3928826
doi
10.5281/zenodo.3928826
oai:zenodo.org:3928826
user-covid-19
ahmedmagds/GNUVID: Globally circulating clonal complexes as of 2020-06-17
Ahmed M Moustafa
Children's Hospital of Philadelphia
url:https://github.com/ahmedmagds/GNUVID/tree/v1.2
info:eu-repo/semantics/openAccess
Other (Open)
Summary:
<ul>
<li><p>18298 GISAID sequences have been included in this analysis.</p>
</li>
<li><p>GNUVID compressed the 182980 ORFs in the 18298 genomes to 10686 unique alleles.</p>
</li>
<li><p>9676 Sequence Types (STs) have been assigned in this dataset and were clustered in 45 clonal complexes (CCs).</p>
</li>
<li><p>21 new CCs have been assigned.</p>
</li>
<li><p>33 CCs have been Inactive (i.e. Last time seen more than 1 month before 2020-06-17).</p>
</li>
<li><p>5 CCs have gone Quiet (i.e. Last seen 2-4 weeks before 2020-06-17).</p>
</li>
<li><p>7 CCs have been Active (i.e. Last seen within the 2 weeks before 2020-06-17).</p>
</li>
<li><p>CC70 and CC26 have now been called CC550 and CC750, respectively.</p>
</li>
<li><p>The three Beijing isolates that are from the <a href="https://www.sciencemag.org/news/2020/06/source-beijing-s-big-new-covid-19-outbreak-still-mystery">recent Beijing's big new COVID-19 outbreak</a> were assigned three new STs that are all Single Locus Variant (SLV) at ORF1ab of ST300, that is mainly found in Europe and founder of CC300.</p>
<ul>
<li><p>Beijing/IVDC-01-06/2020|EPI_ISL_469254|2020-06-11 is assigned to ST9646 (CC300)</p>
</li>
<li><p>Beijing/IVDC-02-06/2020|EPI_ISL_469255|2020-06-11 is assigned to ST9647 (CC300)</p>
</li>
<li><p>Beijing/env/IVDC-03-06/2020|EPI_ISL_469256|2020-06-11 is assigned to ST9648 (CC300)</p>
</li>
</ul>
</li>
</ul>
Zenodo
2020-07-02
info:eu-repo/semantics/other
3927062
user-covid-19
v1.2
1635043030.341297
29604835
md5:e85b8b6a749f3c939b1011c379a93853
https://zenodo.org/records/3928826/files/ahmedmagds/GNUVID-v1.2.zip
public
https://github.com/ahmedmagds/GNUVID/tree/v1.2
Is supplement to
url
10.5281/zenodo.3927062
isVersionOf
doi