Development of a high throughput sequencing and analysis pipeline for West Nile virus

Emmi Mueller1, Rebecca A. Halpin1, Nadia Fedorova1, Timothy B. Stockwell2, Danny Katzel2, Laura Kramer3, Suman R. Das1

1Virology Group and 2Informatics Department, J. Craig Venter Institute, Rockville, MD; and 3 Wadsworth Center, New York State Department of Health, Slingerlands, NY

West Nile virus (WNV) is a member of the Flaviviridae family of enveloped, single-stranded RNA viruses with a linear, non-segmented, positive-sense ~11,000bp genome.  WNV is an enzootic virus of birds and mosquitos, with humans and other mammals serving as spillover hosts, typically via mosquito bites. In humans, WNV is usually asymptomatic, but ~20% of infected people develop a mild flu-like fever (West Nile fever) and ~1% can develop severe symptoms such as encephalitis or meningitis, which can be fatal.  WNV was first isolated from a woman in Uganda in 1937 and first reported in North America in New York City in 1999.  Since then, WNV has caused over 39,000 reported human disease cases in the USA contributing to over 1600 deaths. WNV continues to remain a formidable clinical and public health concern in the USA and worldwide. So far, no human vaccine or specific antiviral treatments for WNV infection are currently available.  As part of the Genomic Center for Infectious Diseases (GCID), the J. Craig Venter Institute is developing a high throughput Next Generation sequencing and analysis pipeline to process ~650 complete WNV genomes from mosquitos, birds, and horses. The development of this pipeline will allow rapid and efficient sequencing and analysis of WNV genomes in order to compare and contrast the genetic diversity and evolutionary dynamics of WNV circulating within animal hosts. Further, the sequencing data will allow us to assess temporal and spatial variation of WNV, as well as to identify selective pressures and genetic correlates of WNV disease transmission.

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