Molecular diagnosis of patients with hepatitis A virus infection using amplicon-based nanopore sequencingopen access
- Authors
- Lee, Geum-Young; Park, Kyungmin; Lee, Young-Sun; Kim, Ji Hoon; Byun, Kwan Soo; Kim, Jongwoo; Kim, Won-Keun; Song, Jin-Won
- Issue Date
- Jul-2023
- Publisher
- Public Library of Science
- Citation
- PLoS ONE, v.18, no.7
- Indexed
- SCIE
SCOPUS
- Journal Title
- PLoS ONE
- Volume
- 18
- Number
- 7
- URI
- https://scholarworks.korea.ac.kr/kumedicine/handle/2021.sw.kumedicine/63838
- DOI
- 10.1371/journal.pone.0288361
- ISSN
- 1932-6203
- Abstract
- High-throughput sequencing is a robust tool used for identifying and tracking pathogen outbreaks. Whole-genome sequencing of hepatitis A virus (HAV) remains poor due to ultra-low viral loads, limitations of next-generation sequencing technology, and its high costs in clinical applications. This study evaluated multiplex polymerase chain reaction (PCR)-based nanopore sequencing to obtain whole-genome sequences of HAV. The HAV genomes were obtained directly from patient specimens for a rapid molecular diagnosis of viral genotypes. Serum and stool samples were collected from six patients with hepatitis A infection. Amplicon-based nanopore sequencing was performed from the clinical specimens to identify HAV genotypes by acquiring nearly complete-genome sequences. TaqMan-based quantitative PCR (qPCR) was conducted to detect and quantify multiple HAV genes. Singleplex-based nanopore sequencing demonstrated high genome coverage rates (90.4-99.5%) of HAV within 8 h, at viral RNA loads of 10 to 10(5) copies/& mu;L. TaqMan qPCR showed multiplex quantification of HAV genes namely, VP0, VP3, and 3C. This study provides useful insights into rapid molecular diagnosis during hepatitis A outbreaks and may ultimately augment public health disease surveillance in the hospital and epidemiology field.
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- Appears in
Collections - 1. Basic Science > Department of Microbiology > 1. Journal Articles
- 2. Clinical Science > Department of Gastroenterology and Hepatology > 1. Journal Articles
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