Development of a Protocol Using Ultra-Deep Pyrosequencing and Phylogenetic Analysis for Source Identification in Two HIV-1 Transmission Lawsuits

As evidence for forensic purposes, conducting phylogenetic analysis has limitations including delayed examinations after the initiation of infection and ambiguity of phyletic relationships. In order to overcome these obstacles, we developed a novel phylogenetic analysis protocol based on ultra-deep pyrosequencing to determine the source. Three criminal cases from different district courts in Taiwan used this protocol. In two of the cases, extremely rare gag and env quasispecies sequences from the plaintiff and defendant were present as clusters with a paraphyletic relationship using the Bayesian tree method.