Genome Monitoring of SARS-CoV-2 Circulating in the Kyrgyz Republic in 2020–2021

Abstract

Introduction: The RNA-containing severe acute respiratory syndrome virus SARS-CoV-2 has spread rapidly around the world by adaptation to the host through genetic evolution. The emergence of variants with genetic mutations that increase contagiousness and transmission may hamper the effectiveness of disease control programs and efficacy of vaccination. Objective: To establish dominant SARS-CoV-2 variants circulating in the Kyrgyz Republic in 2020–2021. Materials and methods: Genomic monitoring was carried out based on positive results of testing nasopharyngeal swabs. SARS-CoV-2 was detected by a real-time reverse transcription –polymerase chain reaction (RT-PCR) assay using registered commercial test kits. Genetic variants (n = 15) were determined by high-throughput sequencing on a MiSeq device (Illumina, USA) using the COVID-19 ARTIC v3 protocol. Mutational variability of SARS-CoV-2 was examined using a cluster analysis of amino acid substitutions in the S protein using Ward’s method. Nucleotide sequences from Kyrgyzstan (n = 15), Russia (n = 16), India (n = 2), and China (n = 2) were aligned using MAFFT. IQ-TREE v1.6.12 was used to infer the phylogenetic tree by maximum likelihood applying Nextstrain processes. Isolates Wuhan/Hu-1/2019 and Wuhan/WH01/2019 downloaded from the GenBank® database were considered to be the root of the tree (reference). Results: Phylogenetic data analysis revealed that SARS-CoV-2 B.1.1.7 (Alpha) was the dominant VOC variant, the proportion of which was as high as 36.4 % (12/33); B.1.351 (Beta) was also found (6.1 % or 2/33). When samples were examined for amino acid substitutions in the S-protein, B.1.1.7 Alpha (British) isolates were found to cluster into two distinct branches. Conclusion: The study of the frequency and influence of mutations on pathogenetic properties of the virus, as well as the analysis of the predominant variants of the virus will allow timely measures to be taken to counteract the spread of SARS-CoV-2 in the country. In this regard, continuous genome monitoring of circulating COVID-19 variants is necessary.