Citation: Yuhang Liu, Zhiqiang Liu, Jian Li, Xiaomin Yan, Weidi Xu, Le Yi, Changchun Tu, Biao He. Rapid diagnosis of a fox's death case using nanopore sequencing reveals the infection with an Artic-like rabies virus .VIROLOGICA SINICA, 2024, 39(5) : 840-842.  http://dx.doi.org/10.1016/j.virs.2024.08.010

Rapid diagnosis of a fox's death case using nanopore sequencing reveals the infection with an Artic-like rabies virus

cstr: 32224.14.j.virs.2024.08.010
  • Corresponding author: Biao He, heb-001001@163.com
  • Received Date: 25 May 2024
    Accepted Date: 23 August 2024
    Available online: 27 August 2024
  • Highlights
    1. We detected a rabies virus (RABV) in a fox's death case within 6 h upon sample receipt using nanopore direct sequencing.
    2. The virus belongs to AL2 sub-lineage, suggesting a high risk of fox-related AL2 RABV on the northeastern border of China.
    3. Nanopore sequencing showed less sensitivity and accuracy, though it helped us rapidly identify the cause of death.

  • 加载中
  • 10.1016j.virs.2024.08.010-ESM.docx
    1. Barbé, L., Schaeffer, J., Besnard, A., Jousse, S., Wurtzer, S., Moulin, L., OBEPINE Consortium, Le Guyader, F. S., Desdouits, M., 2022. SARS-CoV-2 whole-genome sequencing using Oxford Nanopore Technology for variant monitoring in wastewaters. Front. Microbiol. 13, 889811.

    2. Brancaccio, R. N., Robitaille, A., Dutta, S., Rollison, D. E., Tommasino, M., Gheit, T., 2021. MinION nanopore sequencing and assembly of a complete human papillomavirus genome. J. Virol. Methods. 294, 114180.

    3. Croville, G., Walch, M., Secula, A., Lebre, L., Silva, S., Filaire, F., Guerin, J. L., 2024. An amplicon-based nanopore sequencing workflow for rapid tracking of avian influenza outbreaks, France, 2020-2022. Front. Cell. Infect. Microbiol. 14, 1257586.

    4. Dimitrov, K. M., Sharma, P., Volkening, J. D., Goraichuk, I. V., Wajid, A., Rehmani, S. F., Basharat, A., Shittu, I., Joannis, T. M., Miller, P. J. et al., 2017. A robust and cost-effective approach to sequence and analyze complete genomes of small RNA viruses. Virol. J. 14, 72.

    5. Eisenstein, M., 2023. Navigating an increasingly crowded sequencing landscape. Nature. 614, 798-800.

    6. Feng, Y., Wang, Y., Hada, Deijide, Gaosuyilatu, Li, X, Xu, Z., Hasibagen, Bulage, A., Li, L. et al., 2022. Diversity of rabies virus detected in Inner Mongolia, China, 2019-2021. Transbound. Emerg. Dis. 69, 249-253.

    7. Feng, Y., Wang, Y., Xu, W., Tu, Z., Liu, T., Huo, M., Liu, Y., Gong, W., Zeng, Z., Wang, W. et al., 2020. Animal rabies surveillance, China, 2004-2018. Emerg. Infect. Dis. 26, 2825-2834.

    8. Gauthier, N. P. G., Chorlton, S. D., Krajden, M., Manges, A. R., 2023. Agnostic sequencing for detection of viral pathogens. Clin. Microbiol, Rev. 36, e0011922.

    9. Hansen, S., Faye, O., Sanabani, S. S., Faye, M., Bohlken-Fascher, S., Faye, O., Sall, A. A., Bekaert, M., Weidmann, M., Czerny, C. P. et al., 2020. Zika virus amplification using strand displacement isothermal method and sequencing using Nanopore Technology. Methods. Mol. Biol. 2142, 123-136.

    10. Hoenen, T., Groseth, A., Rosenke, K., Fischer, R. J., Hoenen, A., Judson, S. D., Martellaro, C., Falzarano, D., Marzi, A., Squires, R. B. et al., 2016. Nanopore sequencing as a rapidly deployable Ebola outbreak tool. Emerg. Infect. Dis. 22, 331-334.

    11. Jin, Y., Zhang, X., Ma, Y., Qiao, Y., Liu, X., Zhao, K., Zhang, C., Lin, D., Fu, X., Xu, X. et al., 2017. Canine distemper viral infection threatens the giant panda population in China. Oncotarget. 8, 113910-113919.

    12. Li, T., Mbala-Kingebeni, P., Naccache, S. N., Theze, J., Bouquet, J., Federman, S., Somasekar, S., Yu, G., Sanchez-San Martin, C., Achari, A. et al., 2019. Metagenomic Next-Generation Sequencing of the 2014 Ebola virus disease outbreak in the Democratic Republic of the Congo. J. Clin. Microbiol. 57, e00827.-19.

    13. Quick, J., Grubaugh, N. D., Pullan, S. T., Claro, I. M., Smith, A. D., Gangavarapu, K., Oliveira, G., Robles-Sikisaka, R., Rogers, T. F., Beutler, N. A. et al., 2017. Multiplex PCR method for MinION and Illumina sequencing of Zika and other virus genomes directly from clinical samples. Nat. Protoc. 12, 1261-1276.

    14. Sanderson, N. D., Hopkins, K. M. V., Colpus, M., Parker, M., Lipworth, S., Crook, D, Stoesser, N, 2024. Evaluation of the accuracy of bacterial genome reconstruction with Oxford Nanopore R10.4.1 long-read-only sequencing. Microb. Genom. 10, 001246.

    15. Wang, D., Smith, J.L.D., Accatino, F., Ge, J., Wang, T., 2023. Addressing the impact of canine distemper spreading on an isolated tiger population in northeast Asia. Integr. Zool 18, 994-1008.

    16. Wu, F., Zhao, S., Yu, B., Chen, Y. M., Wang, W., Song, Z. G., Hu, Y., Tao, Z. W., Tian, J. H., Pei, Y. Y. et al., 2020. A new coronavirus associated with human respiratory disease in China. Nature. 579, 265-269.

    17. Yu, Z., Wang, T., Sun, H., Xia, Z., Zhang, K., Chu, D., Xu, Y., Xin, Y., Xu, W., Cheng, K. et al., 2013. Contagious caprine pleuropneumonia in endangered Tibetan antelope, China, 2012. Emerg. Infect. Dis. 19, 2051-2053.

  • 加载中

Figures(1)

Article Metrics

Article views(827) PDF downloads(11) Cited by()

Related
Proportional views

    Rapid diagnosis of a fox's death case using nanopore sequencing reveals the infection with an Artic-like rabies virus

      Corresponding author: Biao He, heb-001001@163.com
    • a. Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, State Key Laboratory of Pathogen and Biosecurity, Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Changchun, 130122, China;
    • b. Provincial Wildlife Disease Monitoring Station of Shuanghe, Xunke, 164400, China;
    • c. Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonosis, Yangzhou University, Yangzhou, 225009, China

    Abstract: Highlights
    1. We detected a rabies virus (RABV) in a fox's death case within 6 h upon sample receipt using nanopore direct sequencing.
    2. The virus belongs to AL2 sub-lineage, suggesting a high risk of fox-related AL2 RABV on the northeastern border of China.
    3. Nanopore sequencing showed less sensitivity and accuracy, though it helped us rapidly identify the cause of death.

    Figure (1)  Reference (17) Relative (20)

    目录

    /

    DownLoad:  Full-Size Img  PowerPoint
    Return
    Return