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Viral genome sequence datasets display pervasive evidence of strand-specific substitution biases that are best described using non-reversible nucleotide substitution models Sianga-Mete, Rita; Hartnady, Penelope; Mandikumba, Wimbai Caroline; Rutherford, Kayleigh; Currin, Christopher Brian; Phelanyane, Florence; Stefan, Sabina; Weaver, Steven; Kosakovsky Pond, Sergei L.; Martin, Darren P. Share Save
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Phylogenomic Signatures of a Lineage of Vesicular Stomatitis Indiana Virus Circulating During the 2019-2020 Epidemic in the United States Zarate, Selene; Bertram, Miranda R.; Rodgers, Case; Reed, Kirsten; Pelzel-McCluskey, Angela; Gomez-Romero, Ninnet; Rodriguez, Luis L.; Mayo, Christie; Mire, Chad; Pond, Sergei L. Kosakovsky; Velazquez-Salinas, Lauro Share Save
Positive selection, genetic recombination, and intra-host evolution in novel equine coronavirus genomes and other members of the Embecovirus subgenus Zehr, Jordan D.; Pond, Sergei L. Kosakovsky; Shank, Stephen D.; McQueary, Holly; Grenier, Jennifer K.; Whittaker, Gary R.; Stanhope, Michael J.; Goodman, Laura B. Share Save
The genomic evolutionary dynamics and global circulation patterns of respiratory syncytial virus Langedijk, Annefleur C.; Vrancken, Bram; Lebbink, Robert Jan; Wilkins, Deidre; Kelly, Elizabeth J.; Baraldi, Eugenio; Mascarenas de los Santos, Abiel Homero; Danilenko, Daria M.; Choi, Eun Hwa; Palomino, Maria Angelica; Chi, Hsin; Keller, Christian; Cohen, Robert; Papenburg, Jesse; Pernica, Jeffrey; Greenough, Anne; Richmond, Peter; Martinon-Torres, Federico; Heikkinen, Terho; Stein, Renato T.; Hosoya, Mitsuaki; Nunes, Marta C.; Verwey, Charl; Evers, Anouk; Kragten-Tabatabaie, Leyla; Suchard, Marc A.; Kosakovsky Pond, Sergei L.; Poletto, Chiara; Colizza, Vittoria; Lemey, Philippe; Bont, Louis J. Share Save
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Antigen pressure from two founder viruses induces multiple insertions at a single antibody position to generate broadly neutralizing HIV antibodies Joyce, Collin; Murrell, Sasha; Murrell, Ben; Omorodion, Oluwarotimi; Ver, Lorena S.; Carrico, Nancy; Bastidas, Raiza; Nedellec, Rebecca; Bick, Michael; Woehl, Jordan; Zhao, Fangzhu; Burns, Alison; Barman, Shawn; Appel, Michael; Ramos, Alejandra; Wickramasinghe, Lalinda; Eren, Kemal; Vollbrecht, Thomas; Smith, Davey M.; Pond, Sergei L. Kosakovsky; McBride, Ryan; Worth, Charli; Batista, Facundo; Sok, Devin; Poignard, Pascal; Briney, Bryan; Wilson, Ian A.; Landais, Elise; Burton, Dennis R. Share Save
Identification of Evolutionary Trajectories Shared across Human Betacoronaviruses Escalera-Zamudio, Marina; Pond, Sergei L. Kosakovsky; de la Vina, Natalia Martinez; Gutierrez, Bernardo; Inward, Rhys P. D.; Theze, Julien; van Dorp, Lucy; Castelan-Sanchez, Hugo G.; Bowden, Thomas A.; Pybus, Oliver G.; Hulswit, Ruben J. G. Share Save
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The phylogenomics and evolutionary dynamics of the organellar genomes in carnivorous Utricularia and Genlisea species (Lentibulariaceae) Silva, Saura R.; Miranda, Vitor F. O.; Michael, Todd P.; Plachno, Bartosz J.; Matos, Ramon G.; Adamec, Lubomir; Pond, Sergei L. K.; Lucaci, Alexander G.; Pinheiro, Daniel G.; Varani, Alessandro M. Share Save
Natural selection differences detected in key protein domains between non-pathogenic and pathogenic feline coronavirus phenotypes Zehr, Jordan D.; Kosakovsky Pond, Sergei L.; Millet, Jean K.; Olarte-Castillo, Ximena A.; Lucaci, Alexander G.; Shank, Stephen D.; Ceres, Kristina M.; Choi, Annette; Whittaker, Gary R.; Goodman, Laura B.; Stanhope, Michael J. Share Save
Molecular evidence for SARS-CoV-2 in samples collected from patients with morbilliform eruptions since late 2019 in Lombardy, northern Italy Amendola, Antonella; Canuti, Marta; Bianchi, Silvia; Kumar, Sudhir; Fappani, Clara; Gori, Maria; Colzani, Daniela; Pond, Sergei L. Kosakovsky; Miura, Sayaka; Baggieri, Melissa; Marchi, Antonella; Borghi, Elisa; Zuccotti, Gianvincenzo; Raviglione, Mario C.; Magurano, Fabio; Tanzi, Elisabetta Share Save
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Emergence of SARS-CoV-2 Omicron lineages BA.4 and BA.5 in South Africa Tegally, Houriiyah; Moir, Monika; Everatt, Josie; Giovanetti, Marta; Scheepers, Cathrine; Wilkinson, Eduan; Subramoney, Kathleen; Makatini, Zinhle; Moyo, Sikhulile; Amoako, Daniel G.; Baxter, Cheryl; Althaus, Christian L.; Anyaneji, Ugochukwu J.; Kekana, Dikeledi; Viana, Raquel; Giandhari, Jennifer; Lessells, Richard J.; Maponga, Tongai; Maruapula, Dorcas; Choga, Wonderful; Matshaba, Mogomotsi; Mbulawa, Mpaphi B.; Msomi, Nokukhanya; Naidoo, Yeshnee; Pillay, Sureshnee; Sanko, Tomasz Janusz; San, James E.; Scott, Lesley; Singh, Lavanya; Magini, Nonkululeko A.; Smith-Lawrence, Pamela; Stevens, Wendy; Dor, Graeme; Tshiabuila, Derek; Wolter, Nicole; Preiser, Wolfgang; Treurnicht, Florette K.; Venter, Marietjie; Chiloane, Georginah; McIntyre, Caitlyn; O'Toole, Aine; Ruis, Christopher; Peacock, Thomas P.; Roemer, Cornelius; Kosakovsky Pond, Sergei L.; Williamson, Carolyn; Pybus, Oliver G.; Bhiman, Jinal N.; Glass, Allison; Martin, Darren P.; Jackson, Ben; Rambaut, Andrew; Laguda-Akingba, Oluwakemi; Gaseitsiwe, Simani; von Gottberg, Anne; de Oliveira, Tulio; Bester, Armand Phillip; Claassen, Mathilda; Doolabh, Deelan; Mudau, Innocent; Mbhele, Nokuzola; Engelbrecht, Susan; Goedhals, Dominique; Hardie, Diana; Hsiao, Nei-Yuan; Iranzadeh, Arash; Ismail, Arshad; Joseph, Rageema; Maharaj, Arisha; Mahlangu, Boitshoko; Mahlakwane, Kamela; Davis, Ashlyn; Marais, Gert; Mlisana, Koleka; Mnguni, Anele; Mohale, Thabo; Motsatsi, Gerald; Mwangi, Peter; Ntuli, Noxolo; Nyaga, Martin; Olubayo, Luicer; Radibe, Botshelo; Ramphal, Yajna; Ramphal, Upasana; Strasheim, Wilhelmina; Tebeila, Naume; van Wyk, Stephanie; Wilson, Shannon; Lucaci, Alexander G.; Weaver, Steven; Maharaj, Akhil; Pillay, Yusasha; Davids, Michaela; Mendes, Adriano; Mayaphi, Simnikiwe Share Save
Detection of SARS-CoV-2 intra-host recombination during superinfection with Alpha and Epsilon variants in New York City Wertheim, Joel O.; Wang, Jade C.; Leelawong, Mindy; Martin, Darren P.; Havens, Jennifer L.; Chowdhury, Moinuddin A.; Pekar, Jonathan E.; Amin, Helly; Arroyo, Anthony; Awandare, Gordon A.; Chow, Hoi Yan; Gonzalez, Edimarlyn; Luoma, Elizabeth; Morang'a, Collins M.; Nekrutenko, Anton; Shank, Stephen D.; Silver, Stefan; Quashie, Peter K.; Rakeman, Jennifer L.; Ruiz, Victoria; Torian, Lucia, V; Vasylyeva, Tetyana, I; Pond, Sergei L. Kosakovsky; Hughes, Scott Share Save
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