Elsevier

Infection, Genetics and Evolution

Volume 37, January 2016, Pages 129-136
Infection, Genetics and Evolution

Short communication
The prevalence and genotype diversity of Human Rotavirus A circulating in Thailand, 2011–2014

https://doi.org/10.1016/j.meegid.2015.11.011Get rights and content

Highlights

  • A total of 688 human fecal samples were collected and tested for the RVA genome.

  • Thirty percent of samples were RVA-positive and nine genotypes were identified.

  • Feline-like, porcine-like, and bovine-like genotypes were reported in the study.

Abstract

Human rotavirus A (RVA) is the major infectious virus causing acute watery diarrhea in children, especially those younger than 5 years of age, and is a major public health problem in Thailand. Outbreaks of this virus have been reported worldwide. Besides the common genotypes, unusual genotypes providing evidence of inter-species transmission have also been described. Therefore, the aim of this study was to investigate the prevalence and genotypes of RVA in Thailand. A total of 688 samples were collected from children who were hospitalized with acute diarrhea in Chumphae Hospital in Khon Kaen and Chulalongkorn Hospital in Bangkok. RVA was detected using one-step RT-PCR and the genotypes were evaluated by sequencing. Overall, 204 of the 688 samples (30%) were positive for RVA. Nine genotypes were identified: three common in humans (G1P[8] [53%], G2P[4] [18%], G3P[8] [12%]), one feline-like (G3P[9] [1%]), four porcine-like (G4P[6] [0.5%], G5P[6] [0.5%], G9P[8] [0.5%], G12P[6] [1.5%]), and one bovine-like (G8P[8] [13%]). The variation in virus genotypes and the animal-like genotypes detected in this study suggested that a high diversity of RVA types is circulating in the Thai population. Therefore, continuous molecular epidemiological monitoring of RVA is essential and has implications for the national vaccination program.

Section snippets

Introductions

Rotaviruses belong to the Reoviridae family, genus Rotavirus. Based on their antigenic properties, rotaviruses are classified into eight species designated A through H. Rotavirus A (RVA) is commonly found in humans and causes acute watery diarrhea worldwide, especially in children younger than 5 years of age (Parashar et al., 2006). The virus contains 11 segmented double-stranded RNAs, which are translated into six structural (viral proteins [VPs]) and six non-structural proteins (NSP). The

Study population

A total of 688 stool samples were collected over a 3-year period (26 May 2011 to 9 August 2014). Samples were obtained from individuals presented with acute diarrhea defined by three or more abnormally loose or watery stools within 24 h. A total of 157 samples were collected from the Chulalongkorn Memorial Hospital in Bangkok and 531 samples from the Chumphae Hospital in Khon Kaen. Patients included in this study were between the ages of 1 day and 15 years. Samples were initially tested using the

Study population and RVA prevalence

To determine what proportion of diarrhea in young children was attributable to RVA infection, a total of 688 samples were evaluated (Table S1). The vast majority of the samples comprised children ≤ 5 years old. Children aged 1–5 years old (mode 12 months; median 12 months) represented most individuals, in part due to the many samples from Khon Kaen (Fig. 1A). Meanwhile, samples from Bangkok were mostly from patients between 7–12 months (mode 12 months, median 12 months). Overall, there were more males

Acknowledgments

This study was supported by The National Research University Project, Office of the Higher Education Commission (WCU 58-006-HR, WCU007-HR57, WCU 001-HR57), The National Research Council of Thailand, The Research Chair Grant from The National Science and Technology Development Agency (NSTDA), Chulalongkorn University Centenary Academic Development Project (CU56-HR01), the Ratchadaphiseksomphot Endowment Fund of Chulalongkorn University (RES560530093), the Outstanding Professor of Thailand

References (33)

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    However, this cannot be asserted based on a single gene, but, unfortunately, we were unable to amplify additional genes from this sample from 2013. The phylogenetic study of the VP7 gene of the five G1P[8] isolates from 2014, and the one from 2013 demonstrated that these Argentine strains are very closely related to a group of Thai, Vietnamese, and Russian human strains and a group of Vietnamese porcine strains circulating since 2012 [Chieochansin et al., 2016; Phan et al., 2016]. This relationship is supported by the sequence study of the other three genes, VP4, VP6, and NSP4.

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    Hoa-Tran et al. revealed that the genetic transfer of a bovine G8 VP7 gene, likely from India, to a Taiwanese human G8 sequence was the common ancestor to the strain circulating in Vietnam, a reassortment event estimated to have occurred 2–7 years before its detection. Since each of the analyzed G8P[8] samples shared this genetic reassortment, and due to the geo-temporal proximity of the G8P[8] emergence in Cambodia, Vietnam and Thailand, further evaluation of this reassortant strain and its hypothesized efficiency in human transmission is warranted [16,30]. Remarkable in what is absent from this large Cambodian sample of genotypic data, there was no detection of the G12P[8] genotype.

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  • Clinical and molecular epidemiologic trends reveal the important role of rotavirus in adult infectious gastroenteritis, in Shanghai, China

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    Phylogenetic analysis of the VP7 genes demonstrated that there were six lineages and eleven sublineages in global G9 strains in accordance with an accepted nomenclature (Phan et al., 2007). Thirty-two G9 strains analyzed in the present study were located in sublineage VIe (specific amino acid substitution, H144) of lineage VI together with some other strains reported in Japan, Thailand, Russia, USA, Solomon Islands and Zimbabwe, and primarily, with Chinese strains detected in children from Beijing (BJ-Q94, BJ-CR7611, BJ-CR8537, X1302), Shanghai (SPH0144), Yunnan (ZT-12N-T66) and Zhejiang (WZ810), from 2010 to date (Shen et al., 2013; Yamamoto et al., 2015; Chieochansin et al., 2016; Jones et al., 2016; Li et al., 2016) (Fig. 2A). These G9-VIe strains shared 95.4% to 100% nucleotide (nt) and 95.0% to 100% amino acid (aa) homology, except for strain SH-RV69 (with shared identity of 93.2% nt and 93.9% aa).

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