Using samples from the Texas HIV transmission case (CC samples), for a subset of full-length HIV genomes, the study yielded initial phylogenetic estimates from six non-overlapping genic regions that showed the monophyly of clones sampled from the same recipient individuals; variation in relationships among groups of clones from different individuals; and variation in rates of evolution across different genomic regions. These results are significant in demonstrating the integrity of the phylogenetic signal in these CC molecular clone sequences, since the extrinsic evidence, which was presented in criminal proceedings, strongly suggested that each individual included in the initial analyses acted only as a recipient within the Texas transmission cluster. Distinct relationships among clones from different individuals inferred from numerous genic regions constituted strong evidence of independent evolutionary histories. This provided greater confidence in forensic conclusions. Several technical challenges are currently being addressed. These include optimizing de novo assemblies that will produce larger numbers of successful full-length genome sequences with low SNP counts and also understanding the high estimates of human sequences in the subset of HIV molecular clone reads. Addressing these challenges will facilitate the development of a robust "pathogen toolkit" that can provide a detailed pathway for future forensics studies. 6 figures, 2 tables, and 56 references
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