134 lines
59 KiB
HTML
134 lines
59 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="NCBI Taxonomy: Upcoming Changes to Viruses - NCBI Insights"><meta property="og:description" content="To reflect changes to the International Code of Virus Classification and Nomenclature (ICVCN) made by the International Committee on Taxonomy of Viruses (ICTV), NCBI will add binomial species names to about 3000 viruses. These updates to NCBI Taxonomy are planned for spring 2025, but you can view the changes now in the ICTV’s Virus Metadata Resource. We recognize that the former … Continue reading NCBI Taxonomy: Upcoming Changes to Viruses →"><meta property="og:url" content="https://ncbiinsights.ncbi.nlm.nih.gov/2024/12/11/ncbi-taxonomy-changes-to-viruses/"><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="2024-12-11T19:31:51+00:00"><meta property="og:image" content="https://ncbiinsights.ncbi.nlm.nih.gov/wp-content/uploads/2024/12/Viruses_NCBI-Taxonomy-1-e1733927970690.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 name="twitter:creator" content="@NCBI"><meta name="twitter:site" content="@NCBI"><meta name="twitter:label1" content="Written by"><meta name="twitter:data1" content="NCBI Staff"><meta 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<h1 class="amp-wp-title">NCBI Taxonomy: Upcoming Changes to Viruses</h1>
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<time datetime="2024-12-11T19:31:51+00:00">
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3 months ago </time>
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<figure class="amp-wp-article-featured-image wp-caption">
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<amp-img width="1024" height="535" src="https://i0.wp.com/ncbiinsights.ncbi.nlm.nih.gov/wp-content/uploads/2024/12/Viruses_NCBI-Taxonomy-1-e1733927970690.png?fit=1024%2C535&ssl=1" class="attachment-large size-large wp-post-image amp-wp-enforced-sizes i-amphtml-layout-intrinsic i-amphtml-layout-size-defined" alt="Image of glowing virus cells on a black background. Text says: Coming soon! Updates to Viruses. NCBI Taxonomy" data-hero-candidate="" layout="intrinsic" data-hero i-amphtml-ssr i-amphtml-layout="intrinsic"><i-amphtml-sizer slot="i-amphtml-svc" class="i-amphtml-sizer"><img alt="" aria-hidden="true" class="i-amphtml-intrinsic-sizer" role="presentation" src="data:image/svg+xml;base64,PHN2ZyBoZWlnaHQ9IjUzNSIgd2lkdGg9IjEwMjQiIHhtbG5zPSJodHRwOi8vd3d3LnczLm9yZy8yMDAwL3N2ZyIgdmVyc2lvbj0iMS4xIi8+"></i-amphtml-sizer><img class="i-amphtml-fill-content i-amphtml-replaced-content" decoding="async" loading="lazy" alt="Image of glowing virus cells on a black background. Text says: Coming soon! Updates to Viruses. NCBI Taxonomy" src="https://i0.wp.com/ncbiinsights.ncbi.nlm.nih.gov/wp-content/uploads/2024/12/Viruses_NCBI-Taxonomy-1-e1733927970690.png?fit=1024%2C535&ssl=1"></amp-img> </figure>
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<div class="amp-wp-article-content">
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<p><span data-contrast="none">To reflect changes to the </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"> (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 3000 viruses. These updates 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’s Virus Metadata Resource</span></a><span data-contrast="none">.</span><span data-ccp-props='{"201341983":0,"335557856":16777215,"335559739":0,"335559740":240}'> </span></p>
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<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. </span><i><span data-contrast="none">Lentivirus humimdef1</span></i><span data-contrast="none">) while keeping</span><span data-contrast="none"> the former names available in the 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. </span><span data-ccp-props='{"201341983":0,"335557856":16777215,"335559739":0,"335559740":240}'> </span></p>
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<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"> 11676 </span><span data-contrast="none">will still refer to</span><span data-contrast="none"> HIV-1.</span><span data-contrast="none"> Also, the taxon currently associated with a sequence record will still be displayed prominently on sequence records and BLAST® 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">. </span><span data-ccp-props='{"201341983":0,"335557856":16777215,"335559739":0,"335559740":240}'> </span></p>
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<h5>What’s changing?</h5>
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<p><span data-ccp-props='{"201341983":0,"335557856":16777215,"335559739":0,"335559740":240}'> </span><b><span data-contrast="none">Former lineages</span></b><span data-ccp-props='{"201341983":0,"335557856":16777215,"335559739":0,"335559740":240}'> </span></p>
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<table data-tablestyle="MsoNormalTable" data-tablelook="1184" data-amp-original-style="font-weight: 400;" class="amp-wp-fe3f5cc">
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<tbody>
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<tr>
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<td data-celllook="4369"><span data-amp-original-style="font-size: 17px;" class="amp-wp-8bdd01f"><b>Genus</b> </span></td>
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<td data-celllook="4369"><span data-amp-original-style="font-size: 17px;" class="amp-wp-8bdd01f"><b>Species</b> </span></td>
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</tr>
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<tr>
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<td data-celllook="4369"><span data-amp-original-style="font-size: 17px;" class="amp-wp-8bdd01f"><i>Lentivirus</i> </span></td>
|
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<td data-celllook="4369"><span data-amp-original-style="font-size: 17px;" class="amp-wp-8bdd01f"><i>Human immunodeficiency virus 1</i> </span></td>
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</tr>
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||
<tr>
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<td data-celllook="4369"><span data-amp-original-style="font-size: 17px;" class="amp-wp-8bdd01f"><i>Betacoronavirus</i> </span></td>
|
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<td data-celllook="4369"><span data-amp-original-style="font-size: 17px;" class="amp-wp-8bdd01f"><i>Severe acute respiratory syndrome-related coronavirus</i> </span></td>
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||
</tr>
|
||
<tr>
|
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<td data-celllook="4369"><span data-amp-original-style="font-size: 17px;" class="amp-wp-8bdd01f"><i>Orthopoxvirus</i> </span></td>
|
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<td data-celllook="4369"><span data-amp-original-style="font-size: 17px;" class="amp-wp-8bdd01f"><i>Monkeypox virus</i> </span></td>
|
||
</tr>
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||
</tbody>
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||
</table>
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<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}'> </span></p>
|
||
<table data-tablestyle="MsoNormalTable" data-tablelook="1184">
|
||
<tbody>
|
||
<tr>
|
||
<td data-celllook="4369"><span data-amp-original-style="font-size: 17px;" class="amp-wp-8bdd01f"><b>Genus</b> </span></td>
|
||
<td data-celllook="4369"><span data-amp-original-style="font-size: 17px;" class="amp-wp-8bdd01f"><b>Species</b> </span></td>
|
||
<td data-celllook="4369"><span data-amp-original-style="font-size: 17px;" class="amp-wp-8bdd01f"><b>Below species</b> </span></td>
|
||
</tr>
|
||
<tr>
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<td data-celllook="4369"><span data-amp-original-style="font-size: 17px;" class="amp-wp-8bdd01f"><i>Lentivirus</i> </span></td>
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<td data-celllook="4369"><span data-amp-original-style="font-size: 17px;" class="amp-wp-8bdd01f"><i>Lentivirus humimdef1</i> </span></td>
|
||
<td data-celllook="4369"><span data-amp-original-style="font-size: 17px;" class="amp-wp-8bdd01f"><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> </span></td>
|
||
</tr>
|
||
<tr>
|
||
<td data-celllook="4369"><span data-amp-original-style="font-size: 17px;" class="amp-wp-8bdd01f"><i>Betacoronavirus</i> </span></td>
|
||
<td data-celllook="4369"><span data-amp-original-style="font-size: 17px;" class="amp-wp-8bdd01f"><i>Betacoronavirus pandemicum</i> </span></td>
|
||
<td data-celllook="4369"><span data-amp-original-style="font-size: 17px;" class="amp-wp-8bdd01f"><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> </span></td>
|
||
</tr>
|
||
<tr>
|
||
<td data-celllook="4369"><span data-amp-original-style="font-size: 17px;" class="amp-wp-8bdd01f"><i>Orthopoxvirus</i> </span></td>
|
||
<td data-celllook="4369"><span data-amp-original-style="font-size: 17px;" class="amp-wp-8bdd01f"><i>Orthopoxvirus monkeypox</i> </span></td>
|
||
<td data-celllook="4369"><span data-amp-original-style="font-size: 17px;" class="amp-wp-8bdd01f"><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> </span></td>
|
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</tr>
|
||
</tbody>
|
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</table>
|
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<h5><b><span data-contrast="none">What to consider when accessing or submitting virus data at NCBI</span></b></h5>
|
||
<ul>
|
||
<li data-leveltext="" data-font="Symbol" data-listid="1" data-list-defn-props='{"335552541":1,"335559685":720,"335559991":360,"469769226":"Symbol","469769242":[8226],"469777803":"left","469777804":"","469777815":"multilevel"}' aria-setsize="-1" data-aria-posinset="1" data-aria-level="1"><span data-amp-original-style="font-size: 17px;" class="amp-wp-8bdd01f"><b>Taxonomy-Based Searches:</b> In 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. </span></li>
|
||
<li data-leveltext="" data-font="Symbol" data-listid="1" data-list-defn-props='{"335552541":1,"335559685":720,"335559991":360,"469769226":"Symbol","469769242":[8226],"469777803":"left","469777804":"","469777815":"multilevel"}' aria-setsize="-1" data-aria-posinset="1" data-aria-level="1"><span data-amp-original-style="font-size: 17px;" class="amp-wp-8bdd01f"><b>Data Submissions: </b>Viral data submission to GenBank, BioSample, and Sequence Read Archive (SRA) will remain the same. </span></li>
|
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</ul>
|
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<h5><b><span data-contrast="none">What’s next?</span></b><span data-ccp-props='{"201341983":0,"335557856":16777215,"335559739":0,"335559740":240}'> </span></h5>
|
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<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 <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 <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>
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