Animal virology
The study of animal viruses is important from a veterinary viewpoint and many of these viruses cause diseases that are economically devastating. Many animal viruses are also important from a human medical perspective.  The emergence of the SARS virus in the human population, coming from an animal source, highlights the importance of animals in harbouring infectious agents; avian influenza viruses can directly infect humans. In addition research into animal viruses has made an important contribution to our understanding of viruses in general, their replication, molecular biology, evolution and interaction with the host.

# Foot-and-Mouth Disease Virus
Foot-and-mouth disease virus (FMDV) is the prototypic member of the Aphthovirus genus in the Picornaviridae family. This picornavirus is the etiological agent of an acute systemic vesicular disease that affects cattle worldwide. FMDV is a highly variable and transmissible virus. Soon after infection, the single stranded positive RNA that constitutes the viral genome is efficiently translated using a cap-independent mechanism driven by the internal ribosome entry site element (IRES). This process occurs concomitantly with the inhibition of cellular protein synthesis, caused by the expression of viral proteases. Processing of the viral polyprotein is achieved cotranslationally by viral encoded proteases, giving rise to the different mature viral proteins. Viral RNA as well as viral proteins interact with different components of the host cell, acting as key determinants of viral pathogenesis. In depth knowledge of the molecular basis of the viral cycle is needed to control viral pathogenesis and disease spreading.

# Pestiviruses
Pestiviruses account for important diseases in animals such as Classical swine fever (CSF) and Bovine viral diarrhoea / Mucosal disease (BVD/MD). According to the current O.I.E. list CSF and BVD/MD are notifiable diseases and eradication programms are administered in many countries worldwide. The molecular biology of pestiviruses shares many similarities and peculiarities with the human hepaciviruses. Genome organisation and translation strategy are highly similar for the members of both genera. One hallmark of pestiviruses is their unique strategy to establish persistent infection during pregnancy. Persistent infection with pestiviruses often goes unnoticed; for BVDV frequently nonhomologous RNA recombination events lead to the appearance of genetically distinct viruses that are lethal to the host.

# Arteriviruses
In 1996, the family Arteriviridae was included within the order Nidovirales. Arteriviruses are small, enveloped, animal viruses with an icosahedral core containing a positive-sense RNA genome. The family includes Equine Arteritis Virus (EAV), Porcine Reproductive and Respiratory Syndrome Virus (PRRSV), Lactate Dehydrogenase Elevating Virus (LDV) of mice and Simian Haemorrhagic Fever Virus (SHFV). Three of these viruses were first discovered and characterized in the 1950/60s, whereas PRRSV was first isolated in Europe and in North America in the early 1990s. The arteriviruses are highly species specific, but share many biological and molecular properties, including virion morphology, a unique set of structural proteins, genome organization and replication strategy, and the ability to establish prolonged or true persistent infection in their natural hosts. However, the epidemiology and pathogenesis of the infection caused by each virus is distinct, as are the diseases they cause.

# Coronaviruses
Coronavirus (CoV) genome replication takes place in the cytoplasm in a membrane-protected microenvironment, and starts with the translation of the genome to produce the viral replicase. CoV transcription involves a discontinuous RNA synthesis (template switch) during the extension of a negative copy of the subgenomic mRNAs. The requirement for basepairing during transcription has been formally demonstrated in arteriviruses and CoVs. CoV N protein is required for coronavirus RNA synthesis, and has RNA chaperone activity that may be involved in template switch. Both viral and cellular proteins are required for replication and transcription. CoVs initiate translation by cap-dependent and cap-independent mechanisms. Cell macromolecular synthesis may be controlled after CoV infection by locating some virus proteins in the host cell nucleus. Infection by different coronaviruses cause in the host alteration in the transcription and translation patterns, in the cell cycle, the cytoskeleton, apoptosis and coagulation pathways, inflammation, and immune and stress responses. The balance between genes up- and down-regulated could explain the pathogenesis caused by these viruses. Coronavirus expression systems based on single genome constructed by targeted recombination, or by using infectious cDNAs, have been developed. The possibility of expressing different genes under the control of transcription regulating sequences (TRSs) with programmable strength, and engineering tissue and species tropism indicates that CoV vectors are flexible. CoV based vectors have emerged with high potential for vaccine development and, possibly, for gene therapy. 

# Hendra and Nipah Virus
Over the past decade, the previously unknown paramyxoviruses Hendra virus (HeV) and Nipah virus (NiV) have emerged in humans and livestock in Australia and Southeast Asia. Both viruses are contagious, highly virulent, and capable of infecting a number of mammalian species and causing potentially fatal disease. Due to the lack of a licensed vaccine or antiviral therapies, HeV and NiV are designated as biosafety level (BSL) 4 agents. The genomic structure of both viruses is that of a typical paramyxovirus. However, due to limited sequence homology and little immunological cross-reactivity with other paramyxoviruses, HeV and NiV have been classified into a new genus within the family Paramyxoviridae named Henipavirus.

# Avian Influenza
Wild aquatic birds are the natural hosts for a large variety of influenza A viruses. Occasionally viruses are transmitted from this reservoir to other species and may then cause devastating outbreaks in domestic poultry or give rise to human influenza pandemics. Proteolytic activation of the hemagglutinin is an important determinant for pathogenicity and adaptation of the receptor binding specificity of the hemagglutinin and adaptation of the polymerase to new hosts play important roles in interspecies transmission. 

# Bluetongue Virus
Bluetongue virus (BTV), a member of Orbivirus genus within the Reoviridae family causes serious disease in livestock (sheep, goat, cattle). Partly due to this BTV has been in the forefront of molecular studies for last three decades and now represents one of the best understood viruses at the molecular and structural levels. BTV, like the other members of the family is a complex non-enveloped virus with seven structural proteins and a RNA genome consisting of 10 double-stranded (ds) RNA segments of different sizes. It has been possible to determine the complex nature of the virion through 3D structure reconstructions (diameter ~ 800 A); the atomic structure of proteins and the internal capsid (~ 700 A, the first large highly complex structure ever solved); the definition of the virus encoded enzymes required for RNA replication; the ordered assembly of the capsid shell and the protein sequestration required for it; and the role of host proteins in virus entry and virus release. These areas are important for BTV replication but they also indicate the pathways that may be used by related viruses, which include viruses that are pathogenic to man and animals, thus providing the basis for developing strategies for intervention or prevention. 

# Porcine Circoviruses
Porcine Circoviruses (PCV) are the smallest viruses replicating autonomously in eukaryotic cells. The virions are non-enveloped and spherical with a diameter of 16-18 nm and the covalently closed and single-stranded DNA genomes comprise less than 1800 nucleotides. The genomes encode only two major open reading frames. The gene products Rep, Rep' and Cap are involved in viral replication, regulation of transcription and capsid formation. Due to their highly limited coding capacity, circoviruses are supposed to rely principally on the host's machinery for synthesis of macromolecules. Two types of PCV are known, which differ with respect to their pathogenicity. Porcine circovirus type 1 (PCV1) is not linked with a disease, while porcine circovirus type 2 (PCV2) is the etiological agent of Postweaning Multisystemic Wasting Syndrome (PMWS), a new emerging and multifactorial disease in swine. PCV1 and PCV2 show a high degree of sequence homology and a similar genomic organisation; nevertheless, the basis of the distinct pathogenicity has not yet been unravelled.

# Herpesviruses
Herpesviruses are highly successful pathogens infecting animals and man. Although there is a wide variety of different herpesviruses with different biological characteristics, they have in common basic properties such as morphology of the virion, highly regulated transcription and establishment of latency. In animal virology the most important herpesviruses belong to the Alphaherpesvirinae. Research on pseudorabies virus, the causative agent of Aujeszky's disease in pigs, has pioneered animal disease control with genetically modified vaccines. PrV is now extensively studied as a model for basic processes during lytic herpesvirus infection, and for unravelling molecular mechanisms of herpesvirus neurotropism, whereas bovine herpesvirus 1, the causative agent of bovine infectious rhinotracheitis and pustular vulvovaginitis, is analyzed to elucidate molecular mechanisms of latency. The avian infectious laryngotracheitis virus is phylogenetically distant from these two viruses and serves to underline similarity and diversity within the Alphaherpesvirinae. 

# African Swine Fever Virus
African swine fever virus (ASFV) is a large double-stranded DNA virus which replicates in the cytoplasm of infected cells and is the only member of the Asfarviridae family. In common with other viral haemorrhagic fevers, the main target cells for replication are those of monocyte, macrophage lineage. The virus causes a haemorrhagic fever with high mortality rates in pigs, but persistently infects its natural hosts, warthogs, bushpigs and soft ticks of the Ornithodoros species with no disease signs. The virus encodes enzymes required for replication and transcription of the genome, including elements of a base excision repair system, structural proteins and many proteins that are not essential for replication in cells but have roles in virus survival and transmission in its hosts. Virus replication takes place in perinuclear factory areas. Assembly of the icosahedral capsid occurs on modified membranes from the endoplasmic reticulum. Products from proteolytically processed polyproteins form the core shell between the internal membrane and the nucleoprotein core. An additional outer membrane is gained as particles bud from the plasma membrane. The virus encodes proteins that inhibit signalling pathways in infected macrophages and thus modulate transcriptional activation of immune response genes. In addition the virus encodes proteins which inhibit apoptosis of infected cells to facilitate production of progeny virions. Viral membrane proteins with similarity to cellular adhesion proteins modulate interaction of virus-infected cells and extracellular virions with host components.