Variability of genes encoding nonstructural proteins of rotavirus А (Reoviridae: Rotavirus: Rotavirus A) genotype G9P[8] during the period of dominance in the territory of Nizhny Novgorod (central part of Russia) (2011–2020)

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Abstract

Introduction. In Russia, rotavirus A is the main cause of severe viral gastroenteritis in young children. The molecular features that allow a rotavirus of a particular genotype to gain an evolutionary advantage remain unclear, therefore, the study of the genetic diversity of rotaviruses based on genes encoding nonstructural proteins (NSPs) responsible for the reproduction of the virus in the cell is an urgent task.

Objective. To study the genetic diversity of rotaviruses of genotype G9P[8], which dominated Nizhny Novgorod in 2011–2020, based on genes encoding nonstructural proteins.

Materials and methods. Rotavirus-positive samples were subjected to PCR-genotyping and sequencing of NSP1 – NSP5 genes. Phylogenetic analysis was carried out in the MEGA X program.

Results. In the period 2011–2020, G9P[8] rotaviruses with four variants of the NSP2 gene were co-circulating in Nizhny Novgorod. New alleles were noted in 2012 (N1-a-III), 2016 (N1-a-IV) and in 2019 (N1-a-II). The appearance of new variants of other genes occurred in 2014 (E1-3, NSP4), 2018 (T1-a3-III, NSP3) and in 2019 (A1-b-II, NSP1). NSP2 gene had the most variable amino acid sequence (16 substitutions), 2 to 7 substitutions were observed in NSP1, NSP3 and NSP4, NSP5 was conservative.

Discussion. The results obtained are consistent with the literature data and indicate the participation of NSP genes in maintaining the heterogeneity of the rotavirus population.

Conclusion. Until 2018, the genetic diversity of rotaviruses in Nizhny Novgorod was determined by the circulation of strains carrying several alleles of the NSP2 gene and conservative genes NSP1, NSP3–NSP5. By the end of the study period, new variants of the genotype G9P[8] were formed in the population, carrying previously unknown combinations of alleles of nonstructural genes.

About the authors

Elena I. Velikzhanina

«Academician I.N. Blokhina Nizhny Novgorod Scientific Research Institute of Epidemiology and Microbiology»

Email: www.e_velikzhanina@mail.ru
ORCID iD: 0000-0003-4069-1427

Junior Researcher, laboratory of molecular epidemiology of viral infections

Russian Federation, 603950, Nizhny Novgorod

Tatiana A. Sashina

«Academician I.N. Blokhina Nizhny Novgorod Scientific Research Institute of Epidemiology and Microbiology»

Email: tatyana.sashina@gmail.com
ORCID iD: 0000-0003-3203-7863

PhD, Senior Researcher, laboratory of molecular epidemiology of viral infections

Russian Federation, 603950, Nizhny Novgorod

Olga V. Morozova

«Academician I.N. Blokhina Nizhny Novgorod Scientific Research Institute of Epidemiology and Microbiology»

Email: Olga.morozova.bsc@gmail.com
ORCID iD: 0000-0002-8058-8187

PhD , Research assistant, laboratory of molecular epidemiology of viral infections

Russian Federation, 603950, Nizhny Novgorod

Natalia V. Epifanova

«Academician I.N. Blokhina Nizhny Novgorod Scientific Research Institute of Epidemiology and Microbiology»

Email: epifanovanv@mail.ru
ORCID iD: 0000-0001-7679-8029

PhD, Leading Researcher, laboratory of molecular epidemiology of viral infections

Russian Federation, 603950, Nizhny Novgorod

Nadezhda A. Novikova

«Academician I.N. Blokhina Nizhny Novgorod Scientific Research Institute of Epidemiology and Microbiology»

Author for correspondence.
Email: novikova_na@mail.ru
ORCID iD: 0000-0002-3710-6648

Professor, Head of the laboratory of molecular epidemiology of viral infections

Russian Federation, 603950, Nizhny Novgorod

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2. Fig. 1. Distribution of rotavirus A genotypes in Nizhny Novgorod in the period 2011–2020: a – the percent distribution of basic genotypes of rotaviruses in whole study period; b – the percent of genotype G9P[8] rotaviruses in different seasons of the period of study.

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3. Fig. 2. Phylogenetic tree based on the nucleotide sequences: a – NSP1; b – NSP3; c – NSP5 gene of rotavirus A strains.

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4. Fig. 3. Phylogenetic tree based on the nucleotide sequences: a – NSP2; b – NSP4 gene of rotavirus A strains.

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Copyright (c) 2022 Velikzhanina E.I., Sashina T.A., Morozova O.V., Epifanova N.V., Novikova N.A.

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