Category: Variants
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.
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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.
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
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.
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
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.
Closely tracking the delta+ lineages now across the world, one of the lineages AY.3 seems to be emerging in the United States of America. This tweetorial is to summarise the observations. I will be updating this thread as new evidence emerges.
Thanks pic.twitter.com/2YtsbqmC6y— Vinod Scaria (@vinodscaria) July 24, 2021
Nextstrain makes AY.3 looks pretty widespread in the US already… pic.twitter.com/jO3hrKLRl3
— Ryan M. Ferris (@rferrisx) July 24, 2021
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
CDC: The Covid-19 report that changed the CDC’s view on facemasks
The report that encouraged the CDC to change its facemask mandate this week
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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.
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.”
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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
Image by David Mark from Pixabay
Israel: booster vaccine jab rollout begins – third vaccination in 8 months for some
Israeli Prime Minister Naftali Bennett announced on Thursday the world’s first vaccination drive to inoculate people over 60 with a third Covid vaccine dose, starting Sunday. Speaking at a press conference at Sheba Medical Center in Tel Hashomer, where 60-year-old Herzog received the jab, Bennett said: “We are launching our third jab campaign to protect seniors in Israel. From today there is a new mitzvah: to vaccinate your fathers and mothers.”
Israel: 60% of severely ill Covid patients are fully vaccinated
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 | Lineage | Number 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 |
|---|---|---|---|---|---|
| Alpha | B.1.1.7 | 337 | 34% | 43% | 29 |
| Gamma | P.1 | 168 | 17% | 10% | 12 |
| Epsilon | B.1.429 | 116 | 12% | 15% | 3 |
| Delta | B.1.617.2 | 254 | 26% | 7% | 141 |
| Iota | B.1.526 | 26 | 3% | 3% | 4 |
| Beta | B.1.351 | 10 | 1% | 1% | 0 |
| Epsilon | B.1.427 | 11 | 1% | 2% | 0 |
| Eta | B.1.525 | 4 | 0% | 0% | 0 |
| Kappa | B.1.617.1 | 1 | 0% | 0% | 0 |
| Zeta | P.2 | 0 | 0% | 0% | 0 |
| Other | Other | 54 | 6% | 18% | 4 |
| Total | 981 | 100% | 100% | 193 |
Vaccine Breakthroughs up to 21st July 2021
| 21st July 2021 Variant | Lineage | Number 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 |
|---|---|---|---|---|---|
| Alpha | B.1.1.7 | 308 | 39% | 44% | -1 |
| Gamma | P.1 | 156 | 20% | 10% | 9 |
| Epsilon | B.1.429 | 113 | 14% | 16% | 0 |
| Delta | B.1.617.2 | 113 | 14% | 4% | 23 |
| Iota | B.1.526 | 22 | 3% | 3% | 0 |
| Beta | B.1.351 | 10 | 1% | 1% | -1 |
| Epsilon | B.1.427 | 11 | 1% | 2% | 0 |
| Eta | B.1.525 | 4 | 1% | 0% | 0 |
| Kappa | B.1.617.1 | 1 | 0% | 0% | 0 |
| Zeta | P.2 | 0 | 0% | 0% | 0 |
| Other | Other | 50 | 6% | 19% | 0 |
| Total | 788 | 100% | 100% | 30 |
Vaccine Breakthroughs up to 14th July 2021
| 14th July 2021 Variant | Lineage | Number 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 |
|---|---|---|---|---|---|
| Alpha | B.1.1.7 | 309 | 41% | 44% | 12 |
| Gamma | P.1 | 147 | 19% | 10% | 6 |
| Epsilon | B.1.429 | 113 | 15% | 16% | 0 |
| Delta | B.1.617.2 | 90 | 12% | 4% | 20 |
| Iota | B.1.526 | 22 | 3% | 3% | 1 |
| Beta | B.1.351 | 11 | 1% | 1% | 0 |
| Epsilon | B.1.427 | 11 | 1% | 2% | 0 |
| Eta | B.1.525 | 4 | 1% | 0% | 0 |
| Kappa | B.1.617.1 | 1 | 0% | 0% | 0 |
| Zeta | P.2 | 0 | 0% | 0% | 0 |
| Other | Other | 49 | 6% | 20% | 0 |
| Total | 757 | 100% | 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?
Image by David Mark from Pixabay
Israel: 60% of severely ill Covid patients are fully vaccinated
At least 153 patients in Israel’s hospitals are in serious condition, of whom 28 are ventilated. 93 out of the 153 severely ill patients have been fully vaccinated, or 60% of the total.
According to the Israeli Health Ministry, 102 of the severely ill patients are aged 65 and over, 76 of whom are fully vaccinated. At least 39 of the severely ill are between the age of 40 and 65, while 16 of them are fully vaccinated. Six of the severely ill are below the age of 40 but only one of them is fully vaccinated.
Israel: Are recovered Covid patients more protected than the vaccinated?
Image by Parentingupstream from Pixabay