Show simple item record

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.authorHernández, Kyle M.
dc.contributor.authorMaljkovic Berry, Irina
dc.contributor.authorFoox, Jonathan
dc.contributor.authorBeheshti, Afshin
dc.contributor.authorTernus, Krista
dc.contributor.authorAagaard, Kjersti M.
dc.contributor.authorPosada González, David 
dc.contributor.authorMason, Christopher E.
dc.contributor.authorSedlazeck, Fritz J.
dc.contributor.authorTreangen, Todd J.
dc.date.accessioned2022-02-04T11:49:41Z
dc.date.available2022-02-04T11:49:41Z
dc.date.issued2021-02-18
dc.identifier.citationGenome Research, 31(4): 635-644 (2021)en
dc.identifier.issn10889051
dc.identifier.issn15495469
dc.identifier.urihttp://hdl.handle.net/11093/3015
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
dc.description.sponsorshipNational Institutes of Health | Ref. R01HD091731en
dc.description.sponsorshipNational Institute of Allergy and Infectious Diseases | Ref. U19AI144297-01en
dc.description.sponsorshipNational Aeronautics and Space Administration | Ref. NNX16AO69Aen
dc.description.sponsorshipEuropean Research Council | Ref. ERC-617457-PHYLOCANCERen
dc.description.sponsorshipXunta de Galicia | Ref. CT850A-2spa
dc.description.sponsorshipMinisterio de España de Economía y Competitividad | Ref. PID2019-106247GB-I00spa
dc.language.isoengspa
dc.publisherGenome Researchspa
dc.relationinfo:eu-repo/grantAgreement/AEI/ Plan Estatal de Investigación Científica y Técnica y de Innovación 2017 -2020/PID2019-106247GB-I00/ESen
dc.rightsAttribution-NonCommercial 4.0 International
dc.rights.urihttps://creativecommons.org/licenses/by-nc/4.0/
dc.titleSARS-CoV-2 genomic diversity and the implications for qRT-PCR diagnostics and transmissionen
dc.typearticlespa
dc.rights.accessRightsopenAccessspa
dc.relation.projectIDinfo:eu-repo/grantAgreement/EC/FP7/617457en
dc.identifier.doi10.1101/gr.268961.120
dc.identifier.editorhttp://genome.cshlp.org/lookup/doi/10.1101/gr.268961.120en
dc.publisher.departamentoBioquímica, xenética e inmunoloxíaspa
dc.publisher.grupoinvestigacionXenómica e Biomedicinaspa
dc.subject.unesco2409 Genéticaspa
dc.subject.unesco3202 Epidemiologíaspa
dc.date.updated2022-02-04T11:45:34Z
dc.computerCitationpub_title=Genome Research|volume=31|journal_number=4|start_pag=635|end_pag=644spa
dc.referencesThe authors thank Jamie Purcell for feedback and discussion contributions on the effects of variants on the qRT-PCR detection methods. The authors also thank Dr. Luay Nakhleh for suggestions specific to comparative genomic analyses of SARS-CoV-1 and MERS-COV. The authors thank the GISAID contributors who provided the SARS-CoV-2 assemblies. Finally, the authors also thank all members of the COVID-19 International Research Team (www.cov-irt.org) for their helpful feedback during weekly meetings. N.S. and Y.L. are supported by the Department of Computer Science, Rice University. D.A., Q.W., N.S., R.A.L.E., T.J.T., and Y.L. are supported by startup funds from Rice University. N.S. and T.J.T. are partially supported by a C3.ai Digital Transformation Institute COVID-19 award (C3.ai DTI). M.D.J. is supported under National Institutes of Health (NIH) award No. R01HD091731 from the National Institute of Child Health and Human Development. F.J.S. acknowledges funding and part of the data was produced by Baylor College of Medicine under the Division of Intramural Research, National Institute of Allergy and Infectious Diseases (U19AI144297-01). A.B. is supported by supplemental funds for COVID-19 research from Translational Research Institute for Space Health through National Aeronautics and Space Administration Cooperative Agreement NNX16AO69A (T-0404) and further funding was provided by KBR, Inc. D.P. is supported by the European Research Council (ERC-617457-PHYLOCANCER), Spanish Ministry of Economy and Competitiveness (PID2019-106247GB-I00), Fondo Supera COVID19 (EPICOVIGAL), and Xunta de Galicia (CT850A-2).en


Files in this item

[PDF]

    Show simple item record

    Attribution-NonCommercial 4.0 International
    Except where otherwise noted, this item's license is described as Attribution-NonCommercial 4.0 International