Changes in the distribution of lineage constellations of G2P[4] Rotavirus A strains detected in Japan over 32years (1980–2011)

Doan, Yen Hai; Nakagomi, Toyoko; Agbemabiese, Chantal Ama; Nakagomi, Osamu

doi:10.1016/j.meegid.2015.05.026

Cited by 43 publications

(62 citation statements)

References 27 publications

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“…Recently, interesting studies were conducted on whole genome G2P[4] rotavirus collected for three decades in Italy and Japan . They revealed that globally distributed G2P[4] strains may have undergone intragenotype reassortment, as shown by changes of lineages of all the viral protein genes from the 1970s to 2011.…”

Section: Discussionmentioning

confidence: 99%

“…Nucleotide sequences were aligned with Clustal W and phylogenetic dendrograms were generated from sequences using the neighbor‐joining method with 1000 bootstrap replicates as implemented in MEGA 7 . Lineages and sub‐lineages were defined as published in previous studies . Sequence identity of a pair of gene sequences was determined by using bioedit software (BioEdit).…”

Section: Methodsmentioning

confidence: 99%

“…27 Lineages and sub-lineages were defined as published in previous studies. 28,29 Sequence identity of a pair of gene sequences was determined by using bioedit software (BioEdit). The…”

Section: Rna Extraction and Rt-pcr Genotypingmentioning

confidence: 99%

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Molecular epidemiology of rotavirus gastroenteritis in Japan during 2014‐2015: Characterization of re‐emerging G2P[4] after rotavirus vaccine introduction

Khandoker

Thongprachum

Takanashi

et al. 2018

Journal of Medical Virology

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Rotavirus vaccines have been available in Japan since 2011. This study conducted to monitor the trend of group A rotavirus (RVA) genotypes 3 years after vaccine introduction. A total of, 539 fecal samples were collected from children with acute gastroenteritis in six regions during July 2014-June 2015. Among them, 178 samples (33.0%) were positive for RVA. The most predominant genotype was G1P[8] (35.9%) followed by G2P[4] (26.4%), G9P[8] (21.3%), G3P[8] (4.5%), and G3P[9] (4.5%). The detection rate of G2P[4] was increased soon after vaccine introduction. Sequence analyses of VP7 and VP4 genes of the representative G2P[4] strains were found to be clustered in sub-lineage IVa of lineage IV. It is noteworthy that one amino acid substitution in the antigenic epitope (Q114P) of VP4 gene was found in representative G2P[4] strains of the current study. However, it is unclear whether the change in antigenic epitope is due to the effect of vaccination or due to natural variation, warranting further continuous monitoring of rotavirus evolution after vaccine introduction.

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Section: Discussionmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

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Molecular epidemiology of rotavirus gastroenteritis in Japan during 2014‐2015: Characterization of re‐emerging G2P[4] after rotavirus vaccine introduction

Khandoker

Thongprachum

Takanashi

et al. 2018

Journal of Medical Virology

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“…An extended genotyping system (Gx‐Px‐Ix‐Rx‐Cx‐Mx‐Ax‐Nx‐Tx‐Ex‐Hx) based on the nucleotide identities of all 11 segment genes (VP7‐VP4‐VP6‐VP1‐VP2‐VP3‐NSP1‐NSP2‐NSP3‐NSP4‐NSP5) was proposed in the year 2008, to better define the homology and heterology of RVA strains. Consequently, RVAs are grouped into 3 genotype constellations: Wa (Gx‐P[8]‐I1‐R1‐C1‐M1‐A1‐N1‐T1‐E1‐H1), DS‐1 (Gx‐P[4]‐I2‐R2‐C2‐M2‐A2‐N2‐T2‐E2‐H2), and AU‐1 (G X ‐P[9]‐I3‐R3‐C3‐M3‐A3‐N3‐T3‐E3‐H3) . Globally, the most common combinations in G1, G3, G4, G9, G12, and P[8] are usually associated with Wa‐like constellations, whereas G2 and P[4] strains are closely related to DS‐1–like constellations.…”

Section: Introductionmentioning

confidence: 99%

Phylogenetic analysis of human G9P[8] rotavirus strains circulating in Jiangsu, China between 2010 and 2016

et al. 2018

Journal of Medical Virology

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Rotavirus A (RVA) is the leading cause of acute viral gastroenteritis in children under 5 years of age worldwide. G9P[8] is a common RVA genotype that has been persistently prevalent in Jiangsu, China. To determine the genetic diversity of G9P[8] RVAs, 7 representative G9P[8] strains collected from Suzhou Children's Hospital between 2010 and 2016 (named JS2010-JS2016) were analyzed through whole-genome sequencing. All evaluated strains showed the Wa-like constellation G9-P[8]-I1-R1-C1-M1-A1-N1-T1-E1-H1. Furthermore, phylogenetic analysis revealed that the VP7 genes of all strains clustered into lineage G9-III and G9-VI. With the exception of strain JS2012 (P[8]-4), the VP4 sequences of all strains belonged to the P[8]-3 lineage. Sequencing further revealed that amino acid substitutions were present in the antigenic regions of the VP7 and VP4 genes of all strains. Moreover, there were multiple substitutions in antigenic sites I and II of the nonstructural protein 4 (NSP4) genes, whereas the other NSP genes were relatively conserved. In conclusion, our phylogenetic analysis of these 7 G9P[8] strains suggests that RVA varied across regions and time. Therefore, our findings suggest that continued surveillance is necessary to explore the molecular evolutionary characteristics of RVA for better prevention and treatment of acute viral gastroenteritis.

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“…However, strains from Taiwan were not included in this phylogenetic analysis due to the shortness of these fragments (less than 400 bp). Furthermore, it had been shown using the Bayesian Markov chain Monte Carlo (MCMC) method without porcine G2 sequences that Australian strains CK20037 and CK20055 formed an emergent lineage different from human lineages I-IV, and notably, the divergence time of this emergent lineage from lineage IV was around 1966, yet the date of the most recent common ancestor was 2006 [21]. Therefore, G2 RVAs within the emergent lineage VI may still be circulating throughout the world.…”

mentioning

confidence: 99%

G2 rotavirus within an emergent VP7 evolutionary lineage circulating in children with acute diarrhea in Guangxi Province of China, 2014

et al. 2016

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Routine surveillance revealed that the prevalence of P[4] rotaviruses circulating in children with acute diarrhea in Guangxi Province, China, increased in 2014. However, VP7 genotyping for these P[4] rotaviruses was unsuccessful. Exhaustive database searching and sequence analysis indicated that the G genotype of these P[4] rotaviruses was G2, and the VP7 genes clustered with recently emerging G2 strains in several countries within an emergent evolutionary lineage that was distinct from the previously designated lineages I-IV as well as lineage V including porcine rotaviruses. Further studies are essential to monitor the potential global spread of this emerging G2 rotavirus.

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Changes in the distribution of lineage constellations of G2P[4] Rotavirus A strains detected in Japan over 32years (1980–2011)

Cited by 43 publications

References 27 publications

Molecular epidemiology of rotavirus gastroenteritis in Japan during 2014‐2015: Characterization of re‐emerging G2P[4] after rotavirus vaccine introduction

Molecular epidemiology of rotavirus gastroenteritis in Japan during 2014‐2015: Characterization of re‐emerging G2P[4] after rotavirus vaccine introduction

Phylogenetic analysis of human G9P[8] rotavirus strains circulating in Jiangsu, China between 2010 and 2016

G2 rotavirus within an emergent VP7 evolutionary lineage circulating in children with acute diarrhea in Guangxi Province of China, 2014

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