Development of a culture-independent whole-genome sequencing of Nipah virus using the MinION Oxford Nanopore platform
The development of a culture-independent, high-throughput whole-genome sequencing (WGS) protocol for Nipah virus (NiV) using the Oxford Nanopore MinION technology marks a significant advancement in outbreak response, surveillance, and genomic analysis of NiV. NiV is an RG4 category C pathogen; working with the NiV virus is a deep concern of biosafety and biosecurity. It demands the development of biologically safe procedures to get genetic information. This protocol utilizes biologically safe samples that were collected into recommended lysis solution, multiplex PCR, and third-generation sequencing, effectively addressing challenges in sequencing NiV. This optimized workflow achieved over 95% genome coverage without the need for virus culture. It is a cost-effective, rapid, and efficient approach to the WGS of NiV, making it suitable for resource-limited settings like Bangladesh. The method enhances the capacity for outbreak investigations, epidemiological analyses, and monitoring virus, aiding in detecting emerging strains. This work contributes significantly to global pandemic preparedness and response efforts.
Authors
- Iqbal Kabir Jahid (ORCID: https://orcid.org/0000-0003-0717-0806)
- John D. Klena (ORCID: https://orcid.org/0000-0001-9933-6193)
- Jonathan H. Epstein (ORCID: https://orcid.org/0000-0002-1373-9301)
- Shannon Whitmer (ORCID: https://orcid.org/0000-0002-0819-6736)
- Tahmina Shirin (ORCID: https://orcid.org/0000-0002-5061-3783)
- Christina F. Spiropoulou (ORCID: https://orcid.org/0000-0001-8406-3161)
- Mohammad Enayet Hossain (ORCID: https://orcid.org/0000-0001-5511-1857)
- Mojnu Miah (ORCID: https://orcid.org/0000-0003-0488-1936)
- Samiur Rahim (ORCID: https://orcid.org/0000-0003-1468-395X)
- Maria E. Kaczmarek (ORCID: https://orcid.org/0000-0003-3593-9053)
- Mohammed Ziaur Rahman (ORCID: https://orcid.org/0000-0002-4103-4835)
- Joel M. Montgomery (ORCID: https://orcid.org/0000-0003-0523-4431)
- Ariful Islam (ORCID: https://orcid.org/0000-0001-5195-7572)
- Sharmin Sultana (ORCID: https://orcid.org/0000-0002-2687-1280)
- Md Mahfuzur Rahman (ORCID: https://orcid.org/0000-0002-2917-8991)
- Syed M Satter
Institutions
- University of Science and Technology (YE)
- National Center for Emerging and Zoonotic Infectious Diseases (US)
- Institute of Epidemiology, Disease Control and Research (BD)
- EcoHealth Alliance (US)
- Korea University of Science and Technology (KR)
Publication Details
- Journal
- Microbiology Spectrum
- Published
- 2025-04-16
- DOI
- https://doi.org/10.1128/spectrum.02492-24
- Citations
- 6
- Primary Topic
- Virology and Viral Diseases
- Type
- article
- Field-Weighted Citation Impact
- 8.13