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Relevant SARS-CoV-2 Genome Variation through Six Months of Worldwide Monitoring.
Hakmaoui, Abdelmalek; Khan, Faisal; Liacini, Abdelhamid; Kaur, Amanjot; Berka, Yacine; Machraoui, Safaa; Soualhine, Hafid; Berka, Noureddine; Rais, Hanane; Admou, Brahim.
  • Hakmaoui A; Center of Clinical Research, University Hospital Mohammed VI, Marrakech, Morocco.
  • Khan F; Cumming School of Medicine, University of Calgary, Canada.
  • Liacini A; Immunogenetics Laboratory, Temple University and Hospital, Lewis Katz School of Medicine, USA.
  • Kaur A; Cumming School of Medicine, University of Calgary, Canada.
  • Berka Y; University of Calgary, Alberta, Canada.
  • Machraoui S; Center of Clinical Research, University Hospital Mohammed VI, Marrakech, Morocco.
  • Soualhine H; National Microbiology Laboratory Public Health Agency of Canada, 1015 Arlington Street, Winnipeg, MB, Canada.
  • Berka N; Department of Pathology and Lab Medicine, University of Calgary, Alberta, Canada.
  • Rais H; Center of Clinical Research, University Hospital Mohammed VI, Marrakech, Morocco.
  • Admou B; Center of Clinical Research, University Hospital Mohammed VI, Marrakech, Morocco.
Biomed Res Int ; 2021: 5553173, 2021.
Article in English | MEDLINE | ID: covidwho-1288476
ABSTRACT
Real-time genome monitoring of the SARS-CoV-2 pandemic outbreak is of utmost importance for designing diagnostic tools, guiding antiviral treatment and vaccination strategies. In this study, we present an accurate method for temporal and geographical comparison of mutational events based on GISAID database genome sequencing. Among 42523 SARS-CoV-2 genomes analyzed, we found 23202 variants compared to the reference genome. The Ti/Tv (transition/transversion) ratio was used to filter out possible false-positive errors. Transition mutations generally occurred more frequently than transversions. Our clustering analysis revealed remarkable hotspot mutation patterns for SARS-CoV-2. Mutations were clustered based on how their frequencies changed over time according to each geographical location. We observed some clusters showing a clear variation in mutation frequency and continuously evolving in the world. However, many mutations appeared in specific periods without a clear pattern over time. Various important nonsynonymous mutations were observed, mainly in Oceania and Asia. More than half of these mutations were observed only once. Four hotspot mutations were found in all geographical locations at least once T265I (NSP2), P314L (NSP12), D614G (S), and Q57H (ORF3a). The current analysis of SARS-CoV-2 genomes provides valuable information on the geographical and temporal mutational evolution of SARS-CoV-2.
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Full text: Available Collection: International databases Database: MEDLINE Main subject: Phylogeny / Genome, Viral / Evolution, Molecular / Databases, Nucleic Acid / Pandemics / SARS-CoV-2 / COVID-19 / Mutation Type of study: Diagnostic study / Observational study / Randomized controlled trials Topics: Vaccines / Variants Limits: Humans Language: English Journal: Biomed Res Int Year: 2021 Document Type: Article Affiliation country: 2021

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Full text: Available Collection: International databases Database: MEDLINE Main subject: Phylogeny / Genome, Viral / Evolution, Molecular / Databases, Nucleic Acid / Pandemics / SARS-CoV-2 / COVID-19 / Mutation Type of study: Diagnostic study / Observational study / Randomized controlled trials Topics: Vaccines / Variants Limits: Humans Language: English Journal: Biomed Res Int Year: 2021 Document Type: Article Affiliation country: 2021