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This is Alina Chan, one of the co-authors of Viral: The Search for the Origin of Covid-19. In defense of a natural origin of Omicron, this study describes the

This is Alina Chan, one of the co-authors of Viral: The Search for the Origin of Covid-19. In defense of a natural origin of Omicron, this study describes the remarkable evolution of SARS-CoV-2 during convalescent plasma treatment of an immunosuppressed patient for 3-4 months; the mutations also reduced sensitivity to neutralizing antibodies: https://www.nature.com/articles/s41586-021-03291-y https://www.nature.com/articles/s41586-021-03291-y We know that there is a large immunocompromised population in Africa and that Covid-19 is rampant there. We also know that most hospitals, regardless of country, don't have the resources to track the evolution of SARS-CoV-2 in their immunocompromised patients. So it's not unexpected that a variant like Omicron could have evolved over an entire year in an immunocompromised individual before finally infecting others. If there is any evidence that a lab in the region was serially passaging SARS-CoV-2 in neutralizing antibodies/patient serum, then I'd say there is something to go on for a potential lab origin. But at the moment, there is not even circumstantial evidence pointing to this happening in Africa. Maybe setting up a secure channel for whistleblowers with evidence of the above would be the most productive approach. The above is not to say that I don't think there needs to be much more transparency and accountability from scientists working with pathogens. https://twitter.com/Ayjchan/status/1468582694007279616 https://twitter.com/Ayjchan/status/1468582694007279616

nnx 5y ago
"Omicron could have evolved over an entire year in an immunocompromised individual before finally infecting others" Is it likely that this infected person would not have started any detectable cluster this whole time? How do you explain the ratio of functional vs silent mutations?
- ayjchan 5y ago
  Evolution experiments in the lab mimic natural evolution. The ratio of functional vs silent mutations has also been used to characterize the evolution of viruses under natural selection.
  - netizen-936824 5y ago
    According to the blog post that we are commenting on, there is a strange ratio of silent to functional mutations. How can this be accounted for if it was a natural course of evolution?
    - mbreese 5y ago
      Without looking more at the variants themselves and just going by the numbers in the post, it’s entirely plausible. It’s not likely, but plausible. Mainly because we are talking rare events. If the level of success is 33/3.5 (9.42), we’d expect that 4 (or less) silent variants would happen with a probability of ~ 0.042 (Poisson X <= 4). So, a bit more than a 4% chance. But with millions of people infected, this ratio of S/NS variations would still happen at a pretty high absolute number. Anytime you look at numbers like these, remember with a big denominator, even rare events are expected to happen.
      - sigotirandolas 5y ago
        If it was the case that the absolute number mattered, we would be able to sample different "Omicron-like" variants and observe various ratios such as 33N/10S, 33N/15S, etc. mutations. But according to the data presented, we don't: We only see a single (kind of) Omicron, the one with (about) 33N/4S mutations, presumably spilling over by a single event, so I don't see how your conclusion follows.
        whynotqat 5y ago
        The sequence of mutations leading to Omicron is a one-off. Presumably, if there were a thousand variants with the same N mutations as Omicron, you'd see ratios like the ones you describe, but there's only one Omicron. The previous poster is pointing out it's plausible (~5% chance) that the path Omicron took has only 4 S mutations.
        mbreese 5y ago
        There are two different (and independent) forces at play here: mutation and natural selection. The question is, given a known ratio of 3.5 NS/S, what is the likelihood that there would be only 4 non-silent mutations in any random strain (like omicron)? What the mutations are is irrelevant to this question. (I will use mutations and variants interchangeably below, but both mean a single change in the genetic code for the virus). Because we are dealing with integer counts, you can’t really have 3.5 mutations. You can only have 1, 2, 3, etc. So, 3.5 is just the average of all ratios. When dealing with count data like this, the Poisson distribution is what you use. When you have 33 non-silent mutations, you could have 1, 2, 3, etc silent mutations. We’d expect to see 9.4 (33/3.5), but you can’t have 0.4 of a mutation, only integers. There is a specific probability associated with each possible value (1,2,3…), and that can be calculated using the Poisson distribution. You are most likely to see 9 or 10, but all other values are also possible. To calculate how likely you are to see exactly 4 silent variants, you use the Poisson distribution. Again, we will expect that the rate should be 33/3.5 silent variants. In R, you’d do: dpois(4, 33/3.5) [1] 0.02647255 So, if we had 33 nonsilent variants, we’d expect to see exactly 4 silent variants 2.6% of the time. To put this into context, the most likely number of silent mutations is 9, which is expected only 13% of the time. We normally think in terms of “how likely is it that we’d see 4 or fewer mutations”, so we re-run the test for 0:4 and add them up: sum(dpois(0:4, 33/3.5)) [1] 0.04211515 Which is how I got a probability of 0.042. And which answers the specific question — if we see 33 non silent mutations in a strain, how likely is it that we would be 4 or fewer silent mutations in the same strain? 4.2% of the time. Given these numbers, I’d say it is plausible that you’d see this ratio of NS/S mutations occur naturally. It would be rare, but still somewhat expected to occur. Now this says nothing about what the mutations are, or why the omicron strain is so prevalent. This is where natural selection takes over and this combination of mutations is out competing all others.
- rob_c 5y ago
  More simply, I don't think people tend to remain infected (and infectious) for a whole year (not saying they can't just that this seems a farcical assumption) Yeah I agree with the going undetected too unless they're potentially asymptomatic (in which case why should we ever expect to find/treat them). All leading to the same response of you can't control highly transmissible virus(vurii) once they have infected a large amount of the population. (aka a 0 covid strategy is self-defeating)
  - Taniwha 5y ago
    The mouse theory is interesting .... because omicron is more benign - one of the problems we have with covid is that because of all this modern medicine saving lots of lives (not enough though sadly) there's not a lot of evolutionary pressure to make things more benign. But if omicron has been in a wild mammal population without vaccination or hospitals then there might be more evolutionary pressure to become more benign. It's worth noting that some vaccines in the past have been 'live' vaccines - essentially viruses that get passed around with a sniffle or two but no more harm. This actually what we all hope omicron would be .... I can't see why we shouldn't give the virus a bit of a help along .... the right lab leak might be just what we all need
dqpb 5y ago
Can you also comment on her claim that Delta was a lab leak?
- deleted 5y ago
  [deleted]
- Stevvo 5y ago
  He doesn't claim the origin of Delta was a lab leak. He claims Delta leaked from a lab in Taiwan.
- djrogers 5y ago
  You misread that - there is no claim that delta was initially released by a lab, rather a the known fact that a lab studying delta had an accident. Read the links the author provided.
- sammoody 5y ago
  The claim wasn’t that Delta originated from a lab leak but rather that Delta happened to leak from a lab (after the point that it existed in the wild). Additionally, the phylogenetic points from the article would suggest that Delta is of natural origin
- CamperBob2 5y ago
  She, and yes, she does need to go back over that sentence and clarify it, because it does read that way.
  - dqpb 5y ago
    Thank you, fixed it.
- deleted 5y ago
  [deleted]
- dljones 5y ago
  S/he clarified it now. "[Edited, 5 Jan 2021, to add: Many people have been confused about the statement about delta, so I must have worded it poorly. I’m not saying delta originated in a lab leak. I’m saying delta escaped from a lab late in 2021 where it was being used in research. It’s an example of a research-related lab leak.]"
ufo 5y ago
Another thing that the blog post appears to be unaware of is that the absence of samples showing the step-by-step evolution towards omicron doesn't mean that this didn't happen. A lot of places in the world don't have the resources to do covid testing and genomic surveillance.
- deleted 5y ago
  [deleted]
- mikeyouse 5y ago
  And even if they did do genomic analysis - it's entirely plausible the results are sitting in a hospital database somewhere instead of uploaded to the international gene surveillance repository.
  - Sevaris 5y ago
    Plausible, yes. If the data exists, it should be made public. The article still mostly just makes a hypothesis and makes the argument that this is something that should be seriously investigated, not that the author has determined without a doubt that this is a lab leak.
    - mikeyouse 5y ago
      Sure - but what are the chances that whichever hospitals did the sequencing even know they're in possession of the intermediate data? The OPs' method of "just asking questions" is really bad science and feels a whole lot like the God of the Gaps argument style that Creationists are so fond of using.
      - blix 5y ago
        I'm not sure the best way to judge the quality of a scientific argument is whether it 'feels like good science.' While the author is obviously only scratching the surface in an article targetted at non-scientists, the several PhDs he cites make decent arguments that are based on a little more than feelings. It would probably be more in line with the ideal of 'good science' to actually investigate the possibilities presented than dismiss them from emotional associations. It is a worrying trend that the way science feels is increasingly more important than the actual evidence (or lack thereof). One could even describe the current attitude towards science outside of scientitific institutions as religious.
BearOso 5y ago
That assumes the origin is Africa, but it could have just risen to prevalence there. We know the original COVID-19 was spreading around the world when at the time we thought it was mostly China. It needs only a 12-hour plane ride to get to the other side of the planet.
- throway453sde 5y ago
  With state actor funding it like 30 mins.
dljones 5y ago
The Nature article you mention says, "These data reveal strong selection on SARS-CoV-2 during convalescent plasma therapy, which is associated with the emergence of viral variants that show evidence of reduced susceptibility to neutralizing antibodies in immunosuppressed individuals." Fair enough. So is the hypothesis that this immune compromised person in SA was given a lot of antibodies over a long period of time, creating enough evolutionary pressure to create highly mutated forms of the virus? Such a person might end up with a highly mutated virus that is resistant to existing antibodies. Fair enough. That explains one of the four weirdnesses, and leaves three unexplained. Where are all the missing silent mutations (Weirdness 2)? If someone is followed medically and receiving all these treatments, did no one around them ever get sick with an intermediate variant? (Weirdness 1)? And what about the mouse-related mutations? (Weirdness 4) Did the viruses in the immune compromised person develop those mouse-related mutations independently? I find the "immune compromised person" hypothesis not a very parsimonious or compelling one, although if you can steelman it further, I'm all ears.
- trenchgun 5y ago
  Suggestion: The immunocompromised patient was a humanized mouse, who had HIV.
civilized 5y ago
Thank you for visiting HN, Alina! And I agree, natural evolution seems to make more sense. It's natural to wonder about lab-driven adaptation before COVID was unleashed on the human race... but once it had the entire human race to run its own "gain-of-function experiments", a lab hardly seems necessary anymore. The only question is why we didn't observe some steps on the way. And as you say, poorly monitored infections of the immunocompromised can easily explain this. It hardly seems necessary to posit nefarious secret labs when COVID is constantly spreading among billions of people, a significant fraction of whom are immunocompromised and chronically infected in minimally monitored areas.
- dljones 5y ago
  "poorly monitored infections of the immunocompromised can easily explain this. It hardly seems necessary to posit nefarious secret labs when COVID is constantly spreading among billions of people, a significant fraction of whom are immunocompromised and chronically infected in minimally monitored areas." How do "poorly monitored infections of the immunocompromised" explain weirdnesses 2 and 4? (Referring to the blog post under discussion) Did the blog author "posit nefarious secret labs"? Not that I'm seeing. There are labs all over the world doing things with SARS-CoV-2, probably for what they believe to be legitimate reasons. "Nefariousness" and "secrecy" is not in the article. "Nefariousness" and "secrecy" are not part of the hypothesis. "a significant fraction of whom are immunocompromised and chronically infected in minimally monitored areas": Contrary to people's seeming stereotypes about "Africa," South Africa monitors SARS-CoV-2 really well. The hypothetical immunocompromised person in Alina's discussion would not be someone untreated in some remote village, unnoticed for a year and a half. No, to get that level of immune evasion, Alina must be talking about someone who was being treated medically, with fancy treatments, and being monitored for a very long time. Well, for one thing: My first question is "Who is it? Who is this person who received all the convalescent plasma and all the different monoclonal antibodies for a year and half, in well-monitored South Africa?" But even if we don't know who this hypothetical person is, there are other problems: That person apparently never infected anyone else. And...that person in a year and a half never had any _intermediate_ viruses that infected anyone else either, to account for the gaps in the phylogenetic tree. And...that person had a set of mutations that you might expect to see in a humanized mouse (Weirdness 4). You see, then, that while this is all "possible" it's not very parsimonious. I think we do better to begin with parsimonious hypotheses and try to test those and rule those out. The lab leak is a parsimonious hypothesis -- but instead, mainstream people, for whatever reason, are portraying it as so far-fetched as not to merit consideration -- they would dismiss it, rather unscientifically, as if the hypothesis were really wild and not meriting consideration, like "Space aliens from planet X did it." Then, instead, they put forward hypotheses that are in fact way more far-fetched because they don't account for the data neatly, like "it was an immune compromised person" -- but the set of circumstances in which that would be true, while kinda-sorta possible, is much more unlikely than the circumstances of "lab leak." The failure of the scientific community to address this really makes no sense to me.
cyounkins 5y ago
Welcome to HN. Can you comment on the silent/functional mutation ratio weirdness?
abecedarius 5y ago
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.
  - 5y ago
scrumlord 5y ago
[flagged]
ZeroGravitas 5y ago
The other author of her book is Matt Ridley, the climate change skeptic. But you know what they say, even a person who makes money by telling obvious lies about science is right twice a day, so we should probably evaluate this from first principals as if it wasn't coming from a professional serial liar.
MauroIksem 5y ago
What makes you think omicron started in Africa? There is no proof of this at all.
hidudeurcool 5y ago
Abishek_Muthian 5y ago
> We know that there is a large immunocompromised population in Africa and that Covid-19 is rampant there. The fact that developed countries are hoarding vaccines, essential medications and are willing to let it go to garbage than to send it to those who need it there isn't helping either.

nnx 5y ago

"Omicron could have evolved over an entire year in an immunocompromised individual before finally infecting others" Is it likely that this infected person would not have started any detectable cluster this whole time? How do you explain the ratio of functional vs silent mutations?

ayjchan 5y ago
Evolution experiments in the lab mimic natural evolution. The ratio of functional vs silent mutations has also been used to characterize the evolution of viruses under natural selection.
- netizen-936824 5y ago
  According to the blog post that we are commenting on, there is a strange ratio of silent to functional mutations. How can this be accounted for if it was a natural course of evolution?
  - mbreese 5y ago
    Without looking more at the variants themselves and just going by the numbers in the post, it’s entirely plausible. It’s not likely, but plausible. Mainly because we are talking rare events. If the level of success is 33/3.5 (9.42), we’d expect that 4 (or less) silent variants would happen with a probability of ~ 0.042 (Poisson X <= 4). So, a bit more than a 4% chance. But with millions of people infected, this ratio of S/NS variations would still happen at a pretty high absolute number. Anytime you look at numbers like these, remember with a big denominator, even rare events are expected to happen.
    - sigotirandolas 5y ago
      If it was the case that the absolute number mattered, we would be able to sample different "Omicron-like" variants and observe various ratios such as 33N/10S, 33N/15S, etc. mutations. But according to the data presented, we don't: We only see a single (kind of) Omicron, the one with (about) 33N/4S mutations, presumably spilling over by a single event, so I don't see how your conclusion follows.
      - whynotqat 5y ago
        The sequence of mutations leading to Omicron is a one-off. Presumably, if there were a thousand variants with the same N mutations as Omicron, you'd see ratios like the ones you describe, but there's only one Omicron. The previous poster is pointing out it's plausible (~5% chance) that the path Omicron took has only 4 S mutations.
      - mbreese 5y ago
        There are two different (and independent) forces at play here: mutation and natural selection. The question is, given a known ratio of 3.5 NS/S, what is the likelihood that there would be only 4 non-silent mutations in any random strain (like omicron)? What the mutations are is irrelevant to this question. (I will use mutations and variants interchangeably below, but both mean a single change in the genetic code for the virus). Because we are dealing with integer counts, you can’t really have 3.5 mutations. You can only have 1, 2, 3, etc. So, 3.5 is just the average of all ratios. When dealing with count data like this, the Poisson distribution is what you use. When you have 33 non-silent mutations, you could have 1, 2, 3, etc silent mutations. We’d expect to see 9.4 (33/3.5), but you can’t have 0.4 of a mutation, only integers. There is a specific probability associated with each possible value (1,2,3…), and that can be calculated using the Poisson distribution. You are most likely to see 9 or 10, but all other values are also possible. To calculate how likely you are to see exactly 4 silent variants, you use the Poisson distribution. Again, we will expect that the rate should be 33/3.5 silent variants. In R, you’d do: dpois(4, 33/3.5) [1] 0.02647255 So, if we had 33 nonsilent variants, we’d expect to see exactly 4 silent variants 2.6% of the time. To put this into context, the most likely number of silent mutations is 9, which is expected only 13% of the time. We normally think in terms of “how likely is it that we’d see 4 or fewer mutations”, so we re-run the test for 0:4 and add them up: sum(dpois(0:4, 33/3.5)) [1] 0.04211515 Which is how I got a probability of 0.042. And which answers the specific question — if we see 33 non silent mutations in a strain, how likely is it that we would be 4 or fewer silent mutations in the same strain? 4.2% of the time. Given these numbers, I’d say it is plausible that you’d see this ratio of NS/S mutations occur naturally. It would be rare, but still somewhat expected to occur. Now this says nothing about what the mutations are, or why the omicron strain is so prevalent. This is where natural selection takes over and this combination of mutations is out competing all others.
rob_c 5y ago
More simply, I don't think people tend to remain infected (and infectious) for a whole year (not saying they can't just that this seems a farcical assumption) Yeah I agree with the going undetected too unless they're potentially asymptomatic (in which case why should we ever expect to find/treat them). All leading to the same response of you can't control highly transmissible virus(vurii) once they have infected a large amount of the population. (aka a 0 covid strategy is self-defeating)
- Taniwha 5y ago
  The mouse theory is interesting .... because omicron is more benign - one of the problems we have with covid is that because of all this modern medicine saving lots of lives (not enough though sadly) there's not a lot of evolutionary pressure to make things more benign. But if omicron has been in a wild mammal population without vaccination or hospitals then there might be more evolutionary pressure to become more benign. It's worth noting that some vaccines in the past have been 'live' vaccines - essentially viruses that get passed around with a sniffle or two but no more harm. This actually what we all hope omicron would be .... I can't see why we shouldn't give the virus a bit of a help along .... the right lab leak might be just what we all need

dqpb 5y ago

Can you also comment on her claim that Delta was a lab leak?

deleted 5y ago
[deleted]
Stevvo 5y ago
He doesn't claim the origin of Delta was a lab leak. He claims Delta leaked from a lab in Taiwan.
djrogers 5y ago
You misread that - there is no claim that delta was initially released by a lab, rather a the known fact that a lab studying delta had an accident. Read the links the author provided.
sammoody 5y ago
The claim wasn’t that Delta originated from a lab leak but rather that Delta happened to leak from a lab (after the point that it existed in the wild). Additionally, the phylogenetic points from the article would suggest that Delta is of natural origin
CamperBob2 5y ago
She, and yes, she does need to go back over that sentence and clarify it, because it does read that way.
- dqpb 5y ago
  Thank you, fixed it.
deleted 5y ago
[deleted]
dljones 5y ago
S/he clarified it now. "[Edited, 5 Jan 2021, to add: Many people have been confused about the statement about delta, so I must have worded it poorly. I’m not saying delta originated in a lab leak. I’m saying delta escaped from a lab late in 2021 where it was being used in research. It’s an example of a research-related lab leak.]"

ufo 5y ago

Another thing that the blog post appears to be unaware of is that the absence of samples showing the step-by-step evolution towards omicron doesn't mean that this didn't happen. A lot of places in the world don't have the resources to do covid testing and genomic surveillance.

deleted 5y ago
[deleted]
mikeyouse 5y ago
And even if they did do genomic analysis - it's entirely plausible the results are sitting in a hospital database somewhere instead of uploaded to the international gene surveillance repository.
- Sevaris 5y ago
  Plausible, yes. If the data exists, it should be made public. The article still mostly just makes a hypothesis and makes the argument that this is something that should be seriously investigated, not that the author has determined without a doubt that this is a lab leak.
  - mikeyouse 5y ago
    Sure - but what are the chances that whichever hospitals did the sequencing even know they're in possession of the intermediate data? The OPs' method of "just asking questions" is really bad science and feels a whole lot like the God of the Gaps argument style that Creationists are so fond of using.
    - blix 5y ago
      I'm not sure the best way to judge the quality of a scientific argument is whether it 'feels like good science.' While the author is obviously only scratching the surface in an article targetted at non-scientists, the several PhDs he cites make decent arguments that are based on a little more than feelings. It would probably be more in line with the ideal of 'good science' to actually investigate the possibilities presented than dismiss them from emotional associations. It is a worrying trend that the way science feels is increasingly more important than the actual evidence (or lack thereof). One could even describe the current attitude towards science outside of scientitific institutions as religious.

BearOso 5y ago

That assumes the origin is Africa, but it could have just risen to prevalence there. We know the original COVID-19 was spreading around the world when at the time we thought it was mostly China. It needs only a 12-hour plane ride to get to the other side of the planet.

throway453sde 5y ago
With state actor funding it like 30 mins.

dljones 5y ago

The Nature article you mention says, "These data reveal strong selection on SARS-CoV-2 during convalescent plasma therapy, which is associated with the emergence of viral variants that show evidence of reduced susceptibility to neutralizing antibodies in immunosuppressed individuals." Fair enough. So is the hypothesis that this immune compromised person in SA was given a lot of antibodies over a long period of time, creating enough evolutionary pressure to create highly mutated forms of the virus? Such a person might end up with a highly mutated virus that is resistant to existing antibodies. Fair enough. That explains one of the four weirdnesses, and leaves three unexplained. Where are all the missing silent mutations (Weirdness 2)? If someone is followed medically and receiving all these treatments, did no one around them ever get sick with an intermediate variant? (Weirdness 1)? And what about the mouse-related mutations? (Weirdness 4) Did the viruses in the immune compromised person develop those mouse-related mutations independently? I find the "immune compromised person" hypothesis not a very parsimonious or compelling one, although if you can steelman it further, I'm all ears.

trenchgun 5y ago
Suggestion: The immunocompromised patient was a humanized mouse, who had HIV.

civilized 5y ago

Thank you for visiting HN, Alina! And I agree, natural evolution seems to make more sense. It's natural to wonder about lab-driven adaptation before COVID was unleashed on the human race... but once it had the entire human race to run its own "gain-of-function experiments", a lab hardly seems necessary anymore. The only question is why we didn't observe some steps on the way. And as you say, poorly monitored infections of the immunocompromised can easily explain this. It hardly seems necessary to posit nefarious secret labs when COVID is constantly spreading among billions of people, a significant fraction of whom are immunocompromised and chronically infected in minimally monitored areas.

dljones 5y ago
"poorly monitored infections of the immunocompromised can easily explain this. It hardly seems necessary to posit nefarious secret labs when COVID is constantly spreading among billions of people, a significant fraction of whom are immunocompromised and chronically infected in minimally monitored areas." How do "poorly monitored infections of the immunocompromised" explain weirdnesses 2 and 4? (Referring to the blog post under discussion) Did the blog author "posit nefarious secret labs"? Not that I'm seeing. There are labs all over the world doing things with SARS-CoV-2, probably for what they believe to be legitimate reasons. "Nefariousness" and "secrecy" is not in the article. "Nefariousness" and "secrecy" are not part of the hypothesis. "a significant fraction of whom are immunocompromised and chronically infected in minimally monitored areas": Contrary to people's seeming stereotypes about "Africa," South Africa monitors SARS-CoV-2 really well. The hypothetical immunocompromised person in Alina's discussion would not be someone untreated in some remote village, unnoticed for a year and a half. No, to get that level of immune evasion, Alina must be talking about someone who was being treated medically, with fancy treatments, and being monitored for a very long time. Well, for one thing: My first question is "Who is it? Who is this person who received all the convalescent plasma and all the different monoclonal antibodies for a year and half, in well-monitored South Africa?" But even if we don't know who this hypothetical person is, there are other problems: That person apparently never infected anyone else. And...that person in a year and a half never had any _intermediate_ viruses that infected anyone else either, to account for the gaps in the phylogenetic tree. And...that person had a set of mutations that you might expect to see in a humanized mouse (Weirdness 4). You see, then, that while this is all "possible" it's not very parsimonious. I think we do better to begin with parsimonious hypotheses and try to test those and rule those out. The lab leak is a parsimonious hypothesis -- but instead, mainstream people, for whatever reason, are portraying it as so far-fetched as not to merit consideration -- they would dismiss it, rather unscientifically, as if the hypothesis were really wild and not meriting consideration, like "Space aliens from planet X did it." Then, instead, they put forward hypotheses that are in fact way more far-fetched because they don't account for the data neatly, like "it was an immune compromised person" -- but the set of circumstances in which that would be true, while kinda-sorta possible, is much more unlikely than the circumstances of "lab leak." The failure of the scientific community to address this really makes no sense to me.

cyounkins 5y ago

Welcome to HN. Can you comment on the silent/functional mutation ratio weirdness?

abecedarius 5y ago

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.
- 5y ago

scrumlord 5y ago

[flagged]

ZeroGravitas 5y ago

The other author of her book is Matt Ridley, the climate change skeptic. But you know what they say, even a person who makes money by telling obvious lies about science is right twice a day, so we should probably evaluate this from first principals as if it wasn't coming from a professional serial liar.

MauroIksem 5y ago

What makes you think omicron started in Africa? There is no proof of this at all.

hidudeurcool 5y ago

Abishek_Muthian 5y ago

> We know that there is a large immunocompromised population in Africa and that Covid-19 is rampant there. The fact that developed countries are hoarding vaccines, essential medications and are willing to let it go to garbage than to send it to those who need it there isn't helping either.