International Lockdowns and a Booster

The vaccine booster is progressing. A comprehensive study shows that children are at a very, very low risk for COVID-19. Fauci still wants us all to wear masks. In many places, the Delta variant may be an excuse to keep schools closed in the fall. 

Indonesia, mostly unvaccinated, is having a surge of COVID cases. Japan has barred spectators from the Olympics. Sydney’s lockdown will continue.

In other news:

  • What happens when we wear masks all day? Megan Mansell on the dangers of masks on Rational Ground
  • There still isn’t evidence that masks even work, writes Mike Harris at Less Wrong
  • Where did our curiosity go? Zeynep writes about the origins of COVID at The Insight
  • A look back at lessons from the pandemic by Emily Yoffe at Persuasion

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COVID News

Pfizer to seek FDA authorization for COVID-19 vaccine booster shot

https://theweek.com/coronavirus/1002426/pfizer-to-seek-fda-authorization-for-covid-19-vaccine-booster-shot

Pfizer plans on asking the Food and Drug Administration next month for emergency authorization of a third dose of its COVID-19 vaccine, the company told The Associated Press on Thursday.

Early data from its booster study suggests that after a third shot, antibody levels jump five- to 10-fold, compared to the second dose given months earlier, Pfizer’s Dr. Mikael Dolsten said. He added that data from Britain and Israel shows the vaccine “neutralizes” the highly contagious Delta variant “very well.” The Delta variant now accounts for more than 50 percent of all new infections in the United States. 

In Children, Risk of Covid-19 Death or Serious Illness Remains Extremely Low, New Studies Find

https://www.wsj.com/articles/in-children-risk-of-covid-19-death-or-serious-illness-remain-extremely-low-new-studies-find-11625785260

Children are at extremely slim risk of dying from Covid-19, according to some of the most comprehensive studies to date, which indicate the threat might be even lower than previously thought.

Some 99.995% of the 469,982 children in England who were infected during the year examined by researchers survived, one study found.

In fact, there were fewer deaths among children due to the virus than initially suspected. Among the 61 child deaths linked to a positive Covid-19 test in England, 25 were actually caused by the illness, the study found.

Dr. Fauci says fully vaxxed people should still ‘go the extra mile’ and wear face masks in low vaccination areas

https://www.msn.com/en-us/health/medical/dr-fauci-says-fully-vaxxed-people-should-still-go-the-extra-mile-and-wear-face-masks-in-low-vaccination-areas/ar-AALLi06

Dr. Anthony Fauci, director of the National Institute of Allergy and Infectious Diseases, said even people who are fully vaccinated should still “go the extra mile” to ensure protection in areas with low vaccination rates.

“Even as good as they are and highly effective, nothing is 100%,” Fauci said of vaccines during an interview on NBC’s “Meet the Press” Sunday morning.

“If you put yourself in an environment in which you have a high level of viral dynamics and a very low level of vaccine, you might want to go the extra step and say: ‘When I’m in that area where there’s a considerable degree of viral circulation, I might want to go the extra mile to be cautious enough to make sure that I get the extra added level of protection,’ Fauci said.

Public Schools Still Can’t Figure Out How To Reopen

The masks are off, the planes are full, the deaths are way down, and the thriving is high, yet millions of parents still don’t know whether their children’s schools will be reliably open this fall.

That’s because many government-run schools, which despite an ongoing enrollment decline are still the main providers of instruction for around 90 percent of the country’s 56 million or so K-12 students, have yet to promulgate final rules on the kinds of COVID mitigations that can limit in-person capacity and/or trigger automatic shutdowns.

Commentary/Analysis

Ramifications of restricted breathing

When hearing the terms hypercapnia, hypoxia, and deoxygenation, one might make the assumption that we require a dramatic change in saturation levels for extended periods of time in order for it to be harmful. 

If someone falls into a pool and spends time without oxygen, we have this assumption that just like in the movies, everything snaps back to normal, health-wise, after CPR and a little spit-up. But every second counts with carbon dioxide increases and oxygen decreases – and just like mothers are often rushed into operating rooms to save their unborn children with falling saturation levels during birth, we must consider every moment a child’s breathing is restricted by masks to be just as potentially damaging, as has been found in this recent JAMA publication. 

We Still Don’t Know If Masks Work

https://www.lesswrong.com/posts/fSNp942XBztB352fn/we-still-don-t-know-if-masks-work

Introduction:

Recently a paper was published which got attention by estimating that 100% mask wearing in the population would cause a 25% reduction in the effective transmission number (shortened to transmissiblity throughout).

This study was observational and so inferring causality is always difficult. Thanks to the excellent data availability I was able to replicate and attempt to validate the model.

Based on my analysis, this study does not provide good evidence for such a causal link, and there is evidence to believe that the observed correlation is spurious.

Our Remarkable Media Bubble: The Location Edition

https://www.theinsight.org/p/our-remarkable-media-bubble-the-location

In this newsletter, I continue to explore some of the problems that have been exposed by the way “origins” of SARS-CoV-2 are discussed and debated, rather than the topic itself.

As my New York Times article notes, the biggest reason we’re discussing any of this is that the first of this pandemic outbreak detected a few miles from one of the world’s biggest coronavirus labs. There are only three that are prominent and big and, as far as I’m aware, also have done the kind of advanced bio-engineering work, such as creating chimeric viruses, that have now come under scrutiny.

There’s the one in Wuhan, China; the one in Galveston, Texas; and the one in Chapel Hill, North Carolina. Any outbreak near one of them with the very virus they study would, of course, be worth noting. And I don’t mean this just for Wuhan. I have worked and lived about a mile away from the other coronavirus lab at University of North Carolina for much of the last decade. If there had been a bat coronavirus outbreak in Chapel Hill, NC, of course, we’d all be asking questions to UNC despite the fact that North America also has bats that harbor dangerous viruses.

What We Got Wrong (and Right) About COVID-19

https://www.persuasion.community/p/what-we-got-wrong-and-right-about

Since early 2020, when COVID-19 began its rapid spread around the world, we’ve been told that everyone must “follow the science.” But science is a method, not a monolith. Scientific assertions change with the arrival of new information. Science resists dogma and tribalism. Some of these principles seemed to get lost in the aftermath of the arrival of COVID-19 and the policy response that ensued.

Early in the pandemic, I began following on Twitter a number of distinguished public health professionals who increasingly had views that questioned the public health “consensus” that long-term mass lockdowns and school closures were crucial for stopping the spread of COVID-19. They were advocating for more targeted protection of the most vulnerable while allowing other parts of society to continue functioning. They raised questions about the reluctance to modify restrictions in the face of new data. They said that many people were harmed while the most comfortable were cosseted.

Research

Neutralisation of SARS-CoV-2 lineage P.1 by antibodies elicited through natural SARS-CoV-2 infection or vaccination with an inactivated SARS-CoV-2 vaccine: an immunological study

https://www.thelancet.com/journals/lanmic/article/PIIS2666-5247(21)00129-4/fulltext

Summary

Background

Mutations accrued by SARS-CoV-2 lineage P.1—first detected in Brazil in early January, 2021—include amino acid changes in the receptor-binding domain of the viral spike protein that also are reported in other variants of concern, including B.1.1.7 and B.1.351. We aimed to investigate whether isolates of wild-type P.1 lineage SARS-CoV-2 can escape from neutralising antibodies generated by a polyclonal immune response.

Methods

We did an immunological study to assess the neutralising effects of antibodies on lineage P.1 and lineage B isolates of SARS-CoV-2, using plasma samples from patients previously infected with or vaccinated against SARS-CoV-2. Two specimens (P.1/28 and P.1/30) containing SARS-CoV-2 lineage P.1 (as confirmed by viral genome sequencing) were obtained from nasopharyngeal and bronchoalveolar lavage samples collected from patients in Manaus, Brazil, and compared against an isolate of SARS-CoV-2 lineage B (SARS.CoV2/SP02.2020) recovered from a patient in Brazil in February, 2020. Isolates were incubated with plasma samples from 21 blood donors who had previously had COVID-19 and from a total of 53 recipients of the chemically inactivated SARS-CoV-2 vaccine CoronaVac: 18 individuals after receipt of a single dose and an additional 20 individuals (38 in total) after receipt of two doses (collected 17–38 days after the most recent dose); and 15 individuals who received two doses during the phase 3 trial of the vaccine (collected 134–230 days after the second dose). Antibody neutralisation of P.1/28, P.1/30, and B isolates by plasma samples were compared in terms of median virus neutralisation titre (VNT50, defined as the reciprocal value of the sample dilution that showed 50% protection against cytopathic effects).

Findings

In terms of VNT50, plasma from individuals previously infected with SARS-CoV-2 had an 8·6 times lower neutralising capacity against the P.1 isolates (median VNT50 30 [IQR <20–45] for P.1/28 and 30 [<20–40] for P.1/30) than against the lineage B isolate (260 [160–400]), with a binominal model showing significant reductions in lineage P.1 isolates compared with the lineage B isolate (p≤0·0001). Efficient neutralisation of P.1 isolates was not seen with plasma samples collected from individuals vaccinated with a first dose of CoronaVac 20–23 days earlier (VNT50s below the limit of detection [<20] for most plasma samples), a second dose 17–38 days earlier (median VNT50 24 [IQR <20–25] for P.1/28 and 28 [<20–25] for P.1/30), or a second dose 134–260 days earlier (all VNT50s below limit of detection). Median VNT50s against the lineage B isolate were 20 (IQR 20–30) after a first dose of CoronaVac 20–23 days earlier, 75 (<20–263) after a second dose 17–38 days earlier, and 20 (<20–30) after a second dose 134–260 days earlier. In plasma collected 17–38 days after a second dose of CoronaVac, neutralising capacity against both P.1 isolates was significantly decreased (p=0·0051 for P.1/28 and p=0·0336 for P.1/30) compared with that against the lineage B isolate. All data were corroborated by results obtained through plaque reduction neutralisation tests.

Interpretation

SARS-CoV-2 lineage P.1 might escape neutralisation by antibodies generated in response to polyclonal stimulation against previously circulating variants of SARS-CoV-2. Continuous genomic surveillance of SARS-CoV-2 combined with antibody neutralisation assays could help to guide national immunisation programmes.

Charts and Graphics

International News

Daily Covid-19 Deaths in Indonesia Nearly Double as Delta Variant Drives Surge

https://www.wsj.com/articles/daily-covid-19-deaths-in-indonesia-nearly-double-as-delta-variant-drives-surge-11625674555

SINGAPORE—Deaths in Indonesia from Covid-19 rose sharply on Wednesday, with reported daily fatalities nearly double the number from two days ago, as the fast-spreading Delta variant of the coronavirus overwhelms the largely unvaccinated country’s healthcare system.

Public-health experts have for weeks warned that Indonesia, the world’s fourth most populous nation, could face a surge like the one that caused India’s hospital system to collapse in April and May. Around 5% of Indonesia’s 270 million people are fully vaccinated and infections have been rising for days. The country reported a record 1,040 deaths from Covid-19 on Wednesday, up from 558 deaths two days ago.

Tokyo Olympics Bars Spectators as Japan Declares Covid-19 State of Emergency

https://www.wsj.com/articles/tokyo-olympics-to-be-held-under-covid-19-state-of-emergency-11625733103

TOKYO—The Tokyo Olympics will be held without spectators, the organizers said, after Japan declared a new state of emergency that will continue through the end of the Games due to a rise in Covid-19 infections.

Hundreds of athletes and officials from around the world have already arrived for the Olympics, which open on July 23. Foreign spectators were ruled out in March, but the organizers had intended to allow stadiums and arenas to be around half capacity with local fans.

More than 3.5 million tickets have been purchased by people in Japan for the Olympics, which run through Aug. 8. Most of those tickets would have remained valid.

Sydney locked down for another week as Delta COVID-19 variant spreads

https://news.yahoo.com/sydney-covid-19-lockdown-extended-223338961.html

SYDNEY (Reuters) -The leader of Australia’s New South Wales (NSW) state on Wednesday ordered a week-long extension of Sydney’s COVID-19 lockdown, warning new cases are bound to rise as the country’s biggest city grapples with the highly infectious Delta variant.

Sydney, home to a fifth of Australia’s 25 million people, was plunged into lockdown on June 26 as a Delta variant outbreak persuaded officials to tighten restrictions in a country that has been slow to vaccinate. Strict stay-at-home orders were due to end on Friday, but now remain in place until July 16.

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