Slack / Private Message Drop — page 162

explain (and I can't really fathom a lot of other explanations) why SARS-CoV-2 has not exploded in most of Africa. We're trying to get a dataset to post ASAP on Virological. [2020-09-12 07:27:46] [Robert Garry] Unrelated - I'm looking for a good current Nidovirus tree. Fig 7 here seems good but I'm the *last* to judge a tree: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6211748/ Other trees I've seen have artiviruses closer to toroviruses, but I think that's not correct. I've been looking at some of the spikes of non-CoV Nidoviruses - many have furin sites - some have YUGE mucin-like domains. S2s are more flu-like (one long helix/leash) than the CoV S2s. [2020-09-12 07:38:43] [Kristian Andersen] I'm hopeful vaccines will be able to get us to where we need to be immunity wise, just not so sure about natural immunity and how long-lasting it is - but even if it isn't, there's still no doubt that it's already helping to drive down cases in at-risk areas. Let's see what happens in NYC this late fall / winter... Looking forward to seeing those cross-reaction results - very interesting! [2020-09-12 16:31:15] [Eddie Holmes] I agree Kristian. Open questions. [2020-09-12 16:35:23] [Eddie Holmes] Bob - that nidovirus tree does look a little wobbly in places, esp. the long branches to GAV and PSCNV. I'm not sure of the true branching order. We've actually found a whole bunch of fish ronas. Both freshwater and marine. The tree is proving tricky to resolve though: [shared file(s): coronas_v2_gblocks_tree.pdf] [2020-09-13 05:52:29] [Robert Garry] THANKS - Fascinating - look forward to the manuscript. Interesting how the fish CoVs seem to my naive eye be in "basal" positions leading to the different genuses. Different than the antennaviruses? [2020-09-13 07:20:35] [Robert Garry] Just a note - had not seen the "letovirus." Not too deep a dive -a little occupied with Sally - but spike looks like your snake toroviruses [Guangdong red-banded snake torovirus] not as much like the serpentoviruses [love the name]. [2020-09-13 14:43:13] [Eddie Holmes] Yes, the fish viruses do no look basal but there is no bootstrap support in those parts of the tree and the branches are long so it's all a bit uncertain. Clearly, though, we only have a tiny sample of these viruses from nature. Letovirus was a new one on me as well. [2020-09-14 05:44:02] [Robert Garry] "tiny sample of these viruses from nature" Yes - limiting. But, I'm really curious how your snake toroviruses and serpentoviruses (that are pretty potent pathogens) fit into your tree above . Also that cluster with the pacific salmon nidovirus is really interesting. The salmon virus is the only one I found and it's spike is very interesting to say the least. Here's what i think is the pacific salmon nidovirus s1/s2 junction: ISEAINKVVEAFSHYS*RVTR*TV*RR*VITNTISA*RRRR*STDYGGGVHSN. Three-ish furin sites surrounded by predicted O-linked glycans. [2020-09-14 14:46:56] [Kristian Andersen] [thread - ID: 2020-09-14 14:46:56] Already getting some attention... The long awaited Yan Report. https://zenodo.org/record/4028830#.X1922Wj0nIW