SARS-CoV-2 genomic diversity and the implications for qRT-PCR diagnostics and transmission

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dc.citation.firstpage635
dc.citation.issueNumber4
dc.citation.journalTitleGenome Research
dc.citation.lastpage644
dc.citation.volumeNumber31
dc.contributor.authorSapoval, Nicolae
dc.contributor.authorMahmoud, Medhat
dc.contributor.authorJochum, Michael D.
dc.contributor.authorLiu, Yunxi
dc.contributor.authorElworth, R. A. Leo
dc.contributor.authorWang, Qi
dc.contributor.authorAlbin, Dreycey
dc.contributor.authorOgilvie, Huw A.
dc.contributor.authorLee, Michael D.
dc.contributor.authorVillapol, Sonia
dc.contributor.authorHernandez, Kyle M.
dc.contributor.authorBerry, Irina Maljkovic
dc.contributor.authorFoox, Jonathan
dc.contributor.authorBeheshti, Afshin
dc.contributor.authorTernus, Krista
dc.contributor.authorAagaard, Kjersti M.
dc.contributor.authorPosada, David
dc.contributor.authorMason, Christopher E.
dc.contributor.authorSedlazeck, Fritz J.
dc.contributor.authorTreangen, Todd J.
dc.date.accessioned2021-05-07T19:23:43Z
dc.date.available2021-05-07T19:23:43Z
dc.date.issued2021
dc.description.abstractThe 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.
dc.identifier.citationSapoval, Nicolae, Mahmoud, Medhat, Jochum, Michael D., et al.. "SARS-CoV-2 genomic diversity and the implications for qRT-PCR diagnostics and transmission." <i>Genome Research,</i> 31, no. 4 (2021) Cold Spring Harbor Laboratory Press: 635-644. https://doi.org/10.1101/gr.268961.120.
dc.identifier.digitalGenomeRes-2021-Sapoval-635-44
dc.identifier.doihttps://doi.org/10.1101/gr.268961.120
dc.identifier.urihttps://hdl.handle.net/1911/110490
dc.language.isoeng
dc.publisherCold Spring Harbor Laboratory Press
dc.rightsThis article, published in Genome Research, is available under a Creative Commons License (Attribution-NonCommercial 4.0 International), as described at http://creativecommons.org/licenses/by-nc/4.0/.
dc.rights.urihttp://creativecommons.org/licenses/by-nc/4.0/.
dc.titleSARS-CoV-2 genomic diversity and the implications for qRT-PCR diagnostics and transmission
dc.typeJournal article
dc.type.dcmiText
dc.type.publicationpublisher version
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