Background: Transmitted drug resistance (TDR) remains a significant threat to Human
immunodeficiency virus (HIV) infected patients that are not exposed to antiretroviral treatment. Although,
combined antiretroviral therapy (cART) has reduced deaths among infected individuals,
emergence of drug resistance is gradually on rise.
Objective: To determine the drug resistance mutations and subtypes of HIV-1 among pre-treatment
patients in the Eastern Cape of South Africa.
Methods: Viral RNA was extracted from blood samples of 70 pre-treatment HIV-1 patients while
partial pol gene fragment amplification was achieved with specific primers by RT-PCR followed by
nested PCR and positive amplicons were sequenced utilizing ABI Prism 316 genetic sequencer.
Drug resistance mutations (DRMs) analysis was performed by submitting the generated sequences
to Stanford HIV drug resistance database.
Results: Viral DNA was successful for 66 (94.3%) samples of which 52 edited sequences were obtained
from the protease and 44 reverse transcriptase sequences were also fully edited. Four major protease
inhibitor (PI) related mutations (I54V, V82A/L, L76V and L90M) were observed in seven patients
while several other minor and accessory PIs were also identified. A total of 11(25.0%) patients
had NRTIs related mutations while NNRTIs were observed among 14(31.8%) patients. K103N/S,
V106M and M184V were the most common mutations identified among the viral sequences. Phylogenetic
analysis of the partial pol gene indicated all sequences clustered with subtype C.
Conclusion: This study indicates that HIV-1 subtype C still predominates and responsible for driving
the epidemic in the Eastern Cape of South Africa with slow rise in the occurrence of transmitted