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{"id":14249,"date":"2024-12-11T14:31:51","date_gmt":"2024-12-11T19:31:51","guid":{"rendered":"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/?p=14249"},"modified":"2024-12-11T14:31:51","modified_gmt":"2024-12-11T19:31:51","slug":"ncbi-taxonomy-changes-to-viruses","status":"publish","type":"post","link":"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/2024\/12\/11\/ncbi-taxonomy-changes-to-viruses\/","title":{"rendered":"NCBI Taxonomy: Upcoming Changes to Viruses"},"content":{"rendered":"<p><span data-contrast=\"none\">To reflect\u202fchanges\u202fto the\u202f<\/span><a href=\"https:\/\/ictv.global\/about\/code\"><span data-contrast=\"none\">International Code of Virus Classification and Nomenclature<\/span><\/a><span data-contrast=\"none\">\u202f(ICVCN) made by the International Committee on Taxonomy of Viruses (ICTV), NCBI will a<\/span><span data-contrast=\"none\">dd binomial species names to about\u202f3000 viruses. These\u202fupdates to <\/span><a href=\"https:\/\/www.ncbi.nlm.nih.gov\/taxonomy?utm_source=ncbi_insights&utm_medium=referral&utm_campaign=taxonomy-viruses-20241211\"><span data-contrast=\"none\">NCBI Taxonomy<\/span><\/a><span data-contrast=\"none\"> are planned for spring 2025, but you can view the changes now in the <\/span><a href=\"https:\/\/ictv.global\/vmr\"><span data-contrast=\"none\">ICTV\u2019s Virus Metadata Resource<\/span><\/a><span data-contrast=\"none\">.<\/span><span data-ccp-props=\"{"201341983":0,"335557856":16777215,"335559739":0,"335559740":240}\">\u00a0<\/span><\/p>\n<p><span data-contrast=\"none\">We recognize that the former species names like Human immunodeficiency virus 1 (HIV-1) are broadly used in public health, educational institutions, and research. To minimize the impact of this change on those who use NCBI resources, we will add the new binomial species names (e.g.\u202f<\/span><i><span data-contrast=\"none\">Lentivirus humimdef1<\/span><\/i><span data-contrast=\"none\">) while keeping<\/span><span data-contrast=\"none\">\u202fthe former names available in\u202fthe lineage for each species. The former names will move below the new binomial species name in the taxonomy hierarchy, ensuring continuity. Examples are provided below.\u202f<\/span><span data-ccp-props=\"{"201341983":0,"335557856":16777215,"335559739":0,"335559740":240}\">\u00a0<\/span><!--more--><\/p>\n<p><span data-contrast=\"none\">Taxonomy Identifiers (TaxIds) will remain the same and will continue to refer to the below-species names. For example, TaxId<\/span><span data-contrast=\"none\">\u202f11676\u202f<\/span><span data-contrast=\"none\">will still refer to<\/span><span data-contrast=\"none\">\u202fHIV-1.<\/span><span data-contrast=\"none\">\u202fAlso, the taxon currently associated with a sequence record will still be displayed prominently on sequence records and BLAST\u00ae results. This rollout is similar to the one <\/span><a href=\"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/2023\/02\/21\/influenza-virus-ncbi-taxonomy\/?utm_source=ncbi_insights&utm_medium=referral&utm_campaign=taxonomy-viruses-20241211\"><span data-contrast=\"none\">previously implemented for influenza viruses<\/span><\/a><span data-contrast=\"none\">.\u202f<\/span><span data-ccp-props=\"{"201341983":0,"335557856":16777215,"335559739":0,"335559740":240}\">\u00a0<\/span><\/p>\n<h5>What\u2019s changing?<\/h5>\n<p><span data-ccp-props=\"{"201341983":0,"335557856":16777215,"335559739":0,"335559740":240}\">\u00a0<\/span><b><span data-contrast=\"none\">Former lineages<\/span><\/b><span data-ccp-props=\"{"201341983":0,"335557856":16777215,"335559739":0,"335559740":240}\">\u00a0<\/span><\/p>\n<table style=\"font-weight: 400;\" data-tablestyle=\"MsoNormalTable\" data-tablelook=\"1184\" aria-rowcount=\"4\">\n<tbody>\n<tr aria-rowindex=\"1\">\n<td data-celllook=\"4369\"><span style=\"font-size: 17px;\"><b>Genus<\/b>\u00a0<\/span><\/td>\n<td data-celllook=\"4369\"><span style=\"font-size: 17px;\"><b>Species<\/b>\u00a0<\/span><\/td>\n<\/tr>\n<tr aria-rowindex=\"2\">\n<td data-celllook=\"4369\"><span style=\"font-size: 17px;\"><i>Lentivirus<\/i>\u00a0<\/span><\/td>\n<td data-celllook=\"4369\"><span style=\"font-size: 17px;\"><i>Human immunodeficiency virus 1<\/i>\u00a0<\/span><\/td>\n<\/tr>\n<tr aria-rowindex=\"3\">\n<td data-celllook=\"4369\"><span style=\"font-size: 17px;\"><i>Betacoronavirus<\/i>\u00a0<\/span><\/td>\n<td data-celllook=\"4369\"><span style=\"font-size: 17px;\"><i>Severe acute respiratory syndrome-related coronavirus<\/i>\u202f\u202f\u00a0<\/span><\/td>\n<\/tr>\n<tr aria-rowindex=\"4\">\n<td data-celllook=\"4369\"><span style=\"font-size: 17px;\"><i>Orthopoxvirus<\/i>\u00a0<\/span><\/td>\n<td data-celllook=\"4369\"><span style=\"font-size: 17px;\"><i>Monkeypox virus<\/i>\u00a0<\/span><\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n<p><b><span data-contrast=\"none\">New lineages in spring 2025<\/span><\/b><span data-ccp-props=\"{"201341983":0,"335557856":16777215,"335559739":0,"335559740":240}\">\u00a0<\/span><\/p>\n<table data-tablestyle=\"MsoNormalTable\" data-tablelook=\"1184\" aria-rowcount=\"4\">\n<tbody>\n<tr aria-rowindex=\"1\">\n<td data-celllook=\"4369\"><span style=\"font-size: 17px;\"><b>Genus<\/b>\u00a0<\/span><\/td>\n<td data-celllook=\"4369\"><span style=\"font-size: 17px;\"><b>Species<\/b>\u00a0<\/span><\/td>\n<td data-celllook=\"4369\"><span style=\"font-size: 17px;\"><b>Below species<\/b>\u00a0<\/span><\/td>\n<\/tr>\n<tr aria-rowindex=\"2\">\n<td data-celllook=\"4369\"><span style=\"font-size: 17px;\"><i>Lentivirus<\/i>\u00a0<\/span><\/td>\n<td data-celllook=\"4369\"><span style=\"font-size: 17px;\"><i>Lentivirus humimdef1<\/i>\u00a0<\/span><\/td>\n<td data-celllook=\"4369\"><span style=\"font-size: 17px;\"><a href=\"https:\/\/www.ncbi.nlm.nih.gov\/Taxonomy\/Browser\/wwwtax.cgi?id=11676&utm_source=ncbi_insights&utm_medium=referral&utm_campaign=taxonomy-viruses-20241211\">Human immunodeficiency virus 1<\/a>\u00a0<\/span><\/td>\n<\/tr>\n<tr aria-rowindex=\"3\">\n<td data-celllook=\"4369\"><span style=\"font-size: 17px;\"><i>Betacoronavirus<\/i>\u00a0<\/span><\/td>\n<td data-celllook=\"4369\"><span style=\"font-size: 17px;\"><i>Betacoronavirus pandemicum<\/i>\u00a0<\/span><\/td>\n<td data-celllook=\"4369\"><span style=\"font-size: 17px;\"><a href=\"https:\/\/www.ncbi.nlm.nih.gov\/Taxonomy\/Browser\/wwwtax.cgi?id=694009&utm_source=ncbi_insights&utm_medium=referral&utm_campaign=taxonomy-viruses-20241211\">Severe acute respiratory syndrome-related coronavirus<\/a>\u00a0<\/span><\/td>\n<\/tr>\n<tr aria-rowindex=\"4\">\n<td data-celllook=\"4369\"><span style=\"font-size: 17px;\"><i>Orthopoxvirus<\/i>\u00a0<\/span><\/td>\n<td data-celllook=\"4369\"><span style=\"font-size: 17px;\"><i>Orthopoxvirus monkeypox<\/i>\u00a0<\/span><\/td>\n<td data-celllook=\"4369\"><span style=\"font-size: 17px;\"><a href=\"https:\/\/www.ncbi.nlm.nih.gov\/Taxonomy\/Browser\/wwwtax.cgi?id=10244&utm_source=ncbi_insights&utm_medium=referral&utm_campaign=taxonomy-viruses-20241211\">Monkeypox virus<\/a>\u00a0<\/span><\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n<h5><b><span data-contrast=\"none\">What to consider when accessing or submitting virus data at NCBI<\/span><\/b><\/h5>\n<ul>\n<li data-leveltext=\"\uf0b7\" data-font=\"Symbol\" data-listid=\"1\" data-list-defn-props=\"{"335552541":1,"335559685":720,"335559991":360,"469769226":"Symbol","469769242":[8226],"469777803":"left","469777804":"\uf0b7","469777815":"multilevel"}\" aria-setsize=\"-1\" data-aria-posinset=\"1\" data-aria-level=\"1\"><span style=\"font-size: 17px;\"><b>Taxonomy-Based Searches:<\/b>\u202fIn the taxonomy hierarchy, viral sequence records can be classified to a species or below-species taxon. If you want to retrieve all sequence records for a species, please search using the species name or TaxId.\u00a0<\/span><\/li>\n<li data-leveltext=\"\uf0b7\" data-font=\"Symbol\" data-listid=\"1\" data-list-defn-props=\"{"335552541":1,"335559685":720,"335559991":360,"469769226":"Symbol","469769242":[8226],"469777803":"left","469777804":"\uf0b7","469777815":"multilevel"}\" aria-setsize=\"-1\" data-aria-posinset=\"1\" data-aria-level=\"1\"><span style=\"font-size: 17px;\"><b>Data Submissions:\u202f<\/b>Viral data submission to GenBank, BioSample, and Sequence Read Archive (SRA) will remain the same.\u00a0<\/span><\/li>\n<\/ul>\n<h5><b><span data-contrast=\"none\">What\u2019s next?<\/span><\/b><span data-ccp-props=\"{"201341983":0,"335557856":16777215,"335559739":0,"335559740":240}\">\u00a0<\/span><\/h5>\n<p>We anticipate that over time the scientific community will become familiar with the new binomial species names and update taxonomy-dependent processes. After a transition period, we will evaluate merging the below-species and species-level ranks to make them synonymous where appropriate, recognizing some species names will present challenges. NCBI resources such as\u00a0<a class=\"c-link\" href=\"https:\/\/www.ncbi.nlm.nih.gov\/datasets?utm_source=ncbi_insights&utm_medium=referral&utm_campaign=taxonomy-viruses-20241211\" target=\"_blank\" rel=\"noopener noreferrer\" data-stringify-link=\"https:\/\/www.ncbi.nlm.nih.gov\/datasets\" data-sk=\"tooltip_parent\">NCBI Datasets <\/a>and\u00a0<a class=\"c-link\" href=\"https:\/\/www.ncbi.nlm.nih.gov\/labs\/virus\/vssi\/?utm_source=ncbi_insights&utm_medium=referral&utm_campaign=taxonomy-viruses-20241211#\/\" target=\"_blank\" rel=\"noopener noreferrer\" data-stringify-link=\"https:\/\/www.ncbi.nlm.nih.gov\/labs\/virus\/vssi\/#\/\" data-sk=\"tooltip_parent\">NCBI Virus<\/a> will incorporate updates to facilitate taxonomy-based searches, and NCBI will review the presentation of viral names in other resources. Our goal remains to make the NCBI Taxonomy treatment of viruses reflect the classifications determined by the ICTV while also supporting the needs of the scientific community.<\/p>\n<h5><b><span data-contrast=\"auto\">Questions?<\/span><\/b><span data-ccp-props=\"{"201341983":0,"335559739":0,"335559740":240}\">\u00a0<\/span><\/h5>\n<p><span data-contrast=\"auto\">Please\u202f<\/span><a href=\"https:\/\/support.nlm.nih.gov\/support\/create-case\/\"><span data-contrast=\"none\">reach out to us<\/span><\/a><span data-contrast=\"none\">\u202f<\/span><span data-contrast=\"auto\">if you have questions or would like to provide feedback.<\/span><span data-ccp-props=\"{"201341983":0,"335559739":0,"335559740":240}\">\u00a0<\/span><\/p>\n<h5><b><span data-contrast=\"auto\">Stay up to date<\/span><\/b><span data-ccp-props=\"{"201341983":0,"335559739":0,"335559740":240}\">\u00a0<\/span><\/h5>\n<p><span data-contrast=\"auto\">Follow us on social\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 keep up to date with\u202fNCBI Taxonomy\u202fand other NCBI news.\u202f\u202f<\/span><span data-ccp-props=\"{"201341983":0,"335559739":0,"335559740":240}\">\u00a0<\/span><\/p>\n","protected":false},"excerpt":{"rendered":"<p>To reflect\u202fchanges\u202fto the\u202fInternational Code of Virus Classification and Nomenclature\u202f(ICVCN) made by the International Committee on Taxonomy of Viruses (ICTV), NCBI will add binomial species names to about\u202f3000 viruses. These\u202fupdates to NCBI Taxonomy are planned for spring 2025, but you can view the changes now in the ICTV\u2019s Virus Metadata Resource.\u00a0 We recognize that the former … <a href=\"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/2024\/12\/11\/ncbi-taxonomy-changes-to-viruses\/\" class=\"more-link\">Continue reading <span class=\"screen-reader-text\">NCBI Taxonomy: Upcoming Changes to Viruses<\/span> <span class=\"meta-nav\">→<\/span><\/a><\/p>\n","protected":false},"author":42204617,"featured_media":14254,"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 Taxonomy: Upcoming Changes to Viruses","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":[77187,1201719,29189,693060836,34457,693060764,651448],"table_tags":[],"class_list":["post-14249","post","type-post","status-publish","format-standard","has-post-thumbnail","hentry","category-whats-new","tag-blast","tag-genbank","tag-influenza","tag-ncbi-datasets","tag-taxonomy","tag-ncbi-virus","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 Taxonomy: Upcoming Changes to Viruses - 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\/2024\/12\/11\/ncbi-taxonomy-changes-to-viruses\/\" \/>\n<meta property=\"og:locale\" content=\"en_US\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"NCBI Taxonomy: Upcoming Changes to Viruses - NCBI Insights\" \/>\n<meta property=\"og:description\" content=\"To reflect\u202fchanges\u202fto the\u202fInternational Code of Virus Classification and Nomenclature\u202f(ICVCN) made by the International Committee on Taxonomy of Viruses (ICTV), NCBI will add binomial species names to about\u202f3000 viruses. These\u202fupdates to NCBI Taxonomy are planned for spring 2025, but you can view the changes now in the ICTV\u2019s Virus Metadata Resource.\u00a0 We recognize that the former … Continue reading NCBI Taxonomy: Upcoming Changes to Viruses →\" \/>\n<meta property=\"og:url\" content=\"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/2024\/12\/11\/ncbi-taxonomy-changes-to-viruses\/\" \/>\n<meta property=\"og:site_name\" content=\"NCBI Insights\" \/>\n<meta property=\"article:publisher\" content=\"https:\/\/www.facebook.com\/ncbi.nlm\" \/>\n<meta property=\"article:published_time\" content=\"2024-12-11T19:31:51+00:00\" \/>\n<meta property=\"og:image\" content=\"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/wp-content\/uploads\/2024\/12\/Viruses_NCBI-Taxonomy-1-e1733927970690.png\" \/>\n\t<meta property=\"og:image:width\" content=\"1100\" \/>\n\t<meta property=\"og:image:height\" content=\"575\" \/>\n\t<meta property=\"og:image:type\" content=\"image\/png\" \/>\n<meta name=\"author\" content=\"NCBI Staff\" \/>\n<meta name=\"twitter:card\" content=\"summary_large_image\" \/>\n<meta name=\"twitter:creator\" content=\"@NCBI\" \/>\n<meta name=\"twitter:site\" content=\"@NCBI\" \/>\n<meta name=\"twitter:label1\" content=\"Written by\" \/>\n\t<meta name=\"twitter:data1\" content=\"NCBI Staff\" \/>\n\t<meta name=\"twitter:label2\" content=\"Est. reading time\" \/>\n\t<meta name=\"twitter:data2\" content=\"3 minutes\" \/>\n<script type=\"application\/ld+json\" class=\"yoast-schema-graph\">{\"@context\":\"https:\/\/schema.org\",\"@graph\":[{\"@type\":\"Article\",\"@id\":\"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/2024\/12\/11\/ncbi-taxonomy-changes-to-viruses\/#article\",\"isPartOf\":{\"@id\":\"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/2024\/12\/11\/ncbi-taxonomy-changes-to-viruses\/\"},\"author\":{\"name\":\"NCBI Staff\",\"@id\":\"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/#\/schema\/person\/4f41ea6a31cea38a9a1b1419c048e50b\"},\"headline\":\"NCBI Taxonomy: Upcoming Changes to Viruses\",\"datePublished\":\"2024-12-11T19:31:51+00:00\",\"mainEntityOfPage\":{\"@id\":\"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/2024\/12\/11\/ncbi-taxonomy-changes-to-viruses\/\"},\"wordCount\":457,\"commentCount\":0,\"publisher\":{\"@id\":\"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/#organization\"},\"image\":{\"@id\":\"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/2024\/12\/11\/ncbi-taxonomy-changes-to-viruses\/#primaryimage\"},\"thumbnailUrl\":\"https:\/\/i0.wp.com\/ncbiinsights.ncbi.nlm.nih.gov\/wp-content\/uploads\/2024\/12\/Viruses_NCBI-Taxonomy-1-e1733927970690.png?fit=1100%2C575&ssl=1\",\"keywords\":[\"Basic Local Alignment Search Tool (BLAST)\",\"GenBank\",\"Influenza\",\"NCBI Datasets\",\"NCBI Taxonomy\",\"NCBI Virus\",\"Sequence Read Archive (SRA)\"],\"articleSection\":[\"What's New\"],\"inLanguage\":\"en-US\",\"potentialAction\":[{\"@type\":\"CommentAction\",\"name\":\"Comment\",\"target\":[\"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/2024\/12\/11\/ncbi-taxonomy-changes-to-viruses\/#respond\"]}]},{\"@type\":\"WebPage\",\"@id\":\"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/2024\/12\/11\/ncbi-taxonomy-changes-to-viruses\/\",\"url\":\"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/2024\/12\/11\/ncbi-taxonomy-changes-to-viruses\/\",\"name\":\"NCBI Taxonomy: Upcoming Changes to Viruses - NCBI Insights\",\"isPartOf\":{\"@id\":\"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/#website\"},\"primaryImageOfPage\":{\"@id\":\"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/2024\/12\/11\/ncbi-taxonomy-changes-to-viruses\/#primaryimage\"},\"image\":{\"@id\":\"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/2024\/12\/11\/ncbi-taxonomy-changes-to-viruses\/#primaryimage\"},\"thumbnailUrl\":\"https:\/\/i0.wp.com\/ncbiinsights.ncbi.nlm.nih.gov\/wp-content\/uploads\/2024\/12\/Viruses_NCBI-Taxonomy-1-e1733927970690.png?fit=1100%2C575&ssl=1\",\"datePublished\":\"2024-12-11T19:31:51+00:00\",\"breadcrumb\":{\"@id\":\"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/2024\/12\/11\/ncbi-taxonomy-changes-to-viruses\/#breadcrumb\"},\"inLanguage\":\"en-US\",\"potentialAction\":[{\"@type\":\"ReadAction\",\"target\":[\"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/2024\/12\/11\/ncbi-taxonomy-changes-to-viruses\/\"]}]},{\"@type\":\"ImageObject\",\"inLanguage\":\"en-US\",\"@id\":\"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/2024\/12\/11\/ncbi-taxonomy-changes-to-viruses\/#primaryimage\",\"url\":\"https:\/\/i0.wp.com\/ncbiinsights.ncbi.nlm.nih.gov\/wp-content\/uploads\/2024\/12\/Viruses_NCBI-Taxonomy-1-e1733927970690.png?fit=1100%2C575&ssl=1\",\"contentUrl\":\"https:\/\/i0.wp.com\/ncbiinsights.ncbi.nlm.nih.gov\/wp-content\/uploads\/2024\/12\/Viruses_NCBI-Taxonomy-1-e1733927970690.png?fit=1100%2C575&ssl=1\",\"width\":1100,\"height\":575,\"caption\":\"Image of glowing virus cells on a black background. Text says: Coming soon! Updates to Viruses. 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