The rise and spread of the SARS-CoV-2 AY.122 lineage in Russia

Klink, Galya V.; Safina, Ksenia R; Nabieva, Elena; Shvyrev, Nikita; Garushyants, Sofya K.; Alekseeva, Evgeniia; Komissarov, Andrey; Danilenko, Daria; Pochtovyi, Andrei A.; Divisenko, Elizaveta V.; Vasilchenko, Lyudmila A.; Shidlovskaya, Elena V.; Kuznetsova, Nadezhda A.; Speranskaya, A.S.; Neverov, Alexey D.; Popova, Anfisa V.; Fedonin, Gennady; Акимкин, В. Г.; Lioznov, Dmitry; Гущин, В.А.; Shchur, Vladimir; Bazykin, Georgii A.

doi:10.1093/ve/veac017

Cited by 30 publications

(23 citation statements)

References 53 publications

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“…The ORF7a: P45L mutation of the Delta became dominant in Russia [ 44 ]. It was also found in the Delta variants isolates from India [ 45 ], and in the Omicron samples from South Africa (EPI_ISL_6647958).…”

Section: Discussionmentioning

confidence: 99%

Genome sequence diversity of SARS-CoV-2 obtained from clinical samples in Uzbekistan

Абдуллаев¹,

Abdurakhimov²,

Mirakbarova³

et al. 2022

PLoS ONE

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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.

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Section: Discussionmentioning

confidence: 99%

Genome sequence diversity of SARS-CoV-2 obtained from clinical samples in Uzbekistan

Абдуллаев¹,

Abdurakhimov²,

Mirakbarova³

et al. 2022

PLoS ONE

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“…It should be noted that variant AY.122 (1) prevailed in the third wave of COVID-19 in the Moscow region. One of its characteristic mutations is G8R in the NS8 (ORF8) protein.…”

Section: Resultsmentioning

confidence: 96%

“…The Delta variant of SARS-CoV-2 caused the third wave of the COVID-19 pandemic in mid-2021 in many countries, including Russia (1). The surge in incidence was associated with the high transmissibility of this strain compared to the alpha variant (2).…”

Section: Introductionmentioning

confidence: 99%

HLA-A*01:01 allele vanishing in COVID-19 patients population associated with non-structural epitope abundance in CD8⁺ T-cell repertoire

Shkurnikov

Nersisyan

Averinskaya

et al. 2022

Preprint

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In mid-2021, the SARS-CoV-2 Delta variant caused the third wave of the COVID-19 pandemic in several countries worldwide. The pivotal studies were aimed at studying changes in the efficiency of neutralizing antibodies to the spike protein. However, much less attention was paid to the T-cell response and the presentation of virus peptides by MHC-I molecules. In this study, we compared the features of the HLA-I genotype in symptomatic patients with COVID-19 in the first and third waves of the pandemic. As a result, we could identify the vanishing of carriers of the HLA-A*01:01 allele in the third wave and demonstrate the unique properties of this allele. Thus, HLA-A*01:01-binding immunodominant epitopes are mostly derived from ORF1ab. A set of epitopes from ORF1ab was tested, and their high immunogenicity was confirmed. Moreover, analysis of the results of single-cell phenotyping of T-cells in recovered patients showed that the predominant phenotype in HLA-A*01:01 carriers is central memory T-cells. The predominance of T-lymphocytes of this phenotype may contribute to forming long-term T-cell immunity in carriers of this allele. Our results can be the basis for highly effective vaccines based on ORF1ab peptides.

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“…2 e. Mutations in ORF1ab: P271S, K1763N, S2048F, and K2705R were found only in community samples, whereas mutations in ORF1ab: K261N, A2529V and L829I; and ORF7a: P45L were found in international samples. Although not much is known about these mutations, ORF1ab: K261N and ORF7a: P45L is reported to be prevalent among 90% of AY.122 lineages from Russia( Klink et al 2022 ). These findings suggest that the virus is continuously expanding in the evolutionary space.…”

Section: Discussionmentioning

confidence: 99%

Mutational dynamics across VOCs in International travellers and Community transmission underscores importance of Spike-ACE2 interaction

Mehta

Ravi

Devi

et al. 2022

Microbiological Research

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The rise and spread of the SARS-CoV-2 AY.122 lineage in Russia

Cited by 30 publications

References 53 publications

Genome sequence diversity of SARS-CoV-2 obtained from clinical samples in Uzbekistan

Genome sequence diversity of SARS-CoV-2 obtained from clinical samples in Uzbekistan

HLA-A*01:01 allele vanishing in COVID-19 patients population associated with non-structural epitope abundance in CD8⁺ T-cell repertoire

Mutational dynamics across VOCs in International travellers and Community transmission underscores importance of Spike-ACE2 interaction

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The rise and spread of the SARS-CoV-2 AY.122 lineage in Russia

Cited by 30 publications

References 53 publications

Genome sequence diversity of SARS-CoV-2 obtained from clinical samples in Uzbekistan

Genome sequence diversity of SARS-CoV-2 obtained from clinical samples in Uzbekistan

HLA-A*01:01 allele vanishing in COVID-19 patients population associated with non-structural epitope abundance in CD8+ T-cell repertoire

Mutational dynamics across VOCs in International travellers and Community transmission underscores importance of Spike-ACE2 interaction

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HLA-A*01:01 allele vanishing in COVID-19 patients population associated with non-structural epitope abundance in CD8⁺ T-cell repertoire