HIV-1 Genetic Diversity, Tropism and Drug Resistance Mutations among HIV Infected Patients Attending Comprehensive Care Clinic in Kisii Teaching and Referral Hospital, Kenya

Abstract

Since the initiation of Kenya’s nationwide free antiretroviral therapy (ART) in 2003 and 3 by 5 initiatives the availability of highly active antiretroviral therapy (HAART) has increased dramatically. This initiative has since increased the survival levels of the infected individuals. However, this benefit is often limited by development of drug resistance, leading to treatment failure. Effectiveness of this program requires constant surveillance monitoring and evaluation not only on treatment efficacy but also on circulating viral strains. This exercise is more often poorly implemented or non-existent in most of developing countries. This study aimed at determining HIV-1 genetic diversity, viral tropism, acquired and transmitted drug resistance among treatment naive and experienced HIV infected patients attending Kisii Level Five Hospital, Kenya. Cross sectional and prospective cohort study designs were used. Consecutive sampling was used to select participants. A total of 226 participants consisting of both drug naïve (113) and experienced (113) were consented to participate in this study. Venous blood samples were drawn, CD4 and viral load was estimated using Facs calibur flow cytometry and NucliSens EasyQ HIV monitor respectively. Genotyping of HIV was determined at baseline and at 12th month of follow up. Viral cDNA was extracted using QIAamp ® DSP Virus Spin Kit (Qiagen) and specific HIV-1 genes env C2V3, Integrase and HIV-pol RT were amplified in nested PCR using specific primers and directly sequenced. The generated sequences were phylogenetically analysed. HIV-1 Drug resistance was determined using Stanford HIV drug resistance database and confirmed by International AIDS Society (IAS) algorithm. Viral tropism was predicted using in-silico Geno2pheno [coreceptor] with a false positive rate of 15%. A total of 448 sequences were generated (both drug naïve and experienced); HIV-1 env-C2V3 (164), pol-RT (99) and pol-integrase (129). Phylogenetic analysis revealed that majority of the study subjects were infected with HIV-1 A1 (71%), followed by HIV-1 C (14.3%),HIV-1 D (12.5%),HIV-1 G (1.6%),HIV-1 A2 (0.4%) pure subtypes and (0.2%) each for A2U and 02A1 CRFs. Most drug resistance mutations were NNRTIs (4, 6.8%) followed by NRTI (1, 1.5%). Drug associated mutation K238T 4.5% (n=3) was the most predominant followed by V106A, M184V, G190A and V118I (1.4%). From pooled 284 Kenyan HIV integrase sequences that were analysed for drug resistance, no major mutations conferring resistance to integrase inhibitors were detected. Prevalence of 69% acquired drug resistance was detected. Thirty patients had NRTI resistance mutations with NAMs; K65R, TAMs (23%) and M184V (NRTI). In addition, 46 patients had NNRTIs resistance with V106A as the most common mutation followed by 227L, K103N, Y181C, T238N, V190I, V108I, 230L and 179D.From 164 HIV-1 env gene sequences analysed, 75.6% were CCR5 tropic, 23.2% were CXCR4 tropic while 1.2% were duo tropic. This study showed that viral strains in the study population harbour transmitted intermediate drug resistance with those on treatment having significantly high levels of resistance. The detection of high level of circulating R5 strains and no integrase-associated mutations suggests the likelihood of a successful implementation and use of CCR5 antagonists and INSTIs in Kenya where HIV-1 A1 is the most predominant. Furthermore, transmitted intermediate drug resistance, natural occurring polymorphisms and accumulative drug resistance will in future pose a challenge to the program. This therefore warrants monitoring treatment among drug experienced individuals to combat underlying pre-treatment drug resistance and failure.