Working Paper Article Version 2 This version is not peer-reviewed

Geographic and Genomic Distribution of SARS-CoV-2 Mutations

Version 1 : Received: 29 April 2020 / Approved: 30 April 2020 / Online: 30 April 2020 (11:15:17 CEST)
Version 2 : Received: 1 July 2020 / Approved: 3 July 2020 / Online: 3 July 2020 (09:45:43 CEST)

A peer-reviewed article of this Preprint also exists.


The novel respiratory disease COVID-19 has reached the status of worldwide pandemic and large efforts are currently being undertaken in molecularly characterizing the virus causing it, SARS-CoV-2. The genomic variability of SARS-CoV-2 specimens scattered across the globe can underly geographically specific etiological effects. In the present study, we gather the 48,635 SARS-CoV-2 complete genomes currently available thanks to the collection endeavor of the GISAID consortium and thousands of contributing laboratories. We analyze and annotate all SARS-CoV-2 mutations compared with the reference Wuhan genome NC_045512.2, observing an average of 7.23 mutations per sample. Our analysis shows the prevalence of single nucleotide transitions as the major mutational type across the world. There exist at least three clades characterized by geographic and genomic specificity. In particular, the clade G, prevalent in Europe, carries a D614G mutation in the Spike protein, which is responsible for the initial interaction of the virus with the host human cell. Our analysis may drive local modulation of antiviral strategies based on the molecular specificities of this novel virus.


SARS-CoV-2; genomics coronavirus; COVID-19 evolution


Biology and Life Sciences, Virology

Comments (1)

Comment 1
Received: 3 July 2020
Commenter: Federico Manuel Giorgi
Commenter's Conflict of Interests: Author
Comment: The analysis is now updated to a more than quadrupled data size
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