Spatio-temporal dynamics of intra-host variability in SARS-CoV-2 genomes.
Nucleic Acids Res
; 50(3): 1551-1561, 2022 02 22.
Article
in English
| MEDLINE | ID: covidwho-1636373
ABSTRACT
During the course of the COVID-19 pandemic, large-scale genome sequencing of SARS-CoV-2 has been useful in tracking its spread and in identifying variants of concern (VOC). Viral and host factors could contribute to variability within a host that can be captured in next-generation sequencing reads as intra-host single nucleotide variations (iSNVs). Analysing 1347 samples collected till June 2020, we recorded 16 410 iSNV sites throughout the SARS-CoV-2 genome. We found â¼42% of the iSNV sites to be reported as SNVs by 30 September 2020 in consensus sequences submitted to GISAID, which increased to â¼80% by 30th June 2021. Following this, analysis of another set of 1774 samples sequenced in India between November 2020 and May 2021 revealed that majority of the Delta (B.1.617.2) and Kappa (B.1.617.1) lineage-defining variations appeared as iSNVs before getting fixed in the population. Besides, mutations in RdRp as well as RNA-editing by APOBEC and ADAR deaminases seem to contribute to the differential prevalence of iSNVs in hosts. We also observe hyper-variability at functionally critical residues in Spike protein that could alter the antigenicity and may contribute to immune escape. Thus, tracking and functional annotation of iSNVs in ongoing genome surveillance programs could be important for early identification of potential variants of concern and actionable interventions.
Full text:
Available
Collection:
International databases
Database:
MEDLINE
Main subject:
Genetic Variation
/
Genome, Viral
/
Evolution, Molecular
/
Host-Pathogen Interactions
/
SARS-CoV-2
Type of study:
Observational study
/
Prognostic study
/
Randomized controlled trials
Topics:
Variants
Limits:
Animals
Country/Region as subject:
Asia
Language:
English
Journal:
Nucleic Acids Res
Year:
2022
Document Type:
Article
Affiliation country:
Nar
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