Comparative analysis of SARS-CoV-2 quasispecies in the upper and lower respiratory tract shows an ongoing evolution in the spike cleavage site.
Deep sequencing
Deleterious mutations
Minority variants
SARS-CoV-2
Spike protein
Spillover
Journal
Virus research
ISSN: 1872-7492
Titre abrégé: Virus Res
Pays: Netherlands
ID NLM: 8410979
Informations de publication
Date de publication:
02 07 2022
02 07 2022
Historique:
received:
22
09
2021
revised:
14
03
2022
accepted:
12
04
2022
pubmed:
17
4
2022
medline:
18
5
2022
entrez:
16
4
2022
Statut:
ppublish
Résumé
Studies are needed to better understand the genomic evolution of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). This study aimed to describe viral quasispecies population of upper and lower respiratory tract by next-generation sequencing in patients admitted to intensive care unit. A deep sequencing of the S gene of SARS-CoV-2 from 109 clinical specimens, sampled from the upper respiratory tract (URT) and lower respiratory tract (LRT) of 77 patients was performed. A higher incidence of non-synonymous mutations and indels was observed in the LRT among minority variants. This might be explained by the ability of the virus to invade cells without interacting with ACE2 (e.g. exploiting macrophage phagocytosis). Minority variants are highly concentrated around the gene portion encoding for the Spike cleavage site, with a higher incidence in the URT; four mutations are highly recurring among samples and were found associated with the URT. Interestingly, 55.8% of minority variants detected in this locus were T>G and G>T transversions. Results from this study evidenced the presence of selective pressure and suggest that an evolutionary process is still ongoing in one of the crucial sites of spike protein associated with the spillover to humans.
Identifiants
pubmed: 35429618
pii: S0168-1702(22)00113-7
doi: 10.1016/j.virusres.2022.198786
pmc: PMC9008095
pii:
doi:
Substances chimiques
Spike Glycoprotein, Coronavirus
0
spike protein, SARS-CoV-2
0
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
198786Informations de copyright
Copyright © 2022. Published by Elsevier B.V.
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