BMC infectious diseases, 2018-10, Vol.18 (1), p.521-521, Article 521
2018
Details
- Autor(en) / Beteiligte
- Titel
- Genetic characterization of norovirus GII.4 variants circulating in Canada using a metagenomic technique
- Ist Teil von
- BMC infectious diseases, 2018-10, Vol.18 (1), p.521-521, Article 521
- Ort / Verlag
- England: BioMed Central Ltd
- Erscheinungsjahr
- 2018
- Link zum Volltext
- Quelle
- MEDLINE
- Beschreibungen/Notizen
- 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. A metagenomic, next-generation sequencing method, based on Illumina RNA-Seq, was applied to determine norovirus sequences from clinical samples. 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. Overall this study demonstrated the application of whole genome sequencing as an important tool in molecular characterization of noroviruses.
- Sprache
- Englisch
- Identifikatoren
- ISSN: 1471-2334eISSN: 1471-2334DOI: 10.1186/s12879-018-3419-8Titel-ID: cdi_doaj_primary_oai_doaj_org_article_76326c1f12f84deab938d205e60bcb98
- Format
- –
- Schlagworte
- Amino Acid Sequence, Amino acids, Antigenic drift, Antigens, Caliciviridae Infections - diagnosis, Caliciviridae Infections - epidemiology, Caliciviridae Infections - virology, Canada, Capsid Proteins - genetics, Co-infection, Data processing, Drug resistance, Epidemics, Epitopes, Gastroenteritis, Gene sequencing, Genetic aspects, Genetic diversity, Genomes, Genotype, Genotypes, High-Throughput Nucleotide Sequencing, Humans, Identification and classification, Infections, Innovations, Metagenomics, Methods, Molecular diagnostic techniques, Mutation, Next-generation sequencing, Norovirus, Norovirus - classification, Norovirus - genetics, Norovirus - isolation & purification, Nucleotide sequence, Open Reading Frames - genetics, Pandemics, Phylogeny, Proteins, Recombination, Recombination, Genetic, Ribonucleic acid, RNA, RNA viruses, RNA, Viral - chemistry, RNA, Viral - isolation & purification, RNA, Viral - metabolism, Sequence Analysis, RNA, Viral infections, Viruses, VP1 protein