1. Enteroviruses Future: Omics, Molecular Biology and Control

Karla Kirkegaard

At a time when poliovirus, the flagship Enterovirus, is at the brink of eradication, and while other enteroviruses are simultaneously just emerging as serious public health threats, studies focused on the enteroviruses and other picornaviruses are as important as ever. The true nature of cell exit and cell-to-cell movement by these viruses, for example, is only now being elucidated, particularly taking advantage of recent advances in cell modelling of physiologically relevant cell systems. Modern genomic techniques are just beginning to allow a population-level understanding of mutation and adaptation in these viruses, and are sure to reveal novel drug targets based on the cis/trans genetics of viral genomic regions. Continued understanding of the basic life cycle of these viruses, and of their genomes, will allow novel avenues of vaccine development. In the slightly more distant future, infection by enteroviruses will be rapidly diagnosed and treatments may be tailored by personalized medicine. Finally, enteroviruses are only beginning to be used as tools, particularly as anti-cancer therapeutics. It is impossible to see the future, but as the field moves forward, it is clear that both basic and applied Enterovirus research will remain an important topic for decades to come.

2. Enterovirus Receptors and Entry

Jacqueline D. Corry, Jeffrey M. Bergelson and Carolyn B. Coyne

In order to invade the host, enteroviruses must first attach to receptors expressed on the cell surface and undergo a series of events that culminate in genome release. However, Enterovirus receptors serve functions beyond that of mere docking sites and it is now clear that intracellular signals initiated by receptor binding prime the host cell for virus internalization by promoting modification(s) of the host cell that facilitates endocytic uptake. For many enteroviruses, these processes are complicated by the inaccessibility of their receptors to cellular junctions and/or to the complex environment in which they are interacting with their target cells, such as the gastrointestinal tract. In this chapter, we discuss the diverse cellular factors that serve as enterovirus receptors, the steps involved in enterovirus genome release, and the endocytic pathways utilized by these viruses to gain access to the host cell cytosol.

3. Hijacking Host Functions for Translation and RNA Replication by Enteroviruses

Sonia Maciejewski and Bert L. Semler

The Enterovirus genus includes the species poliovirus, coxsackievirus, rhinovirus, and enterovirus. These viruses can cause severe diseases in certain individuals, including poliomyelitis, myocarditis, and meningitis. Rhinovirus is responsible for one of the most prevalent human diseases in the world, the common cold. Although diseases caused by these infections can be severe, no antiviral against enteroviruses is currently available. To develop broad-spectrum antivirals, the molecular components and mechanistic steps of the viral replication cycle must be identified. Due to the small genomic RNA (≈7.5 kb) of enteroviruses, host proteins are utilized to mediate viral replication. Although some of these cellular proteins have been identified and their roles in picornavirus replication have been characterized, it is necessary to identify and elucidate the replication functions of additional cellular proteins to develop new potential targets for antiviral therapeutics. Enteroviruses are known to modify cellular proteins to stimulate their levels of gene expression and RNA synthesis, but there are some cases where unaltered host proteins can aid in viral replication. Enteroviruses can also evade the antiviral response by altering host proteins involved in the immune and stress response to ensure efficient viral replication. How enteroviruses modify and utilize these host proteins will be discussed in this chapter.

4. The Omics of Rhinoviruses

Ann C. Palmenberg

The human rhinoviruses comprise three species, RV-A, RV-B and RV-C, in the Enterovirus genus of Picornaviridae. Prior to the current 'Omics Era' viruses were typically binned by dominant disease phenotypes after a simple parsing of their RNA or DNA genotypes. But as the 'omics' has piled up, and more and more sequences have emerged, the similarities in genome organization, receptor use, etiology and structures has become ever more apparent. This chapter summarizes key aspects of RV taxonomy and the physical and biochemical parameters by which these viruses are currently studied.

5. Viral Population Dynamics and Sequence Space

Gonzalo Moratorio and Marco Vignuzzi

Without question, the study of enteroviruses at the molecular scale has uncovered the vast majority of our knowledge on the biology of these viruses, how they invade and replicate in host cells, the molecular determinants of pathogenesis, molecular targets for vaccines and antivirals. Molecular studies have also helped understand how these viruses propagate as populations, and being RNA viruses, they have considerably contributed to the study of RNA virus population dynamics. Because at this level we are under the broader umbrella of population genetics and evolutionary sciences, it would be impossible to present a uniquely Enterovirus-specific chapter on the matter. Rather, we have opted to present an overview of the questions that have been addressed in RNA virus population biology, with the state of the art and future directions, giving special attention to instances in which picornaviruses, and more specifically the enteroviruses, have made significant contributions. Here, we describe how RNA viruses have come to be viewed as highly diverse populations, how enteroviruses have heavily contributed to understanding two principal mechanisms by which diversity is maintained (mutation and recombination), the current work attempting to fully characterize the genetic sequence space and the phenotypic fitness landscapes occupied by these viral populations, and several kinds of intra-population dynamics that have been observed and require further study in the future. While Enterovirus studies punctuate the field throughout, it is important to bear in mind that in several cases, even more detailed studies have been performed in other virus families, and the reader is encouraged to seek those out for a more complete picture.

6. Enterovirus Control of Cytoplasmic RNA Granules

Richard E. Lloyd

RNA granules are dynamic structures in cells that are closely linked to repression of gene expression and comprise essential parts of the life cycle of mRNPs. The two general types of RNA granules in somatic cells are stress granules (SGs) and processing bodies (P-bodies, PBs), both of which are manipulated by many types of viruses. Enteroviruses such as poliovirus (PV) and coxsackievirus B3 (CVB3) induce stress granule formation but almost immediately block their formation during the course of infection. PBs are constitutively present, and Enterovirus infection results in their complete dispersal. This review discusses these processes and the current understanding of the underlying mechanisms. In addition, the review discusses reasons viruses control RNA granules, including accumulating data suggesting linkage between RNA granule formation and innate immune sensing and activation.

7. The Autophagic Pathway and Enterovirus Infection

William T. Jackson

A common feature of enteroviruses is the rapid rearrangement of the cytoplasm of infected cells. In general, cellular organelles are altered or disrupted and virus-specific vesicles, which take up a large perinuclear region of the cytoplasm, proliferate. One role of the newly generated vesicles is to act as substrates for RNA-dependent RNA replication complexes. One subset of these vesicles, observed later in infection, is a double-membraned population which strongly resemble autophagosomes, the organelles of the autophagy pathway. Autophagy, a degradative mechanism which maintains cellular homeostasis, is markedly increased during times of cellular stress, including starvation and infection. Autophagy is an important part of the innate immune response, degrading cytosolic pathogens and providing peptides for MHC presentation. However, for a subset of pathogens, including many enteroviruses, the autophagic pathway is subverted to promote replication of the invader. In this chapter we discuss the ways in which enteroviruses are known to interact with the autophagy pathway, often to promote viral replication.

8. The Lipid Blueprints of Replicating Viral Genomes

Nihal Altan-Bonnet, Marianita Santiana and Olha Ilnytska

Plus Strand RNA viruses are the largest group of RNA viruses containing many human, animal and plant pathogens including viruses that are the causative agents of polio, dengue, yellow fever, hepatitis C, common cold and hoof and mouth disease. These viruses dramatically remodel their host cells' preexisting organelles to generate new organelles on which they subsequently assemble their enzymes and replicate. Remarkably the replication organelles from many different viruses end up converging on common lipid blueprints, enriched in specific lipids such as phosphatidylinositol 4-phosphate (PI4P), phosphatidylethanolamine (PE) and cholesterol that facilitate the assembly of macromolecular replication complexes. In addition these lipids impart on the replication organelles a high degree of membrane curvature, which also likely aids the formation and function of the replication complexes. The goal of this article is to examine the mechanisms by which different viruses generate these common lipid blueprints, how they can facilitate replication and how targeting these lipids may be a novel and panviral therapeutic strategy.