{"post_stream":{"posts":[{"id":1215,"name":"Andrew Rambaut","username":"arambaut","avatar_template":"/user_avatar/virological.org/arambaut/{size}/425_2.png","created_at":"2020-02-16T23:46:02.139Z","cooked":"\u003cp\u003eThis paper has now been published here: \u003ca href=\"https://www.nature.com/articles/s41591-020-0820-9\"\u003ehttps://www.nature.com/articles/s41591-020-0820-9\u003c/a\u003e\u003cbr\u003e\nThe published version includes updates and corrections and should be considered the final version (it is also Open Access).\u003c/p\u003e\n\u003ch2\u003eThe Proximal Origin of SARS-CoV-2\u003c/h2\u003e\n\u003cp\u003eKristian G. Andersen\u003csup\u003e1,2*\u003c/sup\u003e, Andrew Rambaut\u003csup\u003e3\u003c/sup\u003e, W. Ian Lipkin\u003csup\u003e4\u003c/sup\u003e, Edward C. Holmes\u003csup\u003e5\u003c/sup\u003e \u0026amp; Robert F. Garry\u003csup\u003e6,7\u003c/sup\u003e\u003c/p\u003e\n\u003cp\u003e\u003csup\u003e1\u003c/sup\u003eDepartment of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA.\u003c/p\u003e\n\u003cp\u003e\u003csup\u003e2\u003c/sup\u003eScripps Research Translational Institute, La Jolla, CA 92037, USA.\u003c/p\u003e\n\u003cp\u003e\u003csup\u003e3\u003c/sup\u003eInstitute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK.\u003c/p\u003e\n\u003cp\u003e\u003csup\u003e4\u003c/sup\u003eCenter for Infection and Immunity, Mailman School of Public Health of Columbia University, New York, New York, USA.\u003c/p\u003e\n\u003cp\u003e\u003csup\u003e5\u003c/sup\u003eMarie Bashir Institute for Infectious Diseases and Biosecurity, School of Life and Environmental Sciences and School of Medical Sciences, The University of Sydney, Sydney, Australia.\u003c/p\u003e\n\u003cp\u003e\u003csup\u003e6\u003c/sup\u003eTulane University, School of Medicine, Department of Microbiology and Immunology, New Orleans, LA, USA.\u003c/p\u003e\n\u003cp\u003e\u003csup\u003e7\u003c/sup\u003eZalgen Labs, LCC, Germantown, MD, USA.\u003c/p\u003e\n\u003cp\u003e\u003csup\u003e*\u003c/sup\u003e\u003cstrong\u003eCorresponding author:\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003e\u003cem\u003eKristian G. Andersen\u003c/em\u003e\u003cbr\u003e\n\u003cem\u003eDepartment of Immunology and Microbiology,\u003c/em\u003e\u003cbr\u003e\n\u003cem\u003eThe Scripps Research Institute,\u003c/em\u003e\u003cbr\u003e\n\u003cem\u003eLa Jolla, CA 92037,\u003c/em\u003e\u003cbr\u003e\n\u003cem\u003eUSA.\u003c/em\u003e\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eSince the first reports of a novel pneumonia (COVID-19) in Wuhan city, Hubei province, China there has been considerable discussion and uncertainty over the origin of the causative virus, SARS-CoV-2. Infections with SARS-CoV-2 are now widespread in China, with cases in every province. As of 14 February 2020, 64,473 such cases have been confirmed, with 1,384 deaths attributed to the virus. These official case numbers are likely an underestimate because of limited reporting of mild and asymptomatic cases, and the virus is clearly capable of efficient human-to-human transmission. Based on the possibility of spread to countries with weaker healthcare systems, the World Health Organization has declared the COVID-19 outbreak a Public Health Emergency of International Concern (PHEIC). There are currently neither vaccines nor specific treatments for this disease.\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eSee here for full text: \u003ca href=\"https://www.nature.com/articles/s41591-020-0820-9\"\u003ehttps://www.nature.com/articles/s41591-020-0820-9\u003c/a\u003e\u003c/p\u003e","post_number":1,"post_type":1,"posts_count":5,"updated_at":"2020-04-16T08:26:09.862Z","reply_count":2,"reply_to_post_number":null,"quote_count":0,"incoming_link_count":84552,"reads":71,"readers_count":70,"score":422756.2,"yours":false,"topic_id":398,"topic_slug":"the-proximal-origin-of-sars-cov-2","display_username":"Andrew Rambaut","primary_group_name":null,"flair_name":null,"flair_url":null,"flair_bg_color":null,"flair_color":null,"flair_group_id":null,"badges_granted":[],"version":10,"can_edit":false,"can_delete":false,"can_recover":false,"can_see_hidden_post":false,"can_wiki":false,"link_counts":[{"url":"https://www.nature.com/articles/s41591-020-0820-9","internal":false,"reflection":false,"clicks":8622},{"url":"https://virological.org/t/ncovs-relationship-to-bat-coronaviruses-recombination-signals-no-snakes-no-evidence-the-2019-ncov-lineage-is-recombinant/331/23","internal":true,"reflection":true,"title":"nCoV's relationship to bat coronaviruses \u0026 recombination signals (no snakes) - no evidence the 2019-nCoV lineage is recombinant","clicks":17}],"read":true,"user_title":"ARTIC Network","title_is_group":false,"bookmarked":false,"actions_summary":[{"id":2,"count":1}],"moderator":true,"admin":true,"staff":true,"user_id":1,"hidden":false,"trust_level":4,"deleted_at":null,"user_deleted":false,"edit_reason":null,"can_view_edit_history":false,"wiki":false,"post_url":"/t/the-proximal-origin-of-sars-cov-2/398/1","can_accept_answer":false,"can_unaccept_answer":false,"accepted_answer":false,"topic_accepted_answer":null,"can_vote":false},{"id":1216,"name":"profbillg1901","username":"profbillg1901","avatar_template":"/letter_avatar_proxy/v4/letter/p/eb8c5e/{size}.png","created_at":"2020-02-17T15:51:19.844Z","cooked":"\u003cp\u003eI concur with this analysis at the amino acid level. I would add, however, that even if two virus isolates have an IDENTICAL amino acid sequence, that would not automatically make one the origin of the other. In my post 10 days ago, \u003ca href=\"//virological.org/t/tackling-rumors-of-a-suspicious-origin-of-ncov2019/384/2\"\u003eTackling Rumors of a Suspicious Origin of nCoV2019\u003c/a\u003e , I showed that mutations in the 3rd wobble base in an otherwise conserved region accumulate as to make seemingly identical viruses very much separated in time – indeed over decades.\u003c/p\u003e\n\u003cp\u003eIt is time to leave playing “who’s ur daddy” to daytime television. No known viral RNA sequence is the daddy of SARS-CoV-2. No match. If it doesn’t fit, you must acquit. It is all bat guano. Whatever analogy you like. A thrust of distrust and recrimination is not the path to protecting the planet from a viral catastrophe.\u003c/p\u003e\n\u003cp\u003eBill Gallaher\u003c/p\u003e","post_number":2,"post_type":1,"posts_count":5,"updated_at":"2020-02-17T15:51:19.844Z","reply_count":0,"reply_to_post_number":null,"quote_count":0,"incoming_link_count":520,"reads":56,"readers_count":55,"score":2611.2,"yours":false,"topic_id":398,"topic_slug":"the-proximal-origin-of-sars-cov-2","display_username":"profbillg1901","primary_group_name":null,"flair_name":null,"flair_url":null,"flair_bg_color":null,"flair_color":null,"flair_group_id":null,"badges_granted":[],"version":1,"can_edit":false,"can_delete":false,"can_recover":false,"can_see_hidden_post":false,"can_wiki":false,"link_counts":[{"url":"http://virological.org/t/tackling-rumors-of-a-suspicious-origin-of-ncov2019/384/2","internal":true,"reflection":false,"title":"Tackling Rumors of a Suspicious Origin of nCoV2019","clicks":0}],"read":true,"user_title":null,"bookmarked":false,"actions_summary":[],"moderator":false,"admin":false,"staff":false,"user_id":56,"hidden":false,"trust_level":1,"deleted_at":null,"user_deleted":false,"edit_reason":null,"can_view_edit_history":false,"wiki":false,"post_url":"/t/the-proximal-origin-of-sars-cov-2/398/2","can_accept_answer":false,"can_unaccept_answer":false,"accepted_answer":false,"topic_accepted_answer":null},{"id":1219,"name":"Kristian Andersen","username":"Kristian_Andersen","avatar_template":"/user_avatar/virological.org/kristian_andersen/{size}/521_2.png","created_at":"2020-02-19T00:36:09.091Z","cooked":"\u003cp\u003eMandarin translation thanks to CHEN Guo from the Center for Infection and Immunity in the Columbia Mailman School of Public Health.\u003c/p\u003e\n\u003cp\u003e\u003ca class=\"attachment\" href=\"/uploads/short-url/dHpDmgjWKLNlBztUWteEJZq4Pvw.pdf\"\u003eThe Proximal Origin of SARS-CoV-2_ChineseSummary.pdf\u003c/a\u003e (198.5 KB)\u003c/p\u003e","post_number":3,"post_type":1,"posts_count":5,"updated_at":"2020-02-19T00:36:09.091Z","reply_count":0,"reply_to_post_number":null,"quote_count":0,"incoming_link_count":233,"reads":50,"readers_count":49,"score":1175.0,"yours":false,"topic_id":398,"topic_slug":"the-proximal-origin-of-sars-cov-2","display_username":"Kristian Andersen","primary_group_name":null,"flair_name":null,"flair_url":null,"flair_bg_color":null,"flair_color":null,"flair_group_id":null,"badges_granted":[],"version":1,"can_edit":false,"can_delete":false,"can_recover":false,"can_see_hidden_post":false,"can_wiki":false,"read":true,"user_title":null,"bookmarked":false,"actions_summary":[],"moderator":true,"admin":true,"staff":true,"user_id":2,"hidden":false,"trust_level":4,"deleted_at":null,"user_deleted":false,"edit_reason":null,"can_view_edit_history":false,"wiki":false,"post_url":"/t/the-proximal-origin-of-sars-cov-2/398/3","can_accept_answer":false,"can_unaccept_answer":false,"accepted_answer":false,"topic_accepted_answer":null},{"id":1299,"name":"Yutao Fu","username":"fuyutao","avatar_template":"/letter_avatar_proxy/v4/letter/f/858c86/{size}.png","created_at":"2020-03-16T00:32:40.076Z","cooked":"\u003caside class=\"quote no-group quote-modified\" data-username=\"arambaut\" data-post=\"1\" data-topic=\"398\"\u003e\n\u003cdiv class=\"title\"\u003e\n\u003cdiv class=\"quote-controls\"\u003e\u003c/div\u003e\n\u003cimg loading=\"lazy\" alt=\"\" width=\"24\" height=\"24\" src=\"https://virological.org/user_avatar/virological.org/arambaut/48/425_2.png\" class=\"avatar\"\u003e arambaut:\u003c/div\u003e\n\u003cblockquote\u003e\n\u003cp\u003eFor a precursor virus to acquire the polybasic cleavage site and mutations in the spike protein suitable for human ACE2 receptor binding, an animal host would likely have to have a high population density – to allow natural selection to proceed efficiently – and an ACE2 gene that is similar to the human orthologue.\u003c/p\u003e\n\u003c/blockquote\u003e\n\u003c/aside\u003e\n\u003cp\u003eThere is one animal species meeting these 3 criteria:\u003c/p\u003e\n\u003col\u003e\n\u003cli\u003eThe species is common with a high population density, some running in the wild;\u003c/li\u003e\n\u003cli\u003eBLASTing the short SARS-CoV-2 furin cleavage site PRRARS against coronavirus, there is only one species ranked above bat, and the hit is also in spike protein;\u003c/li\u003e\n\u003cli\u003eIn a peer reviewed article (\u003ca href=\"https://onlinelibrary.wiley.com/doi/10.1002/jmv.25726\" rel=\"noopener nofollow ugc\"\u003ehttps://onlinelibrary.wiley.com/doi/10.1002/jmv.25726\u003c/a\u003e), the species’ key ACE2 amino acids are closer to human than between pangolin and human. Another paper in preprint (\u003ca href=\"https://www.researchgate.net/publication/339741547_Predicting_the_Angiotensin_Converting_Enzyme_2_ACE2_Utilizing_Capability_as_the_Receptor_of_SARS-CoV-2\" rel=\"noopener nofollow ugc\"\u003ehttps://www.researchgate.net/publication/339741547_Predicting_the_Angiotensin_Converting_Enzyme_2_ACE2_Utilizing_Capability_as_the_Receptor_of_SARS-CoV-2\u003c/a\u003e) predicts the species’ ACE2 can bind SARS-CoV-2.\u003c/li\u003e\n\u003c/ol\u003e","post_number":4,"post_type":1,"posts_count":5,"updated_at":"2020-03-16T00:34:25.633Z","reply_count":0,"reply_to_post_number":null,"quote_count":1,"incoming_link_count":359,"reads":37,"readers_count":36,"score":1802.4,"yours":false,"topic_id":398,"topic_slug":"the-proximal-origin-of-sars-cov-2","display_username":"Yutao Fu","primary_group_name":null,"flair_name":null,"flair_url":null,"flair_bg_color":null,"flair_color":null,"flair_group_id":null,"badges_granted":[],"version":1,"can_edit":false,"can_delete":false,"can_recover":false,"can_see_hidden_post":false,"can_wiki":false,"link_counts":[{"url":"https://onlinelibrary.wiley.com/doi/10.1002/jmv.25726","internal":false,"reflection":false,"clicks":551},{"url":"https://www.researchgate.net/publication/339741547_Predicting_the_Angiotensin_Converting_Enzyme_2_ACE2_Utilizing_Capability_as_the_Receptor_of_SARS-CoV-2","internal":false,"reflection":false,"clicks":405}],"read":true,"user_title":null,"bookmarked":false,"actions_summary":[],"moderator":false,"admin":false,"staff":false,"user_id":198,"hidden":false,"trust_level":1,"deleted_at":null,"user_deleted":false,"edit_reason":null,"can_view_edit_history":false,"wiki":false,"post_url":"/t/the-proximal-origin-of-sars-cov-2/398/4","can_accept_answer":false,"can_unaccept_answer":false,"accepted_answer":false,"topic_accepted_answer":null},{"id":1303,"name":"Xiaowei Jiang","username":"xiaowei.jiang","avatar_template":"/letter_avatar_proxy/v4/letter/x/4bbf92/{size}.png","created_at":"2020-03-18T02:04:46.971Z","cooked":"\u003caside class=\"quote no-group quote-modified\" data-username=\"arambaut\" data-post=\"1\" data-topic=\"398\"\u003e\n\u003cdiv class=\"title\"\u003e\n\u003cdiv class=\"quote-controls\"\u003e\u003c/div\u003e\n\u003cimg loading=\"lazy\" alt=\"\" width=\"24\" height=\"24\" src=\"https://virological.org/user_avatar/virological.org/arambaut/48/425_2.png\" class=\"avatar\"\u003e arambaut:\u003c/div\u003e\n\u003cblockquote\u003e\n\u003cp\u003eglycan\u003c/p\u003e\n\u003c/blockquote\u003e\n\u003c/aside\u003e\n\u003cp\u003eI noticed in the published version on Nature Med it has an extended discussion on the “glycan shield”. The analysis done in this correspondence only refers to one O-linked glycan motif. The “glycan shield” mostly refers to N-linked glycans, which are quite abundant in beta coronavirus and are the major constituents of the “glycan shield”. So there is a big jump in the discussion which may lead to confusion. I just post an initial analysis here in collaboration with David Robertson, and will post a full analysis on this later. \u003ca class=\"attachment\" href=\"/uploads/short-url/uWp3AW1dsBsDYNgjtOz32upPcPo.pdf\"\u003e02_surface.pdf\u003c/a\u003e (170.9 KB) \u003ca class=\"attachment\" href=\"/uploads/short-url/g1DEPAlAKmzcCx04Sbg0GV2o3Fz.pdf\"\u003e02_surface_wuhan_ref_O_linked.pdf\u003c/a\u003e (121.3 KB)\u003c/p\u003e","post_number":5,"post_type":1,"posts_count":5,"updated_at":"2020-03-18T02:38:33.431Z","reply_count":0,"reply_to_post_number":null,"quote_count":1,"incoming_link_count":498,"reads":30,"readers_count":29,"score":2486.0,"yours":false,"topic_id":398,"topic_slug":"the-proximal-origin-of-sars-cov-2","display_username":"Xiaowei Jiang","primary_group_name":null,"flair_name":null,"flair_url":null,"flair_bg_color":null,"flair_color":null,"flair_group_id":null,"badges_granted":[],"version":4,"can_edit":false,"can_delete":false,"can_recover":false,"can_see_hidden_post":false,"can_wiki":false,"link_counts":[{"url":"https://virological.org/t/tackling-rumors-of-a-suspicious-origin-of-ncov2019/384/15","internal":true,"reflection":true,"title":"Tackling Rumors of a Suspicious Origin of 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