Genetic Characterizations and Molecular Evolution of VP7 Gene in Human Group A Rotavirus G1

Zhou, Nan; Lu, Zengjun; Wang, Bei

doi:10.3390/v12080831

Cited by 4 publications

(2 citation statements)

References 45 publications

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“…A previously described algorithm was used to demonstrate the accumulation pattern of amino acid substitutions of the norovirus GI RdRp gene [ 29 , 30 ]. In brief, the number of pairwise amino acid differences was calculated by MEGA 7.0.26 and averaged.…”

Section: Methodsmentioning

confidence: 99%

Molecular Evolution of RNA-Dependent RNA Polymerase Region in Norovirus Genogroup I

Zhou

Huang

et al. 2023

Viruses

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Norovirus is the leading viral agent of gastroenteritis in humans. RNA-dependent RNA polymerase (RdRp) is essential in the replication of norovirus RNA. Here, we present a comprehensive evolutionary analysis of the norovirus GI RdRp gene. Our results show that the norovirus GI RdRp gene can be divided into three groups, and that the most recent common ancestor was 1484. The overall evolutionary rate of GI RdRp is 1.821 × 10−3 substitutions/site/year. Most of the amino acids of the GI RdRp gene were under negative selection, and only a few positively selected sites were recognized. Amino acid substitutions in the GI RdRp gene accumulated slowly over time. GI.P1, GI.P3 and GI.P6 owned the higher evolutionary rates. GI.P11 and GI.P13 had the faster accumulation rate of amino acid substitutions. GI.P2, GI.P3, GI.P4, GI.P6 and GI.P13 presented a strong linear evolution. These results reveal that the norovirus GI RdRp gene evolves conservatively, and that the molecular evolutionary characteristics of each P-genotype are diverse. Sequencing in RdRp and VP1 of norovirus should be advocated in the surveillance system to explore the effect of RdRp on norovirus activity.

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Section: Methodsmentioning

confidence: 99%

Molecular Evolution of RNA-Dependent RNA Polymerase Region in Norovirus Genogroup I

Zhou

Huang

et al. 2023

Viruses

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“…Mutation patterns differed depending on the year of detection. Mutations N94S, S123N, M217T, and K291R have been reported in strains isolated from other countries ( Novikova et al, 2020 ; Zhou et al, 2020 ), suggesting that these substitutions have already been reported in recent G1 epidemic strains. Additionally, in this study, the VP7 gene harbored the L148F mutation in 2012 and 2014, the D100E mutation in 2015 and 2019, the T242M mutation in the G1P[8] (DS-1) strain in 2012–2015, and the N147D mutation in the G1P[8]-E2 strain in 2015 and 2018.…”

Section: Discussionmentioning

confidence: 82%

Molecular evolutionary analysis of novel NSP4 mono-reassortant G1P[8]-E2 rotavirus strains that caused a discontinuous epidemic in Japan in 2015 and 2018

Fujii,

Tsugawa,

Fukuda

et al. 2024

Front. Microbiol.

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In the 2010s, several unusual rotavirus strains emerged, causing epidemics worldwide. This study reports a comprehensive molecular epidemiological study of rotaviruses in Japan based on full-genome analysis. From 2014 to 2019, a total of 489 rotavirus-positive stool specimens were identified, and the associated viral genomes were analyzed by next-generation sequencing. The genotype constellations of those strains were classified into nine patterns (G1P[8] (Wa), G1P[8]-E2, G1P[8] (DS-1), G2P[4] (DS-1), G3P[8] (Wa), G3P[8] (DS-1), G8P[8] (DS-1), G9P[8] (Wa), and G9P[8]-E2). The major prevalent genotype differed by year, comprising G8P[8] (DS-1) (37% of that year’s isolates) in 2014, G1P[8] (DS-1) (65%) in 2015, G9P[8] (Wa) (72%) in 2016, G3P[8] (DS-1) (66%) in 2017, G1P[8]-E2 (53%) in 2018, and G9P[8] (Wa) (26%) in 2019. The G1P[8]-E2 strains (G1-P[8]-I1-R1-C1-M1-A1-N1-T1-E2-H1) isolated from a total of 42 specimens in discontinuous years (2015 and 2018), which were the newly-emerged NSP4 mono-reassortant strains. Based on the results of the Bayesian evolutionary analyses, G1P[8]-E2 and G9P[8]-E2 were hypothesized to have been generated from distinct independent inter-genogroup reassortment events. The G1 strains detected in this study were classified into multiple clusters, depending on the year of detection. A comparison of the predicted amino acid sequences of the VP7 epitopes revealed that the G1 strains detected in different years encoded VP7 epitopes harboring distinct mutations. These mutations may be responsible for immune escape and annual changes in the prevalent strains.

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Whole genome analysis of rotavirus strains circulating in Benin before vaccine introduction, 2016–2018

et al. 2022

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Genetic Characterizations and Molecular Evolution of VP7 Gene in Human Group A Rotavirus G1

Cited by 4 publications

References 45 publications

Molecular Evolution of RNA-Dependent RNA Polymerase Region in Norovirus Genogroup I

Molecular Evolution of RNA-Dependent RNA Polymerase Region in Norovirus Genogroup I

Molecular evolutionary analysis of novel NSP4 mono-reassortant G1P[8]-E2 rotavirus strains that caused a discontinuous epidemic in Japan in 2015 and 2018

Whole genome analysis of rotavirus strains circulating in Benin before vaccine introduction, 2016–2018

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