HIV-1 Subtype C Phylodynamics in the Global Epidemic by Max Essex, Stephen Lagakos, Rui Wang, Vlad Novitsky

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Deciphering Multiplicity of HIV-1C Infection: Transmission of Closely Related Multiple Viral Lineages. by Vlad Novitsky, Sikhulile Moyo, Rui Wang, Simani Gaseitsiwe, M Essex

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Phylodynamic analysis of HIV sub-epidemics in Mochudi, Botswana by Vlad Novitsky, Denise Kühnert, Sikhulile Moyo, Erik Widenfelt, Lillian Okui, M. Essex

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Added Value of Next Generation Sequencing in Characterizing the Evolution of HIV-1 Drug Resistance in Kenyan Youth by Vlad Novitsky, Winstone Nyandiko, Rachel Vreeman, Allison K. DeLong, Mark Howison, Akarsh Manne, Josephine Aluoch, Ashley Chory, Festus Sang, Celestine Ashimosi, Eslyne Jepkemboi, Millicent Orido, Joseph W. Hogan, Rami Kantor

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An Automated Bioinformatics Pipeline Informing Near-Real-Time Public Health Responses to New HIV Diagnoses in a Statewide HIV Epidemic by Mark Howison, Fizza S. Gillani, Vlad Novitsky, Jon A. Steingrimsson, John Fulton, Thomas Bertrand, Katharine Howe, Anna Civitarese, Lila Bhattarai, Meghan MacAskill, Guillermo Ronquillo, Joel Hague, Casey W. Dunn, Utpala Bandy, Joseph W. Hogan, Rami Kantor

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Fostemsavir resistance-associated polymorphisms in HIV-1 subtype C in a large cohort of treatment-naïve and treatment-experienced individuals in Botswana by Boitumelo J. L. Zuze, Botshelo T. Radibe, Wonderful T. Choga, Ontlametse T. Bareng, Natasha O. Moraka, Dorcas Maruapula, Kedumetse Seru, Patrick Mokgethi, Baitshepi Mokaleng, Nokuthula Ndlovu, Nametso Kelentse, Molly Pretorius-Holme, Roger Shapiro, Shahin Lockman, Joseph Makhema, Vlad Novitsky, Kaelo K. Seatla, Sikhulile Moyo, Simani Gaseitsiwe

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Beyond HIV outbreaks: protocol, rationale and implementation of a prospective study quantifying the benefit of incorporating viral sequence clustering analysis into routine public... by Philip A Chan, Joseph W Hogan, John Fulton, Jon A Steingrimsson, Mark Howison, Vlad Novitsky, Fizza S Gillani, Thomas Bertrand, Anna Civitarese, Katharine Howe, Guillermo Ronquillo, Benjamin Lafazia, Zoanne Parillo, Theodore Marak, Lila Bhattarai, Casey Dunn, Utpala Bandy, Nicole Alexander Scott, Rami Kantor

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Epidemiological and viral characteristics of undiagnosed HIV infections in Botswana by Lynnette Bhebhe, Sikhulile Moyo, Simani Gaseitsiwe, Molly Pretorius-Holme, Etienne K. Yankinda, Kutlo Manyake, Coulson Kgathi, Mompati Mmalane, Refeletswe Lebelonyane, Tendani Gaolathe, Pamela Bachanas, Faith Ussery, Mpho Letebele, Joseph Makhema, Kathleen E. Wirth, Shahin Lockman, Max Essex, Vlad Novitsky, Manon Ragonnet-Cronin

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Prediction of Coreceptor Tropism in HIV-1 Subtype C in Botswana by Kenanao Kotokwe, Sikhulile Moyo, Melissa Zahralban-Steele, Molly Pretorius Holme, Pinkie Melamu, Catherine Kegakilwe Koofhethile, Wonderful Tatenda Choga, Terence Mohammed, Tapiwa Nkhisang, Baitshepi Mokaleng, Dorcas Maruapula, Tsotlhe Ditlhako, Ontlametse Bareng, Patrick Mokgethi, Corretah Boleo, Joseph Makhema, Shahin Lockman, Max Essex, Manon Ragonnet-Cronin, Vlad Novitsky, Simani Gaseitsiwe, PANGEA Consortium

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A Challenging Knowledge Gap: Estimating Modes of HIV Acquisition Among Adolescents Entering HIV Care During Adolescence by John Humphrey MD, Miranda Triedman BS, Winstone Nyandiko MBChB, MMed, Edwin Sang MS, Emmanuel Kemboi BS, Marsha Alera MS, Vlad Novitsky MD, PhD, Akarsh Manne MS, Eslyne Jepkemboi BS, Millicent Orido BS, Edith Apondi MBChB, MMed, Rachel Vreeman MD, Kara Wools-Kaloustian MD, Rami Kantor MD

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Doravirine-associated resistance mutations in antiretroviral therapy naïve and experienced adults with HIV-1 subtype C infection in Botswana by Ontlametse T. Bareng, Sekgabo Seselamarumo, Kaelo K. Seatla, Wonderful T. Choga, Blessing Bakae, Dorcas Maruapula, Nametso Kelentse, Natasha O. Moraka, Baitshepi Mokaleng, Patrick T. Mokgethi, Tsotlhe R. Ditlhako, Molly Pretorius-Holme, Mpaphi B. Mbulawa, Refeletswe Lebelonyane, Ebi Celestin Bile, Tendani Gaolathe, Roger Shapiro, Joseph M. Makhema, Shahin Lockman, Max Essex, Vlad Novitsky, Sununguko W. Mpoloka, Sikhulile Moyo, Simani Gaseitsiwe

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Cross-sectional estimates revealed high HIV incidence in Botswana rural communities in the era of successful ART scale-up in 2013-2015. by Sikhulile Moyo, Simani Gaseitsiwe, Terence Mohammed, Molly Pretorius Holme, Rui Wang, Kenanao Peggy Kotokwe, Corretah Boleo, Lucy Mupfumi, Etienne Kadima Yankinda, Unoda Chakalisa, Erik van Widenfelt, Tendani Gaolathe, Mompati O Mmalane, Scott Dryden-Peterson, Madisa Mine, Refeletswe Lebelonyane, Kara Bennett, Jean Leidner, Kathleen E Wirth, Eric Tchetgen Tchetgen, Kathleen Powis, Janet Moore, William A Clarke, Shahin Lockman, Joseph M Makhema, Max Essex, Vlad Novitsky

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Low prevalence of archived integrase strand transfer inhibitors resistance associated mutations in Botswana before the roll out of dolutegravir based first line antiretroviral ther... by Dorcas Maruapula, Doreen Ditshwanelo, Marea N. Pema, Ontlametse T. Bareng, Ontlametse T. Bareng, Wonderful T. Choga, Wonderful T. Choga, Natasha O. Moraka, Natasha O. Moraka, Patrick T. Mokgethi, Patrick T. Mokgethi, Kaelo K. Seatla, Catherine K. Koofhethile, Catherine K. Koofhethile, Boitumelo J. Zuze, Tendani Gaolathe, Molly Pretorius-Holme, Kebaneilwe Lebani, Joseph Makhema, Joseph Makhema, Vlad Novitsky, Roger Shapiro, Roger Shapiro, Shahin Lockman, Shahin Lockman, Shahin Lockman, Sikhulile Moyo, Sikhulile Moyo, Sikhulile Moyo, Simani Gaseitsiwe, Simani Gaseitsiwe

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Global and Regional Estimates for Subtype-Specific Therapeutic and Prophylactic HIV-1 Vaccines: A Modeling Study by Ramyiadarsini Elangovan, Michael Jenks, Jason Yun, Leslie Dickson-Tetteh, Shona Kirtley, Joris Hemelaar, WHO-UNAIDS Network for HIV Isolation and Characterisation, Alash’le G Abimiku, Simon Agwale, Chris Archibald, Boaz Avidor, María Gabriela Barbás, Francoise Barre-Sinoussi, Banson Barugahare, El Hadj Belabbes, Silvia Bertagnolio, Deborah Birx, Aleksei F Bobkov, James Brandful, Helba Bredell, Catherine A Brennan, James Brooks, Marie Bruckova, Luigi Buonaguro, Franco Buonaguro, Stefano Buttò, Anne Buvé, Mary Campbell, Jean Carr, Alex Carrera, Manuel Gómez Carrillo, Connie Celum, Beth Chaplin, Macarthur Charles, Dimitrios Chatzidimitriou, Zhiwei Chen, Katsumi Chijiwa, David Cooper, Philip Cunningham, Anoumou Dagnra, Cillian F de Gascun, Julia Del Amo, Elena Delgado, Ursula Dietrich, Dominic Dwyer, Dennis Ellenberger, Barbara Ensoli, Max Essex, Hervé Fleury, Peter N Fonjungo, Vincent Foulongne, Deepak A Gadkari, Feng Gao, Federico García, Roger Garsia, Guy Michel Gershy-Damet, Judith R Glynn, Ruth Goodall, Zehava Grossman, Monick Lindenmeyer Guimarães, Beatrice Hahn, Raph L Hamers, Osamah Hamouda, Ray Handema, Xiang He, Joshua Herbeck, David D Ho, Africa Holguin, Mina Hosseinipour, Gillian Hunt, Masahiko Ito, Mohamed Ali Bel Hadj Kacem, Erin Kahle, Pontiano Kaleebu, Marcia Kalish, Adeeba Kamarulzaman, Chun Kang, Phyllis Kanki, Edward Karamov, Jean-Claude Karasi, Kayitesi Kayitenkore, Tony Kelleher, Dwip Kitayaporn, Leondios G Kostrikis, Claudia Kucherer, Claudia Lara, Thomas Leitner, Kirsi Liitsola, Jai Lingappa, Marek Linka, Ivette Lorenzana de Rivera, Vladimir Lukashov, Shlomo Maayan, Luzia Mayr, Francine McCutchan, Nicolas Meda, Elisabeth Menu, Fred Mhalu, Doreen Mloka, John L Mokili, Brigitte Montes, Orna Mor, Mariza Morgado, Fausta Mosha, Awatef Moussi, James Mullins, Rafael Najera, Mejda Nasr, Nicaise Ndembi, Joel R Neilson, Vivek R Nerurkar, Florian Neuhann, Claudine Nolte, Vlad Novitsky, Philippe Nyambi, Marianna Ofner, Fem J Paladin, Anna Papa, Jean Pape, Neil Parkin, Chris Parry, Martine Peeters, Alexandra Pelletier, Lucía Pérez-Álvarez, Deenan Pillay, Angie Pinto, Trinh Duy Quang, Cecilia Rademeyer, Filimone Raikanikoda, Mark A. Rayfield, Jean-Marc Reynes, Tobias Rinke de Wit, Kenneth E Robbins, Morgane Rolland, Christine Rousseau, Jesus Salazar-Gonzales, Hanan Salem, Mika Salminen, Horacio Salomon, Paul Sandstrom, Mario L Santiago, Abdoulaye D Sarr, Bryan Schroeder, Michel Segondy, Philippe Selhorst, Sylvester Sempala, Jean Servais, Ansari Shaik, Yiming Shao, Amine Slim, Marcelo A Soares, Elijah Songok, Debbie Stewart, Julie Stokes, Shambavi Subbarao, Ruengpung Sutthent, Jun Takehisa, Amilcar Tanuri, Kok Keng Tee, Kiran Thapa, Michael Thomson, Tyna Tran, Willy Urassa, Hiroshi Ushijima, Philippe van de Perre, Guido van der Groen, Kristel van Laethem, Joep van Oosterhout, Ard van Sighem, Eric van Wijngaerden, Anne-Mieke Vandamme, Jurgen Vercauteren, Nicole Vidal, Lesley Wallace, Carolyn Williamson, Dawit Wolday, Jianqing Xu, Chunfu Yang, Linqi Zhang, Rong Zhang

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Global associations of key populations with HIV-1 recombinants: a systematic review, global survey, and individual participant data meta-analysis by Nkazi Nchinda, Ramyiadarsini Elangovan, Jason Yun, Leslie Dickson-Tetteh, Shona Kirtley, Joris Hemelaar, WHO-UNAIDS Network for HIV Isolation and Characterisation, Alash'le G. Abimiku, Simon Agwale, Chris Archibald, Boaz Avidor, Barbás María Gabriela, Francoise Barre-Sinoussi, Banson Barugahare, El Hadj Belabbes, Silvia Bertagnolio, Deborah Birx, Aleksei F. Bobkov, James Brandful, Helba Bredell, Catherine A. Brennan, James Brooks, Marie Bruckova, Luigi Buonaguro, Franco Buonaguro, Stefano Buttò, Anne Buve, Mary Campbell, Jean Carr, Alex Carrera, Manuel Gómez Carrillo, Connie Celum, Beth Chaplin, Macarthur Charles, Dimitrios Chatzidimitriou, Zhiwei Chen, Katsumi Chijiwa, David Cooper, Philip Cunningham, Anoumou Dagnra, Cillian F. de Gascun, Julia Del Amo, Elena Delgado, Ursula Dietrich, Dominic Dwyer, Dennis Ellenberger, Barbara Ensoli, Max Essex, Herve Fleury, Peter N. Fonjungo, Vincent Foulongne, Deepak A. Gadkari, Feng Gao, Federico García, Roger Garsia, Guy Michel Gershy-Damet, Judith R. Glynn, Ruth Goodall, Zehava Grossman, Monick Lindenmeyer Guimarães, Beatrice Hahn, Raph L. Hamers, Osamah Hamouda, Ray Handema, Xiang He, Joshua Herbeck, David D. Ho, Africa Holguin, Mina Hosseinipour, Gillian Hunt, Masahiko Ito, Mohamed Ali Bel Hadj Kacem, Erin Kahle, Pontiano Kaleebu, Marcia Kalish, Adeeba Kamarulzaman, Chun Kang, Phyllis Kanki, Edward Karamov, Jean-Claude Karasi, Kayitesi Kayitenkore, Tony Kelleher, Dwip Kitayaporn, Leondios G. Kostrikis, Claudia Kucherer, Claudia Lara, Thomas Leitner, Kirsi Liitsola, Jai Lingappa, Marek Linka, Ivette Lorenzana de Rivera, Vladimir Lukashov, Shlomo Maayan, Luzia Mayr, Francine McCutchan, Nicolas Meda, Elisabeth Menu, Fred Mhalu, Doreen Mloka, John L. Mokili, Brigitte Montes, Orna Mor, Mariza Morgado, Fausta Mosha, Awatef Moussi, James Mullins, Rafael Najera, Mejda Nasr, Nicaise Ndembi, Joel R. Neilson, Vivek R. Nerurkar, Florian Neuhann, Claudine Nolte, Vlad Novitsky, Philippe Nyambi, Marianna Ofner, Fem J. Paladin, Anna Papa, Jean Pape, Neil Parkin, Chris Parry, Martine Peeters, Alexandra Pelletier, Lucía Pérez-Álvarez, Deenan Pillay, Angie Pinto, Trinh Duy Quang, Cecilia Rademeyer, Filimone Raikanikoda, Mark A. Rayfield, Jean-Marc Reynes, Tobias Rinke de Wit, Kenneth E. Robbins, Morgane Rolland, Christine Rousseau, Jesus Salazar-Gonzales, Hanan Salem, Mika Salminen, Horacio Salomon, Paul Sandstrom, Mario L. Santiago, Abdoulaye D. Sarr, Bryan Schroeder, Michel Segondy, Philippe Selhorst, Sylvester Sempala, Jean Servais, Ansari Shaik, Yiming Shao, Amine Slim, Marcelo A. Soares, Elijah Songok, Debbie Stewart, Julie Stokes, Shambavi Subbarao, Ruengpung Sutthent, Jun Takehisa, Amilcar Tanuri, Kok Keng Tee, Kiran Thapa, Michael Thomson, Tyna Tran, Willy Urassa, Hiroshi Ushijima, Philippe van de Perre, Guido van der Groen, Kristel van Laethem, Joep van Oosterhout, Ard van Sighem, Eric van Wijngaerden, Anne-Mieke Vandamme, Jurgen Vercauteren, Nicole Vidal, Lesley Wallace, Carolyn Williamson, Dawit Wolday, Jianqing Xu, Chunfu Yang, Linqi Zhang, Rong Zhang

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