Genetic characterization of norovirus GII.4 variants circulating in Canada using a metagenomic technique
| Autor: | Jennifer Ronholm, Nicholas Petronella, Sabah Bidawid, Oksana Mykytczuk, Jennifer Harlow, Nathalie Corneau, Menka Suresh, Neda Nasheri |
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| Rok vydání: | 2018 |
| Předmět: |
0301 basic medicine
Canada Antigenic drift Genotype viruses Biology medicine.disease_cause Genome DNA sequencing lcsh:Infectious and parasitic diseases Astrovirus Open Reading Frames 03 medical and health sciences medicine Humans lcsh:RC109-216 Amino Acid Sequence Gene Phylogeny Caliciviridae Infections Recombination Genetic Whole genome sequencing Genetics Sequence Analysis RNA Norovirus High-Throughput Nucleotide Sequencing virus diseases biology.organism_classification Recombination Co-infection 030104 developmental biology Infectious Diseases Metagenomics Mutation Next-generation sequencing RNA Viral Capsid Proteins Research Article |
| Zdroj: | BMC Infectious Diseases, Vol 18, Iss 1, Pp 1-11 (2018) BMC Infectious Diseases |
| ISSN: | 1471-2334 |
| Popis: | 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. |
| Databáze: | OpenAIRE |
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