Slack / Private Message Drop — page 393

@Kristian Andersen the ruff draft I just posted might be a good place for you to insert a few sentences of some pointed language for the tinfoil hats. [2021-01-12 21:16:09] [Kristian Andersen] I'll take a look Bob - I assume on the GDoc? @Eddie Holmes - I forgot to mention - very interesting about the pangos! Looking forward to seeing some of that data (that'll be another :middle_finger:) [2021-01-12 21:19:44] [Robert Garry] Yes - that would be good if you want to post a Gdoc. Please use the edited version - the paste didn't go well the first time. [2021-01-12 21:22:36] [Robert Garry] Suffered a deletion - go figure... [2021-01-12 21:22:59] [Kristian Andersen] Hang on Bob - which "ruff draft" are you referring to? [2021-01-12 21:24:08] [Robert Garry] *This one in the thread Introduction* SAR-CoV-2 variants carrying multiple mutations have emerged around the world. B.1.1.7 in the United Kingdom acquired 17 mutations, including 8 in spike (Rambaut et al., 2020). B.1.351 in South Africa (Pond et al., 2020) and P.1 in Brazil [ref] represent additional emerging variants with multiple mutations. Among other mutations, B.1.1.7 and B.1.351 have deletions in spike. *Methods* The following sequences were included in this analysis: YP_009724390.1 surface glycoprotein [Severe acute respiratory syndrome coronavirus AAP13441.1 S protein [SARS coronavirus Urbani] AAU04646.1 spike glycoprotein [Civet SARS CoV 007/2004] ```QHR63300.2 spike glycoprotein [Bat coronavirus RaTG13]``` Spike amino acid sequences were aligned using Clustal Omega (Sievers et al., 2011). Figure 1. Amino acid alignment of SARS-CoV, SARS-CoV-2, RatG13 BatCoV spikes. Only part of S2 is shown. The remainder of the alignment does not have additional insertions or deletions. *Results* Divergence of the SARS-CoV and SARS-CoV2 appears to involve insertion of several short sequences in spike (Fig. 1). Except for the insertion that generated the furin cleavage site, the RatG13 BatCov spike has each of the SARS-CoV2 spike insertions. This suggests that a common ancestor of SARS-CoV2 and RatG13 BatCov had already obtained these insertions. The spike of SARS-CoV of civets does not have any insertions or deletions relative to spike of human SARS-CoV (not shown). The spikes of B.1.1.7 variants have deletions of amino acids H69 and V70. The spikes of B.1.351 variants have a deletion at amino acid Y145 and consecutive deletions at amino acids L241, L242 and A243. The deletions in these variants correspond to the apparent insertions that have occurred in the SARS-CoV-2 spike relative to the SARS-CoV spike. Thus, deletions in these emerging variants are in or near sequences that were inserted after the divergence of the embecovirus lineage that produced SARS-CoV-2 from the lineage that produced SARS-CoV. An insertion in or near the coding sequence for amino acid E484 of SARS-CoV-2 spike can also be inferred by the alignment of SARS-CoV, SARS-CoV2 and RatG13-Bat CoV spikes. E484K is one of several mutations of known biological importance that is present in the B.1.351 and P1 lineages of emerging SARS-CoV2 variants.