Cargando…
Genetic characterization of norovirus GII.4 variants circulating in Canada using a metagenomic technique
BACKGROUND: Human norovirus is the leading cause of viral gastroenteritis globally, and the GII.4 has been the most predominant genotype for decades. This genotype has numerous variants that have caused repeated epidemics worldwide. However, the molecular evolutionary signatures among the GII.4 vari...
Autores principales: | , , , , , , , |
---|---|
Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
BioMed Central
2018
|
Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6191920/ https://www.ncbi.nlm.nih.gov/pubmed/30333011 http://dx.doi.org/10.1186/s12879-018-3419-8 |
_version_ | 1783363807754584064 |
---|---|
author | Petronella, Nicholas Ronholm, Jennifer Suresh, Menka Harlow, Jennifer Mykytczuk, Oksana Corneau, Nathalie Bidawid, Sabah Nasheri, Neda |
author_facet | Petronella, Nicholas Ronholm, Jennifer Suresh, Menka Harlow, Jennifer Mykytczuk, Oksana Corneau, Nathalie Bidawid, Sabah Nasheri, Neda |
author_sort | Petronella, Nicholas |
collection | PubMed |
description | BACKGROUND: Human norovirus is the leading cause of viral gastroenteritis globally, and the GII.4 has been the most predominant genotype for decades. This genotype has numerous variants that have caused repeated epidemics worldwide. However, the molecular evolutionary signatures among the GII.4 variants have not been elucidated throughout the viral genome. METHOD: A metagenomic, next-generation sequencing method, based on Illumina RNA-Seq, was applied to determine norovirus sequences from clinical samples. RESULTS: Herein, the obtained deep-sequencing data was employed to analyze full-genomic sequences from GII.4 variants prevailing in Canada from 2012 to 2016. Phylogenetic analysis demonstrated that the majority of these sequences belong to New Orleans 2009 and Sydney 2012 strains, and a recombinant sequence was also identified. Genome-wide similarity analyses implied that while the capsid gene is highly diverse among the isolates, the viral protease and polymerase genes remain relatively conserved. Numerous amino acid substitutions were observed at each putative antigenic epitope of the VP1 protein, whereas few amino acid changes were identified in the polymerase protein. Co-infection with other enteric RNA viruses was investigated and the astrovirus genome was identified in one of the samples. CONCLUSIONS: Overall this study demonstrated the application of whole genome sequencing as an important tool in molecular characterization of noroviruses. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s12879-018-3419-8) contains supplementary material, which is available to authorized users. |
format | Online Article Text |
id | pubmed-6191920 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2018 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-61919202018-10-23 Genetic characterization of norovirus GII.4 variants circulating in Canada using a metagenomic technique Petronella, Nicholas Ronholm, Jennifer Suresh, Menka Harlow, Jennifer Mykytczuk, Oksana Corneau, Nathalie Bidawid, Sabah Nasheri, Neda BMC Infect Dis Research Article BACKGROUND: Human norovirus is the leading cause of viral gastroenteritis globally, and the GII.4 has been the most predominant genotype for decades. This genotype has numerous variants that have caused repeated epidemics worldwide. However, the molecular evolutionary signatures among the GII.4 variants have not been elucidated throughout the viral genome. METHOD: A metagenomic, next-generation sequencing method, based on Illumina RNA-Seq, was applied to determine norovirus sequences from clinical samples. RESULTS: Herein, the obtained deep-sequencing data was employed to analyze full-genomic sequences from GII.4 variants prevailing in Canada from 2012 to 2016. Phylogenetic analysis demonstrated that the majority of these sequences belong to New Orleans 2009 and Sydney 2012 strains, and a recombinant sequence was also identified. Genome-wide similarity analyses implied that while the capsid gene is highly diverse among the isolates, the viral protease and polymerase genes remain relatively conserved. Numerous amino acid substitutions were observed at each putative antigenic epitope of the VP1 protein, whereas few amino acid changes were identified in the polymerase protein. Co-infection with other enteric RNA viruses was investigated and the astrovirus genome was identified in one of the samples. CONCLUSIONS: Overall this study demonstrated the application of whole genome sequencing as an important tool in molecular characterization of noroviruses. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s12879-018-3419-8) contains supplementary material, which is available to authorized users. BioMed Central 2018-10-17 /pmc/articles/PMC6191920/ /pubmed/30333011 http://dx.doi.org/10.1186/s12879-018-3419-8 Text en © The Author(s). 2018 Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated. |
spellingShingle | Research Article Petronella, Nicholas Ronholm, Jennifer Suresh, Menka Harlow, Jennifer Mykytczuk, Oksana Corneau, Nathalie Bidawid, Sabah Nasheri, Neda Genetic characterization of norovirus GII.4 variants circulating in Canada using a metagenomic technique |
title | Genetic characterization of norovirus GII.4 variants circulating in Canada using a metagenomic technique |
title_full | Genetic characterization of norovirus GII.4 variants circulating in Canada using a metagenomic technique |
title_fullStr | Genetic characterization of norovirus GII.4 variants circulating in Canada using a metagenomic technique |
title_full_unstemmed | Genetic characterization of norovirus GII.4 variants circulating in Canada using a metagenomic technique |
title_short | Genetic characterization of norovirus GII.4 variants circulating in Canada using a metagenomic technique |
title_sort | genetic characterization of norovirus gii.4 variants circulating in canada using a metagenomic technique |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6191920/ https://www.ncbi.nlm.nih.gov/pubmed/30333011 http://dx.doi.org/10.1186/s12879-018-3419-8 |
work_keys_str_mv | AT petronellanicholas geneticcharacterizationofnorovirusgii4variantscirculatingincanadausingametagenomictechnique AT ronholmjennifer geneticcharacterizationofnorovirusgii4variantscirculatingincanadausingametagenomictechnique AT sureshmenka geneticcharacterizationofnorovirusgii4variantscirculatingincanadausingametagenomictechnique AT harlowjennifer geneticcharacterizationofnorovirusgii4variantscirculatingincanadausingametagenomictechnique AT mykytczukoksana geneticcharacterizationofnorovirusgii4variantscirculatingincanadausingametagenomictechnique AT corneaunathalie geneticcharacterizationofnorovirusgii4variantscirculatingincanadausingametagenomictechnique AT bidawidsabah geneticcharacterizationofnorovirusgii4variantscirculatingincanadausingametagenomictechnique AT nasherineda geneticcharacterizationofnorovirusgii4variantscirculatingincanadausingametagenomictechnique |