Whole Genomic Analysis of an Unusual Human G6P[14] Rotavirus Strain Isolated from a Child with Diarrhea in Thailand: Evidence for Bovine-To-Human Interspecies Transmission and Reassortment Events.

Ratana Tacharoenmuang,Koki Taniguchi,Kazuhiko Katayama,Tomihiko Ide,Yuya Ouchi,Hiroki Kurahashi,Takao Tsuji,Somchai Sangkitporn,Takema Kato,Satoshi Komoto,Ratigorn Guntapong,Kei Haga,Houssam Attoui

doi:10.1371/journal.pone.0139381

Abstract

An unusual rotavirus strain, SKT-27, with the G6P[14] genotypes (RVA/Human-wt/THA/SKT-27/2012/G6P[14]), was identified in a stool specimen from a hospitalized child aged eight months with severe diarrhea. In this study, we sequenced and characterized the complete genome of strain SKT-27. On whole genomic analysis, strain SKT-27 was found to have a unique genotype constellation: G6-P[14]-I2-R2-C2-M2-A3-N2-T6-E2-H3. The non-G/P genotype constellation of this strain (I2-R2-C2-M2-A3-N2-T6-E2-H3) is commonly shared with rotavirus strains from artiodactyls such as cattle. Phylogenetic analysis indicated that nine of the 11 genes of strain SKT-27 (VP7, VP4, VP6, VP2-3, NSP1, NSP3-5) appeared to be of artiodactyl (likely bovine) origin, while the remaining VP1 and NSP2 genes were assumed to be of human origin. Thus, strain SKT-27 was found to have a bovine rotavirus genetic backbone, and thus is likely to be of bovine origin. Furthermore, strain SKT-27 appeared to be derived through interspecies transmission and reassortment events involving bovine and human rotavirus strains. Of note is that the VP7 gene of strain SKT-27 was located in G6 lineage-5 together with those of bovine rotavirus strains, away from the clusters comprising other G6P[14] strains in G6 lineages-2/6, suggesting the occurrence of independent bovine-to-human interspecies transmission events. To our knowledge, this is the first report on full genome-based characterization of human G6P[14] strains that have emerged in Southeast Asia. Our observations will provide important insights into the origin of G6P[14] strains, and into dynamic interactions between human and bovine rotavirus strains.

Highlights

Group A rotavirus (RVA), a member of the Reoviridae family, is the most important etiological agent of severe gastroenteritis in the young of humans and many animal species worldwide
The full-genomic sequence was determined for strain SKT-27, which was identified as the sole pathogen causing diarrhea in stool specimens from a hospitalized child aged eight months with severe diarrhea in Sukhothai Province in November 2012 during the RVA strain surveillance program in Phetchaboon and Sukhothai Provinces, Thailand in 2012–2014, which involved a total of 685 RVA-positive fecal samples (Tacharoenmuang et al, in preparation)
Stool samples containing strain SKT-27 were kept at −30°C until use

Summary

Introduction

Group A rotavirus (RVA), a member of the Reoviridae family, is the most important etiological agent of severe gastroenteritis in the young of humans and many animal species worldwide. Strain SKT-27 exhibited a unique non-G/P genotype constellation (I2-R2-C2-M2-A3-N2-T6-E2-H3), which is commonly found in RVA strains from artiodactyls such as cattle [17, 18, 42].

Results

Conclusion