Virion-associated nucleic acid-based metagenomics: a decade of advances in molecular characterization of plant viruses

Autor: Moubset, O, François, S, Maclot, F, Palanga, E, Julian, C, Claude, L, Fernandez, E, Rott, PCE, Daugrois, J-H, Antoine-Lorquin, A, Bernardo, P, Blouin, AG, Temple, C, Kraberger, S, Fontenele, RS, Harkins, GW, Marais, A, Candresse, T, Ben Chéhida, S, Lefeuvre, P, Lett, J-M, Varsani, A, Massart, S, Ogliastro, M-H, Martin, DP, Filloux, D, Roumagnac, P

Over the last decade, viral metagenomic studies have resulted in the discovery of thousands of previously unknown viruses. These studies are likely to play a pivotal role in obtaining an accurate and robust understanding of how viruses affect the sta

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=od______1064::8b56879bdc28baca40b166020357f129
https://doi.org/10.1094/phyto-03-22-0096-rvw

Selection Analysis Identifies Clusters of Unusual Mutational Changes in Omicron Lineage BA.1 That Likely Impact Spike Function.

Autor: Martin DP; Institute of Infectious Diseases and Molecular Medicine, Division of Computational Biology, Department of Integrative Biomedical Sciences, University of Cape Town, Cape Town, South Africa., Lytras S; MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, United Kingdom., Lucaci AG; Institute for Genomics and Evolutionary Medicine, Department of Biology, Temple University, Philadelphia, PA, USA., Maier W; Bioinformatics Group, Department of Computer Science, University of Freiburg, Freiburg, Germany, usegalaxy.eu., Grüning B; Bioinformatics Group, Department of Computer Science, University of Freiburg, Freiburg, Germany, usegalaxy.eu., Shank SD; Institute for Genomics and Evolutionary Medicine, Department of Biology, Temple University, Philadelphia, PA, USA., Weaver S; Institute for Genomics and Evolutionary Medicine, Department of Biology, Temple University, Philadelphia, PA, USA., MacLean OA; MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, United Kingdom., Orton RJ; MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, United Kingdom., Lemey P; Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium., Boni MF; Center for Infectious Disease Dynamics, Department of Biology, Pennsylvania State University, University Park, PA, USA., Tegally H; KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine & Medical Sciences, University of KwaZulu-Natal, Durban, South Africa., Harkins GW; South African National Bioinformatics Institute, University of the Western Cape, Cape Town, South Africa., Scheepers C; National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa.; SA MRC Antibody Immunity Research Unit, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa., Bhiman JN; National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa.; SA MRC Antibody Immunity Research Unit, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa., Everatt J; National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa., Amoako DG; National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa., San JE; KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine & Medical Sciences, University of KwaZulu-Natal, Durban, South Africa., Giandhari J; KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine & Medical Sciences, University of KwaZulu-Natal, Durban, South Africa., Sigal A; Africa Health Research Institute, Durban, South Africa., Williamson C; Institute of Infectious Disease and Molecular Medicine, Department of Pathology, University of Cape Town, Cape Town, South Africa.; Division of Medical Virology, University of Cape Town and National Health Laboratory Service, Cape Town, South Africa.; Wellcome Center for Infectious Diseases Research in Africa, Institute of Infectious Disease and Molecular Medicine and Department of Medicine, University of Cape Town, Cape Town, South Africa., Hsiao NY; Division of Medical Virology, University of Cape Town and National Health Laboratory Service, Cape Town, South Africa., von Gottberg A; National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa.; School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa., De Klerk A; Institute of Infectious Diseases and Molecular Medicine, Division of Computational Biology, Department of Integrative Biomedical Sciences, University of Cape Town, Cape Town, South Africa., Shafer RW; Division of Infectious Diseases, Department of Medicine, Stanford University, Stanford, CA, USA., Robertson DL; MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, United Kingdom., Wilkinson RJ; Wellcome Center for Infectious Diseases Research in Africa, Institute of Infectious Disease and Molecular Medicine and Department of Medicine, University of Cape Town, Cape Town, South Africa.; Francis Crick Institute, London, United Kingdom.; Department of Infectious Diseases, Imperial College London, London, United Kingdom., Sewell BT; Structural Biology Research Unit, Department of Integrative Biomedical Sciences, Institute for Infectious Diseases and Molecular Medicine, University of Cape Town, Cape Town, South Africa., Lessells R; KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine & Medical Sciences, University of KwaZulu-Natal, Durban, South Africa., Nekrutenko A; Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, USA, usegalaxy.org., Greaney AJ; Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.; Department of Genome Sciences & Medical Scientist Training Program, University of Washington, Seattle, WA, USA., Starr TN; Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.; Howard Hughes Medical Institute, Seattle, WA, USA., Bloom JD; Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.; Howard Hughes Medical Institute, Seattle, WA, USA., Murrell B; Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden., Wilkinson E; KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine & Medical Sciences, University of KwaZulu-Natal, Durban, South Africa.; Centre for Epidemic Response and Innovation (CERI), School of Data Science, Stellenbosch University, Stellenbosch, South Africa., Gupta RK; Africa Health Research Institute, Durban, South Africa.; Cambridge Institute of Therapeutic Immunology and Infectious Diseases, University of Cambridge, Cambridge, United Kingdom., de Oliveira T; KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine & Medical Sciences, University of KwaZulu-Natal, Durban, South Africa.; Centre for Epidemic Response and Innovation (CERI), School of Data Science, Stellenbosch University, Stellenbosch, South Africa., Kosakovsky Pond SL; Institute for Genomics and Evolutionary Medicine, Department of Biology, Temple University, Philadelphia, PA, USA.

Publikováno v: Molecular biology and evolution [Mol Biol Evol] 2022 Apr 11; Vol. 39 (4).

The emergence and ongoing convergent evolution of the SARS-CoV-2 N501Y lineages.

Autor: Martin DP; Institute of Infectious Diseases and Molecular Medicine, Division Of Computational Biology, Department of Integrative Biomedical Sciences, University of Cape Town, Cape Town 7701, South Africa. Electronic address: darrenpatrickmartin@gmail.com., Weaver S; Institute for Genomics and Evolutionary Medicine, Department of Biology, Temple University, Philadelphia, PA 19122, USA., Tegally H; KwaZulu-Natal Research Innovation and Sequencing Platform, School of Laboratory Medicine & Medical Sciences, University of KwaZulu- Natal, Durban 4001, South Africa., San JE; KwaZulu-Natal Research Innovation and Sequencing Platform, School of Laboratory Medicine & Medical Sciences, University of KwaZulu- Natal, Durban 4001, South Africa., Shank SD; Institute for Genomics and Evolutionary Medicine, Department of Biology, Temple University, Philadelphia, PA 19122, USA., Wilkinson E; KwaZulu-Natal Research Innovation and Sequencing Platform, School of Laboratory Medicine & Medical Sciences, University of KwaZulu- Natal, Durban 4001, South Africa., Lucaci AG; Institute for Genomics and Evolutionary Medicine, Department of Biology, Temple University, Philadelphia, PA 19122, USA., Giandhari J; KwaZulu-Natal Research Innovation and Sequencing Platform, School of Laboratory Medicine & Medical Sciences, University of KwaZulu- Natal, Durban 4001, South Africa., Naidoo S; KwaZulu-Natal Research Innovation and Sequencing Platform, School of Laboratory Medicine & Medical Sciences, University of KwaZulu- Natal, Durban 4001, South Africa., Pillay Y; KwaZulu-Natal Research Innovation and Sequencing Platform, School of Laboratory Medicine & Medical Sciences, University of KwaZulu- Natal, Durban 4001, South Africa., Singh L; KwaZulu-Natal Research Innovation and Sequencing Platform, School of Laboratory Medicine & Medical Sciences, University of KwaZulu- Natal, Durban 4001, South Africa., Lessells RJ; KwaZulu-Natal Research Innovation and Sequencing Platform, School of Laboratory Medicine & Medical Sciences, University of KwaZulu- Natal, Durban 4001, South Africa., Gupta RK; Clinical Microbiology, University of Cambridge, Cambridge CB2 1TN, UK; Africa Health Research Institute, KwaZulu-Natal 4013, South Africa., Wertheim JO; Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA., Nekturenko A; Department of Biochemistry and Molecular Biology, The Pennsylvania State University, State College, PA 16802, USA., Murrell B; Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm 141 83, Sweden., Harkins GW; South African Medical Research Council Capacity Development Unit, South African National Bioinformatics Institute, University of the Western Cape, Bellville 7635, South Africa., Lemey P; Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven 3000, Belgium., MacLean OA; MRC-University of Glasgow Centre for Virus Research, Glasgow 12 8QQ, Scotland, UK., Robertson DL; MRC-University of Glasgow Centre for Virus Research, Glasgow 12 8QQ, Scotland, UK., de Oliveira T; KwaZulu-Natal Research Innovation and Sequencing Platform, School of Laboratory Medicine & Medical Sciences, University of KwaZulu- Natal, Durban 4001, South Africa; Department of Global Health, University of Washington, Seattle, WA 98195-4550, USA. Electronic address: tuliodna@gmail.com., Kosakovsky Pond SL; Institute for Genomics and Evolutionary Medicine, Department of Biology, Temple University, Philadelphia, PA 19122, USA. Electronic address: spond@temple.edu.

Publikováno v: Cell [Cell] 2021 Sep 30; Vol. 184 (20), pp. 5189-5200.e7. Date of Electronic Publication: 2021 Sep 07.

Dispersal dynamics of SARS-CoV-2 lineages during the first epidemic wave in New York City.

Autor: Dellicour S; Spatial Epidemiology Lab (SpELL), Université Libre de Bruxelles, Bruxelles, Belgium.; Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory for Clinical and Epidemiological Virology, KU Leuven, University of Leuven, Leuven, Belgium., Hong SL; Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory for Clinical and Epidemiological Virology, KU Leuven, University of Leuven, Leuven, Belgium., Vrancken B; Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory for Clinical and Epidemiological Virology, KU Leuven, University of Leuven, Leuven, Belgium., Chaillon A; Division of Infectious Diseases and Global Public Health, University of California San Diego, California, United States of America., Gill MS; Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory for Clinical and Epidemiological Virology, KU Leuven, University of Leuven, Leuven, Belgium., Maurano MT; Department of Pathology, NYU Grossman School of Medicine, New York, New York, United States of America.; Institute for Systems Genetics, NYU Grossman School of Medicine, New York, New York, United States of America., Ramaswami S; Genome Technology Center, Office for Science and Research, NYU Langone Health, New York, New York, United States of America., Zappile P; Genome Technology Center, Office for Science and Research, NYU Langone Health, New York, New York, United States of America., Marier C; Genome Technology Center, Office for Science and Research, NYU Langone Health, New York, New York, United States of America., Harkins GW; South African Medical Research Council Capacity Development Unit, South African National Bioinformatics Institute, University of the Western Cape, Bellville, South Africa., Baele G; Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory for Clinical and Epidemiological Virology, KU Leuven, University of Leuven, Leuven, Belgium., Duerr R; Department of Pathology, NYU Grossman School of Medicine, New York, New York, United States of America.; Department of Microbiology, NYU Grossman School of Medicine, New York, New York, United States of America., Heguy A; Department of Pathology, NYU Grossman School of Medicine, New York, New York, United States of America.; Genome Technology Center, Office for Science and Research, NYU Langone Health, New York, New York, United States of America.

Publikováno v: PLoS pathogens [PLoS Pathog] 2021 May 20; Vol. 17 (5), pp. e1009571. Date of Electronic Publication: 2021 May 20 (Print Publication: 2021).

SARS-CoV-2 genomic characterization and clinical manifestation of the COVID-19 outbreak in Uruguay.

Autor: Elizondo V; Laboratorio de Biología Molecular, Asociación Española Primera en Salud, Montevideo, Uruguay., Harkins GW; South African Medical Research Council Capacity Development Unit, South African National Bioinformatics Institute, University of the Western Cape, Bellville, South Africa., Mabvakure B; Department of Medicine, Johns Hopkins School of Medicine, Baltimore, Maryland, United States of America., Smidt S; South African Medical Research Council Capacity Development Unit, South African National Bioinformatics Institute, University of the Western Cape, Bellville, South Africa., Zappile P; Genome Technology Center, Office for Science and Research, NYU Langone Health, New York, New York, United States of America., Marier C; Genome Technology Center, Office for Science and Research, NYU Langone Health, New York, New York, United States of America., Maurano M; Department of Pathology, NYU Grossman School of Medicine, New York, New York, United States of America., Perez V; Laboratorio de Biología Molecular, Asociación Española Primera en Salud, Montevideo, Uruguay.; Departamento de Desarrollo Biotecnológico, Instituto de Higiene, Facultad de Medicina, Udelar, Montevideo, Uruguay., Mazza N; Laboratorio de Biología Molecular, Asociación Española Primera en Salud, Montevideo, Uruguay., Beloso C; Laboratorio de Biología Molecular, Asociación Española Primera en Salud, Montevideo, Uruguay.; Departamento de Biodiversidad y Genética. Instituto de Investigaciones Biológicas Clemente Estable, Montevideo, Uruguay., Ifran S; Laboratorio de Biología Molecular, Asociación Española Primera en Salud, Montevideo, Uruguay., Fernandez M; Laboratorio de Biología Molecular, Asociación Española Primera en Salud, Montevideo, Uruguay., Santini A; Laboratorio de Biología Molecular, Asociación Española Primera en Salud, Montevideo, Uruguay., Perez V; Laboratorio de Biología Molecular, Asociación Española Primera en Salud, Montevideo, Uruguay., Estevez V; Laboratorio de Biología Molecular, Asociación Española Primera en Salud, Montevideo, Uruguay., Nin M; Laboratorio de Biología Molecular, Asociación Española Primera en Salud, Montevideo, Uruguay., Manrique G; Laboratorio de Biología Molecular, Asociación Española Primera en Salud, Montevideo, Uruguay., Perez L; Laboratorio de Biología Molecular, Asociación Española Primera en Salud, Montevideo, Uruguay., Ross F; Laboratorio de Biología Molecular, Asociación Española Primera en Salud, Montevideo, Uruguay., Boschi S; Laboratorio de Biología Molecular, Asociación Española Primera en Salud, Montevideo, Uruguay., Noel Zubillaga M; Laboratorio de Biología Molecular, Asociación Española Primera en Salud, Montevideo, Uruguay., Balleste R; Laboratorio de Biología Molecular, Asociación Española Primera en Salud, Montevideo, Uruguay., Dellicour S; Spatial Epidemiology Lab. (SpELL), Université Libre de Bruxelles, Bruxelles, Belgium.; Department of Microbiology, Immunology and Transplantation, Rega Institute, Leuven, Belgium., Heguy A; Genome Technology Center, Office for Science and Research, NYU Langone Health, New York, New York, United States of America.; Department of Pathology, NYU Grossman School of Medicine, New York, New York, United States of America., Duerr R; Department of Pathology, NYU Grossman School of Medicine, New York, New York, United States of America.

Publikováno v: MedRxiv : the preprint server for health sciences [medRxiv] 2020 Oct 11. Date of Electronic Publication: 2020 Oct 11.