RT Journal Article
SR Electronic
T1 Genomic diversity and evolution of coronavirus (SARS-CoV-2) in France from 309 COVID-19-infected patients
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 2020.09.04.282616
DO 10.1101/2020.09.04.282616
A1 Levasseur, Anthony
A1 Delerce, Jeremy
A1 Caputo, Aurelia
A1 Brechard, Ludivine
A1 Colson, Philippe
A1 Lagier, Jean-Christophe
A1 Fournier, Pierre-Edouard
A1 Raoult, Didier
YR 2020
UL http://biorxiv.org/content/early/2020/09/04/2020.09.04.282616.abstract
AB The novel coronavirus (SARS-CoV-2) causes pandemic of viral pneumonia. The evolution and mutational events of the SARS-CoV-2 genomes are critical for controlling virulence, transmissibility, infectivity, severity of symptoms and mortality associated to this infectious disease. We collected and investigated 309 SARS-CoV-2 genomes from patients infected in France. Detailed genome cartography of all mutational events (SNPs, indels) was reported and correlated to clinical features of patients. A comparative analysis between our 309 SARS-CoV-2 genomes from French patients and the reference Wuhan coronavirus genome revealed 315 substitution mutations and six deletion events: ten were in 5’/3’ UTR, 178 were nonsynonymous, 126 were synonymous and one generated a stop codon. Six different deleted areas were also identified in nine viral variants. In particular, 30 substitution mutations (18 nonsynonymous) and one deletion (Δ21765-21770) concerned the spike S glycoprotein. An average of 7.8 mutational events (+/- 1.7 SD) and a median of 8 (range, 7-9) were reported per viral isolate. Comparative analyses and clustering of specific mutational signatures in 309 genomes disclose several divisions in groups and subgroups combining their geographical and phylogenetic origin. Clinical outcomes of the 309 COVID-19-infected patients were investigated according to the mutational signatures of viral variants. These findings highlight the genome dynamics of the coronavirus 2019-20 and shed light on the mutational landscape and evolution of this virus. Inclusion of the French cohort enabled us to identify 161 novel mutations never reported in SARS-CoV-2 genomes collected worldwide. These results support a global and continuing surveillance of the emerging variants of the coronavirus SARS-CoV-2.Competing Interest StatementThe authors have declared no competing interest.Abbreviations:AAAmino AcidGOgood clinical outcomeIndelInsertion and deletionORFOpen Reading FramePClinOpoor clinical outcomePVirOpoor virological outcomeRBDReceptor Binding DomainSDStandard DeviationSNPSingle Nucleotide PolymorphismUTRUntranslated Transcribed Region