Archiving of mutations in HIV‐1 cellular reservoirs among vertically infected adolescents is contingent with clinical stages and plasma viral load: Evidence from the EDCTP‐READY study

Abstract

Introduction Globally, HIV‐related adolescent deaths have increased about 50%, especially for those who are vertically infected. This could be driven by archived drug resistance mutations (DRMs) as children grow up, which might jeopardize antiretroviral therapy (ART). Our objective was to compare HIV‐1 genotypic variation between plasma RNA and proviral DNA of vertically infected adolescents (aged 10–19 years) failing ART. Methods A comparative study was conducted in 2019 among 296 adolescents with perinatal HIV infection (ALPHI) failing ART in health facilities of the Centre Region of Cameroon. The WHO clinical stage, CD4 count and plasma viral load (PVL) were measured. For those failing ART (PVL ≥ 1000 copies/mL), RNA (plasma) and proviral DNA (buffy coat) were sequenced in the pol gene at Chantal BIYA International Reference Centre (CIRCB), Yaoundé, Cameroon. HIV‐1 subtypes and DRMs were interpreted using Stanford HIVdb v.8.8 and MEGA‐X. Results Of the 30% (89/296) failing ART, 81 had both RNA and DNA sequences generated and three were excluded for APOBEC mutations: the mean age was 16 ± 3 years; female‐to‐male ratio was 3:5; median PVL was 46 856 copies/mL [interquartile range (IQR): 19 898–271 410]; median CD4 count was 264 cells/μL (IQR: 131–574); and 42% were at WHO clinical stage 3/4. Subtype concordance between RNA and DNA viral strains was 100%, with CRF02_AG being predominant (65%) and two potential new recombinants found (A1/G/K; F1/G). Adolescents with DRMs were significantly higher in plasma than in proviral DNA (92% vs. 86%, p < 0.0001). Prevalent DRMs by drug class (RNA vs. DNA respectively) were at position M184 (74% vs. 67%) for nucleoside reverse transcriptase inhibitors (NRTIs), K103 (63% vs. 59%) for non‐NRTIs, and V82, L76 and M46 (2% vs. 2%) for protease inhibitors. A total of 35% (27/78) of adolescents had concordant DRM profiles in RNA and DNA, while 27% (21/78) had DRMs only in proviral DNA. The presence of archived DRMs was associated with advanced clinical stage 3/4 (OR = 0.14, p = 0.0003) and PVL < 5 Log (Copies/mL) (OR: 4.88, p = 0.006). Conclusions Although plasma RNA remains more sensitive for detecting HIV‐1 DRMs, about a quarter of ALPHI experiencing ART failure in an African setting might have archived DRMs in viral reservoirs, indicating clinically occult resistance. Thus, to ensure effective ART success, proviral DNA profiling (alongside RNA genotyping) would provide additional DRMs for adolescents with advanced clinical stages and/or moderate PVL.

Evaluation of archived drug resistance mutations in HIV‐1 DNA among vertically infected adolescents under antiretroviral treatment in Cameroon: Findings during the COVID‐19 pandemic

“…Despite this important rate of virological control, ADRMs were found in 63% of these ALHIV. This burden was below the prevalence (85%) found by Fokam et al in 2019 in HIV-1 DNA of ALHIV experiencing virological failure [17]. However, the burden observed in this current study remains high and could be explained by either undocumented previous therapeutic failure or vertical transmission of resistant viruses [36].…”

“…Concerning amplification, briefly, DNA extracts were directly amplified by two separate PCRs according to a homemade protocol as previously described [17]. The first PCR was done using the primers BS «5 0 -GACAGGC-TAATTTTTTAGGG-3 0 », located at the 2075-2094 (gag) region, and FRAS1 «5 0 -TTTCCCCATATTACTATGCTT-3 0 », located at the 3683-3703 (pol) region.…”

“…The median (IQR) age of the study population was 17 [16][17][18][19] years; 31/60 (51.6%) individuals were female Regarding virological profile at enrolment, 70.0% (42/60) were non-viraemic (VL < 1.60 log 10 copies/mL) and 30.0% (18/60) were viraemic (VL ≥ 1.60 log 10 copies/mL) with a median VL of 2.89 (2.04-3.97) log 10 copies/mL among viraemic ALHIV. More than half of adolescents (15/24, 62.5%) taking PI-based regimens were non-viraemic; 66.7% (8/12) of adolescents on NNRTI-based regimens and 73.7% (14/19) adolescents on dolutegravir-based regimen were also non-viraemic.…”

“…Notably, reservoirs are potential reactivation cells that contain persistent forms of HIV‐1 under effective treatment which may be involved in the pathogenesis of HIV [16]. In Cameroon, as in order countries, although the rate of resistance is higher in plasma than in reservoirs cells, one‐quarter of HIV‐1‐infected adolescents with virological failure have occult resistance [17]. When viral RNA is suppressed, drug resistance mutations (DRMs) may be detected in HIV‐1 DNA obtained from whole blood, peripheral blood mononuclear cells (PBMCs) or buffy coat samples during the virological follow‐up of this susceptible population [18].…”

Evaluation of Circulating and Archived HIV-1 Integrase Drug-Resistance Variants among Patients on Third-Line ART in Cameroon: Implications for Dolutegravir-Containing Regimens in Resource-Limited Settings

“…Finally, the most represented viral clade in this study was the recombinant form CRF02_AG, similar to several reports in Cameroon ( 64 – 69 ). Of note, the broad HIV diversity found in this small sample population could justify the considerable number of polymorphisms observed in viral reservoirs ( 25 , 66 ). Long-term monitoring might help in depicting the potential effects of covariation of these mutants on treatment outcomes under DTG-containing regimens.…”