Slack / Private Message Drop — page 392

Btw all this recent evolution observed in SARS-CoV-2 really is a giant :middle_finger:to all the tinfoil hats out there. [2021-01-12 21:09:16] [Robert Garry] [thread - ID: 2021-01-12 15:14:55] @Robert Garry *@channel Ruff draft: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. *Discussion* The generation of insertions or deletions (indels) in or near the furin cleavage site is a frequent occurrence during coronavirus evolution (Gallaher and Garry, 2020). Passage of SARS-CoV-2 in Vero cells can result in deletion of either the furin cleavage site or a sequence immediately adjacent to it [ref]. Deletions in the spike genes of recent emerging SARS-CoV-2 variants occur preferentially in mutational hotspots that have generated insertions during embecovirus evolution. Another insertion adds amino acid E484 that is subject to further mutation during extended human-to-human passage, and which may impart enhanced fitness and/or immune escape. A caveat of the current analysis is that the amino acid alignments are not intended to precisely represent the underlying nucleotide alignments. A previous analysis suggested that the insertion generating the furin cleavage site in SARS-CoV-2 spike is out-of-frame. The molecular mechanism(s) that generated the insertions present in SASR-CoV-2 spike cannot be determined by sequence analysis. Although coronaviruses have a proof-reading apparatus, their genomes remain subject to recombination as well as copy-choice transcriptional errors [refs]. *Conclusions* It will be important to elucidate genomic features that favor indel formation and to define molecular processes occuring during coronavirus genome replication that produce indels. [2021-01-12 21:13:14] [Robert Garry]