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Viral genomics  
PLOS Biology  
How fast are viruses spreading in the wild?

Simon Dellicour, Paul Bastide, Pauline Rocu, Denis Fargette, Olivier J. Hardy, Marc A. Suchard, Stéphane Guindon, Philippe Lemey

Research Article | published 03 Dec 2024 PLOS Biology

https://doi.org/10.1371/journal.pbio.3002914

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A new lineage nomenclature to aid genomic surveillance of dengue virus

Verity Hill, Sara Cleemput, James Siqueira Pereira, Robert J. Gifford, Vagner Fonseca, Houriiyah Tegally, Anderson F. Brito, Gabriela Ribeiro, Vinicius Carius de Souza, Isabela Carvalho Brcko, Igor Santana Ribeiro, Iago Trezena Tavares De Lima, Svetoslav Nanev Slavov, Sandra Coccuzzo Sampaio, Maria Carolina Elias, Vi Thuy Tran, Duong Thi Hue Kien, Tuyen Huynh, Sophie Yacoub, Idrissa Dieng, Richard Salvato, Gabriel Luz Wallau, Tatiana S. Gregianini, Fernanda M. S. Godinho, Chantal B. F. Vogels, Mallery I. Breban, Mariana Leguia, Suraj Jagtap, Rahul Roy, Chanditha Hapuarachchi, Gaspary Mwanyika, Marta Giovanetti, Luiz C. J. Alcantara, Nuno R. Faria, Christine V. F. Carrington, Kathryn A. Hanley, Edward C. Holmes, Wim Dumon, Alex Ranieri Jerônimo Lima, Tulio de Oliveira, Nathan D. Grubaugh

Consensus View | published 16 Sep 2024 PLOS Biology

https://doi.org/10.1371/journal.pbio.3002834

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Prophage induction can facilitate the in vitro dispersal of multicellular Streptomyces structures

Hoda Jaffal, Mounia Kortebi, Pauline Misson, Paulo Tavares, Malika Ouldali, Hervé Leh, Sylvie Lautru, Virginia S. Lioy, François Lecointe, Stéphanie G. Bury-Moné

Short Reports | published 25 Jul 2024 PLOS Biology

https://doi.org/10.1371/journal.pbio.3002725

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When size matters: A novel compact Cas12a variant for in vivo genome editing

Felix Bubeck, Dirk Grimm

Primer | published 17 Jul 2024 PLOS Biology

https://doi.org/10.1371/journal.pbio.3002637

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Plant viruses traveling without passport

Cristina Sáez, Israel Pagán

Primer | published 10 May 2024 PLOS Biology

https://doi.org/10.1371/journal.pbio.3002626

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Systematic and scalable genome-wide essentiality mapping to identify nonessential genes in phages

Denish Piya, Nicholas Nolan, Madeline L. Moore, Luis A. Ramirez Hernandez, Brady F. Cress, Ry Young, Adam P. Arkin, Vivek K. Mutalik

Methods and Resources | published 04 Dec 2023 PLOS Biology

https://doi.org/10.1371/journal.pbio.3002416

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Copy-back viral genomes induce a cellular stress response that interferes with viral protein expression without affecting antiviral immunity

Lavinia J. González Aparicio, Yanling Yang, Matthew Hackbart, Carolina B. López

Research Article | published 20 Nov 2023 PLOS Biology

https://doi.org/10.1371/journal.pbio.3002381

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ATG9A regulates the dissociation of recycling endosomes from microtubules to form liquid influenza A virus inclusions

Sílvia Vale-Costa, Temitope Akhigbe Etibor, Daniela Brás, Ana Laura Sousa, Mariana Ferreira, Gabriel G. Martins, Victor Hugo Mello, Maria João Amorim

Research Article | published 20 Nov 2023 PLOS Biology

https://doi.org/10.1371/journal.pbio.3002290

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Defining the minimal components of the influenza A virus replication machinery via an in vitro reconstitution system

Zihan Zhu, Haitian Fan, Ervin Fodor

Research Article | published 09 Nov 2023 PLOS Biology

https://doi.org/10.1371/journal.pbio.3002370

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Attenuation hotspots in neurotropic human astroviruses

Hashim Ali, Aleksei Lulla, Alex S. Nicholson, Jacqueline Hankinson, Elizabeth B. Wignall-Fleming, Rhian L. O’Connor, Diem-Lan Vu, Stephen C. Graham, Janet E. Deane, Susana Guix, Valeria Lulla

Methods and Resources | published 17 Jul 2023 PLOS Biology

https://doi.org/10.1371/journal.pbio.3001815

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Development of an amplicon-based sequencing approach in response to the global emergence of mpox

Nicholas F. G. Chen, Chrispin Chaguza, Luc Gagne, Matthew Doucette, Sandra Smole, Erika Buzby, Joshua Hall, Stephanie Ash, Rachel Harrington, Seana Cofsky, Selina Clancy, Curtis J. Kapsak, Joel Sevinsky, Kevin Libuit, Daniel J. Park, Peera Hemarajata, Jacob M. Garrigues, Nicole M. Green, Sean Sierra-Patev, Kristin Carpenter-Azevedo, Richard C. Huard, Claire Pearson, Kutluhan Incekara, Christina Nishimura, Jian Ping Huang, Emily Gagnon, Ethan Reever, Jafar Razeq, Anthony Muyombwe, Vítor Borges, Rita Ferreira, Daniel Sobral, Silvia Duarte, Daniela Santos, Luís Vieira, João Paulo Gomes, Carly Aquino, Isabella M. Savino, Karinda Felton, Moneeb Bajwa, Nyjil Hayward, Holly Miller, Allison Naumann, Ria Allman, Neel Greer, Amary Fall, Heba H. Mostafa, Martin P. McHugh, Daniel M. Maloney, Rebecca Dewar, Juliet Kenicer, Abby Parker, Katharine Mathers, Jonathan Wild, Seb Cotton, Kate E. Templeton, George Churchwell, Philip A. Lee, Maria Pedrosa, Brenna McGruder, Sarah Schmedes, Matthew R. Plumb, Xiong Wang, Regina Bones Barcellos, Fernanda M. S. Godinho, Richard Steiner Salvato, Aimee Ceniseros, Mallery I. Breban, Nathan D. Grubaugh, Glen R. Gallagher, Chantal B. F. Vogels

Research Article | published 13 Jun 2023 PLOS Biology

https://doi.org/10.1371/journal.pbio.3002151

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Cheating leads to the evolution of multipartite viruses

Asher Leeks, Penny Grace Young, Paul Eugene Turner, Geoff Wild, Stuart Andrew West

Research Article | published 24 Apr 2023 PLOS Biology

https://doi.org/10.1371/journal.pbio.3002092

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iPHoP: An integrated machine learning framework to maximize host prediction for metagenome-derived viruses of archaea and bacteria

Simon Roux, Antonio Pedro Camargo, Felipe H. Coutinho, Shareef M. Dabdoub, Bas E. Dutilh, Stephen Nayfach, Andrew Tritt

Methods and Resources | published 21 Apr 2023 PLOS Biology

https://doi.org/10.1371/journal.pbio.3002083

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Distribution and molecular evolution of the anti-CRISPR family AcrIF7

Wendy Figueroa, Adrian Cazares, Daniel Cazares, Yi Wu, Ana de la Cruz, Martin Welch, Luis Kameyama, Franklin L. Nobrega, Gabriel Guarneros

Research Article | published 21 Apr 2023 PLOS Biology

https://doi.org/10.1371/journal.pbio.3002072

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CRISPR-Cas effector specificity and cleavage site determine phage escape outcomes

Michael A. Schelling, Giang T. Nguyen, Dipali G. Sashital

Research Article | published 14 Apr 2023 PLOS Biology

https://doi.org/10.1371/journal.pbio.3002065

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