Next-generation sequencing analysis of barcoded SIV, SHIV, or HIV

  • Analyzes viral populations with a genetic insert used as a viral barcode to track clonotypic viral lineages. 
  • Determines the number, proportion, and unique sequence of each barcode. 

The process: 

  • The Viral Evolution Core extracts nucleic acid from tissues, plasma, or isolated cells. 
  • Polymerase chain reaction amplification of the barcoded region is performed on the extracted DNA/cDNA, and amplicons are sequenced using Illumina next generation deep sequencing.
    • Samples can be run individually or multiplexed up to 10 different samples per run and run simultaneously in one sequencing reaction. 
  • Following sequencing, we use our custom analysis pipeline to determine the number, proportion, and unique sequence of each barcode. 
    • This application is designed to work only with viral populations containing a genetic insert as a viral barcode. 
    • We have recently developed this barcoded virus system for SIV, several SHIV Env clones, and HIV. 

Includes sufficient basic consultation with a subject matter expert. 

Let's Talk

A portrait photo
Brandon Keele Principal Investigator, Retroviral Evolution Section