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Deep sequencing of norovirus genomes defines evolutionary patterns in an urban tropical setting

Title: Deep sequencing of norovirus genomes defines evolutionary patterns in an urban tropical setting
Authors: Cotten, M
Petrova, V
Phan, MVT
Rabaa, MA
Watson, SJ
Ong, SH
Kellam, P
Baker, S
Item Type: Journal Article
Abstract: Norovirus is a highly transmissible infectious agent that causes epidemic gastroenteritis in susceptible children and adults. Norovirus infections can be severe and can be initiated from an exceptionally small number of viral particles. Detailed genome sequence data are useful for tracking norovirus transmission and evolution. To address this need, we have developed a whole-genome deep-sequencing method that generates entire genome sequences from small amounts of clinical specimens. This novel approach employs an algorithm for reverse transcription and PCR amplification primer design using all of the publically available norovirus sequence data. Deep sequencing and de novo assembly were used to generate norovirus genomes from a large set of diarrheal patients attending three hospitals in Ho Chi Minh City, Vietnam, over a 2.5-year period. Positive-selection analysis and direct examination of protein changes in the virus over time identified codons in the regions encoding proteins VP1, p48 (NS1-2), and p22 (NS4) under positive selection and expands the known targets of norovirus evolutionary pressure.
Issue Date: 1-Oct-2014
Date of Acceptance: 10-Jul-2014
URI: http://hdl.handle.net/10044/1/69473
DOI: https://dx.doi.org/10.1128/JVI.01333-14
ISSN: 1098-5514
Publisher: American Society for Microbiology
Start Page: 11056
End Page: 11069
Journal / Book Title: Journal of Virology
Volume: 88
Issue: 19
Copyright Statement: © 2014 Cotten et al. This is an open-access article distributed under the terms of the Creative Commons Attribution 3.0 Unported license (https://creativecommons.org/licenses/by/3.0/).
Keywords: Science & Technology
Life Sciences & Biomedicine
Virology
NORWALK-LIKE VIRUSES
MOLECULAR CHARACTERIZATION
PHYLOGENETIC ANALYSIS
PORCINE NOROVIRUSES
HERD-IMMUNITY
GENOGROUP-II
DYNAMICS
PROTEIN
GASTROENTERITIS
TRANSMISSION
Biological Evolution
Caliciviridae Infections
Child
Child, Preschool
Cities
Codon
Diarrhea
Gastroenteritis
Gene Expression
Genome, Viral
High-Throughput Nucleotide Sequencing
Humans
Infant
Norovirus
Phylogeny
RNA, Viral
Vietnam
Viral Nonstructural Proteins
06 Biological Sciences
07 Agricultural and Veterinary Sciences
11 Medical and Health Sciences
Publication Status: Published
Online Publication Date: 2014-09-08
Appears in Collections:Department of Medicine



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