Comparison of targeted next-generation sequencing for whole- genome sequencing of Hantaan orthohantavirus in Apodemus agrarius lung tissues
- Authors
- No, Jin Sun; Kim, Won-Keun; Cho, Seungchan; Lee, Seung-Ho; Kim, Jeong-Ah; Lee, Daesang; Song, Dong Hyun; Gu, Se Hun; Jeong, Seong Tae; Wiley, Michael R.; Palacios, Gustavo; Song, Jin-Won
- Issue Date
- 12-11월-2019
- Publisher
- NATURE PUBLISHING GROUP
- Citation
- SCIENTIFIC REPORTS, v.9
- Indexed
- SCIE
SCOPUS
- Journal Title
- SCIENTIFIC REPORTS
- Volume
- 9
- URI
- https://scholar.korea.ac.kr/handle/2021.sw.korea/61898
- DOI
- 10.1038/s41598-019-53043-2
- ISSN
- 2045-2322
- Abstract
- Orthohantaviruses, negative-sense single-strand tripartite RNA viruses, are a global public health threat. In humans, orthohantavirus infection causes hemorrhagic fever with renal syndrome or hantavirus cardiopulmonary syndrome. Whole-genome sequencing of the virus helps in identification and characterization of emerging or re-emerging viruses. Next-generation sequencing (NGS) is a potent method to sequence the viral genome, using molecular enrichment methods, from clinical specimens containing low virus titers. Hence, a comparative study on the target enrichment NGS methods is required for whole-genome sequencing of orthohantavirus in clinical samples. In this study, we used the sequence-independent, single-primer amplification, target capture, and amplicon NGS for whole-genome sequencing of Hantaan orthohantavirus (HTNV) from rodent specimens. We analyzed the coverage of the HTNV genome based on the viral RNA copy number, which is quantified by real-time quantitative PCR. Target capture and amplicon NGS demonstrated a high coverage rate of HTNV in Apodemus agrarius lung tissues containing up to 10(3)-10(4) copies/mu L of HTNV RNA. Furthermore, the amplicon NGS showed a 10-fold (10(2) copies/mu L) higher sensitivity than the target capture NGS. This report provides useful insights into target enrichment NGS for whole-genome sequencing of orthohantaviruses without cultivating the viruses.
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Collections - Graduate School > Department of Biomedical Sciences > 1. Journal Articles
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