South Korea: 779 vaccine breakthroughs by vaccine

Janssen’s Covid-19 vaccine recipients reported the largest number of Covid-19 breakthrough infections among the fully vaccinated in South Korea, the Korea Disease Control and Prevention Agency (KDCA) said in a regular briefing on Tuesday.

The KDCA said 779 out of 5,543,933 vaccinated people in Korea, or 14.1 per 100,000, are estimated to have had breakthrough infections as of Thursday.

By type of vaccine, 16.9 per 100,000 people given the AstraZeneca vaccine had breakthrough infections, 5 per 100,000 with the Pfizer vaccine, 38.5 per 100,000 with the Janssen vaccine, and 0.7 per 100,000 with cross vaccination with the first dose of the AZ vaccine and the second dose of the Pfizer vaccine.

Koreabiomed.com report

 

 

 

 

Photo by CDC on Unsplash

UK: 5% of children hospitalized with Covid-19 develop brain or nerve complications

A new UK study has found that around 1 in 20 of children hospitalised with COVID-19 develop brain or nerve complications linked to the viral infection. The research, published in The Lancet Child and Adolescent Health and led by the University of Liverpool, identifies a wide spectrum of neurological complications in children and suggests they may be more common than in adults admitted with COVID-19.

ScienceDaily.com report

 

Kirsty Allsopp: We have to learn to live with Covid

Image by Engin Akyurt from Pixabay

Deepti Gurdasani: “This is a virus that we need to eliminate”, condemns “herd immunity” policies

“There’s no country that has attained herd immunity to SARS-CoV-2. And, certainly, there are countries with different levels of vaccination. I mean, some countries have over 60 percent of their population fully vaccinated. There are also countries that have had natural exposure to the infection at very high rates. But it hasn’t extinguished the pandemic. We’ve always seen surges even after that. And I think that reflects several factors.

One, I think natural immunity can wane over time. And I think the durability of that immunity does depend on the severity of original infection. When infections are mild and asymptomatic, we can have at least weighting of neutralizing antibodies and how that correlates with waning immunity. We don’t know yet, but we know that re-infection, or the getting infected again with the virus, either the same variant or another variant, are far more common than we originally thought. Although there is protection, even over longer duration of time, it’s not absolute.”

WSWS.org interview with Dr. Deepti Gurdasani **

 

** One of just a handful of people on Earth who seems to understand the existential threat that Sars-CoV-2  poses

 

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

 

More…

Hospitals in Texas are also swamped with Covid patients

 

 

 

Image by David Mark from Pixabay

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

Dominic Minghella on “Learning to live with Covid”

This  👆  👆  👆

 

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

 

 

 

Image by Foundry Co from Pixabay

UK: Is Delta already making way for a fitter variant?

One thing that we have been keeping on eye on recently is the possible successor variant to Delta B.1.617.2 in the UK.  The Alpha B.1.1.7 variant had a shelf life of about 5 months before it was displaced by Delta. Will Delta have a similar shelf life?

Delta seems to have been on the wane in the UK over the couple of weeks, so is it already making way for a stronger, fitter variant? If it is, it won’t be long before that successor variant becomes apparent, and the removal of all Covid mitigations on UK “Freedom Day” has given it plenty of opportunity to spread quickly.

 

Below, Alpha had a shelf life of about 5 months in the UK. Delta already seems to be waning. What will take its place?

 

Below, Delta may have peaked worldwide, but there is no clear successor variant yet.

 

Below, It doesn’t look like the successor variant will be Delta AY.3 in the UK from this chart, but it’s too early to tell….

 

Below, Delta peaked in early May 2021 in India, but hasn’t immediately been followed by another stronger variant. The next variant could be waiting for a fall in the population’s antibody levels from the Delta wave which could take 3-6 months, creating an opportunity from August 2021 onwards. The shelf life for Delta in India, in a largely unvaccinated population, was just three months.

The problem for the UK government, though, is that by dropping all mitigations on 19th July 2021, they may have encouraged Delta to peak early and, as a consequence, left enough time for a second larger, and perhaps far worse, autumn or winter wave to form.

As we said in this post in on 16th July:

“According to the UK’s Chief Medical Officer, the idea is that a Covid-19 wave in the summer will prevent an even worse wave in the winter.  Our prediction is that Johnson will simply get two waves for the price of one – the wave he is promoting now, by removing all mitigations, and an even worse winter wave caused by yet another new variant.”

 

 

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

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

Preprint: Emergence and spread of a B.1.1.28-derived lineage with Q675H and Q677H Spike mutations in Uruguay

In a previous study we found a sublineage B.1.1.28+Q675H+Q677H with local transmission in Rocha, a Uruguayan department bordering Brazil. This clade probably arose by early November, 2020, and its introduction from other parts of Uruguay seemed like a reasonable hypothesis. To understand whether these sequences were part of a new emergent SARS-CoV-2 lineage broadly disseminated in Uruguay, herein we analyzed the genetic diversity of B.1.1.28 SARS-CoV-2 viruses circulating in different localities by the end of 2020 and first months of 2021.

Preprint: Emergence and spread of a B.1.1.28-derived lineage with Q675H and Q677H Spike mutations in Uruguay 

 

 

Image by Leandro Ubilla from Pixabay

UK SAGE Bombshell Report: The Long Term Evolution of Sars-CoV-2

Scenario One: A variant that causes severe disease in a greater proportion of the population than has occurred to date.  Scenario Two: A variant that evades current vaccines.  Scenario Three: Emergence of a drug resistant variant after anti-viral strategies.  Scenario Four: SARS-CoV-2 follows an evolutionary trajectory with decreased virulence.

 

Scenario One: A variant that causes severe disease in a greater proportion of the population than has occurred to date. For example, with similar morbidity/mortality to other zoonotic coronaviruses such as SARS-CoV (~10% case fatality) or MERS-CoV (~35% case fatality).

Likelihood of increased severity phenotype: Realistic possibility.

 

Scenario Two: A variant that evades current vaccines. This could be caused by: Antigenic ‘shift’: Natural recombination events that insert a different spike gene sequence (or partial sequence) from human CoVs MERS-CoV (highly unlikely due to the low frequency of MERS-CoV infections), or from currently circulating endemic human CoVs (more likely due to the prevalence of these viruses). This would recombine into the ‘body’ of SARS-CoV-2 that is capable of high replication in human cells. The consequence could be a virus that causes disease at a level similar to COVID-19 when it first emerged but against which our current battery of spike glycoprotein-based vaccines would not work. 

Likelihood: Realistic possibility.

 

Scenario Three: Emergence of a drug resistant variant after anti-viral strategies. This could be caused by: Emergence of new variants following the administration of directly acting antiviral therapies. As we begin to use directly acting antiviral drugs it is highly likely a variant will be selected that had resistance to individual agents. For example, drugs that target the viral 3C protease, drugs that target the polymerase, monoclonal antibodies that target the spike glycoprotein. If the drugs are used as a mono therapy, then resistant variants have a high probability of emerging. This may render all drugs in that category unusable.

Likelihood: Likely – unless the drugs are used correctly.

 

Scenario Four: SARS-CoV-2 follows an evolutionary trajectory with decreased virulence. This could be caused by: Variants arising with increased transmissibility but decreased pathogenesis/virulence as the virus becomes fully adapted to the human host becoming an endemic infection. Coupled with the likelihood of eventual high populations immunity the infection produces less disease. In other words, this virus will become like other human CoV that causes common colds, but with much less severe disease predominantly in the old or clinically vulnerable. 

Likelihood: Unlikely in the short term, realistic possibility in the long term.

 

Download the entire report here

GOV.UK SAGE Website Link

 

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

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