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<!DOCTYPE html>
<html lang="en">
<head>
<meta charset="utf-8">
<meta http-equiv="X-UA-Compatible" content="IE=edge">
<meta name="viewport" content="width=device-width, initial-scale=1">
<title>SARS-CoV-2-Variants by @3dgiordano</title>
<meta name="generator" content="Jekyll v3.9.0" />
<meta property="og:title" content="SARS-CoV-2-Variants" />
<meta name="author" content="David Giordano" />
<meta property="og:locale" content="en_US" />
<meta name="description" content="SARS-CoV-2-Variants by @3dgiordano" />
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<div class="info">
<h1>SARS-CoV-2 Variants</h1>
<div class="info">
This site tries to give a glimpse of the different variants of SAR-CoV-2 in the world.<br />
<br />
<b>Last update: </b><span id="last_update"></span><br>
<br /><br />
<table class="actions"><tr><td><a class="button" href="./">Sequences</a></td><td><a class="button" href="fit">Fitting cases to sequences</a></td><td><a class="button_active" href="about">About</a></td></tr></table><table></table><br>
<br />
<b>About:</b><br />
<br />
The project, site, published data, and graphics are free and open source.<br />
A work in progress project created by <a href="https://github.com/3dgiordano"
target="_blank">@3dgiordano</a>.<br />
They can access the source code and data in their GitHub project <a
href="https://github.com/3dgiordano/SARS-CoV-2-Variants"
target="_blank">https://github.com/3dgiordano/SARS-CoV-2-Variants</a>.</br>
<br />
<b>Genomic data sources:</b><br />
<br />
<b>outbreak.info</b><br />
<br />
Julia L. Mullen, Ginger Tsueng, Alaa Abdel Latif, Manar Alkuzweny, Marco Cano, Emily Haag, Jerry Zhou, Mark
Zeller, Emory Hufbauer, Nate Matteson, Kristian G. Andersen, Chunlei Wu, Andrew I. Su, Karthik Gangavarapu, Laura
D. Hughes, and the Center for Viral Systems Biology outbreak.info. Available online: <a
href="https://outbreak.info/" target="_blank">https://outbreak.info/</a> (2020)<br />
<br />
<b>GISAID Initiative</b><br />
<br />
Elbe, S., and Buckland-Merrett, G. (2017) Data, disease and diplomacy: GISAID’s innovative contribution to global
health. Global Challenges, 1:33-46. DOI: 10.1002/gch2.1018 PMCID: 31565258; Shu, Y., McCauley, J. (2017) GISAID:
Global initiative on sharing all influenza data – from vision to reality. EuroSurveillance, 22(13) DOI:
10.2807/1560-7917.ES.2017.22.13.30494 PMCID: PMC5388101 data license: <a
href="https://www.gisaid.org/registration/terms-of-use/"
target="_blank">https://www.gisaid.org/registration/terms-of-use/</a><br />
<br />
<b>Important:</b>
Sequencing data is not a random sample selection and does not represent actual prevalence, it is an
estimate.<br />
<br />
<b>Naming:</b><br />
<br />
The naming system used is a mix between the names denominated by WHO, the Pango Lineage system and some Nextstrain
Clade names.<br />
<br />
The project use the denomination of:<br />
<ul>
<li>WHO/CDC/ECDC/PHE Variants of Concern (VOC)</li>
<li>WHO/CDC/ECDC Variants of Interest (VOI)</li>
<li>WHO Alerts for Further Monitoring (AFM)</li>
<li>CDC Variants Being Monitored (VBM)</li>
<li>ECDC Variants Under Monitoring (VUM)</li>
<li>PHE Variants Under Investigation (VUI)</li>
</ul>
<br />
If a major variant is detected, the WHO name is used.<br />
If it is some other variant to consider not yet considered by WHO, its Pango lineage is used.<br />
Otherwise, the first letters of the Pango lineage are used.<br />
If the variant is in WHO/CDC/ECDC/PHE VOI, VUI, VOC, AFM or VUM, the label is included.<br />
<br />
For more information about lineages names and classifications<br />
<ul>
<li>WHO <a href="https://www.who.int/en/activities/tracking-SARS-CoV-2-variants/" target="_blank">Tracking
SARS-CoV-2 variants</a></li>
<li>CDC <a href="https://www.cdc.gov/coronavirus/2019-ncov/variants/variant-info.html"
target="_blank">SARS-CoV-2 Variant Classifications and Definitions</a></li>
<li>ECDC <a href="https://www.ecdc.europa.eu/en/covid-19/variants-concern" target="_blank">SARS-CoV-2 variants
of concern</a></li>
<li>PHE <a href="https://www.gov.uk/government/collections/new-sars-cov-2-variant" target="_blank">COVID-19
(SARS-CoV-2) variants</a></li>
</ul>
<br />
</div>
</div>
<script>
start();
</script>
</body>
</html>