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Published January 1, 2024 | Version v1
Journal article Open

Genomic Surveillance and Molecular Characterization of SARS-CoV-2 Variants During the Peak of the Pandemic in Türkiye

Creators

  • 1. Univ Hlth Sci, Hamidiye Fac Med, Dept Basic Med Sci, Div Biostatist & Med Informat, Istanbul, Turkiye
  • 2. Yildiz Tech Univ, Fac Sci & Letters, Dept Mol Biol & Genet, Istanbul, Turkiye
  • 3. TUBITAK Marmara Res Ctr, Life Sci, Kocaeli, Turkiye
  • 4. Univ Hlth Sci, Hamidiye Fac Med, Dept Basic Med Sci, Med Biol, Istanbul, Turkiye
  • 5. Univ Hlth Sci, Hamidiye Fac Med, Dept Biostat & Med Informat, Istanbul, Turkiye
  • 6. Int Univ Sarajevo, Fac Engn & Nat Sci, Dept Comp Sci & Engn, Sarajevo, Bosnia & Herceg
  • 7. Univ Hlth Sci, Hamidiye Inst Sci, Mol Med, Hamidiye Hlth Serv Vocat Sch, Istanbul, Turkiye
  • 8. Univ Hlth Sci, Hamidiye Int Fac Med, Dept Med Biol, Istanbul, Turkiye
  • 9. Adana City Training & Res Hosp, Dept Microbiol, Adana, Turkiye
  • 10. Necmettin Erbakan Univ, Meram Fac Med, Dept Internal Med, Div Gastroenterol, Konya, Turkiye
  • 11. Trabzon Kanuni Training & Res Hosp, Clin Infect Dis & Clin Microbiol, Trabzon, Turkiye
  • 12. Univ Hlth Sci, Basaksehir Cam & Sakura City Hosp, Dept Chest Dis, Istanbul, Turkiye
  • 13. Marmara Univ, Fac Med, Dept Internal Med, Div Geriatr, Istanbul, Turkiye
  • 14. Izmir Tepecik Training & Res Hosp, Clin Infect Dis, Izmir, Turkiye
  • 15. Dokuz Eylul Univ, Dept Internal Med, Div Infect Dis, Izmir, Turkiye

Description

SARS-CoV-2 is a highly transmissible coronavirus and has caused a pandemic of acute respiratory disease. Genomic characterization of SARS-CoV-2 is important for monitoring and assessing its evolution. A total of 1.346 nasopharyngeal swab samples were collected but only 879 SARS-CoV-2 high-quality genomes were isolated, subjected to Next Generation Sequencing and analyzed both statistically and regarding mutations comprehensively. The distribution of clades and lineages in different cities of T & uuml;rkiye and the association of SARS-CoV-2 variants with age groups and clinical characteristics of COVID-19 were also examined. Furthermore, the frequency of the clades and lineages was observed in 10 months. Finally, non-synonymous mutations not defined in specific SARS-CoV-2 variants (during that period) were identified by performing mutation analysis. B.1.1.7 (Alpha) and B.1.617.2 (Delta) SARS-CoV-2 variants which have also been identified in our study from March to December 2021. We observed a significant association of SARS-CoV-2 variants with age groups and cities. Also, E:T9I, S:A27S, S:A67V, S:D796Y, S:K417N, S:N440K, S:R158X, S:S477N (below 1%-frequency) were determined as specific mutations belonging and shared with the Omicron variant that appeared later. Our study has highlighted the importance of constant monitoring of the genetic diversity of SARS-CoV-2 to provide better prevention strategies and it contributes to the understanding of SARS-CoV-2 from the past to the present.

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