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There's so many questions that this raises. - Is it more infectious or just bypasses current immunities? - Will the vaccines basically be voided by this? - I

by zpeti 6y ago

There's so many questions that this raises. - Is it more infectious or just bypasses current immunities? - Will the vaccines basically be voided by this? - Is it less lethal? Could it create more general immunity in communities without killing? - Has is spread yet? I've read the UK gov knew about this in october... seems like it's probably everywhere by now

lucideer 6y ago
No answers on most of those Qs, but the messaging on (2) "Will the vaccines basically be voided by this?" is that no, vaccines should still be effective. I'm not sure how they can no that without restarting extensive trials, but as a sibling commenter points out, viruses mutate constantly so I guess dealing with variants is pretty common when it comes to vaccination.
- xiphias2 6y ago
  Safety is the hardest part of trials, and also the vaccines that were approved are in Phase 4 (post market surveillence).
- SifJar 6y ago
  My understanding is as long as the variant has the same spike protein, vaccines "should" remain effective. So while trials haven't been done yet to verfiy the vaccines are still effective, I'm assuming the spike protein has been observed to be the same so there's no reason to suggest vaccines wouldn't be effective. EDIT: Actually, sounds like a couple of the mutations are in the spike protein and there is some evidence of reduced antibody effectiveness against the mutated version.
  - lbeltrame 6y ago
    N501Y is properly neutralized by vaccination (there's a paper in Science with these data, but I don't have a link handy right now). The deletion seems to reduce antibody neutralization, but: - In the preprint where this was shown, only 4 convalescent sera were tested; - The same 4 sera had large variation in neutralization activity per se; - There is no investigation on potential impaired T cell reactivity (cellular immunity): FTR, the "mink mutation", although it exhibited slightly lower antibody neutralization, did not change the reaction of T cells to it.
    - lbeltrame 6y ago
      I realized I made a mistake here but can't correct now: the sera used were 5, not 4.
  - sjg007 6y ago
    This is being studied.
JetSetWilly 6y ago
> Will the vaccines basically be voided by this? It has been around since September - if vaccines were voided it would have shown up in trials. It seems the human immune system is pretty smart and manufactures many different antibodies against many different sites on the spike protein. So even if some parts of the spike protein mutate, you still have antibodies that will do the job. - Is it less lethal? Could it create more general immunity in communities without killing? It might be - it carries one mutation (a deletion) on a part of the genome that helps it evade the host immune system - but more data is needed. If it was less lethal that is a mechanism that can help it spread - people are asymptomatic for longer, or feel better so are out and about instead of in their bed. But although I have seen rumours on this there's nothing definite and no data. - Has is spread yet? I've read the UK gov knew about this in october... It has been detected in Denmark as well. The UK - especially obviously London where it is prevalent - is highly globally connected. This variant will be everywhere in the world now in small amounts and if it does spread better it is just a matter of time. The UK does a LOT of genome sequencing compares to most countries so it is well equipped to detect the emergence of new strains and their spread.
- spuz 6y ago
  > It has been around since September - if vaccines were voided it would have shown up in trials. The variant didn't reach a significant proportion of infections until November. Evaluation of the efficacy of the Pfizer vaccine was done in July and August. We don't have data to understand how effective the Pfizer vaccine is against this variant yet.
  - DoingIsLearning 6y ago
    This should be the official position when communicating this information. There simply is not enough data at this point. I was really shocked to read German Minister statements saying the vacine is still effective for this variant. Sure theoretical the spike is majority unchanged but there is no evidence or data for a government official to make such an absolute statement.
    - 6y ago
makomk 6y ago
It seems the answer is that we don't know if it's spread yet. To quote the ECDC's briefing, "However, most EU/EEA countries sequence much smaller proportions of virus isolates than the UK, so ongoing circulation of this variant outside of the UK cannot be excluded". https://www.ecdc.europa.eu/sites/default/files/documents/SARS-CoV-2-variant-multiple-spike-protein-mutations-United-Kingdom.pdf https://www.ecdc.europa.eu/sites/default/files/documents/SAR... Basically, the UK is just better set up to detect variants like this than a lot of other countries. The other possibility is that even if this variant hasn't spread yet, there are other variants out there with similar properties that just haven't been detected due to the lack of widespread RNA sequencing. South Africa apparently has one that's similar but unrelated.
- imeron 6y ago
  https://twitter.com/The_Soup_Dragon/status/1340349639946629120 https://twitter.com/The_Soup_Dragon/status/13403496399466291... If this chart is true EU countries announcing the closing borders the last couple of days is waaay to late to prevent the spread of the new strain in Europe.
  - makomk 6y ago
    Yeah, all the evidence seems to point to the border closures being a stupid, counterproductive attempt to close the stable doors after the horse has bolted and maybe shoot the messenger in the process. Unfortunately, there seems to be a bit of a push here in the UK to spin this as a necessary and inevitable measure that the government should have anticipated, including the closure of the border to road freight - which I think is a siginificant escalation compared to the previous EU border closures - for, basically, Brexit-related partistan political reasons.
    - Someone 6y ago
      I think it may be too late, but if it isn’t, bordering of a population where it is more widespread will help. Even if it is too late to prevent this variant from leaving Britain, it will lower the speed at which it spreads, giving time to prepare (assuming it is more widespread in Britain than elsewhere) Because of that, I think this move may be overcautious, but I don’t see how it can be stupid or counterproductive.
hordeallergy 6y ago
Yes, it's in other countries too eg Australia and Netherlands.
- robbiep 6y ago
  If may have been detected in Australia in returned travellers but it is not in Australia in the community. Yesterday Australia had 15 community acquired cases (yes, 15 in total, with a further 11 from international travel in hotel quarantine) in the country and a quarter of sydney is in lockdown due to it, the virus variant is an American strain.
  - sjg007 6y ago
    Maybe but these variants can arise spontaneously as well, probably as a function of the immune response.
    - robbiep 6y ago
      There are a couple of problems with this line of reasoning - yes, as an RNA virus, there is a high rate of mutation. However because of the redundancy of amino acid encoding most mutations will be preservative (ie produce the same protein). Additionally, although there is no reason that chance can’t produce the exact same spike protein mutation in another location in the world, it will be of a different lineage which will clearly show up on sequencing as there will be some clear differences elsewhere (in the preservative mutations). This is highly unlikely to be a result of immune response pressure, in fact I would discount this entirely, mutations arise as a response to copying errors and inside an infection cycle (initial infection, replication, transmission, adaptive immune response). The final immune response will shut down the virus ability to replicate freely due to recognition; selective pressure to avoid immune response is unlikely due to 1) the continually lowering viral load and 2) the very high number of non-selective antibodies produced that recognise a large number of viral epitopes.

by zpeti 6y ago

lucideer 6y ago

No answers on most of those Qs, but the messaging on (2) "Will the vaccines basically be voided by this?" is that no, vaccines should still be effective. I'm not sure how they can no that without restarting extensive trials, but as a sibling commenter points out, viruses mutate constantly so I guess dealing with variants is pretty common when it comes to vaccination.

xiphias2 6y ago
Safety is the hardest part of trials, and also the vaccines that were approved are in Phase 4 (post market surveillence).
SifJar 6y ago
My understanding is as long as the variant has the same spike protein, vaccines "should" remain effective. So while trials haven't been done yet to verfiy the vaccines are still effective, I'm assuming the spike protein has been observed to be the same so there's no reason to suggest vaccines wouldn't be effective. EDIT: Actually, sounds like a couple of the mutations are in the spike protein and there is some evidence of reduced antibody effectiveness against the mutated version.
- lbeltrame 6y ago
  N501Y is properly neutralized by vaccination (there's a paper in Science with these data, but I don't have a link handy right now). The deletion seems to reduce antibody neutralization, but: - In the preprint where this was shown, only 4 convalescent sera were tested; - The same 4 sera had large variation in neutralization activity per se; - There is no investigation on potential impaired T cell reactivity (cellular immunity): FTR, the "mink mutation", although it exhibited slightly lower antibody neutralization, did not change the reaction of T cells to it.
  - lbeltrame 6y ago
    I realized I made a mistake here but can't correct now: the sera used were 5, not 4.
- sjg007 6y ago
  This is being studied.

JetSetWilly 6y ago

> Will the vaccines basically be voided by this? It has been around since September - if vaccines were voided it would have shown up in trials. It seems the human immune system is pretty smart and manufactures many different antibodies against many different sites on the spike protein. So even if some parts of the spike protein mutate, you still have antibodies that will do the job. - Is it less lethal? Could it create more general immunity in communities without killing? It might be - it carries one mutation (a deletion) on a part of the genome that helps it evade the host immune system - but more data is needed. If it was less lethal that is a mechanism that can help it spread - people are asymptomatic for longer, or feel better so are out and about instead of in their bed. But although I have seen rumours on this there's nothing definite and no data. - Has is spread yet? I've read the UK gov knew about this in october... It has been detected in Denmark as well. The UK - especially obviously London where it is prevalent - is highly globally connected. This variant will be everywhere in the world now in small amounts and if it does spread better it is just a matter of time. The UK does a LOT of genome sequencing compares to most countries so it is well equipped to detect the emergence of new strains and their spread.

spuz 6y ago
> It has been around since September - if vaccines were voided it would have shown up in trials. The variant didn't reach a significant proportion of infections until November. Evaluation of the efficacy of the Pfizer vaccine was done in July and August. We don't have data to understand how effective the Pfizer vaccine is against this variant yet.
- DoingIsLearning 6y ago
  This should be the official position when communicating this information. There simply is not enough data at this point. I was really shocked to read German Minister statements saying the vacine is still effective for this variant. Sure theoretical the spike is majority unchanged but there is no evidence or data for a government official to make such an absolute statement.
  - 6y ago

makomk 6y ago

It seems the answer is that we don't know if it's spread yet. To quote the ECDC's briefing, "However, most EU/EEA countries sequence much smaller proportions of virus isolates than the UK, so ongoing circulation of this variant outside of the UK cannot be excluded". https://www.ecdc.europa.eu/sites/default/files/documents/SARS-CoV-2-variant-multiple-spike-protein-mutations-United-Kingdom.pdf https://www.ecdc.europa.eu/sites/default/files/documents/SAR... Basically, the UK is just better set up to detect variants like this than a lot of other countries. The other possibility is that even if this variant hasn't spread yet, there are other variants out there with similar properties that just haven't been detected due to the lack of widespread RNA sequencing. South Africa apparently has one that's similar but unrelated.

imeron 6y ago
https://twitter.com/The_Soup_Dragon/status/1340349639946629120 https://twitter.com/The_Soup_Dragon/status/13403496399466291... If this chart is true EU countries announcing the closing borders the last couple of days is waaay to late to prevent the spread of the new strain in Europe.
- makomk 6y ago
  Yeah, all the evidence seems to point to the border closures being a stupid, counterproductive attempt to close the stable doors after the horse has bolted and maybe shoot the messenger in the process. Unfortunately, there seems to be a bit of a push here in the UK to spin this as a necessary and inevitable measure that the government should have anticipated, including the closure of the border to road freight - which I think is a siginificant escalation compared to the previous EU border closures - for, basically, Brexit-related partistan political reasons.
  - Someone 6y ago
    I think it may be too late, but if it isn’t, bordering of a population where it is more widespread will help. Even if it is too late to prevent this variant from leaving Britain, it will lower the speed at which it spreads, giving time to prepare (assuming it is more widespread in Britain than elsewhere) Because of that, I think this move may be overcautious, but I don’t see how it can be stupid or counterproductive.

hordeallergy 6y ago

Yes, it's in other countries too eg Australia and Netherlands.

robbiep 6y ago
If may have been detected in Australia in returned travellers but it is not in Australia in the community. Yesterday Australia had 15 community acquired cases (yes, 15 in total, with a further 11 from international travel in hotel quarantine) in the country and a quarter of sydney is in lockdown due to it, the virus variant is an American strain.
- sjg007 6y ago
  Maybe but these variants can arise spontaneously as well, probably as a function of the immune response.
  - robbiep 6y ago
    There are a couple of problems with this line of reasoning - yes, as an RNA virus, there is a high rate of mutation. However because of the redundancy of amino acid encoding most mutations will be preservative (ie produce the same protein). Additionally, although there is no reason that chance can’t produce the exact same spike protein mutation in another location in the world, it will be of a different lineage which will clearly show up on sequencing as there will be some clear differences elsewhere (in the preservative mutations). This is highly unlikely to be a result of immune response pressure, in fact I would discount this entirely, mutations arise as a response to copying errors and inside an infection cycle (initial infection, replication, transmission, adaptive immune response). The final immune response will shut down the virus ability to replicate freely due to recognition; selective pressure to avoid immune response is unlikely due to 1) the continually lowering viral load and 2) the very high number of non-selective antibodies produced that recognise a large number of viral epitopes.