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Matsuda EM, da Silva Santos JH, Ahagon CM, Lopes GISL, Brigido LFDM. Transmitted antiretroviral drug resistance to Integrase Strand Transfer Inhibitors class in São Paulo metropolitan area, Brazil. AIDS Res Hum Retroviruses 2024. [PMID: 39041595 DOI: 10.1089/aid.2023.0127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/24/2024] Open
Abstract
Objectives A newer Integrase Strand Transfer Inhibitor (INSTI) cabotegravir was recently approved for both therapy and prophylaxis and can play an essential role in the fight against AIDS. It shares similar resistance profile to dolutegravir, the cornerstone of Brazilian antiretroviral treatment (ARV), with about 600 thousand people living with HIV in Brazil currently on regimens that contain this INSTI. Health services in the São Paulo metropolitan area are responsible to a large proportion of ARV dispensation in the country. Estimating Transmitted Drug Resistance Mutation (TDRM) in the area before cabotegravir introduction may provide a useful baseline information. Methods Partial HIV-1 pol gene was sequenced (Sanger) from 192 newly diagnosed individuals from São Paulo and nearby cities (2020 to March 2023) at integrase, with 85 also at protease/reverse transcriptase regions. Retrotranscribed plasma RNA, amplified with nested PCR, was edited (Recall or Sequencher) and analyzed at Rega and Stanford db. Results Surveillance DRM (SDRM) to INSTI class was detected in three cases (1.6% CI95% 0.5%-5%), two E138K and one R263K, with 7.8% (CI95% 5%-13%) with resistance mutations (major or accessory). SDRM for NRTI, NNRTI, and PI classes were identified in 7 (8.2% CI95% 4%-16%) cases. Subtype B predominated (69%), followed by subtype C (16%), now the second most prevalent infection in this area. Among 131 patients treated for over six months, 92% were virally suppressed below 200 copies/mL, with low TCD4 counts independently associated to failure. Conclusions SDRM to INSTI class is rare in the area. Intermediate rates of transmitted resistance to other ARV classes are comparable to previous estimates. Viral suppression rates may depend on TCD4 counts, another negative impact of late diagnosis in care that deserves more attention.
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Beck IA, Boyce CL, Bishop MD, Vu YL, Fung A, Styrchak S, Panpradist N, Lutz BR, Frenkel LM. Development and Optimization of Oligonucleotide Ligation Assay (OLA) Probes for Detection of HIV-1 Resistance to Dolutegravir. Viruses 2024; 16:1162. [PMID: 39066324 DOI: 10.3390/v16071162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2024] [Revised: 07/17/2024] [Accepted: 07/17/2024] [Indexed: 07/28/2024] Open
Abstract
The WHO currently recommends dolutegravir (DTG)-based ART for persons living with HIV infection in resource-limited-settings (RLS). To expand access to testing for HIV drug resistance (DR) to DTG in RLS, we developed probes for use in the oligonucleotide ligation assay (OLA)-Simple, a near-point of care HIV DR kit. Genotypic data from clinical trials and case reports were used to determine the mutations in HIV-1 integrase critical to identifying individuals with DTG-resistance at virologic failure of DTG-based ART. Probes to detect G118R, Q148H/K/R, N155H and R263K in HIV-1 subtypes A, B, C, D and CRF01_AE were designed using sequence alignments from the Los Alamos database and validated using 61 clinical samples of HIV-1 subtypes A, B, C, D, CRF01_AE genotyped by PacBio (n = 15) or Sanger (n = 46). Initial OLA probes failed to ligate for 16/244 (6.5%) codons (9 at G118R and 7 at Q148H/K/R). Probes revised to accommodate polymorphisms interfering with ligation at codons G118R and Q148R reduced indeterminates to 3.7% (5 at G118R and 4 at Q148H/K/R) and detected DTG-mutations with a sensitivity of 96.5% and 100% specificity. These OLA DTG resistance probes appear highly sensitive and specific across HIV-1 subtypes common in RLS with high burden of HIV infection.
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Affiliation(s)
- Ingrid A Beck
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, WA 98109, USA
| | - Ceejay L Boyce
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, WA 98109, USA
| | - Marley D Bishop
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, WA 98109, USA
| | - Yen L Vu
- Department of Bioengineering, University of Washington, Seattle, WA 98195, USA
| | - Amanda Fung
- Department of Bioengineering, University of Washington, Seattle, WA 98195, USA
| | - Sheila Styrchak
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, WA 98109, USA
| | - Nuttada Panpradist
- Department of Bioengineering, University of Washington, Seattle, WA 98195, USA
| | - Barry R Lutz
- Department of Bioengineering, University of Washington, Seattle, WA 98195, USA
| | - Lisa M Frenkel
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, WA 98109, USA
- Departments of Medicine, Pediatrics and Laboratory Medicine, University of Washington, Seattle, WA 98195, USA
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Januszka J, Drwiega E, Burgos R, Smith R, Badowski M. Real-world prevalence of integrase inhibitor resistance and virological failure since adoption as guideline-preferred therapy. Drugs Context 2024; 13:2023-12-4. [PMID: 38770371 PMCID: PMC11104290 DOI: 10.7573/dic.2023-12-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Accepted: 04/04/2024] [Indexed: 05/22/2024] Open
Abstract
Background Limited data reporting real-world prevalence of integrase strand transfer inhibitor resistance (INSTI-R) in the USA are available because their recommendation as first-line treatment in 2017. Reported national surveillance data in the USA estimated INSTI-R to be 6.3% as of 2018. This article aims to describe estimated prevalence of INSTI-R within a single clinic network in Chicago, IL, USA, and identify risk factors for resistance and virological failure (VF). Methods This was a retrospective, single-centre study of adults with HIV starting an INSTI-containing regimen between September 2017 and 2020. The primary endpoint was the difference in INSTI-R of the sample population compared with the national prevalence. Other outcomes included VF and documented INSTI-R mutations. Results Of 948 participants screened, 321 were included. Eight people had baseline INSTI-R testing results available, of which five had INSTI-R at baseline for an estimated prevalence of 1.6%. This estimation was significantly less than the national estimated prevalence of 6.3% (p<0.001). VF occurred in 26 (7.8%) individuals. Because no participants acquired INSTI-R during the study period, investigators were unable to identify risk factors associated with the development of INSTI-R. People with high pre-treatment viral loads had 1.21 (95% CI 1.05-1.39) higher odds of VF. Conclusions Amongst participants on INSTI-containing regimens, INSTI-R rates were estimated to be lower than the estimated national prevalence. Detectable pre-switch viral loads were more associated with VF than undetectable viral loads.
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Affiliation(s)
- Jenna Januszka
- College of Pharmacy, University of Illinois at Chicago, Chicago, IL, USA
| | - Emily Drwiega
- College of Pharmacy, University of Illinois at Chicago, Chicago, IL, USA
| | - Rodrigo Burgos
- College of Pharmacy, University of Illinois at Chicago, Chicago, IL, USA
| | - Renata Smith
- College of Pharmacy, University of Illinois at Chicago, Chicago, IL, USA
| | - Melissa Badowski
- College of Pharmacy, University of Illinois at Chicago, Chicago, IL, USA
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Chu C, Tao K, Kouamou V, Avalos A, Scott J, Grant PM, Rhee SY, McCluskey SM, Jordan MR, Morgan RL, Shafer RW. Prevalence of Emergent Dolutegravir Resistance Mutations in People Living with HIV: A Rapid Scoping Review. Viruses 2024; 16:399. [PMID: 38543764 PMCID: PMC10975848 DOI: 10.3390/v16030399] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Revised: 02/27/2024] [Accepted: 02/28/2024] [Indexed: 05/23/2024] Open
Abstract
BACKGROUND Dolutegravir (DTG) is a cornerstone of global antiretroviral (ARV) therapy (ART) due to its high efficacy and favorable tolerability. However, limited data exist regarding the risk of emergent integrase strand transfer inhibitor (INSTI) drug-resistance mutations (DRMs) in individuals receiving DTG-containing ART. METHODS We performed a PubMed search using the term "Dolutegravir", last updated 18 December 2023, to estimate the prevalence of VF with emergent INSTI DRMs in people living with HIV (PLWH) without previous VF on an INSTI who received DTG-containing ART. RESULTS Of 2131 retrieved records, 43 clinical trials, 39 cohorts, and 6 cross-sectional studies provided data across 6 clinical scenarios based on ART history, virological status, and co-administered ARVs: (1) ART-naïve PLWH receiving DTG plus two NRTIs; (2) ART-naïve PLWH receiving DTG plus lamivudine; (3) ART-experienced PLWH with VF on a previous regimen receiving DTG plus two NRTIs; (4) ART-experienced PLWH with virological suppression receiving DTG plus two NRTIs; (5) ART-experienced PLWH with virological suppression receiving DTG and a second ARV; and (6) ART-experienced PLWH with virological suppression receiving DTG monotherapy. The median proportion of PLWH in clinical trials with emergent INSTI DRMs was 1.5% for scenario 3 and 3.4% for scenario 6. In the remaining four trial scenarios, VF prevalence with emergent INSTI DRMs was ≤0.1%. Data from cohort studies minimally influenced prevalence estimates from clinical trials, whereas cross-sectional studies yielded prevalence data lacking denominator details. CONCLUSIONS In clinical trials, the prevalence of VF with emergent INSTI DRMs in PLWH receiving DTG-containing regimens has been low. Novel approaches are required to assess VF prevalence with emergent INSTI DRMs in PLWH receiving DTG in real-world settings.
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Affiliation(s)
- Carolyn Chu
- Department of Family and Community Medicine, University of California San Francisco, San Francisco, CA 94110, USA;
| | - Kaiming Tao
- Division of Infectious Diseases, Department of Medicine, Stanford University, Stanford, CA 94305, USA (J.S.); (S.-Y.R.)
| | - Vinie Kouamou
- Faculty of Medicine and Health Sciences, University of Zimbabwe, Harare 00263, Zimbabwe;
| | - Ava Avalos
- Careena Center for Health, Gaborone, Botswana
| | - Jake Scott
- Division of Infectious Diseases, Department of Medicine, Stanford University, Stanford, CA 94305, USA (J.S.); (S.-Y.R.)
| | - Philip M. Grant
- Division of Infectious Diseases, Department of Medicine, Stanford University, Stanford, CA 94305, USA (J.S.); (S.-Y.R.)
| | - Soo-Yon Rhee
- Division of Infectious Diseases, Department of Medicine, Stanford University, Stanford, CA 94305, USA (J.S.); (S.-Y.R.)
| | | | - Michael R. Jordan
- Division of Geographic Medicine and Infectious Diseases, Tufts Medical Center, Boston, MA 02111, USA
- Collaboratory for Emerging Infectious Diseases and Response (CEIDR), Tufts University, Medford, MA 02155, USA
| | - Rebecca L. Morgan
- School of Medicine, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Robert W. Shafer
- Division of Infectious Diseases, Department of Medicine, Stanford University, Stanford, CA 94305, USA (J.S.); (S.-Y.R.)
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Dzinamarira T, Moyo E, Moyo B, Murewanhema G, Cuadros D, Kouamou V, Mpofu A, Musuka G. Strengthening and enhancing national antiretroviral drug resistance surveillance in Zimbabwe-A country that has reached UNAIDS 95-95-95 amongst adults. Front Public Health 2024; 12:1346027. [PMID: 38420022 PMCID: PMC10899673 DOI: 10.3389/fpubh.2024.1346027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Accepted: 02/02/2024] [Indexed: 03/02/2024] Open
Affiliation(s)
- Tafadzwa Dzinamarira
- School of Health Systems and Public Health, University of Pretoria, Pretoria, South Africa
- International Center for AIDS Care and Treatment Programs, Columbia University, Lusaka, Zambia
| | - Enos Moyo
- Department of Public Health Medicine, University of KwaZulu Natal, Durban, South Africa
| | - Brian Moyo
- Ministry of Health and Child Care, Harare, Zimbabwe
| | - Grant Murewanhema
- Faculty of Medicine and Health Sciences, University of Zimbabwe, Harare, Zimbabwe
| | - Diego Cuadros
- University of Cincinnati, Cincinnati, OH, United States
| | - Vinie Kouamou
- Faculty of Medicine and Health Sciences, University of Zimbabwe, Harare, Zimbabwe
| | - Amon Mpofu
- National AIDS Council of Zimbabwe, Harare, Zimbabwe
| | - Godfrey Musuka
- International Initiative for Impact Evaluation, Harare, Zimbabwe
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Henegar C, Letang E, Wang R, Hicks C, Fox D, Jones B, de Ruiter A, Vannappagari V. A Comprehensive Literature Review of Treatment-Emergent Integrase Resistance with Dolutegravir-Based Regimens in Real-World Settings. Viruses 2023; 15:2426. [PMID: 38140667 PMCID: PMC10747437 DOI: 10.3390/v15122426] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Revised: 12/08/2023] [Accepted: 12/12/2023] [Indexed: 12/24/2023] Open
Abstract
After a decade of dolutegravir (DTG) use in various antiretroviral therapy combinations and in diverse populations globally, it is critical to identify HIV strains with reduced drug susceptibility and monitor emergent resistance in people living with HIV who experience virologic failure while on DTG-based regimens. We searched the PubMed, Embase, and Cochrane databases to identify studies that reported DTG resistance-associated mutations (RAMs) emerging under selection pressure. Our review showed that RAMs conferring resistance to DTG were rare in 2-drug and 3-drug regimens used in real-world cohorts, corroborating data from clinical trials. The potency of DTG in maintaining virologic suppression was demonstrated, even in cases of pre-existing resistance to companion drugs in the regimen. Estimates of DTG RAMs depended on the population and certain risk factors, including monotherapy, baseline resistance or lack of genotypic testing, treatment history and prior virologic failure, and suboptimal treatment adherence. The RAMs detected after virologic failure, often in heavily treatment-experienced individuals with prior exposure to integrase strand transfer inhibitors, were G118R, E138K, G140A/C/R/S, Q148H/K/R, N155H, and R263K. Overall, these data highlight the durable effectiveness and high barrier to resistance of DTG as part of combination antiretroviral therapy in a wide variety of settings.
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Affiliation(s)
- Cassidy Henegar
- ViiV Healthcare, 406 Blackwell Street, Suite 300, Durham, NC 27701, USA; (R.W.); (C.H.); (D.F.); (V.V.)
| | - Emilio Letang
- ViiV Healthcare, P.T.M., Severo Ochoa 2, 28760 Tres Cantos, Madrid, Spain
| | - Ruolan Wang
- ViiV Healthcare, 406 Blackwell Street, Suite 300, Durham, NC 27701, USA; (R.W.); (C.H.); (D.F.); (V.V.)
| | - Charles Hicks
- ViiV Healthcare, 406 Blackwell Street, Suite 300, Durham, NC 27701, USA; (R.W.); (C.H.); (D.F.); (V.V.)
| | - Dainielle Fox
- ViiV Healthcare, 406 Blackwell Street, Suite 300, Durham, NC 27701, USA; (R.W.); (C.H.); (D.F.); (V.V.)
| | - Bryn Jones
- ViiV Healthcare, 980 Great West Road, Brentford TW8 9GS, Middlesex, UK
| | | | - Vani Vannappagari
- ViiV Healthcare, 406 Blackwell Street, Suite 300, Durham, NC 27701, USA; (R.W.); (C.H.); (D.F.); (V.V.)
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Tao K, Rhee SY, Chu C, Avalos A, Ahluwalia AK, Gupta RK, Jordan MR, Shafer RW. Treatment Emergent Dolutegravir Resistance Mutations in Individuals Naïve to HIV-1 Integrase Inhibitors: A Rapid Scoping Review. Viruses 2023; 15:1932. [PMID: 37766338 PMCID: PMC10536831 DOI: 10.3390/v15091932] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Revised: 09/08/2023] [Accepted: 09/12/2023] [Indexed: 09/29/2023] Open
Abstract
Background: Dolutegravir (DTG)-based antiretroviral therapy (ART) rarely leads to virological failure (VF) and drug resistance in integrase strand transfer inhibitor (INSTI)-naïve persons living with HIV (PLWH). As a result, limited data are available on INSTI-associated drug resistance mutations (DRMs) selected by DTG-containing ART regimens. Methods: We reviewed studies published through July 2023 to identify those reporting emergent major INSTI-associated DRMs in INSTI-naïve PLWH receiving DTG and those containing in vitro DTG susceptibility results using a standardized assay. Results: We identified 36 publications reporting 99 PLWH in whom major nonpolymorphic INSTI-associated DRMs developed on a DTG-containing regimen and 21 publications containing 269 in vitro DTG susceptibility results. DTG-selected DRMs clustered into four largely non-overlapping mutational pathways characterized by mutations at four signature positions: R263K, G118R, N155H, and Q148H/R/K. Eighty-two (82.8%) viruses contained just one signature DRM, including R263K (n = 40), G118R (n = 24), N155H (n = 9), and Q148H/R/K (n = 9). Nine (9.1%) contained ≥1 signature DRM, and eight (8.1%) contained just other DRMs. R263K and G118R were negatively associated with one another and with N155H and Q148H/K/R. R263K alone conferred a median 2.0-fold (IQR: 1.8-2.2) reduction in DTG susceptibility. G118R alone conferred a median 18.8-fold (IQR:14.2-23.4) reduction in DTG susceptibility. N155H alone conferred a median 1.4-fold (IQR: 1.2-1.6) reduction in DTG susceptibility. Q148H/R/K alone conferred a median 0.8-fold (IQR: 0.7-1.1) reduction in DTG susceptibility. Considerably higher levels of reduced susceptibility often occurred when signature DRMs occurred with additional INSTI-associated DRMs. Conclusions: Among INSTI-naïve PLWH with VF and treatment emergent INSTI-associated DRMs, most developed one of four signature DRMs, most commonly R263K or G118R. G118R was associated with a much greater reduction in DTG susceptibility than R263K.
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Affiliation(s)
- Kaiming Tao
- Division of Infectious Diseases, Department of Medicine, Stanford University, Stanford, CA 94305, USA; (K.T.)
| | - Soo-Yon Rhee
- Division of Infectious Diseases, Department of Medicine, Stanford University, Stanford, CA 94305, USA; (K.T.)
| | - Carolyn Chu
- Department of Family and Community Medicine, University of California San Francisco, San Francisco, CA 94011, USA
| | - Ava Avalos
- Careen Center for Health, Gaborone, Botswana
| | | | - Ravindra K. Gupta
- Cambridge Institute of Therapeutic Immunology and Infectious Disease (CITIID), Cambridge CB2 0AW, UK
| | - Michael R. Jordan
- Division of Geographic Medicine and Infectious Diseases, Tufts Medical Center, Boston, MA 02111, USA
| | - Robert W. Shafer
- Division of Infectious Diseases, Department of Medicine, Stanford University, Stanford, CA 94305, USA; (K.T.)
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