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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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&lt;li&gt;&lt;p&gt;25594 GISAID sequences have been included in this analysis.&lt;/p&gt;
&lt;li&gt;&lt;p&gt;GNUVID compressed the 255940 ORFs in the 25594 genomes to 15025 unique alleles.&lt;/p&gt;
&lt;li&gt;&lt;p&gt;13688 Sequence Types (STs) have been assigned in this dataset and were clustered in 59 clonal complexes (CCs).&lt;/p&gt;
&lt;li&gt;&lt;p&gt;14 new CCs have been assigned.&lt;/p&gt;
&lt;li&gt;&lt;p&gt;42 CCs have been Inactive (i.e. Last time seen more than 1 month before 2020-07-17).&lt;/p&gt;
&lt;li&gt;&lt;p&gt;12 CCs have gone Quiet (i.e. Last seen 2-4 weeks before 2020-07-17).&lt;/p&gt;
&lt;li&gt;&lt;p&gt;5 CCs have been Active (i.e. Last seen within the 2 weeks before 2020-07-17).&lt;/p&gt;
&lt;li&gt;&lt;p&gt;CC70, CC26, CC343, CC927 and CC1434 have now been called CC550, CC750, CC9999, CC1179 and CC2175 respectively.&lt;/p&gt;
&lt;li&gt;&lt;p&gt;Starting from the DB update (07/17/2020), &lt;strong&gt;the nine defining SNPs (C241,C3037,A23403,C8782,G11083,G25563,G26144,T28144,G28882)&lt;/strong&gt; for the six GISAID clades are reported for each CC for easier correlation between the two systems.&lt;/p&gt;
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