Successful Whole Genome Nanopore Sequencing of Swine Influenza A Virus (swIAV) Directly from Oral Fluids Collected in Polish Pig Herds by Nick Vereecke, Aleksandra Woźniak, Marthe Pauwels, Sieglinde Coppens, Hans Nauwynck, Piotr Cybulski, Sebastiaan Theuns, Tomasz Stadejek

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Beyond surveillance: leveraging the potential of next generation sequencing in clinical virology by Paula C. Aulicino, Paula C. Aulicino, Jason T. Kimata

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Novel Insights for Biosurveillance of Bat-Borne Viruses by Adrian C. Paskey, Justin H. J. Ng, Gregory K. Rice, Wan Ni Chia, Casandra W. Philipson, Randy J. H. Foo, Regina Z. Cer, Kyle A. Long, Matthew R. Lueder, Kenneth G. Frey, Theron Hamilton, Ian H. Mendenhall, Gavin J. Smith, Lin-Fa Wang, Kimberly A. Bishop-Lilly

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SARS-CoV-2/COVID-19: Viral Genomics, Epidemiology, Vaccines, and Therapeutic Interventions by Mohammed Uddin, Farah Mustafa, Tahir A. Rizvi, Tom Loney, Hanan Al Suwaidi, Ahmed H. Hassan Al-Marzouqi, Afaf Kamal Eldin, Nabeel Alsabeeha, Thomas E. Adrian, Cesare Stefanini, Norbert Nowotny, Alawi Alsheikh-Ali, Abiola C. Senok

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The Spread of SARS-CoV-2 Omicron Variant in CALABRIA: A Spatio-Temporal Report of Viral Genome Evolution by Claudia Veneziano, Nadia Marascio, Carmela De Marco, Barbara Quaresima, Flavia Biamonte, Enrico Maria Trecarichi, Gianluca Santamaria, Angela Quirino, Daniele Torella, Aldo Quattrone, Giovanni Matera, Carlo Torti, Caterina De Filippo, Francesco Saverio Costanzo, Giuseppe Viglietto

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SEQUENCING PROTOCOL AND BIOINFORMATICS PIPELINE FOR THE AVIAN INFLUENZA VIRUS by Vladimir Gajdov, Tamas Petrovic, Gospava Lazic, Biljana Djurdjevic, Marko Pajic, Slobodan Knezevic, Jakov Nisavic

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Limited Genetic Diversity Detected in Middle East Respiratory Syndrome-Related Coronavirus Variants Circulating in Dromedary Camels in Jordan by Stephanie N. Seifert, Jonathan E. Schulz, Stacy Ricklefs, Michael Letko, Elangeni Yabba, Zaidoun S. Hijazeen, Peter Holloway, Bilal Al-Omari, Hani A. Talafha, Markos Tibbo, Danielle R. Adney, Javier Guitian, Nadim Amarin, Juergen A. Richt, Chester McDowell, John Steel, Ehab A. Abu-Basha, Ahmad M. Al-Majali, Neeltje van Doremalen, Vincent J. Munster

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Intra-Host Evolution Analyses in an Immunosuppressed Patient Supports SARS-CoV-2 Viral Reservoir Hypothesis by Dominique Fournelle, Fatima Mostefai, Elsa Brunet-Ratnasingham, Raphaël Poujol, Jean-Christophe Grenier, José Héctor Gálvez, Amélie Pagliuzza, Inès Levade, Sandrine Moreira, Mehdi Benlarbi, Guillaume Beaudoin-Bussières, Gabrielle Gendron-Lepage, Catherine Bourassa, Alexandra Tauzin, Simon Grandjean Lapierre, Nicolas Chomont, Andrés Finzi, Daniel E. Kaufmann, Morgan Craig, Julie G. Hussin

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Virulent Phages Isolated from a Smear-Ripened Cheese Are Also Detected in Reservoirs of the Cheese Factory by Thomas Paillet, Julien Lossouarn, Clarisse Figueroa, Cédric Midoux, Olivier Rué, Marie-Agnès Petit, Eric Dugat-Bony

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VAPiD: a lightweight cross-platform viral annotation pipeline and identification tool to facilitate virus genome submissions to NCBI GenBank by Ryan C. Shean, Negar Makhsous, Graham D. Stoddard, Michelle J. Lin, Alexander L. Greninger

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A Synthesis of Viral Contribution to Marine Nitrogen Cycling by Shuai Wang, Yu Yang, Jiaojiao Jing, Jiaojiao Jing, Jiaojiao Jing

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Therapeutic Potential of a New Jumbo Phage That Infects Vibrio coralliilyticus, a Widespread Coral Pathogen by Loïc Jacquemot, Yvan Bettarel, Joanne Monjol, Erwan Corre, Sébastien Halary, Christelle Desnues, Thierry Bouvier, Christine Ferrier-Pagès, Anne-Claire Baudoux

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Target-independent high-throughput sequencing methods provide evidence that already known human viral pathogens play a main role in respiratory infections with unexplained etiology by Unai Pérez-Sautu, Michael Ross Wiley, María Iglesias-Caballero, Francisco Pozo, Karla Prieto, Joseph Alex Chitty, María Luz García-García, Cristina Calvo, Inmaculada Casas, Gustavo Palacios

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Genomic Epidemiology of Salmonid Alphavirus in Norwegian Aquaculture Reveals Recent Subtype-2 Transmission Dynamics and Novel Subtype-3 Lineages by Daniel J. Macqueen, Oliver Eve, Manu Kumar Gundappa, Rose Ruiz Daniels, Michael D. Gallagher, Svein Alexandersen, Marius Karlsen

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Genomic evolution, recombination, and inter-strain diversity of chelonid alphaherpesvirus 5 from Florida and Hawaii green sea turtles with fibropapillomatosis by Cheryl L. Morrison, Luke Iwanowicz, Thierry M. Work, Elizabeth Fahsbender, Mya Breitbart, Cynthia Adams, Deb Iwanowicz, Lakyn Sanders, Mathias Ackermann, Robert S. Cornman

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HCV Genetic Diversity Can Be Used to Infer Infection Recency and Time since Infection by Louisa A. Carlisle, Teja Turk, Karin J. Metzner, Herbert A. Mbunkah, Cyril Shah, Jürg Böni, Michael Huber, Dominique L. Braun, Jan Fehr, Luisa Salazar-Vizcaya, Andri Rauch, Sabine Yerly, Aude Nguyen, Matthias Cavassini, Marcel Stoeckle, Pietro Vernazza, Enos Bernasconi, Huldrych F. Günthard, Roger D. Kouyos

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Mapping Data to Deep Understanding: Making the Most of the Deluge of SARS-CoV-2 Genome Sequences by Bahrad A. Sokhansanj, Gail L. Rosen

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Multiple Occurrences of a 168-Nucleotide Deletion in SARS-CoV-2 ORF8, Unnoticed by Standard Amplicon Sequencing and Variant Calling Pipelines by David Brandt, Marina Simunovic, Tobias Busche, Markus Haak, Peter Belmann, Sebastian Jünemann, Tizian Schulz, Levin Joe Klages, Svenja Vinke, Michael Beckstette, Ehmke Pohl, Christiane Scherer, Alexander Sczyrba, Jörn Kalinowski

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Comparative genomic, transcriptomic, and proteomic reannotation of human herpesvirus 6 by Alexander L. Greninger, Giselle M. Knudsen, Pavitra Roychoudhury, Derek J. Hanson, Ruth Hall Sedlak, Hong Xie, Jon Guan, Thuy Nguyen, Vikas Peddu, Michael Boeckh, Meei-Li Huang, Linda Cook, Daniel P. Depledge, Danielle M. Zerr, David M. Koelle, Soren Gantt, Tetsushi Yoshikawa, Mary Caserta, Joshua A. Hill, Keith R. Jerome

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Tsv-N1: A Novel DNA Algal Virus that Infects Tetraselmis striata by António Pagarete, Théophile Grébert, Olga Stepanova, Ruth-Anne Sandaa, Gunnar Bratbak

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