Search Results - "Virus evolution"

Assignment of epidemiological lineages in an emerging pandemic using the pangolin tool by O’Toole, Áine, Scher, Emily, Underwood, Anthony, Jackson, Ben, Hill, Verity, McCrone, John T, Colquhoun, Rachel, Ruis, Chris, Abu-Dahab, Khalil, Taylor, Ben, Yeats, Corin, du Plessis, Louis, Maloney, Daniel, Medd, Nathan, Attwood, Stephen W, Aanensen, David M, Holmes, Edward C, Pybus, Oliver G, Rambaut, Andrew

“…Abstract The response of the global virus genomics community to the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic has been…”
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Bayesian phylogenetic and phylodynamic data integration using BEAST 1.10 by Suchard, Marc A, Lemey, Philippe, Baele, Guy, Ayres, Daniel L, Drummond, Alexei J, Rambaut, Andrew

“…The Bayesian Evolutionary Analysis by Sampling Trees (BEAST) software package has become a primary tool for Bayesian phylogenetic and phylodynamic inference…”
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Temporal signal and the phylodynamic threshold of SARS-CoV-2 by Duchene, Sebastian, Featherstone, Leo, Haritopoulou-Sinanidou, Melina, Rambaut, Andrew, Lemey, Philippe, Baele, Guy

“…Abstract The ongoing SARS-CoV-2 outbreak marks the first time that large amounts of genome sequence data have been generated and made publicly available in…”
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TreeTime: Maximum-likelihood phylodynamic analysis by Sagulenko, Pavel, Puller, Vadim, Neher, Richard A

“…Abstract Mutations that accumulate in the genome of cells or viruses can be used to infer their evolutionary history. In the case of rapidly evolving…”
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RDP4: Detection and analysis of recombination patterns in virus genomes by Martin, Darren P., Murrell, Ben, Golden, Michael, Khoosal, Arjun, Muhire, Brejnev

“…RDP4 is the latest version of recombination detection program (RDP), a Windows computer program that implements an extensive array of methods for detecting and…”
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Exploring the temporal structure of heterochronous sequences using TempEst (formerly Path-O-Gen) by Rambaut, Andrew, Lam, Tommy T., Max Carvalho, Luiz, Pybus, Oliver G.

“…Gene sequences sampled at different points in time can be used to infer molecular phylogenies on a natural timescale of months or years, provided that the…”
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RDP5: a computer program for analyzing recombination in, and removing signals of recombination from, nucleotide sequence datasets by Martin, Darren P, Varsani, Arvind, Roumagnac, Philippe, Botha, Gerrit, Maslamoney, Suresh, Schwab, Tiana, Kelz, Zena, Kumar, Venkatesh, Murrell, Ben

“…Abstract For the past 20 years, the recombination detection program (RDP) project has focused on the development of a fast, flexible, and easy to use…”
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Global patterns in coronavirus diversity by Anthony, Simon J., Johnson, Christine K., Greig, Denise J., Kramer, Sarah, Che, Xiaoyu, Wells, Heather, Hicks, Allison L., Joly, Damien O., Wolfe, Nathan D., Daszak, Peter, Karesh, William, Lipkin, W. I., Morse, Stephen S., Mazet, Jonna A. K., Goldstein, Tracey

“…Abstract Since the emergence of Severe Acute Respiratory Syndrome Coronavirus (SARS-CoV) and Middle East Respiratory Syndrom Coronavirus (MERS-CoV) it has…”
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Evaluation of NGS-based approaches for SARS-CoV-2 whole genome characterisation by Charre, Caroline, Ginevra, Christophe, Sabatier, Marina, Regue, Hadrien, Destras, Grégory, Brun, Solenne, Burfin, Gwendolyne, Scholtes, Caroline, Morfin, Florence, Valette, Martine, Lina, Bruno, Bal, Antonin, Josset, Laurence

“…Abstract Since the beginning of the COVID-19 outbreak, SARS-CoV-2 whole-genome sequencing (WGS) has been performed at unprecedented rate worldwide with the use…”
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Analysis of the virome associated to grapevine downy mildew lesions reveals new mycovirus lineages by Chiapello, M, Rodríguez-Romero, J, Ayllón, M A, Turina, M

“…Abstract The obligatory biotrophic oomycetes Plasmopara viticola is the causal agent of downy mildew, a destructive disease of grapevine worldwide. So far,…”
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The origins and molecular evolution of SARS-CoV-2 lineage B.1.1.7 in the UK by Hill, Verity, Du Plessis, Louis, Peacock, Thomas P, Aggarwal, Dinesh, Colquhoun, Rachel, Carabelli, Alesandro M, Ellaby, Nicholas, Gallagher, Eileen, Groves, Natalie, Jackson, Ben, McCrone, J T, O’Toole, Áine, Price, Anna, Sanderson, Theo, Scher, Emily, Southgate, Joel, Volz, Erik, Barclay, Wendy S, Barrett, Jeffrey C, Chand, Meera, Connor, Thomas, Goodfellow, Ian, Gupta, Ravindra K, Harrison, Ewan M, Loman, Nicholas, Myers, Richard, Robertson, David L, Pybus, Oliver G, Rambaut, Andrew

“…Abstract The first SARS-CoV-2 variant of concern (VOC) to be designated was lineage B.1.1.7, later labelled by the World Health Organization as Alpha…”
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An emergent clade of SARS-CoV-2 linked to returned travellers from Iran by Eden, John-Sebastian, Rockett, Rebecca, Carter, Ian, Rahman, Hossinur, de Ligt, Joep, Hadfield, James, Storey, Matthew, Ren, Xiaoyun, Tulloch, Rachel, Basile, Kerri, Wells, Jessica, Byun, Roy, Gilroy, Nicky, O’Sullivan, Matthew V, Sintchenko, Vitali, Chen, Sharon C, Maddocks, Susan, Sorrell, Tania C, Holmes, Edward C, Dwyer, Dominic E, Kok, Jen

“…Abstract The SARS-CoV-2 epidemic has rapidly spread outside China with major outbreaks occurring in Italy, South Korea, and Iran. Phylogenetic analyses of…”
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Cenote-Taker 2 democratizes virus discovery and sequence annotation by Tisza, Michael J, Belford, Anna K, Domínguez-Huerta, Guillermo, Bolduc, Benjamin, Buck, Christopher B

“…Abstract Viruses, despite their great abundance and significance in biological systems, remain largely mysterious. Indeed, the vast majority of the perhaps…”
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Recurrent SARS-CoV-2 mutations in immunodeficient patients by Wilkinson, S A J, Richter, Alex, Casey, Anna, Osman, Husam, Mirza, Jeremy D, Stockton, Joanne, Quick, Josh, Ratcliffe, Liz, Sparks, Natalie, Cumley, Nicola, Poplawski, Radoslaw, Nicholls, Samuel N, Kele, Beatrix, Harris, Kathryn, Peacock, Thomas P, Loman, Nicholas J

“…Abstract Long-term severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections in immunodeficient patients are an important source of variation for…”
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The virome from a collection of endomycorrhizal fungi reveals new viral taxa with unprecedented genome organization by Sutela, Suvi, Forgia, Marco, Vainio, Eeva J, Chiapello, Marco, Daghino, Stefania, Vallino, Marta, Martino, Elena, Girlanda, Mariangela, Perotto, Silvia, Turina, Massimo

“…Abstract Mutualistic plant-associated fungi are recognized as important drivers in plant evolution, diversity, and health. The discovery that mycoviruses can…”
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An antibody-escape estimator for mutations to the SARS-CoV-2 receptor-binding domain by Greaney, Allison J, Starr, Tyler N, Bloom, Jesse D

“…Abstract A key goal of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) surveillance is to rapidly identify viral variants with mutations that…”
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Fitness effects of mutations to SARS-CoV-2 proteins by Bloom, Jesse D, Neher, Richard A

“…Abstract Knowledge of the fitness effects of mutations to SARS-CoV-2 can inform assessment of new variants, design of therapeutics resistant to escape, and…”
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A threat from both sides: Multiple introductions of genetically distinct H5 HPAI viruses into Canada via both East Asia-Australasia/Pacific and Atlantic flyways by Alkie, Tamiru N, Lopes, Sara, Hisanaga, Tamiko, Xu, Wanhong, Suderman, Matthew, Koziuk, Janice, Fisher, Mathew, Redford, Tony, Lung, Oliver, Joseph, Tomy, Himsworth, Chelsea G, Brown, Ian H, Bowes, Victoria, Lewis, Nicola S, Berhane, Yohannes

“…Abstract From 2016 to 2020, high pathogenicity avian influenza (HPAI) H5 viruses circulated in Asia, Europe, and Africa, causing waves of infections and the…”
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Intra-host evolution during SARS-CoV-2 prolonged infection by Voloch, Carolina M, da Silva Francisco Jr, Ronaldo, de Almeida, Luiz G P, Brustolini, Otavio J, Cardoso, Cynthia C, Gerber, Alexandra L, Guimarães, Ana Paula de C, Leitão, Isabela de Carvalho, Mariani, Diana, Ota, Victor Akira, Lima, Cristiano X, Teixeira, Mauro M, Dias, Ana Carolina F, Galliez, Rafael Mello, Faffe, Débora Souza, Pôrto, Luís Cristóvão, Aguiar, Renato S, Castiñeira, Terezinha M P P, Ferreira, Orlando C, Tanuri, Amilcar, R de Vasconcelos, Ana Tereza

“…Abstract Long-term infection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) represents a challenge to virus dispersion and the control of…”
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Replacement of the Gamma by the Delta variant in Brazil: Impact of lineage displacement on the ongoing pandemic by Giovanetti, Marta, Fonseca, Vagner, Wilkinson, Eduan, Tegally, Houriiyah, San, Emmanuel James, Althaus, Christian L, Xavier, Joilson, Nanev Slavov, Svetoslav, Viala, Vincent Louis, Ranieri Jerônimo Lima, Alex, Ribeiro, Gabriela, Souza-Neto, Jayme A, Fukumasu, Heidge, Lehmann Coutinho, Luiz, Venancio da Cunha, Rivaldo, Freitas, Carla, Campelo de A e Melo, Carlos F, Navegantes de Araújo, Wildo, Do Carmo Said, Rodrigo Fabiano, Almiron, Maria, de Oliveira, Tulio, Coccuzzo Sampaio, Sandra, Elias, Maria Carolina, Covas, Dimas Tadeu, Holmes, Edward C, Lourenço, José, Kashima, Simone, de Alcantara, Luiz Carlos Junior

“…Abstract The coronavirus disease 2019 (COVID-19) epidemic in Brazil was driven mainly by the spread of Gamma (P.1), a locally emerged variant of concern (VOC)…”
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