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CHAPTER 1
OVERVIEW OF RHABDO- AND FILOVIRUSES
Asit K. Pattnaik*,†,§,¶ and Michael A. Whitt‡,§,||
*School of Veterinary Medicine and Biomedical Sciences and
†Nebraska Center for Virology, University of Nebraska-Lincoln, Lincoln, Nebraska 68583, USA
‡Department of Microbiology, Immunology, and Biochemistry, University of Tennessee Health Science Center, Memphis, Tennessee 38163, USA
§These authors contributed equally to this work
Summary
Enveloped viruses with a negative-sense, single-stranded monopartite RNA genome have been classified into the order Mononegavirales. Five families of viruses that constitute the order are: Rhabdoviridae, Filoviridae, Paramyxoviridae, Bornaviridae and Nyamiviridae. Members of these families possess a helical nucleocapsid core containing the viral genome and a host-derived lipid envelope containing viral proteins. This introductory chapter provides a brief overview of the Rhabdoviridae and the Filoviridae, the two families of viruses that are the subject of this book. Many members of these two families are highly significant human and animal pathogens. The rationale and goal of the book is to provide the reader with the most recent information on the structure, genome organization and replication strategy, epidemiology, evolution and emergence, host response to infection, viral countermeasures as well as vaccines and antivirals against these pathogens. More detailed descriptions of these topics are presented in individual chapters of this book.
1. Introduction and Rationale
Rhabdoviridae is one of the most diverse families of viruses with its members having been isolated from vertebrates, invertebrates, and plants. Of the eleven genera of viruses recognized in this family,1 eight are known to infect vertebrates, two infect plants and one infects invertebrates. During the past several decades, understanding of the basic molecular biology and pathogenesis of Rhabdoviridae have been primarily derived from studies using vesicular stomatitis virus (VSV), a member of the Vesiculovirus genus and rabies virus (RABV), a member of the genus Lyssavirus. Both VSV and RABV share many characteristics including structure, genome organization, and replication strategy but differ significantly in their pathogenic attributes. Members of the other genera of the family also appear to have similar characteristics, although many of them differ in the number of additional accessory genes they encode, in addition to the typical set of primary genes common to all members of Rhabdoviridae family (see below).
The family Filoviridae, on the other hand, contains only three genera, Ebola-, Marburg- and Cuevaviruses, with Ebolavirus genus having five recognized species whereas the other two genera contain only one species each.1 Members of Filoviridae cause highly lethal hemorrhagic fever disease in humans and non-human primates with case fatality rates of over 50%. They exhibit pleomorphic structures but their overall genome organization, and the basic replication strategy are similar to each other and to some extent similar to those of Rhabdoviridae, although significant differences have been noted.
The goal of this book is to provide an in-depth review of the most recent information that highlights advances in our understanding of the replication, assembly, epidemiology/evolution and pathogenesis of these two related virus families. We have solicited experts in the field to write chapters that cover these topic areas, as well as how our understanding of virus-host interactions has resulted in the development of novel vaccines and therapeutic strategies to combat infectious diseases (both viral and bacterial) and cancer. Progress in our understanding of virus replication has also led to the development of novel vectors used to study the complex circuitry of the central nervous system (CNS). It is our hope that the information assembled in this book will be a resource for both students seeking advanced degrees as well as seasoned investigators who wish to exploit these viruses in their own research endeavors. The following sections outline the major topic areas found in the book and highlight the most recent advances in our understanding of rhabdovirus and filovirus biology. We hope readers find this book as useful for gaining advanced knowledge about these two important virus families as we found it rewarding to assemble.
2. Structure, Genome Organization, and Replication Strategy (Chapters 2, 3, 4, 5, 6, 8, 14, 17, 19, & 20)
Members of Rhabdoviridae possess a rod- or bullet-shaped morphology and package the five essential viral proteins: the glycoprotein (G), the matrix protein (M), the nucleocapsid protein (N; also called nucleoprotein, NP), the viral RNA polymerase consisting of the phosphoprotein (P) and the large (L) proteins in addition to the viral RNA genome. Both VSV and RABV exhibit bullet-shaped morphology with a flat base and a conical or dome-shaped tip. Studies suggest that the determinants of conical or dome-shape tip formation of VSV appear to reside primarily on the viral N protein.2 The envelope of the virion is studded with the trimeric viral G protein and the virion core contains the viral nucleocapsid (NC) composed of the viral genomic RNA complexed with the N to which the viral RNA-dependent RNA polymerase (L+P) is associated. The M protein bridges the NC core with the G protein on the envelope and provides structural rigidity to the particles. Rhabdovirus genomes are organized in modular fashion with a minimum of five genes encoding the five essential proteins (N, P, M, G, and L) to as many as 15 genes that encode several small accessory proteins,3 which are likely involved in modulating host response pathways and pathogenesis, although their specific role(s) remains to be determined. In recent years, not only the structure of the intact VSV virions, but also the atomic structures of full-length or fragments of individual viral proteins, as well as the nucleocapsid-like particles of VSV and RABV have been described. The structural studies coupled with reverse genetics approaches as well as biochemical and mutagenesis studies have led to greater understanding of the overall architecture of the rhabdovirus particles, the viral NC structure, mechanisms of viral transcription and replication, virus particle assembly from individual components, and the role of viral and host proteins in virus life cycle. Each of these aspects has been described in individual chapters in this book.
Unlike the members of the Rhabdoviridae family, the members of Filoviridae adopt morphologically complex structures from six-shaped, spherical-shaped to long filamentous and flexible doughnut- or toroidal-shaped structures. They range in size from approximately 1µm to 22 µm in length and can package from one to 22 copies of the viral genome, aligned in an end-to-end manner within a single viral envelope.4 This is unique to the members of Filoviridae and is not seen in any of the other families of Mononegavirales. Within the viral envelope, the NC is highly flexible and frequently bent to generate the complex structures that are typical for these viruses. The extremely long filamentous structure of virus particles has been suggested to be an adaptation that likely enhances their attachment to cell surfaces for efficient infection.5 Filovirus entry mechanisms appear to be more complex than Rhabdoviruses and other families of Mononegavirales. Although the virus utilizes the human T cell Ig mucin 1 (TIM-1) protein on mucosal epithelial cells to enter, the receptor(s) in most other cell types remains unidentified. Attachment factors including lectins, signaling factors such as the Tyro3/Axl/Mer (TAM) family of receptor tyrosine kinases, integrins, and endo/lysosomal factors such as cathepsin B and L and Niemann-Pick C1 (NPC1) protein play critical roles in filovirus entry and genome uncoating processes.6,7 The released viral genome in the form of NC undergoes transcription and replication in the cytoplasm. The viral genes are organized in a modular fashion, like those of Rhabdoviridae and are transcribed by similar mechanism(s). The steps in filovirus assembly are poorly understood. However, use of cryo-electron tomography and sub-tomogram averaging principles have revealed both vertical “rocket-like” as well as horizontal “submarine-like” mechanisms of virus budding that occur from infected cells.8 Further details on the structure of filoviruses, processes of entry, uncoating, genome transcription, and replication have been detailed in individual chapters in the book.
Tremendous progress has been made in our understanding of the molecular biology of replication of Rhabdo- and Filoviruses in the past decades; however, many significant questions remain unanswered. As the viral genomes are coated with nucleocapsid proteins, it is still unclear how mechanistically the viral polymerase accesses the genomic RNA for transcription and replication. As challenging as it may appear, structural studies with actively transcribing/replicating templates coupled with biochemical analysis may reveal insights into structural alterations in the viral nucleocapsids induced by the polymerases that allow access to the RNA genome for transcription and replication. Future studies using advanced microscopy techniques and live-cell imaging approaches are likely to provide a clearer picture of the endocytic entry of these viruses and uncoating of their genomes. Identification of receptor(s) for filovirus entry and detailed investigation of the role of various cellular factors in the highly orchestrated pathway of the virus internalization may provide targets for development of therapeutics for filovirus infection and disease.
3. Epidemiology, Evolution, and Eme...
