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A targeted approach with nanopore sequencing for the universal detection and identification of flaviviruses

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Title: A targeted approach with nanopore sequencing for the universal detection and identification of flaviviruses
Authors: Reteng, Patrick Browse this author
Linh, Nguyen Thuy Browse this author
Tam, Tran Thi Minh Browse this author
CelesteTorres, Maria Browse this author
de Filippis, Ana Maria Bispo Browse this author
Orba, Yasuko Browse this author →KAKEN DB
Kobayashi, Shintaro Browse this author →KAKEN DB
Hayashida, Kyoko Browse this author
Sawa, Hirofumi Browse this author →KAKEN DB
Hall, William W. Browse this author
Lan Anh, Nguyen Thi Browse this author
Yamagishi, Junya Browse this author →KAKEN DB
Issue Date: 24-Sep-2021
Publisher: Nature Portfolio
Journal Title: Scientific reports
Volume: 11
Issue: 1
Start Page: 19031
Publisher DOI: 10.1038/s41598-021-98013-9
Abstract: Nucleic acid test (NAT), most typically quantitative PCR, is one of the standard methods for species specific flavivirus diagnosis. Semi-comprehensive NATs such as pan-flavivirus PCR which covers genus Flavivirus are also available; however, further specification by sequencing is required for species level differentiation. In this study, a semi-comprehensive detection system that allows species differentiation of flaviviruses was developed by integration of the pan-flavivirus PCR and Nanopore sequencing. In addition, a multiplexing method was established by adding index sequences through the PCR with a streamlined bioinformatics pipeline. This enables defining cut-off values for observed read counts. In the laboratory setting, this approach allowed the detection of up to nine different flaviviruses. Using clinical samples collected in Vietnam and Brazil, seven different flaviviruses were also detected. When compared to a commercial NAT, the sensitivity and specificity of our system were 66.7% and 95.4%, respectively. Conversely, when compared to our system, the sensitivity and specificity of the commercial NAT were 57.1% and 96.9%, respectively. In addition, Nanopore sequencing detected more positive samples (n = 8) compared to the commercial NAT (n = 6). Collectively, our study has established a semi-comprehensive sequencing-based diagnostic system for the detection of flaviviruses at extremely affordable costs, considerable sensitivity, and only requires simple experimental methods.
Type: article
Appears in Collections:人獣共通感染症国際共同研究所 (International Institute for Zoonosis Control) > 雑誌発表論文等 (Peer-reviewed Journal Articles, etc)

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