- 作者: Yeh-Sheng Chien, Shu-Ting Luo, Kuo-Chien Tsao, Yhu-Chering Huang, Wan-Yu Chung, Yu-Chieh Liao, Yi Tan, Suman R. Das and Min-Shi Lee
- 作者服務機構: 1.Institute of Infectious Disease and Vaccinology, National Health Research Institutes, Zhunan, Miaoli County, Taiwan 2.Department of Life Sciences, National Central University, Taoyuan, Taiwan 3.Department of Medical Biotechnology and Laboratory Science, College of Medicine, Chang Gung University, Guishan, Taoyuan County, Taiwan 4.Department of Pediatrics, Linkou Chang Gung Memorial Hospital, Guishan, Taoyuan County, Taiwan 5.Institute of Population Health Sciences, National Health Research Institutes, Zhunan, Miaoli County, Taiwan 6.Division of Infectious Diseases, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA 7.National Health Research Institutes, R1-7F, 35 Keyan Road, Zhunan, Miaoli County, 350, Taiwan
- 中文摘要:
- 英文摘要:
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. - 中文關鍵字:
- 英文關鍵字: Enterovirus, Virus surveillance, Molecular epidemiology, Next-generation sequencing