Use of a mutation-specific genotyping method to assess for HIV-1 drug resistance in antiretroviral-naïve HIV-1 Subtype C-infected patients in Botswana

Melvin Leteane,Kaelo Seatla,Max Essex,Iain J Macleod,Christopher F Rowley,Kesaobaka Molebatsi,Dorcas Maruapula,Rosemary Musonda,Simani Gaseitsiwe,Sikhulile Moyo

doi:10.12688/aasopenres.13107.1

Abstract

Background:HIV-1 drug resistance poses a major threat to the success of antiretroviral therapy. The high costs of available HIV drug resistance assays prohibit their routine usage in resource-limited settings. Pan-degenerate amplification and adaptation (PANDAA), a focused genotyping approach based on quantitative PCR (qPCR), promises a fast and cost-effective way to detect HIV drug resistance mutations (HIVDRMs). Given the high cost of current genotyping methods, we sought to use PANDAA for screening key HIVDRMs in antiretroviral-naïve individuals at codons 103, 106 and 184 of the HIV-1 reverse transcriptase gene. Mutations selected at these positions have been shown to be the most common driver mutations in treatment failure. Methods:A total of 103 samples from antiretroviral-naïve individuals previously genotyped by Sanger population sequencing were used to assess and verify the performance of PANDAA. PANDAA samples were run on the ABI 7500 Sequence Detection System to genotype the K103N, V106M and M184V HIVDRMs. In addition, the cost per sample and reaction times were compared.Results:Sanger population sequencing and PANDAA detected K103N mutation in three (2.9%) out of 103 participants. There was no evidence of baseline V106M and M184V mutations observed in our study. To genotype the six HIVDRMs it costs approximately 40 USD using PANDAA, while the reagents cost per test for Sanger population sequencing is approximately 100 USD per sample. PANDAA was performed quicker compared to Sanger sequencing, 2 hours for PANDAA versus 15 hours for Sanger sequencing.Conclusion:The performance of PANDAA and Sanger population sequencing demonstrated complete concordance. PANDAA could improve patient management by providing quick and relatively cheap access to drug-resistance information.

Highlights

HIV remains a major global health problem; currently, 37.9 million adults and children are estimated to be living with HIV with Sub-Saharan Africa being the most severely affected region[1]
Our findings proved the potential use of Pan-degenerate amplification and adaptation (PANDAA) assay for testing drug resistance mutations in resource-limited settings
This study demonstrates that applying this cost-effective assay to samples from treatment-naïve individuals where background HIV drug resistance may be increasing can provide valuable insight into baseline resistance and allow for decisions to be made to ensure the best prospect of successful HIV treatment

Summary

Introduction

HIV remains a major global health problem; currently, 37.9 million adults and children are estimated to be living with HIV with Sub-Saharan Africa being the most severely affected region[1]. Given the high cost of current genotyping methods, we sought to use PANDAA for screening key HIVDRMs in antiretroviral-naïve individuals at codons 103, 106 and 184 of the HIV1 reverse transcriptase gene Mutations selected at these positions have been shown to be the most common driver mutations in treatment failure. Reviewer’s comments: The statement that, "Mutations selected at these positions have been shown to be the most common driver mutations in treatment failure" is no longer true in the context of the current regimens. This is a historical statement and it should be clearly stated. We have included more literature which shows that baseline NNRTI resistance are linked to poor response to first-line dolutegravir , it is still important to look at NNRTI resistance mutations (MJ Siedner et al, 2020)

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Results

Discussion

Conclusion