COVID-19 infection and transmission includes complex sequence diversity

SARS-CoV-2 whole genome sequencing has played an important role in documenting the emergence of polymorphisms in the viral genome and its continuing evolution during the COVID-19 pandemic. Here we present data from over 360 patients to characterize the complex sequence diversity of individual infect...

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Bibliographic Details
Published in:PLoS genetics 2022-09, Vol.18 (9), p.e1010200-e1010200
Main Authors: Chan, Ernest R, Jones, Lucas D, Linger, Marlin, Kovach, Jeffrey D, Torres-Teran, Maria M, Wertz, Audric, Donskey, Curtis J, Zimmerman, Peter A
Format: Article
Language:English
Subjects:
Analysis
Biology and life sciences
Conserved sequence
Coronaviruses
COVID-19
COVID-19 - genetics
Disease transmission
DNA sequencing
Genome, Viral - genetics
Genomes
Genomics
HIV
Human immunodeficiency virus
Humans
Infections
Influenza
Medicine and health sciences
Methods
Mutation
Nucleotide sequence
Nucleotide sequencing
Pandemics
Patients
Research and Analysis Methods
RNA polymerase
SARS-CoV-2 - genetics
Severe acute respiratory syndrome coronavirus 2
Single-nucleotide polymorphism
Viruses
Whole genome sequencing
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Summary:SARS-CoV-2 whole genome sequencing has played an important role in documenting the emergence of polymorphisms in the viral genome and its continuing evolution during the COVID-19 pandemic. Here we present data from over 360 patients to characterize the complex sequence diversity of individual infections identified during multiple variant surges (e.g., Alpha and Delta). Across our survey, we observed significantly increasing SARS-CoV-2 sequence diversity during the pandemic and frequent occurrence of multiple biallelic sequence polymorphisms in all infections. This sequence polymorphism shows that SARS-CoV-2 infections are heterogeneous mixtures. Convention for reporting microbial pathogens guides investigators to report a majority consensus sequence. In our study, we found that this approach would under-report sequence variation in all samples tested. As we find that this sequence heterogeneity is efficiently transmitted from donors to recipients, our findings illustrate that infection complexity must be monitored and reported more completely to understand SARS-CoV-2 infection and transmission dynamics. Many of the nucleotide changes that would not be reported in a majority consensus sequence have now been observed as lineage defining SNPs in Omicron BA.1 and/or BA.2 variants. This suggests that minority alleles in earlier SARS-CoV-2 infections may play an important role in the continuing evolution of new variants of concern.
ISSN:1553-7404
1553-7390
1553-7404
DOI:10.1371/journal.pgen.1010200