While I have you all here does anyone have any issues with updating Holmes 2021 as follows: We are updating this post with four additional viruses: RpYN06, PrC31, RaTG15 and RsYN04 (Table 1, yellow highlights). TheseSARSr-CoVs are described in more detail in Zhou et al. (2021), Li et al. (2021) and Guo et al. (2021).```The Spike proteins of RpYN06 and PrC31 share 98.2% identity (99.8% similar) in a 1246 aa overlap. RpYN06 and PrC31 spike are highly similar to Guangdong (GD) pangolin coronavirus in the N-terminus of the protein. RpYN06 and PrC31 have 2 or 3 predicted O-linked glyans near the S1/S2 junction (Indel 8) confirming the highly variable nature of this domain. ```The Spike proteins of RatG15 and RsYN04 share 91.5% identity (96.5% similar) in a 1254 aa overlap. RatG15 and RsYN04 have an apparent insert of three amino acids CXK in the indel referred to here as 4a. Both viruses have acysteine 5 or 4 amino acids towards the N-terminus that is not present in other SARSr-CoVs located within aconserved sequence (underlined). The two additional cysteines may form a tight cysteine loop or potentially these cysteines could coordinate with histidines to bind a metal ion. Variants of interest B.1.427/429 have a mutation inspike W152C that creates an unpaired cysteine. This cysteine in the N-terminal domain of B.1.427/429 spike may coordinate with H69, H146 and H245 to bind a metal ion. RatG15 and RsYN04 have 3 or 4 predicted O-linked glycans near the S1/S2 junction (Indel 8).We note incongruence between the ORF1ab and Spike gene phylogenies of the SARS-CoV-2 related viruses suggesting widespread recombination. This is discussed in more detail in Zhou et al. (2021).*Figure 1 updated*. Amino acid alignment of the spike protein sequences of Cambodian, Thai Japanese and Chinese bat coronaviruses and other sarbecoviruses. The signal peptide, S1 subunit and part of S2 are shown. Positions of selected substitutions or deletions in 'variants of concern' are indicated. Added references:Li L-L, Wang J-L, Ma X-H, Li J-S, Yang X-F, Shi W-F and Duan Z-J. (2021). A novel SARS-CoV-2 related virus with complex recombination isolated from bats in Yunnan province, China bioRxiv 2021.03.17.435823; doi: https://doi.org/10.1101/2021.03.17.435823Guo H, Hu B, Si H-R, Zhu Y, Zhang W, Li B, Li A, Geng R, Lin H-F, Yang X-L, Zhou P and Shi Z-L. (2021).Identification of a novel lineage bat SARS-related coronaviruses that use bat ACE2 receptor. bioRxiv 2021.05.21.445091; doi: https://doi.org/10.1101/2021.05.21.445091Zhou H, Ji J, Chen X, Bi Y, Li J, Hu T, Hao Song H, Chen Y, Cui M, Zhang Y, Hughes AC, Holmes EC and ShiW. (2021).Identification of novel bat coronaviruses sheds light on the evolutionary origins of SARS-CoV-2 and related viruses. bioRxiv 2021.03.08.434390; doi: https://doi.org/10.1101/2021.03.08.434390 (Cell, in press). [shared file(s): image.png, image.png]