Genetic Variations of Three Kazakhstan Strains of the SARS-CoV-2 Virus

Prompt determination of the etiological agent is important in an outbreak of pathogens with pandemic potential, particularly for dangerous infectious diseases. Molecular genetic methods allow for arriving at an accurate diagnosis, employing timely preventive measures, and controlling the spread of the disease-causing agent. In this study, whole-genome sequencing of three SARS-CoV-2 strains was performed using the Sanger method, which provides high accuracy in determining nucleotide sequences and avoids errors associated with multiple DNA amplification. Complete nucleotide sequences of samples, KAZ/Britain/2021, KAZ/B1.1/2021, and KAZ/Delta020/2021 were obtained, with sizes of 29.751 bp, 29.815 bp, and 29.840 bp, respectively. According to the COVID-19 Genome Annotator, 127 mutations were detected in the studied samples compared to the reference strain. The strain KAZ/Britain/2021 contained 3 deletions, 7 synonymous mutations, and 27 non-synonymous mutations, the second strain KAZ/B1.1/2021 contained 1 deletion, 5 synonymous mutations, and 31 non-synonymous mutations, and the third strain KAZ/Delta020/2021 contained 1 deletion, 5 synonymous mutations, and 37 non-synonymous mutations, respectively. The variations C241T, F106F, P314L, and D614G found in the 5' UTR, <i>ORF1ab</i>, and <i>S</i> regions were common to all three studied samples, respectively. According to PROVEAN data, the loss-of-function mutations identified in strains KAZ/Britain/2021, KAZ/B1.1/2021, and KAZ/Delta020/2021 include 5 mutations (P218L, T716I, W149L, R52I, and Y73C), 2 mutations (S813I and Q992H), and 8 mutations (P77L, L452R, I82T, P45L, V82A, F120L, F120L, and R203M), respectively. Phylogenetic analysis showed that the strains studied (KAZ/Britain/2021, KAZ/B1.1/2021, and KAZ/Delta020/2021) belong to different SARS-CoV-2 lineages, which are closely related to samples from Germany (OU141323.1 and OU365922.1), Mexico (OK432605.1), and again Germany (OV375251.1 and OU375174.1), respectively. The nucleotide sequences of the studied SARS-CoV-2 virus strains were registered in the Genbank database with the accession numbers: ON692539.1, OP684305, and OQ561548.1.