Journal Article

Multiplex PCR-Based Nanopore Sequencing and Epidemiological Surveillance of Hantaan orthohantavirus in Apodemus agrarius, Republic of Korea

No, Jin Sun, Park, Kkothanahreum, Kim, Yu-Jin, Lee, Geum-Young, Lee, Seung-Ho, Cho, Seungchan, Kim, Jongwoo, Lee, Jingyeong, Park, Kyungmin, Lee, Seung Ho, Kim, Young-Su, Kim, Won-Keun, Song, Jin-Won, Budhathoki, Shailesh, Klein, Terry A., Kim, Heung-Chul

2021

Overview

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 worldwide. 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.

• Publisher: MDPI AG,MDPI
• Subject: amplicon-based NGS / Annealing / Apodemus agrarius / Decision making / Epidemiology / fever / Genetic diversity / genome / Genomes / Genomics / Hantaan orthohantavirus / Hantaan virus (HTNV) / Hantavirus / Health surveillance / Hemorrhage / Hemorrhagic fever with renal syndrome / hemorrhagic fever with renal syndrome (HFRS) / lungs / Medical research / MinION sequencing / Mitochondrial DNA / monitoring / nanopores / Next-generation sequencing / next-generation sequencing (NGS) / Phylogeny / Polymerase chain reaction / Public health / RNA / RNA polymerase / Severe acute respiratory syndrome / Severe acute respiratory syndrome coronavirus 2 / Small mammals / South Korea / Viruses / Whole genome sequencing