CFAR-Supported Papers, 2016


Papers published in 2016 that acknowledged the SD CFAR

Altice FL, Azbel L, Stone J, Brooks-Pollock E, Smyrnov P, Dvoriak S, Taxman FS, El-Bassel N, Martin NK, Booth R, Stover H, Dolan K, Vickerman P. The perfect storm: incarceration and the high-risk environment perpetuating transmission of HIV, hepatitis C virus, and tuberculosis in Eastern Europe and Central Asia. Lancet. 2016;388(10050):1228-1248. PMCID 5087988

Ann HW, Jun S, Shin NY, Han S, Ahn JY, Ahn MY, Jeon YD, Jung IY, Kim MH, Jeong WY, Ku NS, Kim JM, Smith DM, Choi JY. Characteristics of resting-state functional connectivity in HIV-associated neurocognitive disorderPLoS One. 2016;11(4):e0153493. PMCID: 4841538

Berry SA, Fleishman JA, Yehia BR, Cheever LW, Hauck H, Korthuis PT, Mathews WC, Keruly J, Nijhawan AE, Agwu AL, Somboonwit C, Moore RD, Gebo KA, Network HIVR. Healthcare coverage for HIV provider visits before and after implementation of the Affordable Care ActClin Infect Dis. 2016;63(3):387-395. PMCID: 4946016

Boehme SA, Franz-Bacon K, DiTirro DN, Ly TW, Bacon KB. MAP3K19 Is a novel regulator of TGF-beta signaling that impacts bleomycin-induced lung injury and pulmonary fibrosisPLoS One. 2016;11(5):e0154874. PMCID: 4856290

Director's Choice, January 2017! Borquez A, Cori A, Pufall EL, Kasule J, Slaymaker E, Price A, Elmes J, Zaba B, Crampin AC, Kagaayi J, Lutalo T, Urassa M, Gregson S, Hallett TB. The incidence patterns model to estimate the distribution of new HIV infections in Sub-Saharan Africa: Development and validation of a mathematical modelPLoS Med. 2016;13(9):e1002121. PMCID: 5021265

Bruner KM, Murray AJ, Pollack RA, Soliman MG, Laskey SB, Capoferri AA, Lai J, Strain MC, Lada SM, Hoh R, Ho YC, Richman DD, Deeks SG, Siliciano JD, Siliciano RF. Defective proviruses rapidly accumulate during acute HIV-1 infectionNat Med. 2016;22(9):1043-1049. PMCID: 5014606

Businge CB, Longo-Mbenza B, Mathews V. Risk factors for incident HIV infection among antenatal mothers in rural Eastern Cape, South Africa. Glob Health Action. 2016;9:29060.
PMCID: 4722038

Caceres CF, Borquez A, Klausner JD, Baggaley R, Beyrer C. Implementation of pre-exposure prophylaxis for human immunodeficiency virus infection: progress and emerging issues in research and policyJ Int AIDS Soc. 2016;19(7(Suppl 6)):21108. PMCID: 5071779

Cachay E, Soriano V. Is HIV still a special population for the treatment of hepatitis C? AIDS. 2016;30(12):2001-2003. PMCID: 4955702

Chaillon A, Hoenigl M, Mehta SR, Weibel N, Little SJ, Smith DM. A practical online tool to estimate antiretroviral coverage for HIV infected and susceptible populations needed to reduce local HIV epidemics. Sci Rep. 2016;6:28707. PMCID: 4919622

Chin BS, Chaillon A, Mehta SR, Wertheim JO, Kim G, Shin HS, Smith DM. Molecular epidemiology identifies HIV transmission networks associated with younger age and heterosexual exposure among Korean individualsJ Med Virol. 2016:[Epub ahead of print].

Chin BS, Kim JY, Gianella S, Lee M. Travel pattern and prescription analysis at a single travel clinic specialized for yellow fever vaccination in South KoreaInfect Chemother. 2016;48(1):20-30. PMCID: 4835431

Choi JY, Chaillon A, Oh JO, Ahn JY, Ann HW, Jung IY, Ahn MY, Jeon YD, Ku NS, Smith DM, Kim JM. HIV migration between blood plasma and cellular subsets before and after HIV therapy. J Med Virol. 2016;88(4):606-613. PMCID: 4731240

Colman RE, Anderson J, Lemmer D, Lehmkuhl E, Georghiou SB, Heaton H, Wiggins K, Gillece JD, Schupp JM, Catanzaro DG, Crudu V, Cohen T, Rodwell TC, Engelthaler DM. Rapid drug susceptibility testing of drug-resistant Mycobacterium tuberculosis isolates directly from clinical samples by use of amplicon sequencing: a proof-of-concept studyJ Clin Microbiol. 2016;54(8):2058-2067. PMCID: PMC Journal - in process

Conners EE, Vinetz JM, Weeks JR, Brouwer KC. A global systematic review of Chagas disease prevalence among migrantsActa Trop. 2016;156:68-78. PMC Journal - in process.

Dan JM, Massanella M, Smith DM, Spina CA, Schrier R, Daar ES, Dube MP, Morris SR, Gianella S. Effect of cytomegalovirus and HIV transcription on CD57 and PD-1 T cell expression during suppressive ART.J Acquir Immune Defic Syndr. 2016;72(2):133-7. PMCID: 4868660

Day TR, Smith DM, Heaton RK, Franklin D, Tilghman MW, Letendre S, Jin H, Wu Z, Shi C, Yu X, Perez-Santiago J. Subtype associations with HIV-associated neurocognitive disorder in ChinaJ Neurovirol. 2016;22(2):246-250. PMCID: 4769127

de Almeida SM, Rotta I, Jiang Y, Li X, Raboni SM, Ribeiro CE, Smith D, Potter M, Vaida F, Letendre S, Ellis RJ, and the HNRC Group. Biomarkers of chemotaxis and inflammation in cerebrospinal fluid and serum in individuals with HIV-1 subtype C versus BJ Neurovirol. 2016;22(6):715-724. PMCID: 5130607

Dillon SM, Lee EJ, Kotter CV, Austin GL, Gianella S, Siewe B, Smith DM, Landay AL, McManus MC, Robertson CE, Frank DN, McCarter MD, Wilson CC. Gut dendritic cell activation links an altered colonic microbiome to mucosal and systemic T-cell activation in untreated HIV-1 infectionMucosal Immunol. 2016;9(1):24-37. PMCID: 4626441

Ene L, Voinea C, Stefanescu C, Sima D, Duiculescu D, Mehta SR. Cervical HPV infection in Romanian women infected with HIV during early childhoodInt J STD AIDS. 2016;27(12):1079-1085. PMCID: PMC Journal - in process.

Freeman ML, Lederman MM, Gianella S. Partners in crime: The role of CMV in immune dysregulation and clinical outcome during HIV infectionCurr HIV/AIDS Rep. 2016;13(1):10-19. PMCID: 5079703

Freeman ML, Mudd JC, Shive CL, Younes SA, Panigrahi S, Sieg SF, Lee SA, Hunt PW, Calabrese LH, Gianella S, Rodriguez B, Lederman MM. CD8 T-cell expansion and inflammation linked to CMV coinfection in ART-treated HIV infectionClin Infect Dis. 2016;62(3):392-396. PMCID: 4706630

Geiger R, Smith DM, Little SJ, Mehta SR. Validation of the GeneXpert(R) CT/NG assay for use with male pharyngeal and rectal swabsAustin J HIV AIDS Res. 2016;3(1). PMCID: 4985020

Gianella S, Anderson CM, Var SR, Oliveira MF, Lada SM, Vargas MV, Massanella M, Little SJ, Richman DD, Strain, MC, Perez-Santiago J, Smith DM. Replication of human herpesviruses is associated with higher HIV DNA levels during antiretroviral therapy started at early phases of HIV infectionJ Virol. 2016:90(8);3944-3952. PMCID: 4810527

Gianella S, Ginocchio CC, Daar ES, Dube MP, Morris SR. Genital Epstein Barr Virus is associated with higher prevalence and persistence of anal human papillomavirus in HIV-infected men on antiretroviral therapyBMC infectious diseases. 2016;16:24. PMCID: 4727320

Gianella S, Kosakovsky Pond SL, Oliveira MF, Scheffler K, Strain MC, De la Torre A, Letendre S, Smith DM, Ellis RJ. Compartmentalized HIV rebound in the central nervous system after interruption of antiretroviral therapyVirus Evol. 2016;2(2):vew020. PMCID: 5072458

Gianella S, Letendre S. Cytomegalovirus and HIV: A dangerous pas de deuxJ Infect Dis. 2016;214 Suppl 2:S67-74. PMCID: 5021239

Gianella S, Tsibris A, Barr L, Godfrey C. Barriers to a cure for HIV in womenJ Int AIDS Soc. 2016;19(1):20706. PMCID: 4761692

Glinka ER, Smith DM, Johns ST. Timing matters - Influenza vaccination to HIV-infected patientsHIV Med. 2016;17(8):601-604. PMCID: 4960000

Günthard HF, Saag MS, Benson CA, del Rio C, Eron JJ, Gallant JE, Hoy JF, Mugavero MJ, Sax PE, Thompson MA, Gandhi RT, Landovitz RJ, Smith DM, Jacobsen DM, Volberding PA. Antiretroviral drugs for treatment and prevention of HIV infection in adults: 2016 recommendations of the International Antiviral Society-USA PanelJAMA. 2016;316(2):191-210.

Harris RJ, Martin NK, Rand E, Mandal S, Mutimer D, Vickerman P, Ramsay ME, De Angelis D, Hickman M, Harris HE. New treatments for hepatitis C virus (HCV): scope for preventing liver disease and HCV transmission in EnglandJ Viral Hepat. 2016;23(8):631-643. PMCID: 4982023

Henry BL, Moore DJ. Preliminary findings describing participant experience with iSTEP, an mHealth intervention to increase physical activity and improve neurocognitive function in people living with HIV.J Assoc Nurses AIDS Care. 2016;S1055-3290(16): 2-9. PMCID: 4903897

Hoenigl M, Chaillon A, Kessler HH, Haas B, Stelzl E, Weninger K, Little SJ, Mehta SR. Characterization of HIV transmission in south-east AustriaPLoS One. 2016;11(3):e0151478. PMCID: 4788428

Hoenigl M, Chaillon A, Little, SJ. CD4/CD8 cell ratio in acute HIV infection and the impact of early antiretroviral therapy. Clin Infect Dis. 2016;63(3):425-426. PMCID: 4946020

Hoenigl M, Chaillon A, Moore DJ, Morris SR, Mehta SR, Gianella S, Amico KR, Little SJ. Rapid HIV viral load suppression in those initiating antiretroviral therapy at first visit after HIV diagnosisSci Rep. 2016;6:32947. PMCID: 5011704

Hoenigl M, Green N, Camacho M, Gianella S, Mehta SR, Smith DM, Little SJ. Signs or symptoms of acute HIV infection in a cohort undergoing community-based screeningEmerg Infect Dis. 2016;22(3):532-534. PMCID: 4766914

Hoenigl M, Oliveira MF, Perez-Santiago J, Zhang Y, Morris S, McCutchan AJ, Finkelman M, Marcotte TD, Ellis RJ, Gianella S. (1-->3)-beta-D-glucan levels correlate with neurocognitive functioning in HIV-infected persons on suppressive antiretroviral therapy: a cohort studyMedicine (Baltimore). 2016;95(11):e3162. PMCID: 4839954

Hoenigl M, Perez-Santiago J, Nakazawa M, de Oliveira MF, Zhang Y, Finkelman MA, Letendre S, Smith D, Gianella S. (1-->3)-beta-d-Glucan: A biomarker for microbial translocation in individuals with acute or early HIV infection? Front Immunol. 2016;7:404. PMCID: 5046804

Innes S, Abdullah KL, Haubrich R, Cotton MF, Browne SH. High prevalence of dyslipidemia and insulin resistance in HIV-infected prepubertal African children on antiretroviral therapyPediatr Infect Dis J. 2016;35(1):e1-7. PMCID: 4707556

Karris MY, Jain S, Bowman VQ, Rieg G, Goicoechea M, Dube MP, Kerkar S, Kemper C, Diamond C, Sun X, Daar ES, Haubrich RH, Morris S, California Collaborative Treatment Group 589 Study Team. Nucleoside-sparing regimens with raltegravir and a boosted protease inhibitor: an unsettled issueJ Acquir Immune Defic Syndr. 2016;72(2):e48-50. PMCID 4867124

Karris MY, Umlauf A, Vaida F, Richman D, Little S, Smith D. A randomized controlled clinical trial on the impact of CCR5 blockade with maraviroc in early infection on T-cell dynamicsMedicine (Baltimore). 2016;95(44):e5315. PMCID: PMC Journal - in process.

Kassanjee R, Pilcher CD, Busch MP, Murphy G, Facente SN, Keating SM, McKinney E, Marson K, Price MA, Martin JN, Little SJ, Hecht FM, Kallas EG, Welte A, Consortium for the Evaluation and Performance of HIV Incidence Assays (CEPHIA). Viral load criteria and threshold optimization to improve HIV incidence assay characteristicsAIDS. 2016;30(15):2361-2371. PMCID: 5024345

Kong L, Ju B, Chen Y, He L, Ren L, Liu J, Hong K, Su B, Wang Z, Ozorowski G, Ji X, Hua Y, Chen Y, Deller MC, Hao Y, Feng Y, Garces F, Wilson R, Dai K, O'Dell S, McKee K, Mascola JR, Ward AB, Wyatt RT, Li Y, Wilson IA, Zhu J, Shao Y. Key gp120 glycans pose roadblocks to the rapid development of VRC01-class antibodies in an HIV-1-infected Chinese donorImmunity. 2016;44(4):939-950. PMCID: 4862659

Lee SA, Bacchetti P, Chomont N, Fromentin R, Lewin SR, O'Doherty U, Palmer S, Richman DD, Siliciano JD, Yukl SA, Deeks SG, Burbelo PD. Anti-HIV antibody responses and the HIV reservoir size during antiretroviral therapyPLoS One. 2016;11(8):e0160192. PMCID: 4970722

Lee L, Yehia BR, Gaur AH, Rutstein R, Gebo K, Keruly JC, Moore RD, Nijhawan AE, Agwu AL, Network HR. The impact of youth-friendly structures of care on retention among HIV-infected youthAIDS Patient Care STDS. 2016;30(4):170-177. PMCID: 4827281

Logan C, Todorof K, Fiorillo SP, Campbell TB, Elder JH, Borok M, Gudza I, Gwanzura L, Ndemera B, Lochhead MJ, Benson CA, Schooley RT. Rapid multiplexed immunoassay for detection of antibodies to Kaposi's Sarcoma-associated HerpesvirusPLoS One. 2016;11(9):e0163616. PMCID: 5036886

Martin NK, Thornton A, Hickman M, Sabin C, Nelson M, Cooke GS, Martin TC, Delpech V, Ruf M, Price H, Azad Y, Thomson EC, Vickerman P. Can Hepatitis C Virus (HCV) direct-acting antiviral treatment as prevention reverse the HCV epidemic among men who have sex with men in the United Kingdom? Epidemiological and modeling insightsClin Infect Dis. 2016;62(9):1072-1080. PMCID: 4826456

Martin NK, Vickerman P, Brew IF, Williamson J, Miners A, Irving WL, Saksena S, Hutchinson SJ, Mandal S, O'Moore E, Hickman M. Is increased HCV case-finding combined with current or 8-12 week DAA therapy cost-effective in UK prisons? A prevention benefit analysisHepatology. 2016;63(6):1796-808. PMCID: 4920048

Martin NK, Vickerman P, Dore GJ, Grebely J, Miners A, Cairns J, Foster GR, Hutchinson SJ, Goldberg DJ, Martin TC, Ramsay M, Consortium S-H, Hickman M. Prioritization of HCV treatment in the direct-acting antiviral era: An economic evaluationJ Hepatol. 2016;65(1):17-25. PMCID: 4914770

Martin NK, Vickerman P, Hickman M, Patterson TL, Rand E, Abramovitz D, Strathdee SA. Overlapping substance using high-risk groups and infectious diseases: how dynamic modelling can evaluate risk and target HIV preventionAddiction. 2016:[Epub ahead of print].

Massanella M, Richman DD. Measuring the latent reservoir in vivoJ Clin Invest. 2016;126(2):464-472. PMCID: 4731179

Mehta SR, Murrell B, Anderson CM, Kosakovsky Pond SL, Wertheim JO, Young JA, Freitas L, Richman DD, Mathews WC, Scheffler K, Little SJ, Smith DM. Using HIV sequence and epidemiologic data to assess the effect of self-referral testing for acute HIV infection on incident diagnoses in San Diego, CaliforniaClin Infect Dis. 2016;63(1):101-107. PMCID: 4901863

Milam J, Morris S, Jain S, Sun X, Dube MP, Daar ES, Jimenez G, Haubrich R, and the CCTG 592 Team. Randomized controlled trial of an internet application to reduce HIV transmission behavior among HIV infected men who have sex with menAIDS Behav. 2016;20(6):1173-1181. PMCID: 4838553

Mittal ML, Beletsky L, Patino E, Abramovitz D, Rocha T, Arredondo J, Banuelos A, Rangel G, Strathdee SA. Prevalence and correlates of needle-stick injuries among active duty police officers in Tijuana, MexicoJ Int AIDS Soc. 2016;19(4 Suppl 3):20874. PMCID: 4951532

Nason MC, Patel EU, Kirkpatrick AR, Prodger JL, Shahabi K, Tobian AA, Gianella S, Kalibbala S, Ssebbowa P, Kaul R, Gray RH, Quinn TC, Serwadda D, Reynolds SJ, Redd AD. Immunological signaling during herpes simplex virus-2 and cytomegalovirus vaginal shedding after initiation of antiretroviral treatmentOpen Forum Infect Dis. 2016;3(2):ofw073. PMCID: 4867667

Nikam C, Patel R, Sadani M, Ajbani K, Kazi M, Soman R, Shetty A, Georghiou SB, Rodwell TC, Catanzaro A, Rodrigues C. Redefining MTBDRplus test results: what do indeterminate results actually mean? Int J Tuberc Lung Dis. 2016;20(2):154-159. PMCID: 4874811

Panichsillapakit T, Patel D, Santangelo J, Richman DD, Little SJ, Smith DM. Colorectal disorders in acute human immunodeficiency virus infection: a case seriesOpen Forum Infect Dis. 2016;3(1):ofw014. PMCID: 4766383

Panichsillapakit T, Smith DM, Wertheim JO, Richman DD, Little SJ, Mehta SR. Prevalence of transmitted HIV drug resistance among recently infected persons in San Diego, California 1996-2013J Acquir Immune Defic Syndr. 2016;71(2):228-236. PMCID: 4712087

Perez-Santiago J, Schrier RD, de Oliveira MF, Gianella S, Var SR, Day TR, Ramirez-Gaona M, Suben JD, Murrell B, Massanella M, Cherner M, Smith DM, Ellis RJ, Letendre SL, Mehta SR. Cell-free mitochondrial DNA in CSF is associated with early viral rebound, inflammation, and severity of neurocognitive deficits in HIV infectionJ Neurovirol. 2016;22(2):191-200. PMCID: 4862614

Seifert M, Ajbani K, Georghiou SB, Catanzaro D, Rodrigues C, Crudu V, Victor TC, Garfein RS, Catanzaro A, Rodwell TC. A performance evaluation of MTBDRplus version 2 for the diagnosis of multidrug-resistant tuberculosisInt J Tuberc Lung Dis. 2016;20(5):631-637. PMCID: 4852300

Seifert M, Georghiou SB, Catanzaro D, Rodrigues C, Crudu V, Victor TC, Garfein RS, Catanzaro A, Rodwell TC. MTBDRplus and MTBDRsl assays: Absence of wild-type probe hybridization and implications for detection of drug-resistant tuberculosis. J Clin Microbiol. 2016;54(4):912-918. PMCID: 4809938

Smith LR, Patterson TL, Magis-Rodriguez C, Ojeda VD, Burgos JL, Rojas SA, Zuniga ML, Strathdee SA. Engagement in the HIV care continuum among key populations in Tijuana, MexicoAIDS Behav. 2016;20(5):1017-1025. PMCID: 4785089

Spies G, Ahmed-Leitao F, Fennema-Notestine C, Cherner M, Seedat S. Effects of HIV and childhood trauma on brain morphometry and neurocognitive functionJ Neurovirol. 2016;22(2):149-158. PMCID: 4959545

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. PMCID: 5157837

Stone J, Martin NK, Hickman M, Hellard M, Scott N, McBryde E, Drummer H, Vickerman P. The potential impact of a hepatitis C vaccine for people who inject drugs: Is a vaccine needed in the age of direct-acting antivirals? PLoS One. 2016;11(5):e0156213. PMCID: 4880220

Tokarev A, Stoneham C, Lewinski MK, Mukim A, Deshmukh S, Vollbrecht T, Spina CA, Guatelli J. Pharmacologic inhibition of Nedd8 activation enzyme exposes CD4-induced epitopes within Env on cells expressing HIV-1. J Virol. 2016;90(5):2486-2502. PMCID: 4810708

Toth M, Flandreau EI, Deslauriers J, Geyer MA, Mansuy IM, Merlo Pich E, Risbrough VB. Overexpression of forebrain CRH during early life increases trauma susceptibility in adulthoodNeuropsychopharmacology. 2016;41(6):1681-1690. PMCID: 4832031

Turner SS, Gianella S, Yip MJ, van Seggelen WO, Gillies RD, Foster AL, Barbati ZR, Smith DM, Fierer DS. Shedding of hepatitis C virus in semen of human immunodeficiency virus-infected menOpen Forum Infect Dis. 2016;3(2):ofw057. PMCID: 4866572

Vanpouille C, Introini A, Morris SR, Margolis L, Daar ES, Dube MP, Little SJ, Smith DM, Lisco A, Gianella S. Distinct cytokine/chemokine network in semen and blood characterize different stages of HIV infectionAIDS. 2016;30(2):193-201. PMCID: 4862605

Var SR, Day TR, Vitomirov A, Smith DM, Soontornniyomkij V, Moore DJ, Achim CL, Mehta SR, Perez-Santiago J. Mitochondrial injury and cognitive function in HIV infection and methamphetamine useAIDS. 2016;30(6):839-848. PMCID: 4785088

Voss JE, Macauley MS, Rogers KA, Villinger F, Duan L, Shang L, Fink EA, Andrabi R, Colantonio AD, Robinson JE, Johnson RP, Burton DR, Haase AT. Reproducing SIVDeltanef vaccine correlates of protection: trimeric gp41 antibody concentrated at mucosal front linesAIDS. 2016:30(16):2427-2438. PMCID: 5069161

Wagner GA, Chaillon A, Liu S, Franklin DR, Jr., Caballero G, Kosakovsky Pond SL, Vaida F, Heaton RK, Letendre SL, Grant I, Richman DD, Smith DM. HIV-associated neurocognitive disorder is associated with HIV-1 dual infectionAIDS. 2016;30(17):2591-2597. PMCID: 5083206

White CH, Moesker B, Beliakova-Bethell N, Martins LJ, Spina CA, Margolis DM, Richman DD, Planelles V, Bosque A, Woelk CH. Transcriptomic analysis implicates the p53 signaling pathway in the establishment of HIV-1 latency in central memory CD4 T cells in an in vitro model. PLoS Pathog. 2016;12(11):e1006026. PMCID: 5127598

Yek C, Gianella S, Plana M, Castro P, Scheffler K, Garcia F, Massanella M, Smith DM. Standard vaccines increase HIV-1 transcription during antiretroviral therapy. AIDS. 2016;30(15):2289-2298. PMCID: PMC Journal - in process

Yu V, Rahimy M, Korrapati A, Xuan Y, Zou AE, Krishnan AR, Tsui T, Aguilera JA, Advani S, Crotty Alexander LE, Brumund KT, Wang-Rodriguez J, Ongkeko WM. Electronic cigarettes induce DNA strand breaks and cell death independently of nicotine in cell linesOral Oncol. 2016;52:58-65. PMCID:4891196

Zhao J, Chen L, Chaillon A, Zheng C, Cai W, Yang Z, Li G, Gan Y, Wang X, Hu Y, Zhong P, Zhang C, Smith DM. The dynamics of the HIV epidemic among men who have sex with men (MSM) from 2005 to 2012 in Shenzhen, ChinaSci Rep. 2016;6:28703. PMCID: 4926087

At a Glance