Whole-genome sequencing of infectious agents enables the identification and characterization of emerging viruses. The MinION device is a portable sequencer that allows real-time sequencing in fields or hospitals. Hantaan orthohantavirus (Hantaan virus, HTNV), harbored by Apodemus agrarius, causes hemorrhagic fever with renal syndrome (HFRS) and poses a critical public health threat world-wide. In this study, we aimed to evaluate the feasibility of using nanopore sequencing for whole-genome sequencing of HTNV from samples having different viral copy numbers. Amplicon-based next-generation sequencing was performed in A. agrarius lung tissues collected from the Republic of Korea. Genomic sequences of HTNV were analyzed based on the viral RNA copy numbers. Amplicon-based nanopore sequencing provided nearly full-length genomic sequences of HTNV and showed sufficient read depth for phylogenetic analysis after 8 h of sequencing. The average identity of the HTNV genome sequences for the nanopore sequencer compared to those of generated from Illumina MiSeq revealed 99.8% (L and M segments) and 99.7% (S segment) identities, respectively. This study highlights the potential of the portable nanopore sequencer for rapid generation of accurate genomic sequences of HTNV for quicker decision making in point-of-care testing of HFRS patients during a hantavirus outbreak.
Bibliographical noteFunding Information:
Funding: This study was supported by the Research Program to Solve Social Issues of the National Research Foundation of Korea (NRF) funded by the Ministry of Science and Information and Communication Technology (ICT; NRF-2017M3A9E4061992) and the Agency for Defense Development (UE202026GD). Partial funding was provided by the Research Program to Solve Social Issues of the NRF funded by the Ministry of Science and ICT (NRF-2019R1I1A2A01060902); the Armed Forces Health Surveillance Branch, Global Emerging Infections Surveillance and Response System (AFHSB-GEIS); Silver Spring, MD (ProMIS ID #P0025-2016-2018-ME); and the 65th Medical Brigade, Camp Humphreys, Republic of Korea.
© 2021 by the authors. Licensee MDPI, Basel, Switzerland.
- Amplicon-based NGS
- Genetic diversity
- Hantaan virus (HTNV)
- Hemorrhagic fever with renal syndrome (HFRS)
- MinION sequencing
- Next-generation sequencing (NGS)
- Phylogenetic analysis
- Viral genome surveillance
- Whole-genome sequencing
ASJC Scopus subject areas
- Infectious Diseases