Prevalence of Drug Resistance Mutations and HIV Type 1 Subtypes in an HIV Type 1-Infected Cohort in Rural Tanzania

Abstract

The development of resistance mutations in drug-targeted HIV-1 genes compromises the success of antiretroviral therapy (ART) programs. Genotyping of these mutations enables adjusted therapeutic decisions both at the individual and population level. We investigated over time the prevalence of HIV-1 primary drug resistance mutations in treatment-naive patients and described the HIV-1 subtype distribution in a cohort in rural Tanzania at the beginning of the ART rollout in 2005-2007 and later in 2009. Viral RNA was analyzed in 387 baseline plasma samples from treatment-naive patients over a period of 5 years. The reverse transcriptase (RT) and protease genes were reversely transcribed, polymerase chain reaction (PCR) amplified, and directly sequenced to identify HIV-1 subtypes and single nucleotide polymorphisms associated with drug resistance (DR-SNPs). The prevalence of major DR-SNPs in 2005-2007 in the RT gene was determined: K103N (5.0%), Y181C (2.5%), M184V (2.5%), and G190A (1.7%), and M41L, K65KR, K70KR, and L74LV (0.8%). In samples from 2009 only K103N (3.3%), M184V, and T215FY (0.8%) were detected. Initial frequencies of subtypes C, A, D, and recombinants were 43%, 32%, 18%, and 7%, respectively. Later similar frequencies were found except for the recombinants, which were found twice as often (15%), highlighting the subtype diversity and a relatively stable subtype frequency in the area. DR-SNPs were found at initiation of the cohort despite very low previous ART use in the area. Statistically, frequencies of major mutations did not change significantly over the studied 5-year interval. These mutations could reflect primary resistances and may indicate a possible risk for treatment failure.

Development of HIV drug resistance and therapeutic failure in children and adolescents in rural Tanzania

“…From the 52 available viral genomes from HIV-1-infected children and adolescents, 44.2% (23/52) were subtype C, 32.7% (17/52) subtype A, 21.2% (11/52) subtype D, and the pol gene of one child (1.9%) consisted of a subtype A protease and subtype D reverse transcriptase. This subtype distribution was consistent with the reported viral subtype circulation in treatment-naive patients in Ifakara from 2009 [23]. …”

“…HIV RNA from 400 μl plasma was extracted using the NucleoSpin Virus kit (Macherey-Nagel, Oensingen, Switzerland) according to the manufacturer's protocol. Viral RNA quantification was performed using a validated in-house protocol [23] with the Brilliant III Ultra-Fast QRT-PCR Master Mix (Agilent Technologies, La Jolla, California, USA) using the StepOne Real-Time PCR System (Applied Biosystems, Foster City, California, USA), with a detection limit of 200 viral RNA copies/ml of plasma. HIV drug resistance genotyping was performed by Sanger sequencing on a 3130 Genetic Analyser 4-capillary model (Applied Biosystems, Foster City, California, USA) using a validated in-house PCR protocol [23].…”

Is zidovudine first‐line therapy virologically comparable to tenofovir in resource‐limited settings?

“…VL samples were centrifuged and plasma frozen on place and subsequently transported on dry ice to a reference laboratory in Switzerland for analysis. Viral RNA was prepared using an automated extractor (NucliSENS ® easyMAG ® , Biomerieux, Switzerland) and quantified using a quantitative, validated protocol as published .…”

Different Effects of Nonnucleoside Reverse Transcriptase Inhibitor Resistance Mutations on Cytotoxic T Lymphocyte Recognition between HIV-1 Subtype B and Subtype A/E Infections

“…Drug treatment often increases the risk of subsequent transmission of drug resistance in new cases of an HIV infection. The Y181C mutation was also reported in treatment-naive individuals among different cohorts (see Table S1 in the supplemental material) at 2.3% (1/43), 1.1% (1/91), 0.6% (1/156), 3.0% (3/101), and 1.6% (2/129) of treatment-naive subtype C-infected individuals in Mozambique (42), in South India (43), in KwaZulu-Natal Provinces in South Africa (44), in Tanzania (45), and in China (46), respectively, and 0.43% of 1,389 treatment-naive individuals in southern Vietnam, where subtype A/E virus was the most prevalent subtype (47). The Y181C mutation or the Y181C/I mutation was detected in 0.4%, 0.3% (1/303), 0.2% (4/2,655), and 1.8% (6/336) of treatment-naive individuals in northern Poland (48), Brazil (49), Mexico (50), and Hondurans (51), respectively, where subtype B was the most prevalent.…”