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SARS-CoV-2 genomic diversity and the implications for qRT-PCR diagnostics and transmission.
Sapoval, Nicolae; Mahmoud, Medhat; Jochum, Michael D; Liu, Yunxi; Elworth, R A Leo; Wang, Qi; Albin, Dreycey; Ogilvie, Huw A; Lee, Michael D; Villapol, Sonia; Hernandez, Kyle M; Maljkovic Berry, Irina; Foox, Jonathan; Beheshti, Afshin; Ternus, Krista; Aagaard, Kjersti M; Posada, David; Mason, Christopher E; Sedlazeck, Fritz J; Treangen, Todd J.
  • Sapoval N; Department of Computer Science, Rice University, Houston, Texas 77005, USA.
  • Mahmoud M; Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030, USA.
  • Jochum MD; Department of Obstetrics and Gynecology, Baylor College of Medicine and Texas Children's Hospital, Houston, Texas 77030, USA.
  • Liu Y; Department of Computer Science, Rice University, Houston, Texas 77005, USA.
  • Elworth RAL; Department of Computer Science, Rice University, Houston, Texas 77005, USA.
  • Wang Q; Systems, Synthetic, and Physical Biology (SSPB) Graduate Program, Rice University, Houston, Texas 77005, USA.
  • Albin D; Systems, Synthetic, and Physical Biology (SSPB) Graduate Program, Rice University, Houston, Texas 77005, USA.
  • Ogilvie HA; Department of Computer Science, Rice University, Houston, Texas 77005, USA.
  • Lee MD; Exobiology Branch, NASA Ames Research Center, Mountain View, California 94043, USA.
  • Villapol S; Blue Marble Space Institute of Science, Seattle, Washington 98104, USA.
  • Hernandez KM; Department of Neurosurgery, Houston Methodist Research Institute, Houston, Texas 77030, USA.
  • Maljkovic Berry I; Department of Medicine, University of Chicago, Chicago, Illinois 60637, USA.
  • Foox J; Center for Translational Data Science, University of Chicago, Chicago, Illinois 60637, USA.
  • Beheshti A; Walter Reed Army Institute of Research, Silver Spring, Maryland 20910, USA.
  • Ternus K; Department of Physiology and Biophysics, Weill Cornell Medicine, New York, New York 10021, USA.
  • Aagaard KM; KBR, Space Biosciences Division, NASA Ames Research Center, Moffett Field, California 94035, USA.
  • Posada D; Signature Science, LLC, Austin, Texas 78759, USA.
  • Mason CE; Department of Obstetrics and Gynecology, Baylor College of Medicine and Texas Children's Hospital, Houston, Texas 77030, USA.
  • Sedlazeck FJ; CINBIO, Universidade de Vigo, 36310 Vigo, Spain.
  • Treangen TJ; Department of Biochemistry, Genetics, and Immunology, Universidade de Vigo, 36310 Vigo, Spain.
Genome Res ; 31(4): 635-644, 2021 04.
Article in English | MEDLINE | ID: covidwho-1145214
Preprint
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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.
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Full text: Available Collection: International databases Database: MEDLINE Main subject: Genetic Variation / Genome, Viral / Real-Time Polymerase Chain Reaction / SARS-CoV-2 / COVID-19 Type of study: Diagnostic study / Observational study / Prognostic study Topics: Variants Limits: Humans Language: English Journal: Genome Res Journal subject: Molecular Biology / Genetics Year: 2021 Document Type: Article Affiliation country: Gr.268961.120

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Full text: Available Collection: International databases Database: MEDLINE Main subject: Genetic Variation / Genome, Viral / Real-Time Polymerase Chain Reaction / SARS-CoV-2 / COVID-19 Type of study: Diagnostic study / Observational study / Prognostic study Topics: Variants Limits: Humans Language: English Journal: Genome Res Journal subject: Molecular Biology / Genetics Year: 2021 Document Type: Article Affiliation country: Gr.268961.120