USA: Alabama’s Covid hospitalizations jump by 30% in one night

A report from the Alabama Department of Health’s online dashboard showed 1,883 hospitalized COVID patients, up by 432 over Sunday’s total. That’s an increase of 29.8% in just one day. The total is the highest since Feb. 1, which was during the downward trend of the winter surge in the virus, just as vaccines were first distributed. The pandemic record of 3,084 inpatients was set on Jan. 11. The new total is 11.3 times the low set on June 20 of 166 hospitalized COVID patients and 75% higher than one week ago.

Birminghamwatch.org report

 

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Hospitals in Texas are also swamped with Covid patients

 

 

 

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USA: Republican Mike McCaul’s final report into the origins of the Sars-CoV-2 pandemic

Mike McCaul’s final report on the origins of the pandemic can be downloaded here.

A House Republican lawmaker’s investigation into the origins of COVID-19 is raising concerns that the pandemic outbreak stemmed from a genetically modified virus which leaked from the Wuhan Institute of Virology, the Chinese city where the disease was first detected in December 2019.

The Hill article

Github: AY.3.1 – a new sub-lineage of AY.3 concentrated in Mississippi, USA

AY.3 is the main variant being sequenced weekly in Mississippi (>70% of all recent sequences), most falling within this sub-lineage of AY.3 that is distinguished by the mutations described below (>60% of all recent sequences). For example, of 91 Pangolin-typeable sequences generated on 13 July 2021 by Dr. Robinson’s team, from broad sampling across Mississippi, 68 are AY.3 and 13 are unclassified B.1.617.2. Of those 81 Delta sequences, 60 are this new sub-lineage (those sequences are not yet in GISAID and are thus not included in the counts above for the USA or MS). Thus, there is clear epidemiological relevance of this sub-lineage in a region of the USA.

Github: A new sub-lineage of AY.3 concentrated in Mississippi, US

 

USA: AY.3 genomes increasing faster than Delta B.1.617.2

 

Image by Mark Dawdy from Pixabay

USA: 233 San Francisco healthcare workers in vaccine breakthough outbreak

At least 233 staff members at two major San Francisco hospitals, most of them fully vaccinated, tested positive for the coronavirus this month.  About 75 to 80 percent of the more than 50 staff members infected at Zuckerberg San Francisco General Hospital were fully vaccinated, Dr. Lukejohn Day, the hospital’s chief medical officer, said in an interview on Saturday. The University of California, San Francisco Medical Center said in a statement issued on Friday that 153 of its 183 infected staff members had been fully vaccinated.

NYTimes.com report

 

Finland: 80% vaccine breakthrough in hospital with B16172 Delta #coronavirus variant – PPE no longer effective

 

 

 

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USA: AY.3 genomes increasing faster than Delta B.1.617.2

A long and detailed Twitter thread by Vinod Scaria on the rise of the AY.3 Delta plus variant in the USA which seems to be outcompeting Delta B.1.672 in some states. Outbreak.info is showing that AY.3 genomes are found in 37% of recent sequences.

 

 

 

Github: AY.3.1 – a new sub-lineage of AY.3 concentrated in Mississippi, USA

USA: At least 125,000 vaccine breakthrough infections, 1,400 dead

At least 125,000 fully vaccinated Americans have tested positive for Covid and 1,400 of those have died, according to data collected by NBC News.  The total number of breakthrough cases is likely higher than 125,683, since nine states, including Pennsylvania and Missouri, did not provide any information, while 11, like Florida, did not provide death and hospitalization totals. Four states gave death and hospitalization numbers, but not the full tally of cases.

NBC report

 

WAPO: 35,000 symptomatic Covid-19 infections per week among 162 million vaccinated Americans

USA: Cape Cod superspreader – 79% of breakthrough infections symptomatic, 80% of hospitalized were fully vaccinated

Scientists researching the Provincetown, Cape Cod Covid outbreak reported that 79 percent of the breakthrough infections were symptomatic. Four of five people who were hospitalized were fully vaccinated.

The CDC study “raises the very worrisome possibility that high viral loads can occur in people who have Delta, and this is a fundamental as we have to approach the fall and winter,” said David O’Connor, a professor of pathology and laboratory medicine at the University of Wisconsin School of Medicine and Public Health.

Washington Post report

 

 

Image by Mark Martins from Pixabay

WAPO: 35,000 symptomatic Covid-19 infections per week among 162 million vaccinated Americans

“CDC Director Rochelle Walensky privately briefed members of Congress on Thursday, drawing on much of the material in the document. One of the slides states that there is a higher risk among older age groups for hospitalization and death relative to younger people, regardless of vaccination status. Another estimates that there are 35,000 symptomatic infections per week among 162 million vaccinated Americans.”

Washington Post: The War Has Changed

 

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“vaccinated individuals infected with Delta may be able to transmit the virus as easily as those who are unvaccinated. Vaccinated people infected with Delta have measurable viral loads similar to those who are unvaccinated and infected with the variant.”

Washington Post: The War Has Changed

 

CDC: The Covid-19 report that changed the CDC’s view on facemasks

 

NEJM: Vaccine breakthrough infections leading to long Covid

Image by David Mark from Pixabay

USA: Vaccination is not enough by itself to stop the spread of Covid-19 variants

Vaccination alone won’t stop the rise of new Covid-19 variants and in fact could push the evolution of strains that evade their protection, researchers warned Friday. They said people need to wear masks and take other steps to prevent spread until almost everyone in a population has been vaccinated.

CNN.com report

Nature.com Preprint: Rates of SARS-CoV-2 transmission and vaccination impact the fate of vaccine-resistant strains

USA: Provincetown, Cape Cod outbreak – 882 infections, 74% fully immunized, most reporting symptoms

As of Thursday, 882 people were tied to the Provincetown outbreak. Among those living in Massachusetts, 74% of them were fully immunized, yet officials said the vast majority were also reporting symptoms. Seven people were reported hospitalized.

ABCnews.go report

CDC Report

 

 

 

 

Image by Christophe Schindler from Pixabay

Preprint: Cryptic Sars-CoV-2 Lineages Detected in NYC Wastewater – Possible Animal Reservoir Detected

Researchers find signs of Covid-19 mutations in NYC sewage, pointing to possible dog and rat infections.  After months of testing and re-testing, they found four combinations of COVID mutations that, when compared to a global database of more than 2.5 million sequenced variants, had not been seen before. The four variants are at least somewhat antibody-resistant, which could reduce the effectiveness of vaccines, the researchers found.

As with other animals, COVID-19 could be infecting dogs and rats, leading to new mutations and an outbreak in New York City’s sewers. While animal-to-human transmission of the virus is exceedingly rare, it has been seen in the U.S. in minks

These lineages contain mutations rarely observed in clinical samples, including Q493K, Q498Y, H519N and T572N. Many of these mutations were found to expand the tropism of SARS-CoV-2 pseudoviruses by allowing infection of cells expressing the human, mouse, or rat ACE2 receptor.

TheCity.nyc report

MedrXiv paper: Tracking Cryptic Sars-CoV-2 Lineages Detected in NYC Wastewater

 

USA: Sars-CoV-2 antibodies detected in 33% of White-Tailed Deer samples

USA: Washington State Vaccine Breakthroughs by Variant up to 28th July 2021

This week’s update from Washington State showing vaccine breakthrough cases and which Sars-CoV-2 variant is causing them up to 28th July 2021. Of note this week is huge jump for Delta B.1.617.2 breakthrough cases, which have more than doubled in one week from 113 to 254. There are further increases in vaccine breakthroughs for other variants too.

Vaccine Breakthroughs up to 28th July 2021

28th July 2021

Variant
LineageNumber of Vaccine
Breakthrough Cases
With Variant
Percentage of Vaccine
Breakthrough Cases With
Variant
Percentage of
Sequences From
All Covid-19
Cases With
Variant
Increase in
Number of
Breakthroughs
From Previous
Week
AlphaB.1.1.733734%43%29
GammaP.116817%10%12
EpsilonB.1.42911612%15%3
DeltaB.1.617.225426%7%141
IotaB.1.526263%3%4
BetaB.1.351101%1%0
EpsilonB.1.427111%2%0
EtaB.1.52540%0%0
KappaB.1.617.110%0%0
ZetaP.200%0%0
OtherOther546%18%4
Total981100%100%193

Vaccine Breakthroughs up to 21st July 2021

21st July 2021

Variant
LineageNumber of Vaccine
Breakthrough Cases
With Variant
Percentage of Vaccine
Breakthrough Cases With
Variant
Percentage of
Sequences From
All Covid-19
Cases With
Variant
Increase in
Number of
Breakthroughs
From Previous
Week
AlphaB.1.1.730839%44%-1
GammaP.115620%10%9
EpsilonB.1.42911314%16%0
DeltaB.1.617.211314%4%23
IotaB.1.526223%3%0
BetaB.1.351101%1%-1
EpsilonB.1.427111%2%0
EtaB.1.52541%0%0
KappaB.1.617.110%0%0
ZetaP.200%0%0
OtherOther506%19%0
Total788100%100%30

Vaccine Breakthroughs up to 14th July 2021

14th July 2021

Variant
LineageNumber of Vaccine
Breakthrough Cases
With Variant
Percentage of Vaccine
Breakthrough Cases With
Variant
Percentage of
Sequences From
All Covid-19
Cases With
Variant
Increase in
Number of
Breakthroughs
From Previous
Week
AlphaB.1.1.730941%44%12
GammaP.114719%10%6
EpsilonB.1.42911315%16%0
DeltaB.1.617.29012%4%20
IotaB.1.526223%3%1
BetaB.1.351111%1%0
EpsilonB.1.427111%2%0
EtaB.1.52541%0%0
KappaB.1.617.110%0%0
ZetaP.200%0%0
OtherOther496%20%0
Total757100%100%39

 

USA: Washington State Vaccine Breakthroughs by Variant up to 21st July 2021

 

So what is Plan B if the vaccines fail with a new #coronavirus super-variant?

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NEJM: Vaccine breakthrough infections leading to long Covid

Among 1497 fully vaccinated health care workers, 39 SARS-CoV-2 breakthrough infections were documented.  On follow-up questioning, 31% of all infected workers reported having residual symptoms 14 days after their diagnosis. At 6 weeks after their diagnosis, 19% reported having “long Covid-19” symptoms, which included a prolonged loss of smell, persistent cough, fatigue, weakness, dyspnea, or myalgia.

Nine workers (23%) took a leave of absence from work beyond the 10 days of required quarantine; of these workers, 4 returned to work within 2 weeks. One worker had not yet returned after 6 weeks.

NEJM research article: Covid-19 Breakthrough Infections in Vaccinated Health Care Workers

See also MedrXiv preprint: Breakthrough Symptomatic COVID-19 Infections Leading to Long Covid: Report from Long Covid Facebook Group Poll

 

 

Image by David Mark from Pixabay