Publications

Subtypes A1 and D, and recombinant HIV-1 natural polymorphisms associated with lenacapavir drug resistance in Uganda. Author(s): Omoding D, Musinguzi N, Boum Y 2nd, Muzoora C, Kigozi S, Hunt PW, Martin JN, Bangsberg DR, Haberer JE, Siedner MJ, McCluskey SM, Lee GQ. Citation: J Antimicrob Chemother. 2025 Apr 2;80(4):955-961. doi: 10.1093/jac/dkaf018.

Differences in HIV-1 reservoir size, landscape characteristics, and decay dynamics in acute and chronic treated HIV-1 Clade C infection. Author(s): Reddy K, Lee GQ, Reddy N, Chikowore TJB, Baisley K, Dong KL, Walker BD, Yu XG, Lichterfeld M, Ndung'u T. Citation: Elife. 2025 Feb 20;13:RP96617. doi: 10.7554/eLife.96617.

HIV-1 subtype A1, D, and recombinant proviral genome landscapes during long-term suppressive therapy. Author(s): Lee GQ, Khadka P, Gowanlock SN, Copertino DC Jr, Duncan MC, Omondi FH, Kinloch NN, Kasule J, Kityamuweesi T, Buule P, Jamiru S, Tomusange S, Anok A, Chen Z, Jones RB, Galiwango RM, Reynolds SJ, Quinn TC, Brumme ZL, Redd AD, Prodger JL. Citation: Nat Commun. 2024 Jul 2;15(1):5480. doi: 10.1038/s41467-024-48985-9.

HIV reservoirs are dominated by genetically younger and clonally enriched proviruses. Author(s): Kinloch NN, Shahid A, Dong W, Kirkby D, Jones BR, Beelen CJ, MacMillan D, Lee GQ, Mota TM, Sudderuddin H, Barad E, Harris M, Brumme CJ, Jones RB, Brockman MA, Joy JB, Brumme ZL. Citation: mBio. 2023 Dec 19;14(6):e0241723. doi: 10.1128/mbio.02417-23. Epub 2023 Nov 16.

Near-Full-Length Single-Genome HIV-1 DNA Sequencing. Author(s): Lee GQ, Lichterfeld M. Citation: Methods Mol Biol. 2022;2407:357-364. doi: 10.1007/978-1-0716-1871-4_23.

Attenuated HIV-1 Nef But Not Vpu Function in a Cohort of Rwandan Long-Term Survivors. Author(s): Umviligihozo G, Mann JK, Jin SW, Mwimanzi FM, Hsieh HA, Sudderuddin H, Lee GQ, Byakwaga H, Muzoora C, Hunt PW, Martin JN, Haberer JE, Karita E, Allen S, Hunter E, Brumme ZL, Brockman MA. Citation: Front Virol. 2022 Jun;2:917902. doi: 10.3389/fviro.2022.917902. Epub 2022 Jun 16.

SARS CoV-2 mRNA vaccination exposes latent HIV to Nef-specific CD8(+) T-cells. Author(s): Stevenson EM, Terry S, Copertino D, Leyre L, Danesh A, Weiler J, Ward AR, Khadka P, McNeil E, Bernard K, Miller IG, Ellsworth GB, Johnston CD, Finkelsztein EJ, Zumbo P, Betel D, Dündar F, Duncan MC, Lapointe HR, Speckmaier S, Moran-Garcia N, Papa MP, Nicholes S, Stover CJ, Lynch RM, Caskey M, Gaebler C, Chun TW, Bosque A, Wilkin TJ, Lee GQ, Brumme ZL, Jones RB. Citation: Nat Commun. 2022 Aug 19;13(1):4888. doi: 10.1038/s41467-022-32376-z.

HIV-specific T cell responses reflect substantive in vivo interactions with antigen despite long-term therapy. Author(s): Stevenson EM, Ward AR, Truong R, Thomas AS, Huang SH, Dilling TR, Terry S, Bui JK, Mota TM, Danesh A, Lee GQ, Gramatica A, Khadka P, Alberto WDC, Gandhi RT, McMahon DK, Lalama CM, Bosch RJ, Macatangay B, Cyktor JC, Eron JJ, Mellors JW, Jones RB; AIDS Clinical Trials Group A5321 Team. Citation: JCI Insight. 2021 Feb 8;6(3):e142640. doi: 10.1172/jci.insight.142640.

HIV-1 diversity considerations in the application of the Intact Proviral DNA Assay (IPDA). Author(s): Kinloch NN, Ren Y, Conce Alberto WD, Dong W, Khadka P, Huang SH, Mota TM, Wilson A, Shahid A, Kirkby D, Harris M, Kovacs C, Benko E, Ostrowski MA, Del Rio Estrada PM, Wimpelberg A, Cannon C, Hardy WD, MacLaren L, Goldstein H, Brumme CJ, Lee GQ, Lynch RM, Brumme ZL, Jones RB. Citation: Nat Commun. 2021 Jan 8;12(1):165. doi: 10.1038/s41467-020-20442-3.

Pre-treatment integrase inhibitor resistance is uncommon in antiretroviral therapy-naive individuals with HIV-1 subtype A1 and D infections in Uganda. Author(s): McCluskey SM, Kamelian K, Musinguzi N, Kigozi S, Boum Y 2nd, Bwana MB, Muzoora C, Brumme ZL, Carrington M, Carlson J, Foley B, Hunt PW, Martin JN, Bangsberg DR, Harrigan PR, Siedner MJ, Haberer JE, Lee GQ. Citation: AIDS. 2021 Jun 1;35(7):1083-1089. doi: 10.1097/QAD.0000000000002854.

Chemistry and Bioinformatics Considerations in Using Next-Generation Sequencing Technologies to Inferring HIV Proviral DNA Genome-Intactness. Author(s): Lee GQ. Citation: Viruses. 2021 Sep 19;13(9):1874. doi: 10.3390/v13091874.

Blood and Lymph Node Dissemination of Clonal Genome-Intact Human Immunodeficiency Virus 1 DNA Sequences During Suppressive Antiretroviral Therapy. Author(s): Kuo HH, Banga R, Lee GQ, Gao C, Cavassini M, Corpataux JM, Blackmer JE, Zur Wiesch S, Yu XG, Pantaleo G, Perreau M, Lichterfeld M. Citation: J Infect Dis. 2020 Jul 23;222(4):655-660. doi: 10.1093/infdis/jiaa137.

Tissue memory CD4+ T cells expressing IL-7 receptor-alpha (CD127) preferentially support latent HIV-1 infection. Author(s): Hsiao F, Frouard J, Gramatica A, Xie G, Telwatte S, Lee GQ, Roychoudhury P, Schwarzer R, Luo X, Yukl SA, Lee S, Hoh R, Deeks SG, Jones RB, Cavrois M, Greene WC, Roan NR. Citation: PLoS Pathog. 2020 Apr 30;16(4):e1008450. doi: 10.1371/journal.ppat.1008450. eCollection 2020 Apr.

Differential Vpu-Mediated CD4 and Tetherin Downregulation Functions among Major HIV-1 Group M Subtypes. Author(s): Umviligihozo G, Cobarrubias KD, Chandrarathna S, Jin SW, Reddy N, Byakwaga H, Muzoora C, Bwana MB, Lee GQ, Hunt PW, Martin JN, Brumme CJ, Bangsberg DR, Karita E, Allen S, Hunter E, Ndung'u T, Brumme ZL, Brockman MA. Citation: J Virol. 2020 Jul 1;94(14):e00293-20. doi: 10.1128/JVI.00293-20. Print 2020 Jul 1.

Variation in HIV-1 Nef function within and among viral subtypes reveals genetically separable antagonism of SERINC3 and SERINC5. Author(s): Jin SW, Mwimanzi FM, Mann JK, Bwana MB, Lee GQ, Brumme CJ, Hunt PW, Martin JN, Bangsberg DR, Ndung'u T, Brumme ZL, Brockman MA. Citation: PLoS Pathog. 2020 Sep 14;16(9):e1008813. doi: 10.1371/journal.ppat.1008813. eCollection 2020 Sep.

HIV-1 DNA sequence diversity and evolution during acute subtype C infection. Author(s): Lee GQ, Reddy K, Einkauf KB, Gounder K, Chevalier JM, Dong KL, Walker BD, Yu XG, Ndung'u T, Lichterfeld M. Citation: Nat Commun. 2019 Jun 21;10(1):2737. doi: 10.1038/s41467-019-10659-2.

Intact HIV-1 proviruses accumulate at distinct chromosomal positions during prolonged antiretroviral therapy. Author(s): Einkauf KB, Lee GQ, Gao C, Sharaf R, Sun X, Hua S, Chen SM, Jiang C, Lian X, Chowdhury FZ, Rosenberg ES, Chun TW, Li JZ, Yu XG, Lichterfeld M. Citation: J Clin Invest. 2019 Mar 1;129(3):988-998. doi: 10.1172/JCI124291. Epub 2019 Jan 28.

HIV-1 proviral landscapes distinguish posttreatment controllers from noncontrollers. Author(s): Sharaf R, Lee GQ, Sun X, Etemad B, Aboukhater LM, Hu Z, Brumme ZL, Aga E, Bosch RJ, Wen Y, Namazi G, Gao C, Acosta EP, Gandhi RT, Jacobson JM, Skiest D, Margolis DM, Mitsuyasu R, Volberding P, Connick E, Kuritzkes DR, Lederman MM, Yu XG, Lichterfeld M, Li JZ. Citation: J Clin Invest. 2018 Aug 31;128(9):4074-4085. doi: 10.1172/JCI120549. Epub 2018 Aug 20.

HLA-C downregulation by HIV-1 adapts to host HLA genotype. Author(s): Bachtel ND, Umviligihozo G, Pickering S, Mota TM, Liang H, Del Prete GQ, Chatterjee P, Lee GQ, Thomas R, Brockman MA, Neil S, Carrington M, Bwana B, Bangsberg DR, Martin JN, Kallas EG, Donini CS, Cerqueira NB, O'Doherty UT, Hahn BH, Jones RB, Brumme ZL, Nixon DF, Apps R. Citation: PLoS Pathog. 2018 Sep 4;14(9):e1007257. doi: 10.1371/journal.ppat.1007257. eCollection 2018 Sep.

Genotypic and Mechanistic Characterization of Subtype-Specific HIV Adaptation to Host Cellular Immunity. Author(s): Kinloch NN, Lee GQ, Carlson JM, Jin SW, Brumme CJ, Byakwaga H, Muzoora C, Bwana MB, Cobarrubias KD, Hunt PW, Martin JN, Carrington M, Bangsberg DR, Harrigan PR, Brockman MA, Brumme ZL. Citation: J Virol. 2018 Dec 10;93(1):e01502-18. doi: 10.1128/JVI.01502-18. Print 2019 Jan 1.

Effect of analytical treatment interruption and reinitiation of antiretroviral therapy on HIV reservoirs and immunologic parameters in infected individuals. Author(s): Clarridge KE, Blazkova J, Einkauf K, Petrone M, Refsland EW, Justement JS, Shi V, Huiting ED, Seamon CA, Lee GQ, Yu XG, Moir S, Sneller MC, Lichterfeld M, Chun TW. Citation: PLoS Pathog. 2018 Jan 11;14(1):e1006792. doi: 10.1371/journal.ppat.1006792. eCollection 2018 Jan.

Increasing Prevalence of HIV Pretreatment Drug Resistance in Women But Not Men in Rural Uganda During 2005-2013. Author(s): McCluskey SM, Lee GQ, Kamelian K, Kembabazi A, Musinguzi N, Bwana MB, Muzoora C, Haberer JE, Hunt PW, Martin JN, Boum Y 2nd, Bangsberg DR, Harrigan PR, Siedner MJ. Citation: AIDS Patient Care STDS. 2018 Jul;32(7):257-264. doi: 10.1089/apc.2018.0020.

Anti-apoptotic Protein BIRC5 Maintains Survival of HIV-1-Infected CD4(+) T Cells. Author(s): Kuo HH, Ahmad R, Lee GQ, Gao C, Chen HR, Ouyang Z, Szucs MJ, Kim D, Tsibris A, Chun TW, Battivelli E, Verdin E, Rosenberg ES, Carr SA, Yu XG, Lichterfeld M. Citation: Immunity. 2018 Jun 19;48(6):1183-1194.e5. doi: 10.1016/j.immuni.2018.04.004. Epub 2018 May 22.

Dolutegravir reshapes the genetic diversity of HIV-1 reservoirs. Author(s): Gantner P, Lee GQ, Rey D, Mesplede T, Partisani M, Cheneau C, Beck-Wirth G, Faller JP, Mohseni-Zadeh M, Martinot M, Wainberg MA, Fafi-Kremer S. Citation: J Antimicrob Chemother. 2018 Apr 1;73(4):1045-1053. doi: 10.1093/jac/dkx475.

Distribution and reduction magnitude of HIV-DNA burden in CD4+ T cell subsets depend on art initiation timing. Author(s): Gantner P, Barnig C, Partisani M, Lee GQ, Beck-Wirth G, Faller JP, Martinot M, Mosheni-Zadeh M, Cheneau C, Batard ML, Fischer P, Fuchs A, Uring-Lambert B, Bahram S, Rey D, Fafi-Kremer S. Citation: AIDS. 2018 Apr 24;32(7):921-926. doi: 10.1097/QAD.0000000000001770.

In vitro functional assessment of natural HIV-1 group M Vpu sequences using a universal priming approach. Author(s): Rahimi A, Anmole G, Soto-Nava M, Escamilla-Gomez T, Markle T, Jin SW, Lee GQ, Harrigan PR, Bangsberg DR, Martin J, Avila-Rios S, Reyes-Teran G, Brockman MA, Brumme ZL. Citation: J Virol Methods. 2017 Feb;240:32-41. doi: 10.1016/j.jviromet.2016.11.004. Epub 2016 Nov 16.

Subtype-Specific Differences in Gag-Protease-Driven Replication Capacity Are Consistent with Intersubtype Differences in HIV-1 Disease Progression. Author(s): Kiguoya MW, Mann JK, Chopera D, Gounder K, Lee GQ, Hunt PW, Martin JN, Ball TB, Kimani J, Brumme ZL, Brockman MA, Ndung'u T. Citation: J Virol. 2017 Jun 9;91(13):e00253-17. doi: 10.1128/JVI.00253-17. Print 2017 Jul 1.

Potential for immune-driven viral polymorphisms to compromise antiretroviral-based preexposure prophylaxis for prevention of HIV-1 infection. Author(s): Gatanaga H, Brumme ZL, Adland E, Reyes-Terán G, Avila-Rios S, Mejía-Villatoro CR, Hayashida T, Chikata T, Van Tran G, Van Nguyen K, Meza RI, Palou EY, Valenzuela-Ponce H, Pascale JM, Porras-Cortés G, Manzanero M, Lee GQ, Martin JN, Carrington MN, John M, Mallal S, Poon AFY, Goulder P, Takiguchi M, Oka S; International HIV Adaptation Collaborative. Citation: AIDS. 2017 Sep 10;31(14):1935-1943. doi: 10.1097/QAD.0000000000001575.

Brief Report: Should Abacavir Be a First-Line Alternative for Adults With HIV in Sub-Saharan Africa?. Author(s): Lee GQ, McCluskey S, Boum Y 2nd, Hunt PW, Martin JN, Bangsberg DR, Gao X, Harrigan PR, Haberer JE, Siedner MJ. Citation: J Acquir Immune Defic Syndr. 2017 Oct 1;76(2):188-192. doi: 10.1097/QAI.0000000000001487.

Prevalence and clinical impacts of HIV-1 intersubtype recombinants in Uganda revealed by near-full-genome population and deep sequencing approaches. Author(s): Lee GQ, Bangsberg DR, Mo T, Lachowski C, Brumme CJ, Zhang W, Lima VD, Boum Y 2nd, Mwebesa BB, Muzoora C, Andia I, Mbalibulha Y, Kembabazi A, Carroll R, Siedner MJ, Haberer JE, Mocello AR, Kigozi SH, Hunt PW, Martin JN, Harrigan PR. Citation: AIDS. 2017 Nov 13;31(17):2345-2354. doi: 10.1097/QAD.0000000000001619.

Extensive virologic and immunologic characterization in an HIV-infected individual following allogeneic stem cell transplant and analytic cessation of antiretroviral therapy: A case study. Author(s): Cummins NW, Rizza S, Litzow MR, Hua S, Lee GQ, Einkauf K, Chun TW, Rhame F, Baker JV, Busch MP, Chomont N, Dean PG, Fromentin R, Haase AT, Hampton D, Keating SM, Lada SM, Lee TH, Natesampillai S, Richman DD, Schacker TW, Wietgrefe S, Yu XG, Yao JD, Zeuli J, Lichterfeld M, Badley AD. Citation: PLoS Med. 2017 Nov 28;14(11):e1002461. doi: 10.1371/journal.pmed.1002461. eCollection 2017 Nov.

Clonal expansion of genome-intact HIV-1 in functionally polarized Th1 CD4+ T cells. Author(s): Lee GQ, Orlova-Fink N, Einkauf K, Chowdhury FZ, Sun X, Harrington S, Kuo HH, Hua S, Chen HR, Ouyang Z, Reddy K, Dong K, Ndung'u T, Walker BD, Rosenberg ES, Yu XG, Lichterfeld M. Citation: J Clin Invest. 2017 Jun 30;127(7):2689-2696. doi: 10.1172/JCI93289. Epub 2017 Jun 19.

Non-R5-tropic HIV-1 in subtype A1 and D infections were associated with lower pretherapy CD4+ cell count but not with PI/(N)NRTI therapy outcomes in Mbarara, Uganda. Author(s): Lee GQ, Lachowski C, Cai E, Lima VD, Boum Y, Muzoora C, Mocello AR, Hunt PW, Martin JN, Bangsberg DR, Harrigan PR. Citation: AIDS. 2016 Jul 17;30(11):1781-8. doi: 10.1097/QAD.0000000000001128.

Diversity of HIV-1 reservoirs in CD4+ T-cell subpopulations. Author(s): Lee GQ, Lichterfeld M. Citation: Curr Opin HIV AIDS. 2016 Jul;11(4):383-7. doi: 10.1097/COH.0000000000000281.

Reliable genotypic tropism tests for the major HIV-1 subtypes. Author(s): Cashin K, Gray LR, Harvey KL, Perez-Bercoff D, Lee GQ, Sterjovski J, Roche M, Demarest JF, Drummond F, Harrigan PR, Churchill MJ, Gorry PR. Citation: Sci Rep. 2015 Feb 25;5:8543. doi: 10.1038/srep08543.

HIV drug resistance testing by high-multiplex "wide" sequencing on the MiSeq instrument. Author(s): Lapointe HR, Dong W, Lee GQ, Bangsberg DR, Martin JN, Mocello AR, Boum Y, Karakas A, Kirkby D, Poon AF, Harrigan PR, Brumme CJ. Citation: Antimicrob Agents Chemother. 2015 Nov;59(11):6824-33. doi: 10.1128/AAC.01490-15. Epub 2015 Aug 17.

Highly frequent HIV-1 minority resistant variants at baseline of the ANRS 139 TRIO trial had a limited impact on virological response. Author(s): Charpentier C, Lee GQ, Rodriguez C, Visseaux B, Storto A, Fagard C, Molina JM, Katlama C, Yazdanpanah Y, Harrigan PR, Descamps D. Citation: J Antimicrob Chemother. 2015 Jul;70(7):2090-6. doi: 10.1093/jac/dkv048. Epub 2015 Mar 8.

Limited evolution of inferred HIV-1 tropism while viremia is undetectable during standard HAART therapy. Author(s): Lee GQ, Dong W, Mo T, Knapp DJ, Brumme CJ, Woods CK, Kanters S, Yip B, Harrigan PR. Citation: PLoS One. 2014 Jun 6;9(6):e99000. doi: 10.1371/journal.pone.0099000. eCollection 2014.

Prevalence and virologic consequences of transmitted HIV-1 drug resistance in Uganda. Author(s): Lee GQ, Bangsberg DR, Muzoora C, Boum Y, Oyugi JH, Emenyonu N, Bennett J, Hunt PW, Knapp D, Brumme CJ, Harrigan PR, Martin JN. Citation: AIDS Res Hum Retroviruses. 2014 Sep;30(9):896-906. doi: 10.1089/AID.2014.0043. Epub 2014 Jul 29.

Theoretical and experimental assessment of degenerate primer tagging in ultra-deep applications of next-generation sequencing. Author(s): Liang RH, Mo T, Dong W, Lee GQ, Swenson LC, McCloskey RM, Woods CK, Brumme CJ, Ho CK, Schinkel J, Joy JB, Harrigan PR, Poon AF. Citation: Nucleic Acids Res. 2014 Jul;42(12):e98. doi: 10.1093/nar/gku355. Epub 2014 May 7.

Ability of HIV-1 Nef to downregulate CD4 and HLA class I differs among viral subtypes. Author(s): Mann JK, Byakwaga H, Kuang XT, Le AQ, Brumme CJ, Mwimanzi P, Omarjee S, Martin E, Lee GQ, Baraki B, Danroth R, McCloskey R, Muzoora C, Bangsberg DR, Hunt PW, Goulder PJ, Walker BD, Harrigan PR, Martin JN, Ndung'u T, Brockman MA, Brumme ZL. Citation: Retrovirology. 2013 Sep 16;10:100. doi: 10.1186/1742-4690-10-100.

Comparison of population and 454 "deep" sequence analysis for HIV type 1 tropism versus the original trofile assay in non-B subtypes. Author(s): Lee GQ, Harrigan PR, Dong W, Poon AF, Heera J, Demarest J, Rinehart A, Chapman D, Valdez H, Portsmouth S. Citation: AIDS Res Hum Retroviruses. 2013 Jun;29(6):979-84. doi: 10.1089/aid.2012.0338. Epub 2013 Mar 6.

Prolonged and substantial discordance in prevalence of raltegravir-resistant HIV-1 in plasma versus PBMC samples revealed by 454 "deep" sequencing. Author(s): Lee GQ, Swenson LC, Poon AF, Martin JN, Hatano H, Deeks SG, Harrigan PR. Citation: PLoS One. 2012;7(9):e46181. doi: 10.1371/journal.pone.0046181. Epub 2012 Sep 26.

Convergence of Ser/Thr and two-component signaling to coordinate expression of the dormancy regulon in Mycobacterium tuberculosis. Author(s): Chao JD, Papavinasasundaram KG, Zheng X, Chávez-Steenbock A, Wang X, Lee GQ, Av-Gay Y. Citation: J Biol Chem. 2010 Sep 17;285(38):29239-46. doi: 10.1074/jbc.M110.132894. Epub 2010 Jul 14.