The discussion centers on the various mutations of the SARS-CoV-2 virus, specifically the B.1.1.7, B.1.351, and D614G variants. Participants explore the implications of these mutations on transmissibility, immune response, and detection methods, while referencing recent research and pre-prints related to these variants.
Participants express a range of views regarding the implications of mutations on transmissibility and detection methods, indicating that multiple competing perspectives remain without a clear consensus on the effects of these variants.
Discussions include references to various studies and pre-prints, highlighting the evolving nature of research on SARS-CoV-2 mutations. Limitations in detection methods due to mutations and the context of variant spread are noted but remain unresolved.
This discussion may be of interest to researchers, healthcare professionals, and individuals studying virology, epidemiology, and public health, particularly in relation to COVID-19 variants and their implications.
https://www.cidrap.umn.edu/news-per...dlier-other-covid-19-strains-more-data-affirmThe B117 COVID-19 variant, which was first identified in the United Kingdom in October 2020, may pose a 61% higher risk of 28-day mortality, according to a study published today in Nature.
The finding is in line with last week's BMJ study that reported B117 had a 64% higher 28-day risk of death among people older than 30, although both studies note absolute 28-day mortality risk remains low for most populations.
SARS-CoV-2 lineage B.1.1.7, a variant first detected in the UK in September 20201, has spread to multiple countries worldwide. Several studies have established that B.1.1.7 is more transmissible than preexisting variants, but have not identified whether it leads to any change in disease severity2. Here we analyse a dataset linking 2,245,263 positive SARS-CoV-2 community tests and 17,452 COVID-19 deaths in England from 1 September 2020 to 14 February 2021. For 1,146,534 (51%) of these tests, the presence or absence of B.1.1.7 can be identified because of mutations in this lineage preventing PCR amplification of the spike gene target (S gene target failure, SGTF1). Based on 4,945 deaths with known SGTF status, we estimate that the hazard of death associated with SGTF is 55% (95% CI 39–72%) higher after adjustment for age, sex, ethnicity, deprivation, care home residence, local authority of residence and test date. This corresponds to the absolute risk of death for a 55–69-year-old male increasing from 0.6% to 0.9% (95% CI 0.8–1.0%) within 28 days after a positive test in the community. Correcting for misclassification of SGTF and missingness in SGTF status, we estimate a 61% (42–82%) higher hazard of death associated with B.1.1.7. Our analysis suggests that B.1.1.7 is not only more transmissible than preexisting SARS-CoV-2 variants, but may also cause more severe illness.
Antibodies induced by the Moderna Inc and Pfizer Inc/BioNTech SE vaccines are dramatically less effective at neutralizing some of the most worrying Coronavirus variants, a new study suggests. Researchers obtained blood samples from 99 individuals who had received one or two doses of either vaccine and tested their vaccine-induced antibodies against virus replicas engineered to mimic 10 globally circulating variants. Five of the 10 variants were "highly resistant to neutralization," even when volunteers had received both doses of the vaccines, the researchers reported on Friday in Cell. All five highly resistant variants had mutations in the spike on the virus surface - known as K417N/T, E484K, and N501Y - that characterize a variant rampant in South Africa and two variants spreading rapidly in Brazil.
Astronuc said:Apparently a new variant (double mutation) in India.
https://www.bbc.com/news/world-asia-india-56507988
https://pib.gov.in/PressReleaseIframePage.aspx?PRID=1707177The analysis of samples from Maharashtra has revealed that compared to December 2020, there has been an increase in the fraction of samples with the E484Q and L452R mutations. Such mutations confer immune escape and increased infectivity. These mutations have been found in about 15-20% of samples and do not match any previously catalogued VOCs. These have been categorized as VOCs but require the same epidemiological and public health response of “increased testing, comprehensive tracking of close contacts, prompt isolation of positive cases & contacts as well as treatment as per National Treatment Protocol” by the States/UTs.
From Kerala 2032 samples (from all 14 districts) have been sequenced. The N440K variant that is associated with immune escape has been found in 123 samples from 11 districts. This variant was earlier found in 33% of samples from Andhra Pradesh, and in 53 of 104 samples from Telangana. This variant has also been reported from 16 other countries including UK, Denmark, Singapore, Japan and Australia. As of now these can be at best said to be variant under investigation.
A new triple mutation has been discovered in West Bengal: B.1.618. It contains the E484K mutation.Astronuc said:Apparently a new variant (double mutation) in India.
https://www.bbc.com/news/world-asia-india-56507988
Astronuc said:B.1.617, first identified in India
https://www.dnaindia.com/health/rep...ur-indian-states-all-you-need-to-know-2887254Wrichik Basu said:A new triple mutation has been discovered in West Bengal: B.1.618. It contains the E484K mutation.
The Indian-origin double mutant strain of the coronavirus, B.1.167, that many experts say could be behind the rapid climb of the second COVID-19 wave, was first detected way back on October 5, last year through genome sequencing of a virus sample.
Now, a third mutation in the B.1.167 has been identified and experts are hoping that this time, given the alarm bells ringing all around, the pace of intervention and follow-up picks up.
. . .
A triple mutant refers to variants that have three different strains that have combined together to form a new variant. As of now, multiple SARS-CoV-2 variants are circulating globally and a triple mutant strain could be the next challenge for India.
https://www.nejm.org/doi/full/10.1056/NEJMc2104974The estimated effectiveness of the vaccine against any documented infection with the B.1.1.7 variant was 89.5% (95% confidence interval [CI], 85.9 to 92.3) at 14 or more days after the second dose (Table 1 and Table S2). The effectiveness against any documented infection with the B.1.351 variant was 75.0% (95% CI, 70.5 to 78.9). Vaccine effectiveness against severe, critical, or fatal disease due to infection with any SARS-CoV-2 (with the B.1.1.7 and B.1.351 variants being predominant within Qatar) was very high, at 97.4% (95% CI, 92.2 to 99.5).
Vietnam detects hybrid of Indian and UK COVID-19 variantsAstronuc said:B.1.1.7, first found in the UK
. . . .
B.1.617, first identified in India
I believe the UK and Indian variants were more transmissible than the original or earlier variants, and now the new variant is even more transmissible.Vietnam had previously detected seven virus variants: B.1.222, B.1.619, D614G, B.1.1.7 - known as the UK variant, B.1.351, A.23.1 and B.1.617.2 - the "Indian variant".
Long said Vietnam would soon publish genome data of the newly identified variant, which he said was more transmissible than the previously known types.
The country of about 98 million people has so far received 2.9 million doses and aims to secure 150 million this year.
Cases slowly increasing again in the UK, it's not quite a spike but we went over 4000 cases in 24 hours first time since early April.Astronuc said:Vietnam detects hybrid of Indian and UK COVID-19 variants
https://www.reuters.com/world/asia-...hybrid-indian-uk-covid-19-variant-2021-05-29/
I believe the UK and Indian variants were more transmissible that the original or earlier variants, and now the new variant is even more transmissible.
Any idea whether this is what they expected from the partial relaxation of rules? Probably some would prefer to have a higher percentage with 2 jabs, but 30% with 2 jabs might be ok if coverage in the vulnerable population is 90% or better.pinball1970 said:Cases slowly increasing again in the UK, it's not quite a spike but we went over 4000 cases in 24 hours first time since early April.
Several days over 3000 before that when we had been bubbling along for weeks at 2500.
Approx 60% of the population first jab, a third both
https://coronavirus.data.gov.uk/details/vaccinations
The Indian is 60% more transmissible and the vaccines are also a lot less effective. As low as 33%.
https://www.bmj.com/content/373/bmj.n1346
@PeroK has a handle on UK @Ygggdrasil and Atty
Yes, symptomatic disease includes both mild and severe cases. Vaccines are generally expected to have higher effectiveness against severe disease, so for example if the second dose effectivess against variants for both mild and severe cases is 88%, maybe it's 95% effective against severe disease. Overall, we expect declining vaccine effectiveness as more variants inevitably arise. Hopefully at least the vulnerable population can get a booster early next year (ok I know it sounds terrible to say hopefully some people in the UK will get a third dose in early 2022, when most of the world might still not even have had one dose) ...pinball1970 said:I think the scientists expected an increase due to lifting of restrictions but with cases a lot less likely to end up in ICU because of Vaccine protection.
The BMJ publication mentions 'symptomatic' disease.
That could include serious/hospital?
So we can expect this scenario will be mimicked anywhere we have the Indian variant despite high vaccine numbers? @atyy
Yes we are in a privileged position in the UK unlike India Mexico Brazil Africa...atyy said:Yes, symptomatic disease includes both mild and severe cases. Vaccines are generally expected to have higher effectiveness against severe disease, so for example if the second dose effectivess against variants for both mild and severe cases is 88%, maybe it's 95% effective against severe disease. Overall, we expect declining vaccine effectiveness as more variants inevitably arise. Hopefully at least the vulnerable population can get a booster early next year (ok I know it sounds terrible to say hopefully some people in the UK will get a third dose in early 2022, when most of the world might still not even have had one dose) ...
I really wonder how does this calculated. Regarding an effective R the rate of immunity within the population has really remarkable effect: so a slightly immunity-bypassing variant with an actually lower (!) R0 might spread with higher R in a population which had a bad wave previously - or was thoroughly vaccinated.Astronuc said:I believe the UK and Indian variants were more transmissible that the original or earlier variants, and now the new variant is even more transmissible.
Probably a lot of factors, how viable the virus is on fomites, how long, in droplets/air how effective it is at entering cells, how many copies, where in the respiratory system, antibody evasion...Rive said:I really wonder how does this calculated. Regarding an effective R the rate of immunity within the population has really remarkable effect: so a slightly immunity-bypassing variant with an actually lower (!) R0 might spread with higher R in a population which had a bad wave previously - or was thoroughly vaccinated.
Tweet by Jeffery BarrettRive said:I really wonder how does this calculated. Regarding an effective R the rate of immunity within the population has really remarkable effect: so a slightly immunity-bypassing variant with an actually lower (!) R0 might spread with higher R in a population which had a bad wave previously - or was thoroughly vaccinated.
https://www.statnews.com/2021/05/31/the-name-game-for-coronavirus-variants-just-got-a-little-easier/Each variant will be given a name from the Greek alphabet, in a bid to both simplify the public discussion and to strip some of the stigma from the emergence of new variants. A country may be more willing to report it has found a new variant if it knows the new version of the virus will be identified as Rho or Sigma rather than with the country’s name, Maria Van Kerkhove, the WHO’s Coronavirus lead, told STAT in an interview.
Under the new scheme, B.1.1.7, the variant first identified in Britain, will be known as Alpha and B.1.351, the variant first spotted in South Africa, will be Beta. P.1, the variant first detected in Brazil, will be Gamma and B.1.671.2, the so-called Indian variant, is Delta.
pinball1970 said:Cases slowly increasing again in the UK, it's not quite a spike but we went over 4000 cases in 24 hours first time since early April.
Several days over 3000 before that when we had been bubbling along for weeks at 2500.
Approx 60% of the population first jab, a third both
https://coronavirus.data.gov.uk/details/vaccinations
The Indian is 60% more transmissible and the vaccines are also a lot less effective. As low as 33%.
https://www.bmj.com/content/373/bmj.n1346
@PeroK has a handle on UK @Ygggdrasil and Atty
atyy said:Tweet by Jeffery Barrett
"It's clear that B.1.617.2 has been growing faster than B.1.1.7 in UK for a few weeks. Key question for policy, not yet fully answered, is how much due to:
1. vaccine efficacy
2. intrinsic transmissibility
3. human epidemiological factors"
He has follow up posts discussing data from many sources, but not yet giving a clear picture.
https://www.nature.com/articles/d41586-021-01059-yStudies that tested for SARS-CoV-2 antibodies — an indicator of past infection — in December and January estimated that more than 50% of the population in some areas of India’s large cities had already been exposed to the virus, which should have conferred some immunity, says Manoj Murhekar, an epidemiologist at the National Institute of Epidemiology in Chennai, who led the work. The studies also suggested that, nationally, some 271 million people had been infected1 — about one-fifth of India’s population of 1.4 billion.
These figures made some researchers optimistic that the next stage of the pandemic would be less severe, says Ramanan Laxminarayan, an epidemiologist in Princeton University, New Jersey, who is based in New Delhi. But the latest eruption of COVID-19 is forcing them to rethink.
One explanation might be that the first wave primarily hit the urban poor. Antibody studies might not have been representative of the entire population and potentially overestimated exposure in other groups, he says.
pinball1970 said:This is probably the most relevant thread for this article?
https://www.sciencealert.com/we-hav...-sars-cov-2-can-insert-itself-into-our-genome
Paper here
https://www.pnas.org/content/118/21/e2105968118
A part of our genome is already ERV remnants, about 5%?
Transposons 17%
I have read about these (on a pretty pop level) for Evolution links with other primates
These sequences can do nothing, make copies of themselves, code for “something” or be involved in a regulatory role.
https://www.frontiersin.org/articles/10.3389/fchem.2016.00021/full (or do this)
COVID is not retrovirus and I do not know what consequences this could have if the findings hold up.
ERV sequences are ancient this is be new
Is something our genome just coped with in the past? Without much ado?
Do we know when the last big event was? In terms of this sort of viral insertion?
Some general stuff on ancient ERVs, transposons and epigenetics but it would be nice to get a view from the cell biology guys if they have time
A recent study proposed severe acute respiratory syndrome Coronavirus 2 (SARS-CoV-2) hijacks the LINE-1 (L1) retrotransposition machinery to integrate into the DNA of infected cells. If confirmed, this finding could have significant clinical implications. Here, we applied deep (>50x) long-read Oxford Nanopore Technologies (ONT) sequencing to HEK293T cells infected with SARS-CoV-2, and did not find any evidence of the virus existing as DNA. By examining ONT data from separate HEK293T cultivars, we resolved the complete sequences of 78 L1 insertions arising in vitro in the absence of L1 overexpression systems. ONT sequencing applied to hepatitis B virus (HBV) positive liver cancer tissues located a single HBV insertion. These experiments demonstrate reliable resolution of retrotransposon and exogenous virus insertions via ONT sequencing. That we found no evidence of SARS-CoV-2 integration suggests such events in vivo are highly unlikely to drive later oncogenesis or explain post-recovery detection of the virus.
Alpha has 23 mutations that set it apart from other coronaviruses. When the variant started to surge in Britain, researchers began inspecting these genetic tweaks to look for explanations as to why it was spreading faster than other variants.
To investigate how Alpha achieved this invisibility, the researchers looked at how the Coronavirus replicated inside of infected cells. They found that Alpha-infected cells make a lot of extra copies — some 80 times more than other versions of the virus — of a gene called Orf9b.
Yeah they have been given Greek letters. Indian is DeltaAstronuc said:The B.1.1.7 is now being called 'Alpha' coronavirus, or Alpha SARS-Cov-2?
According to an article in NY Times,
https://www.nytimes.com/2021/06/07/health/covid-alpha-uk-variant.html
Astronuc said:The B.1.1.7 is now being called 'Alpha' coronavirus, or Alpha SARS-Cov-2?
The unvaccinated woman was admitted to hospital in the Belgian city of Aalst on 3 March of this year following a number of falls and was confirmed as being Covid positive on the same day.
Despite showing no initial signs of respiratory distress, she soon deteriorated and died five days after her admission.
When the patient’s respiratory sample was processed for genomic sequencing, researchers discovered that she had been infected by the Alpha and Beta variants, which first emerged in the UK and South Africa respectively.
“This is one of the first documented cases of co-infection with two Sars-CoV-2 variants of concern,” said molecular biologist Dr Anne Vankeerberghen, who helped write a study on the woman.