Detection and molecular characterization of reassortant DS-1-like G1P [8] strains of rotavirus A

Abstract

Group A rotaviruses (RVA) are the main cause of viral gastroenteritis in children worldwide. In this study we provide the molecular characteristics of reassortant DS-1-like G1P[8] RVA strains detected in Russia for the first time. Previously, such reassortant strains were detected in Japan and Thailand. The G1P[8] RVAs with DS-1-like short electropherotype RNA-PAGE were isolated from children hospitalised with an acute gastroenteritis during the 2013-2014 period. The DS-1-like G1P[8] strains accounted for 2.6% of all RVA strains detected continuously throughout the season. A phylogenetic analysis was made on the basis of the established nucleotide sequences of genes VP7, VP8* (VP4), VP6 and NSP4. The Nizhny Novgorod strains belong to G1-I and G1-II alleles of VP7 gene and to P[8]-3 allele of VP4. According to their VP6 sequences, two Russian samples clustered with the reassortant strains isolated in Japan, Thailand and Australia and two other strains were phylogenetically close to the typical G2P[4] DS-1-like RVA. Nucleotide sequences of G1P[8] strains that belong to NSP4 gene form a separate cluster from G3P[8] DS-1-like rotaviruses detected in Thailand and Australia. The RVA alleles included in Rotarix and RotaTeq vaccine strains were clustered separately from the studied reassortant RVAs. On the grounds of phylogenetic analysis we assume a polyphyletic origin of reassortants between Wa- and DS-1-like strains. Mutation rates evaluated by Bayesian inference in clusters with reassortant RVA strains were 1.004Е-3 (VP7), 1.227E-3 (VP4), 3.909E-4 (VP6), and 4.014Е-4 (NSP4). Analysis of tMRCA showed relatively contemporary origin of alleles DS-1-like G1P[8] rotaviruses: VP7 - 1998 (G1-I) and 1981 (G1-II), VP4 - 1998, VP6 - 1994, NSP4 - 1979.

Phylogeographic characteristics of reassortant DS-1-like G3P[8]-strains of rotavirus type A isolated in Nizhny Novgorod (Russia).

“…However, some of the strains belonged to another cluster. In the VP6 phylogenetic tree the isolates considered in our work were related to typical G2P [4] rotaviruses, as well as DS-1-like G1P[8], which were discovered in Nizhny Novgorod in 2014 [10]. The cluster formed by DS-1-like G3P[8] strains identi ed in other countries included only one sequence of the VP6 RVA gene isolated in Nizhny Novgorod.…”

“…The circulation of reassortant DS-1-like G1P[8] rotaviruses in Nizhny Novgorod was established in 2014, but they were not widely distributed [10]. G3P[8] rotaviruses with a "short" pro le of RNA segments migration in PAGE were rst identi ed in Nizhny Novgorod and Novosibirsk in 2017.…”

“…It is noteworthy that the third cluster includes the majority of DS-1-like G3P[8] RVAs described in the literature, including strains isolated in Moscow in 2020. In addition, the third group also included intergroup reassortants with genotype G1P[8] isolated in Nizhny Novgorod in 2014 [10].…”

“…The circulation of DS-1-like G1P[8] RVAs was detected in Japan in 2012-2013, then in Thailand, Vietnam, Malawi, and other countries [6][7][8][9]. This variant was also identi ed in Nizhny Novgorod in 2013-14, but was not widely spread [10]. In 2013, based on a whole genome analysis, it was found that a DS-1-like G3P[8] RVA strains became dominant in children with severe rotavirus gastroenteritis in Australia [11].…”

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

“…It is based on only two genes (VP7 and VP4), and the real contribution of reassortant strains remains unclear. In Nizhny Novgorod, 4 DS-1-like strains with G1-P[8]-I2-E2 genotype were shown by sequencing of four genes (VP7, VP4, VP6 and NSP4) and 2 mono-reassortant strains with G4-P[8]-E2 genotype were found using partial sequencing of all genes [22,23]. Also, G3-P[8]-I2 reassortant strains were detected in Moscow by real-time RT-PCR and Oxford Nanopore sequencing [24].…”