Name of Student:
Chanson Brumme
Research Supervisor: Dr. Richard Harrigan
Title of Presentation: Molecular and functional consequences of immune-mediated evolution in
HIV-1 Nef during the North American epidemic
Abstract
Background: HLA-restricted CTL responses drive evolution of the highly immunogenic Nef
protein, but the extent and functional consequences of population-level adaptation remain
unclear. We have used novel historic Nef data to estimate the date and reconstruct the founder
virus sequence of the North American epidemic, compare patterns of population-level HLAassociated polymorphisms over time, and assess CD4 downregulation activity of historic and
modern Nef sequences.
Methods: Plasma HIV-1 RNA Nef sequencing and HLA typing was performed on 241
historic specimens (1979-89). Modern published HLA/HIV datasets served as controls.
Timing and sequence reconstruction of the founder Nef was performed using BEAST and
HyPhy. HLA-associated polymorphisms were identified using phylogenetically-corrected
methods. CD4 downregulation capacity of 52 historic vs. 52 modern Nef sequences was
compared using flow cytometric methods.
Results: Based on Nef sequences, the most recent common ancestor of the North American
epidemic was dated to 1965. The consensus of the reconstructed founder Nef sequence
differed from 2004 subtype B consensus at codons 15, 22, 51 and 178, while additional sites
remained ambiguous in the reconstruction. Patterns and statistical strengths of HLAassociated polymorphisms remained generally consistent over time (e.g. A*24-associated
Y135F, B*07-R71K, B*08-K94Q and B*57-H116N ranked among the strongest in historic
and modern cohorts); however, a small number of polymorphisms were identified as
candidates for population-level accumulation. Functional assessment of Nef revealed a modest
yet statistically significant increase in CD4 downregulation capacity over time (median 0.93
vs. 1.00 in historic vs. modern sequences; p=0.005).
Conclusions: Modest population-level immune adaptation in Nef, potentially leading to
modest increases in CD4 downregulation capacity, may have occurred in North America since
1979. However, the relatively high similarity between the estimated founder and modern
consensus B, and the observation that CTL escape patterns have remained largely consistent
over time, support Nef as a suitable target for vaccine consideration.