Accumulation of Multiple Mutations In Vivo Confers Cross-Resistance to New and Existing Integrase Inhibitors
Open accessAbstract
Bictegravir (BIC) and cabotegravir (CAB) are the latest available HIV integrase inhibitors in clinical trials. The combination of major integrase inhibitor substitutions G140S/Q148H has been shown to confer high-level resistance to the approved integrase inhibitors raltegravir (RAL) and elvitegravir (EVG) but not necessarily dolutegravir (DTG). We assayed recombinant viruses made from patient-derived RNA extracts for resistance phenotype for a panel of viruses containing G140S/Q148H with additional accessory substitutions. The accumulation of multiple integrase substitutions confers high-level resistance to all 5 integrase inhibitors. There is extensive cross-resistance between DTG, BIC, and CAB (r = 0.96-0.97).
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Claims other papers make about this one
Each is checked against this paper’s own text: does it say what the citing paper says it does?
Dolutegravir, bictegravir, and cabotegravir are second-generation INSTIs with reduced susceptibility to viral mutations that render raltegravir and elvitegravir ineffective.
“The latter three, classified as second-generation compounds, are characterized by reduced susceptibility to viral mutations that render the first-generation drugs, raltegravir and elvitegravir, ineffective151–153.”
From Structure and function of retroviral integrase (2022) · cites this paper as [153]
The Results report that viruses with G140S/Q148H were highly resistant to raltegravir and elvitegravir but had relatively small susceptibility changes to dolutegravir, bictegravir, and cabotegravir. The claim is broader than that finding: the Results also show that additional mutations produced substantial resistance to all three newer inhibitors. (LLM, conf=0.85)
Experimental — accuracy not yet measured
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Cites
Margolis, D. A., González‐García, J., Stellbrink, H.-J., Eron, J. J., Yazdanpanah, Y., Podzamczer, D., Lutz, T., Angel, J. B., Richmond, G. J., Clotet, B., et al. (2017) · The Lancet · doi:10.1016/s0140-6736(17)31917-7 · Cited by 506 · see citing works
Gallant, J. E., Lazzarin, A., Mills, A., Orkin, C. M., Podzamczer, D., Tebas, P., Girard, P., Brar, I., Daar, E. S., Wohl, D. A., et al. (2017) · The Lancet · doi:10.1016/s0140-6736(17)32299-7 · Cited by 394 · see citing works
Castagna, A., Maggiolo, F., Penco, G., Wright, D., Mills, A., Grossberg, R. M., Molina, J., Chas, J., Durant, J., Moreno, S., et al. (2014) · The Journal of Infectious Diseases · doi:10.1093/infdis/jiu051 · Cited by 331 · see citing works
Eron, J. J., Clotet, B., Durant, J., Katlama, C., Kumar, P. N., Lazzarin, A., Poizot‐Martin, I., Richmond, G. J., Soriano, V., Ait‐Khaled, M., et al. (2012) · The Journal of Infectious Diseases · doi:10.1093/infdis/jis750 · Cited by 308 · see citing works
Tsiang, M., Jones, G. S., Goldsmith, J., Mulato, A., Hansen, D., Kan, E., Tsai, L., Bam, R. A., Stepan, G., Stray, K. M., et al. (2016) · Antimicrobial Agents and Chemotherapy · doi:10.1128/aac.01474-16 · Cited by 290 · see citing works
Malet, I., Delelis, O., Valantin, M., Montès, B., Soulié, C., Wirden, M., Tchertanov, L., Peytavin, G., Reynes, J., Mouscadet, J. F., et al. (2008) · Antimicrobial Agents and Chemotherapy · doi:10.1128/aac.01228-07 · Cited by 281 · see citing works
HIV drug resistance against strand transfer integrase inhibitors
Anstett, K., BRENNER, B. G., Mésplède, T., & Wainberg, M. A. (2017) · Retrovirology · doi:10.1186/s12977-017-0360-7 · Cited by 176 · see citing works
Yoshinaga, T., Kobayashi, M., Seki, T., Miki, S., Wakasa-Morimoto, C., Suyama, A., Kawauchi, S., Taishi, T., Kawasuji, T., Johns, B. A., et al. (2014) · Antimicrobial Agents and Chemotherapy · doi:10.1128/aac.03909-14 · Cited by 96 · see citing works
Xue, W., Jin, X., Ning, L., Wang, M., Liu, H., & Yao, X. (2012) · Journal of Chemical Information and Modeling · doi:10.1021/ci300541c · Cited by 75 · see citing works
Fransen, S., Gupta, S., Frantzell, A., Petropoulos, C. J., & Huang, W. (2012) · Journal of Virology · doi:10.1128/jvi.06618-11 · Cited by 42 · see citing works
Seki, T., Suyama, A., Kawauchi, S., Miki, S., Wakasa-Morimoto, C., Akihisa, E., Nakahara, K., Kobayashi, M., Underwood, M., Sato, A., et al. (2015) · Antimicrobial Agents and Chemotherapy · doi:10.1128/aac.04844-14 · Cited by 40 · see citing works
Uncommon Pathways of Immune Escape Attenuate HIV-1 Integrase Replication Capacity
Brockman, M. A., Chopera, D., Olvera, À., Brumme, C. J., Sela, J., Markle, T. J., Martin, E., Carlson, J. M., Le, A. Q., McGovern, R. A., et al. (2012) · Journal of Virology · doi:10.1128/jvi.07133-11 · Cited by 37 · see citing works
Self-citationHachiya, A., Kirby, K. A., Ido, Y., Shigemi, U., Matsuda, M., Okazaki, R., Imamura, J., Sarafianos, S. G., Yokomaku, Y., & Iwatani, Y. (2017) · Antimicrobial Agents and Chemotherapy · doi:10.1128/aac.00315-17 · Cited by 23 · see citing works
Lee, G. Q., Swenson, L. C., Poon, A. F. Y., Martin, J. N., Hatano, H., Deeks, S. G., & Harrigan, P. R. (2012) · PLoS ONE · doi:10.1371/journal.pone.0046181 · Cited by 21 · see citing works
Self-citation
Flagged first, then by citations
Cited by
Sorted by citations
A systematic review of the genetic mechanisms of dolutegravir resistance
Rhee, S., Grant, P., Tzou, P. L., Barrow, G., Harrigan, P. R., Ioannidis, J. P. A., & Shafer, R. W. (2019) · Journal of Antimicrobial Chemotherapy · doi:10.1093/jac/dkz256 · Cited by 154 · see citing works
Self-citationStructure and function of retroviral integrase
Maertens, G. N., Engelman, A. N., & Cherepanov, P. (2022) · Nature Reviews Microbiology · doi:10.1038/s41579-021-00586-9 · Cited by 124 · see citing works
Bictegravir/Emtricitabine/Tenofovir Alafenamide: A Review in HIV-1 Infection
Deeks, E. D. (2018) · Drugs · doi:10.1007/s40265-018-1010-7 · Cited by 118 · see citing works
Structural basis of second-generation HIV integrase inhibitor action and viral resistance
Cook, N. J., Li, W., Berta, D., Badaoui, M., Ballandras-Colas, A., Nans, A., Kotecha, A., Rosta, E., Engelman, A. N., & Cherepanov, P. (2020) · Science · doi:10.1126/science.aay4919 · Cited by 108 · see citing works
Multifaceted HIV integrase functionalities and therapeutic strategies for their inhibition
Engelman, A. (2019) · Journal of Biological Chemistry · doi:10.1074/jbc.rev119.006901 · Cited by 78 · see citing works
“Despite relatively high barriers, second-generation INSTIs do select for resistance (149, 159, 163).”
BackgroundPhillips, A. N., Bansi‐Matharu, L., Cambiano, V., Ehrenkranz, P. D., Serenata, C. M., Venter, F., Pett, S. L., Flexner, C. W., Jahn, A., Revill, P. A., et al. (2021) · The Lancet Global Health · doi:10.1016/s2214-109x(21)00025-5 · Cited by 74 · see citing works
Inzaule, S. C., Hamers, R. L., Doherty, M. C., Shafer, R. W., Bertagnolio, S., & de Wit, T. F. R. (2019) · The Lancet Infectious Diseases · doi:10.1016/s1473-3099(18)30710-2 · Cited by 61 · see citing works
HIV Drug Resistance in Children and Adolescents: Always a Challenge?
Koay, W. L. A., Kose, J., & Rakhmanina, N. Y. (2021) · Current Epidemiology Reports · doi:10.1007/s40471-021-00268-3 · Cited by 47 · see citing works
Going beyond Integration: The Emerging Role of HIV-1 Integrase in Virion Morphogenesis
Elliott, J. L., & Kutluay, S. B. (2020) · Viruses · doi:10.3390/v12091005 · Cited by 46 · see citing works
“However, despite high barriers with the second-generation INSTIs, treatment does select for drug resistance [13–15], and mutations conferring resistance to multiple INSTIs have been reported in clinical settings [16,17], highlighting the need for continued research and development of both improved and novel antiretrov…”
BackgroundParikh, U. M., Koss, C. A., & Mellors, J. W. (2022) · Current HIV/AIDS Reports · doi:10.1007/s11904-022-00616-y · Cited by 44 · see citing works
Genotypic correlates of resistance to the HIV-1 strand transfer integrase inhibitor cabotegravir
Rhee, S., Parkin, N. T., Harrigan, P. R., Holmes, S., & Shafer, R. W. (2022) · Antiviral Research · doi:10.1016/j.antiviral.2022.105427 · Cited by 28 · see citing works
Self-citationSmith, R. A., Raugi, D. N., Wu, V. H., Zavala, C. G., Song, J. K., Diallo, K. M., Seydi, M., Gottlieb, G. S., Sall, F., Diallo, M. B., et al. (2019) · Antimicrobial Agents and Chemotherapy · doi:10.1128/aac.00014-19 · Cited by 25 · see citing works
“0-fold) resistance to bictegravir (33, 39, 51), whereas the T97A/ Y143C mutant did not show resistance to the drug (33) (Table 3).”
BackgroundSaladini, F., Giannini, A., Boccuto, A., Dragoni, F., Appendino, A., Albanesi, E., Vicenti, I., & Zazzi, M. (2019) · Antimicrobial Agents and Chemotherapy · doi:10.1128/aac.01717-19 · Cited by 22 · see citing works
Pham, H. T., & Mésplède, T. (2019) · Expert Opinion on Pharmacotherapy · doi:10.1080/14656566.2018.1560423 · Cited by 21 · see citing works
“In vitro, BIC susceptibility can be compromised in patients with Q148/G140 + ≥1 accessory mutation, similar to what was observed with DTG [61,62].”
BackgroundResultNdashimye, E., Avino, M., Olabode, A. S., Poon, A. F. Y., Gibson, R. M., Li, Y., Meadows, A., Tan, C., Reyes, P. S., Kityo, C. M., et al. (2020) · Journal of Antimicrobial Chemotherapy · doi:10.1093/jac/dkaa355 · Cited by 19 · see citing works
Ndashimye, E., Li, Y., Reyes, P. S., Avino, M., Olabode, A. S., Kityo, C. M., Kyeyune, F., Nankya, I., Quiñones‐Mateu, M. E., Barr, S. D., et al. (2021) · Journal of Antimicrobial Chemotherapy · doi:10.1093/jac/dkab276 · Cited by 17 · see citing works
Santoro, M. M., Fornabaio, C., Malena, M., Galli, L., Poli, A., Menozzi, M., Zazzi, M., White, K., & Castagna, A. (2020) · International Journal of Antimicrobial Agents · doi:10.1016/j.ijantimicag.2020.106027 · Cited by 15 · see citing works
Cheung, P. K., Shahid, A., Dong, W. W. Y., Lepik, K. J., Montaner, J. S. G., Brockman, M. A., Brumme, Z. L., & Brumme, C. J. (2021) · Journal of Antimicrobial Chemotherapy · doi:10.1093/jac/dkab498 · Cited by 14 · see citing works
Self-citationA mini-review on integrase inhibitors: The cornerstone of next-generation HIV treatment
Shalbi, F., & Ali, A. R. (2024) · European Journal of Medicinal Chemistry · doi:10.1016/j.ejmech.2024.116900 · Cited by 11 · see citing works
Engelman, A., & Cherepanov, P. (2020) · FEBS Journal · doi:10.1111/febs.15438 · Cited by 11 · see citing works
Current status of the small molecule anti-HIV drugs in the pipeline or recently approved
Umumararungu, T., Nyandwi, J. B., Katandula, J., Twizeyimana, E. F., Tomani, J. C. D., Gahamanyi, N., Ishimwe, N., Olawode, E. O., Habarurema, G., Mpenda, M., et al. (2024) · Bioorganic & Medicinal Chemistry · doi:10.1016/j.bmc.2024.117860 · Cited by 8 · see citing works
Rossetti, B., Fabbiani, M., Carlo, D. D., Incardona, F., Abecasis, A. B., Gómes, P., Geretti, A. M., Seguin‐Devaux, C., García, F., Kaiser, R., et al. (2022) · HIV Medicine · doi:10.1111/hiv.13262 · Cited by 7 · see citing works
Diez, R. C., Spetz, A., & Sönnerborg, A. B. (2023) · Drug Resistance Updates · doi:10.1016/j.drup.2023.100955 · Cited by 5 · see citing works
Ferrer, P., Ramos, V., Durán, M., Maureira, D., Beltrán, C., & Afani, A. (2025) · Journal of Virus Eradication · doi:10.1016/j.jve.2025.100608 · Cited by 4 · see citing works
“12,16 Four main resistance pathways were identified: Y143R, N155H, R263K, and Q148 H/K/R. 12 N155H was the most prevalent, followed by Q148H, Y143R and R263K.”
Herrera-Espejo, S., Rubio, A., Ceballos-Romero, L., Pachón, J., Cordero, E., Pérez‐Pulido, A. J., & Pachón-Ibáñez, M. E. (2025) · Biomolecules · doi:10.3390/biom15020260 · Cited by 4 · see citing works
“However, the accumulation of multiple mutations could lead to clinical resistance [17].”
Ferrer, P., Rodríguez, C., Sciaraffia, A., Tordecilla, R., Ramos, V., Durán, M., Beltrán, C., & Afani, A. (2020) · Journal of Virus Eradication · doi:10.1016/j.jve.2020.06.002 · Cited by 4 · see citing works
Celotti, A., Gargiulo, F., Quirós-Roldán, E., Properzi, M., Francesco, M. A. D., Coletto, D., Caccuri, F., Izzo, I., Caruso, A., Castelli, F., et al. (2020) · HIV Research & Clinical Practice · doi:10.1080/25787489.2020.1734753 · Cited by 3 · see citing works
Martin, M. A., Reynolds, S. J., Foley, B. T., Nalugoda, F. K., Quinn, T. C., Kemp, S. A., Nakalanzi, M., Kankaka, E. N., Kigozi, G., Ssekubugu, R., et al. (2023) · medRxiv · doi:10.1101/2023.10.14.23297021 · Cited by 3 · see citing works
Giammarino, F., Sönnerborg, A. B., & Diez, R. C. (2024) · Frontiers in Cellular and Infection Microbiology · doi:10.3389/fcimb.2024.1334126 · Cited by 2 · see citing works
Lunkuse, S., Kiiza, R., Ssekagiri, A., Nannyonjo, M., Ntenkaire, N., Nassolo, F., Namagembe, H. S., Kiberu, F., Kabuuka, D., Andia, I., et al. (2025) · Viruses · doi:10.3390/v17121596 · Cited by 2 · see citing works
“The accessory mutations S230R, E157Q, L74F, T97A, and S153YAF observed in this study have minimal effects on DTG susceptibility when independent, but, in combination with other major resistance mutations, they synergistically reduce susceptibility to DTG [37,38].”
Mielczak, K., Serwin, K., Urbańska, A., Aksak‐Wąs, B., Karasińska‐Cieślak, M., Mularska, E., Witor, A., Jakubowski, P., Hlebowicz, M., Bociąga‐Jasik, M., et al. (2024) · Viruses · doi:10.3390/v16101597 · Cited by 2 · see citing works
“It reduces sensitivity to INSTIs only in combination with other mutations [11,45], but in our study, it occurred alone and was observed only in sub-subtype A6.”
Backgrounddos Santos, I. F. C., Moura, A. S., Ferraz, M. M. D., Moreira, C., Meireles, P., & Ceccato, M. D. G. B. (2025) · AIDS Care · doi:10.1080/09540121.2025.2474672 · Cited by 2 · see citing works
“Similarly, the R263K mutation combined with the in vivo accumulation of mutations E138K, G140S, S147G, and Q148R decreases susceptibility to DTG and may confer high-level viral resistance to the drug (Ndashimye et al., 2020; Zhang et al., 2018).”
Martin, M. A., Blenkinsop, A., Moffa, M., Reynolds, S. J., Nalugoda, F. K., Quinn, T. C., Kigozi, G., Ssekubugu, R., Gupta, R. K., Grayson, N. E., et al. (2025) · medRxiv · doi:10.1101/2025.09.01.25334862 · Cited by 2 · see citing works
Martin, M. A., Blenkinsop, A., Moffa, M., Reynolds, S. J., Nalugoda, F. K., Quinn, T. C., Kigozi, G., Ssekubugu, R., Gupta, R. K., Grayson, N. E., et al. (2026) · Clinical Infectious Diseases · doi:10.1093/cid/ciag161 · Cited by 1 · see citing works
New Antiretroviral Agents for HIV Infection
Fong, I. W. (2023) · Emerging infectious diseases of the 21st century · doi:10.1007/978-3-031-26078-0_12 · Cited by 1 · see citing works
Pretreatment integrase strand transfer inhibitor resistance in Tianjin, China
Xia, H., Ge, Z., Zhang, D., Wu, Y., & Ma, P. (2023) · Chinese Medical Journal · doi:10.1097/cm9.0000000000002898 · Cited by 1 · see citing works
“[17] The rare mutation Y143H may be a transitional mutation between the 2-bp mutation R and wild-type Y, which decreases RAL susceptibility by ~3-fold to 20-fold.”
Rodríguez-López, E. R., López, P. L., Rodríguez, Y., Sánchez, R., Acevedo, V.-S., Encarnación-Medina, J., Tirado, G., Ortíz, C., Mésplède, T., & Rivera‐Amill, V. (2024) · AIDS Research and Human Retroviruses · doi:10.1089/aid.2023.0128 · Cited by 1 · see citing works
“22 From multivariate analysis, it has been shown that subtype A6 can be a factor contributing to an increased risk of virological failure with CAB plus rilpivirine.”
InfluentialShahid, A., Zhang, W. W., Montoya, V., Cheung, P. K., Oliveira, N., Sidhu, M. S., Woods, C. K., Robbins, M., Brumme, C. J., & Harrigan, P. R. (2019) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/621755 · Cited by 1 · see citing works
Self-citationMechanisms of Resistance to Antiviral Agents
Shafer, R. W., Boivin, G., Howe, A., & Chou, S. (2023) · ClinMicroNow · doi:10.1002/9781683674849.mcm0115
Mechanisms of Resistance to Antiviral Agents
Shafer, R. W., Boivin, G., Howe, A., & Chou, S. (2023) · ClinMicroNow · doi:10.1002/9781683670438.mcm0115
Godinho, I., Queirós, G., Yefimenko, L., Martins-Pereira, F., & Piedade, J. (2026) · Microorganisms · doi:10.3390/microorganisms14051156
“T97A, found in three sequences, has a modest impact on first-generation INSTIs when present alone [47], but exerts stronger synergistic effects in combination with other DRMs [45].”
Targeting HIV-1 integrase: A review of options, challenges and future directions
Bourquin, R. A., & Schaeffer, P. M. (2026) · International Journal of Biological Macromolecules · doi:10.1016/j.ijbiomac.2026.153092
BindingDB (2026) · UC San Diego · doi:10.7270/q22v2mzm
BindingDB (2026) · UC San Diego · doi:10.7270/q2pg1xnq
- Authors
- Zhang, W. W., Cheung, P. K., Oliveira, N., Robbins, M. A., Harrigan, P. R., & Shahid, A.
- Affiliations
- University of British Columbia (CA)
- BC Centre for Excellence in HIV/AIDS (CA)
- Corresponding author
- Harrigan, P Richard
- Venue
- The Journal of Infectious Diseases
- Publisher
- Oxford University Press (OUP)
- Published
- 2018-07-16
- Volume
- 218
- Issue
- 11
- Pages
- 1773-1776
- ISSN
- 0022-1899 (ISSN-L)
- 1537-6613
- OpenAlex
- W2884916801
- Cited by
- 44
- References
- 14
- Citations by year
- 2026: 5 · 2025: 5 · 2024: 5 · 2023: 6 · 2022: 3 · 2021: 5 · 2020: 7 · 2019: 7 · 2018: 1
- FWCI
- 3.78
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Licence
- academic.oup.com/journals/pages/open_access/funder_policies/chorus/standard_publication_model (vor)
- Locations
- The Journal of Infectious Diseases (publishedVersion)
- PubMed (publishedVersion)
- Funders
- Canadian Institutes of Health Research
- Topics
- Health Sciences › Medicine › Infectious Diseases › HIV/AIDS drug development and treatment
- Life Sciences › Immunology and Microbiology › Virology › HIV Research and Treatment
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Medicine › Antibiotic Resistance in Bacteria
- Keywords
- HIV integrase inhibitors, drug resistance, cross-resistance, bictegravir, cabotegravir, dolutegravir, raltegravir, elvitegravir
- MeSH terms
- Dolutegravir, Amides, Cell Line, Heterocyclic Compounds, 3-Ring, Heterocyclic Compounds, 4 or More Rings, Humans, Oxazines, Piperazines, Pyridones, HIV-1, HIV Infections, HIV Integrase Inhibitors, Drug Resistance, Viral, Diketopiperazines
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review