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We know SARSCoV2 is not a chimeric virus because similar viruses have been identified from other locations, and the pattern-matching (sequence alignment) shows

by pcrh 3y ago

We know SARSCoV2 is not a chimeric virus because similar viruses have been identified from other locations, and the pattern-matching (sequence alignment) shows that SARSCoV2 does not have any insertions or deletions that have a different evolutionary origin compared to its close relatives.

tripletao 3y ago
That doesn't make any sense. I'm assuming by "chimera" that you mean, for example, the spike from natural virus A on the backbone of natural virus B. The WIV could have taken the spike from a virus similar to BANAL-20-52, the backbone from a different, unpublished virus that they'd sampled from nature, and a human-designed FCS. This is basically what they proposed in DEFUSE (in collaboration with Baric at UNC), and what this Times article is now saying they did internally after DEFUSE got rejected. Of course such a virus could also have evolved naturally by a similar path; lots of sarbecoviruses are just a single mutation away from that FCS, and perhaps there's some yet-unknown natural animal host where that gets selected for. The point is that no genomic evidence can distinguish between these two cases, though. For emphasis, it seems like you're assuming that we know all the natural viruses that the WIV was working with. Sampling of novel coronaviruses from nature was a core part of the WIV's research, so that's not a reasonable assumption. RaTG13 was sampled in 2013, but not fully published until 2020. At least one novel coronavirus was identified in contamination of rice samples sequenced on the same equipment that the WIV used: https://www.biorxiv.org/content/10.1101/2023.02.12.528210v2 https://www.biorxiv.org/content/10.1101/2023.02.12.528210v2 That's a merbecovirus, so it couldn't possibly have any relationship to SARS-CoV-2; but if they had one unpublished novel virus, then it's hard to reject the possibility that they had more.

by pcrh 3y ago

tripletao 3y ago

That doesn't make any sense. I'm assuming by "chimera" that you mean, for example, the spike from natural virus A on the backbone of natural virus B. The WIV could have taken the spike from a virus similar to BANAL-20-52, the backbone from a different, unpublished virus that they'd sampled from nature, and a human-designed FCS. This is basically what they proposed in DEFUSE (in collaboration with Baric at UNC), and what this Times article is now saying they did internally after DEFUSE got rejected. Of course such a virus could also have evolved naturally by a similar path; lots of sarbecoviruses are just a single mutation away from that FCS, and perhaps there's some yet-unknown natural animal host where that gets selected for. The point is that no genomic evidence can distinguish between these two cases, though. For emphasis, it seems like you're assuming that we know all the natural viruses that the WIV was working with. Sampling of novel coronaviruses from nature was a core part of the WIV's research, so that's not a reasonable assumption. RaTG13 was sampled in 2013, but not fully published until 2020. At least one novel coronavirus was identified in contamination of rice samples sequenced on the same equipment that the WIV used: https://www.biorxiv.org/content/10.1101/2023.02.12.528210v2 https://www.biorxiv.org/content/10.1101/2023.02.12.528210v2 That's a merbecovirus, so it couldn't possibly have any relationship to SARS-CoV-2; but if they had one unpublished novel virus, then it's hard to reject the possibility that they had more.