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ahmedmagds/GNUVID: GNUVID v1.3: Globally circulating clonal complexes as of 2020-07-17

Ahmed M Moustafa


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  <dc:creator>Ahmed M Moustafa</dc:creator>
  <dc:date>2020-07-30</dc:date>
  <dc:description>Summary

25594 GISAID sequences have been included in this analysis.

GNUVID compressed the 255940 ORFs in the 25594 genomes to 15025 unique alleles.

13688 Sequence Types (STs) have been assigned in this dataset and were clustered in 59 clonal complexes (CCs).

14 new CCs have been assigned.

42 CCs have been Inactive (i.e. Last time seen more than 1 month before 2020-07-17).

12 CCs have gone Quiet (i.e. Last seen 2-4 weeks before 2020-07-17).

5 CCs have been Active (i.e. Last seen within the 2 weeks before 2020-07-17).

CC70, CC26, CC343, CC927 and CC1434 have now been called CC550, CC750, CC9999, CC1179 and CC2175 respectively.

Starting from the DB update (07/17/2020), the nine defining SNPs (C241,C3037,A23403,C8782,G11083,G25563,G26144,T28144,G28882) for the six GISAID clades are reported for each CC for easier correlation between the two systems.

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  <dc:identifier>https://zenodo.org/record/3966904</dc:identifier>
  <dc:identifier>10.5281/zenodo.3966904</dc:identifier>
  <dc:identifier>oai:zenodo.org:3966904</dc:identifier>
  <dc:relation>url:https://github.com/ahmedmagds/GNUVID/tree/v1.3</dc:relation>
  <dc:relation>doi:10.5281/zenodo.3927062</dc:relation>
  <dc:relation>url:https://zenodo.org/communities/covid-19</dc:relation>
  <dc:relation>url:https://zenodo.org/communities/zenodo</dc:relation>
  <dc:rights>info:eu-repo/semantics/openAccess</dc:rights>
  <dc:title>ahmedmagds/GNUVID: GNUVID v1.3: Globally circulating clonal complexes as of 2020-07-17</dc:title>
  <dc:type>info:eu-repo/semantics/other</dc:type>
  <dc:type>software</dc:type>
</oai_dc:dc>
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