Abstract
Tracking temporal and spatial genomic changes and evolution of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are among the most urgent research topics worldwide, which help to elucidate the coronavirus disease 2019 (COVID-19) pathogenesis and the effect of deleterious variants. Our current study concentrates genetic diversity of SARS-CoV-2 variants in Uzbekistan and their associations with COVID-19 severity. Thirty-nine whole genome sequences (WGS) of SARS-CoV-2 isolated from PCR-positive patients from Tashkent, Uzbekistan for the period of July-August 2021, were generated and further subjected to further genomic analysis. Genome-wide annotations of clinical isolates from our study have revealed a total of 223 nucleotide-level variations including SNPs and 34 deletions at different positions throughout the entire genome of SARS-CoV-2. These changes included two novel mutations at the Nonstructural protein (Nsp) 13: A85P and Nsp12: Y479N, which were unreported previously. There were two groups of co-occurred substitution patterns: the missense mutations in the Spike (S): D614G, Open Reading Frame (ORF) 1b: P314L, Nsp3: F924, 5`UTR:C241T; Nsp3:P2046L and Nsp3:P2287S, and the synonymous mutations in the Nsp4:D2907 (C8986T), Nsp6:T3646A and Nsp14:A1918V regions, respectively. The “Nextstrain” clustered the largest number of SARS-CoV-2 strains into the Delta clade (n = 32; 82%), followed by two Alpha-originated (n = 4; 10,3%) and 20A (n = 3; 7,7%) clades. Geographically the Delta clade sample sequences were grouped into several clusters with the SARS-CoV genotypes from Russia, Denmark, USA, Egypt and Bangladesh. Phylogenetically, the Delta isolates in our study belong to the two main subclades 21A (56%) and 21J (44%). We found that females were more affected by 21A, whereas males by 21J variant (χ2 = 4.57; p ≤ 0.05, n = 32). The amino acid substitution ORF7a:P45L in the Delta isolates found to be significantly associated with disease severity. In conclusion, this study evidenced that Identified novel substitutions Nsp13: A85P and Nsp12: Y479N, have a destabilizing effect, while missense substitution ORF7a: P45L significantly associated with disease severity.
【초록키워드】 COVID-19, coronavirus disease, Evolution, SARS-CoV-2, Coronavirus disease 2019, coronavirus, Nsp12, Mutation, Pathogenesis, SARS-CoV, severity, disease severity, Variation, Genome, Russia, SNPs, variant, SARS-CoV-2 variant, COVID-19 severity, Delta, severe acute respiratory syndrome Coronavirus, variants, nsp13, Protein, SARS-CoV-2 variants, male, female, Research, Genotype, Cluster, Deletion, Missense mutation, D614G, clade, SNP, Alpha, clades, Genomic analysis, genetic diversity, Nsp3, clinical isolates, WGS, USA, Denmark, change, association, ORF7a, Amino acid, NSP6, nucleotide, Open reading frame, NSP, Deleterious, Missense, Missense mutations, isolates, followed by, acute respiratory syndrome, two groups, acute respiratory syndrome coronavirus, acute respiratory syndrome coronavirus 2, sequence, help, Substitution, Nextstrain, annotation, SARS-CoV-2 strain, whole genome sequence, reading, amino acid substitution, regions, nsp4, isolate, synonymous, Tashkent, affected, significantly, ORF, two group, evidenced, genomic change, Identified, subclade, the Spike, PCR-positive patient, with COVID-19, 【제목키워드】 SARS-CoV-2, sequence, clinical sample,