Background: HIV-1 drug resistance testing (DRT) is vital for monitoring of individual patient treatment outcomes and for public health surveillance. Access to HIV-1 DRT is limited in resource-poor settings, including Kenya due to its costly nature. Recent inclusion of integrase strand transfer inhibitors (INSTIs) in first-line treatment for all people living with HIV-1 (PLHIV-1) underscores the need for an INSTI DRT. This study aims to validate a cost-effective in-house DRT method to detect HIV-1 Integrase resistance-associated mutations (RAMs) using HIV positive plasma derived samples Methods: Thirty-six plasma derived samples were used to assess the performance characteristics including accuracy, precision, reproducibility and amplification sensitivity of an in-house method in comparison with a reference assay. Cost estimation per test followed an incremental ingredient costing approach. Clinical application of the in-house test was evaluated on a plasma sample from a patient failing an INSTI-based regimen. Results: Comparison of the in-house and reference assay gave mean nucleotide and amino acid sequence identity of 99.49 %, CI [99.21- 99.77] and 99%, CI [98.58, 99.42] respectively. Complete concordance was observed by both assays in detection of the T97TA INSTI RAM. Precision and reproducibility assessment revealed mean nucleotide sequence identities of 100% and 99.14% respectively. The amplification sensitivity was 100% for samples with VL> 1000 copies/mL (n=8) and 50% for samples with VL<1000 copies/mL. Two major (G118R and E188K) and two accessory INSTI mutations (G149A and E157Q) were detected from the clinical sample of a patient failing an INSTI-based therapy. Cost analysis estimated the cost per test at $50.31. Conclusion: The developed HIV-Integrase assay met the validation acceptance criteria and demonstrates the ability to detect clinically relevant INSTI-resistance-associated mutations, highlighting its potential use as an alternative to commercial INSTI tests in resource-limited settings.

At the request of the authors, the article titled 'A low-cost in-house HIV integrase strand transfer inhibitor drug resistance test for resource-limited settings' ([version 1; peer review: awaiting peer review]. F1000Research 2021, 10:260, https://doi.org/10.12688/f1000research.28404.1) has been retracted from F1000Research. Since publication, it has come to the attention of the authors that the primers described in Table 1 were incorrect. As this article contains information which should not be publicly available the content of the article has been removed.  The authors apologise for this honest error, and intend to republish the article with the correct primer information. Unfortunately, Dr Graeme B. Jacobs has passed away since publication of version 1 of this article.