{"post_stream":{"posts":[{"id":927,"name":"edward_holmes","username":"edward_holmes","avatar_template":"/user_avatar/virological.org/edward_holmes/{size}/191_2.png","created_at":"2020-01-11T01:05:33.105Z","cooked":"\u003cblockquote\u003e\n\u003cp\u003e10th January 2020\u003cbr\u003e\nThis posting is communicated by Edward C. Holmes, University of Sydney on behalf of the consortium led by Professor Yong-Zhen Zhang, Fudan University, Shanghai\u003c/p\u003e\n\u003c/blockquote\u003e\n\u003cp\u003eThe Shanghai Public Health Clinical Center \u0026amp; School of Public Health, in collaboration with the Central Hospital of Wuhan, Huazhong University of Science and Technology, the Wuhan Center for Disease Control and Prevention, the National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control, and the University of Sydney, Sydney, Australia is releasing a coronavirus genome from a case of a respiratory disease from the Wuhan outbreak. The sequence has also been deposited on GenBank (\u003ca href=\"https://www.ncbi.nlm.nih.gov/nuccore/MN908947\"\u003eaccession MN908947\u003c/a\u003e) and will be released as soon as possible.\u003c/p\u003e\n\u003cp\u003eUpdate: \u003ca href=\"https://www.ncbi.nlm.nih.gov/nuccore/MN908947\"\u003eThis genome is now available on GenBank and an updated version has been posted\u003c/a\u003e.\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eDisclaimer:\u003c/strong\u003e\u003cbr\u003e\nPlease feel free to download, share, use, and analyze this data\u003csup\u003e1\u003c/sup\u003e. We ask that you communicate with us if you wish to publish results that use these data in a journal. If you have any other questions –then please also contact us directly.\u003c/p\u003e\n\u003cp\u003eProfessor Yong-Zhen Zhang,\u003cbr\u003e\nShanghai Public Health Clinical Center \u0026amp; School of Public Health,\u003cbr\u003e\nFudan University,\u003cbr\u003e\nShanghai, China.\u003c/p\u003e\n\u003cp\u003e\u003ca href=\"mailto:zhangyongzhen@shphc.org.cn\"\u003eemail: zhangyongzhen@shphc.org.cn\u003c/a\u003e\u003c/p\u003e\n\u003chr\u003e\n\u003csup\u003e1\u003c/sup\u003e We know that “data” is plural but we were in a hurry.","post_number":1,"post_type":1,"posts_count":28,"updated_at":"2022-01-27T20:45:01.465Z","reply_count":0,"reply_to_post_number":null,"quote_count":0,"incoming_link_count":106205,"reads":80,"readers_count":79,"score":530451.0,"yours":false,"topic_id":319,"topic_slug":"novel-2019-coronavirus-genome","display_username":"edward_holmes","primary_group_name":null,"flair_name":null,"flair_url":null,"flair_bg_color":null,"flair_color":null,"flair_group_id":null,"badges_granted":[],"version":8,"can_edit":false,"can_delete":false,"can_recover":false,"can_see_hidden_post":false,"can_wiki":false,"link_counts":[{"url":"https://www.ncbi.nlm.nih.gov/nuccore/MN908947","internal":false,"reflection":false,"title":"Wuhan seafood market pneumonia virus isolate Wuhan-Hu-1, complete geno - Nucleotide - NCBI","clicks":35764},{"url":"https://virological.org/t/initial-assessment-of-the-ability-of-published-coronavirus-primers-sets-to-detect-the-wuhan-coronavirus/321","internal":true,"reflection":true,"title":"Initial assessment of the ability of published coronavirus primers sets to detect the Wuhan coronavirus","clicks":59},{"url":"https://virological.org/t/sars-cov-2-diversity-in-uganda-december-2020/571","internal":true,"reflection":true,"title":"SARS-CoV-2 diversity in Uganda, December, 2020","clicks":13}],"read":true,"user_title":"","bookmarked":false,"actions_summary":[{"id":2,"count":2}],"moderator":false,"admin":false,"staff":false,"user_id":57,"hidden":false,"trust_level":3,"deleted_at":null,"user_deleted":false,"edit_reason":null,"can_view_edit_history":false,"wiki":false,"post_url":"/t/novel-2019-coronavirus-genome/319/1","can_accept_answer":false,"can_unaccept_answer":false,"accepted_answer":false,"topic_accepted_answer":null,"can_vote":false},{"id":928,"name":"Andrew Rambaut","username":"arambaut","avatar_template":"/user_avatar/virological.org/arambaut/{size}/425_2.png","created_at":"2020-01-12T12:14:59.344Z","cooked":"\u003cp\u003eFive new genomes have been deposited in the GISAID platform:\u003cbr\u003e\n\u003ca href=\"https://gisaid.org/CoV2020\" class=\"onebox\" target=\"_blank\" rel=\"noopener\"\u003ehttps://gisaid.org/CoV2020\u003c/a\u003e\u003c/p\u003e\n\u003cp\u003e\u003cdiv class=\"lightbox-wrapper\"\u003e\u003ca class=\"lightbox\" href=\"https://virological.org/uploads/default/original/1X/5cff42d15a6560287e0b3b10c9192a7130a659f5.png\" data-download-href=\"https://virological.org/uploads/default/5cff42d15a6560287e0b3b10c9192a7130a659f5\" title=\"image\"\u003e\u003cimg src=\"https://virological.org/uploads/default/optimized/1X/5cff42d15a6560287e0b3b10c9192a7130a659f5_2_690x245.png\" alt=\"image\" data-base62-sha1=\"dgGOVIt88trE1qziIAeA6nVbBeB\" width=\"690\" height=\"245\" srcset=\"https://virological.org/uploads/default/optimized/1X/5cff42d15a6560287e0b3b10c9192a7130a659f5_2_690x245.png, https://virological.org/uploads/default/optimized/1X/5cff42d15a6560287e0b3b10c9192a7130a659f5_2_1035x367.png 1.5x, https://virological.org/uploads/default/optimized/1X/5cff42d15a6560287e0b3b10c9192a7130a659f5_2_1380x490.png 2x\" data-dominant-color=\"DBDFE6\"\u003e\u003cdiv class=\"meta\"\u003e\n\u003csvg class=\"fa d-icon d-icon-far-image svg-icon\" aria-hidden=\"true\"\u003e\u003cuse href=\"#far-image\"\u003e\u003c/use\u003e\u003c/svg\u003e\u003cspan class=\"filename\"\u003eimage\u003c/span\u003e\u003cspan class=\"informations\"\u003e1954×694 161 KB\u003c/span\u003e\u003csvg class=\"fa d-icon d-icon-discourse-expand svg-icon\" aria-hidden=\"true\"\u003e\u003cuse href=\"#discourse-expand\"\u003e\u003c/use\u003e\u003c/svg\u003e\n\u003c/div\u003e\u003c/a\u003e\u003c/div\u003e\u003c/p\u003e","post_number":2,"post_type":1,"posts_count":28,"updated_at":"2020-01-12T12:14:59.344Z","reply_count":0,"reply_to_post_number":null,"quote_count":0,"incoming_link_count":1050,"reads":71,"readers_count":70,"score":5259.2,"yours":false,"topic_id":319,"topic_slug":"novel-2019-coronavirus-genome","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":1,"can_edit":false,"can_delete":false,"can_recover":false,"can_see_hidden_post":false,"can_wiki":false,"link_counts":[{"url":"https://gisaid.org/CoV2020","internal":false,"reflection":false,"clicks":4100}],"read":true,"user_title":"ARTIC Network","title_is_group":false,"bookmarked":false,"actions_summary":[],"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/novel-2019-coronavirus-genome/319/2","can_accept_answer":false,"can_unaccept_answer":false,"accepted_answer":false,"topic_accepted_answer":null},{"id":929,"name":"Trevor Bedford","username":"trvrb","avatar_template":"/user_avatar/virological.org/trvrb/{size}/507_2.png","created_at":"2020-01-14T00:36:27.267Z","cooked":"\u003cp\u003eA preliminary phylogenetic analysis of these 6 genomes is available at \u003ca href=\"https://nextstrain.org/groups/blab/sars-like-cov\" rel=\"nofollow noopener\"\u003ehttps://nextstrain.org/groups/blab/sars-like-cov\u003c/a\u003e. The pipeline to generate this analysis is openly available at \u003ca href=\"https://github.com/blab/sars-like-cov\" rel=\"nofollow noopener\"\u003ehttps://github.com/blab/sars-like-cov\u003c/a\u003e.\u003c/p\u003e","post_number":3,"post_type":1,"posts_count":28,"updated_at":"2020-01-14T00:36:27.267Z","reply_count":0,"reply_to_post_number":null,"quote_count":0,"incoming_link_count":177,"reads":63,"readers_count":62,"score":897.6,"yours":false,"topic_id":319,"topic_slug":"novel-2019-coronavirus-genome","display_username":"Trevor Bedford","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://nextstrain.org/groups/blab/sars-like-cov","internal":false,"reflection":false,"title":"auspice","clicks":2751},{"url":"https://github.com/blab/sars-like-cov","internal":false,"reflection":false,"title":"GitHub - blab/sars-like-cov","clicks":1070}],"read":true,"user_title":"ARTIC Network","title_is_group":false,"bookmarked":false,"actions_summary":[],"moderator":false,"admin":false,"staff":false,"user_id":10,"hidden":false,"trust_level":2,"deleted_at":null,"user_deleted":false,"edit_reason":null,"can_view_edit_history":false,"wiki":false,"post_url":"/t/novel-2019-coronavirus-genome/319/3","can_accept_answer":false,"can_unaccept_answer":false,"accepted_answer":false,"topic_accepted_answer":null},{"id":930,"name":"Andrew Rambaut","username":"arambaut","avatar_template":"/user_avatar/virological.org/arambaut/{size}/425_2.png","created_at":"2020-01-14T11:52:38.078Z","cooked":"\u003cp\u003eThanks \u003ca class=\"mention\" href=\"/u/trvrb\"\u003e@trvrb\u003c/a\u003e. A word of caution about interpreting this tree. I am almost certain that the divergent sequence \u003ccode\u003eIVDC-HB-05/2019\u003c/code\u003e is divergent because of sequencing and assembly artefacts. I strongly suggest not making any epidemic inferences from the 6 genomes available at the moment.\u003c/p\u003e\n\u003cp\u003eI have contacted the authors of this sequence but have not had a reply yet.\u003c/p\u003e","post_number":4,"post_type":1,"posts_count":28,"updated_at":"2020-01-14T11:52:38.078Z","reply_count":0,"reply_to_post_number":null,"quote_count":0,"incoming_link_count":91,"reads":59,"readers_count":58,"score":481.8,"yours":false,"topic_id":319,"topic_slug":"novel-2019-coronavirus-genome","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":1,"can_edit":false,"can_delete":false,"can_recover":false,"can_see_hidden_post":false,"can_wiki":false,"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/novel-2019-coronavirus-genome/319/4","can_accept_answer":false,"can_unaccept_answer":false,"accepted_answer":false,"topic_accepted_answer":null},{"id":931,"name":"Andrew Rambaut","username":"arambaut","avatar_template":"/user_avatar/virological.org/arambaut/{size}/425_2.png","created_at":"2020-01-14T11:55:35.649Z","cooked":"\u003cp\u003eThe SNPs in \u003ccode\u003eIVDC-HB-05/2019\u003c/code\u003e are majority non-synonymous and non-sense:\u003cbr\u003e\n\u003cdiv class=\"lightbox-wrapper\"\u003e\u003ca class=\"lightbox\" href=\"https://virological.org/uploads/default/original/1X/d80f7873b2fd903336d36e4384dc2704524a277d.png\" data-download-href=\"https://virological.org/uploads/default/d80f7873b2fd903336d36e4384dc2704524a277d\" title=\"image\"\u003e\u003cimg src=\"https://virological.org/uploads/default/optimized/1X/d80f7873b2fd903336d36e4384dc2704524a277d_2_689x256.png\" alt=\"image\" data-base62-sha1=\"uPmhiDRAYiIppF6zkiWVmUgNZ4p\" width=\"689\" height=\"256\" srcset=\"https://virological.org/uploads/default/optimized/1X/d80f7873b2fd903336d36e4384dc2704524a277d_2_689x256.png, https://virological.org/uploads/default/optimized/1X/d80f7873b2fd903336d36e4384dc2704524a277d_2_1033x384.png 1.5x, https://virological.org/uploads/default/optimized/1X/d80f7873b2fd903336d36e4384dc2704524a277d_2_1378x512.png 2x\" data-dominant-color=\"DFDDDD\"\u003e\u003cdiv class=\"meta\"\u003e\n\u003csvg class=\"fa d-icon d-icon-far-image svg-icon\" aria-hidden=\"true\"\u003e\u003cuse href=\"#far-image\"\u003e\u003c/use\u003e\u003c/svg\u003e\u003cspan class=\"filename\"\u003eimage\u003c/span\u003e\u003cspan class=\"informations\"\u003e2424×900 284 KB\u003c/span\u003e\u003csvg class=\"fa d-icon d-icon-discourse-expand svg-icon\" aria-hidden=\"true\"\u003e\u003cuse href=\"#discourse-expand\"\u003e\u003c/use\u003e\u003c/svg\u003e\n\u003c/div\u003e\u003c/a\u003e\u003c/div\u003e\u003c/p\u003e\n\u003cp\u003e\u003ccode\u003eIVDC-HB-04/2020\u003c/code\u003e is also suspect - it has 5 non-synonymous mutations and 3 synonymous:\u003cbr\u003e\n\u003cdiv class=\"lightbox-wrapper\"\u003e\u003ca class=\"lightbox\" href=\"https://virological.org/uploads/default/original/1X/5a2c032cffeda022b207007c561a4b9f26264c9e.png\" data-download-href=\"https://virological.org/uploads/default/5a2c032cffeda022b207007c561a4b9f26264c9e\" title=\"image\"\u003e\u003cimg src=\"https://virological.org/uploads/default/optimized/1X/5a2c032cffeda022b207007c561a4b9f26264c9e_2_512x500.png\" alt=\"image\" data-base62-sha1=\"cRHgE3gVbvaOIsd4KqytAiIsBki\" width=\"512\" height=\"500\" srcset=\"https://virological.org/uploads/default/optimized/1X/5a2c032cffeda022b207007c561a4b9f26264c9e_2_512x500.png, https://virological.org/uploads/default/original/1X/5a2c032cffeda022b207007c561a4b9f26264c9e.png 1.5x, https://virological.org/uploads/default/original/1X/5a2c032cffeda022b207007c561a4b9f26264c9e.png 2x\" data-dominant-color=\"959494\"\u003e\u003cdiv class=\"meta\"\u003e\n\u003csvg class=\"fa d-icon d-icon-far-image svg-icon\" aria-hidden=\"true\"\u003e\u003cuse href=\"#far-image\"\u003e\u003c/use\u003e\u003c/svg\u003e\u003cspan class=\"filename\"\u003eimage\u003c/span\u003e\u003cspan class=\"informations\"\u003e654×638 48.2 KB\u003c/span\u003e\u003csvg class=\"fa d-icon d-icon-discourse-expand svg-icon\" aria-hidden=\"true\"\u003e\u003cuse href=\"#discourse-expand\"\u003e\u003c/use\u003e\u003c/svg\u003e\n\u003c/div\u003e\u003c/a\u003e\u003c/div\u003e\u003c/p\u003e","post_number":5,"post_type":1,"posts_count":28,"updated_at":"2020-01-14T11:55:35.649Z","reply_count":0,"reply_to_post_number":null,"quote_count":0,"incoming_link_count":315,"reads":57,"readers_count":56,"score":1586.4,"yours":false,"topic_id":319,"topic_slug":"novel-2019-coronavirus-genome","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":1,"can_edit":false,"can_delete":false,"can_recover":false,"can_see_hidden_post":false,"can_wiki":false,"read":true,"user_title":"ARTIC Network","title_is_group":false,"bookmarked":false,"actions_summary":[],"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/novel-2019-coronavirus-genome/319/5","can_accept_answer":false,"can_unaccept_answer":false,"accepted_answer":false,"topic_accepted_answer":null},{"id":932,"name":"Andrew Rambaut","username":"arambaut","avatar_template":"/user_avatar/virological.org/arambaut/{size}/425_2.png","created_at":"2020-01-14T12:02:02.454Z","cooked":"\u003cp\u003e\u003ccode\u003eIVDC-HB-01/2019\u003c/code\u003e has been cell cultured with one round of passaging. This should be considered the most reliable. It may could have cell adaptations but it is identical to \u003ccode\u003eWIV04/2019\u003c/code\u003e which is direct sequenced so if independent, suggests there are no cell adaptations.\u003c/p\u003e\n\u003cp\u003eThe first genome \u003ccode\u003eWH-Human_1\u003c/code\u003e has one SNP difference from all the others which may mean it is real. However it is not known if this genome is from a sample from one of the same patients as the other 5.\u003c/p\u003e","post_number":6,"post_type":1,"posts_count":28,"updated_at":"2020-01-14T12:02:02.454Z","reply_count":0,"reply_to_post_number":null,"quote_count":0,"incoming_link_count":157,"reads":51,"readers_count":50,"score":790.2,"yours":false,"topic_id":319,"topic_slug":"novel-2019-coronavirus-genome","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":1,"can_edit":false,"can_delete":false,"can_recover":false,"can_see_hidden_post":false,"can_wiki":false,"read":true,"user_title":"ARTIC Network","title_is_group":false,"bookmarked":false,"actions_summary":[],"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/novel-2019-coronavirus-genome/319/6","can_accept_answer":false,"can_unaccept_answer":false,"accepted_answer":false,"topic_accepted_answer":null},{"id":933,"name":"Richard Neher","username":"richard.neher","avatar_template":"/user_avatar/virological.org/richard.neher/{size}/271_2.png","created_at":"2020-01-14T13:14:56.420Z","cooked":"\u003cblockquote\u003e\n\u003cp\u003e\u003ccode\u003eIVDC-HB-04/2020\u003c/code\u003e is also suspect - it has 5 non-synonymous mutations and 3 synonymous\u003c/p\u003e\n\u003c/blockquote\u003e\n\u003cp\u003eThe nextstrain tool-tip is misleading here. The reference used has over-lapping annotations ORF1a and ORF1ab. There is a total of 3 mutations inferred for this branch. C1023T, C1025T, A18460G\u003cbr\u003e\nThe first two change the aa sequence of ORF1a in coding 253 and 245 (and these are the same as the mutations listed in ORF1ab).\u003c/p\u003e\n\u003cp\u003eI was mistaken. This is wrong:\u003c/p\u003e\n\u003cblockquote\u003e\n\u003cp\u003eThe last mutation is synonymous also in ORF1ab after the slippage site.\u003cbr\u003e\nSo: 2 adjacent non-synonymous, 1 synonymous.\u003c/p\u003e\n\u003c/blockquote\u003e\n\u003cp\u003eCorrection:\u003cbr\u003e\nThe last mutation at A18460G is also non-synonymous. All three mutations are non-synonymous\u003c/p\u003e","post_number":7,"post_type":1,"posts_count":28,"updated_at":"2020-01-14T17:03:34.100Z","reply_count":0,"reply_to_post_number":null,"quote_count":0,"incoming_link_count":234,"reads":50,"readers_count":49,"score":1180.0,"yours":false,"topic_id":319,"topic_slug":"novel-2019-coronavirus-genome","display_username":"Richard Neher","primary_group_name":null,"flair_name":null,"flair_url":null,"flair_bg_color":null,"flair_color":null,"flair_group_id":null,"badges_granted":[],"version":2,"can_edit":false,"can_delete":false,"can_recover":false,"can_see_hidden_post":false,"can_wiki":false,"read":true,"user_title":"","bookmarked":false,"actions_summary":[],"moderator":false,"admin":false,"staff":false,"user_id":94,"hidden":false,"trust_level":1,"deleted_at":null,"user_deleted":false,"edit_reason":null,"can_view_edit_history":false,"wiki":false,"post_url":"/t/novel-2019-coronavirus-genome/319/7","can_accept_answer":false,"can_unaccept_answer":false,"accepted_answer":false,"topic_accepted_answer":null},{"id":934,"name":"cupton","username":"cupton","avatar_template":"/letter_avatar_proxy/v4/letter/c/e99b99/{size}.png","created_at":"2020-01-14T19:51:01.511Z","cooked":"\u003cp\u003eHB-04 has a bunch of indels.\u003c/p\u003e\n\u003cp\u003eUse \u003ca href=\"https://4virology.net/virology-ca-tools/base-by-base/\" rel=\"nofollow noopener\"\u003eBase-By-Base\u003c/a\u003e to view the alignment (visual sumary shows all diffs)\u003c/p\u003e","post_number":8,"post_type":1,"posts_count":28,"updated_at":"2020-01-15T07:24:15.404Z","reply_count":1,"reply_to_post_number":null,"quote_count":0,"incoming_link_count":119,"reads":48,"readers_count":47,"score":609.6,"yours":false,"topic_id":319,"topic_slug":"novel-2019-coronavirus-genome","display_username":"cupton","primary_group_name":null,"flair_name":null,"flair_url":null,"flair_bg_color":null,"flair_color":null,"flair_group_id":null,"badges_granted":[],"version":2,"can_edit":false,"can_delete":false,"can_recover":false,"can_see_hidden_post":false,"can_wiki":false,"link_counts":[{"url":"https://4virology.net/virology-ca-tools/base-by-base/","internal":false,"reflection":false,"title":"Base By Base - Viral Bioinformatics Research Centre","clicks":342}],"read":true,"user_title":null,"bookmarked":false,"actions_summary":[],"moderator":false,"admin":false,"staff":false,"user_id":17,"hidden":false,"trust_level":1,"deleted_at":null,"user_deleted":false,"edit_reason":null,"can_view_edit_history":false,"wiki":false,"post_url":"/t/novel-2019-coronavirus-genome/319/8","can_accept_answer":false,"can_unaccept_answer":false,"accepted_answer":false,"topic_accepted_answer":null},{"id":936,"name":"Trevor Bedford","username":"trvrb","avatar_template":"/user_avatar/virological.org/trvrb/{size}/507_2.png","created_at":"2020-01-14T21:02:37.969Z","cooked":"\u003cp\u003eThanks for the feedback Andrew and Richard. I’ve updated \u003ca href=\"https://nextstrain.org/groups/blab/sars-like-cov\" rel=\"nofollow noopener\"\u003ehttps://nextstrain.org/groups/blab/sars-like-cov\u003c/a\u003e to split ORF1a and ORF1b. This makes it clearer how nucleotide mutations map to amino acid substitutions.\u003c/p\u003e\n\u003cp\u003eIgnoring the divergent BetaCoV/Wuhan/IVDC-HB-05/2019 sequence and masking the initial 11 bases of the alignment, we have the following 5 strains and their mutations relative to the base of the outbreak clade:\u003c/p\u003e\n\u003cul\u003e\n\u003cli\u003eWIV04/2019 - no mutations\u003c/li\u003e\n\u003cli\u003eIVDC-HB-01/2019 - no mutations\u003c/li\u003e\n\u003cli\u003eIPBCAMS-WH-01/2019 - 3 nucleotide mutations / 2 AA changes\u003c/li\u003e\n\u003cli\u003eIVDC-HB-04/2020 - 3 nucleotide mutations / 3 AA changes (includes C1023T and C1025T which are suspect being so close together)\u003c/li\u003e\n\u003cli\u003eWH-Human_1 - 2 nucleotide mutations / 1 AA change\u003c/li\u003e\n\u003c/ul\u003e\n\u003cp\u003eThis alignment was stripped to map to reference \u003ca href=\"https://github.com/blab/sars-like-cov/blob/master/config/sars-like-cov_reference.gb\" rel=\"nofollow noopener\"\u003ehttps://github.com/blab/sars-like-cov/blob/master/config/sars-like-cov_reference.gb\u003c/a\u003e and so lacks indels.\u003c/p\u003e","post_number":9,"post_type":1,"posts_count":28,"updated_at":"2020-01-15T01:15:38.896Z","reply_count":0,"reply_to_post_number":null,"quote_count":0,"incoming_link_count":367,"reads":47,"readers_count":46,"score":1844.4,"yours":false,"topic_id":319,"topic_slug":"novel-2019-coronavirus-genome","display_username":"Trevor Bedford","primary_group_name":null,"flair_name":null,"flair_url":null,"flair_bg_color":null,"flair_color":null,"flair_group_id":null,"badges_granted":[],"version":2,"can_edit":false,"can_delete":false,"can_recover":false,"can_see_hidden_post":false,"can_wiki":false,"link_counts":[{"url":"https://nextstrain.org/groups/blab/sars-like-cov","internal":false,"reflection":false,"title":"auspice","clicks":471},{"url":"https://github.com/blab/sars-like-cov/blob/master/config/sars-like-cov_reference.gb","internal":false,"reflection":false,"title":"sars-like-cov/sars-like-cov_reference.gb at master · blab/sars-like-cov · GitHub","clicks":390}],"read":true,"user_title":"ARTIC Network","title_is_group":false,"bookmarked":false,"actions_summary":[],"moderator":false,"admin":false,"staff":false,"user_id":10,"hidden":false,"trust_level":2,"deleted_at":null,"user_deleted":false,"edit_reason":null,"can_view_edit_history":false,"wiki":false,"post_url":"/t/novel-2019-coronavirus-genome/319/9","can_accept_answer":false,"can_unaccept_answer":false,"accepted_answer":false,"topic_accepted_answer":null},{"id":937,"name":"Andrew Rambaut","username":"arambaut","avatar_template":"/user_avatar/virological.org/arambaut/{size}/425_2.png","created_at":"2020-01-15T00:13:36.361Z","cooked":"\u003cp\u003eThe single basepair gaps are in homopolymeric runs suggesting a sequencing platform that maybe has problems with those. There are 2 larger deletions which I assume are missing read coverage.\u003c/p\u003e","post_number":10,"post_type":1,"posts_count":28,"updated_at":"2020-01-15T00:13:36.361Z","reply_count":1,"reply_to_post_number":8,"quote_count":0,"incoming_link_count":93,"reads":46,"readers_count":45,"score":479.2,"yours":false,"topic_id":319,"topic_slug":"novel-2019-coronavirus-genome","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":1,"can_edit":false,"can_delete":false,"can_recover":false,"can_see_hidden_post":false,"can_wiki":false,"read":true,"user_title":"ARTIC Network","title_is_group":false,"reply_to_user":{"id":17,"username":"cupton","name":"cupton","avatar_template":"/letter_avatar_proxy/v4/letter/c/e99b99/{size}.png"},"bookmarked":false,"actions_summary":[],"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/novel-2019-coronavirus-genome/319/10","can_accept_answer":false,"can_unaccept_answer":false,"accepted_answer":false,"topic_accepted_answer":null},{"id":938,"name":"Kristian Andersen","username":"Kristian_Andersen","avatar_template":"/user_avatar/virological.org/kristian_andersen/{size}/521_2.png","created_at":"2020-01-15T00:16:09.916Z","cooked":"\u003cp\u003eI get slightly different stats on the # mutations - HB-04 has some indels that need corrections. Keeping HB-01 as the reference (should maybe be WH-01 though, as that’s the oldest sequence):\u003c/p\u003e\n\u003cp\u003eIVDC-HB-01/2019: [ref]\u003cbr\u003e\nIPBCAMS-WH-01/2019: 3 mutations (2 non-syn / 1 syn)\u003cbr\u003e\nWIV04/2019: 0 mutations\u003cbr\u003e\nHu-1/2019: 1 mutation (1 non-syn)\u003cbr\u003e\nIVDC-HB-04/2020: 2 mutations (2 non-syn) (however, I don’t believe these, so I think this should also be 0 mutations)\u003c/p\u003e\n\u003cp\u003eI agree with Trevor that the mutations in HB-04 are suspect - right next to each other, non-synonymous, close to a poly-T stretch, and this sequence also needed some manual editing for indels. I think these are probably not correct and that sequence would then also be identical.\u003c/p\u003e\n\u003cp\u003eAs for IVDC-HB-05, I agree with everybody that this sequence is definitely wrong (clustering of mutations, wacky ts/tv ratio, etc). If I do my very best to eliminate sequencing errors that I have commonly observed over the years, then I get a maximum of 7 mutations in this sequence, 4 of which are non-synonymous. These 7 can’t be excluded as likely errors (unlike the other 46 mutations in this sequence), but I think they still represent a (substantial) over-estimation.\u003c/p\u003e","post_number":11,"post_type":1,"posts_count":28,"updated_at":"2020-01-15T00:36:25.680Z","reply_count":0,"reply_to_post_number":null,"quote_count":0,"incoming_link_count":153,"reads":46,"readers_count":45,"score":789.2,"yours":false,"topic_id":319,"topic_slug":"novel-2019-coronavirus-genome","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":2,"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":[{"id":2,"count":1}],"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/novel-2019-coronavirus-genome/319/11","can_accept_answer":false,"can_unaccept_answer":false,"accepted_answer":false,"topic_accepted_answer":null},{"id":939,"name":"Kristian Andersen","username":"Kristian_Andersen","avatar_template":"/user_avatar/virological.org/kristian_andersen/{size}/521_2.png","created_at":"2020-01-15T00:19:52.648Z","cooked":"\u003cp\u003eTaking what I said above at face value and making WH-01 the reference (being the earliest sequence), we have three substitutions early in the tree (2 non-synonymous, 1 synonymous), followed by one additional substitution in Hu-1 (non-synonymous).\u003c/p\u003e","post_number":12,"post_type":1,"posts_count":28,"updated_at":"2020-01-15T00:19:52.648Z","reply_count":0,"reply_to_post_number":null,"quote_count":0,"incoming_link_count":61,"reads":44,"readers_count":43,"score":328.8,"yours":false,"topic_id":319,"topic_slug":"novel-2019-coronavirus-genome","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":[{"id":2,"count":1}],"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/novel-2019-coronavirus-genome/319/12","can_accept_answer":false,"can_unaccept_answer":false,"accepted_answer":false,"topic_accepted_answer":null},{"id":943,"name":"Trevor Bedford","username":"trvrb","avatar_template":"/user_avatar/virological.org/trvrb/{size}/507_2.png","created_at":"2020-01-15T06:23:07.948Z","cooked":"\u003cp\u003eThanks for checking this Kristian. I agree with you that the SNP at the end of Hu-1/2019 is spurious as is the SNP at 18460 in BetaCoV/Wuhan/IVDC-HB-04/2020 that appears directly adjacent to a long stretch of ambiguous bases. I’ve masked site 18460 as well as both ends of the alignment. With these changes our counts agree. Additionally, I thought it prudent to drop IVDC-HB-05 from the tree as its divergence is almost certainly spurious.\u003c/p\u003e\n\u003cp\u003eI’ve updated \u003ca href=\"https://nextstrain.org/groups/blab/sars-like-cov\" rel=\"nofollow noopener\"\u003ehttps://nextstrain.org/groups/blab/sars-like-cov\u003c/a\u003e accordingly.\u003c/p\u003e","post_number":13,"post_type":1,"posts_count":28,"updated_at":"2020-01-15T06:30:28.318Z","reply_count":0,"reply_to_post_number":null,"quote_count":0,"incoming_link_count":228,"reads":41,"readers_count":40,"score":1148.2,"yours":false,"topic_id":319,"topic_slug":"novel-2019-coronavirus-genome","display_username":"Trevor Bedford","primary_group_name":null,"flair_name":null,"flair_url":null,"flair_bg_color":null,"flair_color":null,"flair_group_id":null,"badges_granted":[],"version":2,"can_edit":false,"can_delete":false,"can_recover":false,"can_see_hidden_post":false,"can_wiki":false,"link_counts":[{"url":"https://nextstrain.org/groups/blab/sars-like-cov","internal":false,"reflection":false,"title":"auspice","clicks":408}],"read":true,"user_title":"ARTIC Network","title_is_group":false,"bookmarked":false,"actions_summary":[],"moderator":false,"admin":false,"staff":false,"user_id":10,"hidden":false,"trust_level":2,"deleted_at":null,"user_deleted":false,"edit_reason":null,"can_view_edit_history":false,"wiki":false,"post_url":"/t/novel-2019-coronavirus-genome/319/13","can_accept_answer":false,"can_unaccept_answer":false,"accepted_answer":false,"topic_accepted_answer":null},{"id":946,"name":"cupton","username":"cupton","avatar_template":"/letter_avatar_proxy/v4/letter/c/e99b99/{size}.png","created_at":"2020-01-16T19:15:34.888Z","cooked":"\u003cp\u003eOr poor assembly.\u003cbr\u003e\nThink the coverage is so low that regions are missing?\u003c/p\u003e","post_number":14,"post_type":1,"posts_count":28,"updated_at":"2020-01-16T19:15:34.888Z","reply_count":1,"reply_to_post_number":10,"quote_count":0,"incoming_link_count":73,"reads":42,"readers_count":41,"score":378.4,"yours":false,"topic_id":319,"topic_slug":"novel-2019-coronavirus-genome","display_username":"cupton","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,"reply_to_user":{"id":1,"username":"arambaut","name":"Andrew Rambaut","avatar_template":"/user_avatar/virological.org/arambaut/{size}/425_2.png"},"bookmarked":false,"actions_summary":[],"moderator":false,"admin":false,"staff":false,"user_id":17,"hidden":false,"trust_level":1,"deleted_at":null,"user_deleted":false,"edit_reason":null,"can_view_edit_history":false,"wiki":false,"post_url":"/t/novel-2019-coronavirus-genome/319/14","can_accept_answer":false,"can_unaccept_answer":false,"accepted_answer":false,"topic_accepted_answer":null},{"id":947,"name":"Andrew Rambaut","username":"arambaut","avatar_template":"/user_avatar/virological.org/arambaut/{size}/425_2.png","created_at":"2020-01-17T12:56:49.831Z","cooked":"\u003cp\u003eI think it would be unlikely that you would get zero coverage just for 1 basepair. The fact that they are in homopolymeric runs suggests systematic run-length errors. This is probably not Illumina data.\u003c/p\u003e","post_number":15,"post_type":1,"posts_count":28,"updated_at":"2020-01-17T12:56:49.831Z","reply_count":1,"reply_to_post_number":14,"quote_count":0,"incoming_link_count":52,"reads":41,"readers_count":40,"score":273.2,"yours":false,"topic_id":319,"topic_slug":"novel-2019-coronavirus-genome","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":1,"can_edit":false,"can_delete":false,"can_recover":false,"can_see_hidden_post":false,"can_wiki":false,"read":true,"user_title":"ARTIC Network","title_is_group":false,"reply_to_user":{"id":17,"username":"cupton","name":"cupton","avatar_template":"/letter_avatar_proxy/v4/letter/c/e99b99/{size}.png"},"bookmarked":false,"actions_summary":[],"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/novel-2019-coronavirus-genome/319/15","can_accept_answer":false,"can_unaccept_answer":false,"accepted_answer":false,"topic_accepted_answer":null},{"id":975,"name":"Kiho Hong","username":"kihohong","avatar_template":"/letter_avatar_proxy/v4/letter/k/b4bc9f/{size}.png","created_at":"2020-01-20T01:42:13.253Z","cooked":"\u003cp\u003eSeveral sequences including Thailand cases has been added to GISAID today.\u003cbr\u003e\nAlthough GISAID announced their whole genome analysis result, I am wondering if you would update your analysis, since your analysis provide much more information including diversities.\u003cbr\u003e\nSincerely.\u003c/p\u003e","post_number":16,"post_type":1,"posts_count":28,"updated_at":"2020-01-20T02:03:18.801Z","reply_count":0,"reply_to_post_number":15,"quote_count":0,"incoming_link_count":95,"reads":42,"readers_count":41,"score":483.4,"yours":false,"topic_id":319,"topic_slug":"novel-2019-coronavirus-genome","display_username":"Kiho Hong","primary_group_name":null,"flair_name":null,"flair_url":null,"flair_bg_color":null,"flair_color":null,"flair_group_id":null,"badges_granted":[],"version":3,"can_edit":false,"can_delete":false,"can_recover":false,"can_see_hidden_post":false,"can_wiki":false,"read":true,"user_title":null,"reply_to_user":{"id":1,"username":"arambaut","name":"Andrew Rambaut","avatar_template":"/user_avatar/virological.org/arambaut/{size}/425_2.png"},"bookmarked":false,"actions_summary":[],"moderator":false,"admin":false,"staff":false,"user_id":153,"hidden":false,"trust_level":1,"deleted_at":null,"user_deleted":false,"edit_reason":null,"can_view_edit_history":false,"wiki":false,"post_url":"/t/novel-2019-coronavirus-genome/319/16","can_accept_answer":false,"can_unaccept_answer":false,"accepted_answer":false,"topic_accepted_answer":null},{"id":976,"name":"Trevor Bedford","username":"trvrb","avatar_template":"/user_avatar/virological.org/trvrb/{size}/507_2.png","created_at":"2020-01-20T03:18:10.654Z","cooked":"\u003cp\u003e\u003ca href=\"https://nextstrain.org/ncov\" rel=\"nofollow noopener\"\u003ehttps://nextstrain.org/ncov\u003c/a\u003e has been updated with all genomes currently in GISAID.\u003c/p\u003e","post_number":17,"post_type":1,"posts_count":28,"updated_at":"2020-01-20T03:18:10.654Z","reply_count":0,"reply_to_post_number":null,"quote_count":0,"incoming_link_count":76,"reads":42,"readers_count":41,"score":403.4,"yours":false,"topic_id":319,"topic_slug":"novel-2019-coronavirus-genome","display_username":"Trevor Bedford","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://nextstrain.org/ncov","internal":false,"reflection":false,"title":"auspice","clicks":695}],"read":true,"user_title":"ARTIC Network","title_is_group":false,"bookmarked":false,"actions_summary":[{"id":2,"count":1}],"moderator":false,"admin":false,"staff":false,"user_id":10,"hidden":false,"trust_level":2,"deleted_at":null,"user_deleted":false,"edit_reason":null,"can_view_edit_history":false,"wiki":false,"post_url":"/t/novel-2019-coronavirus-genome/319/17","can_accept_answer":false,"can_unaccept_answer":false,"accepted_answer":false,"topic_accepted_answer":null},{"id":983,"name":"Trevor Bedford","username":"trvrb","avatar_template":"/user_avatar/virological.org/trvrb/{size}/507_2.png","created_at":"2020-01-21T18:40:55.733Z","cooked":"\u003cp\u003eThe Zhejiang Provincial Center for Disease Control and Prevention has shared two new genomes via \u003ca href=\"http://gisaid.org\" rel=\"nofollow noopener\"\u003egisaid.org\u003c/a\u003e. We’ve updated \u003ca href=\"https://nextstrain.org/ncov\" rel=\"nofollow noopener\"\u003ehttps://nextstrain.org/ncov\u003c/a\u003e to include them in our analysis bringing total up to 15 highly related samples.\u003c/p\u003e","post_number":18,"post_type":1,"posts_count":28,"updated_at":"2020-01-21T18:40:55.733Z","reply_count":0,"reply_to_post_number":null,"quote_count":0,"incoming_link_count":106,"reads":42,"readers_count":41,"score":538.4,"yours":false,"topic_id":319,"topic_slug":"novel-2019-coronavirus-genome","display_username":"Trevor Bedford","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://nextstrain.org/ncov","internal":false,"reflection":false,"title":"auspice","clicks":236},{"url":"http://gisaid.org","internal":false,"reflection":false,"clicks":96}],"read":true,"user_title":"ARTIC Network","title_is_group":false,"bookmarked":false,"actions_summary":[],"moderator":false,"admin":false,"staff":false,"user_id":10,"hidden":false,"trust_level":2,"deleted_at":null,"user_deleted":false,"edit_reason":null,"can_view_edit_history":false,"wiki":false,"post_url":"/t/novel-2019-coronavirus-genome/319/18","can_accept_answer":false,"can_unaccept_answer":false,"accepted_answer":false,"topic_accepted_answer":null},{"id":985,"name":"Kristian Andersen","username":"Kristian_Andersen","avatar_template":"/user_avatar/virological.org/kristian_andersen/{size}/521_2.png","created_at":"2020-01-21T22:18:52.139Z","cooked":"\u003cp\u003eFour more genomes were released, bringing the total to 19. Note that a couple of these look suspicious:\u003c/p\u003e\n\u003cp\u003eEPI_ISL_403928: A lot of mutations - can’t be trusted at this stage\u003cbr\u003e\nEPI_ISL_403931: Mutations in the 5’ end that are wrong\u003c/p\u003e\n\u003cp\u003eStill not a lot of diversity.\u003c/p\u003e\n\u003cp\u003eBased on this dataset I count 17 SNPs that appear to be real and 35 that do not (this is not including indels in 402120). All SNPs are private - none of them transmitted.\u003c/p\u003e","post_number":19,"post_type":1,"posts_count":28,"updated_at":"2020-01-21T22:25:13.741Z","reply_count":0,"reply_to_post_number":null,"quote_count":0,"incoming_link_count":87,"reads":45,"readers_count":44,"score":459.0,"yours":false,"topic_id":319,"topic_slug":"novel-2019-coronavirus-genome","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":2,"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":[{"id":2,"count":1}],"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/novel-2019-coronavirus-genome/319/19","can_accept_answer":false,"can_unaccept_answer":false,"accepted_answer":false,"topic_accepted_answer":null},{"id":987,"name":"Trevor Bedford","username":"trvrb","avatar_template":"/user_avatar/virological.org/trvrb/{size}/507_2.png","created_at":"2020-01-22T00:17:39.836Z","cooked":"\u003cp\u003eThanks \u003ca class=\"mention\" href=\"/u/kristian_andersen\"\u003e@Kristian_Andersen\u003c/a\u003e. We’ve updated \u003ca href=\"https://nextstrain.org/ncov\" rel=\"nofollow noopener\"\u003ehttps://nextstrain.org/ncov\u003c/a\u003e accordingly, but have also left out Wuhan/IPBCAMS-WH-05/2020 / EPI_ISL_403928 due to appearance of spurious mutations.\u003c/p\u003e\n\u003cp\u003eHowever, I’d note that if there’s been multiple spillover events from the animal reservoir, I would really expect to be seeing clusters of genetically distinct human cases. So, a divergent sequence by itself is an expected thing. What threw me here however, was strange clustering of mutations in Wuhan/IPBCAMS-WH-05/2020.\u003c/p\u003e","post_number":20,"post_type":1,"posts_count":28,"updated_at":"2020-01-22T00:17:39.836Z","reply_count":1,"reply_to_post_number":null,"quote_count":0,"incoming_link_count":99,"reads":48,"readers_count":47,"score":524.6,"yours":false,"topic_id":319,"topic_slug":"novel-2019-coronavirus-genome","display_username":"Trevor Bedford","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://nextstrain.org/ncov","internal":false,"reflection":false,"title":"auspice","clicks":309}],"read":true,"user_title":"ARTIC 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