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1. 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
2. 2021-03-14 09:59 Robert F. Garry open
   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]."
3. 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."
4. 2021-03-14 10:28 Robert F. Garry
   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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