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Virology is the study of viruses. The first viruses were discovered in 1898 and were identified by their ability to pass through filters that were too small to allow the passage of bacteria. Since that time, scientists have been studying viruses to better understand how to prevent epidemics and pandemics, and research on viruses has revealed an abundance of information on how living systems work. Viruses are the most abundant biological entities on Earth and infect all living things, and yet they are not considered to be alive. They share several characteristics with living organisms, but are unable to reproduce independently and maintain metabolic activities. In addition, they do not undergo cell division, like living organisms do, but assemble newly made components from scratch after gaining entry into a cell and its machinery. Viruses appeared around the same time that life began on Earth, but their origin is a much debated issue. The precellular hypothesis proposes that viruses existed before or alongside cells, whereas the escape hypothesis suggests that viruses were once components of living cells. The regressive hypothesis proposes that viruses were once living intracellular parasites that lost their ability to reproduce independently.

The two arms of the immune system, the innate and adaptive immune system, function together to provide long-term immunity against viruses. The innate immune system is activated immediately after infection and consists of nonspecific mechanisms to control viral replication while the adaptive immune system is being activated. Type 1 interferons are important antiviral cytokines produced during this time. Dendritic cells present antigen to cytotoxic T lymphocytes (CTLs) and helper T lymphocytes, which causes their activation. CTLs acquire the ability to kill virally infected cells, while helper T cells induce B cells to produce antibody. Together, the adaptive immune system provides an antigen-specific response that controls infection and creates immunological memory to prevent against reinfection with the same virus. However, many viruses have evolved mechanisms to avoid detection by or interfere with the host immune system.

Influenza viruses are enveloped, −ssRNA viruses with segmented genomes. Influenza A and B viruses are associated with seasonal epidemics, and several pandemics have been caused by influenza A viruses. Virions are transmitted through droplet spread and bind alpha-2,6-linked sialic acids found on the ciliated epithelium of the respiratory tract. Common symptoms include fever, myalgia, sore throat, rhinorrhea, and a nonproductive cough. Children, the elderly, and immunocompromised individuals are at highest risk of secondary bacterial pneumonias. Following receptor binding, the virus undergoes clathrin-mediated endocytosis. The hemagglutinin (HA) protein fuses the viral envelope and endosomal membrane, allowing the release of the ribonucleoproteins. Despite carrying its own RNA-dependent RNA polymerase, viral gene segments enter the nucleus in order to steal the 5′ caps from host mRNAs and splice the smallest two of its transcripts. The virus undergoes assembly at the plasma membrane and buds from the cell. Neuraminidase (NA) cleaves sialic acids upon exit to prevent virion aggregation onto the cell surface. Subtypes of influenza A viruses are categorized by the HA and NA proteins encoded by the virus. Antigenic shifts have led to major pandemics within the last century.

For transmission of a virus to occur, a virus must enter a host through a portal of entry, replicate or disseminate within the host, and be transmitted to a new host through a portal of exit. Unless delivered directly into bodily tissues through a bite or needle, most viruses interact with the epithelium at the site of entry. Localized infections replicate at the initial site of infection, while systemic infections spread to additional areas of the body. Viruses are shed into the environment most often through the same route they entered the body. The stability of virions within the environment is dependent upon virion and environmental factors. Epidemiology is the study of how diseases are transmitted through a population. Epidemiologists perform descriptive or analytic studies to characterize the chain of viral infection throughout a population and design control measures to interrupt it.

T(H)17 cells are the newest member of the T(H) cell family and are characterized by their ability to produce specific cytokines such as IL-17, IL-22, IL-17F, and CCL20. In this review, conditions for the differentiation of T(H)17 cells are defined in both murine and human systems, with discussion of T(H)17-specific cytokines and transcription factors. Functionally, T(H)17 cells contribute to host defense as a new effector T(H) cell subset with a role in protection against extracellular bacteria through activities on immune and nonimmune cells. Their activities, however, are also pivotal in the development of autoimmune diseases under pathologic conditions. T(H)17 cells are also beginning to be associated with the development and pathophysiology of allergic diseases, such as allergic contact dermatitis, atopic dermatitis, and asthma. Lymphoid tissue inducer-like cells and natural killer-like cells, termed RORgammat(+)NKp46(+) or NK-22 cells, might also play a role in allergic diseases because of their propensity to produce IL-17 and IL-22.

Pulmonary arterial remodeling characterized by increased vascular smooth muscle density is a common lesion seen in pulmonary arterial hypertension (PAH), a deadly condition. Clinical correlation studies have suggested an immune pathogenesis of pulmonary arterial remodeling, but experimental proof has been lacking. We show that immunization and prolonged intermittent challenge via the airways with either of two different soluble antigens induced severe muscularization in small- to medium-sized pulmonary arteries. Depletion of CD4+ T cells, antigen-specific T helper type 2 (Th2) response, or the pathogenic Th2 cytokine interleukin 13 significantly ameliorated pulmonary arterial muscularization. The severity of pulmonary arterial muscularization was associated with increased numbers of epithelial cells and macrophages that expressed a smooth muscle cell mitogen, resistin-like molecule α, but surprisingly, there was no correlation with pulmonary hypertension. Our data are the first to provide experimental proof that the adaptive immune response to a soluble antigen is sufficient to cause severe pulmonary arterial muscularization, and support the clinical observations in pediatric patients and in companion animals that muscularization represents one of several injurious events to the pulmonary artery that may collectively contribute to PAH.

Our attempts to prevent and control serious viral illnesses rely upon mass vaccination efforts and the use of antivirals. Live attenuated virus vaccines and inactivated virus vaccines are the most common types of vaccines and have drastically reduced virus-related morbidity and mortality. Recombinant subunit vaccines are also being produced against HBV and HPV, while investigational vaccine formulations use recombinant DNA or live viral vectors. Antivirals inhibit one of the seven stages of viral replication; most antivirals target a viral enzyme or prevent genome replication.

An emerging infectious disease (EID) is defined as a disease caused by a pathogen that has not been observed previously within a population or geographic location. Viruses are a major cause of EIDs, particularly −ssRNA viruses. Many variables are involved in the emergence or reemergence of viruses. These can be classified into human factors, environmental/ecological factors, and viral factors and include urbanization, globalization, weather and climate change, and the genetic composition of the virus. The great majority of emerging viral diseases are zoonoses, notably transmitted by arthropods and nonhuman mammals. Flaviviruses include several notable vector-transmitted viruses, while rodents and bats are thought to be the natural reservoirs of arenaviruses and filoviruses, respectively. This chapter discusses several notable outbreaks of emerging and reemerging viruses, including the 2014–15 outbreak of Ebolavirus in West Africa.

As obligate intracellular parasites, viruses are completely dependent upon a host cell for their replication. They use energy generated by the host cell, and they exploit the host's machinery to manufacture viral proteins. Many of the cell's organelles, as well as the plasma membrane, are involved in viral replication processes. The organelles involved in protein synthesis, processing, and transport—namely the ribosome, rough endoplasmic reticulum, and Golgi complex—are utilized in the manufacture of viral proteins, as well, and viruses use ATP generated by the host cell's mitochondria. The plasma membrane, made of a phospholipid bilayer, is the cell's primary zone of contact with the extracellular world. As such, it is the first obstacle that a virus must overcome for entry into a cell. The Central Dogma of Molecular Biology states that DNA is replicated to create more DNA, DNA is transcribed into mRNA, and mRNA is translated by ribosomes to create proteins. All viruses are dependent upon the host's translation machinery, and many viruses will use other portions of the cell's replication and transcription mechanisms. DNA polymerase is the major enzyme involved in DNA replication, while RNA polymerase creates messenger RNA. Host ribosomes translate the messenger RNA into proteins, composed of amino acids. Viruses also have many unique strategies to ensure the translation of their proteins over host proteins.

Cancer is a leading cause of death in developed nations, and viruses contribute to around 15% of cancer cases worldwide. Despite being disparate viruses, seven major human viruses have been associated with oncogenesis: human T lymphotropic virus type I, hepatitis C virus, hepatitis B virus, Merkel cell polyomavirus, human papillomavirus, Epstein–Barr virus, and Kaposi's sarcoma–associated herpesvirus. Oncogenesis is a by-product of infection and is not required for viral replication. Oncogenic viruses affect pathways that become dysregulated in human cancers. Viral proteins commonly interfere with the cell cycle, target pRB and p53, prevent apoptosis, and interfere with the immune response. These effects contribute to genomic instability and support a cellular state that is more conducive to becoming oncogenic as additional mutations arise within the cell. Viruses are a leading contributory cause to cervical cancer, liver cancer, and oral cancers, among others.

Diagnostic tests are paramount in determining the etiology of viral infections. Direct diagnostic methods assay for the presence of the virus, while indirect methods test for effects of the virus. Cell culture is the process of growing cells or tissues in the laboratory. Cell lines can be infected with patient samples to allow viral replication within the cells; observable cytopathic effects can help to identify the identity of the virus. Infected cells can also be used for immunofluorescence assays, which use fluorescently labeled virus-specific antibodies to identify viruses in fixed cells or tissues. A variety of diagnostic immunoassays exist, including enzyme-linked immunosorbent assays/enzyme immunoassays, western blots, lateral flow immunoassays, and agglutination reactions. Assays that detect viral nucleic acids are based upon the principles of PCR or nucleic acid hybridization, are extremely sensitive, and are specific for a particular virus.

Poliomyelitis (“polio”) is a disease caused by poliovirus, a small, nonenveloped icosahedral virus transmitted through the fecal–oral route. Three poliovirus subtypes exist: type 1, 2, and 3. Following a major viremia, poliovirus replicates within and can cause temporary or permanent damage to the central nervous system, predominantly to the brain stem and motor neurons of the spinal cord. Paralytic poliomyelitis is classified into bulbar, spinal, or bulbospinal poliomyelitis, depending upon the site of the nerves that are damaged. As a +ssRNA virus, translation of the poliovirus genome begins immediately upon entry into the cell, using an internal ribosome entry site in the 5′-region of the genome. A single polyprotein is cleaved sequentially into intermediate precursor and mature proteins responsible for genome replication and virion structure. In 1955, Jonas Salk's laboratory developed a formalin-inactivated virus vaccine, known as the inactivated polio vaccine, and Albert Sabin later developed the oral polio vaccine containing live attenuated poliovirus. Permanent eradication of poliovirus through vaccination is theoretically possible because poliovirus infects only humans, has a limited number of serotypes, and does not cause persistent infections. Global Polio Eradication Initiative efforts have currently reduced the number of countries with endemic wild poliovirus to two, Afghanistan and Pakistan.

To continue the chain of infection, a virus must undergo the process of replication to create new, infectious virions that are able to infect other cells of the body or subsequent hosts. After gaining entry into the body, a virus makes physical contact with and crosses the plasma membrane of a target cell. Inside, it releases and replicates its genome while facilitating the manufacture of its proteins by host ribosomes. How this is carried out depends upon the type of viral nucleic acid. Virus particles are assembled from these newly synthesized biological molecules and become infectious virions. Finally, the virions are released from the cell to continue the process of infection.

Viruses have several common characteristics: they are small, have DNA or RNA genomes, and are obligate intracellular parasites. The virus capsid functions to protect the nucleic acid from the environment, and some viruses surround their capsid with a membrane envelope. Most viruses have icosahedral or helical capsid structure, although a few have complex virion architecture. An icosahedron is a geometric shape with 20 sides, each composed of an equilateral triangle, and icosahedral viruses increase the number of structural units in each face to expand capsid size. The classification of viruses is very useful, and the International Committee on Taxonomy of Viruses is the official body that classifies viruses into order, family, genus, and species taxa. There are currently seven orders of viruses.

The organized lymphoid tissues of the intestine likely play an important role in the balance between tolerance harmless mucosal Ags and commensal bacteria and immunity to mucosal pathogens. We examined the phenotype and function of plasmacytoid dendritic cells (pDCs) from murine Peyer’s patches (PPs). When stimulated with CpG-enriched oligodeoxynucleotides in vitro, PPs and spleen pDCs made equivalent levels of IL-12, yet PP pDCs were incapable of producing significant levels of type I IFNs. Three regulatory factors associated with mucosal tissues, PGE2, IL-10, and TGFβ, inhibited the ability of spleen pDCs to produce type I IFN in a dose-dependent fashion. These studies suggest that mucosal factors may regulate the production of type I IFN as well as IL-12 by pDCs. In the intestine, this may be beneficial in preventing harmful innate and adaptive immune responses to commensal microorganisms.

The innate immune system uses different mechanisms to respond to infectious pathogens. Experiments evaluating the requirements for a type 1 IFN (IFN-αβ) response to lymphocytic choriomeningitis virus (LCMV) resulted in the surprising discovery that mice deficient in B and T cell development, i.e., RAG-deficient and SCID, had profoundly reduced levels of IFN-αβ in serum and spleen, despite high viral replication. In addition to lacking an adaptive immune system, these strains exhibit aberrant splenic architecture, and the defect in type 1 IFN production was also observed in mice lacking normal splenic marginal zone (MZ) organization due to genetic deficiencies in B cell development or in cytokine functions required for development of the MZ, i.e., μMT, lymphotoxin-α, and TNFR1. Interestingly, the IFN-αβ reduction was not observed after murine CMV infection. Depletion of phagocytic cells from normally developed spleens by treatment with clodronate-containing liposomes demonstrated that these populations were required for the type 1 IFN response to LCMV, but not to murine CMV, and for control of viral replication. Complete repopulation of the MZ was necessary to restore normal IFN-αβ production. In contrast, control of LCMV replication correlated with the return of CD11c+ cells. Taken together, these results demonstrate the complexity and sophistication of the splenic MZ in sensing and responding to particular pathogens and reveal the importance of organ architecture in the production of type 1 IFN.

Type 1 interferons (IFNs) are induced in vivo, administered therapeutically, and potential targets for amelioration of autoimmune diseases. The cytokines mediate profound antiproliferative effects. Signal transducer and activator of transcription 1 (STAT1)-dependent signaling pathways are required for inhibition of proliferation, and viral infections can elicit high levels of type 1 IFNs as well as total STAT1 protein expression. Thus, a mechanism must be in place to help antigen-specific T cells overcome IFN-induced inhibition of proliferation. The studies reported here demonstrate that total CD8 T-cell proliferation in the presence of IFNs, ex vivo in response to cytokines and in vivo during viral infection, is inhibited through a STAT1-dependent mechanism. In contrast, major proportions of antigen-specific CD8, but not CD4, T cells are rendered less sensitive to this inhibition, express lower endogenous levels of total STAT1, and are selectively proliferating in the presence of type 1 IFN, at key times after viral challenge. Taken together, these novel results show that differential STAT1 expression is used by the immune system to modify cytokine-mediated effects on T-cell expansion and have implications for the consequences of therapeutic intervention in cytokine function.

Background Biomarkers facilitate early detection of disease and measurement of therapeutic efficacy, both at clinical and experimental levels. Recent advances in analytics and disease models allow comprehensive screening for biomarkers in complex diseases, such as asthma, that was previously not feasible. Objective Using murine and nonhuman primate (NHP) models of asthma, identify biomarkers associated with early and chronic stages of asthma and responses to steroid treatment. Methods The total protein content from thymic stromal lymphopoietin transgenic (TSLP Tg) mouse BAL fluid was ascertained by shotgun proteomics analysis. A subset of these potential markers was further analyzed in BAL fluid, BAL cell mRNA, and lung tissue mRNA during the stages of asthma and following corticosteroid treatment. Validation was conducted in murine and NHP models of allergic asthma. Results Over 40 proteins were increased in the BAL fluid of TSLP Tg mice that were also detected by qRT-PCR in lung tissue and BAL cells, as well as in OVA-sensitive mice and house dust mite-sensitive NHP. Previously undescribed as asthma biomarkers, KLK1, Reg3γ, ITLN2, and LTF were modulated in asthmatic mice, and Clca3, Chi3l4 (YM2), and Ear11 were the first lung biomarkers to increase during disease and the last biomarkers to decline in response to therapy. In contrast, GP-39, LCN2, sICAM-1, YM1, Epx, Mmp12, and Klk1 were good indicators of early therapeutic intervention. In NHP, AMCase, sICAM-1, CLCA1, and GP-39 were reduced upon treatment with corticosteroids. Conclusions and clinical relevance These results significantly advance our understanding of the biomarkers present in various tissue compartments in animal models of asthma, including those induced early during asthma and modulated with therapeutic intervention, and show that BAL cells (or their surrogate, induced sputum cells) are a viable choice for biomarker examination.

Background Interleukin (IL)-19 has been reported to enhance chronic inflammatory diseases such as asthma but the in vivo mechanism is incompletely understood. Because IL-19 is produced by and regulates cells of the monocyte lineage, our studies focused on in vivo responses of CD11c positive (CD11c+) alveolar macrophages and lung dendritic cells. Methodology/Principal Findings IL-19-deficient (IL-19-/-) mice were studied at baseline (naive) and following intranasal challenge with microbial products, or recombinant cytokines. Naive IL-19-/- mixed background mice had a decreased percentage of CD11c+ cells in the bronchoalveolar-lavage (BAL) due to the deficiency in IL-19 and a trait inherited from the 129-mouse strain. BAL CD11c+ cells from fully backcrossed IL-19-/- BALB/c or C57BL/6 mice expressed significantly less Major Histocompatibility Complex class II (MHCII) in response to intranasal administration of lipopolysaccharide, Aspergillus antigen, or IL-13, a pro-allergic cytokine. Neurogenic-locus-notch-homolog-protein-2 (Notch2) expression by lung monocytes, the precursors of BAL CD11c+ cells, was dysregulated: extracellular Notch2 was significantly decreased, transmembrane/intracellular Notch2 was significantly increased in IL-19-/- mice relative to wild type. Instillation of recombinant IL-19 increased extracellular Notch2 expression and dendritic cells cultured from bone marrow cells in the presence of IL-19 showed upregulated extracellular Notch2. The CD205 positive subset among the CD11c+ cells was 3-5-fold decreased in the airways and lungs of naive IL-19-/- mice relative to wild type. Airway inflammation and histological changes in the lungs were ameliorated in IL-19-/- mice challenged with Aspergillus antigen that induces T lymphocyte-dependent allergic inflammation but not in IL-19-/- mice challenged with lipopolysaccharide or IL-13. Conclusions/Significance Because MHCII is the molecular platform that displays peptides to T lymphocytes and Notch2 determines cell fate decisions, our studies suggest that endogenous IL-19 is a constituent of the regulome that controls both processes in vivo.

IL-33 is an IL-1-related cytokine which has been implicated in T(h)2-associated biology and allergic diseases in humans and mice. IL-33 stimulates T(h)2 cells, mast cells, eosinophils, basophils, iNKT cells and circulating CD34(+) stem cells to proliferate and produce pro-allergic cytokines such as IL-5 and IL-13. IL-33 mediates its cytokine effects through a receptor consisting of ST2 and IL-1RAcP. Whereas IL-1RAcP is ubiquitously expressed, ST2 expression is cell-type restricted and determines responsiveness to IL-33. Studies employing ST2-deficient mice have reported variable results on the role of this receptor, and consequently IL-33, with regards to allergic lung inflammation. In this study, we demonstrate that IL-33 is important for allergic lung inflammation. Intra-nasal administration of IL-33 triggered an immediate allergic response in the airways, and more importantly, we show that endogenous IL-33 contributes to airway inflammation and peripheral antigen-specific responses in ovalbumin-induced acute allergic lung inflammation using IL-33-deficient mice. Our results suggest that IL-33 is sufficient and required for severe allergic inflammation in the lung and support the concept of IL-33 as a therapeutic target in allergic lung inflammation.

The best-characterized type 1 interferon (IFN) signaling pathway depends on signal transducer and activator of transcription 1 (STAT1) and STAT2. The cytokines can, however, conditionally activate all STATs. Regulation of their access to particular signaling pathways is poorly understood. STAT4 is important for IFN-γ induction, and NK cells are major producers of this cytokine. We report that NK cells have high basal STAT4 levels and sensitivity to type 1 IFN–mediated STAT4 activation for IFN-γ production. Increases in STAT1, driven during viral infection by either type 1 IFN or IFN-γ, are associated with decreased STAT4 access. Both STAT1 and STAT2 are important for antiviral defense, but STAT1 has a unique role in protecting against sustained NK cell IFN-γ production and resulting disease. The regulation occurs with an NK cell type 1 IFN receptor switch from a STAT4 to a STAT1 association. Thus, a fundamental characteristic of NK cells is high STAT4 bound to the type 1 IFN receptor. The conditions of infection result in STAT1 induction with displacement of STAT4. These studies elucidate the critical role of STAT4 levels in predisposing selection of specific signaling pathways, define the biological importance of regulation within particular cell lineages, and provide mechanistic insights for how this is accomplished in vivo.

CpG-DNA or its synthetic analog CpG-ODN activates innate immunity through Toll-like receptor 9 (TLR9). However, the mechanism of TLR9 activation by CpG-DNA remains elusive. Here we have identified HMGB1 as a CpG-ODN–binding protein. HMGB1 interacts and preassociates with TLR9 in the endoplasmic reticulum-Golgi intermediate compartment (ERGIC), and hastens TLR9's redistribution to early endosomes in response to CpG-ODN. CpG-ODN stimulates macrophages and dendritic cells to secrete HMGB1; in turn, extracellular HMGB1 accelerates the delivery of CpG-ODNs to its receptor, leading to a TLR9-dependent augmentation of IL-6, IL-12, and TNFα secretion. Loss of HMGB1 leads to a defect in the IL-6, IL-12, TNFα, and iNOS response to CpG-ODN. However, lack of intracellular TLR9-associated HMGB1 can be compensated by extracellular HMGB1. Thus, the DNA-binding protein HMGB1 shuttles in and out of immune cells and regulates inflammatory responses to CpG-DNA.

Interleukin 19 (IL-19) is thought to have important roles in the immune control of pathogens, and in enhancing chronic inflammatory diseases of the skin (psoriasis), lung (asthma) and intestine (colitis). However, the biological function and the networked control of IL-19 are poorly understood. Naive mice deficient in IL-19 (IL-19-/-) on a 129xBL6 background had decreased alveolar macrophages and increased eosinophils in the broncho-alveolar lavage (BAL) and decreased B cells in the spleen and bone marrow. However, naïve IL-19-/- mice backcrossed to C57BL/6 or BALB/c, and mice housed in different locations exhibited an attenuated phenotype. Therefore, genetic backcross and challenge experiments with environmental stimuli (allergen, urban particulate matter) were conducted. The studies showed that abnormal composition of the cells in the BAL fluid, spleen and bone marrow in naïve IL-19-/- 129xBL6 mice was due to the deficiency in IL-19 combined with the activity of another gene inherited from the 129 strain. IL-19-/- mice on C57BL/6 or BALB/c backgrounds that were intranasally challenged with antigen or with antigen and urban particulate matter had decreased BAL eosinophils, alveolar macrophages and B cells when compared to wild type. Together our studies indicate that endogenous IL-19 is a critical component of immune homeostasis to the airborne environment and that mouse-strain specific genes control the function of IL-19.