Metagenomic nanopore sequencing: RNA viruses from lab to field
About Liana Kafetzopoulou
Liana is a PhD student based at Public Health England; her project is part of the NIHR Health Protection Research Unit in Emerging and Zoonotic infections, a collaboration between Public Health England and the University of Liverpool. Her work focuses on investigating the application of metagenomic sequencing methods to viral clinical samples. Liana is interested in field sequencing, and utilised the MinION for metagenomic sequencing in Nigeria during the recent Lassa fever outbreak.
Emerging and re-emerging RNA viruses cause a significant global disease burden, ranging from mild febrile illness to haemorrhagic fevers. Rapid and unbiased identification methods, such as metagenomic MinION sequencing, are vital for the identification and characterisation of emerging pathogens for which little prior knowledge is available. Portable methodologies for field use are required during such outbreaks, especially when they occur in resource-limited settings. We have investigated a range of clinical samples using a Sequence Independent Single Primer Amplification approach and have demonstrated that metagenomic MinION sequencing can elucidate full viral genomes directly from clinical samples for Chikungunya, Dengue and Lassa virus; across clinically relevant range of viral titers. Following our results we mobilized a research team and deployed in Nigeria to test and investigate the establishment of field metagenomic sequencing using the MinION. Our pilot study was expedited and utilized to support the largest reported outbreak of Lassa fever (LASV) in Nigeria.