RT Journal Article
SR Electronic
T1 Large scale genomic analysis of 3067 SARS-CoV-2 genomes reveals a clonal geo-distribution and a rich genetic variations of hotspots mutations
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 2020.05.03.074567
DO 10.1101/2020.05.03.074567
A1 Meriem Laamarti
A1 Tarek Alouane
A1 Souad Kartti
A1 M.W. Chemao-Elfihri
A1 Mohammed Hakmi
A1 Abdelomunim Essabbar
A1 Mohamed Laamarti
A1 Haitam Hlali
A1 Loubna Allam
A1 Naima El Hafidi
A1 Rachid El Jaoudi
A1 Imane Allali
A1 Nabila Marchoudi
A1 Jamal Fekkak
A1 Houda Benrahma
A1 Chakib Nejjari
A1 Saaid Amzazi
A1 Lahcen Belyamani
A1 Azeddine Ibrahimi
YR 2020
UL http://biorxiv.org/content/early/2020/05/21/2020.05.03.074567.abstract
AB In late December 2019, an emerging viral infection COVID-19 was identified in Wuhan, China, and became a global pandemic. Characterization of the genetic variants of SARS-CoV-2 is crucial in following and evaluating it spread across countries. In this study, we collected and analyzed 3,067 SARS-CoV-2 genomes isolated from 55 countries during the first three months after the onset of this virus. Using comparative genomics analysis, we traced the profiles of the whole-genome mutations and compared the frequency of each mutation in the studied population. The accumulation of mutations during the epidemic period with their geographic locations was also monitored. The results showed 782 variant sites, of which 512 (65.47%) had a non-synonymous effect. Frequencies of mutated alleles revealed the presence of 38 recurrent non-synonymous mutations, including ten hotspot mutations with a prevalence higher than 0.10 in this population and distributed in six SARS-CoV-2 genes. The distribution of these recurrent mutations on the world map revealed certain genotypes specific to the geographic location. We also found co-occurring mutations resulting in the presence of several haplotypes. Moreover, evolution over time has shown a mechanism of mutation co-accumulation which might affect the severity and spread of the SARS-CoV-2.On the other hand, analysis of the selective pressure revealed the presence of negatively selected residues that could be taken into considerations as therapeutic targetsWe have also created an inclusive unified database (http://genoma.ma/covid-19/) that lists all of the genetic variants of the SARS-CoV-2 genomes found in this study with phylogeographic analysis around the world.Competing Interest StatementThe authors have declared no competing interest.