https://www.biorxiv.org/content/biorxiv/early/2020/02/20/2020.02.19.956581.full.pdf

Structure, Function, and Antigenicity of the SARS-CoV-2 Spike Glycoprotein.

Coronaviruses (CoVs), enveloped positive-sense RNA viruses, are characterized by club-like spikes that project from their surface, an unusually large RNA genome, and a unique replication strategy. Coronaviruses cause a variety of diseases in mammals and birds ranging from enteritis in cows and pigs and upper respiratory disease in chickens to potentially lethal human respiratory infections. Here we provide a brief introduction to coronaviruses discussing their replication and pathogenicity, and current prevention and treatment strategies. We also discuss the outbreaks of the highly pathogenic Severe Acute Respiratory Syndrome Coronavirus (SARS-CoV) and the recently identified Middle Eastern Respiratory Syndrome Coronavirus (MERS-CoV).

/pdf/coronaviruses-an-overview-of-their-replication-and-4lyvr9vdqs.pdf

Coronaviruses: An Overview of Their Replication and Pathogenesis

Coronaviruses are large, enveloped RNA viruses of both medical and veterinary importance. Interest in this viral family has intensified in the past few years as a result of the identification of a newly emerged coronavirus as the causative agent of severe acute respiratory syndrome (SARS). At the molecular level, coronaviruses employ a variety of unusual strategies to accomplish a complex program of gene expression. Coronavirus replication entails ribosome frameshifting during genome translation, the synthesis of both genomic and multiple subgenomic RNA species, and the assembly of progeny virions by a pathway that is unique among enveloped RNA viruses. Progress in the investigation of these processes has been enhanced by the development of reverse genetic systems, an advance that was heretofore obstructed by the enormous size of the coronavirus genome. This review summarizes both classical and contemporary discoveries in the study of the molecular biology of these infectious agents, with particular emphasis on the nature and recognition of viral receptors, viral RNA synthesis, and the molecular interactions governing virion assembly.

The molecular biology of coronaviruses.

The results of the meetings of the International Committee on Taxonomy of Viruses, held in Madrid, September 1975, are briefly reported: rules of viral nomenclature, composition of the new Executive Committee, and a list of the names so far officially agreed. Introduction The International Committee on the Taxonomy of Viruses (ICTV), which is a committee of the Section on Virology of the International Association of Microbiological Societies (IAMS), completed a round of meetings during the Third International Congress for Virology that was held in Madrid from September 10--17, 1975. Since ICTV only meets during these conferences, which are held every four years, the meetings are important occasions for reviewing the classification and nomenclature of viruses. Decisions on new names, which encapsulate the recognition of natural "groups" of viruses, evolve slowly. Official approval for new names depends upon a series of sequential steps ; recommendations by one or more of the subcommittees of the Executive Committee of ICTV (subcommittees on Bacterial, Invertebrate, Plant and Vertebrate Viruses respectively, and for some of the larger viral groups which span several kinds of hos t s the Coordination Subcommittee), which are considered by the Executive Committee of ICTV and may finally be submitted for approval by ICTV itself. Only after this final approval does a name become "official". The results of the last five years of work by ICTV and its committees will be published early this year as a separate volume of "Intervirology", the official journal of the Section on Virology of IAMS, and additional copies will be produced for sale as separates. This "Second P~eport" will include, besides "approved" and common names of virus groups, a brief description of the properties of each

Classification and Nomenclature of Viruses

The Architecture of SARS-CoV-2 Transcriptome.

https://www.cell.com/cell/pdf/0092-8674(89)90766-6.pdf

Amplification, expression, and packaging of a foreign gene by influenza virus

Human coronavirus OC43 and bovine coronavirus elute from agglutinated chicken erythrocytes when incubated at 37 degrees C, suggesting the presence of a receptor-destroying enzyme. Moreover, bovine coronavirus exhibits an acetylesterase activity in vitro using bovine submaxillary mucin as substrate similar to the enzymatic activity found in influenza C viruses. Furthermore, pretreatment of erythrocytes with either influenza C virus or bovine coronavirus eliminates subsequent binding and agglutination by either coronaviruses or influenza C virus, whereas binding of influenza A virus remains intact. In addition, hemagglutination by coronaviruses can be inhibited by pretreatment of erythrocytes with Arthrobacter ureafaciens or Clostridium perfringens neuraminidase or by addition of sialic acid-containing gangliosides. These results suggest that, like influenza C viruses, human coronavirus OC43 and bovine coronavirus recognize O-acetylated sialic acid or a similar derivative as cell receptor.

https://www.pnas.org/content/pnas/85/12/4526.full.pdf

Human and bovine coronaviruses recognize sialic acid-containing receptors similar to those of influenza C viruses.

We succeeded in rescuing infectious influenza virus by transfecting cells with RNAs derived from specific recombinant DNAs. RNA corresponding to the neuraminidase (NA) gene of influenza A/WSN/33 (WSN) virus was transcribed in vitro from plasmid DNA and, following the addition of purified influenza virus RNA polymerase complex, was transfected into MDBK cells. Superinfection with helper virus lacking the WSN NA gene resulted in the release of virus containing the WSN NA gene. We then introduced five point mutations into the WSN NA gene by cassette mutagenesis of the plasmid DNA. Sequence analysis of the rescued virus revealed that the genome contained all five mutations present in the mutated plasmid. The ability to create viruses with site-specific mutations will allow the engineering of influenza viruses with defined biological properties.

https://www.pnas.org/content/pnas/87/10/3802.full.pdf

Introduction of site-specific mutations into the genome of influenza virus.

To generate an extensive set of subgenomic (sg) mRNAs, nidoviruses (arteriviruses and coronaviruses) use a mechanism of discontinuous transcription. During this process, mRNAs are generated that represent the genomic 5′ sequence, the so-called leader RNA, fused at specific positions to different 3′ regions of the genome. The fusion of the leader to the mRNA bodies occurs at a short, conserved sequence element, the transcription-regulating sequence (TRS), which precedes every transcription unit in the genome and is also present at the 3′ end of the leader sequence. Here, we have used site-directed mutagenesis of the infectious cDNA clone of the arterivirus equine arteritis virus to show that sg mRNA synthesis requires a base-pairing interaction between the leader TRS and the complement of a body TRS in the viral negative strand. Mutagenesis of the body TRS of equine arteritis virus RNA7 reduced sg RNA7 transcription severely or abolished it completely. Mutations in the leader TRS dramatically influenced the synthesis of all sg mRNAs. The construction of double mutants in which a mutant leader TRS was combined with the corresponding mutant RNA7 body TRS resulted in the specific restoration of mRNA7 synthesis. The analysis of the mRNA leader–body junctions of a number of mutants with partial transcriptional activity provided support for a mechanism of discontinuous minus-strand transcription that resembles similarity-assisted, copy-choice RNA recombination.

https://www.pnas.org/content/pnas/96/21/12056.full.pdf

Willem Luytjes

Papers

Amplification, expression, and packaging of a foreign gene by influenza virus

Human and bovine coronaviruses recognize sialic acid-containing receptors similar to those of influenza C viruses.

Introduction of site-specific mutations into the genome of influenza virus.

Arterivirus discontinuous mRNA transcription is guided by base pairing between sense and antisense transcription-regulating sequences

Sequence of mouse hepatitis virus A59 mRNA 2: indications for RNA recombination between coronaviruses and influenza C virus.