4 ms·

I’m sure some folks here will chime in with countering/supporting data, but assuming these trends are truly representative, understanding why this is occurring

I’m sure some folks here will chime in with countering/supporting data, but assuming these trends are truly representative, understanding why this is occurring will be imperative. One hypothesis involves the fact that current mRNA vaccines induce an immune response highly targeted toward the spike protein RBD. In contrast, natural infection induces a broader immune response that includes antibodies targeting other proteins (Nucleocapsid protein being one of the most notable; it is commonly used to determine if a prior infection occurred). Omicron in particular is a variant that has accumulated a significant number of mutations in the S protein region. Is this coincidence or are we seeing selective pressure due to mass vaccination campaigns?

_djo_ 5y ago
Given the low vaccination rate in Sub-Saharan Africa at the time this variant emerged from there, it's unlikely that mass vaccination campaigns drove selection pressure in this case. Far more likely that it was a host jump or a long mutation period inside a single immuno-compromised individual.
- wsc981 5y ago
  > Given the low vaccination rate in Sub-Saharan Africa at the time this variant emerged from there, it's unlikely that mass vaccination campaigns drove selection pressure in this case. Far more likely that it was a host jump or a long mutation period inside a single immuno-compromised individual. Perhaps, but it's my understanding that Omicron was first observed in diplomats that had already received multiple vaccinations. See: https://www.nytimes.com/2021/12/03/world/botswana-diplomats-omicron-europe.html https://www.nytimes.com/2021/12/03/world/botswana-diplomats-...
  - _djo_ 5y ago
    No, none of those are suspected of being Patient Zero because they aren’t the earliest cases. Just the first to be detected. Nigeria has found Omicron in samples dating back to October, long before the diplomat cases were identified, and analyses that have compared changes to the genome over time against the infection rate show that it likely emerged in late September / early October.
- peteradio 5y ago
  Just because there is a low vaccination rate doesn't mean there is not a shit load of vaccinated people in the region. Sub-saharan Africa has more than a billion people. Is there any solid evidence this variant actually evolved in Sub-Saharan Africa anyway?
  - _djo_ 5y ago
    It means it’s less likely than other more compelling explanations. For instance, South Africa has previously observed similar huge evolutionary jumps in single immunosuppressed patients with HIV. A similar case was observed in Europe with leukaemia. The case distribution and timing makes it extremely likely that it emerged in the region, yes. Given the evidence, the only reason for claiming that vaccine selective pressure is the only or even most likely explanation is a statement driven by ideology not reality.
    - peteradio 5y ago
      > t means it’s less likely than other more compelling explanations. I don't really think so. We can safely say we are exploring where the latest originated and comparison of hypotheses overall likelihood is difficult to do in even simple cases and huge data in a well defined regime like physics. Our back of the napkin handwaves are piss in the wind. > The case distribution and timing makes it extremely likely that it emerged in the region, yes. It emerged in a population but originated in a particular body, it makes it almost pointless to say it came from this or that country when we are trying to understand the actual body it came from. (I say body because there is another thread discussing mouse origins). > Given the evidence, the only reason for claiming that vaccine selective pressure is the only or even most likely explanation is a statement driven by ideology not reality. Totally. I think someone is exploring one of their pet theory and how it fits with this evidence.

_djo_ 5y ago

Given the low vaccination rate in Sub-Saharan Africa at the time this variant emerged from there, it's unlikely that mass vaccination campaigns drove selection pressure in this case. Far more likely that it was a host jump or a long mutation period inside a single immuno-compromised individual.

wsc981 5y ago
> Given the low vaccination rate in Sub-Saharan Africa at the time this variant emerged from there, it's unlikely that mass vaccination campaigns drove selection pressure in this case. Far more likely that it was a host jump or a long mutation period inside a single immuno-compromised individual. Perhaps, but it's my understanding that Omicron was first observed in diplomats that had already received multiple vaccinations. See: https://www.nytimes.com/2021/12/03/world/botswana-diplomats-omicron-europe.html https://www.nytimes.com/2021/12/03/world/botswana-diplomats-...
- _djo_ 5y ago
  No, none of those are suspected of being Patient Zero because they aren’t the earliest cases. Just the first to be detected. Nigeria has found Omicron in samples dating back to October, long before the diplomat cases were identified, and analyses that have compared changes to the genome over time against the infection rate show that it likely emerged in late September / early October.
peteradio 5y ago
Just because there is a low vaccination rate doesn't mean there is not a shit load of vaccinated people in the region. Sub-saharan Africa has more than a billion people. Is there any solid evidence this variant actually evolved in Sub-Saharan Africa anyway?
- _djo_ 5y ago
  It means it’s less likely than other more compelling explanations. For instance, South Africa has previously observed similar huge evolutionary jumps in single immunosuppressed patients with HIV. A similar case was observed in Europe with leukaemia. The case distribution and timing makes it extremely likely that it emerged in the region, yes. Given the evidence, the only reason for claiming that vaccine selective pressure is the only or even most likely explanation is a statement driven by ideology not reality.
  - peteradio 5y ago
    > t means it’s less likely than other more compelling explanations. I don't really think so. We can safely say we are exploring where the latest originated and comparison of hypotheses overall likelihood is difficult to do in even simple cases and huge data in a well defined regime like physics. Our back of the napkin handwaves are piss in the wind. > The case distribution and timing makes it extremely likely that it emerged in the region, yes. It emerged in a population but originated in a particular body, it makes it almost pointless to say it came from this or that country when we are trying to understand the actual body it came from. (I say body because there is another thread discussing mouse origins). > Given the evidence, the only reason for claiming that vaccine selective pressure is the only or even most likely explanation is a statement driven by ideology not reality. Totally. I think someone is exploring one of their pet theory and how it fits with this evidence.