Phylogenetic characteristics and analysis of the antigenic epitopes of Russian rotaviruses in comparison with vaccine strains

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Abstract

Accumulation of mutations in the amino acid sequence of immunologically significant regions of the outer capsid proteins in locally circulating rotaviruses may reduce the effectiveness of vaccine-generated protection. The aim of the work was to comparatively analyze Russian rotaviruses and strains of the Indian pentavalent vaccine approved for use in the Russian Federation in 2020.

Materials and methods. There were used 38 rotavirus-positive samples derived from children with acute intestinal infection identified in 2022–2023. cDNA fragments of the VP7 gene 877 bp long were sequenced by two strands using “Nanofor 05” device. Phylogenetic analysis was performed using BEAST software package. The final sample included 161 VP7 gene sequences of RVA isolates from three Russian cities (Nizhny Novgorod, Moscow, Novosibirsk), other countries, and vaccine strains.

Results. Based on the results of phylogenetic analysis, Russian rotaviruses were found to belong to 13 lineages and/or sublineages (G1-I-A, G1-II-C, G2-IVa-1, G2-IV-3, G3-I, G3-3-а, G3-3-е, G4-I-с, G6-I, G8-IV, G9-III-d, G9-VI-е, G12-III). Vaccine strains (D, WI79-9, A41CB052A, DS-1, SC2–9, P, WI78-8, ST3, BrB-9, WI79-4, AU-32, 116E) were grouped separately in each case (G1-III, G1-II-A, G2-I, G2-II, G3-3-d, G4-I-а, G6-IV, G9-I, G9-II). Comparative analysis in the regions of antigenic epitopes targeted by neutralizing antibodies showed 3 to 6 amino acid differences between Russian and homotypic vaccine strains. The highest number was observed in isolates of sublineages G1-I-A, G2-IVa-1 and lineage G3-I. In the regions of T-cell epitopes, 1 to 4 substitutions were found. The greatest number of differences had rotaviruses of the G3-I lineage and the G4-I-c sublineage.

Conclusion. For the G3P[8] variant of the G3-I lineage, which is widespread in Russia, 6 substitutions in neutralizing epitopes and 4 substitutions in T-cell epitopes were found in comparison with homotypic vaccine strains. The study results are important for understanding a potential impact of vaccines on the antigenic structure of the rotavirus population in Russia.

About the authors

T. A. Sashina

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

Email: tatyana.sashina@gmail.com

PhD (Biology), Senior Researcher, Laboratory of Molecular Epidemiology of Viral Infections

Russian Federation, Nizhniy Novgorod

O. V. Morozova

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

Email: tatyana.sashina@gmail.com

PhD (Biology), Senior Researcher, Laboratory of Molecular Epidemiology of Viral Infections

Russian Federation, Nizhniy Novgorod

E. I. Velikzhanina

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

Email: tatyana.sashina@gmail.com

Junior Researcher, Laboratory of Molecular Epidemiology of Viral Infections

Russian Federation, Nizhniy Novgorod

N. V. Epifanova

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

Email: tatyana.sashina@gmail.com

PhD (Biology), Leading Researcher, Laboratory of Molecular Epidemiology of Viral Infections

Russian Federation, Nizhniy Novgorod

N. A. Novikova

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

Author for correspondence.
Email: tatyana.sashina@gmail.com

DSc (Biology), Professor, Laboratory of Molecular Epidemiology of Viral Infections, Head of the Laboratory

Russian Federation, Nizhniy Novgorod

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Supplementary files

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2. Figure 1. Phylogenetic tree on the base of rotavirus VP7 gene

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3. Figure 2. Structural model of trimeric VP7

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