Risk of rapid evolutionary escape from biomedical interventions targeting SARS-CoV-2 spike protein. by Debra Van Egeren, Alexander Novokhodko, Madison Stoddard, Uyen Tran, Bruce Zetter, Michael Rogers, Bradley L Pentelute, Jonathan M Carlson, Mark Hixon, Diane Joseph-McCarthy, Arijit Chakravarty

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CD8 T cells targeting adapted epitopes in chronic HIV infection promote dendritic cell maturation and CD4 T cell trans-infection. by Kai Qin, Sushma Boppana, Victor Y Du, Jonathan M Carlson, Ling Yue, Dario A Dilernia, Eric Hunter, Robbie B Mailliard, Simon A Mallal, Anju Bansal, Paul A Goepfert

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Phylogenetic dependency networks: inferring patterns of CTL escape and codon covariation in HIV-1 Gag. by Jonathan M Carlson, Zabrina L Brumme, Christine M Rousseau, Chanson J Brumme, Philippa Matthews, Carl Kadie, James I Mullins, Bruce D Walker, P Richard Harrigan, Philip J R Goulder, David Heckerman

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Prevalence and Characteristics of Hepatitis B Virus (HBV) Coinfection among HIV-Positive Women in South Africa and Botswana. by Philippa C Matthews, Apostolos Beloukas, Amna Malik, Jonathan M Carlson, Pieter Jooste, Anthony Ogwu, Roger Shapiro, Lynn Riddell, Fabian Chen, Graz Luzzi, Manjeetha Jaggernath, Gerald Jesuthasan, Katie Jeffery, Thumbi Ndung'u, Philip J R Goulder, Anna Maria Geretti, Paul Klenerman

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Co-operative additive effects between HLA alleles in control of HIV-1. by Philippa C Matthews, Jennifer Listgarten, Jonathan M Carlson, Rebecca Payne, Kuan-Hsiang Gary Huang, John Frater, Dominique Goedhals, Dewald Steyn, Cloete van Vuuren, Paolo Paioni, Pieter Jooste, Anthony Ogwu, Roger Shapiro, Zenele Mncube, Thumbi Ndung'u, Bruce D Walker, David Heckerman, Philip J R Goulder

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PARV4 prevalence, phylogeny, immunology and coinfection with HIV, HBV and HCV in a multicentre African cohort [version 1; referees: 2 approved] by Colin P. Sharp, William F. Gregory, Louise Hattingh, Amna Malik, Emily Adland, Samantha Daniels, Anriette van Zyl, Jonathan M. Carlson, Susan Wareing, Anthony Ogwu, Roger Shapiro, Lynn Riddell, Fabian Chen, Thumbi Ndung'u, Philip J.R. Goulder, Paul Klenerman, Peter Simmonds, Pieter Jooste, Philippa C. Matthews

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Amino-acid co-variation in HIV-1 Gag subtype C: HLA-mediated selection pressure and compensatory dynamics. by Morgane Rolland, Jonathan M Carlson, Siriphan Manocheewa, J Victor Swain, Erinn Lanxon-Cookson, Wenjie Deng, Christine M Rousseau, Dana N Raugi, Gerald H Learn, Brandon S Maust, Hoosen Coovadia, Thumbi Ndung'u, Philip J R Goulder, Bruce D Walker, Christian Brander, David E Heckerman, James I Mullins

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Progression to AIDS in South Africa is associated with both reverting and compensatory viral mutations. by Kuan-Hsiang Gary Huang, Dominique Goedhals, Jonathan M Carlson, Mark A Brockman, Swati Mishra, Zabrina L Brumme, Stephen Hickling, Christopher S W Tang, Toshiyuki Miura, Chris Seebregts, David Heckerman, Thumbi Ndung'u, Bruce Walker, Paul Klenerman, Dewald Steyn, Philip Goulder, Rodney Phillips, Bloemfontein-Oxford Collaborative Group, Cloete van Vuuren, John Frater

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Role of transmitted Gag CTL polymorphisms in defining replicative capacity and early HIV-1 pathogenesis. by Jessica L Prince, Daniel T Claiborne, Jonathan M Carlson, Malinda Schaefer, Tianwei Yu, Shabir Lahki, Heather A Prentice, Ling Yue, Sundaram A Vishwanathan, William Kilembe, Paul Goepfert, Matthew A Price, Jill Gilmour, Joseph Mulenga, Paul Farmer, Cynthia A Derdeyn, Jiaming Tang, David Heckerman, Richard A Kaslow, Susan A Allen, Eric Hunter

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HLA-associated immune escape pathways in HIV-1 subtype B Gag, Pol and Nef proteins. by Zabrina L Brumme, Mina John, Jonathan M Carlson, Chanson J Brumme, Dennison Chan, Mark A Brockman, Luke C Swenson, Iris Tao, Sharon Szeto, Pamela Rosato, Jennifer Sela, Carl M Kadie, Nicole Frahm, Christian Brander, David W Haas, Sharon A Riddler, Richard Haubrich, Bruce D Walker, P Richard Harrigan, David Heckerman, Simon Mallal

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CD8 and CD4 epitope predictions in RV144: no strong evidence of a T-cell driven sieve effect in HIV-1 breakthrough sequences from trial participants. by Kalpana Dommaraju, Gustavo Kijak, Jonathan M Carlson, Brendan B Larsen, Sodsai Tovanabutra, Dan E Geraghty, Wenjie Deng, Brandon S Maust, Paul T Edlefsen, Eric Sanders-Buell, Silvia Ratto-Kim, Mark S deSouza, Supachai Rerks-Ngarm, Sorachai Nitayaphan, Punnee Pitisuttihum, Jaranit Kaewkungwal, Robert J O'Connell, Merlin L Robb, Nelson L Michael, James I Mullins, Jerome H Kim, Morgane Rolland

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T cell receptor sequencing identifies prior SARS-CoV-2 infection and correlates with neutralizing antibodies and disease severity by Rebecca Elyanow, Thomas M. Snyder, Sudeb C. Dalai, Rachel M. Gittelman, Jim Boonyaratanakornkit, Anna Wald, Stacy Selke, Mark H. Wener, Chihiro Morishima, Alexander L. Greninger, Michael Gale Jr., Tien-Ying Hsiang, Lichen Jing, Michael R. Holbrook, Ian M. Kaplan, H. Jabran Zahid, Damon H. May, Jonathan M. Carlson, Lance Baldo, Thomas Manley, Harlan S. Robins, David M. Koelle

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Selection of an HLA-C*03:04-Restricted HIV-1 p24 Gag Sequence Variant Is Associated with Viral Escape from KIR2DL3+ Natural Killer Cells: Data from an Observational Cohort in South... by Angelique Hölzemer, Christina F Thobakgale, Camilo A Jimenez Cruz, Wilfredo F Garcia-Beltran, Jonathan M Carlson, Nienke H van Teijlingen, Jaclyn K Mann, Manjeetha Jaggernath, Seung-gu Kang, Christian Körner, Amy W Chung, Jamie L Schafer, David T Evans, Galit Alter, Bruce D Walker, Philip J Goulder, Mary Carrington, Pia Hartmann, Thomas Pertel, Ruhong Zhou, Thumbi Ndung'u, Marcus Altfeld

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Longitudinal analysis of T cell receptor repertoires reveals shared patterns of antigen-specific response to SARS-CoV-2 infection by Rachel M. Gittelman, Enrico Lavezzo, Thomas M. Snyder, H. Jabran Zahid, Cara L. Carty, Rebecca Elyanow, Sudeb Dalai, Ilan Kirsch, Lance Baldo, Laura Manuto, Elisa Franchin, Claudia Del Vecchio, Monia Pacenti, Caterina Boldrin, Margherita Cattai, Francesca Saluzzo, Andrea Padoan, Mario Plebani, Fabio Simeoni, Jessica Bordini, Nicola I. Lorè, Dejan Lazarević, Daniela M. Cirillo, Paolo Ghia, Stefano Toppo, Jonathan M. Carlson, Harlan S. Robins, Andrea Crisanti, Giovanni Tonon

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Genotypic and functional impact of HIV-1 adaptation to its host population during the North American epidemic. by Laura A Cotton, Xiaomei T Kuang, Anh Q Le, Jonathan M Carlson, Benjamin Chan, Denis R Chopera, Chanson J Brumme, Tristan J Markle, Eric Martin, Aniqa Shahid, Gursev Anmole, Philip Mwimanzi, Pauline Nassab, Kali A Penney, Manal A Rahman, M-J Milloy, Martin T Schechter, Martin Markowitz, Mary Carrington, Bruce D Walker, Theresa Wagner, Susan Buchbinder, Jonathan Fuchs, Beryl Koblin, Kenneth H Mayer, P Richard Harrigan, Mark A Brockman, Art F Y Poon, Zabrina L Brumme

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A large-scale database of T-cell receptor beta sequences and binding associations from natural and synthetic exposure to SARS-CoV-2 by Sean Nolan, Marissa Vignali, Mark Klinger, Jennifer N. Dines, Ian M. Kaplan, Emily Svejnoha, Tracy Craft, Katie Boland, Mitchell W. Pesesky, Rachel M. Gittelman, Thomas M. Snyder, Christopher J. Gooley, Simona Semprini, Claudio Cerchione, Fabio Nicolini, Massimiliano Mazza, Ottavia M. Delmonte, Kerry Dobbs, Gonzalo Carreño-Tarragona, Santiago Barrio, Vittorio Sambri, Giovanni Martinelli, Jason D. Goldman, Jason D. Goldman, James R. Heath, Luigi D. Notarangelo, Joaquin Martinez-Lopez, Bryan Howie, Jonathan M. Carlson, Harlan S. Robins

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A genome-to-genome analysis of associations between human genetic variation, HIV-1 sequence diversity, and viral control by István Bartha, Jonathan M Carlson, Chanson J Brumme, Paul J McLaren, Zabrina L Brumme, Mina John, David W Haas, Javier Martinez-Picado, Judith Dalmau, Cecilio López-Galíndez, Concepción Casado, Andri Rauch, Huldrych F Günthard, Enos Bernasconi, Pietro Vernazza, Thomas Klimkait, Sabine Yerly, Stephen J O’Brien, Jennifer Listgarten, Nico Pfeifer, Christoph Lippert, Nicolo Fusi, Zoltán Kutalik, Todd M Allen, Viktor Müller, P Richard Harrigan, David Heckerman, Amalio Telenti, Jacques Fellay, for the HIV Genome-to-Genome Study and the Swiss HIV Cohort Study

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Comprehensive sieve analysis of breakthrough HIV-1 sequences in the RV144 vaccine efficacy trial. by Paul T Edlefsen, Morgane Rolland, Tomer Hertz, Sodsai Tovanabutra, Andrew J Gartland, Allan C deCamp, Craig A Magaret, Hasan Ahmed, Raphael Gottardo, Michal Juraska, Connor McCoy, Brendan B Larsen, Eric Sanders-Buell, Chris Carrico, Sergey Menis, Gustavo H Kijak, Meera Bose, RV144 Sequencing Team, Miguel A Arroyo, Robert J O'Connell, Sorachai Nitayaphan, Punnee Pitisuttithum, Jaranit Kaewkungwal, Supachai Rerks-Ngarm, Merlin L Robb, Tatsiana Kirys, Ivelin S Georgiev, Peter D Kwong, Konrad Scheffler, Sergei L Kosakovsky Pond, Jonathan M Carlson, Nelson L Michael, William R Schief, James I Mullins, Jerome H Kim, Peter B Gilbert

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Magnitude and dynamics of the T-cell response to SARS-CoV-2 infection at both individual and population levels by Thomas M. Snyder, Rachel M. Gittelman, Mark Klinger, Damon H. May, Edward J. Osborne, Ruth Taniguchi, H. Jabran Zahid, Ian M. Kaplan, Jennifer N. Dines, Matthew T. Noakes, Ravi Pandya, Xiaoyu Chen, Summer Elasady, Emily Svejnoha, Peter Ebert, Mitchell W. Pesesky, Patricia De Almeida, Hope O’Donnell, Quinn DeGottardi, Gladys Keitany, Jennifer Lu, Allen Vong, Rebecca Elyanow, Paul Fields, Hussein Al-Asadi, Julia Greissl, Lance Baldo, Simona Semprini, Claudio Cerchione, Fabio Nicolini, Massimiliano Mazza, Ottavia M. Delmonte, Kerry Dobbs, Rocio Laguna-Goya, Gonzalo Carreño-Tarragona, Santiago Barrio, Luisa Imberti, Alessandra Sottini, Eugenia Quiros-Roldan, Camillo Rossi, Andrea Biondi, Laura Rachele Bettini, Mariella D’Angio, Paolo Bonfanti, Miranda F. Tompkins, Camille Alba, Clifton Dalgard, Vittorio Sambri, Giovanni Martinelli, Jason D. Goldman, Jason D. Goldman, James R. Heath, Helen C. Su, Luigi D. Notarangelo, Estela Paz-Artal, Joaquin Martinez-Lopez, Bryan Howie, Jonathan M. Carlson, Harlan S. Robins

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