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    Genomic analysis of serologically untypable human enteroviruses in Taiwan

    Chien, Yeh-Sheng
    Luo, Shu-Ting
    Tsao, Kuo-Chien
    Huang, Yhu-Chering
    Chung, Wan-Yu
    Liao, Yu-Chieh
    Tan, Yi
    Das, Suman R.
    Lee, Min-Sh
    : https://ir.vanderbilt.edu/xmlui/handle/1803/9874
    : 2019-07-03

    Abstract

    BackgroundHuman 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.MethodsIn this study, we established an NGS platform to conduct genome sequencing for the serologically untypable enterovirus isolates.ResultsAmong 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.ConclusionsWe successfully integrated VP1-CODEHOP and NGS techniques to conduct genomic analysis of serologically untypable enteroviruses.
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