Category: Recombination
Dominic Minghella on “Learning to live with Covid”
"Learn to live with the virus" either means nothing, or it means, "Learn to be quiet about the unnecessary deaths of your loved ones, friends, and compatriots."
Ain't gonna happen.
— Dominic Minghella (@DMinghella) August 1, 2021
This 👆 👆 👆
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
So what is Plan B if the vaccines fail with a new #coronavirus super-variant?
Kit Yates on “We have to learn to live with the virus”
What do the people who say “learn to live with the virus” actually mean?
They mean: fail to learn any of the lessons of the last 18 months, fail to mitigate against the spread of the virus and tolerate avoidable deaths and disease burden.
I’d rather we didn’t.
— Kit Yates (@Kit_Yates_Maths) July 30, 2021
Over to you Kirsty….
Israel: We have to learn to live with Covid
“We all need to change our thinking and draw a road map for living with Covid,” says Dr. Manfred Green. We disagree, and we will be explaining why we disagree in a post later.
Editors note: This report comes just 48 hours after our warning that Boris Johnson’s government was proposing to his countrymen that they should also “learn to live with Covid” (see original post below).
Have you ever wondered what happens when you search for “We have to learn to live with Ebola”? Try it.
It’s an idea so insane that only one person in recorded history has actually written it down.
We have to learn to live with Covid.
“Learning to live with Covid” will be coming to your country soon. Be prepared.
Boris Johnson tells Britons to “learn to live with Covid”
English Freedom Day: Lions led by Zombies
A short reminder of what happened after “Freedom Day” was announced in the Czech Republic on July 2nd 2020:
Covid-19 cases after “Freedom Day” in the Czech Republic in 2020:
Covid-19 deaths after “Freedom Day” in the Czech Republic in July 2020:
English Freedom Day – Lions led by Zombies.
Gupta Lab: Delta variant emergence, replication and immune evasion
Bad news from the Gupta Lab who have been looking at the Delta variant.
“Taking replication we originally showed increased growth of Delta virus in vitro using airway organoids compared to Alpha. Now we show increased virus production in two other systems: Calu-3 epithelial lung cell lines (shown here) and airway epithelial cells”
“We now further define Delta immune evasion using a panel of 38 monoclonal antibodies, showing significant loss of potency of NTD and RBD targeting antibodies. Imdevimab, part of the REGN2 dual monoclonal antibody cocktail is compromised by Delta.”
“We also show loss of activity for casivirimab, part of the Lily dual therapy cocktail. These dual therapies could be less effective against Delta particularly in the setting of immune compromise could lead to escape variants emerging/ transmitting.”
“We also found that the Delta virus appears to be in a predominantly cleaved form as compared to Alpha. This may suggest that each virus particle is more infectious in addition to more virus particles being produced“
BiorXiv Preprint: SARS-CoV-2 B.1.617.2 Delta variant emergence, replication and immune evasion
Photo by British Library on Unsplash
UK Chief Medical Officer – lockdown in 5 weeks
“I don’t think we should underestimate the fact that we could get into trouble again surprisingly fast”
The UK Government’s top medic has warned the number of people in hospital with coronavirus could reach “quite scary” levels within weeks and new coronavirus restrictions in England could be needed in just five weeks.
Chris Whitty’s stark warning came just days before has warned just days before Boris Johnsons’ ‘Freedom Day’ on Monday (July 19). The Chief Medical Officer sounded the alarm over a potential “scary” growth in hospitalisations which could leave the NHS “in trouble again surprisingly fast” once restrictions are lifted.
UK: International summit condemns Boris Johnson’s THIRD Covid-19 catastrophe
Boris Johnson’s “Freedom Day” plan to create herd immunity in the UK by having one huge summer Delta wave has been rightly criticised from scientists from around the globe. 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.
Watch this space.
Indian scientists explored the “unconventional evolution” of Sars-CoV-2 in January 2020
“One of such studies that was brought to the notice of Fauci was a research paper by some scientists from India. In January 2020, Indian researchers had published a paper, where they had found that the spike glycoprotein (S) of SARS-CoV-2 had four insertions which are not found in any other Coronavirus, and the insertions are similar to those found in HIV virus. The study had raised that possibility that SARS-CoV-2 may have been bio-engineered using the existing Coronavirus and HIV virus.”
Preprint: Uncanny similarity of unique inserts in the 2019-nCoV spike protein to HIV-1 gp120 and Gag
** UPDATE 1 **
A day after the authors withdrew the above paper, on 2 February 2020, the director of the Center for Emerging Infectious Diseases at the Wuhan Institute of Virology, Shi Zhengli, and her team, published the sequence of a bat coronavirus called RaTG13 in what was the very first paper to properly describe and characterise what would eventually become known as the SARS-CoV-2 virus.
** Update 2 **
Indian researcher still backs their study and says they were forced by vested interests to withdraw
OpIndia talked to Ashutosh Kumar Pandey, one of the researchers of the study. Earlier he had commented on Twitter that they stand by their conclusion that the SARS-CoV-2 is not natural. “We said this in Jan 2020, we are saying it again”, he had tweeted.
Vietnam: No new hybrid #coronavirus strain detected in Vietnam says WHO
“There is no new hybrid variant in Vietnam at this moment based on WHO definition,” Kidong Park, the WHO representative in Vietnam, told Nikkei Asia on Wednesday. “The variant detected is Delta variant (B.1.617.2), with additional mutations, and needs more observation. We need to monitor during next couple of weeks,”
“This is within the existing [Delta] variant. It is an additional mutation” Park explained, adding “as for now, there is no alarming alert from WHO. Park also stressed the Delta variant is dangerous as it is highly contagious and spreads very quickly.
Vietnam: recombinant/hybrid #coronavirus announced – B.1.617.2 Delta variant with Y144 mutation from B.1.1.7 Alpha variant
Vietnam has detected a coronavirus hybrid variant with characteristics from the existing B16172 Delta variant and B117 Alpha variant, the Ministry of Health announced Saturday. Minister Nguyen Thanh Long said a new coronavirus variant has recently been detected in Vietnam with characteristics from both the Alpha and the Delta variants. More specifically, it is a Delta variant B.1.617.2 with mutations that originally belong to the Alpha variant B.1.1.7.
Laboratory cultures of the new variant, which is much more transmissible than the previously known types, revealed that the virus replicated itself very quickly, explaining why so many new cases appeared in different locations in a short period, Long was quoted as saying.
More…
According to the Central Institute of Hygiene and Epidemiology, the results of viral gene sequencing of 32 Covid-19 patient samples, detected 4 samples infected with the Delta B16172 strain but carrying a gene mutation of the Alpha B117 strain.
“We found that there is a Y144 deletion mutation on the S protein of the virus B.1.617.2 (first detected in India). This mutation is similar to the mutation detected on variant B.1.1.7 (first detected in the UK)”, Professor Le Thi Quynh Mai, Deputy Director of the Central Institute of Hygiene and Epidemiology, said on the evening of May 29.
Up to now, Vietnam has recorded a total of 7 strains of nCoV, including: B.1.222, B.1.619, D614G, B.1.1.7 (Alpha variant), B.1.351, A.23.1 and B.1.617.2 (Delta variant).
Vietnam: No new hybrid #coronavirus strain detected in Vietnam says WHO
Vietnam: first case of #coronavirus variant B.1.617.2 found in Ho Chi Minh City
Gamaleya Institute: ‘The next stage of the epidemic is the infection with the #coronavirus of farm and domestic animals’
Alexander Gintsburg, head of the Gamaleya institute that developed Russia’s Sputnik V human vaccine, was quoted in Izvestia newspaper as saying COVID-19 was likely to hit animals next. “The next stage of the epidemic is the infection with the coronavirus of farm and domestic animals,” Gintsburg said.
Russia has produced the world’s first batch – 17,000 doses – of COVID-19 vaccines for animals, its agricultural regulator said on Friday. Russia registered Carnivac-Cov in March after tests showed it generated antibodies against COVID-19 in dogs, cats, foxes and mink.
NEJM “a recombination event between B.1.1.7 and B.1.526” #coronavirus variants
Examination of the SARS-CoV-2 sequences revealed that both patients were infected with variant viruses. Rapid identification of sequence variants by targeted PCR amplification showed that neither sequence precisely fit any known clade. Some of the substitutions in Patient 1 (T95I, del144, E484K, A570D, D614G, P681H, and D796H) were shared with B.1.526 (T95I, E484K, and D614G6), and three substitutions were shared with Patient 2 (in whom the variants T95I, G142V and del144, F220I, R190T, R237K, R246T, and D614G were detected). Whole viral genome sequencing revealed several additional substitutions, including D796H, present in a guanine–cytosine–rich region not identified by targeted PCR. These substitutions may decrease sensitivity to convalescent serum11 and may have some unique noncoding changes as compared with the clades first identified in Wuhan, the United Kingdom, and New York City.
Although more detailed analysis of whole-genome sequencing from Patient 1 was undertaken, we could not conclude that the variant in this patient was a Pango lineage because it was only present in a single person.
Its closest links on the phylogenetic tree were the variant first identified in the United Kingdom (B.1.1.7) and the variant first identified in New York City (B.1.526), but with considerable differences. It will be of interest to determine whether this may have resulted from a recombination event between B.1.1.7 and B.1.526, as has been recently reported for recombination between the B.1.1.7 lineage and the “wild-type” lineage first identified in Wuhan. Alternatively, shared substitutions may be the result of convergent evolution.
NEJM: Vaccine Breakthrough Infections with SARS-CoV-2 Variants
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