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Slack / Private Message Drop, p.593 [SLACK_000807] · slack_pm:msg:06197

Date: 2021-03-14 11:38
Type: chat message · slack
recipient: Kristian G. Andersen, Robert F. Garry, Edward C. Holmes
speaker: Andrew Rambaut
Topics: Wuhan Institute of Virology collaboration

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From our nomenclature paper: https://www.nature.com/articles/s41564-020-0770-5 ```At the root of the phylogeny of SARS-CoV-2 are two lineages that we simply denote as lineages A and B. The earliest lineage A viruses, such as Wuhan/WH04/2020 (EPI_ISL_406801), sampled on 5 January 2020, share two nucleotides (positions 8,782 in ORF1ab and 28,144 in ORF8) with the closest known bat viruses (RaTG13 and RmYN02). Different nucleotides are present at those sites in viruses assigned to lineage B, of which Wuhan-Hu-1 (GenBank accession no. MN908947) sampled on 26 December 2019 is an early representative. Hence, although viruses from lineage B happen to have been sequenced and published first8,9,10, it is likely (based on current data) that the most recent common ancestor (MRCA) of the SARS-CoV-2 phylogeny shares the same genome sequenceas the early lineage A sequences (for example, Wuhan/WH04/2020). ```

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journal https://www.nature.com/articles/s41564-020-0770-5

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A single line often inverts meaning once you see what it answers, so neighbouring messages are always shown.

2021-03-14 11:38 Andrew Rambaut

From our nomenclature paper: https://www.nature.com/articles/s41564-020-0770-5 ```At the root of the phylogeny of SARS-CoV-2 are two lineages that we simply denote as lineages A and B. The earliest lineage A viruses, such as Wuhan/WH04/2020 (EPI_ISL_406801), sampled on 5 January 2020, share two nucleotides (positions 8,782 in ORF1ab and 28,144 in ORF8) with the closest known bat viruses (RaTG13 and RmYN02). Different nucleotides are present at those sites in viruses assigned to lineage B, of which Wuhan-Hu-1 (GenBank accession no. MN908947) sampled on 26 December 2019 is an early representative. Hence, although viruses from lineage B happen to have been sequenced and published first8,9,10, it is likely (based on current data) that the most recent common ancestor (MRCA) of the SARS-CoV-2 phylogeny shares the same genome sequenceas the early lineage A sequences (for example, Wuhan/WH04/2020). ```
2021-03-14 11:40 Andrew Rambaut open

But actually the haplotype that was WA1 in Seattle (a traveller from Wuhan) is one SNP closer to the bat viruses andI think that may be the earliest sampled haplotype.
2021-03-14 11:47 Robert F. Garry open

Yes - the authors rediscovered what you already taught. The smoking raccoon dog/grate data puts this into a somewhat new context.
2021-03-14 11:57 Robert F. Garry open

https://pubmed.ncbi.nlm.nih.gov/32912998/ So this paper takes on even more significance...

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