SARS-CoV-2 genomic diversity and the implications for qRT-PCR diagnostics and transmission.
Journal
Genome research
ISSN: 1549-5469
Titre abrégé: Genome Res
Pays: United States
ID NLM: 9518021
Informations de publication
Date de publication:
04 2021
04 2021
Historique:
received:
16
07
2020
accepted:
12
02
2021
pubmed:
20
2
2021
medline:
15
4
2021
entrez:
19
2
2021
Statut:
ppublish
Résumé
The COVID-19 pandemic has sparked an urgent need to uncover the underlying biology of this devastating disease. Though RNA viruses mutate more rapidly than DNA viruses, there are a relatively small number of single nucleotide polymorphisms (SNPs) that differentiate the main SARS-CoV-2 lineages that have spread throughout the world. In this study, we investigated 129 RNA-seq data sets and 6928 consensus genomes to contrast the intra-host and inter-host diversity of SARS-CoV-2. Our analyses yielded three major observations. First, the mutational profile of SARS-CoV-2 highlights intra-host single nucleotide variant (iSNV) and SNP similarity, albeit with differences in C > U changes. Second, iSNV and SNP patterns in SARS-CoV-2 are more similar to MERS-CoV than SARS-CoV-1. Third, a significant fraction of insertions and deletions contribute to the genetic diversity of SARS-CoV-2. Altogether, our findings provide insight into SARS-CoV-2 genomic diversity, inform the design of detection tests, and highlight the potential of iSNVs for tracking the transmission of SARS-CoV-2.
Identifiants
pubmed: 33602693
pii: gr.268961.120
doi: 10.1101/gr.268961.120
pmc: PMC8015855
doi:
Types de publication
Journal Article
Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't
Research Support, U.S. Gov't, Non-P.H.S.
Langues
eng
Sous-ensembles de citation
IM
Pagination
635-644Subventions
Organisme : NICHD NIH HHS
ID : R01 HD091731
Pays : United States
Organisme : NINDS NIH HHS
ID : R21 NS106640
Pays : United States
Commentaires et corrections
Type : UpdateOf
Informations de copyright
© 2021 Sapoval et al.; Published by Cold Spring Harbor Laboratory Press.
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