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{"id":11683,"date":"2023-06-27T13:19:30","date_gmt":"2023-06-27T17:19:30","guid":{"rendered":"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/?p=11683"},"modified":"2023-06-27T13:19:30","modified_gmt":"2023-06-27T17:19:30","slug":"ncbi-virus-mutation-based-search-sars-cov-2-data","status":"publish","type":"post","link":"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/2023\/06\/27\/ncbi-virus-mutation-based-search-sars-cov-2-data\/","title":{"rendered":"NCBI Virus: Mutation-Based Search for SARS-CoV-2 Data"},"content":{"rendered":"<p><span class=\"TextRun SCXW18102055 BCX8\" lang=\"EN-US\" xml:lang=\"EN-US\" data-contrast=\"auto\"><span class=\"NormalTextRun SCXW18102055 BCX8\">Millions of SARS-CoV-2 samples <\/span><span class=\"NormalTextRun SCXW18102055 BCX8\">from around the world <\/span><span class=\"NormalTextRun SCXW18102055 BCX8\">have been made <\/span><span class=\"NormalTextRun SCXW18102055 BCX8\">publicly available as assembled and unassembled sequence data <\/span><span class=\"NormalTextRun SCXW18102055 BCX8\">in GenBank and the Sequence Read Archive (SRA)<\/span><span class=\"NormalTextRun SCXW18102055 BCX8\">.<\/span><span class=\"NormalTextRun SCXW18102055 BCX8\"> Now you can find sequences <\/span><span class=\"NormalTextRun SCXW18102055 BCX8\">with<\/span><span class=\"NormalTextRun SCXW18102055 BCX8\"> a particular <\/span><span class=\"NormalTextRun SCXW18102055 BCX8\">muta<\/span><span class=\"NormalTextRun SCXW18102055 BCX8\">tion<\/span> <span class=\"NormalTextRun SCXW18102055 BCX8\">by searching with <\/span><span class=\"NormalTextRun SCXW18102055 BCX8\">the <\/span><span class=\"NormalTextRun SCXW18102055 BCX8\">protein and the amino acid change (e.g<\/span><span class=\"NormalTextRun SCXW18102055 BCX8\">.<\/span> <\/span><a class=\"Hyperlink SCXW18102055 BCX8\" href=\"https:\/\/www.ncbi.nlm.nih.gov\/activ\/mutations?search=S%3AF486V&utm_source=ncbi_insights&utm_medium=referral&utm_campaign=ncbi-virus-search-sars-cov2-20230627\" target=\"_blank\" rel=\"noreferrer noopener\"><span class=\"TextRun Underlined SCXW18102055 BCX8\" lang=\"EN-US\" xml:lang=\"EN-US\" data-contrast=\"none\"><span class=\"NormalTextRun SCXW18102055 BCX8\" data-ccp-charstyle=\"Hyperlink\">S<\/span><span class=\"NormalTextRun SCXW18102055 BCX8\" data-ccp-charstyle=\"Hyperlink\">:<\/span><span class=\"NormalTextRun SCXW18102055 BCX8\" data-ccp-charstyle=\"Hyperlink\">F486V<\/span><\/span><\/a><span class=\"TextRun SCXW18102055 BCX8\" lang=\"EN-US\" xml:lang=\"EN-US\" data-contrast=\"auto\"><span class=\"NormalTextRun CommentStart SCXW18102055 BCX8\">)<\/span><span class=\"NormalTextRun SCXW18102055 BCX8\">. <\/span><span class=\"NormalTextRun SCXW18102055 BCX8\">Visit our <\/span><\/span><a class=\"Hyperlink SCXW18102055 BCX8\" href=\"https:\/\/www.ncbi.nlm.nih.gov\/activ?utm_source=ncbi_insights&utm_medium=referral&utm_campaign=ncbi-virus-search-sars-cov2-20230627\" target=\"_blank\" rel=\"noreferrer noopener\"><span class=\"TextRun Underlined SCXW18102055 BCX8\" lang=\"EN-US\" xml:lang=\"EN-US\" data-contrast=\"none\"><span class=\"NormalTextRun SCXW18102055 BCX8\" data-ccp-charstyle=\"Hyperlink\">SARS-CoV-2 Variant Overview<\/span><\/span><\/a><span class=\"TextRun SCXW18102055 BCX8\" lang=\"EN-US\" xml:lang=\"EN-US\" data-contrast=\"auto\"> <span class=\"NormalTextRun SCXW18102055 BCX8\">on<\/span> <\/span><a class=\"Hyperlink SCXW18102055 BCX8\" href=\"https:\/\/www.ncbi.nlm.nih.gov\/labs\/virus\/vssi\/?utm_source=ncbi_insights&utm_medium=referral&utm_campaign=ncbi-virus-search-sars-cov2-20230627#\/\" target=\"_blank\" rel=\"noreferrer noopener\"><span class=\"TextRun Underlined SCXW18102055 BCX8\" lang=\"EN-US\" xml:lang=\"EN-US\" data-contrast=\"none\"><span class=\"NormalTextRun SCXW18102055 BCX8\" data-ccp-charstyle=\"Hyperlink\">NCBI Virus<\/span><\/span><\/a><span class=\"TextRun SCXW18102055 BCX8\" lang=\"EN-US\" xml:lang=\"EN-US\" data-contrast=\"auto\"><span class=\"NormalTextRun SCXW18102055 BCX8\"> and click on the <\/span><span class=\"NormalTextRun SCXW18102055 BCX8\">\u2018<\/span><span class=\"NormalTextRun SCXW18102055 BCX8\">Mutation<\/span><span class=\"NormalTextRun SCXW18102055 BCX8\">\u2019<\/span><\/span> <span class=\"TextRun SCXW18102055 BCX8\" lang=\"EN-US\" xml:lang=\"EN-US\" data-contrast=\"auto\"><span class=\"NormalTextRun SCXW18102055 BCX8\">tab <\/span><span class=\"NormalTextRun SCXW18102055 BCX8\">to get started<\/span>\u00a0<span class=\"NormalTextRun SCXW18102055 BCX8\">(Figure 1).<\/span><\/span><span class=\"EOP SCXW18102055 BCX8\" data-ccp-props=\"{"201341983":0,"335559739":0,"335559740":240}\">\u00a0<\/span><\/p>\n<p><img data-recalc-dims=\"1\" loading=\"lazy\" decoding=\"async\" data-attachment-id=\"11687\" data-permalink=\"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/2023\/06\/27\/ncbi-virus-mutation-based-search-sars-cov-2-data\/variants_overview_mutations\/\" data-orig-file=\"https:\/\/i0.wp.com\/ncbiinsights.ncbi.nlm.nih.gov\/wp-content\/uploads\/2023\/06\/Variants_overview_mutations.png?fit=1062%2C904&ssl=1\" data-orig-size=\"1062,904\" data-comments-opened=\"1\" data-image-meta=\"{"aperture":"0","credit":"","camera":"","caption":"","created_timestamp":"0","copyright":"","focal_length":"0","iso":"0","shutter_speed":"0","title":"","orientation":"0"}\" data-image-title=\"Variants_overview_mutations\" data-image-description=\"\" data-image-caption=\"\" data-medium-file=\"https:\/\/i0.wp.com\/ncbiinsights.ncbi.nlm.nih.gov\/wp-content\/uploads\/2023\/06\/Variants_overview_mutations.png?fit=300%2C255&ssl=1\" data-large-file=\"https:\/\/i0.wp.com\/ncbiinsights.ncbi.nlm.nih.gov\/wp-content\/uploads\/2023\/06\/Variants_overview_mutations.png?fit=1024%2C872&ssl=1\" class=\"alignright size-full wp-image-11687\" src=\"https:\/\/i0.wp.com\/ncbiinsights.ncbi.nlm.nih.gov\/wp-content\/uploads\/2023\/06\/Variants_overview_mutations.png?resize=1062%2C904&ssl=1\" alt=\"\" width=\"1062\" height=\"904\" srcset=\"https:\/\/i0.wp.com\/ncbiinsights.ncbi.nlm.nih.gov\/wp-content\/uploads\/2023\/06\/Variants_overview_mutations.png?w=1062&ssl=1 1062w, https:\/\/i0.wp.com\/ncbiinsights.ncbi.nlm.nih.gov\/wp-content\/uploads\/2023\/06\/Variants_overview_mutations.png?resize=300%2C255&ssl=1 300w, https:\/\/i0.wp.com\/ncbiinsights.ncbi.nlm.nih.gov\/wp-content\/uploads\/2023\/06\/Variants_overview_mutations.png?resize=1024%2C872&ssl=1 1024w, https:\/\/i0.wp.com\/ncbiinsights.ncbi.nlm.nih.gov\/wp-content\/uploads\/2023\/06\/Variants_overview_mutations.png?resize=150%2C128&ssl=1 150w, https:\/\/i0.wp.com\/ncbiinsights.ncbi.nlm.nih.gov\/wp-content\/uploads\/2023\/06\/Variants_overview_mutations.png?resize=768%2C654&ssl=1 768w, https:\/\/i0.wp.com\/ncbiinsights.ncbi.nlm.nih.gov\/wp-content\/uploads\/2023\/06\/Variants_overview_mutations.png?resize=270%2C230&ssl=1 270w\" sizes=\"auto, (max-width: 1062px) 100vw, 1062px\" \/><\/p>\n<p><span data-contrast=\"auto\"><em>Figure 1: SARS-CoV-2 Variants Overview. Arrows indicate important features on the page, including the \u201cLineages\u201d and \u201cMutations\u201d tabs to switch between views, the search box, and the information box describing the mutation format. The results are also indicated, including a summary of the total records found that contain the searched term as well as the results table.<\/em>\u00a0<\/span><span data-ccp-props=\"{"201341983":0,"335559739":0,"335559740":240}\">\u00a0<\/span><!--more--><\/p>\n<p><span data-contrast=\"auto\">The SARS-CoV-2 Variants Overview is based on sequence data analysis from the <\/span><a href=\"https:\/\/www.ncbi.nlm.nih.gov\/sra\/docs\/sars-cov-2-variant-calling\/?utm_source=ncbi_insights&utm_medium=referral&utm_campaign=ncbi-virus-search-sars-cov2-20230627\"><span data-contrast=\"none\">SARS-CoV-2 Variant Calling<\/span><\/a><span data-contrast=\"auto\"> pipeline. We compare sequence records that pass validation to the SARS-CoV-2 reference genome sequence (<\/span><a href=\"https:\/\/www.ncbi.nlm.nih.gov\/nuccore\/NC_045512?utm_source=ncbi_insights&utm_medium=referral&utm_campaign=ncbi-virus-search-sars-cov2-20230627\"><span data-contrast=\"none\">NC_045512<\/span><\/a><span data-contrast=\"auto\">) to identify changes in the genomes and translate these mutations into amino acid changes. We use these to assign lineages to the sequences. The \u2018Lineages\u2019 tab provides information on <\/span><i><span data-contrast=\"auto\">where<\/span><\/i><span data-contrast=\"auto\"> and <\/span><i><span data-contrast=\"auto\">when<\/span><\/i><span data-contrast=\"auto\"> lineages with a <\/span><a href=\"https:\/\/www.cdc.gov\/coronavirus\/2019-ncov\/variants\/variant-classifications.html\"><span data-contrast=\"none\">CDC status \u2013 Variant Being Monitored (VBM) Variant of Interest (VOI), or Variant of Concern (VOC)<\/span><\/a><span data-contrast=\"auto\"> \u2014 were sequenced.\u00a0<\/span><span data-ccp-props=\"{"201341983":0,"335559739":0,"335559740":240}\">\u00a0<\/span><\/p>\n<h5>What\u2019s new?<\/h5>\n<p><span data-contrast=\"auto\">In the recently added Mutations tab, you can search with a mutation to find matches from all analyzed sequences collected over the past 6 months, links to access the sequence records, and metadata describing the samples. An information box describing the format accepted for mutations is provided below the search box.<\/span><span data-ccp-props=\"{"201341983":0,"335559739":0,"335559740":240}\">\u00a0<\/span><span data-ccp-props=\"{"201341983":0,"335559739":0,"335559740":240}\">\u00a0<\/span><\/p>\n<p><span data-contrast=\"auto\">If you have used our Excel Variant Reports to get mutation-related data in the past, please be aware that these reports will be discontinued on July 31, 2023. Published reports will continue to be available on our <\/span><a href=\"https:\/\/ftp.ncbi.nlm.nih.gov\/pub\/ACTIV-TRACE\/\"><span data-contrast=\"none\">FTP public site<\/span><\/a><span data-contrast=\"none\">,<\/span><span data-contrast=\"auto\"> but no new reports will be added after July 31. 2023. While we will continue to process SARS-CoV-2 sequences through the <\/span><a href=\"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/2022\/12\/01\/sars-cov-2-variant-calling-pipeline\/?utm_source=ncbi_insights&utm_medium=referral&utm_campaign=ncbi-virus-search-sars-cov2-20230627\"><span data-contrast=\"none\">SARS-CoV-2 Variant Calling Pipeline<\/span><\/a><span data-contrast=\"auto\"> and curate mutations, the up-to-date data will be available through the Mutations tab as described above.<\/span><span data-ccp-props=\"{"201341983":0,"335559739":0,"335559740":240}\">\u00a0<\/span><\/p>\n<p><span data-contrast=\"auto\">We are working on expanding the SARS-CoV-2 Variants Overview mutations search. For example, we will add the ability to search for sequences containing a set of mutations.<\/span><span data-ccp-props=\"{"201341983":0,"335559739":0,"335559740":240}\">\u00a0<\/span><\/p>\n<h5>We want to hear from you!<\/h5>\n<p><span data-contrast=\"auto\">Try it out and let us know what you think. We are making improvements based on your feedback. We would love to hear from you about other ways to make mutation-based search more useful. Please use the yellow Feedback button at the bottom right of the webpage and remember to include your email if you would like a response.<\/span><span data-ccp-props=\"{"201341983":0,"335559739":0,"335559740":240}\">\u00a0<\/span><\/p>\n<h5>Stay up to date<\/h5>\n<p><span data-contrast=\"auto\">Follow us on Twitter\u202f<\/span><a href=\"https:\/\/twitter.com\/ncbi\"><span data-contrast=\"none\">@NCBI<\/span><\/a><span data-contrast=\"none\">\u202f<\/span><span data-contrast=\"auto\">and<\/span><span data-contrast=\"none\">\u202f<\/span><a href=\"https:\/\/public.govdelivery.com\/accounts\/USNLMOCPL\/subscriber\/new?topic_id=USNLMOCPL_52\"><span data-contrast=\"none\">join our mailing list<\/span><\/a><span data-contrast=\"none\">\u202f<\/span><span data-contrast=\"auto\">to<\/span> <span data-contrast=\"auto\">keep up to date with\u202fNCBI Virus\u202fand other NCBI news.\u202f\u202f<\/span><span data-ccp-props=\"{"134233117":false,"134233118":false,"201341983":0,"335559738":0,"335559739":0,"335559740":240}\">\u00a0<\/span><\/p>\n<h5>Questions?<\/h5>\n<p><span data-contrast=\"auto\">If you have questions, please reach out to us at\u202f<\/span><a href=\"mailto:info@ncbi.nlm.nih.gov\"><span data-contrast=\"none\">info@ncbi.nlm.nih.gov<\/span><\/a><span data-contrast=\"none\">.\u202f\u202f<\/span><span data-ccp-props=\"{"134233117":false,"134233118":false,"201341983":0,"335559738":0,"335559739":0,"335559740":240}\">\u00a0<\/span><\/p>\n<hr \/>\n<p><em>Note: We developed the SARS-CoV-2 Variants Overview as part of NLM\u2019s participation in the National Institutes of Health (NIH) <a href=\"https:\/\/www.nih.gov\/research-training\/medical-research-initiatives\/activ\">ACTIV initiative<\/a>.<\/em><\/p>\n<p><span data-ccp-props=\"{"201341983":0,"335559739":0,"335559740":240}\">\u00a0<\/span><\/p>\n<p><span data-ccp-props=\"{"201341983":0,"335559739":0,"335559740":240}\">\u00a0<\/span><\/p>\n","protected":false},"excerpt":{"rendered":"<p>Millions of SARS-CoV-2 samples from around the world have been made publicly available as assembled and unassembled sequence data in GenBank and the Sequence Read Archive (SRA). Now you can find sequences with a particular mutation by searching with the protein and the amino acid change (e.g. S:F486V). Visit our SARS-CoV-2 Variant Overview on NCBI … <a href=\"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/2023\/06\/27\/ncbi-virus-mutation-based-search-sars-cov-2-data\/\" class=\"more-link\">Continue reading <span class=\"screen-reader-text\">NCBI Virus: Mutation-Based Search for SARS-CoV-2 Data<\/span> <span class=\"meta-nav\">→<\/span><\/a><\/p>\n","protected":false},"author":42204617,"featured_media":11685,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"_coblocks_attr":"","_coblocks_dimensions":"","_coblocks_responsive_height":"","_coblocks_accordion_ie_support":"","jetpack_post_was_ever_published":false,"_jetpack_newsletter_access":"","_jetpack_dont_email_post_to_subs":false,"_jetpack_newsletter_tier_id":0,"_jetpack_memberships_contains_paywalled_content":false,"_jetpack_memberships_contains_paid_content":false,"footnotes":"","jetpack_publicize_message":"NCBI Virus: Mutation-Based Search for SARS-CoV-2 Data","jetpack_publicize_feature_enabled":true,"jetpack_social_post_already_shared":true,"jetpack_social_options":{"image_generator_settings":{"template":"highway","enabled":false},"version":2}},"categories":[2248],"tags":[1201719,693060764,693060688,651448],"table_tags":[],"class_list":["post-11683","post","type-post","status-publish","format-standard","has-post-thumbnail","hentry","category-whats-new","tag-genbank","tag-ncbi-virus","tag-sars-cov-2","tag-sra"],"jetpack_publicize_connections":[],"yoast_head":"<!-- This site is optimized with the Yoast SEO plugin v24.6 - https:\/\/yoast.com\/wordpress\/plugins\/seo\/ -->\n<title>NCBI Virus: Mutation-Based Search for SARS-CoV-2 Data - NCBI Insights<\/title>\n<meta name=\"robots\" content=\"index, follow, max-snippet:-1, max-image-preview:large, max-video-preview:-1\" \/>\n<link rel=\"canonical\" href=\"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/2023\/06\/27\/ncbi-virus-mutation-based-search-sars-cov-2-data\/\" \/>\n<meta property=\"og:locale\" content=\"en_US\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"NCBI Virus: Mutation-Based Search for SARS-CoV-2 Data - NCBI Insights\" \/>\n<meta property=\"og:description\" content=\"Millions of SARS-CoV-2 samples from around the world have been made publicly available as assembled and unassembled sequence data in GenBank and the Sequence Read Archive (SRA). Now you can find sequences with a particular mutation by searching with the protein and the amino acid change (e.g. S:F486V). 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