Back to Search
Start Over
Multiplex PCR-Based Nanopore Sequencing and Epidemiological Surveillance of Hantaan orthohantavirus in Apodemus agrarius, Republic of Korea
- Source :
- Viruses, Volume 13, Issue 5, Viruses, Vol 13, Iss 847, p 847 (2021)
- Publication Year :
- 2021
- Publisher :
- Multidisciplinary Digital Publishing Institute, 2021.
-
Abstract
- 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.
- Subjects :
- 0301 basic medicine
Apodemus agrarius
amplicon-based NGS
030106 microbiology
MinION sequencing
Microbiology
Hantaan virus (HTNV)
03 medical and health sciences
Virology
Multiplex polymerase chain reaction
next-generation sequencing (NGS)
Hantaan virus
Hantavirus
Whole genome sequencing
biology
hemorrhagic fever with renal syndrome (HFRS)
phylogenetic analysis
virus diseases
genetic diversity
Amplicon
biology.organism_classification
QR1-502
030104 developmental biology
Infectious Diseases
whole-genome sequencing
Minion
viral genome surveillance
Nanopore sequencing
Subjects
Details
- Language :
- English
- ISSN :
- 19994915
- Database :
- OpenAIRE
- Journal :
- Viruses
- Accession number :
- edsair.doi.dedup.....b9826e5a64c9c89dd5f80bb2d88e1a98
- Full Text :
- https://doi.org/10.3390/v13050847