The present outbreak of a coronavirus-associated acute respiratory disease called coronavirus disease 19 (COVID-19) is the third documented spillover of an animal coronavirus to humans in only two decades that has resulted in a major epidemic. The Coronaviridae Study Group (CSG) of the International Committee on Taxonomy of Viruses, which is responsible for developing the classification of viruses and taxon nomenclature of the family Coronaviridae, has assessed the placement of the human pathogen, tentatively named 2019-nCoV, within the Coronaviridae. Based on phylogeny, taxonomy and established practice, the CSG recognizes this virus as forming a sister clade to the prototype human and bat severe acute respiratory syndrome coronaviruses (SARS-CoVs) of the species Severe acute respiratory syndrome-related coronavirus, and designates it as SARS-CoV-2. In order to facilitate communication, the CSG proposes to use the following naming convention for individual isolates: SARS-CoV-2/host/location/isolate/date. While the full spectrum of clinical manifestations associated with SARS-CoV-2 infections in humans remains to be determined, the independent zoonotic transmission of SARS-CoV and SARS-CoV-2 highlights the need for studying viruses at the species level to complement research focused on individual pathogenic viruses of immediate significance. This will improve our understanding of virus–host interactions in an ever-changing environment and enhance our preparedness for future outbreaks.

/pdf/the-species-severe-acute-respiratory-syndrome-related-1dzcs2z0y0.pdf

The species Severe acute respiratory syndrome-related coronavirus: classifying 2019-nCoV and naming it SARS-CoV-2

Isolation and Maintenance.- Isolation and Differentiation of Medaka Embryonic Stem Cells.- Maintenance of Chicken Embryonic Stem Cells In Vitro.- Derivation and Culture of Mouse Trophoblast Stem Cells In Vitro.- Derivation, Maintenance, and Characterization of Rat Embryonic Stem Cells In Vitro.- Derivation, Maintenance, and Induction of the Differentiation In Vitro of Equine Embryonic Stem Cells.- Generation and Characterization of Monkey Embryonic Stem Cells.- Derivation and Propagation of Embryonic Stem Cells in Serum- and Feeder-Free Culture.- Signaling in Embryonic Stem Cell Differentiation.- Internal Standards in Differentiating Embryonic Stem Cells In Vitro.- Matrix Assembly, Cell Polarization, and Cell Survival.- Phosphoinositides, Inositol Phosphates, and Phospholipase C in Embryonic Stem Cells.- Cripto Signaling in Differentiating Embryonic Stem Cells.- The Use of Embryonic Stem Cells to Study Hedgehog Signaling.- Transfection and Promoter Analysis in Embryonic Stem Cells.- SAGE Analysis to Identify Embryonic Stem Cell-Predominant Transcripts.- Utilization of Digital Differential Display to Identify Novel Targets of Oct3/4.- Gene Silencing Using RNA Interference in Embryonic Stem Cells.- Genetic Manipulation of Embryonic Stem Cells.- Efficient Transfer of HSV-1 Amplicon Vectors Into Embryonic Stem Cells and Their Derivatives.- Lentiviral Vector-Mediated Gene Transfer in Embryonic Stem Cells.- Use of the Cytomegalovirus Promoter for Transient and Stable Transgene Expression in Mouse Embryonic Stem Cells.- Use of Simian Immunodeficiency Virus Vectors for Simian Embryonic Stem Cells.- Generation of Green Fluorescent Protein-Expressing Monkey Embryonic Stem Cells.- DNA Damage Response and Mutagenesis in Mouse Embryonic Stem Cells.- Ultraviolet-Induced Apoptosis in Embryonic Stem Cells In Vitro.- Use of Embryonic Stem Cells in Pharmacological and Toxicological Screens.- Use of Differentiating Embryonic Stem Cells in Pharmacological Studies.- Embryonic Stem Cells as a Source of Differentiated Neural Cells for Pharmacological Screens.- Use of Murine Embryonic Stem Cells in Embryotoxicity Assays.- Use of Chemical Mutagenesis in Mouse Embryonic Stem Cells.- Epigenetic Analysis of Embryonic Stem Cells.- Nuclear Reprogramming of Somatic Nucleus Hybridized With Embryonic Stem Cells by Electrofusion.- Methylation in Embryonic Stem Cells In Vitro.- Tumor-Like Properties.- Identification of Genes Involved in Tumor-Like Properties of Embryonic Stem Cells.- In Vivo Tumor Formation From Primate Embryonic Stem Cells.- Animal Models and Therapy.- Directed Differentiation and Characterization of Genetically Modified Embryonic Stem Cells for Therapy.- Use of Differentiating Embryonic Stem Cells in the Parkinsonian Mouse Model.

Isolation and characterization

If stretched end to end, the estimated 1030viruses in the oceans would span farther than the nearest 60 galaxies. This reservoir of genetic and biological diversity continues to yield exciting discoveries and, in this Review, Curtis A. Suttle highlights the areas that are likely to be of greatest interest in the next few years. Viruses are by far the most abundant 'lifeforms' in the oceans and are the reservoir of most of the genetic diversity in the sea. The estimated 1030 viruses in the ocean, if stretched end to end, would span farther than the nearest 60 galaxies. Every second, approximately 1023 viral infections occur in the ocean. These infections are a major source of mortality, and cause disease in a range of organisms, from shrimp to whales. As a result, viruses influence the composition of marine communities and are a major force behind biogeochemical cycles. Each infection has the potential to introduce new genetic information into an organism or progeny virus, thereby driving the evolution of both host and viral assemblages. Probing this vast reservoir of genetic and biological diversity continues to yield exciting discoveries.

Marine viruses — major players in the global ecosystem

Classification of Papillomaviruses (PVs) Based on 189 PV Types and Proposal of Taxonomic Amendments

Possible emergence of new geminiviruses by frequent recombination.

Virus taxonomy : eighth report of the International Committee on Taxonomy of Viruses

Virus Taxonomy: VIIIth Report of the International Committee on Taxonomy of Viruses.

Bacterial viruses have been classified into 13 families and 1 unassigned genus. A new order, Caudovirales, has now been established, comprising the three families of tailed bacterial viruses, based on similarities in tailed virus morphology, replication, and assembly. In addition, genera have been established for some species in each tailed virus family, based on properties involving viral DNA replication and packaging, and on some features specific to particular genera (e.g., DNA-termini linked proteins, virus-encoded polymerases, and ability to establish temperate infections). At present, there are six genera in the family Myoviridae (viruses with contractile tails), six in the family Siphoviridae (viruses with long, noncontractile tails), and three in the family Podoviridae (viruses with short noncontractile tails). In recognition that the definitions of tailed virus genera represent a “work in progress” and to keep the nomenclature flexible, tailed virus genera have been assigned vernacular names based on their type species.

/pdf/taxonomy-of-bacterial-viruses-establishment-of-tailed-virus-4rdvxezld9.pdf

Taxonomy of bacterial viruses: establishment of tailed virus genera and the order Caudovirales.

1 UPR 9021-Immunochimie des Peptides et des Virus, Institut de Biologie Moléculaire et Cellulaire du CNRS, Strasbourg, France 20xford University, St. Cross College, St. Giles, Oxford, U.K. 30RSTOM/ILTAB, The Scripps Research Institute, Division of Plant Biology, La Jolla, California, U.S.A. 4 Scottish Crop Research lnstitute, Invergowrie, Dundee, U.K. 'Department of Microbiology and Immunology, University of Rochester, Rochester, New Y ark. U.S.A. 6 Arthropod Borne & Infectious Disease Labaratory, Department of Microbiology, Colorado State University, Ft. Collins, Colorado, U.S.A.

Guidelines to the demarcation of virus species

A recent, highly polemical contribution to these columns [10] criticized the workings of the International Committee on Taxonomy of Viruses (ICTV) and suggested that the new Rules about the orthography of virus species names approved by ICTV were leading virus nomenclature into chaos. References to receding or impending chaos are frequently made by those who approve [6, 7] or disapprove [10] of the work done by the ICTV on behalf of the world community of virologists. In his one-sided and unbalanced diatribe against the work of the ICTV, Gibbs [10] raises several issues that need to be answered. We have gauged the opinions of the ICTV Executive Committee and of the ICTV Life Members regarding the various criticisms levelled by Gibbs and summarize the responses below. Several of the respondents deplored the derogatory tone used by Gibbs to refer to the activities of the ICTV, an organization of which he is a Life Member, and stated that they regard the ICTV as a valuable international body which, in spite of certain organizational concerns, has served virologists well.

/pdf/virus-nomenclature-consensus-versus-chaos-iyijqmohyo.pdf

J. Maniloff

Papers

Virus taxonomy : eighth report of the International Committee on Taxonomy of Viruses

Virus Taxonomy: VIIIth Report of the International Committee on Taxonomy of Viruses.

Taxonomy of bacterial viruses: establishment of tailed virus genera and the order Caudovirales.

Guidelines to the demarcation of virus species

Virus nomenclature: consensus versus chaos.