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A targeted approach with nanopore sequencing for the universal detection and identification of flaviviruses
| 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 |
| URI: | http://hdl.handle.net/2115/83175 |
| 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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