Publications
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Predicting the mutational drivers of future SARS-CoV-2 variants of concern M. Cyrus Maher, Istvan Bartha, Steven Weaver, Julia di Iulio, Elena Ferri, Leah Soriaga, Florian A. Lempp, Brian L. Hie, Bryan Bryson, Bonnie Berger, David L. Robertson, Gyorgy Snell, Davide Corti, Herbert W. Virgin, Sergei L. Kosakovsky Pond, Amalio Telenti Science Translational Medicine (2022) Continued Emergence and Evolution of Omicron in South Africa: New BA.4 and BA.5 lineages Houriiyah Tegally, Monika Moir, Josie Everatt, Marta Giovanetti, Cathrine Scheepers, Eduan Wilkinson, Kathleen Subramoney, Sikhulile Moyo, Daniel G. Amoako, Cheryl Baxter, Christian L. Althaus, Ugochukwu J. Anyaneji, Dikeledi Kekana, Raquel Viana, Jennifer Giandhari, Richard J. Lessells, Tongai Maponga, Dorcas Maruapula, Wonderful Choga, Mogomotsi Matshaba, Simnikiwe Mayaphi, Nokuzola Mbhele, Mpaphi B. Mbulawa, Nokukhanya Msomi, Yeshnee Naidoo, Sureshnee Pillay, Tomasz Janusz Sanko, James E. San, Lesley Scott, Lavanya Singh, Nonkululeko A. Magini, Pamela Smith-Lawrence, Wendy Stevens, Graeme Dor, Derek Tshiabuila, Nicole Wolter, Wolfgang Preiser, Florette K. Treurnicht, Marietjie Venter, Michaela Davids, Georginah Chiloane, Adriano Mendes, Caitlyn McIntyre, Aine O’Toole, Christopher Ruis, Thomas P. Peacock, Cornelius Roemer, Carolyn Williamson, Oliver G. Pybus, Jinal Bhiman, Allison Glass, Darren P. Martin, Andrew Rambaut, Simani Gaseitsiwe, Anne von Gottberg, Tulio de Oliveira medRxiv (2022) Emergence of SARS-CoV-2 Omicron lineages BA.4 and BA.5 in South Africa Houriiyah Tegally, Monika Moir, Josie Everatt, Marta Giovanetti, Cathrine Scheepers, Eduan Wilkinson, Kathleen Subramoney, Zinhle Makatini, Sikhulile Moyo, Daniel G. Amoako, Cheryl Baxter, Christian L. Althaus, Ugochukwu J. Anyaneji, Dikeledi Kekana, Raquel Viana, Jennifer Giandhari, Richard J. Lessells, Tongai Maponga, Dorcas Maruapula, Wonderful Choga, Mogomotsi Matshaba, Mpaphi B. Mbulawa, Nokukhanya Msomi, Armand Phillip Bester, Mathilda Claassen, Deelan Doolabh, Innocent Mudau, Nokuzola Mbhele, Susan Engelbrecht, Dominique Goedhals, Diana Hardie, Nei-Yuan Hsiao, Arash Iranzadeh, Arshad Ismail, Rageema Joseph, Arisha Maharaj, Boitshoko Mahlangu, Kamela Mahlakwane, Ashlyn Davis, Gert Marais, Koleka Mlisana, Anele Mnguni, Thabo Mohale, Gerald Motsatsi, Peter Mwangi, Noxolo Ntuli, Martin Nyaga, Luicer Olubayo, Botshelo Radibe, Yajna Ramphal, Upasana Ramphal, Wilhelmina Strasheim, Naume Tebeila, Stephanie van Wyk, Shannon Wilson, Alexander G. Lucaci, Steven Weaver, Akhil Maharaj, Yusasha Pillay, Michaela Davids, Adriano Mendes, Simnikiwe Mayaphi, Yeshnee Naidoo, Sureshnee Pillay, Tomasz Janusz Sanko, James E. San, Lesley Scott, Lavanya Singh, Nonkululeko A. Magini, Pamela Smith-Lawrence, Wendy Stevens, Graeme Dor, Derek Tshiabuila, Nicole Wolter, Wolfgang Preiser, Florette K. Treurnicht, Marietjie Venter, Georginah Chiloane, Caitlyn McIntyre, Aine O’Toole, Christopher Ruis, Thomas P. Peacock, Cornelius Roemer, Sergei L. Kosakovsky Pond, Carolyn Williamson, Oliver G. Pybus, Jinal N. Bhiman, Allison Glass, Darren P. Martin, Ben Jackson, Andrew Rambaut, Oluwakemi Laguda-Akingba, Simani Gaseitsiwe, Anne von Gottberg, Tulio de Oliveira Nature Medicine (2022) Rapid epidemic expansion of the SARS-CoV-2 Omicron variant in southern Africa Raquel Viana, Sikhulile Moyo, Daniel G. Amoako, Houriiyah Tegally, Cathrine Scheepers, Christian L. Althaus, Ugochukwu J. Anyaneji, Phillip A. Bester, Maciej F. Boni, Mohammed Chand, Wonderful T. Choga, Rachel Colquhoun, Michaela Davids, Koen Deforche, Deelan Doolabh, Louis du Plessis, Susan Engelbrecht, Josie Everatt, Jennifer Giandhari, Marta Giovanetti, Diana Hardie, Verity Hill, Nei-Yuan Hsiao, Arash Iranzadeh, Arshad Ismail, Charity Joseph, Rageema Joseph, Legodile Koopile, Sergei L. Kosakovsky Pond, Moritz U. G. Kraemer, Lesego Kuate-Lere, Oluwakemi Laguda-Akingba, Onalethatha Lesetedi-Mafoko, Richard J. Lessells, Shahin Lockman, Alexander G. Lucaci, Arisha Maharaj, Boitshoko Mahlangu, Tongai Maponga, Kamela Mahlakwane, Zinhle Makatini, Gert Marais, Dorcas Maruapula, Kereng Masupu, Mogomotsi Matshaba, Simnikiwe Mayaphi, Nokuzola Mbhele, Mpaphi B. Mbulawa, Adriano Mendes, Koleka Mlisana, Anele Mnguni, Thabo Mohale, Monika Moir, Kgomotso Moruisi, Mosepele Mosepele, Gerald Motsatsi, Modisa S. Motswaledi, Thongbotho Mphoyakgosi, Nokukhanya Msomi, Peter N. Mwangi, Yeshnee Naidoo, Noxolo Ntuli, Martin Nyaga, Lucier Olubayo, Sureshnee Pillay, Botshelo Radibe, Yajna Ramphal, Upasana Ramphal, James E. San, Lesley Scott, Roger Shapiro, Lavanya Singh, Pamela Smith-Lawrence, Wendy Stevens, Amy Strydom, Kathleen Subramoney, Naume Tebeila, Derek Tshiabuila, Joseph Tsui, Stephanie van Wyk, Steven Weaver, Constantinos K. Wibmer, Eduan Wilkinson, Nicole Wolter, Alexander E. Zarebski, Boitumelo Zuze, Dominique Goedhals, Wolfgang Preiser, Florette Treurnicht, Marietje Venter, Carolyn Williamson, Oliver G. Pybus, Jinal Bhiman, Allison Glass, Darren P. Martin, Andrew Rambaut, Simani Gaseitsiwe, Anne von Gottberg, Tulio de Oliveira Nature (2022) Selection Analysis Identifies Clusters of Unusual Mutational Changes in Omicron Lineage BA.1 That Likely Impact Spike Function Darren P. Martin, Spyros Lytras, Alexander G. Lucaci, Wolfgang Maier, Björn Grüning, Stephen D. Shank, Steven Weaver, Oscar A. MacLean, Richard J. Orton, Philippe Lemey, Maciej F. Boni, Houriiyah Tegally, Gordon W. Harkins, Cathrine Scheepers, Jinal N. Bhiman, Josie Everatt, Daniel G. Amoako, James Emmanuel San, Jennifer Giandhari, Alex Sigal, Carolyn Williamson, Nei-yuan Hsiao, Anne von Gottberg, Arne De Klerk, Robert W. Shafer, David L. Robertson, Robert J. Wilkinson, B. Trevor Sewell, Richard Lessells, Anton Nekrutenko, Allison J. Greaney, Tyler N. Starr, Jesse D. Bloom, Ben Murrell, Eduan Wilkinson, Ravindra K. Gupta, Tulio de Oliveira, Sergei L. Kosakovsky Pond Molecular Biology and Evolution (2022) Selection analysis identifies unusual clustered mutational changes in Omicron lineage BA.1 that likely impact Spike function Darren P Martin, Spyros Lytras, Alexander G Lucaci, Wolfgang Maier, Björn Grüning, Stephen D Shank, Steven Weaver, Oscar A MacLean, Richard J Orton, Philippe Lemey, Maciej F Boni, Houriiyah Tegally, Gordon Harkins, Cathrine Scheepers, Jinal N Bhiman, Josie Everatt, Daniel G Amoako, James Emmanuel San, Jennifer Giandhari, Alex Sigal, Carolyn Williamson, Nei-yuan Hsiao, Anne von Gottberg, Arne De Klerk, Robert W Shafer, David L Robertson, Robert J Wilkinson, B Trevor Sewell, Richard Lessells, Anton Nekrutenko, Allison J. Greaney, Tyler N. Starr, Jesse D. Bloom, Ben Murrell, Eduan Wilkinson, Ravindra K Gupta, Tulio de Oliveira, Sergei L Kosakovsky Pond bioRxiv (2022) The emergence and ongoing convergent evolution of the SARS-CoV-2 N501Y lineages Darren P. Martin, Steven Weaver, Houriiyah Tegally, James Emmanuel San, Stephen D. Shank, Eduan Wilkinson, Alexander G. Lucaci, Jennifer Giandhari, Sureshnee Naidoo, Yeshnee Pillay, Lavanya Singh, Richard J. Lessells, Ravindra K. Gupta, Joel O. Wertheim, Anton Nekturenko, Ben Murrell, Gordon W. Harkins, Philippe Lemey, Oscar A. MacLean, David L. Robertson, Tulio de Oliveira, Sergei L. Kosakovsky Pond Cell (2021) Characteristics and growth of the genetic HIV transmission network of Mexico City during 2020 Vanessa Dávila‐Conn, Claudia García‐Morales, Margarita Matías‐Florentino, Eduardo López‐Ortiz, Héctor E. Paz‐Juárez, Ángeles Beristain‐Barreda, Miroslava Cárdenas‐Sandoval, Daniela Tapia‐Trejo, Dulce M. López‐Sánchez, Manuel Becerril‐Rodríguez, Pedro García‐Esparza, Israel Macías‐González, Patricia Iracheta‐Hernández, Steven Weaver, Joel O. Wertheim, Gustavo Reyes‐Terán, Andrea González‐Rodríguez, Santiago Ávila‐Ríos Journal of the International AIDS Society (2021) Detection of a SARS-CoV-2 variant of concern in South Africa Houriiyah Tegally, Eduan Wilkinson, Marta Giovanetti, Arash Iranzadeh, Vagner Fonseca, Jennifer Giandhari, Deelan Doolabh, Sureshnee Pillay, Emmanuel James San, Nokukhanya Msomi, Koleka Mlisana, Anne von Gottberg, Sibongile Walaza, Mushal Allam, Arshad Ismail, Thabo Mohale, Allison J. Glass, Susan Engelbrecht, Gert Van Zyl, Wolfgang Preiser, Francesco Petruccione, Alex Sigal, Diana Hardie, Gert Marais, Nei-yuan Hsiao, Stephen Korsman, Mary-Ann Davies, Lynn Tyers, Innocent Mudau, Denis York, Caroline Maslo, Dominique Goedhals, Shareef Abrahams, Oluwakemi Laguda-Akingba, Arghavan Alisoltani-Dehkordi, Adam Godzik, Constantinos Kurt Wibmer, Bryan Trevor Sewell, José Lourenço, Luiz Carlos Junior Alcantara, Sergei L. Kosakovsky Pond, Steven Weaver, Darren Martin, Richard J. Lessells, Jinal N. Bhiman, Carolyn Williamson, Tulio de Oliveira Nature (2021) Escape of SARS-CoV-2 501Y.V2 from neutralization by convalescent plasma Sandile Cele, Inbal Gazy, Laurelle Jackson, Shi-Hsia Hwa, Houriiyah Tegally, Gila Lustig, Jennifer Giandhari, Sureshnee Pillay, Eduan Wilkinson, Yeshnee Naidoo, Farina Karim, Yashica Ganga, Khadija Khan, Mallory Bernstein, Alejandro B. Balazs, Bernadett I. Gosnell, Willem Hanekom, Mahomed-Yunus S. Moosa, Richard J. Lessells, Tulio de Oliveira, Alex Sigal Nature (2021) HIV-1 and SARS-CoV-2: Patterns in the evolution of two pandemic pathogens Will Fischer, Elena E. Giorgi, Srirupa Chakraborty, Kien Nguyen, Tanmoy Bhattacharya, James Theiler, Pablo A. Goloboff, Hyejin Yoon, Werner Abfalterer, Brian T. Foley, Houriiyah Tegally, James Emmanuel San, Tulio de Oliveira, Eduan Wilkinson, Nokukhanya Msomi, Arash Iranzadeh, Vagner Fonseca, Deelan Doolabh, Koleka Mlisana, Anne von Gottberg, Sibongile Walaza, Mushal Allam, Arshad Ismail, Thabo Mohale, Allison J. Glass, Susan Engelbrecht, Gert Van Zyl, Wolfgang Preiser, Francesco Petruccione, Alex Sigal, Diana Hardie, Gert Marais, Marvin Hsiao, Stephen Korsman, Mary-Ann Davies, Lynn Tyers, Innocent Mudau, Denis York, Caroline Maslo, Dominique Goedhals, Shareef Abrahams, Oluwakemi Laguda-Akingba, Arghavan Alisoltani-Dehkordi, Adam Godzik, Constantinos Kurt Wibmer, Bryan Trevor Sewell, José Lourenço, Sergei L. Kosakovsky Pond, Steven Weaver, Marta Giovanetti, Luiz Carlos Junior Alcantara, Darren Martin, Jinal N. Bhiman, Carolyn Williamson, Sandrasegaram Gnanakaran, Bette Korber Cell Host and Microbe (2021) Multiplex qPCR discriminates variants of concern to enhance global surveillance of SARS-CoV-2 Chantal B. F. Vogels, Mallery I. Breban, Isabel M. Ott, Tara Alpert, Mary E. Petrone, Anne E. Watkins, Chaney C. Kalinich, Rebecca Earnest, Jessica E. Rothman, Jaqueline Goes de Jesus, Ingra Morales Claro, Giulia Magalhães Ferreira, Myuki A. E. Crispim, Lavanya Singh, Houriiyah Tegally, Ugochukwu J. Anyaneji, Emma B. Hodcroft, Christopher E. Mason, Gaurav Khullar, Jessica Metti, Joel T. Dudley, Matthew J. MacKay, Megan Nash, Jianhui Wang, Chen Liu, Pei Hui, Steven Murphy, Caleb Neal, Eva Laszlo, Marie L. Landry, Anthony Muyombwe, Randy Downing, Jafar Razeq, Tulio de Oliveira, Nuno R. Faria, Ester C. Sabino, Richard A. Neher, Joseph R. Fauver, Nathan D. Grubaugh PLoS Biology (2021) PCR assay to enhance global surveillance for SARS-CoV-2 variants of concern Chantal B.F. Vogels, Mallery I. Breban, Tara Alpert, Mary E. Petrone, Anne E. Watkins, Isabel M. Ott, Jaqueline Goes de Jesus, Ingra Morales Claro, Giulia Magalhães Ferreira, Myuki A.E. Crispim, Lavanya Singh, Houriiyah Tegally, Ugochukwu J. Anyaneji, Emma B. Hodcroft, Christopher E. Mason, Gaurav Khullar, Jessica Metti, Joel T. Dudley, Matthew J. MacKay, Megan Nash, Jianhui Wang, Chen Liu, Pei Hui, Steven Murphy, Caleb Neal, Eva Laszlo, Marie L. Landry, Anthony Muyombwe, Randy Downing, Jafar Razeq, Tulio de Oliveira, Nuno R. Faria, Ester C. Sabino, Richard A. Neher, Joseph R. Fauver, Nathan D. Grubaugh medRxiv (2021) The emergence and ongoing convergent evolution of the N501Y lineages coincides with a major global shift in the SARS-CoV-2 selective landscape Darren P Martin, Steven Weaver, Houryiah Tegally, Emmanuel James San, Stephen D Shank, Eduan Wilkinson, Alexander G Lucaci, Jennifer Giandhari, Sureshnee Naidoo, Yeshnee Pillay, Lavanya Singh, Richard J Lessells, Ravindra K Gupta, Joel O Wertheim, Anton Nekturenko, Ben Murrell, Gordon W Harkins, Philippe Lemey, Oscar A MacLean, David L Robertson, Tulio de Oliveira, Sergei L Kosakovsky Pond medRxiv (2021) Emergence and rapid spread of a new severe acute respiratory syndrome-related coronavirus 2 (SARS-CoV-2) lineage with multiple spike mutations in South Africa Houriiyah Tegally, Eduan Wilkinson, Marta Giovanetti, Arash Iranzadeh, Vagner Fonseca, Jennifer Giandhari, Deelan Doolabh, Sureshnee Pillay, Emmanuel James San, Nokukhanya Msomi, Koleka Mlisana, Anne von Gottberg, Sibongile Walaza, Mushal Allam, Arshad Ismail, Thabo Mohale, Allison J Glass, Susan Engelbrecht, Gert Van Zyl, Wolfgang Preiser, Francesco Petruccione, Alex Sigal, Diana Hardie, Gert Marais, Marvin Hsiao, Stephen Korsman, Mary-Ann Davies, Lynn Tyers, Innocent Mudau, Denis York, Caroline Maslo, Dominique Goedhals, Shareef Abrahams, Oluwakemi Laguda-Akingba, Arghavan Alisoltani-Dehkordi, Adam Godzik, Constantinos Kurt Wibmer, Bryan Trevor Sewell, José Lourenço, Luiz Carlos Junior Alcantara, Sergei L Kosakovsky Pond, Steven Weaver, Darren Martin, Richard J Lessells, Jinal N Bhiman, Carolyn Williamson, Tulio de Oliveira medRxiv (2020) HyPhy 2.5 - A Customizable Platform for Evolutionary Hypothesis Testing Using Phylogenies Sergei L Kosakovsky Pond, Art F Y Poon, Ryan Velazquez, Steven Weaver, N Lance Hepler, Ben Murrell, Stephen D Shank, Brittany Rife Magalis, Dave Bouvier, Anton Nekrutenko, Sadie Wisotsky, Stephanie J Spielman, Simon D W Frost, Spencer V Muse Molecular Biology and Evolution (2020) No more business as usual: Agile and effective responses to emerging pathogen threats require open data and open analytics Dannon Baker, Marius van den Beek, Daniel Blankenberg, Dave Bouvier, John Chilton, Nate Coraor, Frederik Coppens, Ignacio Eguinoa, Simon Gladman, Björn Grüning, Nicholas Keener, Delphine Larivière, Andrew Lonie, Sergei Kosakovsky Pond, Wolfgang Maier, Anton Nekrutenko, James Taylor, Steven Weaver PLoS Pathogens (2020) Rapid sequencing of complete env genes from primary HIV-1 Samples Melissa Laird Smith, Ben Murrell, Kemal Eren, Caroline Ignacio, Elise Landais, Steven Weaver, Pham Phung, Colleen Ludka, Lance Hepler, Gemma Caballero, Tristan Pollner, Yan Guo, Douglas Richman, Pascal Poignard, Ellen E. Paxinos, Sergei L. Kosakovsky Pond, Davey M. Smith Virus Evolution (2016) Gene-wide identification of episodic selection Molecular biology and evolution (2015)
OCCAMS: An Open Source Clinical Content Analysis and Management System. Applications for HIV Primary Infection Research.