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

Objectives: We assessed SARS-CoV-2 genome diversity and probable impact on epidemiology, immune response and clinical disease in Turkey. Materials and methods: Complete genomes and partial Spike (S) sequences were accessed from the Global Initiative on Sharing Avian Influenza Data (GISAID) database. The genomes were analysed for variations and recombinations using appropriate softwares. Results: Four hundred ten complete genomes and 206 S region sequences were included. Overall, 1,200 distinct nucleotide variations were noted. Mean variation count was 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%). Most 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 B.1.1.7, B.1.351 and P.1 were detected, with a statistically-significant time-associated increase in B.1.1.7 prevalence. Conclusions: We described prominent SARS-CoV-2 variations as well as comparisons with global virus diversity. Continuing a molecular surveillance in agreement with local disease epidemiology appears to be crucial, as vaccination and mitigation efforts are ongoing.

Automated summary

This study assessed the genome diversity of SARS-CoV-2 in Turkey and found a significant increase in nucleotide variations during the pandemic. The most frequent variations included D614G and P323L. The majority of genomes belonged in the SARS-CoV-2 haplogroup A, and no evidence of recombination was found. Variants B.1.1.7, B.1.351, and P.1 were detected, with a statistically significant increase in the prevalence of B.1.1.7 over time.