Crystal Gigante - Evaluation of the Oxford Nanopore MinION for Rabies Virus Sequence Typing
Nanopore Community Meeting 2017
Rabies is a fatal zoonotic disease. Across the globe, rabies prevention efforts are hampered by a lack of information regarding the distribution and spread of rabies virus variants. Rapid, cost-effective variant typing using sequencing could help guide control and vaccination strategies and increase understanding of virus-host relations and viral evolution. We evaluated the MinION for rabies monitoring because of its potential for deployment in resource-limited areas and real-time data analysis. Overlapping PCR amplicons were sequenced producing high coverage across the rabies virus genome. The error rate in raw reads was dramatically reduced in error-corrected consensus sequences, which achieved high accuracy compared to more costly sequencing methods. Our evaluation suggests MinION sequencing can produce informative sequences from rabies clinical and surveillance samples. Future work will focus on increasing throughput and pipeline automation, with the ultimate goal of live sequence typing for deployment in public health labs and in the field. Disclaimer: Use of trade names and commercial sources is for identification only and does not imply endorsement by the Centers for Disease Control and Prevention, the Public Health Service, or the U.S. Department of Health and Human Services.