Slack / Private Message Drop — page 592

[2021-03-13 12:50:17] [Eddie Holmes] The branch lengths to our Black Death Yersinia pestis sequences have always been too short. I bet they had shitty lab safety protocols in the 14th century. [2021-03-13 16:53:15] [Robert Garry] Angie :shushing_face: [shared file(s): image.png] [2021-03-13 23:14:32] [Eddie Holmes] Nice one! The University of Sydney are NOT going to release those emails for the FOI request. They believe that they will lead to more online abuse and they have a duty of care not to let that happen. Good. The Right to Know people will probably challenge it so let's see what happens. [2021-03-14 07:08:34] [Robert Garry] We will have ample opportunity to reiterate that we deeply considered the "lab leak" hypothesis and found no evidence for it. RtK, Alina and DRASTIC will apply yet another layer of tinfoil and moan about yet another conspiracy and cover-up, but let them have at it. [2021-03-14 07:41:18] [Robert Garry] https://www.skynews.com.au/details/_6240160351001 tells you all you need to know about Josh Rogin - selling books making $ -same with head Parisite Jamie Metzl [2021-03-14 09:59:22] [Robert Garry] 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 09:59:46] [Robert 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 consensus at 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 mentioning is that the patient of sample Wuhan/WH04/2020 did not visit the market but stayed in a hotel nearby between 23 and 27 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 10:00:08] [Robert Garry] 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