Comparison of targeted next-generation sequencing for whole-genome sequencing of Hantaan orthohantavirus in Apodemus agrarius lung tissues

Jin Sun No, Won Keun Kim, Seungchan Cho, Seung Ho Lee, Jeong Ah Kim, Daesang Lee, Dong Hyun Song, Se Hun Gu, Seong Tae Jeong, Michael R. Wiley, Gustavo Palacios, Jin Won Song

Research output: Contribution to journalArticlepeer-review

24 Citations (Scopus)

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 103–104 copies/μL of HTNV RNA. Furthermore, the amplicon NGS showed a 10-fold (102 copies/μL) 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.

Original languageEnglish
Article number16631
JournalScientific reports
Volume9
Issue number1
DOIs
Publication statusPublished - 2019 Dec 1

Bibliographical note

Funding Information:
We thank Mr. Charles Hong from Defense Threat Reduction Agency (DTRA) for critical discussion and experimental support. We thank Dr. Gary Schroth and Dr. Stephen Gross (Illumina) for technical supports. We thank Dr. Man-Seong Park (Korea University College of medicine) for supporting NGS facility. This work was supported by the Agency for Defense Development (UD160022ID), the Research Program To Solve Social Issues of the National Research Foundation of Korea (NRF) funded by the Ministry of Science and ICT (NRF-2017M3A9E4061992), and the Institute of Biomedical Science & Food Safety, Korea University (K1909531).

Publisher Copyright:
© 2019, The Author(s).

ASJC Scopus subject areas

  • General

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