Slack / Private Message Drop — page 311

As for chronic infection - I can totally believe that. Here's a case we recently picked up - seven month of SARS2 infection with negative PCRs in-between. Sky high titers when picked up in late October (6 months after infection - he remained positive into December). [shared file(s): fake-reinfection.pdf] [2020-12-14 09:42:07] [Andrew Rambaut] I am normally fairly relaxed about RBD mutations - sure they happen and they may have antigenic effects but we can be pretty sure that they are not being antigenically selected for because there isn't enough standing immunity (in most places) or vaccination yet. BUT... this chronic infection scenario worries me because it may well have selected for escape from the immune response raised by the wild type virus (and thus the vaccine). And now it is circulating widely. [2020-12-14 09:44:03] [Andrew Rambaut] This is the set of mutations that are unique to this cluster: [shared file(s): image.png] [2020-12-14 09:44:10] [Kristian Andersen] Yes, agreed. Although reinfections also a concern here - I'm worried about selection in e.g., healthcare settings. Mink transmission also a concern here. My default is always "probably not an issue", but SARS2 really does appear to be pretty 'adaptable' and there's A LOT of transmission going on. [2020-12-14 09:44:35] [Andrew Rambaut] Here is the tree... [shared file(s): Kent_N501Y_836.ml_annotated_collapsed_tree.pdf] [2020-12-14 09:44:38] [Kristian Andersen] That's A LOT of mutations - all in one 'jump'? [2020-12-14 09:45:01] [Andrew Rambaut] There is one intermediate with some of the mutations... hence thought of a chronic shedder [2020-12-14 09:46:25] [Kristian Andersen] Yeah, the spike mutations would suggest chronic - but a lot of mutations outside spike too, which is a little peculiar to me. [2020-12-14 09:51:50] [Robert Garry] Chronic shedding with immune selection definitely a possibility. N501 is next to a short disordered region in S structures - a clear signal that it's an epitope. [2020-12-14 09:56:19] [Robert Garry] [thread - ID: 2020-12-14 09:56:19] P681H is also VERY interesting....how common is this? [2020-12-14 10:06:18] [Andrew Rambaut] There is an ORF8 stop at amino acid 27 and then a number appear after that suggesting it has become non functional.