Dataset Information
Genomic analysis of serologically untypable human enteroviruses in Taiwan.
Ontology highlight
ABSTRACT: Background
Human enteroviruses contain over 100 serotypes. We have routinely conducted enterovirus surveillance in northern Taiwan; but about 10% of isolates could not be serotyped using traditional assays. Next-generation sequencing (NGS) is a powerful tool for genome sequencing.Methods
In this study, we established an NGS platform to conduct genome sequencing for the serologically untypable enterovirus isolates.Results
Among 130 serologically untypable isolates, 121 (93%) of them were classified into 29 serotypes using CODEHOP (COnsensus-DEgenerate Hybrid Oligonucleotide Primer)-based RT-PCR to amplify VP1 genes (VP1-CODEHOP). We further selected 52 samples for NGS and identified 59 genome sequences from 51 samples, including 8 samples containing two virus genomes. We also detected 23 genome variants (nucleotide identity < 90% compared with genome sequences in the public domain) which were potential genetic recombination, including 9 inter-serotype recombinants and 14 strains with unknown sources of recombination.Conclusions
We successfully integrated VP1-CODEHOP and NGS techniques to conduct genomic analysis of serologically untypable enteroviruses.
SUBMITTER: Chien YS
PROVIDER: S-EPMC6607526 | biostudies-literature | 2019 Jul
REPOSITORIES: biostudies-literature
Publications
Genomic analysis of serologically untypable human enteroviruses in Taiwan.
Journal of biomedical science 20190703 1
<h4>Background</h4>Human enteroviruses contain over 100 serotypes. We have routinely conducted enterovirus surveillance in northern Taiwan; but about 10% of isolates could not be serotyped using traditional assays. Next-generation sequencing (NGS) is a powerful tool for genome sequencing.<h4>Methods</h4>In this study, we established an NGS platform to conduct genome sequencing for the serologically untypable enterovirus isolates.<h4>Results</h4>Among 130 serologically untypable isolates, 121 (93 ...[more]