Publications

1: Lee GQ, Lichterfeld M. Near-Full-Length Single-Genome HIV-1 DNA Sequencing.

Methods Mol Biol. 2022;2407:357-364. doi: 10.1007/978-1-0716-1871-4_23. PMID:

34985675.

2: Lee GQ. Chemistry and Bioinformatics Considerations in Using Next-Generation

Sequencing Technologies to Inferring HIV Proviral DNA Genome-Intactness.

Viruses. 2021 Sep 19;13(9):1874. doi: 10.3390/v13091874. PMID: 34578455; PMCID:

PMC8473067.

3: Kinloch NN, Ren Y, Alberto WDC, 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. Author Correction: HIV-1 diversity

considerations in the application of the Intact Proviral DNA Assay (IPDA). Nat

Commun. 2021 May 13;12(1):2958. doi: 10.1038/s41467-021-23515-z. Erratum for:

Nat Commun. 2021 Jan 8;12(1):165. PMID: 33986282; PMCID: PMC8119429.

4: 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. Pre-treatment

integrase inhibitor resistance is uncommon in antiretroviral therapy-naive

individuals with HIV-1 subtype A1 and D infections in Uganda. AIDS. 2021 Jun

1;35(7):1083-1089. doi: 10.1097/QAD.0000000000002854. PMID: 33635845; PMCID:

PMC8102316.

5: 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. HIV-1 diversity considerations in the

application of the Intact Proviral DNA Assay (IPDA). Nat Commun. 2021 Jan

8;12(1):165. doi: 10.1038/s41467-020-20442-3. Erratum in: Nat Commun. 2021 May

13;12(1):2958. PMID: 33420062; PMCID: PMC7794580.

6: 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. HIV-specific T cell

responses reflect substantive in vivo interactions with antigen despite long-

term therapy. JCI Insight. 2021 Feb 8;6(3):e142640. doi:

10.1172/jci.insight.142640. PMID: 33400687; PMCID: PMC7934865.

7: 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. Variation in HIV-1 Nef

function within and among viral subtypes reveals genetically separable

antagonism of SERINC3 and SERINC5. PLoS Pathog. 2020 Sep 14;16(9):e1008813. doi:

10.1371/journal.ppat.1008813. PMID: 32925973; PMCID: PMC7515180.

8: 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. Differential Vpu-

Mediated CD4 and Tetherin Downregulation Functions among Major HIV-1 Group M

Subtypes. J Virol. 2020 Jul 1;94(14):e00293-20. doi: 10.1128/JVI.00293-20. PMID:

32376625; PMCID: PMC7343213.

9: 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. Tissue memory CD4+ T cells expressing IL-7 receptor-alpha (CD127)

preferentially support latent HIV-1 infection. PLoS Pathog. 2020 Apr

30;16(4):e1008450. doi: 10.1371/journal.ppat.1008450. PMID: 32353080; PMCID:

PMC7192375.

10: 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. Blood and Lymph Node

Dissemination of Clonal Genome-Intact Human Immunodeficiency Virus 1 DNA

Sequences During Suppressive Antiretroviral Therapy. J Infect Dis. 2020 Jul

23;222(4):655-660. doi: 10.1093/infdis/jiaa137. PMID: 32236405; PMCID:

PMC8493664.

11: Lee GQ, Reddy K, Einkauf KB, Gounder K, Chevalier JM, Dong KL, Walker BD, Yu

XG, Ndung'u T, Lichterfeld M. HIV-1 DNA sequence diversity and evolution during

acute subtype C infection. Nat Commun. 2019 Jun 21;10(1):2737. doi:

10.1038/s41467-019-10659-2. PMID: 31227699; PMCID: PMC6588551.

12: 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. Intact HIV-1

proviruses accumulate at distinct chromosomal positions during prolonged

antiretroviral therapy. J Clin Invest. 2019 Mar 1;129(3):988-998. doi:

10.1172/JCI124291. Epub 2019 Jan 28. PMID: 30688658; PMCID: PMC6391088.

13: 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. Genotypic and Mechanistic Characterization

of Subtype-Specific HIV Adaptation to Host Cellular Immunity. J Virol. 2018 Dec

10;93(1):e01502-18. doi: 10.1128/JVI.01502-18. PMID: 30305354; PMCID:

PMC6288327.

14: 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. HLA-C downregulation by HIV-1 adapts

to host HLA genotype. PLoS Pathog. 2018 Sep 4;14(9):e1007257. doi:

10.1371/journal.ppat.1007257. PMID: 30180214; PMCID: PMC6138419.

15: 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. HIV-1 proviral landscapes distinguish posttreatment

controllers from noncontrollers. J Clin Invest. 2018 Aug 31;128(9):4074-4085.

doi: 10.1172/JCI120549. Epub 2018 Aug 20. PMID: 30024859; PMCID: PMC6118642.

16: 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. Increasing Prevalence of HIV Pretreatment Drug Resistance in

Women But Not Men in Rural Uganda During 2005-2013. AIDS Patient Care STDS. 2018

Jul;32(7):257-264. doi: 10.1089/apc.2018.0020. PMID: 29985647; PMCID:

PMC6034395.

17: 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.

Anti-apoptotic Protein BIRC5 Maintains Survival of HIV-1-Infected

CD4⁺ T Cells. Immunity. 2018 Jun 19;48(6):1183-1194.e5. doi:

10.1016/j.immuni.2018.04.004. Epub 2018 May 22. PMID: 29802019; PMCID:

PMC6013384.

18: 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. Distribution and reduction magnitude of HIV-DNA

burden in CD4+ T cell subsets depend on art initiation timing. AIDS. 2018 Apr

24;32(7):921-926. doi: 10.1097/QAD.0000000000001770. PMID: 29424775.

19: 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. Effect of analytical treatment interruption and reinitiation of

antiretroviral therapy on HIV reservoirs and immunologic parameters in infected

individuals. PLoS Pathog. 2018 Jan 11;14(1):e1006792. doi:

10.1371/journal.ppat.1006792. PMID: 29324842; PMCID: PMC5764487.

20: 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. Dolutegravir

reshapes the genetic diversity of HIV-1 reservoirs. J Antimicrob Chemother. 2018

Apr 1;73(4):1045-1053. doi: 10.1093/jac/dkx475. PMID: 29244129.

21: 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. Extensive virologic and

immunologic characterization in an HIV-infected individual following allogeneic

stem cell transplant and analytic cessation of antiretroviral therapy: A case

study. PLoS Med. 2017 Nov 28;14(11):e1002461. doi: 10.1371/journal.pmed.1002461.

PMID: 29182633; PMCID: PMC5705162.

22: 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.

Prevalence and clinical impacts of HIV-1 intersubtype recombinants in Uganda

revealed by near-full-genome population and deep sequencing approaches. AIDS.

2017 Nov 13;31(17):2345-2354. doi: 10.1097/QAD.0000000000001619. PMID: 28832407;

PMCID: PMC5656522.

23: 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. Potential for immune-driven viral

polymorphisms to compromise antiretroviral-based preexposure prophylaxis for

prevention of HIV-1 infection. AIDS. 2017 Sep 10;31(14):1935-1943. doi:

10.1097/QAD.0000000000001575. PMID: 28650381; PMCID: PMC8171589.

24: Lee GQ, McCluskey S, Boum Y 2nd, Hunt PW, Martin JN, Bangsberg DR, Gao X,

Harrigan PR, Haberer JE, Siedner MJ. Brief Report: Should Abacavir Be a First-

Line Alternative for Adults With HIV in Sub-Saharan Africa? J Acquir Immune

Defic Syndr. 2017 Oct 1;76(2):188-192. doi: 10.1097/QAI.0000000000001487. PMID:

28639996; PMCID: PMC5597467.

25: 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. Clonal expansion of genome-intact HIV-1 in functionally

polarized Th1 CD4+ T cells. J Clin Invest. 2017 Jun 30;127(7):2689-2696. doi:

10.1172/JCI93289. Epub 2017 Jun 19. PMID: 28628034; PMCID: PMC5490740.

26: 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. Subtype-Specific Differences in

Gag-Protease-Driven Replication Capacity Are Consistent with Intersubtype

Differences in HIV-1 Disease Progression. J Virol. 2017 Jun 9;91(13):e00253-17.

doi: 10.1128/JVI.00253-17. PMID: 28424286; PMCID: PMC5469260.

27: 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. In vitro functional assessment of natural HIV-1 group M Vpu

sequences using a universal priming approach. J Virol Methods. 2017

Feb;240:32-41. doi: 10.1016/j.jviromet.2016.11.004. Epub 2016 Nov 16. PMID:

27865749; PMCID: PMC5183569.

28: Lee GQ, Lachowski C, Cai E, Lima VD, Boum Y, Muzoora C, Mocello AR, Hunt PW,

Martin JN, Bangsberg DR, Harrigan PR. 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. AIDS. 2016 Jul 17;30(11):1781-8.

doi: 10.1097/QAD.0000000000001128. PMID: 27124899; PMCID: PMC4925292.

29: Lee GQ, Lichterfeld M. Diversity of HIV-1 reservoirs in CD4+ T-cell

subpopulations. Curr Opin HIV AIDS. 2016 Jul;11(4):383-7. doi:

10.1097/COH.0000000000000281. PMID: 27023286; PMCID: PMC4915926.

30: Charpentier C, Lee GQ, Rodriguez C, Visseaux B, Storto A, Fagard C, Molina

JM, Katlama C, Yazdanpanah Y, Harrigan PR, Descamps D. Highly frequent HIV-1

minority resistant variants at baseline of the ANRS 139 TRIO trial had a limited

impact on virological response. J Antimicrob Chemother. 2015 Jul;70(7):2090-6.

doi: 10.1093/jac/dkv048. Epub 2015 Mar 8. PMID: 25755001.

31: 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. Reliable

genotypic tropism tests for the major HIV-1 subtypes. Sci Rep. 2015 Feb

25;5:8543. doi: 10.1038/srep08543. PMID: 25712827; PMCID: PMC4894445.

32: Lee GQ, Bangsberg DR, Muzoora C, Boum Y, Oyugi JH, Emenyonu N, Bennett J,

Hunt PW, Knapp D, Brumme CJ, Harrigan PR, Martin JN. Prevalence and virologic

consequences of transmitted HIV-1 drug resistance in Uganda. AIDS Res Hum

Retroviruses. 2014 Sep;30(9):896-906. doi: 10.1089/AID.2014.0043. Epub 2014 Jul

29. PMID: 24960249; PMCID: PMC4151058.

33: Lee GQ, Dong W, Mo T, Knapp DJ, Brumme CJ, Woods CK, Kanters S, Yip B,

Harrigan PR. Limited evolution of inferred HIV-1 tropism while viremia is

undetectable during standard HAART therapy. PLoS One. 2014 Jun 6;9(6):e99000.

doi: 10.1371/journal.pone.0099000. PMID: 24905411; PMCID: PMC4048224.

34: 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. Theoretical and

experimental assessment of degenerate primer tagging in ultra-deep applications

of next-generation sequencing. Nucleic Acids Res. 2014 Jul;42(12):e98. doi:

10.1093/nar/gku355. Epub 2014 May 7. PMID: 24810852; PMCID: PMC4081055.

35: 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. Ability of HIV-1 Nef to downregulate CD4 and HLA class I differs

among viral subtypes. Retrovirology. 2013 Sep 16;10:100. doi:

10.1186/1742-4690-10-100. PMID: 24041011; PMCID: PMC3849644.

36: Lee GQ, Harrigan PR, Dong W, Poon AF, Heera J, Demarest J, Rinehart A,

Chapman D, Valdez H, Portsmouth S. Comparison of population and 454 "deep"

sequence analysis for HIV type 1 tropism versus the original trofile assay in

non-B subtypes. AIDS Res Hum Retroviruses. 2013 Jun;29(6):979-84. doi:

10.1089/aid.2012.0338. Epub 2013 Mar 6. PMID: 23350534; PMCID: PMC3653393.

37: Lee GQ, Swenson LC, Poon AF, Martin JN, Hatano H, Deeks SG, Harrigan PR.

Prolonged and substantial discordance in prevalence of raltegravir-resistant

HIV-1 in plasma versus PBMC samples revealed by 454 "deep" sequencing. PLoS One.

2012;7(9):e46181. doi: 10.1371/journal.pone.0046181. Epub 2012 Sep 26. PMID:

23049972; PMCID: PMC3458959.

38: Chao JD, Papavinasasundaram KG, Zheng X, Chávez-Steenbock A, Wang X, Lee GQ,

Av-Gay Y. Convergence of Ser/Thr and two-component signaling to coordinate

expression of the dormancy regulon in Mycobacterium tuberculosis. J Biol Chem.

2010 Sep 17;285(38):29239-46. doi: 10.1074/jbc.M110.132894. Epub 2010 Jul 14.

PMID: 20630871; PMCID: PMC2937955.