3 ms·

What do you think of this suggestion that labs in southern Africa are not the only relevant ones? > Omicron COVID was in Italy as early as 2021-10-13 – 7 weeks

What do you think of this suggestion that labs in southern Africa are not the only relevant ones? > Omicron COVID was in Italy as early as 2021-10-13 – 7 weeks before alarm from South Africa. > per upthread, Italy also where SARS-CoV2 immune-escape gain-of-function variants bred, since 2020, in less-than-max-biosecurity labs. https://twitter.com/gojomo/status/1473471612112441344 https://twitter.com/gojomo/status/1473471612112441344 (IANA biologist)

gojomo 5y ago
Thanks for referencing my tweet - & asking some questions I would! I 1st learned of the referenced Italy antibody-escape gain-of-function paper via an HN post which appeared almost concurrently with the first reports of the (not-yet-named) Omicron variant: https://news.ycombinator.com/item?id=29359125 https://news.ycombinator.com/item?id=29359125 As Twitter user @Vbruttel has pointed out (https://twitter.com/VBruttel/status/1466930489026093056 https://twitter.com/VBruttel/status/1466930489026093056), similar published research was done in Durban South Africa, which has at most a BSL-3 lab. This is not to say either of those are the origin; just that this kind of research seems pretty common: within the capability & interest of many labs, who cheerfully report their creation, via selective pressure, of immune-escape variants in published papers.
fer 5y ago
First detection is an indicator of that, when it was first detected, not a guarantee that it was first there. Only a very small fraction of RT-PCR positive samples are sent for sequencing under normal conditions. > Omicron COVID was in Italy as early as 2021-10-13 – 7 weeks before alarm from South Africa. 7 weeks before the alarm, but only 10 days before in retrospective sampling, and even less in other places in Africa. Saying it appeared in Italy but somehow it spread in Southern Africa first goes against normal epidemiological dynamics, especially given how contagious Omicron is. The chances are it started where the first cluster is detected, not where the first retrospective case is detected, because the possibility of it escaping in Italy, flying to SA, and somehow staying dormant in Italy while giving SA a head-start is extremely unlikely.
- gojomo 5y ago
  But Italy, hit extremely hard by early waves, and now with a much-higher vax rate than South Africa, could more easily miss a rising wave of mild cases in already-immune that don't seek treatment. There are plenty of factors in all directions, and only very spotty variant surveillance most places.
  - fer 5y ago
    South Africa has absurdly higher seroprevalence though, which generally provides higher protection.

gojomo 5y ago

Thanks for referencing my tweet - & asking some questions I would! I 1st learned of the referenced Italy antibody-escape gain-of-function paper via an HN post which appeared almost concurrently with the first reports of the (not-yet-named) Omicron variant: https://news.ycombinator.com/item?id=29359125 https://news.ycombinator.com/item?id=29359125 As Twitter user @Vbruttel has pointed out (https://twitter.com/VBruttel/status/1466930489026093056 https://twitter.com/VBruttel/status/1466930489026093056), similar published research was done in Durban South Africa, which has at most a BSL-3 lab. This is not to say either of those are the origin; just that this kind of research seems pretty common: within the capability & interest of many labs, who cheerfully report their creation, via selective pressure, of immune-escape variants in published papers.

fer 5y ago

First detection is an indicator of that, when it was first detected, not a guarantee that it was first there. Only a very small fraction of RT-PCR positive samples are sent for sequencing under normal conditions. > Omicron COVID was in Italy as early as 2021-10-13 – 7 weeks before alarm from South Africa. 7 weeks before the alarm, but only 10 days before in retrospective sampling, and even less in other places in Africa. Saying it appeared in Italy but somehow it spread in Southern Africa first goes against normal epidemiological dynamics, especially given how contagious Omicron is. The chances are it started where the first cluster is detected, not where the first retrospective case is detected, because the possibility of it escaping in Italy, flying to SA, and somehow staying dormant in Italy while giving SA a head-start is extremely unlikely.

gojomo 5y ago
But Italy, hit extremely hard by early waves, and now with a much-higher vax rate than South Africa, could more easily miss a rising wave of mild cases in already-immune that don't seek treatment. There are plenty of factors in all directions, and only very spotty variant surveillance most places.
- fer 5y ago
  South Africa has absurdly higher seroprevalence though, which generally provides higher protection.