HIV drug resistance (HIVDR) in antiretroviral therapy-naïve patients in Tanzania not eligible for WHO threshold HIVDR survey is dramatically high

Abstract

Background: The World Health Organization (WHO) has recommended guidelines for a HIV drug resistance (HIVDR) survey for resource-limited countries. Eligibility criteria for patients include age below 25 years in order to focus on the prevalence of transmitted HIVDR (tHIVDR) in newly-infected individuals. Most of the participating sites across Africa have so far reported tHIVDR prevalences of below 5%. In this study we investigated whether the rate of HIVDR in patients <25 years is representative for HIVDR in the rest of the therapy-naïve population.

Methods and findings: HIVDR was determined in 88 sequentially enrolled ART-naïve patients from Mwanza, Tanzania (mean age 35.4 years). Twenty patients were aged <25 years and 68 patients were aged 25-63 years. The frequency of HIVDR in the study population was 14.8% (95%; CI 0.072-0.223) and independent of NVP-resistance induced by prevention of mother-to-child transmission programs. Patients >25 years had a significantly higher HIVDR frequency than younger patients (19.1%; 95% CI 0.095-0.28) versus 0%, P = 0.0344). In 2 out of the 16 patients with HIVDR we found traces of antiretrovirals (ARVs) in plasma.

Conclusions: ART-naïve patients aged over 25 years exhibited significantly higher HIVDR than younger patients. Detection of traces of ARVs in individuals with HIVDR suggests that besides transmission, undisclosed misuse of ARVs may constitute a significant factor in the generation of the observed high HIVDR rate. The current WHO tHIVDR survey that is solely focused on the transmission of HIVDR and that excludes patients over 25 years of age may therefore result in substantial underestimation of the prevalence of HIVDR in the therapy-naïve population. Similar studies should be performed also in other areas to test whether the so far reported optimistic picture of low HIVDR prevalence in young individuals is really representative for the rest of the ART-naïve HIV-infected population.

Figure 1. The frequency of HIVDR is age-dependent.

HIVDR was determined by bulk sequencing from ART-naïve patients. A.: Frequency of WHO-defined HIVDR in patients aged under 25 years (n = 20, left bar), patients aged over 25 years (n = 68, middle bar), and in the total study population (n = 88, right white bar). B: Frequency of WHO-defined HIVDR peaks in different age groups. Numbers in brackets indicate the number of individuals tested in each age group. Data as means ± S.E.M.. For statistical analysis, Fisher's exact test was performed. Differences with a P<0.05 were regarded as statistically significant. C: Number of WHO-defined RAM per individual (“RAM burden”). D: Number of affected antiretroviral drug classes (NRTI, NNRTI, PI) per individual in relation to the number of WHO-defined RAM per individual.

Figure 2. HIVDR affects efficacy of local first- and second-line ART regimens.

Effects of HIVDR (high- and low-level resistances) on drugs included in the local antiretroviral regimens. A: Effects on local first-line ART regimen. HIVDR that affects at least one of the drugs included in first-line therapy (AZT/D4T plus 3TC plus NVP/EFV) scored positive. B: Effects on local second-line ART regimen. HIVDR that affects at least one of the drugs included in second-line therapy (ddI/ABC plus LPV/SQV plus RTV) scored positive. C: Proportion of patients with HIVDR that affects first-line ART regimen who also carry HIVDR that affects second-line ART regimen.

Figure 3. Phylogenetic analysis of RT and PR sequences from the Tanzanian cohort.

A neighbour-joining phylogenetic tree was constructed from the 88 patient derived HIV-1 sequences from the Tanzania cohort and the two partner-derived sequences. Reference sequences were obtained from the Los Alamos HIV sequence database. The analyzed 1302 bp region includes the complete Protease and Reverse Transcriptase coding region. The tree was constructed using Mega software version 4, and the evolutionary distances were calculated using the Kimura 2-parameter method. The bootstrap consensus tree was inferred from 50000 replicates and values greater than 70% are indicated on the branch lengths. The scale at the bottom left indicates the calculated genetic distances between the branches of the phylogenetic tree. Circles represent the 88 samples from our cohort. Black-dotted circles are without RAM, open-circled sequences are with RAM, open triangles are sequences with RAM from HIV-infected partners of two study subjects, which were not included in the determination of HIVDR as these patients received ART. Sequences without symbols are subtype reference sequences derived from Los Alamos database. The subtype is indicated at the end of each sequence name. Relative subtype frequency: A1: 34%, A1D: 7%, C: 26%, CRF10_CD: 4%, D: 28%, B: 1%. Sequences isolated from two couples (couple I, couple II) with NVP resistances.