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Whole genome sequencing of SARS-CoV2 strains circulating in Iran during five waves of pandemic

Yavarian, J ; Sharif University of Technology | 2022

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  1. Type of Document: Article
  2. DOI: 10.1371/journal.pone.0267847
  3. Publisher: Public Library of Science , 2022
  4. Abstract:
  5. Purpose Whole genome sequencing of SARS-CoV2 is important to find useful information about the viral lineages, variants of interests and variants of concern. As there are not enough data about the circulating SARS-CoV2 variants in Iran, we sequenced 54 SARS-CoV2 genomes during the 5 waves of pandemic in Iran. Methods After viral RNA extraction from clinical samples collected during the COVID-19 pandemic, next generation sequencing was performed using the Nextseq platform. The sequencing data were analyzed and compared with reference sequences. Results During the 1st wave, V and L clades were detected. The second wave was recognized by G, GH and GR clades. Circulating clades during the 3rd wave were GH and GR. In the fourth wave GRY (alpha variant), GK (delta variant) and one GH clade (beta variant) were detected. All viruses in the fifth wave were in clade GK (delta variant). There were different mutations in all parts of the genomes but Spike-D614G, NSP12-P323L, N-R203K and N-G204R were the most frequent mutants in these studied viruses. Conclusions These findings display the significance of SARS-CoV2 monitoring to help on time detection of possible variants for pandemic control and vaccination plans. © 2022 Yavarian et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited
  6. Keywords:
  7. Virus RNA ; Cladistics ; Coronavirus disease 2019 ; Data analysis ; High throughput sequencing ; Human ; Infection control ; Mutational analysis ; Nonhuman ; RNA extraction ; SARS-CoV-2 Alpha ; SARS-CoV-2 Beta ; SARS-CoV-2 Delta ; Severe acute respiratory syndrome coronavirus 2 ; Vaccination ; Variant of concern ; Variant of interest ; Virus detection ; Virus mutant ; Virus strain ; Genetics ; Influenza ; Pandemic ; Whole genome sequencing ; COVID-19 ; Humans ; Influenza, Human ; Iran ; Pandemics ; RNA, Viral ; SARS-CoV-2
  8. Source: PLoS ONE ; Volume 17, Issue 5 May , 2022 ; 19326203 (ISSN)
  9. URL: https://pubmed.ncbi.nlm.nih.gov/35499994