4 ms·

Another recent study [1], discussed on This Week in Virology [2], also found T-cell immunity to be robust against mutations. However, there seems to be an open

Another recent study [1], discussed on This Week in Virology [2], also found T-cell immunity to be robust against mutations. However, there seems to be an open question of how well natural T cells, trained on the whole virus, will compare to T cells trained on vaccines that only have the spike protein or some other subset. [1]: https://www.biorxiv.org/content/10.1101/2021.02.27.433180v1 https://www.biorxiv.org/content/10.1101/2021.02.27.433180v1 [2]: https://www.microbe.tv/twiv/twiv-736/ https://www.microbe.tv/twiv/twiv-736/

jonny_eh 6y ago
I recall reading that the enhanced immune response from the vaccines were more protective than a natural infection.
- dragontamer 6y ago
  Why is this post downvoted? I know that P.1 (Brazil variant) seems to totally avoid natural immunity. The proof is from the city of Manaus, which was over 75% infected in October 2020. A resurgent wave of COVID19 hit in January 2021. At first, this didn't seem possible. But upon further study, it seemed that P.1 was avoiding natural immunity. So its reinfecting a ton of people in Manaus. ------------ In contrast, the Pfizer vaccine has shown to confer immunity to both the original strain AND to P.1. As such, the immune response created from Pfizer absolutely offers better protection, once we account for the variants (especially P.1 and B.1.351, which both have defenses against natural immunity) B.1.351 is the other "immune avoiding" variant. And I await for more studies before making a conclusion on that matter. -------- EDIT: It seems like the article is discussing B.1.351 among its list of variants. That's good: the South African strain seemed like it had some ability to avoid our immune system, but our T-cells are still functioning against it. So a P.1 / Manaus event probably won't happen.
  - anonuser123456 6y ago
    >The proof is from the city of Manaus, The Manaus data was not very compelling. Lots of selection bias in their sampling.
    - dragontamer 6y ago
      There's multiple studies and multiple sets of data from Manaus. You'll have to be more specific. Which data, from which study, is untrustworthy?
      - anonuser123456 6y ago
        I do not have the citation handy, but in one study, they recruited individuals by enticing them with the results; e.g. if you take take part in the study, we will give you the antibody result. This would obviously bias the results toward people that believed they had the virus, but didn't have a test when sick.
      - eindiran 6y ago
        OP is likely talking about: https://science.sciencemag.org/content/371/6526/288?ijkey=0164586a5cf47a56724f873706982763e64356b8&keytype2=tf_ipsecsha https://science.sciencemag.org/content/371/6526/288?ijkey=01... Which was originally reported in the popular press as "herd immunity doesn't real". The methodology seems weak to me, both in terms of sampling and how poorly some of the adjustments in the attack rate/seropositivity estimates were justified. This paper, Buss et al 2021, was cited wrt 67% attack rate and 75%+ seroprevalence in Faria et al 2021: https://www.biorxiv.org/content/10.1101/2021.03.12.435194v2 https://www.biorxiv.org/content/10.1101/2021.03.12.435194v2 This in turn was cited in eg Dejnirattisai et al 2021, as if it were the original source of the seroprevalence claims/data: https://www.biorxiv.org/content/10.1101/2021.03.12.435194v2 https://www.biorxiv.org/content/10.1101/2021.03.12.435194v2 Note the lack of a citation for Buss et al 2021. The error bars in Buss et al 2021 are awfully narrow given how uncertain many of the assumptions made were in correcting the seroprevalence estimates. Further, the idea that P1 seems to "totally avoid natural immunity" (in comparison to vaccine immunity) is not borne out by the experimental data (eg Dejnirattisai et al 2021, linked above, or Tarke et al 2021: https://www.biorxiv.org/content/10.1101/2021.02.27.433180v1 https://www.biorxiv.org/content/10.1101/2021.02.27.433180v1). Both convalescent and vaccine sera showed reduced neutralization rates for P1; you see similar behavior in other potent VOCs like B1.1.7 (Dejnirattisai et al 2021 bis: https://www.cell.com/cell/fulltext/S0092-8674(21)00222-1 https://www.cell.com/cell/fulltext/S0092-8674(21)00222-1) and B1.351 (Zhou et al 2021: https://www.researchgate.net/publication/349058926_Reduced_Neutralization_of_SARS-CoV-2_B117_Variant_from_Naturally_Acquired_and_Vaccine_Induced_Antibody_Immunity https://www.researchgate.net/publication/349058926_Reduced_N...). And given the lack of transparency in any of these papers regarding how the antibodies sourced from convalescent sera were chosen for use, it's hard to say for certain that there isn't yet another selection issue here. > There's multiple studies and multiple sets of data from Manaus. If you are aware of another data set from Manaus from the period prior to P1 emergence which used a different methodology to claim 75%+ seroprevalence, I'd love to take a look at it. Otherwise, it seems like all the claims are ultimately sourced from the estimates of Buss et al 2021.
  - timr 6y ago
    > I know that P.1 (Brazil variant) seems to totally avoid natural immunity. This is completely false, and is a poor extrapolation from a faulty initial data point. There have now been several publications -- including the J&J clinical trial data itself [1] -- which show that immune responses induced by non-variant virus (or vaccine) are protective against the Brazilian variant. There is some evidence that a particular mutation in the spike protein of the Brazilian variant can partially evade neutralization by particular antibodies, but this is far from "totally avoiding natural immunity". > The proof is from the city of Manaus, which was over 75% infected in October 2020. This number is based on a study that was written in summer 2020 [2], and used a number of questionable "adjustments" to the raw seroprevalence data to arrive at their conclusion. Raw seroprevalence data (Figure 2) was closer to 30%, not 75%. The parsimonious conclusion is that the paper citing 75% seroprevalence in Manaus was wrong. Science really should retract this paper, or publish an addendum. It's an example where low-quality science is leading to a lot of unnecessary panic and speculation. [1] https://www.ucsf.edu/news/2021/03/420071/how-effective-johnson-johnson-covid-19-vaccine-heres-what-you-should-know https://www.ucsf.edu/news/2021/03/420071/how-effective-johns... [2] https://science.sciencemag.org/content/371/6526/288 https://science.sciencemag.org/content/371/6526/288
    - splistud 6y ago
      You say totally false, but your own favored hand-on-the-scale (which could be reasonable) adjustment leaves it at NOT in any way totally false
      - timr 6y ago
        There is no adjustment. Those are the raw values.
    - lamontcg 6y ago
      Use of blood donors is itself questionable and open to selection bias. Particularly if blood donors were getting free antibody testing and seeing the results, but even if they weren't. The authors seem to only have considered the demographics of the sample selection, and somewhat poorly.
  - jupp0r 6y ago
    You make it sound as if immune evasion is a binary thing. It's a spectrum. We don't need to worry about 100% evasion suddenly appearing and it's definitely not what we are seeing with B.1.351 and P.1. There are somewhat lower antibody titers with current vaccines, but they are still very effective both in antibody and T-Cell response it seems. "Proof" from Manaus would have to be replicated in lab settings and all the data from lab tests show that there is some slight immune escape for P.1, but by no means is it total.
- dreamcompiler 6y ago
  Same here, but that's adaptive immune response with antibodies. T-cell response is a different matter, and we're just beginning to learn how it works with COVID.

jonny_eh 6y ago

I recall reading that the enhanced immune response from the vaccines were more protective than a natural infection.

dragontamer 6y ago
Why is this post downvoted? I know that P.1 (Brazil variant) seems to totally avoid natural immunity. The proof is from the city of Manaus, which was over 75% infected in October 2020. A resurgent wave of COVID19 hit in January 2021. At first, this didn't seem possible. But upon further study, it seemed that P.1 was avoiding natural immunity. So its reinfecting a ton of people in Manaus. ------------ In contrast, the Pfizer vaccine has shown to confer immunity to both the original strain AND to P.1. As such, the immune response created from Pfizer absolutely offers better protection, once we account for the variants (especially P.1 and B.1.351, which both have defenses against natural immunity) B.1.351 is the other "immune avoiding" variant. And I await for more studies before making a conclusion on that matter. -------- EDIT: It seems like the article is discussing B.1.351 among its list of variants. That's good: the South African strain seemed like it had some ability to avoid our immune system, but our T-cells are still functioning against it. So a P.1 / Manaus event probably won't happen.
- anonuser123456 6y ago
  >The proof is from the city of Manaus, The Manaus data was not very compelling. Lots of selection bias in their sampling.
  - dragontamer 6y ago
    There's multiple studies and multiple sets of data from Manaus. You'll have to be more specific. Which data, from which study, is untrustworthy?
    - anonuser123456 6y ago
      I do not have the citation handy, but in one study, they recruited individuals by enticing them with the results; e.g. if you take take part in the study, we will give you the antibody result. This would obviously bias the results toward people that believed they had the virus, but didn't have a test when sick.
    - eindiran 6y ago
      OP is likely talking about: https://science.sciencemag.org/content/371/6526/288?ijkey=0164586a5cf47a56724f873706982763e64356b8&keytype2=tf_ipsecsha https://science.sciencemag.org/content/371/6526/288?ijkey=01... Which was originally reported in the popular press as "herd immunity doesn't real". The methodology seems weak to me, both in terms of sampling and how poorly some of the adjustments in the attack rate/seropositivity estimates were justified. This paper, Buss et al 2021, was cited wrt 67% attack rate and 75%+ seroprevalence in Faria et al 2021: https://www.biorxiv.org/content/10.1101/2021.03.12.435194v2 https://www.biorxiv.org/content/10.1101/2021.03.12.435194v2 This in turn was cited in eg Dejnirattisai et al 2021, as if it were the original source of the seroprevalence claims/data: https://www.biorxiv.org/content/10.1101/2021.03.12.435194v2 https://www.biorxiv.org/content/10.1101/2021.03.12.435194v2 Note the lack of a citation for Buss et al 2021. The error bars in Buss et al 2021 are awfully narrow given how uncertain many of the assumptions made were in correcting the seroprevalence estimates. Further, the idea that P1 seems to "totally avoid natural immunity" (in comparison to vaccine immunity) is not borne out by the experimental data (eg Dejnirattisai et al 2021, linked above, or Tarke et al 2021: https://www.biorxiv.org/content/10.1101/2021.02.27.433180v1 https://www.biorxiv.org/content/10.1101/2021.02.27.433180v1). Both convalescent and vaccine sera showed reduced neutralization rates for P1; you see similar behavior in other potent VOCs like B1.1.7 (Dejnirattisai et al 2021 bis: https://www.cell.com/cell/fulltext/S0092-8674(21)00222-1 https://www.cell.com/cell/fulltext/S0092-8674(21)00222-1) and B1.351 (Zhou et al 2021: https://www.researchgate.net/publication/349058926_Reduced_Neutralization_of_SARS-CoV-2_B117_Variant_from_Naturally_Acquired_and_Vaccine_Induced_Antibody_Immunity https://www.researchgate.net/publication/349058926_Reduced_N...). And given the lack of transparency in any of these papers regarding how the antibodies sourced from convalescent sera were chosen for use, it's hard to say for certain that there isn't yet another selection issue here. > There's multiple studies and multiple sets of data from Manaus. If you are aware of another data set from Manaus from the period prior to P1 emergence which used a different methodology to claim 75%+ seroprevalence, I'd love to take a look at it. Otherwise, it seems like all the claims are ultimately sourced from the estimates of Buss et al 2021.
- timr 6y ago
  > I know that P.1 (Brazil variant) seems to totally avoid natural immunity. This is completely false, and is a poor extrapolation from a faulty initial data point. There have now been several publications -- including the J&J clinical trial data itself [1] -- which show that immune responses induced by non-variant virus (or vaccine) are protective against the Brazilian variant. There is some evidence that a particular mutation in the spike protein of the Brazilian variant can partially evade neutralization by particular antibodies, but this is far from "totally avoiding natural immunity". > The proof is from the city of Manaus, which was over 75% infected in October 2020. This number is based on a study that was written in summer 2020 [2], and used a number of questionable "adjustments" to the raw seroprevalence data to arrive at their conclusion. Raw seroprevalence data (Figure 2) was closer to 30%, not 75%. The parsimonious conclusion is that the paper citing 75% seroprevalence in Manaus was wrong. Science really should retract this paper, or publish an addendum. It's an example where low-quality science is leading to a lot of unnecessary panic and speculation. [1] https://www.ucsf.edu/news/2021/03/420071/how-effective-johnson-johnson-covid-19-vaccine-heres-what-you-should-know https://www.ucsf.edu/news/2021/03/420071/how-effective-johns... [2] https://science.sciencemag.org/content/371/6526/288 https://science.sciencemag.org/content/371/6526/288
  - splistud 6y ago
    You say totally false, but your own favored hand-on-the-scale (which could be reasonable) adjustment leaves it at NOT in any way totally false
    - timr 6y ago
      There is no adjustment. Those are the raw values.
  - lamontcg 6y ago
    Use of blood donors is itself questionable and open to selection bias. Particularly if blood donors were getting free antibody testing and seeing the results, but even if they weren't. The authors seem to only have considered the demographics of the sample selection, and somewhat poorly.
- jupp0r 6y ago
  You make it sound as if immune evasion is a binary thing. It's a spectrum. We don't need to worry about 100% evasion suddenly appearing and it's definitely not what we are seeing with B.1.351 and P.1. There are somewhat lower antibody titers with current vaccines, but they are still very effective both in antibody and T-Cell response it seems. "Proof" from Manaus would have to be replicated in lab settings and all the data from lab tests show that there is some slight immune escape for P.1, but by no means is it total.
dreamcompiler 6y ago
Same here, but that's adaptive immune response with antibodies. T-cell response is a different matter, and we're just beginning to learn how it works with COVID.