Slack / Private Message Drop — page 421

[2021-01-19 00:25:13] [Eddie Holmes] shared file(s): Pangos.pptx [2021-01-19 00:25:31] [Eddie Holmes] "1. Yes, deletion at 69,70. 2. Yes. no deletion but HL at 69,70. Note human WH1 is HV at 69,70. 3. GD pangolin-CoV one is actually more genetic distant to human WH1 than than GX pangolin-CoV does. It is not deletion but with TK at 69,70. 4.For the existence of two copies in either GX-P2V (isolate) or GX-P4L (lung original sample), I have checked the read assembly, none of them contain both copies." [2021-01-19 00:26:40] [Eddie Holmes] Of note, he did this completely independently of Bob...he just observed the same thing (but he's only looked at this site) [2021-01-19 00:43:08] [Andrew Rambaut] Email from Bogner after I queried the 10th Jan release of data on GISAID: [2021-01-19 00:43:08] [Andrew Rambaut] ```GISAID did indeed acknowledge a) the anniversary of learning that the respiratory illnesses reported in Wuhan were not caused by an influenza virus, but by a previously unknown human coronavirus, and b) the anniversary of GISAID releasing the first whole-genome sequences and metadata. The January 10th date is not a "mistake". Rather, reports that those genomes were first made available on GISAID on a later date are wrong. Ever since GISAID went live in May 2008, whenever there is word of a noteworthy event in which influenza-like symptoms are noted, GISAID goes into "first-responder-mode" and awaits feedback from its colleagues involved in the investigations. Last January was no exception. On January 8th 2020 at 3:38am PST, we received a message from George Gao, who I copy here, saying: "It's a novel coronavirus". As you know, it is typical that GISAID receives such an alert when a novel strain appears, as in 2009, when GISAID was advised by the US CDC of H1N1p, and in 2013, when the China CDC gave GISAID a heads up on the HPAI H7N9, and on numerous other occasions when it seemed an outbreak could occur. In almost all cases when we are alerted, GISAID receives the first data generated between 36-48 hours later, well prepared to process these data. George's alert gave us a chance to prepare, and gave our technical team time to set up an HTML area. We received the first 3x genomes and metadata in the afternoon of January 9th at 3:29 pm PST (2020-01-09 23:29 UTC). Two of these genomes, HB-01 and HB-05, were released on GISAID after processing, a little more than an hour later, at 4:41 pm PST and 4:44 pm PST (2020-01-10 0:41 UTC and 2020-01-10 0:44 UTC), respectively. GISAID understood at that time that it would be dealing with only a few hundred cases, yet by the time you and I spoke on January 17th, it was apparent to us both that this outbreak would likely see significantly more cases. Our GISAID technical team was immensely grateful for the technical advice you provided over the next several days, which helped them scale up and steadily improve the platform. You and I had subsequent interactions over the next few months. For example: on March 10th, when we discussed the inclusion of genomes with low coverage; on March 13th, when we debated which reference sequence from the early Wuhan cluster would be most suitable for use by GISAID, and on April 23rd, when you introduced your lineage naming system (which GISAID subsequently integrated). During all of our interactions, you never questioned that the first genomes were made available on GISAID on January 10th, even though that date was prominently displayed on the website and in the database, the entire time that our discussions were taking place. Wouldn't you have said something if our date was wrong? Not even Prof. Holmes, who wrote to my colleague on January 20th, passing on an update request of metadata for BetaCoV/Wuhan-Hu-1/2019, took issue with the dates of the first genomes, clearly visible in the database. To be clear Andrew; it is certainly not my intention to challenge your statement about the date and time, that Prof.