Investigation of the HIV diversity in the Cape Winelands, Overberg and West Coast districts of the Western Cape Province of South Africa

[摘要] ENGLISH SUMMARY: The Western Cape Province of South Africa has a well-established program that monitorsactive combination antiretroviral therapy (cART) against HIV-1. The HIV-1 prevalence ratein the Province has increased from 5.0% in 2011 to 18.0% in 2015. South Africa has thehighest rate of infections worldwide (19.2%). In this study, we analyzed the Protease (PR),Reverse Transcriptase (RT) and Intergrase (IN) regions of HIV-1 for diversity and resistanceassociatedmutations (RAMs) from samples obtained from the Cape Winelands, West Coastand Overberg districts of the Province, where no such study has ever been conducted.Samples were received from our diagnostic laboratory for HIV-1 viral load testing, throughthe National Health Laboratory Services (NHLS). Two hundred and five (205) patientsamples with a viral load of 2000 copies/ml and above were included, based on Gall et al.,(2012) who showed that a sensitivity of at least 2000 copies/ml is a limit of amplification forthe SuperScsript ® III one-step RT with Platinum Taq DNA Polymerase kit, used in thisstudy. We screened for HIV-1 diversity and RAMs using the pol PR, RT and IN regions witha laboratory-based PCR and sequencing protocol. Sequence-specific subtype analyses wereexecuted with the REGA HIV subtyping tool 3.0, Recombinant Identification Program (RIP)3.0 and subtype classification using evolutionary algorithms (SCUEAL) software. Sequenceswere screened for RAMs using the Stanford University HIV Drug Resistance Database(HIVdb) 8.1. We successfully PCR amplified 170 (82.9%) PR and 166 (80.9%) RTfragments. For the IN region, only 176 samples had sufficient plasma and RNA left aftergenotyping of the PR and RT regions. For IN we successfully amplified 143 (81.3%) of thepatient samples. A total of 197 (96.1%) samples could be amplified for at least one of the polregions. Of these, 62 (53.4%) PR, 103 (62.0%) RT and 93 (86.1%) IN sequences wereobtained, respectively. We could successfully sequence 173 (84.4%) of the samples included.HIV-1 subtype C was predominant (n = 144; 93.7%), with 5.3% of other subtypes detected.This includes A1 (n = 2; 1.3%), B (n = 4; 2.6%), D (n = 1; 0.7%) and H (n =1; 0.7%). Nomajor RAMs were detected against PI and IN inhibitors. Minor RAMs were detected in 4 PR(3.7%) and 15 IN (16.1%) sequences analysed. RAMs against RT inhibitors were detected in63 (61.7%) of the sequences analyzed. This includes 39 NRTI mutations (36.1%) and 71NNRTI mutations (63.5%) identified. As the national cART program continues to expand,HIV-1 diversity, viral load monitoring and drug resistance screening remains critical for thesuccess of cART outcomes and reducing transmission rates. Our results reflect that subtype Cis still the driving force of the epidemic in South Africa. However, we cannot ignore thepotential impact of non-C subtypes. Sequence analyses confirm that the majority of patients receiving viral load testing have major RAMs against RT inhibitors used in first line therapy.Better surveillance systems for HIV diversity and drug resistance testing are required toensure success of cART.

[发布机构] Stellenbosch University