Detection and full-genotype determination of rare and reassortant rotavirus A strains in Nizhny Novgorod in the European part of Russia.

Reassortant DS-1-like rotavirus A strains have been shown to circulate widely in many countries around the world. In Russia, the prevalence of such strains remains unclear due to the preferred use of the traditional binary classification system. In this work, we obtained partial sequence data from all 11 genome segments and determined the full-genotype constellations of rare and reassortant rotaviruses circulating in Nizhny Novgorod in 2016-2019. DS-1-like G3P[8] and G8P[8] strains were found, reflecting the global trend. Most likely, these strains were introduced into the territory of Russia from other countries but subsequently underwent further evolutionary changes locally. G3P[8], G9P[8], and G12P[8] Wa-like strains of subgenotypic lineages that are unusual for the territory of Russia were also identified. Reassortant G2P[8], G4P[4], and G9P[4] strains with one Wa-like gene (VP4 or VP7) on a DS-1-like backbone were found, and these apparently had a local origin. Feline-like G3P[9] and G6P[9] strains were found to be phylogenetically close to BA222 isolated from a cat in Italy but carried some traces of reassortment with human strains from Russia and other countries. Thus, full-genotype determination of rotavirus A strains in Nizhny Novgorod has clarified some questions related to their origin and evolution.

Increasing detection of rotavirus G2P[4] strains in Nizhny Novgorod, Russia, between 2016 and 2019.

Rotavirus infection is one of the leading causes of acute gastroenteritis in children in their first years of life. We studied the genotypic diversity of rotavirus A (RVA) strains in Nizhny Novgorod, Russia, during the period 2016-19. In total, 4714 samples of faeces from children admitted to the Nizhny Novgorod Hospital for Infectious Diseases with acute gastroenteritis were examined. The share of rotavirus-positive samples was 31.5% in 2016-17. It decreased to 21.6% in 2018-19. In Nizhny Novgorod, all six global types of RVA were detected (G1P[8], G2P[4], G3P[8], G4P[8], G9P[8] and G12P[8]), as well as sporadic samples with genotypes G9P[4], G3P[9], G9P[9], G8P[8], G2P[8], G4P[4], G3P[9]. The fraction of strains with genotype G2P[4] gradually increased from 5.9% in 2016-17 to 39.1% in 2018-19. Simultaneously, the proportion of G9P[8] strains decreased from 63.2% to 27.7% in the same period. Phylogenetic analysis showed that rotaviruses with the G2P[4] genotype carried ubiquitous alleles of the VP7 and VP4 genes during the period of their prevalence: G2-IVa-1 and G2-IVa-3; P[4]-IVa and P[4]-IVb. As rotavirus vaccination is not widely used in the region because it is not included in the national vaccination calendar in Russia so far, the increase in the number of G2P[4] RVA is likely due to natural strain fluctuations.

Genotype constellations of the rotavirus A strains circulating in Nizhny Novgorod, Russia, 2017-2018.

Currently, the full-genome-based classification is widely used to investigate rotavirus A (RVA) strains found in different countries around the world. However, the information on the full genotypes of rotaviruses circulating in Russia is limited. Using partial sequencing, this study determined the full genotype constellations of 15 RVA strains in total commonly detected in Nizhny Novgorod (European part of Russia) in 2017-2018, three from each of the following genotypes G1P[8], G4P[8], and G9P[8] and six from G2P[4]. There were two intergenogroup mono-reassortants possessing an identical genotype constellation of G4-P[8]-I1-R1-C1-M1-A1-N1-T1-E2-H1 with the DS-1-like NSP4 gene of probably local origin. A variety of subgenotype lineages and their combinations of Wa-like rotaviruses and genetic heterogeneity among G9P[8] and G1P[8] strains were shown on the basis of phylogenetic analysis of each gene. Moreover, two distinct co-circulating variants that differed in all 11 genome segments were found among DS-1-like rotaviruses.

Phylodynamics of G4P[8] and G2P[4] strains of rotavirus A isolated in Russia in 2017 based on full-genome analyses.

Rotavirus A is a dynamically evolving pathogen causing acute gastroenteritis in children during the first years of life. In the present study, we conducted a phylodynamic analysis based on the complete sequences of 11 segments of rotaviruses with the G4P[8] and G2P[4] genotypes isolated in Russia in 2017. Since rotavirus has a segmented genome, our analysis was performed using the Bayesian approach based on separate samples of nucleotide sequences for each gene of the strains studied. For the strain with the genotype G4P[8], the most likely geographical locations of the nearest common ancestor were Russia (VP7, VP4, VP6), China (VP1), Thailand (VP3), Belgium (NSP1), Hungary (VP2, NSP2, NSP3), Italy (NSP4) and Japan (NSP5). For the strain with the G2P[4] genotype, India (VP7, VP4, VP6, NSP1, NSP4), Malawi (VP2, NSP2, NSP3), Australia (VP1), Italy (NSP5) and Bangladesh (VP3). The closest common ancestor of the strain with the genotype G4P[8] circulated in 2001-2012, depending on the gene being analyzed. For the strain with the G2P[4] genotype, the closest common ancestor dates from 2006 to 2013.