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 HLA-associated
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 HLA-associated 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).
Conclusion: 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.
Background US Food and Drug Administration-approved enzyme-linked immunoassays (EIA) for determining type-specific herpes simplex virus (HSV) serostatus are widely used in clinical practice. We compared the performance of such assays with the University of Washington Western blot (UW WB) in patients who sought confirmation of their HSV serology result. Methods We reviewed charts of all persons evaluated at the Westover Heights Clinic in Portland, Oregon, from July 2010 through September 2015, who had a HSV EIA, followed by UW WB. Results Of 864 persons, 47% were women. The median age was 36 years (range, 18–73 years). Using UW WB to define infection status, 286 (33%) persons were HSV-1 seropositive only, 104 (12%) were HSV-2 seropositive only, 134 (16%) were both HSV-1 and HSV-2 seropositive, 235 (27%) were HSV seronegative, and 105 (12%) had indeterminate results. Compared with the UW WB as the criterion standard, EIA was 70.2% sensitive and 91.6% specific for HSV-1, and 91.9% sensitive and 57.4% specific for HSV-2. Among 278 persons who were HSV-1 seropositive by EIA, 255 were confirmed by the UW WB (positive predictive value [PPV], 91.7%). Of the 360 persons that were HSV-1 seronegative by the EIA, 252 were seronegative by UW WB (negative predictive value [NPV], 70.0%). Among 381 persons with HSV-2 EIA seropositivity, 193 tested HSV-2 seropositive by the UW WB (PPV, 50.7%). Of the 270 persons HSV-2 seronegative by EIA, 17 were seropositive with the UW WB (NPV, 93.7%). Among 261 persons with an EIA HSV-2 index value = 1.1–2.9, 39.8% of results were confirmed by UW WB, compared with 78.6% of the 70 persons with an EIA index value of 3 or greater ( P < 0.001). The risk of false-positive HSV-2 EIA results was higher in those with HSV-1 antibody (47.1% vs 37.1%, P = 0.036). Conclusions US Food and Drug Administration-approved EIAs have poor PPV for HSV-2 and poor NPV for HSV-1 in clinical practice. More accurate rapid type-specific HSV antibody tests are needed.
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