Skip to main content
University of Wisconsin–Madison
Wisconsin National Primate Research Center
A legacy of life-saving research and humane animal care

Genetics Services – Viral Pathogen Sequencing

A WNPRC Genetic Services technician checks the progress of a viral pathogen deep-sequencing run on an instrument monitor.

WNPRC Genetic Services staff member Ryan Moriarty checks the progress of a viral pathogen deep-sequencing run.

COVID-19 pandemic update:

As of 1 June 2020, UW-Madison is beginning a phased reopening of research operations, but limitations on occupancy of campus buildings remain in place. These will continue to impact our ability to provide research support. The situation remains fluid, so we request your patience as we all navigate the process. Please contact us for updates if you wish to initiate a new project or restart one that has been paused due to COVID-19. 

We specialize in RNA viral genome sequencing with an emphasis on simian immunodeficiency viruses (e.g., SIVmac239, SIVmac251, and SIVsmE660) and emerging pathogens (e.g., Zika virus). We use Illumina MiSeq technology to sequence the entire coding sequence of RNA viruses, shorter amplicons, and plasmids.

Sequencing data can be produced from various starting materials, including plasma, cell culture, RNA, and DNA. In our method, each genome is molecularly barcoded, and 20-30 viral genomes are pooled together for each MiSeq run. After images are processed and nucleotides are called on the MiSeq instrument, we bin the sequence reads by barcode tag. We routinely provide fastq files for each read. If a reference genome is available, we can also generate BAM or SAM alignments. Additional data analyses may be performed after consultation with Pathogen sequencing lead, Dr. Shelby O’Connor.

Viral pathogen stocks used to infect animals will be deep sequenced  free of charge*  provided investigators agree to make this important information publicly available via the SRA database.

Please see our pathogen sequencing white paper (pdf) for additional details.

To learn more, contact Pathogen sequencing lead, Shelby O’Connor, PhD.

Pricing examples:

Service Cost/Sample**
SIV Sequencing from Plasma $339

**All pricing examples cover the cost of reagents, labor & BAM alignment. Prices shown are cost recovery rates for UW-Madison investigators. Other investigators are charged overhead rates ranging from 17% (federal or not-for-profit) to 72% (for-profit entities).

Return to WNPRC Research Services