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Published in final edited form as: Lancet HIV. 2025 Jun 18;12(9):e664–e668. doi: 10.1016/S2352-3018(25)00108-0

Do We Need Routine Integrase Resistance Testing Before Starting Antiretroviral Therapy?

Rami Kantor 1, Alice K Pau 2, Michael J Kozal 3, Emily P Hyle 4,5
PMCID: PMC12265005  NIHMSID: NIHMS2092809  PMID: 40541216

Summary

Oral second-generation integrase strand transfer inhibitors are now anchor drugs of ART globally due to their high resistance barriers. In high-income settings, guidelines recommend routine protease and reverse transcriptase resistance testing before ART initiation but recommend routine integrase resistance testing only for individuals at higher risk of integrase resistance. Improved characterization of transmitted integrase resistance, its detection, and its clinical impact will guide future recommendations for clinical decision-making. Balancing the need to protect this critical drug class against concerns about resource allocation and care complexity presents a substantial challenge. Shifting the responsibility to providers to decide whether and when to test for integrase resistance before ART initiation can be problematic, particularly given the uncertainty around the need to reassess related current recommendations. As our understanding of integrase resistance evolves, prioritizing this discussion is essential, and we urge providers, researchers, and policymakers to engage in addressing this critical issue.

Keywords: Integrase Strand Transfer Inhibitors, Drug Resistance, Genotypic Testing, HIV, Antiretroviral Therapy

Introduction

HIV remains a global epidemic with almost 40 million people living with HIV at the end of 2023 worldwide who will need lifetime antiretroviral therapy (ART).1 Since ART’s introduction, drug resistance has remained a challenge, threatening its effectiveness.2 However, oral second-generation integrase strand transfer inhibitors (INSTIs) (e.g., dolutegravir, bictegravir) are now the cornerstone of ART globally3 and have a high resistance barrier, prompting questions about whether resistance concerns could be diminished or even eliminated.4,5

HIV drug resistance testing before ART initiation has been guidelines-recommended since 2006, enabling providers to detect transmitted resistance and tailor ART selection.6,7 Until the late 2010s, non-nucleoside reverse transcriptase inhibitors (NNRTIs) were common anchor drugs in initial regimens globally. However, rising global NNRTI resistance had led to a significant worldwide shift to INSTIs.8,9 Current guidelines in high-income settings recommend protease and reverse transcriptase (PRRT) resistance testing for all before initiating ART, with INSTI resistance testing reserved for people at higher risk of exposure to major INSTI mutations, including people with prior exposure to INSTI-based pre- or post-exposure prophylaxis (PrEP; PEP) or a partner with INSTI resistance (appendix p1). With the global rise in INSTI use for treatment and prevention of HIV, it is uncertain whether routine INSTI resistance testing should be recommended for all individuals before initiating ART, in settings where resources are available. Providing clear guidance on this issue is challenging. Here, we examine the pros and cons of routine INSTI resistance testing at ART initiation, currently primarily relevant for high-income settings, and provide recommendations regarding data needed that could further inform clinical decision-making.

Pros for conducting INSTI resistance testing before ART initiation (Table 1)

Table 1.

Pros and cons for conducting INSTI resistance testing before ART initiation

Pros Cons
INSTI major drug resistance mutations are transmissible Many INSTI resistance mutations do not impact the effectiveness of ART with 2nd-generation INSTIs
INSTI acquired drug resistance may be increasing Transmitted INSTI resistance affecting 2nd-generation INSTIs remains rare
INSTI transmitted drug resistance may be increasing Guidance on ART regimens for INSTI resistance is limited and ART initiation of non-INSTI regimens could risk deterring people with HIV from taking ART
Selective testing for INSTI transmitted resistance may be inadequate Limited downside in monitoring for viral suppression after ART initiation with INSTI resistance testing for people who do not attain viral suppression promptly
Push for better assays, antiretrovirals and science Clinical care should be driven by patient benefits, not public health surveillance or research
Be prepared; lessons from COVID-19 Opportunity costs of testing with resources that could be used more effectively to support the care of people with HIV
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Abbreviations: ART, antiretroviral therapy; INSTI, integrase strand transfer inhibitors.

INSTI major resistance mutations are transmissible. INSTI resistance mutations can be considered ‘major’ - raising concern for compromising the INSTI antiviral activity, and ‘minor’ - requiring combination with other mutations for clinical significance. All drug resistance mutations can theoretically be transmitted, with the likelihood primarily influenced by their impact on viral fitness. However, their occurrence depends on their resistance barrier – the ease with which a mutation develops against a drug or drug class. Mutations are less likely to emerge to drugs with a high resistance barrier, making their transmission less common. Second-generation INSTIs have a high resistance barrier, with resistance upon virologic failure uncommonly observed in clinical trials.10 Therefore, it may be reasonable to question the transmissibility of significant INSTI resistance. However, since 2011 (in a 42-year-old woman from Cameroon11) and most recently (in a 14 month-old infant from Haiti12), cases have demonstrated that transmission of major INSTI resistance mutations is indeed possible.

Examination of the widely-used Stanford HIV Sequence Database reveals 433 literature references incorporating integrase sequences from 33,666 individuals not exposed to INSTIs.13 Reported cases of major 2nd-generation INSTI resistance mutations included E92Q (3 individuals), G118R (1), E138K (51), G140 SAC (11), Y143RCH (8), Q148HRK (21), N155H (2), and R263K (32). Even if combined - assuming each mutation occurred alone and did not arise de novo – the estimated occurrence of major resistance mutations likely impacting 2nd-generation INSTIs in this publicly available dataset remains low at 0.4%. However, many references predate INSTI availability, and these figures rely solely on published or contributed data, including INSTI-naïve but other ART experienced individuals, likely underestimating the true global prevalence of transmitted INSTI resistance. Nonetheless, this evidence confirms the existence of transmitted resistance potentially impacting responses to 2nd-generation INSTIs.

Acquired INSTI resistance may be increasing. With significant increase in the use of 2nd-generation INSTIs for HIV treatment and prevention globally, reports of acquired resistance are steadily accumulating.14 Such reports, along with World Health Organization (WHO) data, show 4–20% prevalence of INSTI resistance among adults and especially children and adolescents with viremia on dolutegravir-based ART, prompting intensified monitoring.9,15 This concern is further compounded by the risk of INSTI monotherapy, with unacceptably high failure rates and INSTI resistance. This may arise when INSTI-based ART is started in people with unrecognized transmitted nucleoside reverse transcriptase (NRTI) resistance. Misinterpretation and overextrapolation of data suggesting NRTI resistance can be ignored further compound the issue.16

Transmitted INSTI resistance may be increasing. The emergence and detection of transmitted resistance is a gradual process, spanning stages from clinical trial publication to drug approval, usage in real-life setting, acquired resistance, and eventually transmission, as has been observed previously.17 This progression may take even longer for drugs with a higher resistance barrier and mutations with greater impacts on viral fitness, such as 2nd-generation INSTIs. Nevertheless, transmitted INSTI resistance mutations may already be increasing or are expected to rise, and ongoing efforts will be informative to provide further guidance.8,9,18,19

Selective testing for INSTI transmitted resistance may be inadequate. INSTI resistance testing only in certain individuals before ART initiation through surveys or based on perceived risk, rather than implementing it routinely for all, is problematic. Surveys9,20 are often periodic and sample only a subset of the population, leading to demographic and geographic underrepresentation, delayed resistance detection, and reduced sensitivity to low-prevalence resistance. Moreover, such approaches fail to align with individualized patient care principles, and, notably, some institutions perform INSTI resistance testing despite the currently low reported prevalence. Guidelines recommendations that limit integrase resistance testing before ART initiation only to people deemed at high risk places an undue burden on providers, who must decide who should undergo this testing, especially given the lack of reliable data to accurately identify high risk individuals. With the widespread use of INSTIs for both treatment and prevention, virtually anyone could be at risk.

Assays, antiretrovirals and science will be advanced. Conducting drug resistance testing for all individuals before ART initiation will inevitably increase testing volume. This demand could drive development of more affordable and streamlined assays - a process already advocated by the WHO.21 Integrating integrase genotyping with PRRT genotyping adds minimal cost, but currently, the tests often have to be ordered separately, complicating consistent INSTI resistance testing at ART initiation for all. Beyond testing, if increased transmitted INSTI resistance is detected through routine testing, it will further support development of improved medications and new formulations to address resistance and support individualized care effectively. Additionally, the data may stimulate research by identifying new mutations or profiles that suggest alternative resistance mechanisms, thereby enhancing our understanding of drug resistance and strategies to combat it.22

We should take lessons from COVID-19 and be prepared. While HIV has taught us how to address pandemics like COVID-19, we must also embrace lessons from COVID-19 itself. The rapid detection of the SARS-CoV-2 Omicron variant in Southern Africa was possible because the region was prepared – swiftly responding to unusual case surges and sequencing viruses for variant identification.23 Without this readiness, detection would have been delayed, potentially worsening global consequences. Similarly, we must proactively prepare for a potential rise in transmitted INSTI resistance to avoid reactive responses. Waiting for resistance levels to become critical risks missing timely intervention opportunities.

Cons for conducting INSTI resistance testing before ART initiation (Table 1)

Many INSTI resistance mutations may not impact the efficacy of 2nd-generation INSTIs. Although a wide range of INSTI mutations have been reported, the effects of non-major mutations on 2nd-generation INSTI efficacy remain unclear.13 Reports of increasing INSTI mutation prevalence often include mutations that do not reduce the efficacy of ART regimens with oral 2nd-generation INSTIs, warranting cautious interpretation.24,25

Transmitted INSTI resistance affecting 2nd-generation INSTI-based regimens remains rare. Across multiple observational studies examining resistance patterns among people at ART initiation, the prevalence of major INSTI resistance affecting ART with 2nd-generation INSTIs is reported to be <1%.9,24–26 Since INSTI resistance testing prior to ART initiation is typically recommended only for people with a history of prior exposure to INSTI-based PrEP or PEP, or a partner with INSTI resistance, the available data likely reflect a bias toward people with increased risk factors for INSTI resistance. This makes the finding of extremely low prevalence in ART-naïve individuals particularly reassuring, suggesting that transmitted INSTI resistance to date is not a common problem that would merit a clinical recommendation for routine testing in all people at ART initiation. Additionally, most people starting 2nd-generation INSTI-based ART regimens will attain virologic suppression promptly even without testing for INSTI resistance, reinforcing the view that routine pre-ART INSTI resistance testing may not be required for individualized care decisions.27–29

Guidance on crafting ART regimens in the presence of INSTI resistance mutations is limited, which can lead to delays in ART initiation and appropriate selection. Data are limited to support current guidance on how to interpret the wide range of reported INSTI resistance mutations, and expert opinion on ART selection in the setting of resistance is varied.30 In particular, the impact of some INSTI mutations on the efficacy of 2nd-generation INSTI-based regimens remains unclear. This limited ability to provide clear guidance regarding ART selection in the setting of detected INSTI mutations in ART-naïve people risks delays in ART initiation and selection of unnecessarily complicated ART regimens while awaiting specialist consultation. Such delays in ART initiation and selection can have substantial implications for newly diagnosed people at a time when building trust in care providers is essential. Importantly, ART regimens designed for use with 2nd-generation INSTI resistance often have a higher pill burden or increased risk of adverse side effects or drug-drug interactions. The unnecessary use of non-INSTI-based regimens with poorer tolerability may foster a negative perception of ART as toxic among people newly starting ART.

Clinical outcomes are unlikely to be affected if ART is initiated with INSTI resistance testing performed only if virologic suppression is not promptly achieved. Testing for conditions is typically recommended when clinical decisions that would be influenced by the test results would affect patient outcomes. However, clinically relevant transmitted resistance to 2nd-generation INSTIs is currently infrequent, and it is unclear whether initiation of guideline-recommended 2nd-generation INSTI-based regimens would be less likely to result in viral suppression. It is also unlikely that major INSTI resistance mutations would occur in the absence of other mutations (e.g. NRTI-associated), further strengthening this point. It is already critical to advise people newly initiating ART to follow-up closely to confirm virologic suppression, which would allow for timely detection of existing INSTI-resistance and regimen switch within weeks of ART initiation, if viremia persists.

Expanding pre-ART testing will have opportunity costs. Some institutions and insurers often require additional paperwork and justification to test for INSTI resistance at ART initiation, which can lead to increased costs, administrative burden, and delayed results. Additionally, the financial burden of clinical care continues to pose challenges, affecting people with HIV due to out-of-pocket expenses and the healthcare system overall. Testing for which a short delay in diagnosis is unlikely to change clinical outcomes will add costs without clinical benefit. The costs and effort needed for additional resistance testing prior to ART initiation are likely to have a bigger impact on clinical outcomes if exerted on other elements of clinical care.

The foundation of clinical decision-making is that clinical testing should benefit the patient. At current estimates of transmitted INSTI resistance and uncertainty in interpreting the clinical implications of many INSTI mutations, it is not clear that routine testing prior to ART initiation will provide better outcomes for people newly initiating ART than close follow-up to ensure virologic suppression. Surveillance for transmitted drug-resistance, innovation in resistance testing, further understanding of drug resistance patterns, and protecting ART efficacy are all extremely important; but routine clinical care, where costs can be incurred by patients and clinical guidance on decision-making is unclear, should not be the setting to generate these data.31

Geographical considerations

Testing for transmitted resistance for PRRT and/or integrase is currently recommended for individual care primarily in high-income settings (appendix p1). In low- and middle-income countries (LMICs), where cost and infrastructure limitations are substantial, population-level surveillance is the recommended approach,8,9 and individualized testing upon virologic failure is typically limited. However, this Viewpoint may also be important for treatment management in LMICs. First, 2nd-generation INSTIs are not only recommended in first-line regimens globally, but also in more advanced lines of ART, and soon will be for prevention. Second, in many lower-resource settings, limited past and current access to routine viral load and drug resistance monitoring increased the risk of undetected resistance development with past ART regimens.8 Third, multiple HIV-1 subtypes predominate in these regions, yet research and knowledge are limited on whether and how these subtypes impact resistance development. Fourth, especially in settings of increased restrictions in resources for most LMICs, the opportunity costs of using limited resources for diagnostics that are not uniformly recommended in high-income settings would be very high. These factors collectively may contribute to a higher risk of developing and transmitting resistance, with a particular gap in knowledge regarding the more recently used ART regimens with 2nd-generation INSTIs. Given the interconnected nature of health outcomes worldwide, ensuring that transmitted drug resistance is effectively monitored and managed across all regions is increasingly important, even if implementing comprehensive testing for it in many settings may currently be challenging.

Conclusions

While there is broad agreement on the importance of reducing the development of INSTI resistance and safeguarding the long-term effectiveness of this powerful antiretroviral class, the need to reassess current recommendations for transmitted INSTI resistance testing at ART initiation remains unclear, even in settings where individualized care makes it feasible. Relying solely on providers and patients to decide whether and when to conduct such testing could be problematic, especially given the uncertainty around whether current guidelines on this topic should be reassessed. This issue has compelling arguments on both sides, leaving some uncertain, while others may hold definitive views. The absence of routine testing risks jeopardizing this critical class of medications, but unnecessary routine testing could lead to unintended consequences, such as resource misuse or overly complex care that can delay or deter care engagement.

Based on the earlier discussion of advantages and limitations, we offer recommendations to guide the collection of additional data to inform decision-making on this critical topic (Panel). Guideline panels and policymakers should define the key data needed to inform their decisions, while providers and researchers should assess and report outcomes related to INSTI resistance. Transmitted INSTI resistance should be closely monitored and aggregated to track real-time trends where it is feasible to perform it, alongside comprehensive, frequent, and globally representative surveillance. Such data can advance understanding of transmitted INSTI resistance patterns and refine resistance interpretation algorithms and regimen recommendations, enabling more accurate and actionable insights and supporting evidence-based clinical management decisions. Collectively, these efforts will help shape and advance the ongoing discussion. As our understanding of INSTI resistance grows, we urge providers, researchers and policymakers to engage in the discussion of this critical issue.

Panel: Data needs for reassessing INSTI resistance testing at ART initiation.

  • Outline data required to support informed decisions on recommending pre-ART INSTI resistance testing. This will help generate evidence for guideline committees and policymakers, to determine whether and for whom integrase resistance testing should be performed before ART initiation.

  • Characterize viral and clinical outcomes associated with INSTI resistance. This will help refine resistance interpretation algorithms, deepen understanding of the clinical significance of specific mutations and mutation profiles and elucidate their relationships with particular drugs and combinations, which will enhance clinical guidance and optimize outcomes for people with INSTI resistance.

  • Conduct global surveillance of INSTI resistance systematically across regions, subtypes, and populations, with frequent, real time data collection.

  • Encourage the reporting of observed cases of transmitted INSTI resistance, even if limited, to enhance understanding of resistance patterns and their extent.

  • Encourage innovation of antiretroviral resistance testing, including assay simplification, point-of-care technology, and lower costs.

  • Establish or leverage data repositories to compile, organize and aggregate raw sequences alongside relevant clinical and epidemiological data on transmitted INSTI resistance. 13

Supplementary Material

Appendix

Appendix Table. Selected guidelines recommendations for drug resistance testing before ART initiation.

Acknowledgements

RK is partly supported by R01AI186632, R01136058, R01AI147333, K24AI134359, and P30AI042853. EPH is partly supported by R01AI042006 and the MGH Jerome and Celia Reich Endowed Scholar Award. Funders had no role in the writing of the manuscript or the decision to submit it for publication. The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health or Massachusetts General Hospital. The content and discussion points emerged from a debate at the DHHS Panel retreat. The authors confirm that the paper has not been submitted to another journal and has not been published in whole or in part elsewhere previously.

Footnotes

Conflict of Interest

Rami Kantor reports receiving support from the NIH paid to his institution, support from Gilead Sciences for a research grant on COVID-19 paid to his institution, honoraria from Thermofisher for a lecture at a conference workshop on INSTI drug resistance, and support for attending meetings and/or travel from the WHO for a HIV drug resistance meeting.

Alice Pau reports being the Executive Secretary of the HHS Panel on Antiretroviral Treatment Guidelines for Adults and Adolescents; the Executive Secretary of the NIH COVID-19 Treatment Guidelines (ended August 2024); and the Co-Chair of the Guidelines for the Prevention and Treatment of Opportunistic Infections in Adults and Adolescents with HIV.

Emily Hyle reports receiving support from the NIH and Massachusetts General Hospital paid to her institution, support from UpToDate paid to herself, and support for attending meetings and/or travel from the WHO for a HIV drug resistance meeting.

Michael Kozal declared no conflict of interest.

Declaration of generative AI and AI-assisted technologies in the writing process

During the preparation of this work the author(s) used ChatGPT version 2.0 in order to improve clarity and language. After using this tool/service, the author(s) reviewed and edited the content as needed and take(s) full responsibility for the content of the publication.

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Associated Data

This section collects any data citations, data availability statements, or supplementary materials included in this article.

Supplementary Materials

Appendix

Appendix Table. Selected guidelines recommendations for drug resistance testing before ART initiation.

NIHMS2092809-supplement-Appendix.docx (28.1KB, docx)

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