Natural selection in the evolution of SARS-CoV-2 in bats, not humans, created a highly capable human pathogen

Autor: Maciej F. Boni, Kosakovsky Pond Sl, Joshua B Singer, Philippe Lemey, David Robertson, Spyros Lytras, Oscar A. MacLean, Steven Weaver

RNA viruses are proficient at switching host species, and evolving adaptations to exploit the new host’s cells efficiently. Surprisingly, SARS-CoV-2 has apparently required no significant adaptation to humans since the start of the COVID-19 pandemi

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_________::1b8aafa0f0307dad1022300d567237d5
https://doi.org/10.1101/2020.05.28.122366

Multiple emergences of amphibian chytridiomycosis include a globalised hypervirulent recombinant lineage

Autor: Farrer RA, Weinert LA, Bielby J, Garner TWJ, Balloux F, Clare F, Bosch J, Cunningham AA, Weldon C, du Preez LH, Anderson L, Kosakovsky Pond SL, Shahar-Golan R, Henk DA, MC Fisher

Publikováno v: PNAS.

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=erc_________::434d0c13a43bd98872e495089bfe5cf5

Ecological diversification of sea catfishes is accompanied by genome-wide signatures of positive selection.

Autor: Rincon-Sandoval M; Department of Biology, The University of Oklahoma, Norman, OK, 73019, USA., De-Kayne R; Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, CA, 95064, USA., Shank SD; Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, PA, 19122, USA., Pirro S; Iridian Genomes, Silver Spring, MD, 20904, USA., Ko'ou A; School of Natural & Physical Sciences, The University of Papua New Guinea, University 134, National Capital District, Port Moresby, Papua New Guinea., Abueg L; Vertebrate Genome Lab, The Rockefeller University, New York, NY, 10065, USA., Tracey A; Vertebrate Genome Lab, The Rockefeller University, New York, NY, 10065, USA., Mountcastle J; Vertebrate Genome Lab, The Rockefeller University, New York, NY, 10065, USA., O'Toole B; Vertebrate Genome Lab, The Rockefeller University, New York, NY, 10065, USA., Balacco J; Vertebrate Genome Lab, The Rockefeller University, New York, NY, 10065, USA., Formenti G; Vertebrate Genome Lab, The Rockefeller University, New York, NY, 10065, USA., Jarvis ED; Vertebrate Genome Lab, The Rockefeller University, New York, NY, 10065, USA., Arcila D; Scripps Institution of Oceanography, University of California San Diego, 8622 Kennel Way, La Jolla, CA, 92037, USA., Kosakovsky Pond SL; Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, PA, 19122, USA., Davis A; Centre for Tropical Water and Aquatic Ecosystem Research, School of Marine and Tropical Biology, James Cook University, Townsville, QLD 4811, Australia., Bloom DD; Department of Biological Sciences, Western Michigan University, Kalamazoo, MI, 49008, USA., Betancur-R R; Scripps Institution of Oceanography, University of California San Diego, 8622 Kennel Way, La Jolla, CA, 92037, USA. rbetancur@ucsd.edu.

Publikováno v: Nature communications [Nat Commun] 2024 Nov 20; Vol. 15 (1), pp. 10040. Date of Electronic Publication: 2024 Nov 20.

AUTO-TUNE: selecting the distance threshold for inferring HIV transmission clusters.

Autor: Weaver S; Center for Viral Evolution, Temple University, Philadelphia, PA, United States., Dávila Conn VM; Center for Research in Infectious Diseases, National Institute of Respiratory Diseases, Mexico City, Mexico., Ji D; Department of Medicine, University of California San Diego, La Jolla, CA, United States., Verdonk H; Center for Viral Evolution, Temple University, Philadelphia, PA, United States., Ávila-Ríos S; National Institute of Respiratory Diseases, Mexico City, Mexico., Leigh Brown AJ; Department of Medicine, University of California San Diego, La Jolla, CA, United States., Wertheim JO; Department of Medicine, University of California San Diego, La Jolla, CA, United States., Kosakovsky Pond SL; Center for Viral Evolution, Temple University, Philadelphia, PA, United States.

Publikováno v: Frontiers in bioinformatics [Front Bioinform] 2024 Jul 10; Vol. 4, pp. 1400003. Date of Electronic Publication: 2024 Jul 10 (Print Publication: 2024).

The genomic evolutionary dynamics and global circulation patterns of respiratory syncytial virus.

Autor: Langedijk AC; Department of Paediatric Immunology and Infectious Diseases, Wilhelmina Children's Hospital, University Medical Centre Utrecht, Lundlaan 6, 3584 EA, Utrecht, the Netherlands., Vrancken B; Department of Microbiology, Immunology and Transplantation, Laboratory of Clinical and Epidemiological Virology, Herestraat 49, 3000, Leuven, Belgium.; Spatial Epidemiology Lab (SpELL), Université Libre de Bruxelles, Bruxelles, Belgium., Lebbink RJ; Department of Medical Microbiology, University Medical Center Utrecht, Heidelberglaan 100, 3584 CX, Utrecht, the Netherlands., Wilkins D; Translational Medicine, Vaccines & Immune Therapies, BioPharmaceuticals R&D, AstraZeneca, 1 MedImmune Way, Gaithersburg, MD, USA., Kelly EJ; Translational Medicine, Vaccines & Immune Therapies, BioPharmaceuticals R&D, AstraZeneca, 1 MedImmune Way, Gaithersburg, MD, USA., Baraldi E; Department of Woman's and Child's Health, University Hospital of Padova, Padova, Italy.; ReSViNET Foundation, Zeist, the Netherlands.; Institute of Pediatric Research 'Città della Speranza', Padova, Italy., Mascareñas de Los Santos AH; Jose Eluterio Gonzalez Hospital Universitario, Monterrey, Mexico., Danilenko DM; Smorodintsev Research Institute of Influenza, St. Petersburg, Russia., Choi EH; Seoul National University Children's Hospital, Seoul, South Korea., Palomino MA; Hospital Roberto del Río, Universidad de Chile, Santiago, Chile., Chi H; MacKay Children's Hospital, New Taipei, Taiwan, ROC., Keller C; Institute of Virology, University Hospital Giessen and Marburg, Marburg, Germany., Cohen R; Université Paris XII, Créteil, France., Papenburg J; McGill University Health Centre, Montreal, QC, Canada., Pernica J; McMaster University, Hamilton, ON, Canada., Greenough A; ReSViNET Foundation, Zeist, the Netherlands.; King's College London, London, UK., Richmond P; University of Western Australia, Perth, WA, Australia., Martinón-Torres F; ReSViNET Foundation, Zeist, the Netherlands.; Hospital Clínico Universitario de Santiago, Galicia, Spain., Heikkinen T; ReSViNET Foundation, Zeist, the Netherlands.; University of Turku and Turku University Hospital, Turku, Finland., Stein RT; ReSViNET Foundation, Zeist, the Netherlands.; Pontificia Universidade Catolica de Rio Grande do Sul, Porto Alegre, Brazil., Hosoya M; Fukushima Medical University School of Medicine, Fukushima, Japan., Nunes MC; ReSViNET Foundation, Zeist, the Netherlands.; Department of Paediatrics and Child Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.; South African Medical Research Council, Vaccines & Infectious Diseases Analytics Research Unit, and Department of Science and Technology/National Research Foundation, South African Research Chair Initiative in Vaccine Preventable Diseases, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa., Verwey C; Department of Paediatrics and Child Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.; Hospices Civils de Lyon and the Centre International de Recherche en Infectiologie (CIRI) Inserm U1111, CNRS UMR5308, ENS de Lyon, UCBL1, Lyon, France., Evers A; Department of Medical Microbiology, University Medical Center Utrecht, Heidelberglaan 100, 3584 CX, Utrecht, the Netherlands., Kragten-Tabatabaie L; ReSViNET Foundation, Zeist, the Netherlands., Suchard MA; Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, CA, 90095, USA.; Department of Biostatistics, Jonathan and Karin Fielding School of Public Health, University of California, Los Angeles, CA, 90095, USA.; Department of Biomathematics, David Geffen School of Medicine, University of California, Los Angeles, CA, 90095, USA., Kosakovsky Pond SL; Institute for Genomics and Evolutionary Medicine, Department of Biology, Temple University, 801 N Broad St, Philadelphia, PA, 19122, USA., Poletto C; INSERM, Sorbonne Université, Institut Pierre Louis d'Epidémiologie et de Santé Publique IPLESP, F75012, Paris, France., Colizza V; INSERM, Sorbonne Université, Institut Pierre Louis d'Epidémiologie et de Santé Publique IPLESP, F75012, Paris, France., Lemey P; Department of Microbiology, Immunology and Transplantation, Laboratory of Clinical and Epidemiological Virology, Herestraat 49, 3000, Leuven, Belgium., Bont LJ; Department of Paediatric Immunology and Infectious Diseases, Wilhelmina Children's Hospital, University Medical Centre Utrecht, Lundlaan 6, 3584 EA, Utrecht, the Netherlands. l.bont@umcutrecht.nl.; ReSViNET Foundation, Zeist, the Netherlands. l.bont@umcutrecht.nl.

Publikováno v: Nature communications [Nat Commun] 2024 Apr 10; Vol. 15 (1), pp. 3083. Date of Electronic Publication: 2024 Apr 10.