Skip to main content

A pipeline for viral population analysis using the Primer ID method

Wednesday, September 24, 2014 — Poster Session IV

10:00 a.m. –12:00 p.m.

FAES Academic Center




  • A.J. Oler
  • W.L. Ince
  • J.R. Bennink
  • J.W. Yewdell
  • D.E. Hurt


​RNA viruses, such as influenza, have the ability to rapidly evolve in response to host immune pressure because of their high mutation rates. High-throughput sequencing allows researchers to deeply sample viral populations in order to determine low-frequency variants in the population and their relative fitness over time. The ability to determine genotypes exhibiting increased fitness as they emerge in an infection could help biologists understand the genetic landscape of a virus and develop better vaccines; however, researchers' ability to confidently detect low-frequency variants in a viral population is limited by the error rate of the sample preparation procedure and the sequencing platform. The Primer ID sequencing method allows for removal of errors introduced by polymerase chain reaction (PCR) or sequencing in order to detect low-frequency variants with greater confidence. Currently no tools exist for integrated analysis of Primer ID data. In response, a pipeline was developed for Primer ID analysis of amplicons directed to the influenza hemagglutinin (HA) segment. The pipeline is able to determine variants present within the virus sample (at the level of nucleotide, codon, and amino acid), incorporate biological replicates, determine significant differential abundance of variants between samples, and determine linkage disequilibrium between variants.

back to top