Virus evolution

Keyphrases

Publications

volume 10, number 1, 2024

Babil Torralba, Stéphane Blanc, Yannis Michalakis
Reassortments in single-stranded DNA multipartite viruses: Confronting expectations based on molecular constraints with field observations. Virus evolution 10 (1) (2024)
Bin Ma, Huimin Gong, Qianshuai Xu, Yuan Gao, Aohan Guan, Haoyu Wang, Kexin Hua, Rui Luo, Hui Jin
Bases-dependent Rapid Phylogenetic Clustering (Bd-RPC) enables precise and efficient phylogenetic estimation in viruses. Virus evolution 10 (1) (2024)
Sambit Kumar Mishra, Chase W Nelson, Bin Zhu, Maisa Pinheiro, Hyo Jung Lee, Michael Dean, Laurie Burdett, Meredith Yeager, Lisa Mirabello
Improved detection of low-frequency within-host variants from deep sequencing: A case study with human papillomavirus. Virus evolution 10 (1) (2024)
Idrissa Nonmon Sanogo, Claire Guinat, Simon Dellicour, Mohamed Adama Diakité, Mamadou Niang, Ousmane A Koita, Christelle Camus, Mariette F Ducatez
Genetic insights of H9N2 avian influenza viruses circulating in Mali and phylogeographic patterns in Northern and Western Africa. Virus evolution 10 (1) (2024)
Anton Labutin, Gerald Heckel
Genome-wide support for incipient Tula hantavirus species within a single rodent host lineage. Virus evolution 10 (1) (2024)
Chapin S Korosec, Lindi M Wahl, Jane M Heffernan
Within-host evolution of SARS-CoV-2: how often are de novo mutations transmitted from symptomatic infections? Virus evolution 10 (1) (2024)
Jordan Romeyer Dherbey, Frederic Bertels
The untapped potential of phage model systems as therapeutic agents. Virus evolution 10 (1) (2024)
Christopher J R Illingworth, Jose A Guerra-Assuncao, Samuel Gregg, Oscar Charles, Juanita Pang, Sunando Roy, Rana Abdelnabi, Johan Neyts, Judith Breuer
Genetic consequences of effective and suboptimal dosing with mutagenic drugs in a hamster model of SARS-CoV-2 infection. Virus evolution 10 (1) (2024)
Sambit Kumar Mishra, Chase W Nelson, Bin Zhu, Maisa Pinheiro, Hyo Jung Lee, Michael Dean, Laurie Burdett, Meredith Yeager, Lisa Mirabello
Improved detection of low-frequency within-host variants from deep sequencing: A case study with human papillomavirus. Virus evolution 10 (1) (2024)
Adriano de Bernardi Schneider, Michelle Su, Angie S Hinrichs, Jade Wang, Helly Amin, John Bell, Debra A Wadford, Áine Niamh O'Toole, Emily Scher, Marc D Perry, Yatish Turakhia, Nicola de Maio, Scott Hughes, Russ Corbett-Detig
SARS-CoV-2 lineage assignments using phylogenetic placement/UShER are superior to pangoLEARN machine-learning method. Virus evolution 10 (1) (2024)
Chapin S Korosec, Lindi M Wahl, Jane M Heffernan
Within-host evolution of SARS-CoV-2: how often are de novo mutations transmitted from symptomatic infections? Virus evolution 10 (1) (2024)
Bin Ma, Huimin Gong, Qianshuai Xu, Yuan Gao, Aohan Guan, Haoyu Wang, Kexin Hua, Rui Luo, Hui Jin
Bases-dependent Rapid Phylogenetic Clustering (Bd-RPC) enables precise and efficient phylogenetic estimation in viruses. Virus evolution 10 (1) (2024)
Áine Niamh O'Toole, Rachel Colquhoun, Corey Ansley, Catherine Troman, Daniel Maloney, Zoe Vance, Joyce Akello, Erika Bujaki, Manasi Majumdar, Adnan Khurshid, Yasir Arshad, Muhammad Masroor Alam, Javier Martin, Alexander G Shaw, Nicholas C Grassly, Andrew Rambaut
Automated detection and classification of polioviruses from nanopore sequencing reads using piranha. Virus evolution 10 (1) (2024)
Babil Torralba, Stéphane Blanc, Yannis Michalakis
Reassortments in single-stranded DNA multipartite viruses: Confronting expectations based on molecular constraints with field observations. Virus evolution 10 (1) (2024)
Idrissa Nonmon Sanogo, Claire Guinat, Simon Dellicour, Mohamed Adama Diakité, Mamadou Niang, Ousmane A Koita, Christelle Camus, Mariette F Ducatez
Genetic insights of H9N2 avian influenza viruses circulating in Mali and phylogeographic patterns in Northern and Western Africa. Virus evolution 10 (1) (2024)
Barney I Potter, Marijn Thijssen, Nídia Sequeira Trovão, Andrea Pineda-Peña, Marijke Reynders, Thomas Mina, Carolina Alvarez, Samad Amini-Bavil-Olyaee, Frederik Nevens, Piet Maes, Philippe Lemey, Marc Van Ranst, Guy Baele, Mahmoud Reza Pourkarim
Contemporary and historical human migration patterns shape hepatitis B virus diversity. Virus evolution 10 (1) (2024)
William M Switzer, Anupama Shankar, Hongwei Jia, Sergey Knyazev, Frank Ambrosio, Reagan Kelly, HaoQiang Zheng, Ellsworth M Campbell, Roxana Cintron, Yi Pan, Neeraja Saduvala, Nivedha Panneer, Rhiannon Richman, Manny B Singh, Douglas A Thoroughman, Erin F Blau, George M Khalil, Sheryl Lyss, Walid Heneine
High HIV diversity, recombination, and superinfection revealed in a large outbreak among persons who inject drugs in Kentucky and Ohio, USA. Virus evolution 10 (1) (2024)
Marco Forgia, Stefania Daghino, Marco Chiapello, Marina Ciuffo, Massimo Turina
New clades of viruses infecting the obligatory biotroph Bremia lactucae representing distinct evolutionary trajectory for viruses infecting oomycetes. Virus evolution 10 (1) (2024)
Wen-Jian Chung, Elizabeth Connick, Dominik Wodarz
Human immunodeficiency virus dynamics in secondary lymphoid tissues and the evolution of cytotoxic T lymphocyte escape mutants. Virus evolution 10 (1) (2024)
Ji-Yun Kim, Sol Jeong, Da-Won Kim, Dong-Wook Lee, Dong-Hun Lee, Daehun Kim, Jung-Hoon Kwon
Genomic epidemiology of highly pathogenic avian influenza A (H5N1) virus in wild birds in South Korea during 2021-2022: Changes in viral epidemic patterns. Virus evolution 10 (1) (2024)
Paula Lagan Tregaskis, Michael Hamil, Susan Cull, Anthony Hanrahan, Rosanna M Wregor, Ken Lemon
Swine influenza A virus infection dynamics and evolution in intensive pig production systems. Virus evolution 10 (1) (2024)
Barney I Potter, Marijn Thijssen, Nídia Sequeira Trovão, Andrea Pineda-Peña, Marijke Reynders, Thomas Mina, Carolina Alvarez, Samad Amini-Bavil-Olyaee, Frederik Nevens, Piet Maes, Philippe Lemey, Marc Van Ranst, Guy Baele, Mahmoud Reza Pourkarim
Contemporary and historical human migration patterns shape hepatitis B virus diversity. Virus evolution 10 (1) (2024)
Maxime Courcelle, Habib Salami, Kadidia Tounkara, Modou Moustapha Lo, Aminata Ba, Mariame Diop, Mamadou Niang, Cheick Abou Kounta Sidibe, Amadou Sery, Marthin Dakouo, Lanceï Kaba, Youssouf Sidime, Mohamed Keyra, Alpha Oumar Sily Diallo, Ahmed Bezeid El Mamy, Ahmed Salem El Arbi, Yahya Barry, Ekaterina Isselmou, Habiboullah Habiboullah, Baba Doumbia, Mohamed Baba Gueya, Joseph Awuni, Theophilus Odoom, Patrick Tetteh Ababio, Daniel Nana Yaw TawiahYingar, Caroline Coste, Samia Guendouz, Olivier Kwiatek, Geneviève Libeau, Arnaud Bataille
Comparative evolutionary analyses of peste des petits ruminants virus genetic lineages. Virus evolution 10 (1) (2024)
Marco Forgia, Stefania Daghino, Marco Chiapello, Marina Ciuffo, Massimo Turina
New clades of viruses infecting the obligatory biotroph Bremia lactucae representing distinct evolutionary trajectory for viruses infecting oomycetes. Virus evolution 10 (1) (2024)
Song Zhang, Caixia Yang, Yuanjian Qiu, Ruiling Liao, Zhiyou Xuan, Fang Ren, Yafeng Dong, Xiaoying Xie, Yanhong Han, Di Wu, Pedro Luis Ramos-González, Juliana Freitas-Astúa, Huadong Yang, Changyong Zhou, Mengji Cao
Conserved untranslated regions of multipartite viruses: Natural markers of novel viral genomic components and tags of viral evolution. Virus evolution 10 (1) (2024)
Áine Niamh O'Toole, Rachel Colquhoun, Corey Ansley, Catherine Troman, Daniel Maloney, Zoe Vance, Joyce Akello, Erika Bujaki, Manasi Majumdar, Adnan Khurshid, Yasir Arshad, Muhammad Masroor Alam, Javier Martin, Alexander G Shaw, Nicholas C Grassly, Andrew Rambaut
Automated detection and classification of polioviruses from nanopore sequencing reads using piranha. Virus evolution 10 (1) (2024)
Song Zhang, Caixia Yang, Yuanjian Qiu, Ruiling Liao, Zhiyou Xuan, Fang Ren, Yafeng Dong, Xiaoying Xie, Yanhong Han, Di Wu, Pedro Luis Ramos-González, Juliana Freitas-Astúa, Huadong Yang, Changyong Zhou, Mengji Cao
Conserved untranslated regions of multipartite viruses: Natural markers of novel viral genomic components and tags of viral evolution. Virus evolution 10 (1) (2024)
Ana Del Arco, Matthias G Fischer, Lutz Becks
Evolution of exploitation and replication of giant viruses and virophages. Virus evolution 10 (1) (2024)
Wen-Jian Chung, Elizabeth Connick, Dominik Wodarz
Human immunodeficiency virus dynamics in secondary lymphoid tissues and the evolution of cytotoxic T lymphocyte escape mutants. Virus evolution 10 (1) (2024)
Jia-Xin Lv, Xiang Liu, Yuan-Yuan Pei, Zhi-Gang Song, Xiao Chen, Shu-Jian Hu, Jia-Lei She, Yi Liu, Yan-Mei Chen, Yong-Zhen Zhang
Evolutionary trajectory of diverse SARS-CoV-2 variants at the beginning of COVID-19 outbreak. Virus evolution 10 (1) (2024)
Zhiyong Wu, Tong Chang, Decheng Wang, Hongliang Zhang, Haizhou Liu, Xinyi Huang, Zhijun Tian, Xiaoxiao Tian, Di Liu, Tong-Qing An, Yi Yan
Genomic surveillance and evolutionary dynamics of type 2 porcine reproductive and respiratory syndrome virus in China spanning the African swine fever outbreak. Virus evolution 10 (1) (2024)
Zhiyong Wu, Tong Chang, Decheng Wang, Hongliang Zhang, Haizhou Liu, Xinyi Huang, Zhijun Tian, Xiaoxiao Tian, Di Liu, Tong-Qing An, Yi Yan
Genomic surveillance and evolutionary dynamics of type 2 porcine reproductive and respiratory syndrome virus in China spanning the African swine fever outbreak. Virus evolution 10 (1) (2024)
Stephanie J Waller, Pablo Tortosa, Tertia Thurley, Colin F J O'Donnell, Rebecca Jackson, Gillian Dennis, Rebecca M Grimwood, Edward C Holmes, Kate McInnes, Jemma L Geoghegan
Virome analysis of New Zealand's bats reveals cross-species viral transmission among the Coronaviridae . Virus evolution 10 (1) (2024)
Jia-Xin Lv, Xiang Liu, Yuan-Yuan Pei, Zhi-Gang Song, Xiao Chen, Shu-Jian Hu, Jia-Lei She, Yi Liu, Yan-Mei Chen, Yong-Zhen Zhang
Evolutionary trajectory of diverse SARS-CoV-2 variants at the beginning of COVID-19 outbreak. Virus evolution 10 (1) (2024)
Miguel Álvarez-Herrera, Jordi Sevilla, Paula Ruiz-Rodriguez, Andrea Vergara, Jordi Vila, Pablo Cano-Jiménez, Fernando González-Candelas, Iñaki Comas, Mireia Coscollá
VIPERA: Viral Intra-Patient Evolution Reporting and Analysis. Virus evolution 10 (1) (2024)
William M Switzer, Anupama Shankar, Hongwei Jia, Sergey Knyazev, Frank Ambrosio, Reagan Kelly, HaoQiang Zheng, Ellsworth M Campbell, Roxana Cintron, Yi Pan, Neeraja Saduvala, Nivedha Panneer, Rhiannon Richman, Manny B Singh, Douglas A Thoroughman, Erin F Blau, George M Khalil, Sheryl Lyss, Walid Heneine
High HIV diversity, recombination, and superinfection revealed in a large outbreak among persons who inject drugs in Kentucky and Ohio, USA. Virus evolution 10 (1) (2024)
Anton Labutin, Gerald Heckel
Genome-wide support for incipient Tula hantavirus species within a single rodent host lineage. Virus evolution 10 (1) (2024)
Miguel Álvarez-Herrera, Jordi Sevilla, Paula Ruiz-Rodriguez, Andrea Vergara, Jordi Vila, Pablo Cano-Jiménez, Fernando González-Candelas, Iñaki Comas, Mireia Coscollá
VIPERA: Viral Intra-Patient Evolution Reporting and Analysis. Virus evolution 10 (1) (2024)
Maxime Courcelle, Habib Salami, Kadidia Tounkara, Modou Moustapha Lo, Aminata Ba, Mariame Diop, Mamadou Niang, Cheick Abou Kounta Sidibe, Amadou Sery, Marthin Dakouo, Lanceï Kaba, Youssouf Sidime, Mohamed Keyra, Alpha Oumar Sily Diallo, Ahmed Bezeid El Mamy, Ahmed Salem El Arbi, Yahya Barry, Ekaterina Isselmou, Habiboullah Habiboullah, Baba Doumbia, Mohamed Baba Gueya, Joseph Awuni, Theophilus Odoom, Patrick Tetteh Ababio, Daniel Nana Yaw TawiahYingar, Caroline Coste, Samia Guendouz, Olivier Kwiatek, Geneviève Libeau, Arnaud Bataille
Comparative evolutionary analyses of peste des petits ruminants virus genetic lineages. Virus evolution 10 (1) (2024)
Christopher J R Illingworth, Jose A Guerra-Assuncao, Samuel Gregg, Oscar Charles, Juanita Pang, Sunando Roy, Rana Abdelnabi, Johan Neyts, Judith Breuer
Genetic consequences of effective and suboptimal dosing with mutagenic drugs in a hamster model of SARS-CoV-2 infection. Virus evolution 10 (1) (2024)
Stephanie J Waller, Pablo Tortosa, Tertia Thurley, Colin F J O'Donnell, Rebecca Jackson, Gillian Dennis, Rebecca M Grimwood, Edward C Holmes, Kate McInnes, Jemma L Geoghegan
Virome analysis of New Zealand's bats reveals cross-species viral transmission among the Coronaviridae . Virus evolution 10 (1) (2024)
Ana Del Arco, Matthias G Fischer, Lutz Becks
Evolution of exploitation and replication of giant viruses and virophages. Virus evolution 10 (1) (2024)
Ophelie Lebrasseur, Kuldeep Dilip More, Ludovic Orlando
Equine herpesvirus 4 infected domestic horses associated with Sintashta spoke-wheeled chariots around 4,000 years ago. Virus evolution 10 (1) (2024)
Ophelie Lebrasseur, Kuldeep Dilip More, Ludovic Orlando
Equine herpesvirus 4 infected domestic horses associated with Sintashta spoke-wheeled chariots around 4,000 years ago. Virus evolution 10 (1) (2024)
Oumaima Moubset, Denis Filloux, Hugo Fontes, Charlotte Julian, Emmanuel Fernandez, Serge Galzi, Laurence Blondin, Sélim Ben Chehida, Jean-Michel Lett, François Mesléard, Simona Kraberger, Joy M Custer, Andrew Salywon, Elizabeth Makings, Armelle Marais, Frédéric Chiroleu, Pierre Lefeuvre, Darren P Martin, Thierry Candresse, Darren P Martin, Virginie Ravigné, Philippe Roumagnac
Virome release of an invasive exotic plant species in southern France. Virus evolution 10 (1) (2024)
Oumaima Moubset, Denis Filloux, Hugo Fontes, Charlotte Julian, Emmanuel Fernandez, Serge Galzi, Laurence Blondin, Sélim Ben Chehida, Jean-Michel Lett, François Mesléard, Simona Kraberger, Joy M Custer, Andrew Salywon, Elizabeth Makings, Armelle Marais, Frédéric Chiroleu, Pierre Lefeuvre, Darren P Martin, Thierry Candresse, Darren P Martin, Virginie Ravigné, Philippe Roumagnac
Virome release of an invasive exotic plant species in southern France. Virus evolution 10 (1) (2024)
Paula Lagan Tregaskis, Michael Hamil, Susan Cull, Anthony Hanrahan, Rosanna M Wregor, Ken Lemon
Swine influenza A virus infection dynamics and evolution in intensive pig production systems. Virus evolution 10 (1) (2024)
Ji-Yun Kim, Sol Jeong, Da-Won Kim, Dong-Wook Lee, Dong-Hun Lee, Daehun Kim, Jung-Hoon Kwon
Genomic epidemiology of highly pathogenic avian influenza A (H5N1) virus in wild birds in South Korea during 2021-2022: Changes in viral epidemic patterns. Virus evolution 10 (1) (2024)
Jordan Romeyer Dherbey, Frederic Bertels
The untapped potential of phage model systems as therapeutic agents. Virus evolution 10 (1) (2024)
Adriano de Bernardi Schneider, Michelle Su, Angie S Hinrichs, Jade Wang, Helly Amin, John Bell, Debra A Wadford, Áine Niamh O'Toole, Emily Scher, Marc D Perry, Yatish Turakhia, Nicola de Maio, Scott Hughes, Russ Corbett-Detig
SARS-CoV-2 lineage assignments using phylogenetic placement/UShER are superior to pangoLEARN machine-learning method. Virus evolution 10 (1) (2024)