The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.Ĭompeting interests: I have read the journal’s policy and the authors of this manuscript have the following competing interests: CJD has received research grants from Clorox, Pfizer, and PDI. The work is made available under the Creative Commons CC0 public domain dedication.ĭata Availability: All of our sequence data have been reported to GenBank (NCBI – GenBank Accession numbers OM988245-OM988384).įunding: This work was supported by a Merit Review grant (CX001848) from the US Department of Veterans Affairs to CJD and by a grant from the US Department of Veterans Affairs Office of Research and Development as part of funding for VASeqCURE (grant number N/A) which in turn received funding from the American Rescue Plan Act funds.
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Received: ApAccepted: JPublished: September 8, 2022 PLoS Genet 18(9):Įditor: Susana Campino, London School of Hygiene & Tropical Medicine, UNITED KINGDOM (2022) COVID-19 infection and transmission includes complex sequence diversity. 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.Ĭitation: Chan ER, Jones LD, Linger M, Kovach JD, Torres-Teran MM, Wertz A, et al. 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. 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. In our study, we found that this approach would under-report sequence variation in all samples tested. Convention for reporting microbial pathogens guides investigators to report a majority consensus sequence. This sequence polymorphism shows that SARS-CoV-2 infections are heterogeneous mixtures.
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. 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). 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.
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