In Reply Dr Goldman and colleagues highlight aspects of the phylogenetic analyses used to investigate HIV transmission events in the PARTNER study.1 Previous studies have taken advantage of the now-discontinued Roche 454 deep-sequencing platform to obtain sequence reads of sufficient length to allow reliable phylogenetic analyses of minority viral species. We have been conducting work to optimize the Illumina deep-sequencing platform to perform an analysis of minority species in couples in our study. The reconstruction of HIV haplotypes presents notorious technical and interpretative challenges when applied to the short sequence reads currently obtained by Illumina. We are also using conventional limiting dilution techniques to obtain single and near full-length genomes using established methods.2 These further analyses will be submitted for publication once completed.
Geretti AM, Rodger AJ, Lundgren J. HIV Transmission During Condomless Sex With a Seropositive Partner With Suppressed Infection—Reply. JAMA. 2016;316(19):2045. doi:10.1001/jama.2016.16033