Virus nomenclature below the species level : a standardized nomenclature for filovirus strains and variants rescued from cDNA

Specific alterations (mutations, deletions, insertions) of virus genomes are crucial for the functional characterization of their regulatory elements and their expression products, as well as a prerequisite for the creation of attenuated viruses that could serve as vaccine candidates. Virus genome tailoring can be performed either by using traditionally cloned genomes as starting materials, followed by site-directed mutagenesis, or by de novo synthesis of modified virus genomes or parts thereof. A systematic nomenclature for such recombinant viruses is necessary to set them apart from wild-type and laboratoryadapted viruses, and to improve communication and collaborations among researchers who may want to use recombinant viruses or create novel viruses based on them. A large group of filovirus experts has recently proposed nomenclatures for natural and laboratory animal-adapted filoviruses that aim to simplify the retrieval of sequence data from electronic databases. Here, this work is extended to include nomenclature for filoviruses obtained in the laboratory via reverse genetics systems. The previously developed template for natural filovirus genetic variant naming,\virus name[(\strain[/)\isolation host-suffix[/ \country of sampling[/\year of sampling[/\genetic variant designation[-\isolate designation[, is retained, but we propose to adapt the type of information added to each field for cDNA clone-derived filoviruses. For instance, the full-length designation of an Ebola virus Kikwit variant rescued from a plasmid developed at the US Centers for Disease Control and Prevention could be akin to ‘‘Ebola virus H.sapiens-rec/COD/1995/Kikwit-abc1’’ (with the suffix ‘‘rec’’ identifying the recombinant nature of the virus and ‘‘abc1’’ being a placeholder for any meaningful isolate designator). Such a full-length designation should be used in databases and the methods section of publications. Shortened designations (such as ‘‘EBOV H.sap/COD/95/ Kik-abc1’’) and abbreviations (such as ‘‘EBOV/Kik-abc1’’) could be used in the remainder of the text, depending on how critical it is to convey information contained in the full-length name. ‘‘EBOV’’ would suffice if only one EBOV strain/variant/isolate is addressed.http://link.springer.com/journal/705hb201

2021 Taxonomic update of phylum Negarnaviricota (Riboviria: Orthornavirae), including the large orders Bunyavirales and Mononegavirales.

In March 2021, following the annual International Committee on Taxonomy of Viruses (ICTV) ratification vote on newly proposed taxa, the phylum Negarnaviricota was amended and emended. The phylum was expanded by four families (Aliusviridae, Crepuscuviridae, Myriaviridae, and Natareviridae), three subfamilies (Alpharhabdovirinae, Betarhabdovirinae, and Gammarhabdovirinae), 42 genera, and 200 species. Thirty-nine species were renamed and/or moved and seven species were abolished. This article presents the updated taxonomy of Negarnaviricota as now accepted by the ICTV

Ensuring vaccine safety

There is an urgent need for vaccines to protect against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection to reduce COVID-19 and stop the current pandemic. Although bureaucratic delays should be reduced to accelerate vaccine availability, there remains the need for extensive safety testing protocols developed by the U.S. Food and Drug Administration (FDA) and other regulatory agencies. COVID-19 vaccines will be safe if regulatory agencies maintain their well-documented safety testing protocols. Safety should be considered at every phase of vaccine discovery, development, and testing. History provides a strong scientific basis for safety evaluation of all vaccine candidates, which must be maintained to realize their enormous potential

Multiplexed Metagenomic Deep Sequencing To Analyze the Composition of High-Priority Pathogen Reagents.

Laboratories studying high-priority pathogens need comprehensive methods to confirm microbial species and strains while also detecting contamination. Metagenomic deep sequencing (MDS) inventories nucleic acids present in laboratory stocks, providing an unbiased assessment of pathogen identity, the extent of genomic variation, and the presence of contaminants. Double-stranded cDNA MDS libraries were constructed from RNA extracted from in vitro-passaged stocks of six viruses (La Crosse virus, Ebola virus, canine distemper virus, measles virus, human respiratory syncytial virus, and vesicular stomatitis virus). Each library was dual indexed and pooled for sequencing. A custom bioinformatics pipeline determined the organisms present in each sample in a blinded fashion. Single nucleotide variant (SNV) analysis identified viral isolates. We confirmed that (i) each sample contained the expected microbe, (ii) dual indexing of the samples minimized false assignments of individual sequences, (iii) multiple viral and bacterial contaminants were present, and (iv) SNV analysis of the viral genomes allowed precise identification of the viral isolates. MDS can be multiplexed to allow simultaneous and unbiased interrogation of mixed microbial cultures and (i) confirm pathogen identity, (ii) characterize the extent of genomic variation, (iii) confirm the cell line used for virus propagation, and (iv) assess for contaminating microbes. These assessments ensure the true composition of these high-priority reagents and generate a comprehensive database of microbial genomes studied in each facility. MDS can serve as an integral part of a pathogen-tracking program which in turn will enhance sample security and increase experimental rigor and precision. IMPORTANCE Both the integrity and reproducibility of experiments using select agents depend in large part on unbiased validation to ensure the correct identity and purity of the species in question. Metagenomic deep sequencing (MDS) provides the required level of validation by allowing for an unbiased and comprehensive assessment of all the microbes in a laboratory stock

Taxonomy of the order Mononegavirales: second update 2018

In October 2018, the order Mononegavirales was amended by the establishment of three new families and three new genera, abolishment of two genera, and creation of 28 novel species. This article presents the updated taxonomy of the order Mononegavirales as now accepted by the International Committee on Taxonomy of Viruses (ICTV).status: publishe

Taxonomy of the order Mononegavirales: update 2019

In February 2019, following the annual taxon ratification vote, the order Mononegavirales was amended by the addition of four new subfamilies and 12 new genera and the creation of 28 novel species. This article presents the updated taxonomy of the order Mononegavirales as now accepted by the International Committee on Taxonomy of Viruses (ICTV).status: publishe

Taxonomy of the order Mononegavirales: update 2018

In 2018, the order Mononegavirales was expanded by inclusion of 1 new genus and 12 novel species. This article presents the updated taxonomy of the order Mononegavirales as now accepted by the International Committee on Taxonomy of Viruses (ICTV) and summarizes additional taxonomic proposals that may affect the order in the near future.status: publishe

Annual (2023) taxonomic update of RNA-directed RNA polymerase-encoding negative-sense RNA viruses (realm Riboviria: kingdom Orthornavirae: phylum Negarnaviricota)

Laulima Government Solutions, LLC, prime contract with the U.S. National Institute of Allergy and Infectious Diseases (NIAID) under Contract No. HHSN272201800013C. J.H.K. performed this work as an employee of Tunnell Government Services (TGS), a subcontractor of Laulima Government Solutions, LLC, under Contract No. HHSN272201800013C. U.J.B. was supported by the Division of Intramural Resarch, NIAID. This work was also funded in part by Contract No. HSHQDC15-C-00064 awarded by DHS S and T for the management and operation of The National Biodefense Analysis and Countermeasures Centre, a federally funded research and development centre operated by the Battelle National Biodefense Institute (V.W.); and NIH contract HHSN272201000040I/HHSN27200004/D04 and grant R24AI120942 (N.V., R.B.T.). S.S. acknowledges support from the Mississippi Agricultural and Forestry Experiment Station (MAFES), USDA-ARS project 58-6066-9-033 and the National Institute of Food and Agriculture, U.S. Department of Agriculture, Hatch Project, under Accession Number 1 021 494.National Institutes of Health. National Institute of Allergy and Infectious Disease. Division of Clinical Research. Integrated Research Facility at Fort Detrick. Frederick, MD, USA.Hokkaido Research Organization. Agricultural Research Department. Ornamental Plants and Vegetables Research Center. Takikawa, Hokkaido, Japan.United States Department of Agriculture. Agricultural Research Service. US Horticultural Research Laboratory. Fort Pierce, FL, USA.D.I. Ivanovsky Institute of Virology of N.F. Gamaleya National Center on Epidemiology and Microbiology of Ministry of Health of Russian Federation. Moscow, Russia.University of Ljubljana. Faculty of Medicine. Institute of Microbiology and Immunology. 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Department of Microbiology and Immunology. Bronx, NY, USA.Unite des Virus Emergents -Aix-Marseille Univ-IRD 190-Inserm 1207. Marseille, France.ICAR-Indian Agricultural Statistics Research Institute. Centre for Agricultural Bioinformatics. New Delhi, India.The New Zealand Institute for Plant and Food Research Limited. Auckland, New Zealand.National Institutes of Health. National Institute of Allergy and Infectious Diseases. Integrated Research Facility at Fort Detrick. Frederick, MD, USA.Universidad de La Plata. Facultad de Ciencias Agrarias y Forestales. CIDEFI. La Plata, Argentina.The Scripps Research Institute. Department of Immunology and Microbiology IMM-6. La Jolla, CA, USA.The University of Texas Medical Branch at Galveston. Department of Microbiology and Immunology. World Reference Center for Emerging Viruses and Arboviruses. Galveston, TX, USA.Wageningen Bioveterinary Research. Department of Virology. Lelystad, Netherlands.Instituto de Patología Vegetal. 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School of Life Sciences. Coventry, UK.Hacettepe University. Faculty of Medicine. Department of Medical Microbiology. Virology Unit. Ankara, Turkey.Museum Support Center. Smithsonian Institution. Walter Reed Biosystematics Unit. Suitland, MD, USA / Walter Reed Army Institute of Research. One Health Branch. Silver Spring, MD, USA / Smithsonian Institution-National Museum of Natural History. Department of Entomology. Washington, DC, USA / China National Rice Research Institute. Hangzhou, PR China.University of Cambridge. Department of Pathology. Cambridge, UK.Animal and Plant Health Agency. eybridge, Surrey, UK.World Health Organization. Geneva, Switzerland.Embrapa Cassava and Fruits. Cruz das Almas, BA, Brazil.Martin Luther University Halle-Wittenberg. Institute of Biochemistry and Biotechnology. Halle/Saale, Germany.Instituto de Biotecnología y Biología Molecular. Facultad de Ciencias Exactas. La Plata, Argentina.Icahn School of Medicine at Mount Sinai. New York, NY, USA.Brandenburg State Office of Rural Development. Agriculture and Land Consolidation. Frankfurt, Germany.Humboldt-Universität Zu Berlin. Thaer-Institute of Agricultural and Horticultural Sciences. Division Phytomedicine. Berlin, Germany.Ministry of Education. Jilin University. College of Veterinary Medicine. Key Laboratory of Zoonoses Research. State Key Laboratory for Zoonotic Diseases. Changchun, PR China / Georgetown University. School of Medicine. Division of Biomedical Graduate Research Organization. Department of Microbiology and Immunology. Washington, DC, USA.Institute of Vertebrate Biology of the Czech Academy of Sciences. Brno, CzechiaBoston University. National Emerging Infectious Diseases Laboratories. Chobanian and Avedisian School of Medicine. Department of Virology, Immunology and Microbiology. Boston, MA, USA.Friedrich-Loeffler-Institut. Institute of Novel and Emerging Infectious Diseases. Greifswald-Insel Riems, Germany.Bernhard-Nocht Institute for Tropical Medicine. WHO Collaborating Centre for Arboviruses and Hemorrhagic Fever Reference and Research. Department of Virology. Hamburg, Germany.United States Department of Agriculture. Agricultural Research Service / United States Naval Academy. Floral and Nursery Plants Research Unit. Beltsville, MD, USA.Hosei University. Department of Clinical Plant Science. Koganei, Tokyo, Japan.Kochi Agricultural Research Center. Nankoku, Kochi, Japan.University of Helsinki. Department of Virology. Medicum, Helsinki, Finland.University of Zurich. Institute of Veterinary Pathology, Vetsuisse Faculty. Zurich, Switzerland.Auckland University of Technology. The School of Science. Auckland, New Zealand.Yamagata University. Faculty of Medicine. Department of Infectious Diseases. Yamagata, Japan / Osaka Metropolitan University. Graduate School of Veterinary Science / Osaka Metropolitan University. International Research Center for Infectious Diseases. Izumisano, Osaka, Japan.Centers for Disease Control and Prevention. Fort Collins, CO, USA.Murdoch University. School of Veterinary Medicine. Murdoch, WA, Australia.Kobe University. Graduate School of Agricultural Science. Kobe, Hyogo, Japan.Huazhong Agricultural University. State Key Laboratory of Agricultural Microbiology. Wuhan, Hubei Province, PR China.International Rice Research Institute. College. Los Baños, Laguna, Philippines.Charité-Universitätsmedizin Berlin. Freie Universität Berlin. Corporate Member. Humboldt-Universität zu Berlin. Berlin Institute of Health. Institute of Virology. Berlin, Germany.Slovak Academy of Sciences. Biomedical Research Center. Institute of Virology. Bratislava, Slovakia.Linköping University. Department of Biomedical and Clinical Sciences. Linköping, Sweden.Okayama University. Institute of Plant Science and Resources. Kurashiki, Japan.National Institutes of Health. National Library of Medicine. 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School of Biological Sciences. Auckland, New Zealand.KU Leuven. Rega Institute. Zoonotic Infectious Diseases unit. Leuven, Belgium.FIND - The Global Alliance for Diagnostics. Geneva, Switzerland.Pontificia Universidad Católica de Valparaíso-Campus Curauma. Instituto de Biología-Laboratorio de Genética Molecular. Valparaíso, Chile.United States Department of Agriculture. Agricultural Research Service. Toledo, OH, USA.Folkhalsomyndigheten. Stockholm, Sweden.Yamagata University. Department of Agriculture. Tsuruoka, Japan.Washington State University. Irrigated Agricultural Research and Extension Center. Department of Plant Pathology. Prosser, WA, USA.Utsunomiya University. Utsunomiya, Japan.Universitat Politècnica de València-Consejo Superior de Investigaciones Científicas. Instituto de Biología Molecular y Celular de Plantas. Valencia, Spain.Utsunomiya University. School of Agriculture. Utsunomiya, Japan.Novosibirsk State University. Novosibirsk Oblast, Russia.University of Wisconsin-Madison. Department of Pathobiological Sciences. Influenza Research Institute. Madison, USA.University of Veterinary Medicine Vienna. Institute of Virology. Vienna, Austria.Mohammed Bin Rashid University of Medicine and Health Sciences. College of Medicine. Dubai, United Arab Emirates.Ministério da Saúde. Secretaria de Vigilância em Saúde e Ambiente. Instituto Evandro Chagas. Ananindeua, PA, Brasil.Oklahoma State University. Institute for Biosecurity and Microbial Forensics. Stillwater. Oklahoma, USA.Icahn School of Medicine at Mount Sinai. Department of Microbiology. New York, NY, USA.Universitat Politècnica de Valencia - Consejo Superior de Investigaciones Cientificas. Instituto de Biología Molecular y Celular de Plantas. Valencia, Spain.Aristotle University of Thessaloniki. Department of Microbiology, Medical School. National Reference Centre for Arboviruses and Haemorrhagic Fever viruses. Thessaloniki, Greece.Robert Koch Institute. Genome Competence Center. Berlin, Germany / Cornell University. College of Veterinary Medicine. Baker Institute for Animal Health. Ithaca, NY, USA.Ministério da Saúde. Secretaria de Vigilância em Saúde e Ambiente. Instituto Evandro Chagas. Ananindeua, PA, Brasil.National Institute for Communicable Diseases of the National Health Laboratory Service. Center for Emerging Zoonotic and Parasitic Diseases. Sandringham-Johannesburg, Gauteng, South Africa.University of Georgia. College of Veterinary Medicine. Department of Population Health. Athens, GA, USA.Georgia State University Institute for Biomedical Sciences. Center for Translational Antiviral Research. Atlanta, GA, USA.International AIDS Vaccine Initiative. Vaccine Design and Development Laboratory. Brooklyn, NY, USA.Auckland University of Technology. The School of Science / The New Zealand Institute for Plant and Food Research Limited. 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Raleigh, NC, USA.Chinese Academy of Sciences. Wuhan Institute of Virology. Key Laboratory of Special Pathogens and Biosafety. Wuhan, PR China.Agricultural University of Athens. School of Agricultural Production, Infrastructure and Environment. Department of Crop Science. Plant Pathology Laboratory. Votanikos, Athens, Greece.Yokohama Plant Protection Station. Yokohama, Kanagawa, Japan.Zhejiang University. Institute of Insect Sciences. Hangzhou, PR China.Universidade Federal de Viçosa. Dep. de Fitopatologia/BIOAGRO. Viçosa, MG, Brazil.Center for Disease Control and Prevention of Xinjiang Military Command Area. Xinjiang, PR China.Guangxi Academy of Specialty Crops. Guangxi, PR China / Fudan University. School of Life Sciences and Human Phenome Institute. Shanghai, PR China.University of Chinese Academy of Sciences. Beijing, PR China.Pharmaq Analytiq. Bergen, Norway.Francis Crick Institute. Worldwide Influenza Centre. London, UK.Navarro, BeatrizIn April 2023, following the annual International Committee on Taxonomy of Viruses (ICTV) ratification vote on newly proposed taxa, the phylum Negarnaviricota was amended and emended. The phylum was expanded by one new family, 14 new genera, and 140 new species. Two genera and 538 species were renamed. One species was moved, and four were abolished. This article presents the updated taxonomy of Negarnaviricota as now accepted by the ICTV