SARS-CoV-2 genomic diversity and the implications for qRT-PCR diagnostics and transmission
dc.citation.firstpage | 635 | |
dc.citation.issueNumber | 4 | |
dc.citation.journalTitle | Genome Research | |
dc.citation.lastpage | 644 | |
dc.citation.volumeNumber | 31 | |
dc.contributor.author | Sapoval, Nicolae | |
dc.contributor.author | Mahmoud, Medhat | |
dc.contributor.author | Jochum, Michael D. | |
dc.contributor.author | Liu, Yunxi | |
dc.contributor.author | Elworth, R. A. Leo | |
dc.contributor.author | Wang, Qi | |
dc.contributor.author | Albin, Dreycey | |
dc.contributor.author | Ogilvie, Huw A. | |
dc.contributor.author | Lee, Michael D. | |
dc.contributor.author | Villapol, Sonia | |
dc.contributor.author | Hernandez, Kyle M. | |
dc.contributor.author | Berry, Irina Maljkovic | |
dc.contributor.author | Foox, Jonathan | |
dc.contributor.author | Beheshti, Afshin | |
dc.contributor.author | Ternus, Krista | |
dc.contributor.author | Aagaard, Kjersti M. | |
dc.contributor.author | Posada, David | |
dc.contributor.author | Mason, Christopher E. | |
dc.contributor.author | Sedlazeck, Fritz J. | |
dc.contributor.author | Treangen, Todd J. | |
dc.date.accessioned | 2021-05-07T19:23:43Z | |
dc.date.available | 2021-05-07T19:23:43Z | |
dc.date.issued | 2021 | |
dc.description.abstract | The 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.citation | Sapoval, 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.digital | GenomeRes-2021-Sapoval-635-44 | |
dc.identifier.doi | https://doi.org/10.1101/gr.268961.120 | |
dc.identifier.uri | https://hdl.handle.net/1911/110490 | |
dc.language.iso | eng | |
dc.publisher | Cold Spring Harbor Laboratory Press | |
dc.rights | This 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.uri | http://creativecommons.org/licenses/by-nc/4.0/. | |
dc.title | SARS-CoV-2 genomic diversity and the implications for qRT-PCR diagnostics and transmission | |
dc.type | Journal article | |
dc.type.dcmi | Text | |
dc.type.publication | publisher version |
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