Comparison of Methods to Detect HIV Dual Infection

Current methods to detect intraclade HIV dual infection are poorly suited for determining its prevalence in large cohorts. To investigate the potential of ultra-deep sequencing to screen for dual infection, we compared it to bulk-sequence based synonymous mixture index and the current standard of single genome sequencing. The synonymous mixture index identified samples likely to harbor dual infection, while ultra-deep sequencing identified additional cases of dual infection not identified by single genome sequencing in our study set. At approximately 40% of the cost and 20% of laboratory and analysis time, ultra-deep sequencing captured more intra-host viral diversity than single genome sequencing. The synonymous mixture index and ultra-deep sequencing are promising methods for rapid and cost-effective systematic identification of HIV dual infection.