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

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Title: Unbiased whole-genome deep sequencing of human and porcine stool samples reveals circulation of multiple groups of rotaviruses and a putative zoonotic infection
Authors: Phan, MVT
Hong Anh, P
Van Cuong, N
Oude Munnink, B
Van der Hoek, L
Tran My, P
Ngo Tri, T
Bryant, J
Baker, S
Thwaites, G
Woolhouse, M
Kellam, P
Rabaa, M
Cotten, M
Item Type: Working Paper
Abstract: Coordinated and synchronous virological surveillance for zoonotic viruses in both human clinical cases and animal reservoirs provides an opportunity to identify interspecies virus movement. Rotavirus is an important cause of viral gastroenteritis in humans and animals. We have documented the rotavirus 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 60 human rotaviruses (all group A) and 31 porcine rotaviruses (13 group A, 7 group B, 6 group C and 5 group H). Phylogenetic analyses showed the co-circulation of multiple distinct rotavirus 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.
Issue Date: 14-Jun-2016
URI: http://hdl.handle.net/10044/1/72073
DOI: https://doi.org/10.1101/058875
Publisher: Oxford University Press
Copyright Statement: © 2019 The Author(s). This item is made available under a CC-BY 4.0 International license (https://creativecommons.org/licenses/by/4.0/).
Sponsor/Funder: Wellcome Trust
Funder's Grant Number: 093724/E/10/Z
Keywords: on behalf of the VIZIONS Consortium
Publication Status: Published
Appears in Collections:Department of Medicine



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