2015-2017

Resistance of Major Histocompatibility Complex Class B (MHC-B) to Nef-Mediated Downregulation Relative to that of MHC-A Is Conserved among Primate Lentiviruses and Influences Antiviral T Cell Responses in HIV-1-Infected Individuals. Mwimanzi F, Toyoda M, Mahiti M, Mann JK, Martin JN, Bangsberg D, Brockman MA, Goulder P, Kirchhoff F, Brumme ZL, Ndung'u T, Ueno T. J Virol. 2017 Dec 14;92(1):e01409-17. doi: 10.1128/JVI.01409-17. Print 2018 Jan 1.

Sociodemographic correlates of HIV drug resistance and access to drug resistance testing in British Columbia, Canada. Rocheleau G, Franco-Villalobos C, Oliveira N, Brumme ZL, Rusch M, Shoveller J, Brumme CJ, Harrigan PR. PLoS One. 2017 Sep 22;12(9):e0184848. doi: 10.1371/journal.pone.0184848. eCollection 2017.

Mapping the human T cell repertoire to recurrent driver mutations in MYD88 and EZH2 in lymphoma. Nielsen JS, Chang AR, Wick DA, Sedgwick CG, Zong Z, Mungall AJ, Martin SD, Kinloch NN, Ott-Langer S, Brumme ZL, Treon SP, Connors JM, Gascoyne RD, Webb JR, Berry BR, Morin RD, Macpherson N, Nelson BH. Oncoimmunology. 2017 Apr 28;6(7):e1321184. doi: 10.1080/2162402X.2017.1321184. eCollection 2017.

Potential for immune-driven viral polymorphisms to compromise antiretroviral-based preexposure prophylaxis for prevention of HIV-1 infection. 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. AIDS. 2017 Sep 10;31(14):1935-1943. doi: 10.1097/QAD.0000000000001575.

Mother-to-Child HIV Transmission Bottleneck Selects for Consensus Virus with Lower Gag-Protease-Driven Replication Capacity. Naidoo VL, Mann JK, Noble C, Adland E, Carlson JM, Thomas J, Brumme CJ, Thobakgale-Tshabalala CF, Brumme ZL, Brockman MA, Goulder PJR, Ndung'u T. J Virol. 2017 Aug 10;91(17):e00518-17. doi: 10.1128/JVI.00518-17. Print 2017 Sep 1.

Subtype-Specific Differences in Gag-Protease-Driven Replication Capacity Are Consistent with Intersubtype Differences in HIV-1 Disease Progression. 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. J Virol. 2017 Jun 9;91(13):e00253-17. doi: 10.1128/JVI.00253-17. Print 2017 Jul 1.

In vitro functional assessment of natural HIV-1 group M Vpu sequences using a universal priming approach. 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. J Virol Methods. 2017 Feb;240:32-41. doi: 10.1016/j.jviromet.2016.11.004. Epub 2016 Nov 16.

Sesterterpenoids Isolated from the Sponge Phorbas sp. Activate Latent HIV-1 Provirus Expression. Wang M, Tietjen I, Chen M, Williams DE, Daoust J, Brockman MA, Andersen RJ. J Org Chem. 2016 Nov 18;81(22):11324-11334. doi: 10.1021/acs.joc.6b02312. Epub 2016 Nov 4. PMID: 27768313

Novel Acylguanidine-Based Inhibitor of HIV-1. Mwimanzi P, Tietjen I, Miller SC, Shahid A, Cobarrubias K, Kinloch NN, Baraki B, Richard J, Finzi A, Fedida D, Brumme ZL, Brockman MA. J Virol. 2016 Sep 29;90(20):9495-508. doi: 10.1128/JVI.01107-16. Print 2016 Oct 15.

Afri-Can Forum 2 : Johannesburg, South Africa. 16-18 February 2015. BMC Infect Dis. 2016 Jul 12;16 Suppl 2(Suppl 2):315. doi: 10.1186/s12879-016-1466-6.

Croton megalobotrys Müll Arg. and Vitex doniana (Sweet): Traditional medicinal plants in a three-step treatment regimen that inhibit in vitro replication of HIV-1. Tietjen I, Gatonye T, Ngwenya BN, Namushe A, Simonambanga S, Muzila M, Mwimanzi P, Xiao J, Fedida D, Brumme ZL, Brockman MA, Andrae-Marobela K. J Ethnopharmacol. 2016 Sep 15;191:331-340. doi: 10.1016/j.jep.2016.06.040. Epub 2016 Jun 24.

Transmitted/Founder HIV-1 Subtype C Viruses Show Distinctive Signature Patterns in Vif, Vpr, and Vpu That Are Under Subsequent Immune Pressure During Early Infection. Rossenkhan R, MacLeod IJ, Brumme ZL, Magaret CA, Sebunya TK, Musonda R, Gashe BA, Edlefsen PT, Novitsky V, Essex M. AIDS Res Hum Retroviruses. 2016 Oct/Nov;32(10-11):1031-1045. doi: 10.1089/AID.2015.0330. Epub 2016 Jul 26.

Impact of pre-adapted HIV transmission. Carlson JM, Du VY, Pfeifer N, Bansal A, Tan VY, Power K, Brumme CJ, Kreimer A, DeZiel CE, Fusi N, Schaefer M, Brockman MA, Gilmour J, Price MA, Kilembe W, Haubrich R, John M, Mallal S, Shapiro R, Frater J, Harrigan PR, Ndung'u T, Allen S, Heckerman D, Sidney J, Allen TM, Goulder PJ, Brumme ZL, Hunter E, Goepfert PA. Nat Med. 2016 Jun;22(6):606-13. doi: 10.1038/nm.4100. Epub 2016 May 16.

HIV-1 Vpu Mediates HLA-C Downregulation. Apps R, Del Prete GQ, Chatterjee P, Lara A, Brumme ZL, Brockman MA, Neil S, Pickering S, Schneider DK, Piechocka-Trocha A, Walker BD, Thomas R, Shaw GM, Hahn BH, Keele BF, Lifson JD, Carrington M. Cell Host Microbe. 2016 May 11;19(5):686-95. doi: 10.1016/j.chom.2016.04.005.

Differences in the Selection Bottleneck between Modes of Sexual Transmission Influence the Genetic Composition of the HIV-1 Founder Virus. Tully DC, Ogilvie CB, Batorsky RE, Bean DJ, Power KA, Ghebremichael M, Bedard HE, Gladden AD, Seese AM, Amero MA, Lane K, McGrath G, Bazner SB, Tinsley J, Lennon NJ, Henn MR, Brumme ZL, Norris PJ, Rosenberg ES, Mayer KH, Jessen H, Kosakovsky Pond SL, Walker BD, Altfeld M, Carlson JM, Allen TM. PLoS Pathog. 2016 May 10;12(5):e1005619. doi: 10.1371/journal.ppat.1005619. eCollection 2016 May.

Diagnostic Accuracy of the HemoCue Hb 301, STAT-Site MHgb and URIT-12 Point-of-Care Hemoglobin Meters in a Central Laboratory and a Community Based Clinic in Durban, South Africa. Jaggernath M, Naicker R, Madurai S, Brockman MA, Ndung'u T, Gelderblom HC. PLoS One. 2016 Apr 5;11(4):e0152184. doi: 10.1371/journal.pone.0152184. eCollection 2016.

Rapid HIV-1 Disease Progression in Individuals Infected with a Virus Adapted to Its Host Population. Katoh J, Kawana-Tachikawa A, Shimizu A, Zhu D, Han C, Nakamura H, Koga M, Kikuchi T, Adachi E, Koibuchi T, Gao GF, Brumme ZL, Iwamoto A. PLoS One. 2016 Mar 8;11(3):e0150397. doi: 10.1371/journal.pone.0150397. eCollection 2016.

Relative Resistance of HLA-B to Downregulation by Naturally Occurring HIV-1 Nef Sequences. Mahiti M, Toyoda M, Jia X, Kuang XT, Mwimanzi F, Mwimanzi P, Walker BD, Xiong Y, Brumme ZL, Brockman MA, Ueno T. mBio. 2016 Jan 19;7(1):e01516-15. doi: 10.1128/mBio.01516-15.

Nef Proteins from HIV-1 Elite Controllers Are Inefficient at Preventing Antibody-Dependent Cellular Cytotoxicity. Alsahafi N, Ding S, Richard J, Markle T, Brassard N, Walker B, Lewis GK, Kaufmann DE, Brockman MA, Finzi A. J Virol. 2015 Dec 30;90(6):2993-3002. doi: 10.1128/JVI.02973-15.

Differential evolution of a CXCR4-using HIV-1 strain in CCR5wt/wt and CCR5∆32/∆32 hosts revealed by longitudinal deep sequencing and phylogenetic reconstruction. Le AQ, Taylor J, Dong W, McCloskey R, Woods C, Danroth R, Hayashi K, Milloy MJ, Poon AF, Brumme ZL. Sci Rep. 2015 Dec 3;5:17607. doi: 10.1038/srep17607.

Toward Personalized Lymphoma Immunotherapy: Identification of Common Driver Mutations Recognized by Patient CD8+ T Cells. Nielsen JS, Sedgwick CG, Shahid A, Zong Z, Brumme ZL, Yu S, Liu L, Kroeger DR, Treon SP, Connors JM, Gascoyne RD, Berry BR, Marra MA, Morin RD, Macpherson N, Nelson BH. Clin Cancer Res. 2016 May 1;22(9):2226-36. doi: 10.1158/1078-0432.CCR-15-2023. Epub 2015 Dec 2.

A strong association of human leukocyte antigen-associated Pol and Gag mutations with clinical parameters in HIV-1 subtype A/E infection. Van Tran G, Chikata T, Carlson JM, Murakoshi H, Nguyen DH, Tamura Y, Akahoshi T, Kuse N, Sakai K, Sakai S, Cobarrubias K, Oka S, Brumme ZL, Van Nguyen K, Takiguchi M; NHTD Treatment-Naive Cohort Study Group. AIDS. 2016 Mar 13;30(5):681-9. doi: 10.1097/QAD.0000000000000969.

Lack of a significant impact of Gag-Protease-mediated HIV-1 replication capacity on clinical parameters in treatment-naive Japanese individuals. Sakai K, Chikata T, Brumme ZL, Brumme CJ, Gatanaga H, Oka S, Takiguchi M. Retrovirology. 2015 Nov 19;12:98. doi: 10.1186/s12977-015-0223-z.

Population-Level Immune-Mediated Adaptation in HIV-1 Polymerase during the North American Epidemic. Kinloch NN, MacMillan DR, Le AQ, Cotton LA, Bangsberg DR, Buchbinder S, Carrington M, Fuchs J, Harrigan PR, Koblin B, Kushel M, Markowitz M, Mayer K, Milloy MJ, Schechter MT, Wagner T, Walker BD, Carlson JM, Poon AF, Brumme ZL. J Virol. 2015 Nov 11;90(3):1244-58. doi: 10.1128/JVI.02353-15. Print 2016 Feb 1.

Challenges and Opportunities for T-Cell-Mediated Strategies to Eliminate HIV Reservoirs. Brockman MA, Jones RB, Brumme ZL. Front Immunol. 2015 Oct 2;6:506. doi: 10.3389/fimmu.2015.00506. eCollection 2015.

Unciaphenol, an Oxygenated Analogue of the Bergman Cyclization Product of Uncialamycin Exhibits Anti-HIV Activity. Williams DE, Bottriell H, Davies J, Tietjen I, Brockman MA, Andersen RJ. Org Lett. 2015 Nov 6;17(21):5304-7. doi: 10.1021/acs.orglett.5b02664. Epub 2015 Oct 14.

Consequences of HLA-B*13-Associated Escape Mutations on HIV-1 Replication and Nef Function. Shahid A, Olvera A, Anmole G, Kuang XT, Cotton LA, Plana M, Brander C, Brockman MA, Brumme ZL. J Virol. 2015 Nov;89(22):11557-71. doi: 10.1128/JVI.01955-15. Epub 2015 Sep 9.

A robust and scalable TCR-based reporter cell assay to measure HIV-1 Nef-mediated T cell immune evasion. Anmole G, Kuang XT, Toyoda M, Martin E, Shahid A, Le AQ, Markle T, Baraki B, Jones RB, Ostrowski MA, Ueno T, Brumme ZL, Brockman MA. J Immunol Methods. 2015 Nov;426:104-13. doi: 10.1016/j.jim.2015.08.010. Epub 2015 Aug 28.

Global Database-Driven Assessment of HIV-1 Adaptation to the Immune Repertoires of Human Populations. Karakas A, Brumme ZL, Poon AF. J Virol. 2015 Oct;89(20):10693-5. doi: 10.1128/JVI.01355-15. Epub 2015 Aug 5.

Differential Ability of Primary HIV-1 Nef Isolates To Downregulate HIV-1 Entry Receptors. Toyoda M, Ogata Y, Mahiti M, Maeda Y, Kuang XT, Miura T, Jessen H, Walker BD, Brockman MA, Brumme ZL, Ueno T. J Virol. 2015 Sep;89(18):9639-52. doi: 10.1128/JVI.01548-15. Epub 2015 Jul 15.

Dynamic range of Nef-mediated evasion of HLA class II-restricted immune responses in early HIV-1 infection. Mahiti M, Brumme ZL, Jessen H, Brockman MA, Ueno T. Biochem Biophys Res Commun. 2015 Jul 31;463(3):248-54. doi: 10.1016/j.bbrc.2015.05.038. Epub 2015 May 19.

Geographic and temporal trends in the molecular epidemiology and genetic mechanisms of transmitted HIV-1 drug resistance: an individual-patient- and sequence-level meta-analysis. Rhee SY, Blanco JL, Jordan MR, Taylor J, Lemey P, Varghese V, Hamers RL, Bertagnolio S, Rinke de Wit TF, Aghokeng AF, Albert J, Avi R, Avila-Rios S, Bessong PO, Brooks JI, Boucher CA, Brumme ZL, Busch MP, Bussmann H, Chaix ML, Chin BS, D'Aquin TT, De Gascun CF, Derache A, Descamps D, Deshpande AK, Djoko CF, Eshleman SH, Fleury H, Frange P, Fujisaki S, Harrigan PR, Hattori J, Holguin A, Hunt GM, Ichimura H, Kaleebu P, Katzenstein D, Kiertiburanakul S, Kim JH, Kim SS, Li Y, Lutsar I, Morris L, Ndembi N, Ng KP, Paranjape RS, Peeters M, Poljak M, Price MA, Ragonnet-Cronin ML, Reyes-Terán G, Rolland M, Sirivichayakul S, Smith DM, Soares MA, Soriano VV, Ssemwanga D, Stanojevic M, Stefani MA, Sugiura W, Sungkanuparph S, Tanuri A, Tee KK, Truong HM, van de Vijver DA, Vidal N, Yang C, Yang R, Yebra G, Ioannidis JP, Vandamme AM, Shafer RW. PLoS Med. 2015 Apr 7;12(4):e1001810. doi: 10.1371/journal.pmed.1001810. eCollection 2015 Apr.

Screening of the Pan-African natural product library identifies ixoratannin A-2 and boldine as novel HIV-1 inhibitors. Tietjen I, Ntie-Kang F, Mwimanzi P, Onguéné PA, Scull MA, Idowu TO, Ogundaini AO, Meva'a LM, Abegaz BM, Rice CM, Andrae-Marobela K, Brockman MA, Brumme ZL, Fedida D. PLoS One. 2015 Apr 1;10(4):e0121099. doi: 10.1371/journal.pone.0121099. eCollection 2015.

Modest attenuation of HIV-1 Vpu alleles derived from elite controller plasma. Chen J, Tibroni N, Sauter D, Galaski J, Miura T, Alter G, Mueller B, Haller C, Walker BD, Kirchhoff F, Brumme ZL, Ueno T, Fackler OT. PLoS One. 2015 Mar 20;10(3):e0120434. doi: 10.1371/journal.pone.0120434. eCollection 2015.

Anti-APOBEC3G activity of HIV-1 Vif protein is attenuated in elite controllers. Kikuchi T, Iwabu Y, Tada T, Kawana-Tachikawa A, Koga M, Hosoya N, Nomura S, Brumme ZL, Jessen H, Pereyra F, Trocha A, Walker BD, Iwamoto A, Tokunaga K, Miura T. J Virol. 2015 May;89(9):4992-5001. doi: 10.1128/JVI.03464-14. Epub 2015 Feb 25.

HIV-1 adaptation to HLA: a window into virus-host immune interactions. Carlson JM, Le AQ, Shahid A, Brumme ZL. Trends Microbiol. 2015 Apr;23(4):212-24. doi: 10.1016/j.tim.2014.12.008. Epub 2015 Jan 19.

Immune screening identifies novel T cell targets encoded by antisense reading frames of HIV-1. Berger CT, Llano A, Carlson JM, Brumme ZL, Brockman MA, Cedeño S, Harrigan PR, Kaufmann DE, Heckerman D, Meyerhans A, Brander C. J Virol. 2015 Apr;89(7):4015-9. doi: 10.1128/JVI.03435-14. Epub 2015 Jan 14.