Unbiased whole-genome deep sequencing of human and porcine stool samples reveals circulation of multiple groups of rotaviruses and a putative zoonotic infection

Phan, M. V. T. et al. (2016) Unbiased whole-genome deep sequencing of human and porcine stool samples reveals circulation of multiple groups of rotaviruses and a putative zoonotic infection. Virus Evolution, 2(2), vew027. (doi: 10.1093/ve/vew027) (PMID:28748110) (PMCID:PMC5522372)

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Abstract

Coordinated and synchronous surveillance for zoonotic viruses in both human clinical cases and animal reservoirs provides an opportunity to identify interspecies virus movement. Rotavirus (RV) is an important cause of viral gastroenteritis in humans and animals. In this study, we document the RV diversity within co-located humans and animals sampled from the Mekong delta region of Vietnam using a primer-independent, agnostic, deep sequencing approach. A total of 296 stool samples (146 from diarrhoeal human patients and 150 from pigs living in the same geographical region) were directly sequenced, generating the genomic sequences of sixty human rotaviruses (all group A) and thirty-one porcine rotaviruses (thirteen group A, seven group B, six group C, and five group H). Phylogenetic analyses showed the co-circulation of multiple distinct RV group A (RVA) genotypes/strains, many of which were divergent from the strain components of licensed RVA vaccines, as well as considerable virus diversity in pigs including full genomes of rotaviruses in groups B, C, and H, none of which have been previously reported in Vietnam. Furthermore, the detection of an atypical RVA genotype constellation (G4-P[6]-I1-R1-C1-M1-A8-N1-T7-E1-H1) in a human patient and a pig from the same region provides some evidence for a zoonotic event.

Item Type:Articles
Additional Information:This study was supported by the Wellcome Trust of the UK through the VIZIONS strategic award (WT/093724), and the British Council of the UK through the Researchers Link Travel Award (MVTP, Grant application number 127624851).
Status:Published
Refereed:Yes
Glasgow Author(s) Enlighten ID:Cotten, Professor Matthew
Authors: Phan, M. V. T., Anh, P. H., Cuong, N. V., Munnink, B. B. O., van der Hoek, L., My, P. T., Tri, T. N., Bryant, J. E., Baker, S., Thwaites, G., Woolhouse, M., Kellam, P., Rabaa, M. A., and Cotten, M.
College/School:College of Medical Veterinary and Life Sciences > School of Infection & Immunity
College of Medical Veterinary and Life Sciences > School of Infection & Immunity > Centre for Virus Research
Journal Name:Virus Evolution
Publisher:Oxford University Press
ISSN:2057-1577
ISSN (Online):2057-1577
Published Online:03 October 2016
Copyright Holders:Copyright © 2016 The Authors
First Published:First published in Virus Evolution 2(2): vew027
Publisher Policy:Reproduced under a Creative Commons License

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