mallapaty, Nature

The ZyCoV-D vaccine heralds a wave of DNA vaccines for various diseases that are undergoing clinical trials around the world.

9/1/2021   Coronavirus California: Bay Area business group recommends wider workplace vaccine requirements, by Amanda del Castillo, ABC7 News San Francisco

9/1/2021   Opinion: The keys to ending anti-vaccine madness: Fear and the law, by Jennifer Rubin, The Washington Post

9/1/2021   Covid vaccines remain ‘stunningly effective,’ even as Delta concerns grow, by Chloe Taylor, CNBC

A piece of research funded by Pfizer, published in July, showed that the efficacy of the Pfizer-BioNTech vaccine was strongest between one week and two months after receiving the second dose, coming in at 96.2%. It then, however, declined by an average of 6% every two months. Four to six months after a second dose, its effectiveness fell to around 84%.

9/1/2021   An Instagram user who went by ‘AntiVaxMomma’ sold hundreds of fake covid vaccine cards, prosecutors say, by Julian Mark, The Washington Post

Nadayza Barkley, 27, was also charged in the alleged conspiracy. Prosecutors allege Barkley entered at least 10 people who bought the cards into the New York State Immunization Information System database.

8/30/2021   CDC advisory panel unanimously recommends Pfizer-BioNtech vaccine for those 16 and older, by Frances Stead Sellers, The Washington Post

Since Dec. 14, more than 369 million doses of coronavirus vaccines have been administered in the United States — with 210 million of those being Pfizer-BioNTech, according to the Centers for Disease Control and Prevention.

8/30/2021   Pfizer booster shot protects against coronavirus infection and severe disease, Israeli scientists report, by Lenny Bernstein, The Washington Post

Researchers at a variety of Israeli institutions looked at data from the nation’s Health Ministry for 1.1 million people 60 or older this month. They concluded that the shots significantly helped in blocking infection from the highly transmissible delta variant of the virus as well as severe forms of the disease. They said the improvement kicked in about 12 days after the booster was administered.

8/30/2021   Study finds vaccine booster shots effective as WHO Europe head says they’re ‘not a luxury’, The Washington Post

August 2021    Vaccine Refusers Don’t Get to Dictate Terms Anymore, by Juliette Kayyem, The Atlantic

People who opt out of shots shouldn’t expect their employers, health insurers, and fellow citizens to accommodate them.  Getting a shot to protect yourself and others from COVID-19 is both a social responsibility and the best way to hasten the end of the pandemic, and if you don’t believe that, we’re not waiting around for you to step up.


I know, I know: I should try harder to understand the feelings of unvaccinated Americans. Being more patient and empathetic would make me sound nicer. But do you know what’s really nice? Going back to school safely. Traveling without feeling vulnerable. Seeing a nation come back to life.


2021 08 29 JacobsonVMassachusetts ProVaxSupremes

Jacobson v. Massachusetts,  197 U.S. 11 (1905)


2021 08 29 TweetOfMichaelHarriot AfricanSmallpoxVaccine

AntiVaxxing: The Background of Jacobson v. Massachusetts (ThreadUnrolled)

4/2/2020   Onesimus: The Slave Who Helped Boston Battle Smallpox, by Lashyra Nolen, Undark



2021 08 29 TweetOfEricTopol Israel Booster Data



2021 08 29 VOC Odds Ratios DFisman Tuite Comeau

by Bill Comeau @Billius27 August 28, 2021

NEW - major Lancet study: Delta is not just much more transmissible, it is much more severe. 

In above findings, HR = Hazard ratio.

That's the probability of a treatment event (like Delta variant hospitalization) 

compared to the probability in a control group (like Alpha variant hospitalization).


2021 08 28 DeltaVsVaccine BritainStudy

Confused and confusing


2021 08 29 BritishCovidDeaths

by William Ku, Ph.D.   

"#COVID19 continues its resurgence since 9 days after.reedom Day".

3.2k Brits will die over the next 4 weeks. This study suggests more

cases and hospitalizations as schools continue to reopen."


LancetStudy 2021 08 27 Delta tweet1


8/27/2021   Opinion: The confusion surrounding booster shots could paralyze vaccination efforts. The government must step up. by Kavita Patel M.D., The Washington Post

Clinicians across the country are managing three outbreaks simultaneously. The first, of course, is the surge in covid-19 cases due to more transmissible variants. The second is rapidly spreading lies and misinformation about vaccines on social media. And the third outbreak has emerged only recently: The chaos and confusion surrounding the administration of booster shots.

8/25/2021   Moderna completes submission for full FDA approval of COVID vaccine, by Jamie Gumbrecht and Jen Christensen, CNN


2021 08 29 Pfizer Booster Data


8/20/2021   Why America’s Largest Teachers’ Union Refuses to Support Vaccine Mandates, by Emma Green, The Atlantic

8/16/2021   Cardinal Raymond Leo Burke, a Covid-19 vaccination critic, is hospitalized and on a ventilator, by Jennifer Henderson and Polo Sandoval, CNN

8/12/2021   The Vaccine Scientist Spreading Vaccine Misinformation, by Tom Bartlett, The Atlantic

Robert Malone claims to have invented mRNA technology. Why is he trying so hard to undermine its use?

7/27/2021   San Francisco bars saw a ‘surge’ of breakthrough covid cases. Now they’re requiring vaccine cards to enter. By Julian Mark, The Washington Post

7/12/2021    ‘Potentially a death sentence’: White House goes off on vaccine fearmongers, by Natasha Korecki and Eugene Daniels, Politico

The White House is adopting a more aggressive political posture to hit back harder on misinformation and scare tactics after Republican lawmakers and conservative activists pledged to fight the administration’s stated plans to go “door-to-door” to increase vaccination rates.  The Biden administration is casting conservative opponents of its Covid-19 vaccine campaign as dangerous and extreme.

Coloured scanning electron micrograph of a cell infected with B.1.1.7 variant Covid-19 coronavirus particles

A cell infected with particles (yellow; artificially coloured) of the SARS-CoV-2 variant called B.1.1.7

Credit: National Institutes of Health/Science Photo Library


5/24/2021   What scientists know about new, fast-spreading coronavirus variants, by David Adam

Key questions remain about how quickly B.1.617 variants can spread, their potential to evade immunity and how they might affect the course of the pandemic.

5/5/2021    COVID research: a year of scientific milestones, Nature

4/26/2021   The Biden administration is expected to share AstraZeneca doses with other nations after a safety review, by Sheryl Gay Stolberg and David E Sanger, The New York Times

AstraZeneca’s vaccine, unlike those of Pfizer, Moderna and Johnson & Johnson, has not been granted emergency use authorization by the Food and Drug Administration. And the administration would not specify which countries will receive the vaccine.


Mr. Biden, who has already released a total of 4 million doses of AstraZeneca vaccine to Canada and Mexico, said last week that he was considering sending more overseas: “We’re looking at what is going to be done with some of the vaccines that we are not using,” the president said. “We’ve got to make sure they are safe to be sent.”


Jen Psaki, the White House press secretary, cautioned at a news conference that the donations of doses would not happen right away. She said about 10 million doses could be released “in the coming weeks” if the F.D.A. determines that the vaccine meets “our own bar and our own guidelines,” and that another 50 million doses are in various stages of production.


“Right now we have zero doses available of AstraZeneca,” Ms. Psaki said.



4/26/2021   Breathless headlines about 8% of Americans "skipping" their second doses aside, by Jeff Linder.'s actually pretty amazing, especially given that Americans pretty regularly get about HALF of recommended medical services.


12/2016   The Quality of Outpatient Care Delivered to Adults in the United States, 2002 to 2013, by David M. Levine, MD, JAMA Internal Medicine

4/25/2021    Millions Are Skipping Their Second Doses of Covid Vaccines, by Rebecca Robbins, The New York Times

Nearly 8 percent of those who got initial Pfizer or Moderna shots missed their second doses. State officials want to prevent the numbers from rising.

4/20/2021   Opinion: The covid-19 vaccines are an extraordinary success story. The media should tell it that way, by Leana S. Wen, M.D., The Washington Post

“So far, 5,800 fully vaccinated people have caught Covid anyway in the US, CDC says,” read one headline. “CDC reports 5,800 COVID-19 infections, 74 deaths in fully vaccinated people,” said another.


By themselves, the numbers sound concerning. But let’s take a closer look. An infection rate of 5,800 infections out of 77 million fully vaccinated people is less than 0.008 percent — a remarkably low rate. Compare this with 68,000 daily new infections in the United States — which, over a 30-day period, is nearly 100 times higher than the infection rate for those vaccinated. Put another way: A total of 5,800 infections among the inoculated is orders of magnitude better than 68,000 infections per day in the general population.

4/20/2021    Virginia Uses Emergency Alert System to Notify of Coronavirus Vaccine Availability, by Gregory S. Schneider and Erin Cox, The Washington Post

Virginia officials startled some residents Monday by using the wireless emergency alert system to send out notice that coronavirus vaccines are now available to everyone over age 16.

4/20/2021   ‘I’m still a zero’: Vaccine-resistant Republicans warn that their skepticism is worsening, by Dan Diamond, The Washington Post

Many vaccine-hesitant Americans are increasingly entrenched in their decisions to resist the shots, said Frank Luntz, a longtime GOP communications expert who convened Sunday’s focus group over Zoom.   Unlike a similar focus group five weeks ago, when most participants told Luntz and Frieden that the session persuaded them to get shots, attendees Sunday said they were swayed only moderately by doctors’ urging — or not moved at all.


“The further we go into the vaccination process, the more passionate the hesitancy is,” Luntz said after the session. “If you’ve refused to take the vaccine this long, it’s going to be hard to switch you.”

4/19/2021   The race to untangle the secrets of rare, severe blood clots after Johnson & Johnson vaccination, by Carolyn Y. Johnson, The Washington Post

A protein found inside platelets that also coated the surface of arteries and veins, called platelet factor 4, could bind strongly to heparin, forming a two-part complex.  In some people, when heparin and the protein bonded, the body’s disease-fighting system went on alert, triggering antibodies against platelet factor 4. The antibodies could activate platelets, but with seemingly contradictory consequences: Some platelets would clot, while others would vanish. The antibodies could damage the cells lining blood vessels, helping trigger clots in more ways than one.   It appears that something in the vaccine bound to platelet factor 4 and triggered a similar response.


“Just as an occasional patient zings off one of these huge responses after being given heparin and gets in trouble, the occasional person given these vaccines loses the regulatory control that keeps this immune response and zings off one of these high-titer antibody responses,” In five of the six U.S. patients who developed clots after receiving the Johnson & Johnson vaccine, physicians performed tests and found those same HIT antibodies. A 25-year-old man who received the vaccine in the clinical trial of the vaccine and suffered a brain clot also had HIT antibodies. The existence of those tests — and the ability to treat the condition — is a tribute to the years of experience studying HIT.

4/18/2021   Drones are delivering COVID-19 vaccines in Africa through ‘highways in the sky’, by Emmett Smith, Mashable

4/16/2021   Biden admin hunts for clues to J&J blood-clot mystery, by Erin Banco, Dan Goldberg, Rachel Roubein and Sarah Owermohle, Politico

The data gap may not be fully resolved by next Friday, when the Centers for Disease Control and Prevention’s vaccine advisory panel is set to gather for the second time to discuss the concerns about the shot

4/16/2021   The Blood-Clot Problem Is Multiplying, by Roxanne Khamsi, The Atlantic

The world is now engaged in a vaccination program unlike anything we have seen in our lifetimes, and with it, unprecedented scrutiny of ultra-rare but dangerous side effects. An estimated 852 million COVID-19 vaccine doses have been administered across 154 countries, according to data collected by Bloomberg. Last week, the European Medicines Agency, which regulates medicines in the European Union, concluded that the unusual clotting events were indeed a side effect of the AstraZeneca vaccine; by that point, more than 220 cases of dangerous blood abnormalities had been identified. Only half a dozen cases have been documented so far among Americans vaccinated with the Johnson & Johnson vaccine, and a causal link has not yet been established. But the latest news suggests that the scope of this problem might be changing.

4/16/2021   The Danger of a ‘Dudes Only’ Vaccine, by Katherine J. Wu, The Atlantic

The Johnson & Johnson shot is teetering on the precipice of becoming America’s “dudes only” vaccine.

 4/15/2021   COVID-19 Vaccines Are Entering Uncharted Immune Territory, by Katherine J. Wu, The Atlantic

A transplant infectious-disease physician at the University of Pittsburgh, told me that his team did not detect antibodies in about 46 percent of blood-cancer patients who had received both doses of the Pfizer or Moderna vaccine. Two studies out of Johns Hopkins University found no evidence of antibodies in 26 percent of people with rheumatic or musculoskeletal disease (a group that includes rheumatoid arthritis and lupus), and 83 percent of organ-transplant recipients, after their first dose of the Pfizer or Moderna vaccine.


For now, immunocompromised people will have to rely on those who can confidently derive protection from vaccines, such as household members, health-care providers, and other close contacts. That puts some of the onus on the rest of the world: “Every vaccine that goes into an arm is protection for these people,” Longbrake, of Yale, said.

4/14/2021   Livingston County COVID-19 vaccine tracker: 19% people fully vaccinated, by Chastity Laskey, Livingston Daily/ USA TODAY NETWORK

The five counties with the highest percentage of their population fully vaccinated in Michigan as of April 12 are Leelanau County (35%), Emmet County (32%), Grand Traverse County (31%), Schoolcraft County (30%) and Ontonagon County (30%).

4/14/2021   The Rural Pandemic Isn’t Ending, by Elaine Godfrey, The Atlantic

Rural Americans are twice as likely as people in urban areas to say they will “definitely not” get a shot, and nearly three-quarters of them identify as Republican or Republican-leaning, according to new survey data from the nonpartisan Kaiser Family Foundation. Rural Americans are more apt to see vaccination as a civil-liberties issue: “More (58%) rural residents view getting vaccinated as a personal choice rather than part of everyone’s responsibility to protect the health of others (42%),” the KFF survey found. (The reverse is true for urban residents.) This group is also much more likely than any other to say that the news media have exaggerated the pandemic’s seriousness, Liz Hamel, who directs KFF’s polling work, told me.

4/14/2021   CDC vaccine panel considers limiting J&J shot by age or sex, by Sarah Owermohle and Erin Banco, Politico

Officials stressed that these clots are of concern in part because the typical treatment for clotting — the blood thinner heparin — can make them worse.

4/14/2021   The mRNA Vaccines Are Looking Better and Better, by Sarah Zhang, The Atlantic

The blood-clot events with the AstraZeneca and J&J vaccines are so rare—appearing in one in 100,000 to one in 1 million vaccine recipients—that they would not have shown up in clinical trials, even ones conducted within more leisurely, non-pandemic timelines. (The COVID-19 vaccine trials, which generally included tens of thousands of participants each, were actually unusually large because researchers wanted data as quickly as possible.) “It’s true with all new medications of any sort. You only find rare events when things are rolled out to very vast numbers of people,” says John Grabenstein, the associate director of scientific communication for the Immunization Action Coalition, who used to work on vaccines for the pharmaceutical giant Merck. “One-in-a-million events are just barely measurable.” That faint signal is especially difficult to see against a noisy background: Some people get blood clots for reasons unrelated to the vaccine, too.


Some scientists now hypothesize that the immune reaction is triggered by some part of the adenovirus-vector technology. If that’s true, these blood clots might show up as a rare side effect with other adenovirus-vector vaccines. But they clearly are very infrequent. The AstraZeneca and J&J coronavirus vaccines are the first adenovirus-vector shots to even be deployed widely enough in the U.S. and Europe for such rare events to emerge, but vaccines including Russia’s Sputnik V,  China’s CanSino, and J&J’s Ebola vaccine also use the technology.

4/11/2021   Why covid arm and other post-vaccine rashes might actually be a ‘good thing’, by Marlene Cimons, The Washington Post

She thought the rash could be a side effect of the vaccine — in her case Moderna — and worried she wouldn’t be able to get her second dose.

“That was my biggest fear,” she says. “I wanted to be able to get it. I was more anxious about not getting it, than I was about the reaction itself.”

4/10/2021   Vaccines won’t be enough. New Covid variants have changed the game, by Susan Michie, et al, The Print

4/8/2021   Colorado vaccination site shuts down early after 11 people have 'expected' adverse reactions to the Covid-19 vaccine, officials say, by Rebekah Riess, Joe Sutton and Scottie Andrew, CNN

More than 1,700 people received the Johnson & Johnson vaccine on Wednesday at Dick's Sporting Goods Park, a soccer stadium where the state of Colorado and health care provider Centura Health operate a mass vaccination site. The 11 people reported feeling nauseous and dizzy after they were vaccinated, Colorado health officials said.

4/6/2021   Among 1.7 million fully vaccinated Michiganders, state identifies small number of COVID-19 infections and deaths, by Samuel Dodge,

There are 246 fully-vaccinated Michiganders that tested positive for COVID-19, as well as three that died according to numbers from the state health department.  These cases account for just .0001% of the 1.7 million Michigan residents that received both doses of the COVID-19 vaccine as of March 30. The three patients that died were all age 65 or older.


The very small percentage of infections from fully vaccinated people falls well within the expected protectiveness of the Pfizer and Moderna vaccines, which provide 95% and 94% efficacy respectively. Health experts told MLive that 95% effectiveness means that if 1,000 people are fully vaccinated, you can expect around 50 infections among that group.

4/6/2021   Clear link between AstraZeneca vaccine and rare blood clots in brain, EMA official tells paper

“In my opinion we can now say it, it is clear that there is an association with the vaccine. However, we still do not know what causes this reaction,” Marco Cavaleri, chair of the vaccine evaluation team at the EMA, told Italian daily Il Messaggero when asked about the possible relation between the AstraZeneca shot and cases of brain blood clots.  The regulator has consistently said the benefits outweigh the risks as it investigates 44 reports of an extremely rare brain clotting ailment known as cerebral venous sinus thrombosis (CVST) out of 9.2 million people in the European Economic Area who have received the AstraZeneca vaccine.

4/6/2021   Biden Speeds It Up: All Adults Will Be Eligible for Vaccine by April 19, by Jamie Ross, Daily Beast

Last month, President Joe Biden promised America that every adult would be eligible for their first coronavirus vaccine by May 1. According to CNN, he’s now chopping two weeks off that deadline.

GlobalConvergenceInMaleLifeExpectancy Kashnitsky

4/5/2021   Demography 101:  What is Life Expectancy? and, even more important, What it Isn't, by Ilya Kashnitsky, PhD


 4/5/2021   The Story of One Dose, by Jeff Wise, Intelligencer

As an object, it’s not much: an inch and a half of glass with a stopper and some liquid inside. But a thimbleful of the stuff has amazing power — the ability to liberate us from our yearlong collective trauma. The fact that it’s available, scarcely a year after the start of a pandemic, is both an industrial miracle and a freakish stroke of luck; a decade ago, technology did not exist that could bring vaccines so quickly to the public’s arms.


The story of the vaccine’s path from development to mass distribution is a lesson in the power of the global capitalist system — the network of corporations and supply chains that, though it can suffocate and disempower us as individuals, can also summon forth immense material and intellectual resources and deploy them for the greater good.


To turn the original virus into a harmless vaccine, researchers had deleted genes the virus needs for replication; in order to make copies of itself, the Ad26.COV2.S vector required a special environment. The solution was to insert the virus’s missing genes into a unique human-cell line that had originated in the eye of a human fetus aborted in the mid-1980s. This genetically modified cell line was named PER.C6. Unlike normal human cells, which can multiply only so many times before dying, these cells are immortal; as long as they’re fed the right nutrients and kept at the right temperature, they can grow forever. Because PER.C6 contained the genes that Ad26 needed to reproduce, it held the key to growing the viral vectors.


The nurse chooses a needle based on the heft of your arm — an inch and a half for larger people, an inch otherwise — and pushes the tip into the rubber gasket atop the vial containing your dose. She slips the needle into your muscle. Inside your arm, 50 billion genetically engineered nanoscale robot assassins, carrying genetic payloads downloaded from the internet and bred in a soup of immortal human-eye cells, begin prying their way through your cells’ defenses.

4/5/2021   His Patient Refused the Vaccine. She Died of COVID in the ICU, by Michael Daly, Daily Beast

As he drove past reopened churches on Sunday, critical care nurse John Haacke figured Easter will prove to be yet another holiday followed by a surge in COVID-19.


“Things are picking up again. It seems like it won’t stop.” he said. “I have two sets of husbands and wives that died in the last week and a half, right in beds next to each other. I think in both families, the children infected them.”


None of the patients had been vaccinated. They either had not yet been able to get a shot or they had declined the opportunity. One clerical worker in her 50s had been given the chance but refused and ended up in the ICU with COVID-19.


The woman’s chest x-ray looked like a white sheet of paper, something increasingly common among recent patients.


“The worst chest x-rays I’ve ever seen in my life,” Haacke said. “Some of these x-rays, with an untrained eye you wouldn’t know there’s a lung that exists in there.”


The ICU team decided the woman’s best chance was extracorporeal membrane oxygenation (ECMO), where a machine pumps and oxygenates the blood outside the body.


“We tried to send her out Friday to put her on ECMO, but they didn’t have any beds available,” Haacke said. “It’s been that way.”

4/4/2021   Las goticas milagrosas del doctor Maduro, por Alberto Barrera Tyszka, The New York Rimes 

¿Por qué precisamente ahora, en la peor circunstancia, el chavismo rechaza vacunas? Porque su lógica es otra, porque su prioridad no son las víctimas, porque sus acciones no están destinadas a atender la emergencia sino —más bien— a aprovecharla en función de sus objetivos, de su plan de acumulación y permanencia en el poder.


You can hit the google translate button to read this in English, but it loses a little bite.


2021 04 03 Share of pop with at least one does of vaccine

2021 03 28 CDC VaccinationsByCounty WaPost

4/3/2021   U.S. Taps Johnson & Johnson to Run Emergent's Troubled Vaccine Plant, by Sheryl Gay Stolberg, The New York Times

WASHINGTON — The Biden administration on Saturday put Johnson & Johnson in charge of a troubled Baltimore manufacturing plant that ruined 15 million doses of the Johnson & Johnson coronavirus vaccine and moved to stop the plant from making another vaccine by AstraZeneca, senior federal health officials said.


The extraordinary move by the Department of Health and Human Services came just days after officials had learned that Emergent BioSolutions, a contract manufacturer that has been making both the Johnson & Johnson and the AstraZeneca vaccines, mixed up ingredients from the two, which led regulators to delay authorization of the plant’s production lines.


The Department of Health and Human Services directed Johnson & Johnson to install a new leadership team to oversee all aspects of production and manufacturing at the Emergent Baltimore plant.


The ingredient mix-up, and Saturday’s move by the administration, is a significant setback and a public relations debacle for Emergent, a Maryland-based biotech company that has built a profitable business by teaming up with the federal government, primarily by selling its anthrax vaccines to the Strategic National Stockpile.


Emergent’s Baltimore plant is one of two that are federally designated as “Centers for Innovation in Advanced Development and Manufacturing” and were built with taxpayer support. Last June, the government paid Emergent $628 million to reserve space there as part of Operation Warp Speed, the Trump administration’s fast-track initiative to develop coronavirus vaccines.


Last month, Mr. Biden canceled a visit to Emergent’s Baltimore plant, and his spokeswoman announced that the administration would conduct an audit of the Strategic National Stockpile, the nation’s emergency medical reserve. Both actions came after a New York Times investigation into how the company had gained outsize influence over the repository.

3/8/2021   Biden Cancels Visit to Vaccine Maker After Times Report on Its Tactics, by Sheryl Gay Stolberg and Chris Hamby, The New York Times

Decisions about how to spend the repository’s limited budget are supposed to be based on careful assessments by government officials of how best to save lives, but The Times found that they were largely driven by the demands and financial interests of a handful of biotech companies that have specialized in products that address terrorist threats rather than infectious disease.


Chief among them is Emergent. Throughout most of the past decade, the government has spent nearly half of the stockpile’s half-billion-dollar annual budget on Emergent’s anthrax vaccines, The Times found.


In the competition for funding, products for pandemic preparedness — including N95s — repeatedly lost out, according to the Times investigation, which relied on more than 40,000 pages of documents and interviews with more than 60 people with inside knowledge of the stockpile.


The image of some health care workers wearing trash bags for personal protection has become an enduring symbol of the government’s failed response. Yet the government paid Emergent $626 million in 2020 for products that included vaccines to protect against a terrorist attack using anthrax.


For much of Emergent’s two-decade history, its primary product has been an anthrax vaccine, first licensed in 1970, that the company purchased in 1998 from the State of Michigan. Over time, the price per dose that the government agreed to pay Emergent increased nearly sixfold, accounting for inflation.

3/6/2021   A Who’s Who of Revolving-Door Influence at Emergent BioSolutions, by Sheryl Gay Stolberg and Chris Hamby, The New York Times

As in previous years, Emergent’s biggest single source of revenue in 2020 was products for the Strategic National Stockpile, the country’s emergency medical reserve, which was woefully ill prepared for the pandemic. Even with the country focused on Covid-19, the government last year paid Emergent $626 million for products that included anthrax and smallpox vaccines.

3/31/2021   Up to 15M Johnson & Johnson coronavirus vaccine doses ruined due to human error: NYT, by Eric Sagonowsky, Fierce Pharma

The manufacturing issues at J&J and AstraZeneca underscore the impressive production efforts underway at mRNA players Pfizer-BioNTech and Moderna. CDC data show 98 million Pfizer-BioNTech doses have been delivered to states, while 90 million Moderna doses have been sent. Moderna this week said it shipped its 100 millionth dose to the government.

3/31/2021   Johnson & Johnson’s vaccine is delayed by a U.S. factory mixup, by Sharon LaFraniere and Noah Weiland, The New York Times

The mistake is a major embarrassment both for Johnson & Johnson, whose one-dose vaccine has been credited with speeding up the national immunization program, and for Emergent, its subcontractor, which has faced fierce criticism for its heavy lobbying for federal contracts, especially for the government’s emergency health stockpile.


3/8/2021   How One Firm Put an ‘Extraordinary Burden’ on the U.S.’s Troubled Stockpile, by Chris Hamby and Sheryl Gay Stolberg, The New York Times

  • The shortage of lifesaving medical equipment last year was a searing example of the government’s failed coronavirus response. 
  • Explanations about what went wrong devolved into partisan finger pointing, with Mr. Trump blaming the Obama administration for leaving the cupboard bare, and Democrats in Congress accusing Mr. Trump of negligence.
  • An investigation by The New York Times found a hidden explanation: Government purchases for the Strategic National Stockpile, the country’s emergency medical reserve where such equipment is kept, have largely been driven by the demands and financial interests of a handful of biotech firms that have specialized in products that address terrorist threats rather than infectious disease.

4/1/2021   Biden Administration Announces Ad Campaign to Combat Vaccine Hesitancy, by Annie Karni, The New York Times

A new poll by the Kaiser Family Foundation this week found that the number of Black adults willing to be vaccinated had increased substantially since February. But 13 percent of respondents over all said that they would “definitely not” get a vaccine. Among Republicans and white evangelical Christians, almost 30 percent of each group said that they would “definitely not” get a shot.


“I’ve got some pockets where they cite religious reasons with the Johnson & Johnson vaccine,” said Shirley Bloomfield, the chief executive of N.T.C.A. — The Rural Broadband Association, who has been sharing with the White House what she hears from her group’s members. “There are a lot of pockets where people have already had Covid and a sense of, ‘Well, we’ve all already gotten it, so we’re not really pressed.’”

3/29.2021    Interim Estimates of Vaccine Effectiveness of BNT162b2 and mRNA-1273 COVID-19 Vaccines in Preventing SARS-CoV-2 Infection Among Health Care Personnel, First Responders, and Other Essential and Frontline Workers — Eight U.S. Locations, December 2020–March 2021, by Mark G. Thompson, PhD; Jefferey L. Burgess, MD; Allison L. Naleway, PhD; Harmony L. Tyner, MD; Sarang K. Yoon, DO; Jennifer Meece, PhD; Lauren E.W. Olsho, PhD; Alberto J. Caban-Martinez, DO; Ashley Fowlkes, ScD; Karen Lutrick, PhD; Jennifer L. Kuntz, PhD; Kayan Dunnigan, MPH; Marilyn J. Odean, MS; Kurt T. Hegmann, MD; Elisha Stefanski; Laura J. Edwards, MPH; Natasha Schaefer-Solle, PhD; Lauren Grant, MS; Katherine Ellingson, PhD; Holly C. Groom, MPH; Tnelda Zunie; Matthew S. Thiese, PhD; Lynn Ivacic; Meredith G. Wesley, MPH; Julie Mayo Lamberte, MSPH; Xiaoxiao Sun, PhD; Michael E. Smith; Andrew L. Phillips, MD; Kimberly D. Groover, PhD; Young M. Yoo, MSPH; Joe Gerald, MD; Rachel T. Brown, PhD; Meghan K. Herring, MPH; Gregory Joseph, MPH; Shawn Beitel, MSc; Tyler C. Morrill, MS; Josephine Mak, MPH; Patrick Rivers, MPP; Katherine M. Harris, PhD; Danielle R. Hunt, PhD; Melissa L. Arvay, PhD; Preeta Kutty, MD; Alicia M. Fry, MD; Manjusha Gaglani, MBBS, MMWR, CDC

Under real-world conditions, mRNA vaccine effectiveness of full immunization (≥14 days after second dose) was 90% against SARS-CoV-2 infections regardless of symptom status; vaccine effectiveness of partial immunization (≥14 days after first dose but before second dose) was 80%.

3/29/2021   How mRNA Technology Could Change the World, by Derek Thompson, The Atlantic

More than 40 years had passed between the 1970s, when a Hungarian scientist pioneered early mRNA research, and the day the first authorized mRNA vaccine was administered in the United States, on December 14, 2020. In the interim, the idea’s long road to viability nearly destroyed several careers and almost bankrupted several companies.

3/29/2021   Scientists figured out the Moderna COVID-19 vaccine's code and posted it on Github, by Matt Binder, Mashable

As Motherboard mentions, COVID-19 vaccines have been reverse-engineered before. In late 2020, the founder of PowerDNS, an open source software provider, was able to figure out the mRNA sequence of the BioNTech/Pfizer vaccine using only information that was available online.

3/29/2021   Stanford Scientists Reverse Engineer Moderna Vaccine, Post Code on Github, by Matthew Gault, Motherboard

The Pfizer/BioNTech data [Figure 1] verified the reported sequence for that vaccine
(, while
the Moderna sequence [Figure 2] could not be checked against a published reference.

3/23/2021  Assemblies-of-putative-SARS-CoV2-spike-encoding-mRNA-sequences-for-vaccines-BNT-162b2-and-mRNA-1273, GitHub


  • Dae Eun Jeong,
  • Matthew McCoy,
  • Karen Artiles,
  • Orkan Ilbay,
  • Andrew Fire*,
  • Kari Nadeau,
  • Helen Park,
  • Brooke Betts,
  • Scott Boyd,
  • Ramona Hoh, and
  • Massa Shoura*, 

Departments of Pathology, Genetics, Pediatrics, and Medicine, Stanford University School of Medicine and Veterans Affairs Palo Alto Medical Center, Github

Moderna mRNA 1273


BioNTech Pfizer BNT 162b2



3/25/2021   12 people are behind most of the anti-vaxxer disinformation you see on social media, by Matt Binder, Mashable

Health misinformation was a huge problem in 2020 amid the ongoing COVID-19 pandemic. According to the Center for Countering Digital Hate, more than 59 million people were reached on social media platforms at the end of last year by the 425 anti-vaxxer accounts which the organization tracks. 

3/22/2021   Israeli company claims oral COVID-19 vaccine on its way, By MAAYAN JAFFE-HOFFMAN, The Jerusalem Post

Oramed Pharmaceuticals Inc., a clinical-stage pharmaceutical company based on technology developed by Hadassah-University Medical Center, announced over the weekend a joint venture with India-based Premas Biotech to develop a novel oral vaccine. Together they formed the company Oravax Medical Inc. The vaccine is based on Oramed’s “POD” oral delivery technology and Premas’s vaccine technology.

The new Oravax vaccine candidate targets three structural proteins of the novel coronavirus, as opposed to the single spike protein targeted via the Moderna and Pfizer vaccines, Kidron said. As such, this vaccine should be much more resistant to COVID-19 variants.


Oramed’s technology can be used to orally administer a number of protein-based therapies, which would otherwise be delivered by injection. Oramed is in the midst of a Phase III clinical trial through the US Food and Drug Administration of an oral insulin capsule for Type 1 and Type 2 diabetes.

3/18/2021   Understanding and Explaining mRNA COVID-19 Vaccines, CDC

Beyond vaccines, numerous preclinical and clinical studies have used mRNA to encode cancer antigens to stimulate immune responses targeted at clearing or reducing malignant tumors.

3/16/2021   The Disinformation Dozen, Center for Countering Digital Hate

Tracking of 425 anti-vaccine accounts by CCDH shows that their total following across platforms now stands at 59.2 million as a result of these failures.


The 20 anti-vaxxers with the largest followings account for over two-thirds of this total.

The Disinformation Dozen account for up to 73% of Facebook’s anti-vaxx content.


TweetOfDrToshnerReClotting 2021 03 16

Threadreader version, rolled up and readable in a browser


TweetOfVaccine 2pt2PctMortality



3/15/2021   As Biden Confronts Vaccine Hesitancy, Republicans Are a Particular Challenge, by Annie Karni and Zolan Kanno-Youngs, The New York Times

While there are degrees of opposition to vaccination for the coronavirus among a number of groups, including African-Americans and antivaccine activists, polling suggests that opinions in this case are breaking substantially along partisan lines.


A third of Republicans said in a CBS News poll that they would not be vaccinated — compared with 10 percent of Democrats — and another 20 percent of Republicans said they were unsure.


Widespread opposition to vaccination, if not overcome, could slow the United States from reaching the point where the virus can no longer spread easily, setting back efforts to get the economy humming again and people back to a more normal life.


But many conservative and rural voters continue to point to a variety of worries. Some conservatives harbor religious concerns about the Johnson & Johnson vaccine, which uses abortion-derived fetal cell lines.

3/5/2021   Americans are increasingly willing to get vaccinated, according to a new survey, by Ruth Graham, The New York Times

The proportion of adults in the country who intend to get vaccinated has increased significantly over the last several months, according to a survey released Friday by the Pew Research Center. Sixty-nine percent of the public now plans to get vaccinated — or already has — up from 60 percent who said in November that they intended to pursue it.


The issue has become more partisan over time, however. The new survey finds a 27-percentage point political gap, with 83 percent of Democrats saying they plan to get the vaccine or have already received it, compared to just 56 percent of Republicans.

2/18/2021   Delay a Shot? Skip One? Vaccine-Dosing Messaging Is a Nightmare, by Katherine Wu, The Atlantic

Vaccine regimens need both science and public trust to succeed.

2/8/2021   A Few Covid Vaccine Recipients Developed a Rare Blood Disorder, by Denise Grady, The New York Times

One day after receiving her first dose of Moderna’s Covid vaccine, Luz Legaspi, 72, woke up with bruises on her arms and legs, and blisters that bled inside her mouth.  Ms. Legaspi was strong and in good health before receiving the Moderna vaccine. But when she was admitted to the city hospital in Elmhurst, Queens, her platelet count was zero. Normal readings range from 150,000 to 450,000, and anything under 10,000 is considered very dangerous and in urgent need of treatment.  It is not known whether this blood disorder is related to the Covid vaccines.

1/26/2021   Luck, foresight and science: How an unheralded team developed a COVID-19 vaccine in record time, by David Heath and Gus Garcia-Roberts, USA Today

EXPERTS KNEW there had never been a vaccine created in less than four years. That was for the mumps, and even that vaccine was an outlier. “I think the goal of 18 months is one that will be very, very difficult to achieve,” Michael Osterholm, director of the Center for Infectious Disease Research and Policy at the University of Minnesota, said in the early months. “But it just may be our moon shot.”

1/12/2021   How COVID unlocked the power of RNA vaccines, by Elie Dolgin, Nature

RNA vaccines seem built for speed. From the genetic sequence of a pathogen, researchers can quickly pull out a potential antigen-encoding segment, insert that sequence in a DNA template and then synthesize the corresponding RNA before packaging the vaccine for delivery into the body.


Moderna, for example, managed this within 4 days of receiving the SARS-CoV-2 genome sequence. It focused on the virus’s spike protein, a surface protein used to enter cells. Collaborating with the US National Institutes of Health, the company then ran proof-of-concept experiments in mice before kicking off first-in-human testing in a span of just two months.

1/10/2021   Exploring the Supply Chain of the Pfizer/BioNTech and Moderna COVID-19 vaccines, by Jonas Neubert

I’ll start with the bad news: Nobody will be making an mRNA vaccine in their garage any time soon.


Both Pfizer-BioNTech and Moderna each have two largely independent supply chains in Europe and the United States. This makes sense in order to maximize utilization of available manufacturing capacity and to add resilience through redundancy. Bloomberg’s Supply Lines newsletter points out that it also appeases certain “protectionist governments intent on hobbling international cooperation by exerting sovereignty over supply chains”. In fact, “America exports virtually nothing out of its borders” (says German chancellor Merkel)12 and supply agreements with manufacturers specifically prohibit sending vaccine from Europe to the US, for example Moderna’s contract with Lonza.


Following the active ingredient from beginning (DNA synthesis) to end (fill-and-finish into vials) takes on the order of weeks. For example, Moderna’s first ever batch of the COVID-19 vaccine was sent off to the National Institutes of Health (NIH) for phase 1 clinical trials 42 days after the design of the vaccine was completed.14 (The final 14 of those 42 days were spent waiting for the fixed-length sterility test experiment to complete.)


A note about the relationship between BioNTech and Pfizer: BioNTech is the original developer of several COVID-19 vaccine candidates. In March 2020, BioNTech announced a collaboration with Pfizer that involves jointly pursuing clinical trials for the candidates, development of the final vaccine, and all other remaining steps towards global distribution including manufacturing, distribution, finances, and marketing.15 Pfizer owns marketing and distribution rights for all but three countries in the world.16 Those three exceptions are: Germany and Turkey where BioNTech themselves markets and distributes, and China where Shanghai Fosun Pharma holds the marketing rights.17 Pfizer and BioNTech share gross profits generated outside of China 50:50.


Fun fact: BioNTech’s headquarter’s street address is “An der Goldgrube 12” which literally translates to “At the Goldmine 12”.



TweetOfBertHubert ReverseEngineeringBioNTechVaccine 2020 12 27



The BNT162b2 mRNA vaccine has this digital code at its heart. It is 4284 characters long, so it would fit in a bunch of tweets. At the very beginning of the vaccine production process, someone uploaded this code to a DNA printer (yes), which then converted the bytes on disk to actual DNA molecules.


A Codex DNA BioXp 3200 DNA printer

The Codex DNA BioXp 3200 DNA printer



12/19/2021   Moderna's groundbreaking coronavirus vaccine was designed in just 2 days, by Susie Neilson, Andrew Dunn and Aria Bendix, Business Insider

11/25/2021   COVID-19 vaccines poised for launch, but impact on pandemic unclear, by Elie Dolgin, Nature


11/23/2020   Why Oxford’s positive COVID vaccine results are puzzling scientists, by Ewen Callaway, Nature

Preliminary data suggest that the immunization was more effective in trial participants who received a lower dose.

11/17/2020   A vial, a vaccine and hopes for slowing a pandemic — how a shot comes to be, by Carolyn Y. Johnson, The Washington Post

“There’s a lot of times in this industry, you work on something that you know someone — a family member or friend” affected by a disease, said Pamela Siwik, vice president of Pfizer Global Supply. “In this case, it’s the world.”

11/16/2020   COVID vaccine excitement builds as Moderna reports third positive result, by Ewen Callaway, Nature

Preliminary data show that the immunization is 94% effective and seems to prevent severe infections.

11/10/2020   The story of mRNA: How a once-dismissed idea became a leading technology in the Covid vaccine race, by Damian Garde — STAT and Jonathan Saltzman — Boston Globe

As he listened to Rossi describe his use of modified mRNA, Langer recalled, he realized the young professor had discovered something far bigger than a novel way to create stem cells. Cloaking mRNA so it could slip into cells to produce proteins had a staggering number of applications, Langer thought, and might even save millions of lives.


“I think you can do a lot better than that,” Langer recalled telling Rossi, referring to stem cells. “I think you could make new drugs, new vaccines — everything.”

11/9/2020   What Pfizer’s landmark COVID vaccine results mean for the pandemic, by Ewen Callaway, Nature

10/14/2020   How anti-ageing drugs could boost COVID vaccines in older people, by Cassandra Willyard, nature

COVID-19 poses the greatest threat to older people, but vaccines often don’t work well in this group. Scientists hope drugs that rejuvenate the immune system will help.

9/25/2020   COVID-vaccine results are on the way — and scientists’ concerns are growing, by Smriti Mallapaty & Heidi Ledford, Nature

Researchers warn that vaccines could stumble on safety trials, be fast-tracked because of politics or fail to meet the public’s expectations.

9/11/2020   China’s coronavirus vaccine shows military’s growing role in medical research, by Dyani Lewis, Nature

Scientists in the People’s Liberation Army helped to develop the world’s first COVID-19 vaccine to be approved for restricted use.

4/28/2020   The race for coronavirus vaccines: a graphical guide, by Ewen Callaway, Nature

More than 90 vaccines are being developed against SARS-CoV-2 by research teams in companies and universities across the world.  Nature’s graphical guide explains each vaccine design.


3/21/2020   About mRNA-1273, Moderna's Potential Vaccine Against COVID-19


2/4/2020   The promise of mRNA vaccines: a biotech and industrial perspective, by Nicholas A. C. Jackson, Kent E. Kester, Danilo Casimiro, Sanjay Gurunathan & Frank DeRosa, NPJ/Vaccines

Assuming that mRNA vaccines will be proven clinically efficacious and safe, one of the central advantages hinges on rapidity of manufacture. Within weeks, clinical batches can be generated after the availability of a sequence encoding the immunogen. The process is cell-free and scalable. Of paramount advantage, a facility dedicated to mRNA production should be able to rapidly manufacture vaccines against multiple targets, with minimal adaptation to processes and formulation. In addition, new targets requiring multi-antigen approaches will benefit from the speed in which mRNA can render multiple constructs.

1/13/2020  The NIH and Moderna’s infectious disease research team finalized the sequence for mRNA-1273. Moderna mobilized toward clinical manufacture, Moderna

NIAID, part of NIH, disclosed their intent to run a Phase 1 study using mRNA-1273 in response to the coronavirus threat. Manufacture of this batch was funded by the Coalition for Epidemic Preparedness Innovations (CEPI).

1/11/2020    Chinese authorities shared the genetic sequence of the novel coronavirus, Moderna



10/16/2019   Unlocking the potential of vaccines built on messenger RNA, by Elie Dolgin, Nature

Brad Kremer had waited months to receive an experimental cancer vaccine called BNT122, during which time the melanoma on his skin had spread to his liver and spine. His back pain was getting worse, he was rapidly losing weight and new cancerous lesions kept appearing on his left thigh. “It was very scary,” says Kremer, a 52-year-old sales representative from Acton, Massachusetts.


But within weeks of his first injection in March, Kremer could see that the vaccine was working. The coin-sized melanoma spots that popped up from his skin were now flat discolourations measuring millimetres across. “I was actually witnessing the cancer cells shrinking before my eyes,” he says. Several doses later, his appetite has returned, his back pain has subsided and scans show that his cancer is continuing to retreat.


Kremer’s dramatic response exemplifies the medical potential of vaccines built on messenger RNA. In this method, strings of lab-synthesized nucleotides train the immune system to recognize and destroy disease-causing agents — be they cancer cells or infectious viruses.

10/16/2019   How RNA therapies could be used to tackle the world’s biggest killer, by Chris Woolston, Nature

Researchers hope that understanding the many roles of non-coding RNA in heart health and cardiovascular disease could deliver a therapeutic breakthrough.

10/16/2019   Pharma’s roller-coaster relationship with RNA therapies, by Michael Eisenstein, Nature

After a groundswell of hype and a sceptical backlash, the pharmaceutical industry is learning how to leverage RNA interference in the clinic.

10/16/2019   RNA therapies explained, by Sarah DeWeerdt, Nature

Treatments that target RNA or deliver it to cells fall into three broad categories, with hybrid approaches also emerging.

4/10/2019   mRNA as a Transformative Technology for Vaccine Development to Control Infectious Diseases, by Giulietta Maruggi, Cuiling Zhang, Junwei Li, Jeffrey B. Ulmer, and Dong Yu1, NIH US National Library of Medicine

Due to the ability of the host’s innate system to sense and respond to RNA sequences of viral origin (reviewed in Chen et al.9 and Vabret et al.22), mRNA vaccines induce robust innate responses, including production of chemokines and cytokines such as interleukin-12 (IL-12) and tumor necrosis factor (TNF) at the injection site.23, 24, 25 These are factors crucial to successful induction of effective adaptive responses against the encoded antigen.26 Currently, two forms of mRNA vaccines have been developed: conventional mRNA encoding the antigen of interest flanked by 5′ and 3′ UTRs, and self-amplifying mRNA derived from the genome of positive-stranded RNA viruses. Self-amplifying mRNA encodes not only the antigen but also the viral replication machinery required for intracellular RNA amplification leading to high levels of antigen expression (Figure 1). Unique attributes of each mRNA technology, as well as the roadblocks that need to be overcome for advancement, are summarized in Table 1.

1/12/2018   mRNA vaccines — a new era in vaccinology, by Norbert Pardi, Michael J. Hogan, Frederick W. Porter & Drew Weissman, Nature Reviews/Drug Discovery

4/21/2016   Genetic secrets of the healthy elderly unveiled, by Erika Check Hayden, Nature

Scientists who have studied the genomes of hundreds of healthy older people say that one of their secrets might be genetic protection against the loss of mental function.The researchers' study, published on 21 April in Cell1, is the largest ever to sequence the genomes of people who have lived long, disease-free lives. Cardiologist Eric Topol of the Scripps Translational Science Institute in La Jolla, California, a leader of the work, says that one of the most difficult challenges was simply to find people who have lived to an old age (around 80 and upwards in this instance) without suffering autoimmune disease, blood clots, most cancers, diabetes, dementia, heart attack, kidney failure or stroke.

4/18/2011   The Vaccine Safety Datalink: a model for monitoring immunization safety, National Library of Medicine


Moderna Site:   mRNA Design Studio™ – Digital Design and Ordering of mRNA for Research

Our proprietary in-house digital application suite contains a Sequence Designer module to tailor an entire mRNA, with ever-improving rule sets that contain our accumulated learning about mRNA design. Drug Design Studio utilizes cloud-based computational capacity to run various algorithms we have developed to design each mRNA sequence. The utility of cloud-based capacity allows us to provide flexible computational capacity on demand, allowing the Research Engine to power parallel intake and design of multiple mRNA sequences. 


A statement by Moderna on Intellectual Property Matters during the COVID-19 Pandemic can be found here. Representative US patents relevant to our mRNA-1273 vaccine against COVID-19, are available here.

Wikipedia:   Polio Eradication

Wikipedia:   The Polio Vaccine 




Plague Poems – The Forty-Fourth Week

CitadelJohnSmith 960w540h

 3/26/2021   Citadel, a film by John Smith, Playing now on

Against a visual backdrop of London skyscrapers, roofs, chimneypots, snow and rain, sunlit and shadowed, days pass into nights. Skylines fade into nightlit peerings into windows and middle class lives.  Platings and dinners, coffee and desks.  Against this backdrop play Boris Johnson's speechs, lies and lesser lies, the tow-haired bluster of February through May of 2020. This is a brief film: 16 minutes 16 seconds of exteriors.  Boris dishes fantasy. The U.K. pandemic worsens into Europe's worst and the U.K economy slides off the twinned Brexit and Covid cliffs. .

1/5/2021   Blurbed to Death: How one of publishing’s most hyped books became its biggest horror story — and still ended up a best seller, by Lila Shapiro, Vulture


11/24/2020   Lord of Misrule: Thomas Morton’s American Subversions, By Ed Simon, The Public Domain Rieview

When we think of early New England, we tend to picture stern-faced Puritans and black-hatted Pilgrims, but in the same decade that these more famous settlers arrived, a man called Thomas Morton founded a very different kind of colony — a neo-pagan experiment he named Merrymount. Ed Simon explores the colony’s brief existence and the alternate vision of America it represents.



"Steps off a scraped March sky and sinks

Up into the blind Atlantic morning One small

Red dog jumping across the beach miles below

Like a freed shadow"


- from Geryoneis, by Stesichoros, 620BC-ish, fragments in the translation by Anne Carson, Autobiography of Red (Vintage Contemporaries)  Knopf Doubleday Publishing Group, 2013.

Anne Carson - interviewed at NYU -  Her "obsession with Herakles" and most recent evocation, in denim: "H of H Playbook," arriving on Kindle November 4


 A Journal of the Plague Year, Daniel Defoe

“that this necessity of going out of our houses to buy provisions was in a great measure the ruin of the whole city, for the people catched the distemper on these occasions one of another, and even the provisions themselves were often tainted.


“But when the physicians assured us that the danger was as well from the sound (that is, the seemingly sound) as the sick, and that those people who thought themselves entirely free were oftentimes the most fatal, and that it came to be generally understood that people were sensible of it, and of the reason of it; then, I say, they began to be jealous of everybody, and a vast number of people locked themselves up, so as not to come abroad into any company at all, nor suffer any that had been abroad in promiscuous company to come into their houses, or near them—at least not so near them as to be within the reach of their breath or of any smell from them; and when they were obliged to converse at a distance with strangers, they would always have preservatives in their mouths and about their clothes to repel and keep off the infection. It must be acknowledged that when people began to use these cautions they were less exposed to danger, and the infection did not break into such houses so furiously as it did into others before; and thousands of families were preserved (speaking with due reserve to the direction of Divine Providence) by that means.


"Every visited House to be marked. 'That each residence visited be marked with a red pass of a foot long inside the center of the door, obtrusive to be seen, and with these traditional printed words, that is to mention, "Lord, have mercy upon us," to be set close over the equal move, there to hold till lawful starting of the equal house. 


"But it was impossible to beat anything into the heads of the poor. They went on with the usual impetuosity of their tempers, full of outcries and lamentations when taken, but madly careless of themselves, foolhardy and obstinate, while they were well. Where they could get employment they pushed into any kind of business, the most dangerous and the most liable to infection; and if they were spoken to, their answer would be, ‘I must trust to God for that; if I am taken, then I am provided for, and there is an end of me’, and the like. Or thus, ‘Why, what must I do? I can’t starve. I had as good have the plague as perish for want. I have no work; what could I do? I must do this or beg.’ Suppose it was burying the dead, or attending the sick, or watching infected houses, which were all terrible hazards; but their tale was generally the same. It is true, necessity was a very justifiable, warrantable plea, and nothing could be better; but their way of talk was much the same where the necessities were not the same. This adventurous conduct of the poor was that which brought the plague among them in a most furious manner; and this, joined to the distress of their circumstances when taken, was the reason why they died so by heaps; for I cannot say I could observe one jot of better husbandry among them, I mean the labouring poor, while they were all well and getting money than there was before, but as lavish, as extravagant, and as thoughtless for tomorrow as ever; so that when they came to be taken sick they were immediately in the utmost distress, as well for want as for sickness, as well for lack of food as lack of health.


"But it was all to no purpose; the audacious creatures were so possessed with the first joy and so surprised with the satisfaction of seeing a vast decrease in the weekly bills, that they were impenetrable by any new terrors, and would not be persuaded but that the bitterness of death was past; and it was to no more purpose to talk to them than to an east wind; but they opened shops, went about streets, did business, and conversed with anybody that came in their way to converse with, whether with business or without, neither inquiring of their health or so much as being apprehensive of any danger from them, though they knew them not to be sound.

"This imprudent, rash conduct cost a great many their lives who had with great care and caution shut themselves up and kept retired, as it were, from all mankind, and had by that means, under God’s providence, been preserved through all the heat of that infection.

"This rash and foolish conduct, I say, of the people went so far that the ministers took notice to them of it at last, and laid before them both the folly and danger of it; and this checked it a little, so that they grew more cautious. But it had another effect, which they could not check; for as the first rumour had spread not over the city only, but into the country, it had the like effect: and the people were so tired with being so long from London, and so eager to come back, that they flocked to town without fear or forecast, and began to show themselves in the streets as if all the danger was over. It was indeed surprising to see it, for though there died still from 1000 to 1800 a week, yet the people flocked to town as if all had been well.

"The consequence of this was, that the bills increased again 400 the very first week in November; and if I might believe the physicians, there was above 3000 fell sick that week, most of them new-comers, too.


Link to Virology explainers, Virologists and to the outer, more accessible edges of the science.  Assembled and organized for my own use. If these help you, great..

NB: I haven't written out their full names, titles, or affiliations. Assume they've PhDs and more. There's no point in quoting randos or facebook foolishness.


Ed Rybicki   @edrybicki

Björn Meyer  @_b_meyer

Trevor Bedford   @trvrb     Bedford Lab

Isabella Eckerle, MD   @EckerleIsabella

Dr. Zoë Hyde   @DrZoeHyde 

Dr. Krutika Kuppalli   @KrutikaKuppalli

Ian M. Mackay, PhD   @MackayIM

Dr. Angela Rasmussen   @angie_rasmussen

Dr Emma Hodcraft   @firefoxx66


Prof. Akiko Iwasaki   @VirusesImmunity

Marion Koopmans   @MarionKoopmans 

Brian Wasik   @BrianRWasik 

Lauring Lab   @LauringLab

Bloom Lab   @jbloom_lab

Tyler Starr   @tylernstarr

Marija Backovic   @marija_backovic

Dr. Arinjay Banerjee   @sci_questions



DIY? SEC-MALS Validated SARS-CoV-2 Prefusion Trimeric Spike Variant Proteins


Close-up of orange experimental COVID-19 treatment pills called molnupiravir

10/8/2021   How antiviral pill molnupiravir shot ahead in the COVID drug hunt, by Cassandra Willyard, Nature

Molnupiravir, like remdesivir, is a nucleoside analogue, which means it mimics some of the building blocks of RNA. But the compounds work in entirely different ways. When SARS-CoV-2 enters a cell, the virus needs to duplicate its RNA genome to form new viruses. Remdesivir is a ‘chain terminator’. It stops the enzyme that builds these RNA ‘chains’ from adding further links. Molnupiravir, on the other hand, gets incorporated into burgeoning RNA strands and, once inside, wreaks havoc. The compound can shift its configuration, sometimes mimicking the nucleoside cytidine and sometimes mimicking uridine. Those RNA strands become faulty blueprints for the next round of viral genomes. Anywhere the compound gets inserted and that conformational shift happens, a point mutation occurs, Plemper says. When enough mutations accumulate, the viral population collapses. “That is what we term lethal mutagenesis,” he adds. “The virus essentially mutates itself to death.” And because the mutations accumulate randomly, it’s difficult for viruses to evolve resistance to molnupiravir — another plus for the compound.


Whether this clinical-trial success story will translate into a global game-changer in the fight against the pandemic isn’t yet clear. This week, two Indian drugmakers testing molnupiravir in people with moderate illness due to COVID-19 sought to end their trials because they saw no “significant efficacy” for the experimental drug. Also, Merck’s findings, which apply to people with mild-to-moderate cases of COVID-19, were disclosed only in a press release — and have yet to be pored over by scientists and submitted to regulators for approval


The United States has agreed to purchase 1.7 million courses of molnupiravir for US$1.2 billion, which works out to about $700 per 5-day course. That’s far less than the price of remdesivir or monoclonal antibodies, but still too costly for much of the world. Merck, which is co-developing the compound with Ridgeback, has struck licensing agreements with five Indian manufacturers of generic drugs. Those deals allow the manufacturers to set their own price in India and 100 other low- and lower-middle-income countries.



TweetReNeanderthalGene 2021 09 30

9/28/2021   A prenylated dsRNA sensor protects against severe COVID-19, Science, for list of 50+ authors, follow link

Inherited genetic factors can influence the severity of COVID-19, but the molecular explanation underpinning a genetic association is often unclear. Intracellular antiviral defenses can inhibit the replication of viruses and reduce disease severity. To better understand the antiviral defenses relevant to COVID-19, we used interferon-stimulated gene (ISG) expression screening to reveal that OAS1, through RNase L, potently inhibits SARS-CoV-2. We show that a common splice-acceptor SNP (Rs10774671) governs whether people express prenylated OAS1 isoforms that are membrane-associated and sense specific regions of SARS-CoV-2 RNAs, or only express cytosolic, nonprenylated OAS1 that does not efficiently detect SARS-CoV-2. Importantly, in hospitalized patients, expression of prenylated OAS1 was associated with protection from severe COVID-19, suggesting this antiviral defense is a major component of a protective antiviral response.

10/11/2021   A Neanderthal OAS1 isoform Protects Against COVID-19 Susceptibility and Severity: Results from Mendelian Randomization and Case-Control Studies, medRxIv

by Sirui Zhou, Guillaume Butler-Laporte, Tomoko Nakanishi, David Morrison, Jonathan Afilalo, Marc Afilalo, Laetitia Laurent, Maik Pietzner, Nicola Kerrison,  Kaiqiong Zhao, Elsa Brunet-Ratnasingham, Danielle Henry, Nofar Kimchi, Zaman Afrasiabi, Nardin Rezk, Meriem Bouab, Louis Petitjean, Charlotte Guzman, Xiaoqing Xue, Chris Tselios, Branka Vulesevic, Olumide Adeleye, Tala Abdullah, Noor Almamlouk, Yiheng Chen, Michaël Chassé, Madeleine Durand, Michael Pollak, Clare Paterson,  Hugo Zeberg, Johan Normark,  Robert Frithiof, Miklós Lipcsey, Michael Hultström, Celia M T Greenwood, Claudia Langenberg, Elin Thysell, Vincent Mooser, Vincenzo Forgetta, Daniel E. Kaufmann, ichards

9/26/2021   Key Stages of the SARS-CoV-2 Life Cycle, Pfizer

SARS-CoV-2 proteolysis is driven by two virally encoded proteases, the 3C-like protease, 3CL (known as the main protease); and the papain-like protease.2,4 The 3CL protease cleaves the viral pp1ab polyprotein at 11 sites, while the papain-like protease cleaves at 3 sites, generating proteins critical for viral replication.2,4  Despite coronaviruses being subject to extensive mutagenesis, proteases are highly conserved among coronaviruses. SARS-CoV-2 proteases are potential targets for stopping replication.2,3,6,7 


[ some brief animations, mainly ]

9/25/2021   Lack of Evidence of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Spillover in Free-Living Neotropical Non-Human Primates, Brazil, by Lívia Sacchetto 1,†OrcID,Bárbara Aparecida Chaves 2,3,4,†OrcID,Edson Rodrigues Costa 2OrcID,Aline Souza de Menezes Medeiros 2,Marcelo Gordo 5OrcID,Danielle Bastos Araújo 6,7,Danielle Bruna Leal Oliveira 6,7,8OrcID,Ana Paula Betaressi da Silva 9,Andréia Francesli Negri 9,Edison Luiz Durigon 6,10OrcID,Kathryn A. Hanley 11,Nikos Vasilakis 12,13,14,15,16OrcID,Marcus Vinícius Guimarães de Lacerda 2,3,17,* andMaurício Lacerda Nogueira 1,*OrcID, Viruses

Marion Koopmans: Twitter[ @MarionKoopmans ]:  "Primates are sensitive to SARS COV 2 and in zoo’s have been infected. This study looked at free-living primates, found no evidence for reverse spillover."

9/24/2021   Caspase-4/11 exacerbates disease severity in SARS-CoV-2 infection by promoting inflammation and thrombosis, by Mostafa Eltobgy, Ashley Zani, Adam Kenney, Shady Estfanous, Eunsoo Kim, Asmaa Badr, Cierra Carafice, Kylene Daily, Owen Whitham, Maciej Pietrzak, Amy Webb, Jeffrey Kawahara, Adrian Eddy, Parker Denz, Mijia Lu, Mahesh KC, Mark Peeples, Jianrong Li, Jian Zhu, Jianwen Que, Richard Robinson, Oscar Rosas Mejia, Rachael Rayner, Luanne Hall-Stoodley, Stephanie Seveau, Mikhail A Gavrilin, Andrea Tedeschi, Santiago Partida-Sanchez, Frank Roberto, Emily Hemann, Eman Abdelrazik, Adriana Forero, Shahid Nimjee, Prosper Boyaka, Estelle Cormet-Boyaka, Jacob Yount, Amal Amer, bioRxiv

9/13/2021   Some thoughts on gain of function (GoF) and virology research in general, by Stuart Neil, PhD  @stuartjdneil on twitter

One of these links takes you to a browser friendly threadreaderapp version of Neil's twitter thread. The other takes you to his twitter bio.

Animated sequence of the SARS-CoV-2 virus.

Credit: Janet Iwasa, University of Utah

2021/07/28   How the coronavirus infects cells — and why Delta is so dangerous, by Megan Scudellari, Nature

Scientists are unpicking the life cycle of SARS-CoV-2 and how the virus uses tricks to evade detection.


Virosphere 800w VG


9/1/2021:   "We argue that the virosphere proper, here termed orthovirosphere, consists of a distinct variety of replicators that encode structural proteins encasing the replicators’ genomes, thereby providing protection and facilitating transmission among hosts."  

6/17/2021   The quest for a pill to fight viruses gets a $3.2 billion boost, by Carolyn Y. Johnson, The Washngton Post

“Investors are totally uninterested in antivirals. Even if you can demonstrate you can make a couple billion dollars, nobody cares,” said Ann Kwong, a virologist who played a leading role in developing an antiviral approved against hepatitis C at Vertex Pharmaceuticals, along with an influenza treatment. “What they really want is a chronic treatment. Nobody ever gets cured of high cholesterol.” 


4/29/2021   Hopes rise for coronavirus drug remdesivir, by Heidi Ledford, Nature

Despite conflicting studies, results from largest trial yet show the antiviral speeds up recovery, putting it on track to become a standard of care in the United States.

TweetOfCovid 2ndstudydemonstratingairborneviability

4/23/2021   Isolation of SARS-CoV-2 from the air in a car driven by a COVID patient with mild illness, by John A. Lednicky, Michael Lauzardo Md.,  M. Alam, Maha A. Elbadry, Caroline J. Stephenson, Julia C. Gibson, J. Glenn Morris Jr., International Journal of Infectious Diseases

  • SARS-CoV-2 was isolated from air in a car driven by a COVID patient.
  • Virus was cultured from samples with a particle range of 0.25 to 0.50 μm.
  • A substantial component of transmission risk appears to be via aerosolized virus.


We used a Sioutas personal cascade impactor sampler (PCIS) to screen for SARS-CoV-2 in a car driven by a COVID-19 patient. The patient, who had only mild illness without fever or cough and was not wearing a mask, drove the car for 15 minutes with the air conditioning turned on and windows closed. The PCIS was clipped to the sun-visor above the front passenger seat and was retrieved from the car two hours after completion of the drive.


SARS-CoV-2 was detectable at all PCIS stages by PCR and was cultured from the section of the sampler collecting particles in the 0.25 to 0.50 μm size range.



Our data highlight the potential risk of SARS-CoV-2 transmission by minimally symptomatic persons in the closed space inside of a car and suggest that a substantial component of that risk is via aerosolized virus.

4/22/2020   Coronavirus: the first three months as it happened

Nature recorded major events as the pandemic spread across the globe.

4/14/2021   The race for antiviral drugs to beat COVID — and the next pandemic, by Elie Dolgin, Nature

Despite dire warnings, a stockpile of ready compounds to fight viral pandemics was sorely lacking. Can drugmakers finally do the right thing?

3/11/2021   mRNA vaccine protects monkeys against HIV-like virus, by Liz Highleyman, nam/aidsmap

The same messenger RNA (mRNA) approach used for the highly effective Pfizer-BioNTech and Moderna COVID-19 vaccines also shows promise for protection against HIV, according to a presentation this week at the virtual Conference on Retroviruses and Opportunistic Infections.


Despite more than three decades of research, scientists have had little success developing vaccines to prevent HIV. To date, only one vaccine regimen – a canarypox vector primer followed by a gp120 protein booster – has demonstrated partial protection in human studies; however, it was not effective in a recent large trial.


Dr Peng Zhang of the US National Institute of Allergy and Infectious Diseases (NIAID) and colleagues, in collaboration with Moderna, are taking a different approach. The investigators designed a vaccine regimen that introduces mRNA into a cell and instructs it to make the outer, envelope proteins of three different subtypes of HIV, plus the structural gag protein from SIV, HIV's simian cousin. The cells then assemble these proteins to make virus-like particles that trigger an immune response. These particles are not viruses because they have no genetic material of their own and cannot reproduce – but they look like viruses to the immune system.

3/2/2021   Study looks at the impact of Stabilising SARS-Cov-2 Spike through “PP” mutations and Cleavage site removal. Combination of PP and Cleavage site removal (as seen in J&J/Novavax vaccine) was beneficial, “PP” mutation alone (as seen in Pfizer/Moderna) was not, COVID Data Review

3/2/2021   Introduction of Two Prolines and Removal of the Polybasic Cleavage Site Lead to Higher Efficacy of a Recombinant Spike-Based SARS-CoV-2 Vaccine in the Mouse Model, by Fatima Amanat, Shirin Strohmeier, Raveen Rathnasinghe, Michael Schotsaert, Lynda Coughlan, Adolfo García-Sastre, Florian Krammer, American Society for Microbiology

3/2/2021   SARS-CoV-2 RBD-Tetanus toxoid conjugate vaccine induces a strong neutralizing immunity in preclinical studies, [by dozens of scientists], bioRxiv

2/23/2021   "We have completely mapped #SARS_CoV_2 mutations that escape binding by LY-CoV555 (antibody that forms the basis for Eli Lilly's bamlanivimab) both alone & in cocktail with LY-CoV016 in a new study," Bloom Lab

2/22/2021   Complete map of SARS-CoV-2 RBD mutations that escape the monoclonal antibody LY-CoV555 and its cocktail with LY-CoV016, by Tyler N. Starr,  Allison J. Greaney,  Adam S. Dingens, Jesse D. Bloom, bioRxiv


TweetOfBloomLab bamlanivimabEscapeMutations

The dynamics of adaptation on correlated fitness landscapes, by Sergey Kryazhimskiya, Gašper Tkacikˇ and Joshua B. Plotkina, Proceedings of the National Academy of Sciences of the United States of America

2021-01-31   NYC Reveals White New Yorkers Have Received Lion's Share Of COVID-19 Vaccine Doses, by Sydney Pereira, Jake Dobkin and Nsikan Akpan, the Gothamist

Three white residents receive a COVID-19 vaccine for every Black or Latino person in the city, according to new demographic data released by the mayor’s office on Sunday.

2021-01-29   Virus expert Trevor Bedford warns of "convergent evolution" amid COVID-19 mutations, Margaret Brennan, Face the Nation

2021-01-27   We Cannot Rely Exclusively on Vaccines to End the Pandemic, Angela Rasmussen, Slate

2021/01/21   mRNA Vaccines: What Happens, Derek Lowe, Sciencemag

2021/01/02   Putting PCR into real-time, Ian M Mackay, PhD, Virology Down Under

2020/12/28   The mechanics of the polymerase chain reaction (PCR)…a primer, Ian M Mackay, PhD

2020/10/24   The Swiss Cheese Respiratory Virus Pandemic Defence, Mackay


2020/10/23   Virology, transmission, and pathogenesis of SARS-CoV-2, Cevik, Kuppalli and Kindrachuk, BMJ

2020/05/15   The sprint to solve coronavirus protein structures — and disarm them with drugs, by Megan Scudellari, 

Lying in bed on the night of 10 January, scrolling through news on his smartphone, Andrew Mesecar got an alert. He sat up. It was here. The complete genome of a coronavirus causing a cluster of pneumonia-like cases in Wuhan, China, had just been posted online.

2020/05/14   Dozens of coronavirus drugs are in development — what happens next? by Heidi Ledford, Nature

2020/05/04   Profile of a killer: the complex biology powering the coronavirus pandemic, by David Cyranoski, Nature

In 1912, German veterinarians puzzled over the case of a feverish cat with an enormously swollen belly. That is now thought to be the first reported example of the debilitating power of a coronavirus. Veterinarians didn’t know it at the time, but coronaviruses were also giving chickens bronchitis, and pigs an intestinal disease that killed almost every piglet under two weeks old.


The link between these pathogens remained hidden until the 1960s, when researchers in the United Kingdom and the United States isolated two viruses with crown-like structures causing common colds in humans. Scientists soon noticed that the viruses identified in sick animals had the same bristly structure, studded with spiky protein protrusions. Under electron microscopes, these viruses resembled the solar corona, which led researchers in 1968 to coin the term coronaviruses for the entire group.


Of the viruses that attack humans, coronaviruses are big. At 125 nanometres in diameter, they are also relatively large for the viruses that use RNA to replicate, the group that accounts for most newly emerging diseases. But coronaviruses really stand out for their genomes. With 30,000 genetic bases, coronaviruses have the largest genomes of all RNA viruses. Their genomes are more than three times as big as those of HIV and hepatitis C, and more than twice influenza’s.

2020/04/28   The race for coronavirus vaccines: a graphical guide, by Ewen Callaway, Nature

Eight ways in which scientists hope to provide immunity to SARS-CoV-2 .

2020/04/20   How does COVID-19 kill? Uncertainty is hampering doctors’ ability to choose treatments, by Heidi Ledford, Nature

Doctors are reaching for drugs that dampen the immune response — but these also undermine the body’s own fight against the coronavirus.

2020/04/07   Why measles deaths are surging — and coronavirus could make it worse, by Leslie Roberts, Nature

2020/02/18   When will the coronavirus outbreak peak? by David Cyranoski, Nature

On 11 February, Zhong Nanshan, a prominent Chinese physician leading a panel of experts helping to control the outbreak, said that the coronavirus will possibly peak by the end of February. Zhong, who is famous for discovering the SARS virus, said the situation had improved with government control measures, such as travel restrictions and extended holidays, although he admitted that it was still a “difficult period” for Wuhan.


Sebastian Funk, a statistician who models infectious diseases and who coauthored the analysis, says the prediction is based on an estimate that one infected person in Wuhan was, on average, infecting between 1.5 and 4.5 others — a measure known as the virus’s effective reproduction number, or R — before the travel restrictions were introduced on 23 January.

2020/02/15   More than 80 clinical trials launch to test coronavirus treatments, by Amy Maxmen, Nature

As HIV drugs, stem cells and traditional Chinese medicines vie for a chance to prove their worth, the World Health Organization attempts to bring order to the search.

2020/01/24   Wuhan scientists: What it’s like to be on lockdown, by David Cyranoski & Andrew Silver, Nature

Measures to contain a new virus’s spread have cut off the city's researchers.

2020/01/22    China coronavirus: Six questions scientists are asking, by Ewen Callaway & David Cyranoski, Nature

Researchers are racing to find out more about the epidemiology and genetic sequence of the coronavirus spreading in Asia and beyond.

2020/01/21   Stop the Wuhan virus, Nature

The virus has been spreading. On 21 January, as Nature went to press, there were almost 300 reported cases — seven times the figure stated five days earlier. Over the past week, authorities in South Korea, Thailand and Japan have also reported cases. Researchers at Imperial College London who have modelled the outbreak on the basis of estimates of travel out of Wuhan say the virus might have infected as many as 1,700 people.


The virus, which still lacks a formal name, is being called 2019-nCOV. It is a relative of both the deadly severe acute respiratory syndrome (SARS) and the Middle East respiratory syndrome (MERS) viruses. People with the virus report a fever along with other symptoms of lower-respiratory infection such as a cough or breathing difficulties. The first people infected in China are understood to have caught the virus in one of Wuhan’s live animal and seafood markets — probably from an animal. Some 95% of the total cases, including those in Japan, South Korea and Thailand, also involved people who had been to Wuhan.

2020/01/21   How quickly does the Wuhan virus spread? by Nicky Phillips , Smriti Mallapaty & David Cyranoski, Nature

Chinese officials have confirmed that the virus is spreading between people, but it’s still unclear how easily this happens.

2020/01/20   New virus surging in Asia rattles scientists, by David Cyranoski, Nature

Chinese officials reported more than 100 new infections and South Korea confirmed its first case.

2020/01/08   New virus identified as likely cause of mystery illness in China, by David Cyranoski, Nature

As of 5 January, 59 people in the east-central city of Wuhan have been infected with the mystery virus, with 7 in a critical condition, according to the Wuhan Municipal Health Commission.


Update: On 9 January, Chinese state media reported that scientists have identified a new coronavirus as the likely cause of a pneumonia-like illness that has sickened dozens of people. Researchers have sequenced the virus's genome, and fifteen patients have tested positive to the virus, according to Xinhua news agency.

2019/10/31   Measles erases immune ‘memory’ for other diseases, by Giorgia Guglielmi, Nature

Measles infections in children can wipe out the immune system’s memory of other illnesses such as influenza, according to a pair of studies[[1]] [[2]]. This can leave kids who recover from measles vulnerable to other pathogens that they might have been protected from before their bout with the virus.


The Science study is the first to show definitive evidence that measles can destroy this immune memory, says Harvard T. H. Chan School of Public Health in Boston, Massachusetts, infectious-disease immunologist Michael Mina.

2019/10/30   South Korea deploys snipers and drones to fend off deadly pig virus, by Mark Zastrow, Nature

Outbreaks of African swine fever have killed millions of pigs across Asia, and the virus has recently been detected in wild boars near the North Korean border.

Scientists and doctors riding syringes and capsules, and surfing on tablets at a coronavirus

2019/09/18    Nature Outlook: Influenza, Nature

2019/09/18   Towards a universal flu vaccine, by Michael Eisenstein, Nature

So far, antibodies have been the primary focus of the vaccine community because they represent a crucial first line of defence against circulating virus particles, but T cells provide critical protection by containing infection once it is under way. “People get exposed and infected every two or three years on average,” says Sarah Gilbert, who heads vaccine development at the University of Oxford’s Jenner Institute, UK. “The vast majority of these infections are either asymptomatic or mild,” she says, “and the reason is that people have a T-cell response that’s strong enough to protect them.”

2019/09/18   Flu on the farm, by Cassandra Willyard, Nature

Farms help to spread influenza but they might be an early warning system for the next human pandemic.

2019/04/25    Spread of deadly pig virus in China hastens vaccine research, by Smriti Mallapaty, Nature

The virus is not harmful to humans, but is taking a huge economic toll on the pork industry.

2018/11/01   Machine learning helps to identify the animals that deadly viruses call home, by Ewen Callaway, Nature

But the model will need further refining before it can pinpoint species-level disease reservoirs.

2018/11/01   Machine learning spots natural selection at work in human genome, by Amy Maxmen, Nature

Scientists are using artificial intelligence to identify genetic sequences molded by evolutionary pressures.

2018/03/19   Machine learning spots treasure trove of elusive viruses, by Amy Maxmen, Nature

In recent years, researchers have hunted for unknown viruses by sequencing DNA in samples taken from various environments. To identify the microbes present, researchers search for the genetic signatures of known viruses and bacteria — just as a word processor’s ‘find’ function highlights words containing particular letters in a document. But that method often fails, because virologists cannot search for what they do not know. A form of AI called machine learning gets around this problem because it can find emergent patterns in mountains of information. Machine-learning algorithms parse data, learn from them and then classify information autonomously.


“Previously, people had no method to study viruses well,” says Jie Ren, a computational biologist at the University of Southern California in Los Angeles. “But now we have tools to find them.”

2018/01/03   Deep learning sharpens views of cells and genes, by Amy Maxmen, Nature

Neural networks are making biological images easier to process.

2017/12/01   Bat cave solves mystery of deadly SARS virus — and suggests new outbreak could occur, by David Cyranoski, Nature

Chinese scientists find all the genetic building blocks of SARS in a single population of horseshoe bats.

2017/06/15   Bats are global reservoir for deadly coronaviruses, by Amy Maxmen, Nature

2017/04/05   Machine learning predicts the look of stem cells, by Amy Maxen, Nature

2017/02/23   Inside the Chinese lab poised to study world's most dangerous pathogens, by David Cyranoski, Nature

A laboratory in Wuhan is on the cusp of being cleared to work with the world’s most dangerous pathogens. The move is part of a plan to build between five and seven biosafety level-4 (BSL-4) labs across the Chinese mainland by 2025, and has generated much excitement, as well as some concerns.


The lab was certified as meeting the standards and criteria of BSL-4 by the China National Accreditation Service for Conformity Assessment (CNAS) in January. The CNAS examined the lab’s infrastructure, equipment and management, says a CNAS representative, paving the way for the Ministry of Health to give its approval.


BSL-4 is the highest level of biocontainment: its criteria include filtering air and treating water and waste before they leave the laboratory, and stipulating that researchers change clothes and shower before and after using lab facilities. Such labs are often controversial. The first BSL-4 lab in Japan was built in 1981, but operated with lower-risk pathogens until 2015, when safety concerns were finally overcome.


The expansion of BSL-4-lab networks in the United States and Europe over the past 15 years — with more than a dozen now in operation or under construction in each region — also met with resistance, including questions about the need for so many facilities.

2012/08/28   Pig fever sweeps across Russia, by Ewen Callaway, Nature

Scientists first encountered African swine fever in the 1920s in domestic pigs in Kenya, where the vicious haemorrhagic fever felled nearly every animal infected. The virus, which is also carried by warthogs and ticks without causing disease, is now endemic in much of sub-Saharan Africa, limiting pig farming there. It does not infect humans. In 1957, the virus jumped to Portugal after pigs near Lisbon’s airport were fed infected human food scraps (the virus particles can survive meat curing processes). It then hit Spain, and import of the region’s ham — including the coveted jamón ibérico — was banned by many countries, until the disease was eradicated in Spain and Portugal in the mid-1990s.





ImpactOfOpeningAndClosingDecisionsInMichigan JHU LiveChart


Clicking the above graphic takes you to the Johns Hopkins University live version of this graphic.  Each dotted vertical line is a 2020 policy change, an opening, a closing, something..  Click them for their meaning.



9/3/2021    What we now know about how to fight the delta variant of COVID, by J. Stacey Klutts, M.D., Tampa Bay Times

Klutts is Special Assistant to the National Director of Pathology and Lab Medicine for the entire Veterans Affairs system, with a specific role in advising on elements of COVID testing for the system.

  • 1. Like Gorilla Glue. The delta variant (lineage B.1.617.2) has a particular collection of mutations in the spike protein (that knob-like projection you see in renderings of the virus) that make it extremely effective in attaching to human cells and gaining entry. If the original COVID strains were covered in syrup, this variant is covered in ultrafast-drying Gorilla Super Glue (industrial strength).
  • 2. 1,000 times higher. There are two recent publications which demonstrate that the viral loads in the back of the throats of infected patients are 1,000 times higher with the delta than with previous variants. I can tell you from data in my own labs, that is absolutely true. We are seeing viral signals we never saw last year using the exact same assays.
  • 3. Much more infectious. This much higher load plus the ultra “stickiness” of the delta strains for adhering to human cells makes it remarkably more infectious than previous strains. You may have heard of R0 (Pronounced R naught) which is, in a nutshell, the number of people to which an infected person would be expected to transmit the virus. Early versions of the virus had a 2 to 2.5 R0 value. So one infected person would infect two or so people on average. Delta has an R0 of about eight! In the infectious disease world, that’s almost unheard of. Chickenpox and measles are about all we have ever seen that spread that efficiently from human to human. This changes the story line completely from earlier in the pandemic and makes this surge, in many ways, like a completely different pandemic event.
  • 4. Five days. There is another recent publication out of Singapore with data that confirms something we suspected. I will explain more about the “why” on this below when I talk about vaccines, but the gist is this: The viral loads in the throats of vaccinated persons who become infected with delta rises at identical rates as in unvaccinated persons, but only for the first few days. After five days or so, the viral loads in the vaccinated person start to quickly drop whereas those in the unvaccinated person persist. This key set of observations is important for several reasons relating to vaccinated persons serving as vectors for spread (see below).
  • 5. Young people. This pandemic, Round 2, is primarily being observed in younger patients than in Round 1. Our children’s hospitals are even already filling up or full. Because of the delta viral dynamics, it is much more capable of causing severe disease in a larger swath of the population. You spew enough of any human pathogen on someone without immunity, and it’s not going to end well. This sets up very poorly for the beginning of the school year — which has already started in Florida — and it scares me. Check that. It is actually terrifying. I sure hope we have vaccines for the 5- to 11-year-olds soon.
  • 6. Vaccines work! Speaking of vaccines. Are they working? Yes! They are absolutely doing their expected job. We know a lot about vaccines for upper respiratory viruses, as we have been giving the population one every year for decades (influenza). To explain all of this, I need to provide some biological context. When you get a vaccine as a “shot,” the “antigen” in the vaccine leads to formation of an antibody response. You probably knew that. What’s important, though, is that it primarily leads to a specific Immunoglobulin G (IgG) response. That’s the antibody type that circulates around in really high numbers in the blood, is located some in tissues and is more easily detectable by blood tests, etc.

    What that shot does not do is produce an Immunoglobulin A (IgA) antibody response to the virus at the surface of the throat mucosa. That’s the antibody type that could prevent the virus from ever binding in the first place. As such, in a vaccinated person, the virus can still attach like it’s about to break into the house, but it doesn’t realize that there is an armed homeowner on the other side of the door. When that virus is detected, the IgG beats it up and clears it before the person gets very ill (or ill at all). (Sidebar: Anyone ever had their kid — or themselves — get the “Flumist” vaccine as their annual flu booster? The idea there is to introduce the antigens at the surface of the throat mucosa leading to that IgA response that will prevent infection from happening at all. Sounds good and still has a place, but it isn’t quite as effective overall as the shot.)

  • 7. Preventing disease and death. The COVID-19 vaccines are designed to prevent disease/death through that IgG response (though it does also reduce infections somewhat). How good are the vaccines at doing all of this with delta? The Centers for Disease Control and Prevention has just released data addressing that very question. Punchline: They’re remarkably good! The vaccine shows an 8-fold reduction in the development of any symptomatic disease secondary to delta. For hospitalization, it is a 25-fold reduction. That’s 25 times! Remarkable. For death, it is also 25 times! This is a very effective pharmaceutical class when looking at overall efficacy toward the intended/expected purpose. When looking at the very tiny side effect profile, I’d personally consider it one of the best overall pharmaceuticals on the market in any class of drugs.
  • 8. So, you’re vaccinated? First of all, a sincere, heart-felt thank you! But you may now ask, so why do I again need to wear a mask? We talked about disease, hospitalizations and death above, but what about infections themselves? The vaccines are now estimated to provide a 3-times reduction in infection. For reasons that I tried to make clear above, it isn’t surprising that the vaccine is less effective at preventing infection vs. preventing disease. We are indeed seeing detectable virus, at high levels, in asymptomatic, vaccinated persons when we test them prior to procedures, etc. We have a few that are mildly symptomatic, too.

    While we now understand that the virus fades from the back of the throat pretty quickly in a vaccinated person, we also know that an infected, vaccinated person can transmit this very infectious virus to others for at least a couple of days. So, as before, you are being asked to wear a mask to primarily protect others.

    We need you again to interrupt the transmission cycle of the virus, as you don’t know when you might be infectious. The vaccine alone cannot interrupt this cycle when there is a lot of virus in the community within unprotected persons.

    9. What’s next? I live and practice in Iowa, and I see the tsunami wave on the horizon. It’s typical for respiratory viruses to begin in the southern United States (where it is hot and everyone clusters indoors in the air conditioning to escape the heat) and then creep north to affect those areas when it gets colder (and people go inside because it’s getting colder). If you live in the north and are not vaccinated, it is not too late, but it’s getting damn close. It’s also time to start wearing masks in public again (ugh...I hate it, too).

    Those of you in the south, particularly in Florida, know that the tsunami is already on your shores. If you weren’t already off the beach, you might be in trouble. However, if you are there and haven’t yet been affected, run like hell to metaphorical higher ground — get vaccinated, wear a mask.

    I beg of you, watch that wave and don’t ignore it. I have zero political agenda (I hate politics). I’m just a nerdy scientist and physician who loves you all, and I certainly don’t want to see a mass of my friends grieving — or dead — because I didn’t yell loud enough to get you and your families off that beach. So, run! (to your pharmacy ... driving is allowed). You don’t want any part of this thing without vaccine on board.

    Dr. J. Stacey Klutts is a clinical associate professor of pathology and clinical microbiology at the University of Iowa and is the chief of the Pathology and Laboratory Service for the Central Iowa VA Health Care System. He is the past president of the Academy of Clinical Laboratory Physicians and Scientists (ACLPS) and chairs the National VA Clinical Microbiology Council in addition to his national roles referenced above. This is adapted from a Facebook post with permission of the author.


7/30/2021   How Contagious Are Chickenpox, Measles As CDC Document Reveals Delta Variant's R0, by Aristos Georgiou, Newsweek

7/29/2021   ‘The war has changed’: Internal CDC document urges new messaging, warns delta infections likely more severe, by Yasmeen Abutaleb, Carolyn Y. Johnson and Joel Achenbach, The Washington Post

A person working in partnership with the CDC on investigations of the delta variant, who spoke on the condition of anonymity because they were not authorized to speak, said the data came from a July 4 outbreak in Provincetown, Mass. Genetic analysis of the outbreak showed that people who were vaccinated were transmitting the virus to other vaccinated people. The person said the data was “deeply disconcerting” and a “canary in the coal mine” for scientists who had seen the data.


Matthew Seeger, a risk communication expert at Wayne State University in Detroit, said a lack of communication about breakthrough infections has proved problematic. Because public health officials had emphasized the great efficacy of the vaccines, the realization that they aren’t perfect may feel like a betrayal.

7/29/2021    'The War Has Changed: Delta Strain Equally Contagious in Vaccinated Cases, Masks a Must, CDC Says, by Daniel Villareal, Newsweek

Symptomatic breakthrough infections seem to be happening among 0.0098 percent of all fully vaccinated people, according to an ABC News study of cases reported by the CDC last week. Put another way, out of 156 million fully vaccinated Americans, 153,000 contracted symptomatic COVID last week, the CDC reported.

7/27/2021   Tennessee evangelical pastor demands churchgoers ditch their masks: ‘Don’t believe this delta variant nonsense’, by Jaclyn Peiser, The Washington Post

If “you start showing up [with] all these masks and all this nonsense, I will ask you to leave,” Locke, 45, told scores of Global Vision Bible Church parishioners during his sermon on Sunday. His statement was followed by cheers and applause.


“I am not playing these Democrat games up in this church,” he added.


Tennessee recently reported that 98 percent of people who died of covid and 97 percent of covid hospitalizations are among the unvaccinated.

CovidVariants 2021 08 02

CovidVariants 2021 08 02 pic1



4/28/2021   Characteristics of SARS-CoV-2 variants of concern B.1.1.7, B.1.351 or P.1: data from seven EU/EEA countries, weeks 38/2020 to 10/2021, by Tjede Funk, et al


2021 04 06 Michigan b117 variant infection rates

4/6/2021   As Variants Have Spread, Progress Against the Virus in U.S. Has Stalled, by Lauren Leatherby, The New York Times

The country’s vaccine rollout has sped up since the first doses were administered in December, recently reaching a rolling average of more than three million doses per day. And new U.S. cases trended steeply downward in the first quarter of the year, falling by almost 80 percent from mid-January through the end of March.


But during that period, states also rolled back virus control measures, and now mobility data shows a rise in people socializing and traveling.


Amid all this, more-contagious variants have been gaining a foothold, and new cases are almost 20 percent higher than they were at the lowest point in March. The B.1.526 variant, which first appeared in New York City in samples from November, appears in two forms: one with a mutation that may help the virus evade antibodies and another that may help it bind more tightly to human cells.

4/1/2021   Michigan Confirms First Case Of The Brazil Variant, by Allen Lengel, Deadline Detroit

The news came on the same day the state reported 6,036 new Covid cases and 49 deaths.

4/1/2021   Michigan's 1st case of Brazil COVID-19 variant identified in Bay County, by Christina Hall, Detroit Free Press

This is the second new variant of COVID-19 to be identified in Bay County since last week, said Joel Strasz, the county's public health officer, adding, "The rise of these new variants definitely impact the progress we have made this year with vaccinations."


TweetOfDrEricFeigl Ding P1Variant 2021 04 01


3/30/2021   The Fourth Surge Is Upon Us. This Time, It’s Different., by Zeynep Tufekci, The Atlantic

The twists and turns of a pandemic can be hard to predict, but this most recent increase was almost inevitable: A more transmissible and more deadly variant called B.1.1.7 has established itself at the precise moment when many regions are opening up rapidly by lifting mask mandates, indoor-gathering restrictions, and occupancy limits on gyms and restaurants.


TweetOfDrEricFeigl Ding P1Variant 2021 03 26

4) One Brazil @obscovid19br study puts #P1 transmission at 2.5x faster than old

common strain. This 150% increase is much faster than even #B117 if it holds up.

As ever, if it's a tweet, click it to follow the thread.


TweetOfVariance 2021 03 17 Bolze

SARS-CoV-2 Variants, updated Mar. 16, 2021, CDC


2/26/2021   Worst fears of Denmark CDC coming true, B117 will be the dominant #SARSCoV2 variant, by Dr Erid Feigl-Ding

2) The steady inevitable March of #B117 replacing the old strain is as constant as time. B117 will replace older less contagious common strains - and it certainly has. Denmark Data is best because they now genetically sequence 100% of all cases!!!

3) Denmark cases surge is now very different than before - a lot more reports of children not seen before. Here is an outbreak of #B117.

4) The global decline in cases **HAS NOW REVERSED**. Cases are once again on the rise worldwide, especially in Europe where #B117 is most common and surging.

5) I warned about this divergence - old strain pandemic is ending. But new #B117 led pandemic is on the rise. And we didn’t see it / it was hard to see because of the initial B117 growing in the underbelly of an overall decline.

TWO DIFFERENT #COVID19 PANDEMICS—Many think with cases dropping that pandemic is nearly over. But truth is, there are now 2 different #SARSCoV2 pandemics diverging—old strain is waning, while the more contagious #B117 strain is dominating. We will be soon slammed very hard.


Here is what is going to happen... currently R is ~0.9 in many places, but with the more infectious #B117, the R will jump 50% approximately. And it is inevitable (all CDC and Danish models say this) that B117 will take over as the reigning dominant variant soon...  and when that happens, what worked before to keep the pandemic contained at R of 0.9 will no longer work. Here is the model for Alberta, by @GosiaGasperoPhD.   The B117 dotted red line will soon dominate and drive a new surge in latter half of March and April.

TweetOfEricFeiglDing ProjectionOfCovidAlbertaCurrent 2021 02 05


The solution to defeating the #B117 is to chase a #ZeroCovid approach and slam the R even lower to below 0.7.... but optimally 0.6 or less. So that even when the #B117 arises, it will keep R under 1 (0.6*1.5=0.9). And by keeping R at 0.6 now—we will have buffer room for B117.  And again Denmark CDC agrees with that assessment. Their model for R of 0.8 shows it is insufficient to defeat #B117. But its model for R 0.7 shows it can be enough.  The problem is that of the declining states, only 1 state is under R 0.7... which is Wyoming (figure below sorted from lowest to highest R). Every other state’s R is over 0.7. Thus while they would yield decreases now—they won’t once #B117 takes over.

2/22/2021   Coronavirus Mutations: A Visual Guide to New, More-Infectious Variants, by Alberto Cervantes and Josh Ulick, The Wall Street Journal 

2/20/2021   National and Subnational estimates for the United States of America

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2021 02 21 EPINowGlobal 900w528h


Danish scientists have been extremely worried and anxious about the growing #B117 underbelly despite case drop. They knew it was coming. And they kept warning the world.

Denmark even more worried than ever  about new #B117 variant—B117 cases increasing 70% a week **despite strict lockdown**, says Denmark’s CDC genome sequencing *every single case in the country* for mutation. By contrast, United States sequencing 0.3%.

2/18/2021   Nextstrain, retweeted by the Covid-19 Genomics (COG-UK) Consortium

About Nextstrain

NAmerFocusedGenomicEvolution Radial 801w994h


NAmerFocusedGenomicEvolution Rect 800w817h

2/24/2021   Research Futures: The Sequencing and Tracking Of Phylogeny in COVID-19, University of Portsmouth

As the virus passes from person to person, mutations can occur that can be monitored and traced to identify chains of infection. Working as part of the COVID-19 Genomics UK Consortium (COG-UK), Dr Robson and his team work with NHS sites across the South and Lighthouse Labs throughout the UK to help with infection control processes and to provide a UK-wide database of viral genomes. The UK leads this field by a wide margin, and these data are used to track and trace novel variants of concern.

2/22/2021   How to Vaccinate the World, BBC, 28 minutes

Professor Emma Thomson (twitter: @emcat1 ) joined the panel of experts on @BBCRadio4’s How to Vaccinate the World, to discuss sequencing #SARSCoV2 & why monitoring global #COVID19 infection is vital for vaccine effectivenessMicrobe


2/22/2021   Introducing the COG-UK Mutation Explorer (COG-UK-ME), Covid-19 Genomics Consortium (COG-UK)

COG-UK-ME is an open-access dashboard that provides access to data on #SARSCoV2 mutations and variants of interest Microbe


Explore COG-UK-ME:


Read our explainer blog:


2/21/2021   Officials confirm the first case of the South Africa variant in a New York resident, by Mihir Zaveri, The New York Times

The variant, known as B.1.351, was originally identified in South Africa in December, and has since been found in dozens of other countries and at least nine states, including California, Texas and Virginia. The variant carries mutations that help it latch on more tightly to human cells and that may help the virus evade some antibodies.


Two weeks ago, South Africa halted the use of the AstraZeneca-Oxford vaccine after evidence emerged that it did not protect participants in a clinical trial from mild or moderate illness caused by the variant.

2/21/2021   Virus variants deliver fresh blow to Europe’s open borders, by Matina Stevis-Gridneff, The New York Times

Thousands of people in Austria and the Czech Republic commute daily to jobs in Germany, and after the new checks came into force, long lines began to form. By the end of the week, business groups were writing desperate letters asking Germany to ease or lift the restrictions.

2/18/2021   Coronavirus Variants and Mutations, by Jonathan Corum and Carl Zimmer, The New York Times

After its discovery in December, coronaviruses from the B.1.1.7 lineage quickly emerged in other countries and surged at an exponential rate. It is doubling in the United States every ten days. Preliminary evidence suggests that B.1.1.7 is about 35 percent more deadly than other variants. But testing suggests that vaccines still work well against it.


Lineages covered in this assemblage of reports:


B.   aka 20I/501Y.V1

B.1.351     aka 20H/501Y.V2

P.1             aka 20J/501Y.V3


D614G Spike Mutation

N501Y Spike Mutation

E484K Spike Mutation

L452R Spike Mutation

Q677 Spike Mutation


CAL.20C Variant


 On the NYTimes site, this diagram and dozens more from the report are actually readable



2/14/2021   7 Virus Variants Found in U.S. Carrying the Same Mutation, by Carl Zimmer, The New York Times

It’s difficult to answer even basic questions about the prevalence of these seven lineages because the United States sequences genomes from less than 1 percent of coronavirus test samples.

1/19/2021   As Coronavirus Mutates, the World Stumbles Again to Respond, by Matt Apuzzo, Selam Gebrekidan and Apoorva Mandavilli, The New York Times

“We do know how to dial down the transmission of the virus by a lot with our behavior,” said Carl T. Bergstrom, an evolutionary biologist at the University of Washington in Seattle. “We’ve got a lot of agency there.”

1/16/2021   Why the New Covid-19 Variants Could Be More Infectious, by Daniela Hernandez and Alberto Cervantes, The Wall Street Journal

The Receptor Binding Domain isn’t the only portion of the spike protein that is affected in the two variants found in the U.K. and South Africa.


1/6/2021   U.S. Is Blind to Contagious New Virus Variant, Scientists Warn, by Carl Zimmer, The New York Times

It’s not too late to curb the contagious variant’s spread in the U.S., experts say — but only with a national program for genetic sequencing.


Britain has sequenced 146,463 coronavirus genomes since March, nearly half of all the sequenced coronavirus genomes in the world.


Over the past month, American researchers have only sequenced a few hundred genomes a day, according to GISAID, an international database where researchers share new genomes from coronaviruses. And just a few states have been responsible for most of the effort. California is in the lead, with 8,896 genomes. In North Dakota, which has had more than 93,500 cases so far, researchers haven’t sequenced a single genome.



TweetOfEricFeiglDing B117SARSCoV2Variant 2021 01 05


Click to jump into Dr. Eric Feigl-Ding's ten post explanation of  the future we face

if mitigation protocols are not taken and followed seriously.