CFAR-Supported Papers


How do I get my papers on the list?

If your research was supported through CFAR cores or grant funding, please include our grant number (P30 AI036214) in the funding or acknowledgements section of your papers. Follow these instructions and examples.

We'll add your papers to the list below when you notify us that they are in press or when we receive notice from the NIH. Who knows? One of your papers may be selected as the Directors' Choice on the CFAR home page.

Papers Supported by the San Diego CFAR


Beliakova-Bethell, Nadejda; Hezareh, Marjan; Wong, Joseph K; Strain, Matthew C; Lewinski, Mary K; Richman, Douglas D; Spina, Celsa A. Relative efficacy of T cell stimuli as inducers of productive HIV-1 replication in latently infected CD4 lymphocytes from patients on suppressive cART. Virology. 2017 Aug;508:127-133. PMID: 28527342. 

Boehme SA, Franz-Bacon K, Ludka J, DiTirro DN, Ly TW, Bacon KB. MAP3K19 Is Overexpressed in COPD and Is a Central Mediator of Cigarette Smoke-Induced Pulmonary Inflammation and Lower Airway Destruction. PLoS One. 2016;11(12):e0167169. PMID: 27935962. PMCID: 5147866

Cachay, Edward R; Agmas, Wollelaw; Christopher Mathews, Wm. Disparities in the clinical evolution of anal neoplasia in an HIV-infected cohort. J Racial Ethn Health Disparities. 2017 Mar 23. PMID: 28332090. PMCID: 5610590.

Carter, Christoph; Akrami, Kevan; Hall, Drew; Smith, Davey; Aronoff-Spencer, Eliah. Lyophilized visually readable loop-mediated isothermal reverse transcriptase nucleic acid amplification test for detection Ebola Zaire RNAJ Virol Methods. 2017 Jun;244:32-38. PMID: 28242293. PMCID: 5568651.

Caskey M, Schoofs T, Gruell H, Settler A, Karagounis T, Kreider EF, Murrell B, Pfeifer N, Nogueira L, Oliveira TY, Learn GH, Cohen YZ, Lehmann C, Gillor D, Shimeliovich I, Unson-O'Brien C, Weiland D, Robles A, Kummerle T, Wyen C, Levin R, Witmer-Pack M, Eren K, Ignacio C, Kiss S, West AP, Jr., Mouquet H, Zingman BS, Gulick RM, Keler T, Bjorkman PJ, Seaman MS, Hahn BH, Fatkenheuer G, Schlesinger SJ, Nussenzweig MC, Klein F. Antibody 10-1074 suppresses viremia in HIV-1-infected individualsNat Med. 2017;23(2):185-191. PMID: 28092665. PMCID: 5467219.

Chaillon A, Smith DM, Vanpouille C, Lisco A, Jordan P, Caballero G, Vargas M, Gianella S, Mehta SR. HIV trafficking between blood and semen during early untreated HIV infectionJ Acquir Immune Defic Syndr. 2017;74(1):95-102. PMCID: 5140710

Chaillon A, Nakazawa M, Wertheim JO, Little SJ, Smith DM, Mehta SR, Gianella S. No Substantial Evidence for Sexual Transmission of Minority HIV Drug Resistance Mutations in Men Who Have Sex with Men. J Virol. 2017;91(21). PMID: 28794047. PMCID: 5640831

Chaillon, Antoine; Essat, Asma; Frange, Pierre; Smith, Davey M; Delaugerre, Constance; Barin, Francis; Ghosn, Jade; Pialoux, Gilles; Robineau, Olivier; Rouzioux, Christine; Goujard, Cécile; Meyer, Laurence; Chaix, Marie-Laure; on behalf the ANRS PRIMO Cohort Study. Spatiotemporal dynamics of HIV-1 transmission in France (1999-2014) and impact of targeted prevention strategies. Retrovirology. 2017 Feb 21;14(1):15. PMID: 28222757. PMCID: 5322782.

de Almeida, Sergio M; Rotta, Indianara; Ribeiro, Clea E; Oliveira, Michelli F; Chaillon, Antoine; de Pereira, Ana Paula; Cunha, Ana Paula; Zonta, Marise; Bents, Joao França; Raboni, Sonia M; Smith, Davey; Letendre, Scott; Ellis, Ronald J. Dynamic of CSF and serum biomarkers in HIV-1 subtype C encephalitis with CNS genetic compartmentalization-case study. J Neurovirol. 2017 Jun;23(3):460-473. PMID: 28247269. PMCID: 5441962.

Drozd DR, Saag MS, Westfall AO, Mathews WC, Haubrich R, Boswell SL, Cole SR, Porter D, Kitahata MM, Juday T, Rosenblatt L, CFAR Network of Integrated Clinical Systems. Comparative effectiveness of single versus multiple tablet antiretroviral therapy regimens in clinical HIV practiceMedicine (Baltimore). 2017;96(14):e6275. PMID: 28383402. PMCID: 5411186.

Fatukasi TV, Cole SR, Moore RD, Mathews WC, Edwards JK, Eron JJ, and the CNICS investigators. Risk factors for delayed antiretroviral therapy initiation among HIV-seropositive patientsPLoS One. 2017;12(7):e0180843. PMID: 28700693. PMCID: 5507276.

Fraser, Hannah; Zibbell, Jon; Hoerger, Thomas; Hariri, Susan; Vellozzi, Claudia; Martin, Natasha K; Kral, Alex H; Hickman, Matthew; Ward, John W; Vickerman, Peter. Scaling up HCV prevention and treatment interventions in rural USA - model projections for tackling an increasing epidemic. Addiction. 2017 Jul 22. PMID: 28734093. 

Gianella S, Chaillon A, Mutlu EA, Engen PA, Voigt RM, Keshavarzian A, Losurdo J, Chakradeo P, Lada SM, Nakazawa M, Landay AL. Effect of cytomegalovirus and Epstein-Barr virus replication on intestinal mucosal gene expression and microbiome composition of HIV-infected and uninfected individuals. AIDS. 2017;31(15):2059-2067.PMID: 28906277 PMCID: 5654609

Gianella S, Taylor J, Brown TR, Kaytes A, Achim CL, Moore DJ, Little SJ, Ellis RJ, Smith DM. Can research at the end of life be a useful tool to advance HIV cure? AIDS. 2017;31(1):1-4. PMCID: 5137789

Gountas, Ilias; Sypsa, Vana; Anagnostou, Olga; Martin, Natasha; Vickerman, Peter; Kafetzopoulos, Evangelos; Hatzakis, Angelos. Treatment and primary prevention in people who inject drugs for chronic hepatitis C infection: is elimination possible in a high-prevalence setting? Addiction. 2017 Jul;112(7):1290-1299. PMID: 28107585. PMCID: 5553636. 

Graves SK, Little SJ, Hoenigl M. Risk profile and HIV testing outcomes of women undergoing community-based testing in San Diego 2008-2014Sci Rep. 2017;7:42183. PMID: 28165056. PMCID: 5292713.

Green N, Hoenigl M, Chaillon A, Anderson CM, Kosakovsky Pond SL, Smith DM, Little SJ. Partner services in adults with acute and early HIV infectionAIDS. 2017;31(2):287-293. PMCID: 5177524

Hartzler, Bryan; Carlini, Beatriz H; Newville, Howard; Crane, Heidi M; Eron, Joseph J; Geng, Elvin H; Mathews, W Christopher; Mayer, Kenneth H; Moore, Richard D; Mugavero, Michael J; Napravnik, Sonia; Rodriguez, Benigno; Donovan, Dennis M. Identifying HIV care enrollees at-risk for cannabis use disorder. AIDS Care. 2017 Jul;29(7):846-850. PMID: 28006972. PMCID: 5573588 

Hickman M, Martin NK, Huxtable R. Hepatitis C virus prevention and treatment prioritization-ethical, economic and evidential dimensions of early rather than delayed treatment for people who inject drugsAddiction. 2017;112(2):201-203. PMCID: 5233591

Hoenigl M, Braun DL, Kouyos R, Gunthard HF, Little SJ. Evaluation of the predictive potential of the short acute retroviral syndrome severity score for HIV-1 disease progression in individuals with acute HIV infection. J Acquir Immune Defic Syndr. 2017;74(4):e114-e117. PMID: 28225720. PMCID: 5324781.

Hoenigl, Martin; Braun, Dominique L; Kouyos, Roger; Günthard, Huldrych F; Little, Susan J. Evaluation of the Predictive Potential of the Short Acute Retroviral Syndrome Severity Score for HIV-1 Disease Progression in Individuals With Acute HIV Infection. J Acquir Immune Defic Syndr. 2017 Apr 1;74(4):e114-e117. PMID: 28225720. PMCID: 5324781.

Innes S, van Toorn R, Otwombe K, Dobbels E, van Zyl G, Cotton MF, Laughton B. Late onset HIV encephalopathy in children with long-standing virologic suppression followed by slow spontaneous recovery despite no change in antiretroviral therapy - four case reportsPediatr Infect Dis J. 2017:[Epub ahead of print]  doi: 10.1097/INF.0000000000001694. PMID: 28719495. 

Johnson CE, Crawford BE, Stavridis M, Ten Dam G, Wat AL, Rushton G, Ward CM, Wilson V, van Kuppevelt TH, Esko JD, Smith A, Gallagher JT, Merry CL. Essential alterations of heparan sulfate during the differentiation of embryonic stem cells to Sox1-enhanced green fluorescent protein-expressing neural progenitor cells. Stem Cells. 2007;25(8):1913-1923. PMID: 17464092

Karris, Maile Y; Jain, Sonia; Day, Tyler R C; Pérez-Santiago, Josué; Goicoechea, Miguel; Dubé, Michael P; Sun, Xiaoying; Spina, Celsa; Daar, Eric S; Haubrich, Richard H; Morris, Sheldon; California Collaborative Treatment Group (CCTG) 589 Study Team. HIV viral kinetics and T cell dynamics in antiretroviral naïve persons starting an integrase strand transfer inhibitor and protease inhibitor regimen. HIV Clin Trials. 2017 Mar;18(2):67-74. PMID: 28134057. PMCID: 5613656.

Martin, Natasha K; Skaathun, Britt; Vickerman, Peter; Stuart, David. Modeling combination HCV prevention among HIV-infected men who have sex with men and people who inject drugs. AIDS Rev. 2017 Apr - Jun;19(2):97-104. PMID: 28534885. PMCID: 5560483. 

Martin, Natasha K; Vickerman, Peter; Hickman, Matthew. How to eliminate HCV infection by antiviral treatment. J Hepatol. 2017 Jul;67(1):5-6. PMID: 28323120. 

Oliveira MF, Chaillon A, Nakazawa M, Vargas M, Letendre SL, Strain MC, Ellis RJ, Morris S, Little SJ, Smith DM, Gianella S. Early antiretroviral therapy is associated with lower HIV DNA molecular diversity and lower inflammation in cerebrospinal fluid but does not prevent the establishment of compartmentalized HIV DNA populationsPLoS Pathog. 2017;13(1):e1006112. PMCID: 5266327

Osorio G, Hoenigl M, Quartarolo J, Barger K, Morris SR, Reed SL, Lee J, Little SJ. Evaluation of opt-out inpatient HIV screening at an urban teaching hospitalAIDS Care. 2017:1-5. PMID: 28114789. PMCID: 5469710.

Patel, Eshan U; Gianella, Sara; Newell, Kevin; Tobian, Aaron A R; Kirkpatrick, Allison R; Nalugoda, Fredrick; Grabowski, Mary K; Gray, Ronald H; Serwadda, David; Quinn, Thomas C; Redd, Andrew D; Reynolds, Steven J. Elevated cytomegalovirus IgG antibody levels are associated with HIV-1 disease progression and immune activation. AIDS. 2017 Mar 27;31(6):807-813. PMID: 28121712. PMCID: 5352830. 

Spies G, Fennema-Notestine C, Cherner M, Seedat S. Changes in cognitive function in women with HIV infection and early life stressAIDS Care. 2017;29(1):14-23. PMID: 27396980. PMCID: 5157837.

Stoneham, Charlotte A; Singh, Rajendra; Jia, Xiaofei; Xiong, Yong; Guatelli, John. Endocytic activity of HIV-1 Vpu: Phosphoserine-dependent interactions with clathrin adaptors. Traffic. 2017 Aug;18(8):545-561. PMID: 28504462. PMCID: 5600163.

Vesa, Jouni; Chaillon, Antoine; Wagner, Gabriel A; Anderson, Christy M; Richman, Douglas D; Smith, Davey M; Little, Susan J. Increased HIV-1 superinfection risk in carriers of specific human leukocyte antigen alleles. AIDS. 2017 May 15;31(8):1149-1158. PMID: 28244954. PMCID: 5559224.

Vitomirov A, Ramirez-Gaona M, Mehta SR, Perez-Santiago J. Random shearing as an alternative to digestion for mitochondrial DNA processing in droplet digital PCRMitochondrion. 2017;32:16-18. PMID: 27838478. PMCID: 5218872.

Wagner, Gabriel A; Landais, Elise; Caballero, Gemma; Phung, Pham; Kosakovsky Pond, Sergei L; Poignard, Pascal; Richman, Douglas D; Little, Susan J; Smith, Davey M. Intrasubtype B HIV-1 superinfection correlates with delayed neutralizing antibody response. J Virol. 2017 Aug 10;91(17). PMID: 28615205. PMCID: 5553187.

Wertheim JO, Kosakovsky Pond SL, Forgione LA, Mehta SR, Murrell B, Shah S, Smith DM, Scheffler K, Torian LV. Social and genetic networks of HIV-1 transmission in New York CityPLoS Pathog. 2017;13(1):e1006000. PMCID: 5221827.


At a Glance