Virus Satellites Drive Viral Evolution and Ecology. by Belén Frígols, Nuria Quiles-Puchalt, Ignacio Mir-Sanchis, Jorge Donderis, Santiago F Elena, Angus Buckling, Richard P Novick, Alberto Marina, José R Penadés

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Viral evolution sustains a dengue outbreak of enhanced severity by Catherine Inizan, Marine Minier, Matthieu Prot, Olivia O’Connor, Carole Forfait, Sylvie Laumond, Ingrid Marois, Antoine Biron, Ann-Claire Gourinat, Marie-Amélie Goujart, Elodie Descloux, Anavaj Sakuntabhai, Arnaud Tarantola, Etienne Simon-Lorière, Myrielle Dupont-Rouzeyrol

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Rates of viral evolution are linked to host geography in bat rabies. by Daniel G Streicker, Philippe Lemey, Andres Velasco-Villa, Charles E Rupprecht

“…Although the tempo of viral evolution is often ascribed to viral features such as mutation rates and transmission mode, these factors alone cannot explain variation among closely related viruses, where host biology might operate more strongly on viral evolution. …”
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Flavivirus and Filovirus EvoPrinters: New alignment tools for the comparative analysis of viral evolution. by Thomas Brody, Amarendra S Yavatkar, Dong Sun Park, Alexander Kuzin, Jermaine Ross, Ward F Odenwald

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The mutational landscape of SARS-CoV-2 provides new insight into viral evolution and fitness by Jori Symons, Claire Chung, Bert M. Verheijen, Sarah J. Shemtov, Dorien de Jong, Gimano Amatngalim, Monique Nijhuis, Marc Vermulst, Jean-Francois Gout

“…In this work, we show that the biased mutation spectrum of SARS-CoV-2 is likely a result of frequent cytidine deamination and that the secondary structure of the virus plays an important role in this process, providing new insight into the parameters that guide viral evolution and highlighting fundamental weaknesses of the virus that may be exploited for therapeutic purposes.…”
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Higher Rates of Viral Evolution in Chronic Hepatitis B Patients Linked to Predicted T Cell Epitopes by Magnus Illum Dalegaard, Anni Winckelmann, Ulrik Fahnøe, Alexander P. Underwood, Anders Gorm Pedersen, Signe Bollerup, Jens Bukh, Nina Weis

“…This study aims to compare intra-individual viral evolution in two groups of chronic hepatitis B (CHB) patients, using antiviral treatment initiation as a measure of lack of immunological control. …”
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Correction: Evidence of Differential HLA Class I-Mediated Viral Evolution in Functional and Accessory/Regulatory Genes of HIV-1

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Integrated Analysis of the 2022 SARS-CoV-2 Omicron Lineage Replacement Dynamics in Connecticut, US by Nicholas F. G. Chen, Kien Pham, Chrispin Chaguza, Rafael Lopes, Fayette Klaassen, Chaney C. Kalinich, Yale SARS-CoV-2 Genomic Surveillance Initiative, Nicholas Kerantzas, Sameer Pandya, David Ferguson, Wade Schulz, Daniel M. Weinberger, Virginia E. Pitzer, Joshua L. Warren, Nathan D. Grubaugh, Anne M. Hahn

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SIV/SARS-CoV-2 coinfection in rhesus macaques impacts viral shedding, host immunity, the microbiome, and viral evolution by Megan N. Fredericks, Megan N. Fredericks, Zohar Kolodner, Zohar Kolodner, Adam Waalkes, Kaitlin Sawatzki, Linhui Hao, Dustin R. Long, Kelsi Penewit, Cecily C. Midkiff, Carter J. McCormick, Semira Beraki, Semira Beraki, Paul T. Edlefsen, Jeana Barrow, Alexander L. Greninger, Michael Gale, Michael Gale, Michael Gale, Robert V. Blair, Stephen J. Salipante, Deborah H. Fuller, Deborah H. Fuller, Megan A. O’Connor, Megan A. O’Connor, Megan A. O’Connor

“…We show that SIV impairs anti-SARS-CoV-2 immunity, potentially leading to prolonged viral shedding, altered pathogenesis, and viral evolution. This highlights the importance of HIV status in COVID-19 and supports the use of this model for HIV/SARS-CoV-2 coinfection.…”
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Apollo: a comprehensive GPU-powered within-host simulator for viral evolution and infection dynamics across population, tissue, and cell by Deshan Perera, Evan Li, Paul MK Gordon, Frank van der Meer, Tarah Lynch, John Gill, Deirdre L. Church, A. P. Jason de Koning, Christian D. Huber, Guido van Marle, Alexander Platt, Quan Long

“…Abstract Modern sequencing instruments bring unprecedented opportunity to study within-host viral evolution in conjunction with viral transmissions between hosts. …”
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Genetic diversity and antigenic variations of porcine circovirus type 2 genotypes in Brazilian swine herds: Implications for vaccine efficacy and viral evolution by H.I.J. Nascimento, J.L.R. Cunha, A.L.S. Fraiha, B.S.A.S. Santos, B.M.M. Rocha, N.R. Aguilar, B.F.S. Ribeiro, D.C. Veit, K.A. Franz, É.G. Franco, V.L.A. Fernandes, D.P. Três, L.T.S. Hanna, T.B.S. Silva, L. Santos, G.C. Gallinari, M.I.M.C. Guedes, Z.I.P. Lobato, E.A. Costa

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Host taxonomy and environment shapes insectivore viromes and viral spillover risks in Southwestern China by Ji-Hu Yang, Chun-Feng Luo, Rong Xiang, Jiu-Meng Min, Zong-Ti Shao, Yi-Lin Zhao, Lu Chen, Lin Huang, Yun Zhang, Shun-Shuai Liu, Yu-Qiong Li, En-Nian Pu, Wen-Qiang Shi, Hai-Feng Pan, Wei-Jun Chen, Chun-Hong Du, Jia-Fu Jiang

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Amino acid mutations of porcine circovirus type 2 (PCV2) capsid protein increase virus binding to host and evade immune responses: An evaluation of viral evolution by Dongliang Wang, Wenfeng Zhou, Qing He, Yihan Bai, Luhua Zhang, Yang Zhan, Yi Yang, Naidong Wang

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Secondary structure of the SARS-CoV-2 genome is predictive of nucleotide substitution frequency by Zach Hensel

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Fixation and reversion of mutations in the receptor-binding domain of the SARS-CoV-2 spike protein: A 2020–2024 analysis by Daniele Focosi, Pietro Giorgio Spezia, Fabrizio Maggi

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Yaravirus brasiliense genomic structure analysis and its possible influence on the metabolism by Ana Karoline Nunes-Alves, Jônatas Santos Abrahão, Sávio Torres de Farias

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Predicting pathogen evolution and immune evasion in the age of artificial intelligence by D.J. Hamelin, M. Scicluna, I. Saadie, F. Mostefai, J.C. Grenier, C. Baron, E. Caron, J.G. Hussin

Subjects: “…Viral evolution…”
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Identification of Clinical and Genomic Features Associated with SARS-CoV-2 Reinfections by Francisco Muñoz-López, Antoni E. Bordoy, Francesc Català-Moll, Verónica Saludes, David Panisello Yagüe, Mariona Parera, Ignacio Blanco, Pere-Joan Cardona, Cristina Casañ, Ana Blanco-Suárez, Sandra Franco, Álvaro F. García-Jiménez, Roger Paredes, Bonaventura Clotet, Lourdes Mateu, Marc Noguera-Julian, Elisa Martró, José Ramón Santos, Marta Massanella

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A codon usage-based approach for the stratification of Influenza A across recent spillovers by Tommaso Alfonsi, Matteo Chiara, Anna Bernasconi

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Discovery of novel mycoviruses from fungi associated with mango leaf spots by Qihua Wang, Mengyi Chen, Yanling Xie

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