Steven Weaver

Minus the Error: Testing for Positive Selection in the Presence of Residual Alignment Errors

Avery Selberg, Nathan L Clark, Timothy B Sackton, Spencer V Muse, Alexander G Lucaci, Steven Weaver, Anton Nekrutenko, Maria Chikina, Sergei L Kosakovsky Pond

(2025)

Viral genome sequence datasets display pervasive evidence of strand-specific substitution biases that are best described using non-reversible nucleotide substitution models

Rita Sianga-Mete, Penelope Hartnady, Wimbai Caroline Mandikumba, Kayleigh Rutherford, Christopher Brian Currin, Florence Phelanyane, Sabina Stefan, Steven Weaver, Sergei L Kosakovsky Pond, Darren P Martin

eLife 12 : RP87361 (2025)

HIV molecular network in Mexico City (2021-2022): Understanding transmission dynamics through the role of newly diagnosed cases

Samuel E Schulz-Medina, Daniela Tapia-Trejo, Margarita Matías-Florentino, Dulce M López-Sánchez, Claudia García-Morales, Jessica Monreal-Flores, Ángeles Beristain-Barreda, Miroslava Cárdenas-Sandoval, Manuel Becerril-Rodríguez, Silvia Del Arenal-Sánchez, Verónica Quiroz-Morales, Steven Weaver, Joel O Wertheim, Raúl Adrián Cruz-Flores, Gustavo Reyes-Terán, Andrea González-Rodríguez, Santiago Ávila-Ríos, Vanessa Dávila-Conn

HIV Medicine 26 (7) : 1046-1059 (2025)

Nationwide Implementation of HIV Molecular Cluster Detection by Centers for Disease Control and Prevention and State and Local Health Departments, United States

Anne Marie France, Camden J Hallmark, Nivedha Panneer, Rachael Billock, Olivia O Russell, Mary Plaster, Jessica Alberti, Fathima Nuthan, Neeraja Saduvala, David Philpott, M Cheryl Bañez Ocfemia, Scott Cope, Angela L Hernandez, Sergei L Kosakovsky Pond, Joel O Wertheim, Steven Weaver, Saja Khader, Kevin Johnson, Alexandra M Oster

Emerging Infectious Diseases 31 (13) : 80-88 (2025)

Continued Emergence and Evolution of Omicron in South Africa: New BA.4 and BA.5 lineages

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, 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 28 (9) : 1785-1790 (2022)

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 14 (633) : eabk3445 (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 603 (7902) : 679-686 (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 39 (4) (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)

TopHap: rapid inference of key phylogenetic structures from common haplotypes in large genome collections with limited diversity

Marcos A Caraballo-Ortiz, Sayaka Miura, Maxwell Sanderford, Tenzin Dolker, Qiqing Tao, Steven Weaver, Sergei L K Pond, Sudhir Kumar

Bioinformatics 38 (10) : 2719-2726 (2022)

An Evolutionary Portrait of the Progenitor SARS-CoV-2 and Its Dominant Offshoots in COVID-19 Pandemic

Sudhir Kumar, Qiqing Tao, Steven Weaver, Maxwell Sanderford, Marcos A Caraballo-Ortiz, Sudip Sharma, Sergei L K Pond, Sayaka Miura

Molecular Biology and Evolution 38 (8) : 3046-3059 (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 24 (11) : e25836 (2021)

Contrast-FEL - A Test for Differences in Selective Pressures at Individual Sites among Clades and Sets of Branches

Sergei L Kosakovsky Pond, Sadie R Wisotsky, Ananias Escalante, Brittany Rife Magalis, Steven Weaver

Molecular Biology and Evolution 38 (3) : 1184-1198 (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 592 (7854) : 438-443 (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 593 (7857) : 142-146 (2021)

Extra base hits: Widespread empirical support for instantaneous multiple-nucleotide changes

Alexander G Lucaci, Sadie R Wisotsky, Stephen D Shank, Steven Weaver, Sergei L Kosakovsky Pond

PLOS ONE 16 (3) : e0248337 (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, Sandrasegaram Gnanakaran, Bette Korber

Cell Host and Microbe 29 (7) : 1093-1110 (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 19 (5) : e3001236 (2021)

Natural selection in the evolution of SARS-CoV-2 in bats created a generalist virus and highly capable human pathogen

Oscar A MacLean, Spyros Lytras, Steven Weaver, Joshua B Singer, Maciej F Boni, Philippe Lemey, Sergei L Kosakovsky Pond, David L Robertson

PLOS Biology 19 (3) : e3001115 (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)

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 184 (20) : 5189-5200.e7 (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

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 37 (1) : 295-299 (2020)

Natural selection in the evolution of SARS-CoV-2 in bats, not humans, created a highly capable human pathogen

Oscar A MacLean, Spyros Lytras, Steven Weaver, Joshua B Singer, Maciej F Boni, Philippe Lemey, Sergei L Kosakovsky Pond, David L Robertson

bioRxiv (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 16 (8) : e1008643 (2020)

Evolution of viral genomes: Interplay between selection, recombination, and other forces

Stephanie J Spielman, Steven Weaver, Stephen D Shank, Brittany Rife Magalis, Michael Li, Sergei L Kosakovsky Pond

Methods in Molecular Biology 1910 : 427-468 (2019)

Full-Length Envelope Analyzer (FLEA): A tool for longitudinal analysis of viral amplicons

Kemal Eren, Steven Weaver, Robert Ketteringham, Morné Valentyn, Melissa Laird Smith, Venkatesh Kumar, Sanjay Mohan, Sergei L Kosakovsky Pond, Ben Murrell

PLoS Computational Biology 14 (12) : e1006498 (2018)

HIV-TRACE (TRAnsmission Cluster Engine): A tool for large scale molecular epidemiology of HIV-1 and other rapidly evolving pathogens

Sergei L Kosakovsky Pond, Steven Weaver, Andrew J Leigh Brown, Joel O Wertheim

Molecular Biology and Evolution 35 (7) : 1812-1819 (2018)

phylotree.js - a JavaScript library for application development and interactive data visualization in phylogenetics

Stephen D Shank, Steven Weaver, Sergei L Kosakovsky Pond

BMC Bioinformatics 19 (1) : 276 (2018)

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 2 (2) : vew018 (2016)

Gene-wide identification of episodic selection

Ben Murrell, Steven Weaver, Martin D Smith, Joel O Wertheim, Sasha Murrell, Anthony Aylward, Kemal Eren, Tristan Pollner, Darren P Martin, Davey M Smith, Konrad Scheffler, Sergei L Kosakovsky Pond

Molecular Biology and Evolution 32 (5) : 1365-71 (2015)

Less is more: An adaptive branch-site random effects model for efficient detection of episodic diversifying selection

Martin D Smith, Joel O Wertheim, Steven Weaver, Ben Murrell, Konrad Scheffler, Sergei L Kosakovsky Pond

Molecular Biology and Evolution 32 (5) : 1342-53 (2015)

IDEPI: Rapid Prediction of HIV-1 Antibody Epitopes and Other Phenotypic Features from Sequence Data Using a Flexible Machine Learning Platform

N Lance Hepler, Konrad Scheffler, Steven Weaver, Ben Murrell, Douglas D Richman, Dennis R Burton, Pascal Poignard, Davey M Smith, Sergei L Kosakovsky Pond

PLoS Computational Biology 10 (9) : e1003842 (2014)