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

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dc.citation.firstpage635en_US
dc.citation.issueNumber4en_US
dc.citation.journalTitleGenome Researchen_US
dc.citation.lastpage644en_US
dc.citation.volumeNumber31en_US
dc.contributor.authorSapoval, Nicolaeen_US
dc.contributor.authorMahmoud, Medhaten_US
dc.contributor.authorJochum, Michael D.en_US
dc.contributor.authorLiu, Yunxien_US
dc.contributor.authorElworth, R. A. Leoen_US
dc.contributor.authorWang, Qien_US
dc.contributor.authorAlbin, Dreyceyen_US
dc.contributor.authorOgilvie, Huw A.en_US
dc.contributor.authorLee, Michael D.en_US
dc.contributor.authorVillapol, Soniaen_US
dc.contributor.authorHernandez, Kyle M.en_US
dc.contributor.authorBerry, Irina Maljkovicen_US
dc.contributor.authorFoox, Jonathanen_US
dc.contributor.authorBeheshti, Afshinen_US
dc.contributor.authorTernus, Kristaen_US
dc.contributor.authorAagaard, Kjersti M.en_US
dc.contributor.authorPosada, Daviden_US
dc.contributor.authorMason, Christopher E.en_US
dc.contributor.authorSedlazeck, Fritz J.en_US
dc.contributor.authorTreangen, Todd J.en_US
dc.date.accessioned2021-05-07T19:23:43Zen_US
dc.date.available2021-05-07T19:23:43Zen_US
dc.date.issued2021en_US
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.en_US
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.en_US
dc.identifier.digitalGenomeRes-2021-Sapoval-635-44en_US
dc.identifier.doihttps://doi.org/10.1101/gr.268961.120en_US
dc.identifier.urihttps://hdl.handle.net/1911/110490en_US
dc.language.isoengen_US
dc.publisherCold Spring Harbor Laboratory Pressen_US
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/.en_US
dc.rights.urihttp://creativecommons.org/licenses/by-nc/4.0/.en_US
dc.titleSARS-CoV-2 genomic diversity and the implications for qRT-PCR diagnostics and transmissionen_US
dc.typeJournal articleen_US
dc.type.dcmiTexten_US
dc.type.publicationpublisher versionen_US
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