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Early Wuhan Coronavirus: 3 Extra Mutations Discovered
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[QUOTE="atyy, post: 6508405, member: 123698"] As pointed out in a [URL='https://twitter.com/stgoldst/status/1407494774236483586']tweet[/URL] by Stephen Goldstein, the original article by Wang et al (2020) [URL]https://onlinelibrary.wiley.com/doi/full/10.1002/smll.202002169[/URL] has been available since August 2020, and explicitly lists the key mutations in Table 1. Wang et al also explicitly discuss "Tang et al. (2020) have found that SARS-CoV-2 genomes evolved into two major types (designated L and S) that are well defined by two different SNPs at position 8782 (T8782C, synonymous) and 28144 (T28144C, Leu→Ser).[[URL='https://onlinelibrary.wiley.com/doi/full/10.1002/smll.202002169#smll202002169-bib-0037']37[/URL]] Based on the classification of 50 NTS positive samples (Experimental Section), 31 samples had a ≥10× depth at position 28144 (Table S5, Supporting Information), of which 22 (71.0%) were classified as L type, 8 (25.8%) were classified as S type, and one (3.2%) was uncertain ([B]Figure[/B] [URL='https://onlinelibrary.wiley.com/doi/full/10.1002/smll.202002169#smll202002169-fig-0007']7c[/URL]). These results were consistent with those previously reported,[[URL='https://onlinelibrary.wiley.com/doi/full/10.1002/smll.202002169#smll202002169-bib-0037']37[/URL]] which indicated that the L type was more prevalent in the early stages of the outbreak in Wuhan." The nomenclature used by Wang et al about L and S types is slightly different from that used by Rambaut et al (2020) [URL]https://www.nature.com/articles/s41564-020-0770-5[/URL]. However, the S and L seem to map onto Rambaut's A and B respectively. Rambaut had already commented that "Hence, although viruses from lineage B happen to have been sequenced and published first, it is likely (based on current data) that the most recent common ancestor (MRCA) of the SARS-CoV-2 phylogeny shares the same genome sequence as the early lineage A sequences (for example, Wuhan/WH04/2020)." As noted by [URL='https://virological.org/t/early-appearance-of-two-distinct-genomic-lineages-of-sars-cov-2-in-different-wuhan-wildlife-markets-suggests-sars-cov-2-has-a-natural-origin/691']Robert Garry[/URL], from the [URL='https://www.who.int/publications/i/item/who-convened-global-study-of-origins-of-sars-cov-2-china-part']WHO report[/URL], it seems that the Huanan market genomes are to date mainly from lineage B. It is uncertain whether Rambaut et al's conjecture that lineage A is earlier is correct. But it points to extant data already suggesting scenarios in which Huanan is not the origin. Further, as acknowledged by Bloom, one of the progenitors he suggests had already been suggested by [URL='https://academic.oup.com/mbe/advance-article/doi/10.1093/molbev/msab118/6257226']Kumar et al (2021)[/URL] by different methods. Kumar et al suggest "This progenitor genome differs from genomes of the first coronaviruses sampled in China by three variants, implying that none of the earliest patients represent the index case or gave rise to all the human infections." [/QUOTE]
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