A cross-sectional overview of SARS-CoV-2 genome variations in Turkey

Abstract Introduction: Nearly a year following the emergence of COVID-19 in Turkey, we analysed SARS-CoV-2 sequences to identify virus genome variations and their probable impact on epidemiology, immune response and clinical disease.Materials and Methods: Complete genomes and partial Spike (S) region sequences originating from Turkey were accessed from the Global Initiative on Sharing Avian Influenza Data (GISAID) database. The genomes were aligned and analysed for variations and recombinations using appropriate softwares. Results: 410 complete genomes and 206 S region sequences were included. Overall, 1200 distinct nucleotide variations were noted. Mean variation count was noted as 14.2 per genome and increased significantly during the course of the pandemic. The most frequent variations were identified as A23403G (D614G; 92.9,%), C14408T (P323L, 92.2%), C3037T (89.8%), C241T (83.4%) and GGG28881AAC (RG203KR, 62.6%). The A23403G mutation was the most frequent variation in the S region sequences (99%). Majority of the genomes (%98.3) belonged in the SARS-CoV-2 haplogroup A. No evidence for recombination was identified in genomes representing sub-haplogroup branches. The variants of concern B.1.1.7, B.1.351 and P.1 were detected, with a statistically-significant time-associated increase in the variant B.1.1.7 prevalence. Discussion: We described prominant SARS-CoV-2 variantions as well as comparisons with global virus diversity. Continuing a molecular surveillence in agreement with local disease epidemiology appears to be crucial, as vaccination and mitigation efforts are ongoing.