93 lines
63 KiB
HTML
93 lines
63 KiB
HTML
<!DOCTYPE html>
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/*# sourceURL=/css/ampshared.css*/</style><meta property="og:locale" content="en_US"><meta property="og:type" content="article"><meta property="og:title" content="Automated Lineage Definitions Now Available in NCBI Virus SARS-CoV-2 Variants Overview - NCBI Insights"><meta property="og:description" content="Recently, NCBI Virus SARS-CoV-2 Variants Overview moved from a manual to an automated process for selecting mutations required to define a lineage (e.g., Omicron, BA.2, JN.1, etc.). With this update, the SARS-CoV-2 Variant Overview provides coverage for all SARS-CoV-2 lineages and is no longer limited to only lineages with CDC status. The SARS-CoV-2 Variants Overview … Continue reading Automated Lineage Definitions Now Available in NCBI Virus SARS-CoV-2 Variants Overview →"><meta property="og:url" content="https://ncbiinsights.ncbi.nlm.nih.gov/2024/05/02/automated-lineage-definitions-ncbi-virus-sars-cov-2-variants-overview/"><meta property="og:site_name" content="NCBI Insights"><meta property="article:publisher" content="https://www.facebook.com/ncbi.nlm"><meta property="article:published_time" content="2024-05-02T17:00:44+00:00"><meta property="article:modified_time" content="2024-05-02T17:10:23+00:00"><meta property="og:image" content="https://ncbiinsights.ncbi.nlm.nih.gov/wp-content/uploads/2024/05/NCBI_Virus_Automated_Lineage_Definitions-e1714600345598.png"><meta property="og:image:width" content="1100"><meta property="og:image:height" content="575"><meta property="og:image:type" content="image/png"><meta name="author" content="NCBI Staff"><meta name="twitter:card" content="summary_large_image"><meta 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<h1 class="amp-wp-title">Automated Lineage Definitions Now Available in NCBI Virus SARS-CoV-2 Variants Overview</h1>
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<p><span class="TextRun SCXW80774363 BCX8" lang="EN-US" data-contrast="auto"><span class="NormalTextRun SCXW80774363 BCX8">Recently</span><span class="NormalTextRun SCXW80774363 BCX8">, NCBI Virus </span></span><a class="Hyperlink SCXW80774363 BCX8" href="https://www.ncbi.nlm.nih.gov/activ?utm_source=ncbi_insights&utm_medium=referral&utm_campaign=virus-sars-cov2-automated-20240502" target="_blank" rel="noreferrer noopener"><span class="TextRun Underlined SCXW80774363 BCX8" lang="EN-US" data-contrast="none"><span class="NormalTextRun SCXW80774363 BCX8" data-ccp-charstyle="Hyperlink">SARS-CoV-2 Variants Overview</span></span></a><span class="TextRun SCXW80774363 BCX8" lang="EN-US" data-contrast="auto"> <span class="NormalTextRun SCXW80774363 BCX8">moved </span><span class="NormalTextRun SCXW80774363 BCX8">from a </span><span class="NormalTextRun SCXW80774363 BCX8">manual </span><span class="NormalTextRun SCXW80774363 BCX8">to</span><span class="NormalTextRun SCXW80774363 BCX8"> an automated process </span><span class="NormalTextRun SCXW80774363 BCX8">for </span></span><span class="TextRun SCXW80774363 BCX8" lang="EN-US" data-contrast="none"><span class="NormalTextRun SCXW80774363 BCX8">selecting mutations required to define a lineage</span></span><span class="TextRun SCXW80774363 BCX8" lang="EN-US" data-contrast="auto"><span class="NormalTextRun SCXW80774363 BCX8"> (e.g.</span><span class="NormalTextRun SCXW80774363 BCX8">,</span> <span class="NormalTextRun CommentStart SCXW80774363 BCX8">Omicron, </span><span class="NormalTextRun SCXW80774363 BCX8">BA.2, </span><span class="NormalTextRun SCXW80774363 BCX8">JN.1</span><span class="NormalTextRun SCXW80774363 BCX8">, etc.)</span><span class="NormalTextRun SCXW80774363 BCX8">.</span> <span class="NormalTextRun SCXW80774363 BCX8">With this update, the SARS-CoV-2 Variant Overview </span><span class="NormalTextRun SCXW80774363 BCX8">provides </span><span class="NormalTextRun CommentStart SCXW80774363 BCX8">coverage for</span> <span class="NormalTextRun SCXW80774363 BCX8">all </span><span class="NormalTextRun SCXW80774363 BCX8">SARS-CoV-2 </span><span class="NormalTextRun SCXW80774363 BCX8">lineages</span><span class="NormalTextRun SCXW80774363 BCX8"> and is no longer limited to </span><span class="NormalTextRun SCXW80774363 BCX8">only lineages with </span><span class="NormalTextRun CommentStart SCXW80774363 BCX8">CDC</span><span class="NormalTextRun SCXW80774363 BCX8"> status</span><span class="NormalTextRun SCXW80774363 BCX8">.</span> <span class="NormalTextRun SCXW80774363 BCX8">The </span><span class="NormalTextRun SCXW80774363 BCX8">SARS-CoV-2 Variants Overview </span><span class="NormalTextRun SCXW80774363 BCX8">website </span><span class="NormalTextRun SCXW80774363 BCX8">reports results from analyzing both </span></span><a class="Hyperlink SCXW80774363 BCX8" href="https://www.ncbi.nlm.nih.gov/genbank/?utm_source=ncbi_insights&utm_medium=referral&utm_campaign=virus-sars-cov2-automated-20240502" target="_blank" rel="noreferrer noopener"><span class="TextRun Underlined SCXW80774363 BCX8" lang="EN-US" data-contrast="none"><span class="NormalTextRun SCXW80774363 BCX8" data-ccp-charstyle="Hyperlink">GenBank</span></span></a><span class="TextRun SCXW80774363 BCX8" lang="EN-US" data-contrast="auto"><span class="NormalTextRun SCXW80774363 BCX8"> and unassembled </span></span><a class="Hyperlink SCXW80774363 BCX8" href="https://www.ncbi.nlm.nih.gov/sra?utm_source=ncbi_insights&utm_medium=referral&utm_campaign=virus-sars-cov2-automated-20240502" target="_blank" rel="noreferrer noopener"><span class="TextRun Underlined SCXW80774363 BCX8" lang="EN-US" data-contrast="none"><span class="NormalTextRun SCXW80774363 BCX8" data-ccp-charstyle="Hyperlink">Sequence Read Archive (</span><span class="NormalTextRun SCXW80774363 BCX8" data-ccp-charstyle="Hyperlink">SRA</span><span class="NormalTextRun SCXW80774363 BCX8" data-ccp-charstyle="Hyperlink">)</span></span></a><span class="TextRun SCXW80774363 BCX8" lang="EN-US" data-contrast="auto"><span class="NormalTextRun SCXW80774363 BCX8"> sequence data</span><span class="NormalTextRun CommentStart SCXW80774363 BCX8">.</span> <span class="NormalTextRun SCXW80774363 BCX8">It</span> <span class="NormalTextRun SCXW80774363 BCX8">allows </span><span class="NormalTextRun SCXW80774363 BCX8">you </span><span class="NormalTextRun SCXW80774363 BCX8">to</span> </span><a class="Hyperlink SCXW80774363 BCX8" href="https://www.ncbi.nlm.nih.gov/activ/?utm_source=ncbi_insights&utm_medium=referral&utm_campaign=virus-sars-cov2-automated-20240502" target="_blank" rel="noreferrer noopener"><span class="TextRun Underlined SCXW80774363 BCX8" lang="EN-US" data-contrast="none"><span class="NormalTextRun SCXW80774363 BCX8" data-ccp-charstyle="Hyperlink">view geographic and frequency trends</span></span></a><span class="TextRun SCXW80774363 BCX8" lang="EN-US" data-contrast="auto"> <span class="NormalTextRun SCXW80774363 BCX8">of </span><span class="NormalTextRun SCXW80774363 BCX8">records assigned to <a href="https://cov-lineages.org/lineage_list.html">Pango lineages</a> </span><span class="NormalTextRun SCXW80774363 BCX8">and </span></span><a class="Hyperlink SCXW80774363 BCX8" href="https://www.ncbi.nlm.nih.gov/activ/mutations?utm_source=ncbi_insights&utm_medium=referral&utm_campaign=virus-sars-cov2-automated-20240502" target="_blank" rel="noreferrer noopener"><span class="TextRun Underlined SCXW80774363 BCX8" lang="EN-US" data-contrast="none"><span class="NormalTextRun SCXW80774363 BCX8" data-ccp-charstyle="Hyperlink">search for sequence records</span></span></a> using <span class="TextRun SCXW80774363 BCX8" lang="EN-US" data-contrast="auto"><span class="NormalTextRun SCXW80774363 BCX8">lineage-defining or other </span><span class="NormalTextRun SCXW80774363 BCX8">mutations</span><span class="NormalTextRun SCXW80774363 BCX8"> (example shown in Figure 1)</span><span class="NormalTextRun SCXW80774363 BCX8">. </span></span><span class="EOP SCXW80774363 BCX8" data-ccp-props='{"201341983":0,"335559739":0,"335559740":240}'> </span></p>
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<p><em>Figure 1: On the “Lineage Frequency and Location” tab, select a Pango lineage such as JN.1 to access details including the lineage-defining mutations, the change in frequency of the lineage in GenBank and SRA records, and the geographic locations where the samples were collected.</em><span data-ccp-props='{"201341983":0,"335559739":0,"335559740":240}'> </span></p>
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<h5><b><span data-contrast="auto">Automated lineage definition</span></b><span data-ccp-props='{"201341983":0,"335551550":6,"335551620":6,"335559739":0,"335559740":240}'> </span></h5>
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<p><span data-contrast="auto"><a href="https://cov-lineages.org/resources/pangolin.html">Pangolin</a> in UShER mode is run daily to assign lineages to all GenBank sequences. The new automated lineage definition pipeline identifies the mutations that are characteristic and unique to each Pango lineage. Specifically, the pipeline creates a set of mutations defining a single lineage according to the following rules:</span><span data-ccp-props='{"201341983":0,"335551550":6,"335551620":6,"335559739":0,"335559740":240}'> </span></p>
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<ul>
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<li data-leveltext="" data-font="Wingdings" data-listid="3" data-list-defn-props='{"335552541":1,"335559685":720,"335559991":360,"469769226":"Wingdings","469769242":[9642],"469777803":"left","469777804":"","469777815":"hybridMultilevel"}' aria-setsize="-1" data-aria-posinset="1" data-aria-level="1"><span data-amp-original-style="font-size: 17px;" class="amp-wp-8bdd01f">The lineage must have at least 10 GenBank records assigned to it by Pangolin </span></li>
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||
<li data-leveltext="" data-font="Wingdings" data-listid="3" data-list-defn-props='{"335552541":1,"335559685":720,"335559991":360,"469769226":"Wingdings","469769242":[9642],"469777803":"left","469777804":"","469777815":"hybridMultilevel"}' aria-setsize="-1" data-aria-posinset="2" data-aria-level="1"><span data-amp-original-style="font-size: 17px;" class="amp-wp-8bdd01f">Lineage-defining mutations from the set must occur in at least 80% of records assigned to that lineage by Pangolin </span></li>
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||
<li data-leveltext="" data-font="Wingdings" data-listid="3" data-list-defn-props='{"335552541":1,"335559685":720,"335559991":360,"469769226":"Wingdings","469769242":[9642],"469777803":"left","469777804":"","469777815":"hybridMultilevel"}' aria-setsize="-1" data-aria-posinset="3" data-aria-level="1"><span data-amp-original-style="font-size: 17px;" class="amp-wp-8bdd01f">Mutations must be specific to a single lineage, i.e., if more than 20% of the records containing a candidate lineage-defining mutation were assigned to a <i>different</i> lineage by Pangolin, the candidate mutation is ineligible</span><span data-ccp-props='{"201341983":0,"335559739":0,"335559740":240}'> </span></li>
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</ul>
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<p><span data-contrast="auto">The pipeline subsequently uses these predefined sets of mutations to assign lineages to SRA and GenBank sequence records. A sequence record must contain 100% of the lineage-defining mutations for it to be assigned to that lineage. After a sequence is released to the public, it is usually classified into a lineage and available through the NCBI Virus SARS-CoV-2 Variants Overview webpage within a couple of days. Mutation sets are recalculated weekly, and all sequence records are reclassified periodically. More details on the lineage definition pipeline can be found in NCBI Virus </span><a href="https://ncbi.nlm.nih.gov/activ/help?utm_source=ncbi_insights&utm_medium=referral&utm_campaign=virus-sars-cov2-automated-20240502#howLineagesAssigned"><span data-contrast="none">help documentation</span></a><span data-contrast="auto">.</span><span data-ccp-props='{"201341983":0,"335559739":0,"335559740":240}'> </span></p>
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<p><span data-contrast="auto">Follow us on social media </span><a href="https://twitter.com/ncbi"><span data-contrast="none">@NCBI</span></a><span data-contrast="auto"> and </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="auto"> to keep up to date with NCBI Virus and other NCBI news.</span><span data-ccp-props='{"134233117":false,"134233118":false,"201341983":0,"335557856":16777215,"335559738":0,"335559739":0,"335559740":240}'> </span></p>
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<p aria-level="2"><span data-contrast="auto">Please </span><a href="https://support.nlm.nih.gov/support/create-case/"><span data-contrast="none">reach out to us</span></a><span data-contrast="auto"> with questions or feedback.</span><span data-ccp-props='{"134245418":true,"134245529":true,"201341983":0,"335559738":0,"335559739":0,"335559740":240}'> </span></p>
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