Phylogenetics And Networks for Generalised HIV Epidemics in Africa


University of North Carolina

The University of North Carolina at Chapel Hill (UNC) is a partner with PANGEA. Through the Institute for Global Health & Infectious Diseases (IGHID), directed by Dr. Myron Cohen, and the UNC Center for AIDS Research, UNC has a long history of internationally recognized HIV research.  With approximately $60 million in research revenue, more than 75 affiliated faculty members, and strong sustainable programs, the IGHID is a leader in global health research.  

As consortium partners, UNC investigators will provide scientific expertise and guidance to PANGEA. In the laboratory of Dr. Ron Swanstrom, UNC investigators will explore the utility of including Primer ID in the whole genome sequencing of HIV-1 genomes.  The goal of the sequencing group is two-fold.  First, create sequence data sets that allow the identification of transmission networks through phylogenetic linkage using next generation sequencing platforms.  Second, in creating these data sets have them be of sufficient quality that they will be useful to the broader research community.  In the context of the second goal we propose to test a subset of samples that have whole genome sequencing done at the Sanger Center and repeat the sequencing using Primer ID, random sequence tags in the cDNA primer that tag each amplicon. PCR resampling allows multiple reads of each template sequence allowing errors to be corrected through the creation of a consensus sequence, and the depth of sampling is defined by the number of Primer ID consensus sequences created.  This approach should add important information about the deep sequencing data that will significantly improve its utility to the larger research community.

University of North Carolina

UNC team: Mike Cohen (not pictured), Ron Swanstrom, Ann Dennis, and Shuntai Zhou.