A high prevalence of potential HIV elite controllers identified over 30 years in Democratic Republic of Congo

Abstract

Background: In-depth analysis of the HIV pandemic at its epicenter in the Congo basin has been hampered by 40 years of political unrest and lack of functional public health infrastructure. In recent surveillance studies (2017-18), we found that the prevalence of HIV in Kinshasa, Democratic Republic of Congo (11%) far exceeded previous estimates.

Methods: 10,457 participants were screened in Kinshasa with rapid tests from 2017-2019. Individuals confirmed as reactive by the Abbott ARCHITECT HIV Ag/Ab Combo assay (n=1968) were measured by the Abbott RealTime HIV-1 viral load assay. Follow up characterization of samples was performed with alternate manufacturer viral load assays, qPCR for additional blood borne viruses, unbiased next generation sequencing, and HIV Western blotting.

Findings: Our data suggested the existence of a significant cohort (n=429) of HIV antibody positive/viral load negative individuals. We systematically eliminated collection site bias, sample integrity, and viral genetic diversity as alternative explanations for undetectable viral loads. Mass spectroscopy unexpectedly detected the presence of 3TC antiviral medication in approximately 60% of those tested (209/354), and negative Western blot results indicated false positive serology in 12% (49/404). From the remaining Western blot positives (n=53) and indeterminates (n=31) with reactive Combo and rapid test results, we estimate 2.7-4.3% of infections in DRC to be potential elite controllers. We also analyzed samples from the DRC collected in 1987 and 2001-03, when antiretroviral drugs were not available, and found similarly elevated trends.

Interpretation: Viral suppression to undetectable viral loads without therapy occurs infrequently in HIV-1 infected patients around the world. Mining of global data suggests a unique ability to control HIV infection arose early in central Africa and occurs in <1% of founder populations. Identification of this group of elite controllers presents a unique opportunity to study potentially novel genetic mechanisms of viral suppression.

Funding: Abbott Laboratories funded surveillance in DRC and subsequent research efforts. Additional funding was received from a MIZZOU Award from the University of Missouri. Research was supported in part by the Division of Intramural Research, National Institute of Allergy and Infectious Diseases, NIH.

Keywords: Democratic Republic of Congo; Elite controller; HIV; Viral controller.

Fig. 1

High percentage of viral load ‘TND’ in DRC. a) Map of collection sites in Kinshasa, DRC. b) Surveillance testing algorithm. FP = false positive, IDR = gp41 immunodominant region, outside test = alternate VL manufacturer. c) Plot of HIV Combo S/CO vs HIV-1 viral load. Legend indicates color for year sample was received. Samples on the y-axis with viral load results of ‘target not detected’ (TND) are circled. d) Histogram relating the number of tentative TNDs among HIV viral load positives for each cohort.

Fig. 2

TND are confirmed sero-positives collected from numerous sites and observed over decades. a) Number of TND (orange) and VL+ (blue) collected at each site from 2017-2019. b) Western blot results according to year (top) and corresponding HIV Combo S/CO values (bottom).

Fig. 3

Sample integrity and sequence diversity do not explain absence of HIV RNA detection. a) Bioanalyzer profiles of mNGS libraries. PBS5635 (lane 2) and PBS829 (lane 15) samples (red) were heat-treated. The table beneath lists each sample's viral load (log copies/ml), Multiplex qPCR Ct, HIV Combo S/CO, Western blot, and total number of NGS reads (in millions). The histogram plots the # HIV reads/million (green) and the % HIV genome coverage (brown) on both linear and log scales (PC = positive control, an HIV+ sample of 4.0 log₁₀ cp/ml; (-) = negative PCR; IND = indeterminate Western Blot; (+) = positive Western Blot; n.d.= not done). b) TNDs were reassessed by a multiplex qPCR that detects HIV-1/-2, HBV, and HCV. Ct values for each positive sample are plotted by virus. c) S/CO values of antigen assays for HBV and HCV qPCR positives shown in 3b.

Fig. 4

A sizeable population of potential elite controllers reside in the Democratic Republic of Congo. a) Breakdown by cohort of TND that were positive (grey) and negative (orange) for 3TC by mass spec. b) Breakdown by collection site of TND that were positive (grey) and negative (orange) for 3TC by mass spec. c). Percentage range by year of potential elite controllers in DRC are represented by the slices extending from the pie, which include VL-|ART-|WB IND|RAPID POS and VL-|ART-|WB POS samples. Total number of HIV Combo+ samples evaluated are listed beneath each year.