Affordable drug resistance genotyping of HIV-1 reverse transcriptase, protease and integrase genes, for resource limited settings

Abstract

Background As use of dolutegravir (DTG) becomes more common in resource limited settings (RLS), the demand for integrase resistance testing is increasing. Affordable methods for genotyping all relevant HIV-1 pol genes (i.e., protease (PR), reverse transcriptase (RT) and integrase (IN)) are required to guide choice of future antiretroviral therapy (ART). We designed an in-house HIV-1 drug resistance (HIVDR) genotyping method that is affordable and suitable for use in RLS. Methods We obtained remnant plasma samples from CAPRISA 103 study and amplified HIV-1 PR, RT and IN genes, using an innovative PCR assay. We validated the assay using remnant plasma samples from an external quality assessment (EQA) programme. We genotyped samples by Sanger sequencing and assessed HIVDR mutations using the Stanford HIV drug resistance database. We compared drug resistance mutations with previous genotypes and calculated method cost-estimates. Results From 96 samples processed, we obtained sequence data for 78 (81%), of which 75 (96%) had a least one HIVDR mutation, with no major-IN mutations observed. Only one sample had an E157Q INSTI-accessory mutation. When compared to previous genotypes, 18/78 (23%) had at least one discordant mutation, but only 2/78 (3%) resulted in different phenotypic predictions that could affect choice of subsequent regimen. All CAPRISA 103 study sequences were HIV-1C as confirmed by phylogenetic analysis. Of the 7 EQA samples, 4 were HIV-1C, 2 were HIV-1D, and 1 was HIV-1A. Genotypic resistance data generated using the IDR method were 100% concordant with EQA panel results. Overall genotyping cost per sample was estimated at ~ US$43–$US49, with a processing time of ~ 2 working days. Conclusions We successfully designed an in-house HIVDR method that is suitable for genotyping HIV-1 PR, RT and IN genes, at an affordable cost and shorter turnaround time. This HIVDR genotyping method accommodates changes in ART regimens and will help to guide HIV-1 treatment decisions in RLS.

Strengthening and enhancing national antiretroviral drug resistance surveillance in Zimbabwe—A country that has reached UNAIDS 95-95-95 amongst adults

“…The prevalence of HIVDR is a growing concern globally, particularly in regions with widespread access to antiretroviral therapy (ART). Africa has witnessed a significant increase in ART availability, accompanied by a rise in HIVDR cases (9)(10)(11). This is particularly concerning in newly infected individuals and those starting ART in sub-Saharan Africa, as it impacts the effectiveness of first-line treatment regimens and threatens the overall success of HIV control programs.…”

HIV drug resistance monitoring in the era of dolutegravir and injectable long-acting cabotegravir in resource-limited settings

“…HIV-1 Genotyping kit Amplification Module from Thermosteric Scientific) for sequencing the integrase region are still being optimized. Affordable in-house protocols are also being developed to include all reverse transcriptase, protease, and integrase regions for the clinical management [15]. Despite these efforts, many national laboratories in RLS including Zimbabwe are still not fully equipped to perform sequencing of the HIV pol gene, and the cost associated with Sanger sequencing remains exorbitant (200 USD--300 USD) [16] in RLS for many PWH and their families who often pay out of their pocket.…”