| Query Trace: Hiv[orginal query] |
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| Phylogenetic methods inconsistently predict direction of HIV transmission among heterosexual pairs in the HPTN052 cohort. Rebecca Rose, Matthew Hall, Andrew D Redd, Susanna Lamers, Andrew E Barbier, Stephen F Porcella, Sarah E Hudelson, Estelle Piwowar-Manning, Marybeth McCauley, Theresa Gamble, Ethan A Wilson, Johnstone Kumwenda, Mina C Hosseinipour, James G Hakim, Nagalingeswaran Kumarasamy, Suwat Chariyalertsak, Jose H Pilotto, Beatriz Grinsztejn, Lisa A Mills, Joseph Makhema, Breno R Santos, Ying Q Chen, Thomas C Quinn, Christophe Fraser, Myron S Cohen, Susan H Eshleman, and Oliver Laeyendecker The Journal of infectious diseases 2018 Dec |
| Maintenance and reappearance of extremely divergent intra-host HIV-1 variants. Joel O Wertheim, Alexandra M Oster, Ben Murrell, Neeraja Saduvala, Walid Heneine, William M Switzer, and Jeffrey A Johnson Virus evolution 2018 Jul (2) vey030 |
| Diagnosis of Human Immunodeficiency Virus Infection. Bharat S Parekh, Chin-Yih Ou, Peter N Fonjungo, Mireille B Kalou, Erin Rottinghaus, Adrian Puren, Heather Alexander, Mackenzie Hurlston Cox, and John N Nkengasong Clinical microbiology reviews 2019 Jan (1) |
| A large HCV transmission network enabled a fast-growing HIV outbreak in rural Indiana, 2015. Sumathi Ramachandran, Hong Thai, Joseph C Forbi, Romeo Regi Galang, Zoya Dimitrova, Guo-Liang Xia, Yulin Lin, Lili T Punkova, Pamela R Pontones, Jessica Gentry, Sara J Blosser, Judith Lovchik, William M Switzer, Eyasu Teshale, Philip Peters, John Ward, Yury Khudyakov, and EBioMedicine 2018 Nov |
| Completeness of HIV nucleotide sequence ascertainment and its potential impact on understanding HIV transmission - Maryland, 2011-2013. Richard B Brooks, Katherine A Feldman, David Blythe, and Colin Flynn AIDS care 2018 Nov 1-8 |
| Estimating effects of HIV sequencing data completeness on transmission network patterns and detection of growing HIV transmission clusters. Sharoda Dasgupta, Anne Marie France, Mary-Grace Brandt, Jennifer Reuer, Tianchi Zhang, Nivedha Panneer, Angela L Hernandez, and Alexandra M Oster AIDS research and human retroviruses 2018 Nov |
| HIV-genetic diversity and drug resistance transmission clusters in Gondar, Northern Ethiopia, 2003-2013. Dawit Assefa Arimide, Almaz Abebe, Yenew Kebede, Fekadu Adugna, Tesfaye Tilahun, Desta Kassa, Yibeltal Assefa, Taye Tolera Balcha, Per Björkman, and Patrik Medstrand PloS one 2018 13(10) e0205446 |
| Identifying Clusters of Recent and Rapid HIV Transmission Through Analysis of Molecular Surveillance Data. Alexandra M Oster, Anne Marie France, Nivedha Panneer, M Cheryl Bañez Ocfemia, Ellsworth Campbell, Sharoda Dasgupta, William M Switzer, Joel O Wertheim, and Angela L Hernandez Journal of acquired immune deficiency syndromes (1999) 2018 Dec 79(5) 543-550 |
| Progestin-based contraception regimens modulate expression of putative HIV risk factors in the vaginal epithelium of pig-tailed Macaques. Steven E Bosinger, Gregory K Tharp, Nirav B Patel, Chunxia Zhao, Tamika L Payne, Sharon Dietz Ostergaard, Katherine Butler, Shanon Ellis, Ryan L Johnson, Ellen N Kersh, Janet M McNicholl, and Sundaram A Vishwanathan American journal of reproductive immunology (New York, N.Y. : 1989) 2018 Aug e13029 |
| HCV adaptation to HIV coinfection. James Lara, Mahder A Teka, Seth Sims, Guo-Liang Xia, Sumathi Ramachandran, and Yury Khudyakov Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases 2018 Nov 65216-225 |
| Association between HIV genotype, viral load and disease progression in a cohort of Thai men who have sex with men with estimated dates of HIV infection. Wanna Leelawiwat, Sarika Pattanasin, Anuwat Sriporn, Punneeporn Wasinrapee, Oranuch Kongpechsatit, Famui Mueanpai, Jaray Tongtoyai, Timothy H Holtz, and Marcel E Curlin PloS one 2018 13(7) e0201386 |
| Detection of minority drug resistant mutations in Malawian HIV-1 subtype C-positive patients initiating and on first-line antiretroviral therapy. Zhiyong Zhou, Kevin Tang, Guoqing Zhang, Nellie Wadonda-Kabondo, Kundai Moyo, Lori A Rowe, Joshua R DeVos, Nick Wagar, Du-Ping Zheng,Hongxiong Guo, John Nkengasong, Mike Frace, Scott Sammons, and Chunfu Yang African journal of laboratory medicine 2018 (1) 708 |
| Prevalence of pretreatment HIV drug resistance in Cameroon following a nationally representative WHO survey. Gaëlle F Tchouwa, Sabrina Eymard-Duvernay, Amandine Cournil, Nadine Lamare, Laetitia Serrano, Christelle Butel, Silvia Bertagnolio, Eitel Mpoudi-Ngole, Elliot Raizes, Avelin F Aghokeng, and The Journal of antimicrobial chemotherapy 2018 Jun |
| Characterization of real-time microarrays for simultaneous detection of HIV-1, HIV-2, and hepatitis viruses. Timothy C Granade, Maja Kodani, Susan K Wells, Ae S Youngpairoj, Silvina Masciotra, Kelly A Curtis, Saleem Kamili, and S Michele Owen Journal of virological methods 2018 09 60-65 |
| Impact of the griffithsin anti-HIV microbicide and placebo gels on the rectal mucosal proteome and microbiome in non-human primates. Lauren Girard, Kenzie Birse, Johanna B Holm, Pawel Gajer, Mike S Humphrys, David Garber, Patricia Guenthner, Laura Noël-Romas, Max Abou, Stuart McCorrister, Garrett Westmacott, Lin Wang, Lisa C Rohan, Nobuyuki Matoba, Janet McNicholl, Kenneth E Palmer, Jacques Ravel, and Adam D Burgener Scientific reports 2018 May (1) 8059 |
| Discovery of genetic variants of the kinases that activate tenofovir among individuals in the United States, Thailand, and South Africa: HPTN067. Dominique B Figueroa, Joseph Tillotson, Maoji Li, Estelle Piwowar-Manning, Craig W Hendrix, Timothy H Holtz, Kevin Bokoch, Linda-Gail Bekker, Frits van Griensven, Sharon Mannheimer, James P Hughes, Robert M Grant, and Namandjé N Bumpus PloS one 2018 (4) e0195764 |
| Molecular Epidemiology and the Transformation of HIV Prevention. Alexandra M Oster, Anne Marie France, and Jonathan Mermin JAMA 2018 Apr 319(16) 1657-1658 |
| Cross-Sectional HIV Incidence Surveillance: A Benchmarking of Approaches for Estimating the 'Mean Duration of Recent Infection'. Reshma Kassanjee, Daniela De Angelis, Marian Farah, Debra Hanson, Jan Phillipus Lourens Labuschagne, Oliver Laeyendecker, Stéphane Le Vu, Brian Tom, Rui Wang, and Alex Welte Statistical communications in infectious diseases 2017 Mar (1) |
| Association of maternal KIR gene content polymorphisms with reduction in perinatal transmission of HIV-1. Yusuf O Omosun, Anna J Blackstock, John Williamson, Anne Maria van Eijk, John Ayisi, Juliana Otieno, Renu B Lal, Feiko O ter Kuile, Laurence Slutsker, and Ya Ping Shi PloS one 2018 (1) e0191733 |
| Detailed Transmission Network Analysis of a Large Opiate-Driven Outbreak of HIV Infection in the United States. Ellsworth M Campbell, Hongwei Jia, Anupama Shankar, Debra Hanson, Wei Luo, Silvina Masciotra, S Michele Owen, Alexandra M Oster, Romeo R Galang, Michael W Spiller, Sara J Blosser, Erika Chapman, Jeremy C Roseberry, Jessica Gentry, Pamela Pontones, Joan Duwve, Paula Peyrani, Ron M Kagan, Jeannette M Whitcomb, Philip J Peters, Walid Heneine, John T Brooks, and William M Switzer The Journal of infectious diseases 2017 Oct |
| The Female Genital Tract Microbiome Is Associated With Vaginal Antiretroviral Drug Concentrations in Human Immunodeficiency Virus-Infected Women on Antiretroviral Therapy. Renee Donahue Carlson, Anandi N Sheth, Timothy D Read, Michael B Frisch, C Christina Mehta, Amy Martin, Richard E Haaland, Anar S Patel, Chou-Pong Pau, Colleen S Kraft, and Igho Ofotokun The Journal of infectious diseases 2017 Oct |
| Time to first positive HIV-1 DNA PCR may differ with antiretroviral regimen in infants infected with non-B subtype HIV-1. Raji Balasubramanian, Mary Glenn Fowler, Kenneth Dominguez, Shahin Lockman, Pat A Tookey, Nicole Ngo Giang Huong, Steven Nesheim, Michael D Hughes, Marc Lallemant, Jennifer Tosswill, Nathan Shaffer, Gayle Sherman, Paul Palumbo, and David E Shapiro AIDS (London, England) 2017 Nov 31(18) 2465-2474 |
| Decoding noises in HIV computational genotyping. Mingrui Jia, Timothy Shaw, Xing Zhang, Dong Liu, Ye Shen, Amara E Ezeamama, Chunfu Yang, and Ming Zhang Virology 2017 Nov 511249-255 |
| HIV Transmission Dynamics among Foreign-born Persons in the United States. Eduardo E Valverde, Alexandra M Oster, Songli Xu, Joel O Wertheim, and Angela L Hernandez Journal of acquired immune deficiency syndromes (1999) 2017 Sep |
| Polymorphisms in the vitamin D receptor gene are associated with reduced rate of sputum culture conversion in multidrug-resistant tuberculosis patients in South Africa. Matthew J Magee, Yan V Sun, James C M Brust, N Sarita Shah, Yuming Ning, Salim Allana, Angela Campbell, Qin Hui, Koleka Mlisana, Pravi Moodley, and Neel R Gandhi PloS one 2017 (7) e0180916 |
| Increased Risk for Meningococcal Disease among Men who have Sex with Men in the United States, 2012-2015. Temitope A Folaranmi, Cecilia B Kretz, Hajime Kamiya, Jessica R MacNeil, Melissa J Whaley, Amy Blain, Mike Antwi, Marie Dorsinville, Massimo Pacilli, Shamika Smith, Rachel Civen, Van Ngo, Kathleen Winter, Kathleen Harriman, Xin Wang, Virginia B Bowen, Manisha Patel, Stacey Martin, Lara Misegades, and Sarah A Meyer Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2017 May |
| Transmission fitness of drug-resistant HIV revealed in a surveillance system transmission network. Joel O Wertheim, Alexandra M Oster, Jeffrey A Johnson, William M Switzer, Neeraja Saduvala, Angela L Hernandez, H Irene Hall, and Walid Heneine Virus evolution 2017 Jan (1) vex008 |
| Emergence of untreatable, multidrug-resistant HIV-1 in patients failing second-line therapy in Kenya. Seth C Inzaule, Raph L Hamers, Irene Mukui, Kennedy Were, Prestone Owiti, Daniel Kwaro, Tobias F Rinke de Wit, and Clement Zeh AIDS (London, England) 2017 Apr |
| Mutational Correlates of Virological Failure in Individuals Receiving a WHO-Recommended Tenofovir-Containing First-Line Regimen: An International Collaboration. Soo-Yon Rhee, Vici Varghese, Susan P Holmes, Gert U Van Zyl, Kim Steegen, Mark A Boyd, David A Cooper, Sabin Nsanzimana, Shanmugam Saravanan, Charlotte Charpentier, Tulio de Oliveira, Mary-Ann A Etiebet, Federico Garcia, Dominique Goedhals, Perpetua Gomes, Huldrych F Günthard, Raph L Hamers, Christopher J Hoffmann, Gillian Hunt, Awachana Jiamsakul, Pontiano Kaleebu, Phyllis Kanki, Rami Kantor, Bernhard Kerschberger, Vincent C Marconi, Jean D'amour Ndahimana, Nicaise Ndembi, Nicole Ngo-Giang-Huong, Casper Rokx, Maria M Santoro, Jonathan M Schapiro, Daniel Schmidt, Lillian Seu, Kim C E Sigaloff, Sunee Sirivichayakul, Lindiwe Skhosana, Henry Sunpath, Michele Tang, Chunfu Yang, Sergio Carmona, Ravindra K Gupta, and Robert W Shafer EBioMedicine 2017 Apr 18225-235 |
| Evaluation of Automated Molecular Testing Rollout for Tuberculosis Diagnosis Using Routinely Collected Surveillance Data - Uganda, 2012-2015. Colleen Scott, Simon Walusimbi, Bruce Kirenga, Moses Joloba, Muttamba Winters, Nyombi Abdunoor, Rommel Bain, Heather Alexander, Tom Shinnick,Sean Toney, Rosemary Odeke, Christine Mwangi, Estella Birabwa, Seyoum Dejene, Frank Mugabe, Mukadi YaDiul, and J Sean Cavanaugh MMWR. Morbidity and mortality weekly report 2017 Mar (12) 339-342 |
| Increasing HIV-1 subtype diversity in seven states, United States, 2006-2013. Alexandra M Oster, William M Switzer, Angela L Hernandez, Neeraja Saduvala, Joel O Wertheim, Ndidi Nwangwu-Ike, M Cheryl Ocfemia, Ellsworth Campbell, and H Irene Hall Annals of epidemiology 2017 Feb |
| Ebola Virus RNA in Semen from an HIV-Positive Survivor of Ebola. Lawrence J Purpura, Emerson Rogers, April Baller, Stephen White, Moses Soka, Mary J Choi, Nuha Mahmoud, Christine Wasunna, Moses Massaquoi, Jomah Kollie, Straker Dweh, Philip Bemah, Victor Ladele, Jonathan Kpaka, Mary Jawara, Margaret Mugisha, Onyekachi Subah, Mylene Faikai, Jeff A Bailey, Pierre Rollin, Barbara Marston, Tolbert Nyenswah, Alex Gasasira, Barbara Knust, Stuart Nichol, and Desmond Williams Emerging infectious diseases 2017 Apr (4) |
| Highlights from the 2016 HIV diagnostics conference: The new landscape of HIV testing in laboratories, public health programs and clinical practice. Laura G Wesolowski, Monica M Parker, Kevin P Delaney, and S Michele Owen Journal of clinical virology : the official publication of the Pan American Society for Clinical Virology 2017 Jun 63-68 |
| Surveillance of HIV-1 pol transmitted drug resistance in acutely and recently infected antiretroviral drug-naïve persons in rural western Kenya. Harris Onywera, David Maman, Seth Inzaule, Erick Auma, Kennedy Were, Harrison Fredrick, Prestone Owiti, Valarie Opollo, Jean-François Etard, Irene Mukui, Andrea A Kim, and Clement Zeh PloS one 2017 (2) e0171124 |
| Transmission of Extensively Drug-Resistant Tuberculosis in South Africa. N Sarita Shah, Sara C Auld, James C M Brust, Barun Mathema, Nazir Ismail, Pravi Moodley, Koleka Mlisana, Salim Allana, Angela Campbell, Thuli Mthiyane, Natashia Morris, Primrose Mpangase, Hermina van der Meulen, Shaheed V Omar, Tyler S Brown, Apurva Narechania, Elena Shaskina, Thandi Kapwata, Barry Kreiswirth, and Neel R Gandhi The New England journal of medicine 2017 Jan (3) 243-253 |
| A Pan-Lyssavirus Taqman Real-Time RT-PCR Assay for the Detection of Highly Variable Rabies virus and Other Lyssaviruses. Ashutosh Wadhwa, Kimberly Wilkins, Jinxin Gao, Rene Edgar Condori Condori, Crystal M Gigante, Hui Zhao, Xiaoyue Ma, James A Ellison, Lauren Greenberg, Andres Velasco-Villa, Lillian Orciari, and Yu Li PLoS neglected tropical diseases 2017 11(1) e0005258 |
| Subtypes and risk behaviors among incident HIV cases in the Bangkok Men Who Have Sex with Men Cohort Study, Thailand, 2006-2015. Caitlin R Lam, Timothy H Holtz, Wanna Leelawiwat, Philip A Mock, Wannee Chonwattana, Wipas Wimonsate, Anchalee Varangrat, Warunee Thienkrua,Charles Rose, Anupong Chitwarakorn, and Marcel E Curlin AIDS research and human retroviruses 2016 Dec |
| HIV-1 Infection and Transmission Networks of Younger People in Chicago, Illinois, 2005-2011. Ethan Morgan, Alexandra M Oster, Stephanie Townsell, Donna Peace, Nanette Benbow, and John A Schneider Public health reports (Washington, D.C. : 1974) (1) 48-55 |
| Severity of Respiratory Syncytial Virus Lower Respiratory Tract Infection with Viral Coinfection in HIV-uninfected Children. Natalie I Mazur, Louis Bont, Adam L Cohen, Cheryl Cohen, Anne von Gottberg, Michelle J Groome, Orienka Hellferscee, Kerstin Klipstein-Grobusch, Omphile Mekgoe, Fathima Naby, Jocelyn Moyes, Stefano Tempia, Florette K Treurnicht, Marietje Venter, Sibongile Walaza, Nicole Wolter, Shabir A Madhi, and Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2016 Dec |
| The rectal mucosa and condomless receptive anal intercourse in HIV-negative MSM: implications for HIV transmission and prevention. C F Kelley, C S Kraft, T Jb de Man, C Duphare, H-W Lee, J Yang, K A Easley, G K Tharp, M J Mulligan, P S Sullivan, S E Bosinger, and R R Amara Mucosal immunology 2016 Nov |
| Optimizing Infant HIV Diagnosis in Resource-Limited Settings: Modeling the Impact of HIV DNA PCR Testing at Birth. Alexander Chiu, Surbhi Modi, Emilia D Rivadeneira, and Emilia H Koumans Journal of acquired immune deficiency syndromes (1999) 2016 Dec 73(4) 454-462 |
| 1970s and 'Patient 0' HIV-1 genomes illuminate early HIV/AIDS history in North America. Michael Worobey, Thomas D Watts, Richard A McKay, Marc A Suchard, Timothy Granade, Dirk E Teuwen, Beryl A Koblin, Walid Heneine, Philippe Lemey, and Harold W Jaffe Nature 2016 Oct |
| Time until emergence of HIV test reactivity following infection with HIV-1: Implications for interpreting test results and retesting after exposure. Kevin P Delaney, Debra L Hanson, Silvina Masciotra, Steven F Ethridge, Laura Wesolowski, and Sherry Michele Owen Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2016 Oct |
| Xpert MTB/RIF - why the lack of morbidity and mortality impact in intervention trials? Andrew F Auld, Katherine L Fielding, Ankur Gupta-Wright, and Stephen D Lawn Transactions of the Royal Society of Tropical Medicine and Hygiene 2016 Sep |
| Executive Summary: Official American Thoracic Society/Centers for Disease Control and Prevention/Infectious Diseases Society of America Clinical Practice Guidelines: Treatment of Drug-Susceptible Tuberculosis. Payam Nahid, Susan E Dorman, Narges Alipanah, Pennan M Barry, Jan L Brozek, Adithya Cattamanchi, Lelia H Chaisson, Richard E Chaisson, Charles L Daley, Malgosia Grzemska, Julie M Higashi, Christine S Ho, Philip C Hopewell, Salmaan A Keshavjee, Christian Lienhardt, Richard Menzies, Cynthia Merrifield, Masahiro Narita, Rick O'Brien, Charles A Peloquin, Ann Raftery, Jussi Saukkonen, H Simon Schaaf, Giovanni Sotgiu, Jeffrey R Starke, Giovanni Battista Migliori, and Andrew Vernon Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2016 Oct 63(7) 853-67 |
| Maternal colonization with Streptococcus agalactiae and associated stillbirth and neonatal disease in coastal Kenya. Anna C Seale, Angela C Koech, Anna E Sheppard, Hellen C Barsosio, Joyce Langat, Emily Anyango, Stella Mwakio, Salim Mwarumba, Susan C Morpeth, Kirimi Anampiu, Alison Vaughan, Adam Giess, Polycarp Mogeni, Leahbell Walusuna, Hope Mwangudzah, Doris Mwanzui, Mariam Salim, Bryn Kemp, Caroline Jones, Neema Mturi, Benjamin Tsofa, Edward Mumbo, David Mulewa, Victor Bandika, Musimbi Soita, Maureen Owiti, Norris Onzere, A Sarah Walker, Stephanie J Schrag, Stephen H Kennedy, Greg Fegan, Derrick W Crook, and James A Berkley Nature microbiology 2016 1(7) 16067 |
| Treatment as Prevention: Characterization of partner infections in the HIV Prevention Trials Network 052 trial. Susan H Eshleman, Sarah E Hudelson, Andrew D Redd, Ronald Swanstrom, San-San Ou, Xinyi Cindy Zhang, Li-Hua Ping, Estelle Piwowar-Manning, Stephen F Porcella, Matthew F Sievers, Craig A Martens, Daniel Bruno, Elena Dukhovlinova, Marybeth McCauley, Theresa Gamble, Jessica M Fogel, Devin Sabin, Thomas C Quinn, Laurence Gunde, Madalitso Maliwichi, Nehemiah Nhando, Victor Akelo, Sikhulile Moyo, Ravindre Panchia, Nagalingeswaran Kumarasamy, Nuntisa Chotirosniramit, Marineide Gonçalves de Melo, Jose Pilotto, Beatriz Grinsztejn, Kenneth Mayer, Ying Q Chen, James P Hughes, and Myron S Cohen Journal of acquired immune deficiency syndromes (1999) 2016 Aug |
| Official American Thoracic Society/Centers for Disease Control and Prevention/Infectious Diseases Society of America Clinical Practice Guidelines: Treatment of Drug-Susceptible Tuberculosis. Payam Nahid, Susan E Dorman, Narges Alipanah, Pennan M Barry, Jan L Brozek, Adithya Cattamanchi, Lelia H Chaisson, Richard E Chaisson, Charles L Daley, Malgosia Grzemska, Julie M Higashi, Christine S Ho, Philip C Hopewell, Salmaan A Keshavjee, Christian Lienhardt, Richard Menzies, Cynthia Merrifield, Masahiro Narita, Rick O'Brien, Charles A Peloquin, Ann Raftery, Jussi Saukkonen, H Simon Schaaf, Giovanni Sotgiu, Jeffrey R Starke, Giovanni Battista Migliori, and Andrew Vernon Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2016 Aug |
| HIV Infection Linked to Injection Use of Oxymorphone in Indiana, 2014-2015. Philip J Peters, Pamela Pontones, Karen W Hoover, Monita R Patel, Romeo R Galang, Jessica Shields, Sara J Blosser, Michael W Spiller, Brittany Combs, William M Switzer, Caitlin Conrad, Jessica Gentry, Yury Khudyakov, Dorothy Waterhouse, S Michele Owen, Erika Chapman, Jeremy C Roseberry,Veronica McCants, Paul J Weidle, Dita Broz, Taraz Samandari, Jonathan Mermin, Jennifer Walthall, John T Brooks, Joan M Duwve, and The New England journal of medicine 2016 Jul 375(3) 229-39 |
| Antiretroviral Therapy for the Prevention of HIV-1 Transmission. Myron S Cohen, Ying Q Chen, Marybeth McCauley, Theresa Gamble, Mina C Hosseinipour, Nagalingeswaran Kumarasamy, James G Hakim, Johnstone Kumwenda, Beatriz Grinsztejn, Jose H S Pilotto, Sheela V Godbole, Suwat Chariyalertsak, Breno R Santos, Kenneth H Mayer, Irving F Hoffman, Susan H Eshleman, Estelle Piwowar-Manning, Leslie Cottle, Xinyi C Zhang, Joseph Makhema, Lisa A Mills, Ravindre Panchia, Sharlaa Faesen, Joseph Eron, Joel Gallant, Diane Havlir, Susan Swindells, Vanessa Elharrar, David Burns, Taha E Taha, Karin Nielsen-Saines, David D Celentano, Max Essex, Sarah E Hudelson, Andrew D Redd, Thomas R Fleming, and The New England journal of medicine 2016 375(9) 830-9 |
| Molecular Typing of Treponema pallidum in Ocular Syphilis. Sara Oliver, Sharon K Sahi, Lauren C Tantalo, Charmie Godornes, Robyn Neblett Fanfair, Lauri E Markowitz, Sheila A Lukehart, and Christina M Marra Sexually transmitted diseases 2016 Aug (8) 524-527 |
| Origin and spread of HIV-1 in persons who inject drugs in Bulgaria. Ivailo Alexiev, Anupama Shankar, Reneta Dimitrova, Anna Gancheva, Asia Kostadinova, Pavel Teoharov, Elitsa Golkocheva, Maria Nikolova, Mariya Muhtarova, Ivaylo Elenkov, Mariyana Stoycheva, Daniela Nikolova, Tonka Varleva, and William M Switzer Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases 2016 May |
| Protocol for a population-based molecular epidemiology study of tuberculosis transmission in a high HIV-burden setting: the Botswana Kopanyo study. N M Zetola, C Modongo, P K Moonan, E Click, J E Oeltmann, J Shepherd, and A Finlay BMJ open 2016 (5) e010046 |
| The International Dimension of the U.S. HIV Transmission Network and Onward Transmission of HIV Recently Imported into the United States. Joel O Wertheim, Alexandra M Oster, Angela L Hernandez, Neeraja Saduvala, M Cheryl Bañez Ocfemia, and H Irene Hall AIDS research and human retroviruses 2016 Apr |
| HIV virological failure and drug resistance in a cohort of Tanzanian HIV-infected adults. Claudia Hawkins, Nzovu Ulenga, Enju Liu, Said Aboud, Ferdinand Mugusi, Guerino Chalamilla, David Sando, Eric Aris, Deborah Carpenter, and Wafaie Fawzi The Journal of antimicrobial chemotherapy 2016 Jul (7) 1966-74 |
| Sensitive sentinel mutation screening reveals differential underestimation of transmitted HIV drug resistance among demographic groups. Jin-Fen Li, Laurie Linley, Richard Kline, Rebecca Ziebell, Walid Heneine, and Jeffrey A Johnson AIDS (London, England) 2016 Mar |
| Prevalence and dynamics of the K65R drug resistance mutation in HIV-1-infected infants exposed to maternal therapy with lamivudine, zidovudine and either nevirapine or nelfinavir in breast milk. Seth C Inzaule, Paul J Weidle, Chunfu Yang, Kenneth Ndiege, Raph L Hamers, Tobias F Rinke de Wit, Timothy Thomas, and Clement Zeh The Journal of antimicrobial chemotherapy 2016 Mar |
| Molecular Epidemiology and Transmission Dynamics of Recent and Long-Term HIV-1 Infections in Rural Western Kenya. Clement Zeh, Seth C Inzaule, Pascale Ondoa, Lillian G Nafisa, Alex Kasembeli, Fredrick Otieno, Hilde Vandenhoudt, Pauli N Amornkul, Lisa A Mills, and John N Nkengasong PloS one 2016 (2) e0147436 |
| HIV-1 Drug Resistance Mutations: Potential Applications for Point-of-Care Genotypic Resistance Testing. Soo-Yon Rhee, Michael R Jordan, Elliot Raizes, Arlene Chua, Neil Parkin, Rami Kantor, Gert U Van Zyl, Irene Mukui, Mina C Hosseinipour, Lisa M Frenkel, Nicaise Ndembi, Raph L Hamers, Tobias F Rinke de Wit, Carole L Wallis, Ravindra K Gupta, Joseph Fokam, Clement Zeh, Jonathan M Schapiro, Sergio Carmona, David Katzenstein, Michele Tang, Avelin F Aghokeng, Tulio de Oliveira, Annemarie M J Wensing, Joel E Gallant, Mark A Wainberg, Douglas D Richman, Joseph E Fitzgibbon, Marco Schito, Silvia Bertagnolio, Chunfu Yang, and Robert W Shafer PloS one 2015 (12) e0145772 |
| Sustainable HIV treatment in Africa through viral-load-informed differentiated care. , Andrew Phillips, Amir Shroufi, Lara Vojnov, Jennifer Cohn, Teri Roberts, Tom Ellman, Kimberly Bonner, Christine Rousseau, Geoff Garnett, Valentina Cambiano, Fumiyo Nakagawa, Deborah Ford, Loveleen Bansi-Matharu, Alec Miners, Jens D Lundgren, Jeffrey W Eaton, Rosalind Parkes-Ratanshi, Zachary Katz, David Maman, Nathan Ford, Marco Vitoria, Meg Doherty, David Dowdy, Brooke Nichols, Maurine Murtagh, Meghan Wareham, Kara M Palamountain, Christine Chakanyuka Musanhu, Wendy Stevens, David Katzenstein, Andrea Ciaranello, Ruanne Barnabas, R Scott Braithwaite, Eran Bendavid, Kusum J Nathoo, David van de Vijver, David P Wilson, Charles Holmes, Anna Bershteyn, Simon Walker, Elliot Raizes, Ilesh Jani, Lisa J Nelson, Rosanna Peeling, Fern Terris-Prestholt, Joseph Murungu, Tsitsi Mutasa-Apollo, Timothy B Hallett, and Paul Revill Nature 2015 Dec (7580) S68-76 |
| Simultaneous Detection of Major Drug Resistance Mutations of HIV-1 Subtype B Viruses from Dried Blood Spot Specimens by Multiplex Allele-specific Assay. Guoqing Zhang, Fangping Cai, Ivette Lorenzana de Rivera, Zhiyong Zhou, Jing Zhang, John Nkengasong, Feng Gao, and Chunfu Yang Journal of clinical microbiology 2015 Nov |
| Molecular analysis allows inference into HIV transmission among young men who have sex with men in the United States. Y Omar Whiteside, Ruiguang Song, Joel O Wertheim, and Alexandra M Oster AIDS (London, England) 2015 Nov (18) 2517-22 |
| Prevalence of transmitted HIV-1 drug resistance among young adults attending HIV counselling and testing clinics in Kigali, Rwanda. Mwumvaneza Mutagoma, Jean d'Amour Ndahimana, Eugenie Kayirangwa, Anicet G Dahourou, Helen Balisanga, Joshua R DeVos, David McAlister,Chunfu Yang, Silvia Bertagnolio, David J Riedel, and Sabin Nsanzimana Antiviral therapy 2016 (3) 247-51 |
| Longitudinal Detection and Persistence of Minority Drug-Resistant Populations and Their Effect on Salvage Therapy. Masako Nishizawa, Masakazu Matsuda, Junko Hattori, Teiichiro Shiino, Tetsuro Matano, Walid Heneine, Jeffrey A Johnson, and Wataru Sugiura PLoS ONE 2015 (9) e0135941 |
| Using Molecular HIV Surveillance Data to Understand Transmission Between Subpopulations in the United States. Alexandra M Oster, Joel O Wertheim, Angela L Hernandez, Marie Cheryl Bañez Ocfemia, Neeraja Saduvala, and H Irene Hall Journal of acquired immune deficiency syndromes (1999) 2015 Dec 70(4) 444-51 |
| Prevalence of Diagnosed and Undiagnosed HIV Infection - United States, 2008-2012. H Irene Hall, Qian An, Tian Tang, Ruiguang Song, Mi Chen, Timothy Green, Jian Kang, and MMWR Morb. Mortal. Wkly. Rep. 2015 Jun 26. 64(24) 657-62 |
| Detection of Acute HIV-1 Infection by RT-LAMP. Donna L Rudolph, Vickie Sullivan, S Michele Owen, and Kelly A Curtis PLoS ONE 2015 (5) e0126609 |
| Trends in use of genotypic resistance testing and frequency of major drug resistance among antiretroviral-naive persons in the HIV Outpatient Study, 1999-2011. Kate Buchacz, Benjamin Young, Frank J Palella, Carl Armon, John T Brooks, , J. Antimicrob. Chemother. 2015 May 15. |
| Public Health Practice of Population-Based Birth Defects Surveillance Programs in the United States. Cara T Mai, Russell S Kirby, Adolfo Correa, Deborah Rosenberg, Michael Petros, and Michael C Fagen Journal of public health management and practice : JPHMP 22(3) E1-8 |
| Dried blood spots for viral load monitoring in Malawi: feasible and effective. Sarah E Rutstein, Mina C Hosseinipour, Deborah Kamwendo, Alice Soko, Memory Mkandawire, Andrea K Biddle, William C Miller, Morris Weinberger, Stephanie B Wheeler, Abdoulaye Sarr, Sundeep Gupta, Frank Chimbwandira, Reuben Mwenda, Steve Kamiza, Irving Hoffman, and Ronald Mataya PloS one 2015 10(4) e0124748 |
| 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. Soo-Yon Rhee, Jose Luis Blanco, Michael R Jordan, Jonathan Taylor, Philippe Lemey, Vici Varghese, Raph L Hamers, Silvia Bertagnolio, Tobias F Rinke de Wit, Avelin F Aghokeng, Jan Albert, Radko Avi, Santiago Avila-Rios, Pascal O Bessong, James I Brooks, Charles A B Boucher, Zabrina L Brumme, Michael P Busch, Hermann Bussmann, Marie-Laure Chaix, Bum Sik Chin, Toni T D'Aquin, Cillian F De Gascun, Anne Derache, Diane Descamps, Alaka K Deshpande, Cyrille F Djoko, Susan H Eshleman, Herve Fleury, Pierre Frange, Seiichiro Fujisaki, P Richard Harrigan, Junko Hattori, Africa Holguin, Gillian M Hunt, Hiroshi Ichimura, Pontiano Kaleebu, David Katzenstein, Sasisopin Kiertiburanakul, Jerome H Kim, Sung Soon Kim, Yanpeng Li, Irja Lutsar, Lynn Morris, Nicaise Ndembi, Kee Peng Ng, Ramesh S Paranjape, Martine Peeters, Mario Poljak, Matt A Price, Manon L Ragonnet-Cronin, Gustavo Reyes-Terán, Morgane Rolland, Sunee Sirivichayakul, Davey M Smith, Marcelo A Soares, Vincent V Soriano, Deogratius Ssemwanga, Maja Stanojevic, Mariane A Stefani, Wataru Sugiura, Somnuek Sungkanuparph, Amilcar Tanuri, Kok Keng Tee, Hong-Ha M Truong, David A M C van de Vijver, Nicole Vidal, Chunfu Yang, Rongge Yang, Gonzalo Yebra, John P A Ioannidis, Anne-Mieke Vandamme, and Robert W Shafer PLoS Med. 2015 Apr 12(4) e1001810 |
| Viral Genetic Diversity and Polymorphisms in a Cohort of HIV-1-Infected Patients Eligible for Initiation of Antiretroviral Therapy in Abuja, Nigeria. Karidia Diallo, Du-Ping Zheng, Erin K Rottinghaus, Orji Bassey, and Chunfu Yang AIDS Res. Hum. Retroviruses 2015 May (5) 564-75 |
| An HIV-1 RNA test following a reactive fourth-generation antigen/antibody combination assay confirms a high proportion of HIV infections. Emily Westheimer, Jie Fu, Anita Radix, Francesca R Giancotti, Laura Hall, Demetre C Daskalakis, Benjamin Tsoi, and Philip J Peters J. Clin. Virol. 2014 Dec 61(4) 623-4 |
| Increasing HIV-1 molecular complexity among men who have sex with men in Bangkok. Wanna Leelawiwat, Wiriya Rutvisuttinunt, Miguel Arroyo, Famui Mueanpai, Oranuch Kongpechsatit, Wannee Chonwattana, Supaporn Chaikummao, Mark de Souza, Frits vanGriensven, Janet M McNicholl, and Marcel E Curlin AIDS research and human retroviruses 2015 Apr (4) 393-400 |
| Limited utility of dried-blood- and plasma spot-based screening for antiretroviral treatment failure with Cobas Ampliprep/TaqMan HIV-1 version 2.0. Souleymane Sawadogo, Andreas Shiningavamwe, Joy Chang, Andrew D Maher, Guoqing Zhang, Chunfu Yang, Esegiel Gaeb, Harold Kaura, Dennis Ellenberger, and David W Lowrance J. Clin. Microbiol. 2014 Nov 52(11) 3878-83 |
| Reference panel of cloned HIV-2 plasmid DNA for nucleic acid assay development, evaluation, and quality monitoring. Ae S Youngpairoj, Kelly A Curtis, Susan K Wells, Chou-Pong Pau, Timothy C Granade, and S Michele Owen J. Clin. Virol. 2014 Oct 61(2) 293-7 |
| HIV reverse-transcriptase drug resistance mutations during early infection reveal greater transmission diversity than in envelope sequences. Jonathan T Lipscomb, William M Switzer, Jin-Fen Li, Silvina Masciotra, S Michele Owen, and Jeffrey A Johnson The Journal of infectious diseases 2014 Dec (11) 1827-37 |
| Dense genotyping of immune-related loci identifies variants associated with clearance of HPV among HIV-positive women in the HIV epidemiology research study (HERS). Staci L Sudenga, Howard W Wiener, Caroline C King, Anne M Rompalo, Susan Cu-Uvin, Robert S Klein, Keerti V Shah, Jack D Sobel, Denise J Jamieson, and Sadeep Shrestha PLoS ONE 2014 9(6) e99109 |
| Field study of dried blood spot specimens for HIV-1 drug resistance genotyping. C M Parry, N Parkin, K Diallo, S Mwebaza, R Batamwita, J DeVos, N Bbosa, F Lyagoba, B Magambo, M R Jordan, R Downing, G Zhang, P Kaleebu, C Yang, and S Bertagnolio J. Clin. Microbiol. 2014 Aug 52(8) 2868-75 |
| Recombinant viruses initiated the early HIV-1 epidemic in Burkina Faso. Peter N Fonjungo, Marcia L Kalish, Amanda Schaefer, Mark Rayfield, Jennifer Mika, Laura E Rose, Orville Heslop, Robert Soudré, and Danuta Pieniazek PLoS ONE 2014 9(3) e92423 |
| Development of a loop-mediated isothermal amplification method for detection of Histoplasma capsulatum DNA in clinical samples. Christina M Scheel, Yitian Zhou, Raquel C Theodoro, Bethany Abrams, S Arunmozhi Balajee, and Anastasia P Litvintseva J. Clin. Microbiol. 2014 Feb 52(2) 483-8 |
| Sensitive testing of plasma HIV-1 RNA and Sanger sequencing of cellular HIV-1 DNA for the detection of drug resistance prior to starting first-line antiretroviral therapy with etravirine or efavirenz. Anna Maria Geretti, Tim Conibear, Andrew Hill, Jeffrey A Johnson, Lotke Tambuyzer, Kim Thys, Johan Vingerhoets, Yvon van Delft, and J. Antimicrob. Chemother. 2014 Apr 69(4) 1090-7 |
| Molecular characterization of ambiguous mutations in HIV-1 polymerase gene: implications for monitoring HIV infection status and drug resistance. Du-Ping Zheng, Margarida Rodrigues, Ebi Bile, Duc B Nguyen, Karidia Diallo, Joshua R DeVos, John N Nkengasong, and Chunfu Yang PLoS ONE 2013 8(10) e77649 |
| Simultaneous detection of major drug resistance mutations in the protease and reverse transcriptase genes for HIV-1 subtype C by use of a multiplex allele-specific assay. Guoqing Zhang, Fangping Cai, Zhiyong Zhou, Joshua DeVos, Nick Wagar, Karidia Diallo, Isaac Zulu, Nellie Wadonda-Kabondo, Jeffrey S A Stringer, Paul J Weidle, Clement B Ndongmo, Izukanji Sikazwe, Abdoulaye Sarr, Matthew Kagoli, John Nkengasong, Feng Gao, and Chunfu Yang J. Clin. Microbiol. 2013 Nov 51(11) 3666-74 |
| Evaluation of a dried blood and plasma collection device, SampleTanker(®), for HIV type 1 drug resistance genotyping in patients receiving antiretroviral therapy. Karidia Diallo, Erica Lehotzky, Jing Zhang, Zhiyong Zhou, Ivette Lorenzana de Rivera, Wendy E Murillo, John Nkengasong, Jennifer Sabatier, Guoqing Zhang, and Chunfu Yang AIDS Res. Hum. Retroviruses 2014 Jan 30(1) 67-73 |
| Unusual Enterocytozoon bieneusi genotypes and Cryptosporidium hominis subtypes in HIV-infected patients on highly active antiretroviral therapy. Frederick O Akinbo, Christopher E Okaka, Richard Omoregie, Haileeyesus Adamu, and Lihua Xiao Am. J. Trop. Med. Hyg. 2013 Jul 89(1) 157-61 |
| Recent advances in research of HIV infection: implications of viral and host genetics on treatment and prevention. R E Haaland, J A Johnson, and J Tang Public Health Genomics 2013 16(1-2) 31-6 |
| Detailed molecular epidemiologic characterization of HIV-1 infection in Bulgaria reveals broad diversity and evolving phylodynamics. Ivailo Alexiev Ivanov, Danail Beshkov, Anupama Shankar, Debra L Hanson, Dimitrios Paraskevis, Viara Georgieva, Lyudmila Karamacheva, Hristo Taskov, Tonka Varleva, Ivaylo Elenkov, Mariana Stoicheva, Daniela Nikolova, and William M Switzer PLoS ONE 2013 8(3) e59666 |
| Susceptibility to repeated, low-dose, rectal SHIVSF162P3 challenge is independent of TRIM5 genotype in rhesus macaques. Katherine Butler, Jennifer S Morgan, Debra L Hanson, Debra Adams, J Gerardo Garcia-Lerma, Walid Heneine, Dennis Ellenberger, R Michael Hendry,Janet McNicholl, Welkin E Johnson, and Ellen N Kersh AIDS Res. Hum. Retroviruses 2013 Jul 29(7) 1091-4 |
| Association between immunoglobulin GM and KM genotypes and placental malaria in HIV-1 negative and positive women in western Kenya. Nnaemeka C Iriemenam, Janardan P Pandey, John Williamson, Anna J Blackstock, Ajay Yesupriya, Aryan M Namboodiri, Keith M Rocca, Anna Maria van Eijk, John Ayisi, Juliana Oteino, Renu B Lal, Feiko O ter Kuile, Richard Steketee, Bernard Nahlen, Laurence Slutsker, and Ya Ping Shi PLoS ONE 2013 8(1) e53948 |
| Impact of minority nonnucleoside reverse transcriptase inhibitor resistance mutations on resistance genotype after virologic failure. Jonathan Z Li, Roger Paredes, Heather J Ribaudo, Michael J Kozal, Evguenia S Svarovskaia, Jeffrey A Johnson, Anna Maria Geretti, Karin J Metzner, Martin R Jakobsen, Katherine Huppler Hullsiek, Lars Ostergaard, Michael D Miller, and Daniel R Kuritzkes J. Infect. Dis. 2013 Mar 15. 207(6) 893-7 |
| Field evaluation of a broadly sensitive HIV-1 in-house genotyping assay for use with both plasma and dried blood spot specimens in a resource-limited country. Seth Inzaule, Chunfu Yang, Alex Kasembeli, Lillian Nafisa, Jully Okonji, Boaz Oyaro, Richard Lando, Lisa A Mills, Kayla Laserson, Timothy Thomas, John Nkengasong, and Clement Zeh J. Clin. Microbiol. 2013 Feb 51(2) 529-39 |
| Zoonotic Cryptosporidium species and Enterocytozoon bieneusi genotypes in HIV-positive patients on antiretroviral therapy. Lin Wang, Hongwei Zhang, Xudong Zhao, Longxian Zhang, Guoqing Zhang, Meijin Guo, Lili Liu, Yaoyu Feng, and Lihua Xiao J. Clin. Microbiol. 2013 Feb 51(2) 557-63 |
| Comparison of Ahlstrom grade 226, Munktell TFN, and Whatman 903 filter papers for dried blood spot specimen collection and subsequent HIV-1 load and drug resistance genotyping analysis. Erin Rottinghaus, Ebi Bile, Mosetsanagape Modukanele, Maruping Maruping, Madisa Mine, John Nkengasong, and Chunfu Yang J. Clin. Microbiol. 2013 Jan 51(1) 55-60 |
| Deletion of specific immune-modulatory genes from modified vaccinia virus Ankara-based HIV vaccines engenders improved immunogenicity in rhesus macaques. David A Garber, Leigh A O'Mara, Sailaja Gangadhara, Monica McQuoid, Xiugen Zhang, Rui Zheng, Kiran Gill, Meena Verma, Tianwei Yu, Brent Johnson, Bing Li, Cynthia A Derdeyn, Chris Ibegbu, John D Altman, Eric Hunter, and Mark B Feinberg J. Virol. 2012 Dec 86(23) 12605-15 |
| Evaluation of blood collection filter papers for HIV-1 DNA PCR. Silvina Masciotra, Samoel Khamadi, Ebi Bilé, Adrian Puren, Peter Fonjungo, Shon Nguyen, Mulu Girma, Robert Downing, Artur Ramos, Shambavi Subbarao, and Dennis Ellenberger J. Clin. Virol. 2012 Oct 55(2) 101-6 |
| Virological and molecular characterization of a simian human immunodeficiency virus (SHIV) encoding the envelope and reverse transcriptase genes from HIV-1. Ranajit Pal, Lindsey Galmin, Lara E Pereira, Bin Li, Jining Zhang, Daniel Li, Jesse Francis, Janet M McNicholl, Deborah E Weiss, and James M Smith Virology 2012 Oct 10. 432(1) 173-83 |
| Relaxation of adaptive evolution during the HIV-1 infection owing to reduction of CD4+ T cell counts. Élcio Leal, Jorge Casseb, Michael Hendry, Michael P Busch, and Ricardo Sobhie Diaz PLoS ONE 2012 7(6) e39776 |
| Differential association of gene content polymorphisms of killer cell immunoglobulin-like receptors with placental malaria in HIV- and HIV+ mothers. Yusuf O Omosun, Anna J Blackstock, Wangeci Gatei, Allen Hightower, Anne Maria van Eijk, John Ayisi, Juliana Otieno, Renu B Lal, Richard Steketee,Bernard Nahlen, Feiko O ter Kuile, Laurence Slutsker, and Ya Ping Shi PLoS ONE 2012 7(6) e38617 |
| Comparison of HIV-1 resistance profiles in plasma RNA versus PBMC DNA in heavily treated patients in Honduras, a resource-limited country. Karidia Diallo, Wendy E Murillo, Ivette Lorenzana de Rivera, Jan Albert, Zhiyong Zhou, John Nkengasong, Guoqing Zhang, Jennifer F Sabatier, and Chunfu Yang Int J Mol Epidemiol Genet 2012 3(1) 56-65 |
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