Molecular characterization of SARS-CoV-2 in the first COVID-19 cluster in France reveals an amino-acid deletion in nsp2 (Asp268Del)-Reference-Cited by-同舟云学术

Molecular characterization of SARS-CoV-2 in the first COVID-19 cluster in France reveals an amino-acid deletion in nsp2 (Asp268Del)

Published:2020-03-21 Issue: Volume: Page:
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Author:

Bal Antonin,Destras Grégory,Gaymard Alexandre,Bouscambert-Duchamp Maude,Valette Martine,Escuret Vanessa,Frobert Emilie,Billaud Geneviève,Trouillet-Assant Sophie,Cheynet Valérie,Brengel-Pesce Karen,Morfin Florence,Lina Bruno,Josset Laurence

Abstract

AbstractWe present the first genetic characterization of a COVID-19 cluster in Europe using metagenomic next-generation sequencing (mNGS). Despite low viral loads, the mNGS workflow used herein allowed to characterize the whole genome sequences of SARS-CoV2 isolated from an asymptomatic patient, in 2 clinical samples collected 1 day apart. Comparison of these sequences suggests viral evolution with development of quasispecies. In addition, the present workflow identified a new deletion in nsp2 (Asp268Del) which was found in all 3 samples originating from this cluster as well as in 37 other viruses collected in England and in Netherlands, suggesting the spread of this deletion in Europe. The impact of Asp268Del on SARS-CoV-2 transmission and pathogenicity, as well as on PCR performances and anti-viral strategy should be rapidly evaluated in further studies.

Publisher

Cold Spring Harbor Laboratory

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