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Slack / Private Message Drop, p.592 [SLACK_000806] · slack_pm:msg:06194

Date: 2021-03-14 09:59
Type: chat message · slack
recipient: Kristian G. Andersen, Edward C. Holmes, Andrew Rambaut
speaker: Robert F. Garry
Topics: Natural origin / zoonotic spillover Furin cleavage site and molecular features Wuhan Institute of Virology collaboration

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This paragraphs sticks out "Next, to address the question of whether those two sites are evolutionarily conserved,we generated a phylogenetic tree of the seven patient samples linked with the Huanan Seafood Wholesale Market(hereinafter named as the Market) and the related coronaviruses from animal reservoirs by nucleotide sequence alignment [14]. Interestingly, we found the most related coronaviruses from pangolins and bats showed consensusat the orthologous sites of 8782 base as T and 28144 base as C. A complete linkage at both sites was also observed in these highly related coronaviruses including the most closely related bat coronavirus RaTG13 (96.2%identical) (Fig. 1a). This result suggests that the T8782 and C28144 genotype existing in 19.1% of SARS-CoV-2 genomes is more conserved during evolution as an ancestral genotype. On the opposite, the samples from the seven patients demonstrate identical concurrent mutations on those two sites (T8782C and C28144T).Coincidentally, all seven patients had worked or visited the Market before the onset of illness. Also worth mentioningis that the patient of sample Wuhan/WH04/2020 did not visit the market but stayed in a hotel nearby between 23 and27 December, 2019 [2,7]. Different from the aforementioned seven Market samples, the genotype of this patient sample showed no mutations on the two sites (i.e. T8782 and C28144), suggesting this patient had been infected from somewhere else in Wuhan instead of the Market. Noteworthily, the first sequenced SARS-CoV-2 genome, Wuhan-Hu-1 which was from a worker at the Market, also acquired the two point mutations [2]."

Extracted statements

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Statement	Grade	Attribution	Stance
This paragraphs sticks out "Next, to address the question of whether those two sites are evolutionarily conserved,we generated a phylogenetic tree of the seven patient samples linked with the Huanan Seafood Wholesale Market(hereinafter named as the Market) and the related coronaviruses from animal reservoirs by nucleotide sequence alignment [14].	own voice, substantive	speaker_own	asserts
Interestingly, we found the most related coronaviruses from pangolins and bats showed consensusat the orthologous sites of 8782 base as T and 28144 base as C.	quoted / not their view	quoted_external inside quotation marks	asserts

Statement

Grade

Attribution

Stance

own voice, substantive

speaker_own

asserts

Interestingly, we found the most related coronaviruses from pangolins and bats showed consensusat the orthologous sites of 8782 base as T and 28144 base as C.

quoted / not their view

quoted_external inside quotation marks

asserts

In context

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

2021-03-14 09:59 Robert F. Garry open

Since the market is likely to become a hotbed of interest over the next few weeks this recent analysis seems important: https://www.biorxiv.org/content/10.1101/2021.01.05.425339v3.full.pdf
2021-03-14 09:59 Robert F. Garry

This paragraphs sticks out "Next, to address the question of whether those two sites are evolutionarily conserved,we generated a phylogenetic tree of the seven patient samples linked with the Huanan Seafood Wholesale Market(hereinafter named as the Market) and the related coronaviruses from animal reservoirs by nucleotide sequence alignment [14]. Interestingly, we found the most related coronaviruses from pangolins and bats showed consensusat the orthologous sites of 8782 base as T and 28144 base as C. A complete linkage at both sites was also observed in these highly related coronaviruses including the most closely related bat coronavirus RaTG13 (96.2%identical) (Fig. 1a). This result suggests that the T8782 and C28144 genotype existing in 19.1% of SARS-CoV-2 genomes is more conserved during evolution as an ancestral genotype. On the opposite, the samples from the seven patients demonstrate identical concurrent mutations on those two sites (T8782C and C28144T).Coincidentally, all seven patients had worked or visited the Market before the onset of illness. Also worth mentioningis that the patient of sample Wuhan/WH04/2020 did not visit the market but stayed in a hotel nearby between 23 and27 December, 2019 [2,7]. Different from the aforementioned seven Market samples, the genotype of this patient sample showed no mutations on the two sites (i.e. T8782 and C28144), suggesting this patient had been infected from somewhere else in Wuhan instead of the Market. Noteworthily, the first sequenced SARS-CoV-2 genome, Wuhan-Hu-1 which was from a worker at the Market, also acquired the two point mutations [2]."
2021-03-14 10:00 Robert F. Garry open

And this one:"Early cases reported from Wuhan was extremely critical to answer how the outbreak took place at the very beginning. In this study, we were able to collate 34 viral genomes sampled from Wuhan between December 24,2019 to January 18, 2020, although the number of confirmed case by then were 121 according to Chinese officials (Fig. 4b). There were two distinct clusters of the 34 early samples. 30 out of 34 viral genomes were categorized into the M type (T8782C/C28144T) with a great extent of genetic diversity. Among these 30 genomes, 17 acquired extra mutations apart from two M type mutations resulting in 14 different genotypes. All of the 11 viral genomes linked with the Market (including 8 samples of patients who worked at the Market and 3 positive environmental samples collected from the Market) were in this cluster [7]. Although the M type was the dominant type during the early outbreak of COVID-19 in Wuhan, the non-Market genotypes from four patients forms the second cluster that alsoco-existed with M type cluster at that time. Two of them were ancestral type and the other two had their own unique mutations."
2021-03-14 10:28 Robert F. Garry open

https://www.biorxiv.org/content/10.1101/2020.08.27.270637v1.full.pdf The nS mutation T28144C: ORF8: T251C, L84S. Not trivial.

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