A comparative analysis of HIV drug resistance interpretation based on short reverse transcriptase sequences versus full sequences

Abstract

Background: As second-line antiretroviral treatment (ART) becomes more accessible in resource-limited settings (RLS), the need for more affordable monitoring tools such as point-of-care viral load assays and simplified genotypic HIV drug resistance (HIVDR) tests increases substantially. The prohibitive expenses of genotypic HIVDR assays could partly be addressed by focusing on a smaller region of the HIV reverse transcriptase gene (RT) that encompasses the majority of HIVDR mutations for people on ART in RLS. In this study, an in silico analysis of 125,329 RT sequences was performed to investigate the effect of submitting short RT sequences (codon 41 to 238) to the commonly used virco®TYPE and Stanford genotype interpretation tools.

Results: Pair-wise comparisons between full-length and short RT sequences were performed. Additionally, a non-inferiority approach with a concordance limit of 95% and two-sided 95% confidence intervals was used to demonstrate concordance between HIVDR calls based on full-length and short RT sequences.The results of this analysis showed that HIVDR interpretations based on full-length versus short RT sequences, using the Stanford algorithms, had concordance significantly above 95%. When using the virco®TYPE algorithm, similar concordance was demonstrated (>95%), but some differences were observed for d4T, AZT and TDF, where predictions were affected in more than 5% of the sequences. Most differences in interpretation, however, were due to shifts from fully susceptible to reduced susceptibility (d4T) or from reduced response to minimal response (AZT, TDF) or vice versa, as compared to the predicted full RT sequence. The virco®TYPE prediction uses many more mutations outside the RT 41-238 amino acid domain, which significantly contribute to the HIVDR prediction for these 3 antiretroviral agents.

Conclusions: This study illustrates the acceptability of using a shortened RT sequences (codon 41-238) to obtain reliable genotype interpretations by virco®TYPE and Stanford algorithms. Implementation of this simplified protocol could significantly reduce the cost of both resistance testing and ARV treatment monitoring in RLS.

Figure 1

Representation of the definition of minor and major changes in predicted HIVDR calls between full RT and short RT sequences . * MA: maximal response; RE: reduced response; MI: minimal response; CCO1: lower clinical cut-off; CCO2: upper clinical cut-off; S: susceptible; R: resistant; BCO: biological cut-off ** S: susceptible; pLR: potential low-level resistant; LR: low-level resistant; I: intermediate resistant; R: high-level resistant

Figure 2

Dataset, based on subtype and drug-specific full-length RT HIVDR profile by virco^®TYPE. The subtypes are arranged by decreasing prevalence of in the Virco database. MA: maximal response, S: susceptible

Figure 3

virco^®TYPE call changes between full length and short RT HIVDR interpretations for sequences with a 'susceptible' profile, based on full RT interpretation (group 1). A. Minor call changes. Minor changes are not possible for drugs with a BCO only as a shift can only occur from susceptible to resistant (or vice versa), which is a major call change; therefore EFV and NVP are not depicted in this graph. B. Major call changes MA: maximal response, S: susceptible

Figure 4

virco^®TYPE call changes between full length and short RT HIVDR interpretations for sequences with a 'resistant' profile based on full RT interpretation (group 2). A. Minor call changes. Minor changes are not possible for drugs with a BCO only as a shift can only occur from susceptible to resistant (or vice versa), which is a major call change; therefore EFV and NVP are not depicted in this graph. B. Major call changes RE: reduced response, MI: minimal response, R: resistant