Strong adaptive evolutionary forces shape the interactions between pathogens and their hosts and typically lead to a stable co-existence. In this process of co-evolution, mammals have developed restriction factors that limit retrovirus infectivity, replication or assembly and narrow the spectrum of potential host species. These restriction factors are either constitutively expressed, such as APOBEC3 proteins, cytidine deaminases that interfere with reverse transcription, or form part of the type I interferon-induced innate immunity, such as TRIM5, a member of the tripartite motif protein family that induces degradation of retroviral capsid, blocks reverse transcription, or tetherin (BST-2, CD317), which inhibits release of nascent viral particles from infected cells. Conversely, viruses have evolved antagonists of restriction factors or proteins that limit IFN-induced gene expression, thus evading immune surveillance. The interaction between host and viral components is delicately balanced and has a significant impact on disease outcome. Feline immunodeficiency virus (FIV), a lentivirus closely related to human immunodeficiency virus (HIV), is a recent introduction into domestic cats and causes an immunodeficiency syndrome analogous to human AIDS. Interestingly, non-domestic cats such as lion or pumas have co-existed with lentiviruses for prolonged periods of time and FIV infections are largely benign. Although plasma viral and proviral loads are high in both domestic and non-domestic cats, in vitro studies have shown that FIV infection of non-domestic cat T lymphocytes is significantly less efficient than that of domestic cat T cells. Thus, this thesis tests the hypothesis that the differential disease outcome of FIV infections in felids is caused by differences in lentiviral restriction factor activities or their sensitivities to FIV restriction factor antagonists. Data presented in this study show for the first time that feline APOBEC3 proteins are expressed in tissues and cell types relevant for FIV infection. The APOBEC3 proteins A3H and A3CH exhibited a high antiviral activity against FIV lacking the APOBEC3 antagonist Vif in single-cycle replication assays, with no difference in activity being detected between domestic and non-domestic cat proteins. However, domestic cat A3CH was significantly more sensitive to antagonism by FIV Vif than lion or puma A3CH, which would allow efficient viral replication in domestic cat T lymphocytes and subsequently lead to T cell loss and immunodeficiency. Furthermore, this thesis provides evidence that felid tetherins can prevent FIV particle release from producer cells in single-cycle replication assays; however, stable expression of domestic and non-domestic cat tetherins in feline cell lines did not abrogate FIV replication. Indeed, syncytium formation indicative of viral cell-to-cell spread was significantly enhanced in type I interferon-treated feline cells infected with CD134-independent strains of FIV which often arise in chronic (late) stages of FIV infections in vivo. Finally, this work reports the generation of a synthetic domestic cat TRIM5α-cyclophilin A fusion protein which was highly efficient at preventing FIV pseudotype and productive infection. This novel feline restriction factor represents a potent antiviral defence agent with very low potential for toxicity and could in future be used in gene therapy approaches to treat FIV-infected cats.

There is a delicate evolutionary balance between viruses and their hosts. The host has evolved the intrinsic, innate and adaptive immunity to fight viral infections. However, viruses have acquired several counteracting measures to evade host defences. Ovine Betaretroviruses, including the exogenous and pathogenic Jaagsiekte sheep retrovirus (JSRV) and the highly related endogenous enJSRVs are a unique model system to investigate virus-host interaction over long evolutionary periods. Sheep have co-opted some defective enJSRV loci to (i) counteract infection by exogenous viruses and likely (ii) to cope with the continuous retroviral invasion of their genome. In addition, various genes of the innate and intrinsic immunity of the host have evolved to block viral replication. The work presented in this thesis focuses on the ovine bone marrow stromal cell antigen 2 (Bst-2)/ tetherin, a recently identified cellular restriction factor with a broad antiviral activity, and its interaction with sheep Betaretroviruses. In sheep, the BST-2 gene is duplicated into two paralogs termed oBST-2A and -2B. Studies presented in this thesis show that oBST-2B possesses several biological properties distinct from the paralog oBST-2A and from all the other BST-2 orthologs. oBST-2A prevents the release of JSRV/enJSRV viral particles by ‘tethering’ them at the cell membrane similarly to what observed by human BST-2. On the other hand, oBST-2B, does not reach the cell membrane but remains within the Golgi stacks and the trans-Golgi network. Several lines of evidence obtained in this thesis suggest that oBST-2B reduces significantly Env incorporation into viral particles. Therefore, oBST-2B possesses a unique antiviral activity that complements the classical tethering restriction provided by oBST-2A.

Trypanosoma brucei is an evolutionarily divergent eukaryotic parasite of mammals in sub-Saharan Africa and is transmitted by the tsetse fly vector. To evade the mammalian immune response, T. brucei utilises antigenic variation, which involves switches in the Variant Surface Glycoprotein (VSG) expressed on the cell surface. Such reactions can occur at very high rates (~10-3 switches/cell/generation) and occur primarily by the recombination of VSG genes, selected from an enormous silent archive, into specialised expression sites. It has been previously shown that such VSG switching is a form of homologous recombination, as mutation of RAD51 and a related gene, RAD51-3, impairs the process. BRCA2 has emerged as a significant regulatory factor during RAD51-catalysed recombination. In humans, BRCA2 contains eight BRC repeats, six of which have been shown to bind RAD51. Similar repeats are present in BRCA2 from other organisms, though normally in smaller numbers. This thesis describes a T. brucei BRCA2 homologue that appears exceptional in that it contains up to 12 BRC repeats. Furthermore, the sequence degeneracy that is observed between the BRC repeats in most organisms is absent in T. brucei, with all but the C-terminal proximal repeat being identical. It was hypothesised that this unusual BRCA2 organisation is due to the high levels of RAD51-directed recombination needed during antigenic variation. To examine the function of the putative T. brucei BRCA2 homologue, mutants were generated and found to display impaired growth, sensitivity to induced DNA damage, impairment in the ability to form sub-nuclear RAD51 foci, a reduced ability to recombine DNA constructs into their genome and a reduction in frequency of VSG switching, all of which are consistent with roles for BRCA2 in DNA repair and recombination. Furthermore, genome instability in the mutants was observed through the loss of silent VSG gene copies and substantial reductions in the size of the mega-base chromosomes. Interestingly, other chromosome classes (the so-called mini- and intermediate-chromosomes) appear not to be susceptible to such instability. A potentially novel function for BRCA2 was identified through DNA content analysis of the T. brucei BRCA2 mutants. Mutation of BRCA2 was shown to result in an accumulation of cells with aberrant DNA content that is most readily explained by an increased number of cells that undergo cytokinesis without having completed nuclear division, phenotypes that are not observed in other T. brucei recombination mutants, such as RAD51. This result suggests that BRCA2 has a role in the regulation of cell division, with mutation causing impaired replication of T. brucei nuclear DNA, but without a cell cycle stall, leading to the accumulation of chromosomal aberrations. In order to investigate the potential role of T. brucei BRCA2 in DNA replication and the unusual BRC repeat organisation phenotypes further, various truncations of BRCA2 were expressed in a mutant background. Cell lines expressing BRCA2 with only 1 BRC repeat displayed reduced efficiency in recombination, DNA repair and RAD51 foci formation, indicating that the large BRC repeat expansion in T. brucei BRCA2 plays a critical role in the proteins function. Expression of a BRCA2 variant encompassing only the region of the protein, C-terminal to the BRC repeats appeared able to function, at least partially, in regulating cell cycle progression. Moreover, this DNA replication role appears not to be provided by conserved DNA binding motifs present within the C terminus of BRCA2 since a fusion of T. brucei BRCA2 and the parasites homologue of the replication protein A 70 kDa subunit was impaired in cell division, but was proficient in repair of DNA damage. Taken together, these data infer that T. brucei BRCA2 possesses a function that is distinct from BRCA2’s role as a regulator of RAD51, and acts in DNA replication or cell division. In addition to the above research on BRCA2, I sought to examine the factors that interact with RAD51 in T. brucei. This work demonstrated that it is possible to add an epitope tag for tandem affinity purification (TAP) to the N-terminus of RAD51 in both the bloodstream and procyclic stages of T. brucei without disrupting its function. Preliminary data suggest that TAP is potentially a feasible way of examining RAD51 interacting factors.

Evidence is presented to indicate that: a) The cuticular layer of the shell is rarely present as an even covering at any stage in the laying year. So, its role as a first line of defence is questionable. b) The shell membranes do inhibit bacterial transfer to some degree, even when they are structurally disrupted; however, if the challenge is great enough, then their function as effective barriers is reduced. c) In the absence of the shell membranes, Salmonella enteritidis Phage type 4 does not move freely across the shell, but it is either facilitated or inhibited in its passage by structural variation in the true shell, particularly at the level of the mammillary layer. Statistical data support in most instances a significant and positive correlation between the presence of structural defects and bacterial transfer. d) In a three tier battery system, a tier effect exists with respect to ease of translocation of microoganisms, with eggs from the top tier being more susceptible, i.e. structurally inferior. e) The results confirm earlier work that shell quality declines with age, and extends this finding to show that this morphological deterioration is accompanied by a decreased resistance to bacterial movement. f) Patent gas exchange pores, whilst obvious portals for bacterial ingress, are in this respect of secondary importance to structural defects within the shell. Evidence is also provided to substantiate the assumption that birds, irrespective of strain, display diverse shell structural quality. One of the strains evaluated (strain B) was structurally better than the other (strain A), at the beginning and middle of lay, and was also more capable of withstanding bacterial challenge in all three laying periods tested. 4. The housing system can influence shell quality; thus Barn and Battery eggs were structurally superior to their Range counterparts, at the end of lay. 5. The tagging of Salmonella with immunogold markers proved to be a valuable technique, which allowed a more precise localisation of the bacteria within the shell's ultrastructure, as viewed by the Scanning Electron Microscope (S.E.M.). This method gave support to other findings in this work, confirming that bacterial transfer was specifically encouraged by late fusion and alignment of the mammillae and pitting occurrences, with the cone layer probably implicated in the process of penetration in vivo. (now derestricted)

Feline chronic gingivostomatitis (FCGS) is an inflammatory disease of the oral cavity that causes severe pain and distress. No specific treatment methods are available and little is known about its aetiology. The aims of this study were:- 1) to identify the bacterial flora, including uncultivable and potentially novel species, in healthy cats and those with FCGS, using 16S rRNA gene sequencing in combination with conventional culture methods; 2) to investigate the viral status of cats with and without FCGS; 3) to assess the immune response by investigating the expression of cytokine and Toll-like receptor (TLR) genes in tissue biopsies from normal cats and those with FCGS; 4) to investigate the histopathological changes in tissue biopsies from normal cats and those with FCGS, 5) to assess putative risk factors for FCGS by the use of a questionnaire-based study. Oral swabs, mucosal biopsies and blood were collected and the location of the oral lesions was recorded. A total of 32 cats with FCGS and 16 normal cats were included in the study. Bacteria were identified from swabs by use of 16S rRNA gene sequencing and by conventional culture methods. Blood samples and swabs were used for diagnosis of infection with feline leukaemia virus (FeLV), feline immunodeficiency virus (FIV), feline herpes virus 1 (FHV-1), feline calicivirus (FCV) and for blood biochemistry and haematology. Gene expression levels for TLR2, TLR3, TLR4, TLR7 and TLR9, and cytokines IL-1β, IL-4, IL-6, IL-10, TNF-α and IFN-γ mRNA were determined using quantitative PCR in biopsy samples from healthy cats and cats with FCGS. Histopathological examination of the tissue biopsies was done using hematoxylin and eosin (H&E) staining. In the healthy group, 16S rRNA gene sequencing demonstrated that the most prevalent bacteria were part of the Proteobacteria and Bacteroidetes phyla, plus a group of uncultured bacteria. The most prevalent species in the healthy group were Xanthomonadaceae bacterium (6.2 % of clones analysed), Capnocytophaga canimorsus (5.4%), Capnocytophaga cynodegmi (4.8%), Bergeyella species (4.5%) and Pasteurella multocida subspecies septica (4.4%). Uncultured bacteria accounted for 29% of the clones analysed. In the FCGS group most of the identified species were part of the phylum Proteobacteria. The most prevalent species in the FCGS group were P. multocida subsp. multocida (14.1%) P. multocida subsp. septica (11.5%), Pseudomonas sp. (7.3%), Tannerella forsythia (6.6%) and Porphyromonas circumdentaria (5.6%). A variety of uncultured bacteria represented 7.7% of all analysed FCGS clones. The culture data showed the most prevalent bacteria in the healthy group were P. multocida subsp. septica (9.9%), and uncultured bacteria (30.5%). In the FCGS group the most prevalent isolates were P. multocida subsp septica and P. multocida subsp. multocida (both 9.9%). Uncultured bacteria accounted for 21.7% of all isolates. FCV was detected in 71% of cats with FCGS and in 13.3% of normal cats. FeLV antigen was detected in 33.3% of normal cats but not in any cats with FCGS. FIV antibodies were detected in 3.4% of cats with FCGS and in 33.3% of normal cats. FHV-1 was detected in 6.9% of cats with FCGS, but was not detected any of the normal cats. In the FCGS group a significant increase was seen in the expression of TLR2 and TLR7 genes as well as TNF-α, IFN-γ, IL-1β and IL-6 cytokine genes. The healthy cats and cats with FCGS in the study that were found to harbour T. forsythia and P. circumdentaria showed an increase in the expression of several TLR and cytokine genes when compared to the group of cats in which these bacterial species were absent. The most severely inflamed sites in the oral cavity of cats with FCGS included the tissue lateral to the palatoglossal folds and the maxillary attached gingiva. Histopathological analysis of the tissue from the palatoglossal folds showed two types of infiltrates:- 1) a combination of lymphocytes and plasma cells, most often seen in the milder inflamed tissue samples; 2) a predominantly plasmacytic infiltration, most often seen in the severely inflamed tissue samples. Preliminary data from a questionnaire-based epidemiological study showed that the presence of potential environmental stress factors such as no ability to roam outdoors and the presence of more than one cat in the household is significantly higher in cats with FCGS when compared to normal cats. This study highlights the possibility of a multifactorial aetiology for FCGS in which FCV, specific bacteria and stress factors may play an important role. Although species from the Bacteroidetes phylum appeared to be capable of eliciting an immune response, these were not the most prevalent species in the FCGS group. A shift could be seen in the composition of the bacterial flora when healthy cats and those with FCGS were compared.

The work described in this thesis was designed to investigate the current impact of parasitic gastroenteritis on organic and conventional dairy farms in first season grazing youngstock in Scotland, and to elucidate a marker of significant parasite challenge within individual calves, in order to target these calves with an anthelmintic treatment. It was felt particularly that any recommendations should be practical and easily implemented on-farm, and optimise anthelmintic usage, with regard to animal health, welfare and performance on both organic and conventional farms. There is world-wide recognition that nematode parasite infections are one of the greatest causes of lost productivity of grazing livestock. In the UK, the single most important cause of parasitic gastroenteritis in cattle is infection with the abomasal nematode, Ostertagia ostertagi, although concomitant infection with the less pathogenic intestinal nematode, Cooperia oncophora is common. Often, non-organic (conventional) producers use anthelmintic treatment programmes that prevent disease or treat all animals in a group without necessarily considering the basic epidemiological information needed for an optimal strategic control. Organic producers are encouraged to avoid this approach, thus it may be hypothesised that organic livestock harbour higher parasite burdens compared to livestock in conventional systems. However, little information is available on current UK organic dairy anthelmintic use and subsequent parasite challenge to youngstock. This thesis aimed to investigate current management practices on three Scottish organic farms compared to three Scottish conventional farms and examine different ways of assessing parasite challenge (including novel markers) with a view to the implementation of a targeted selective treatment (TST) programme. Liveweight gain assessment by means of weigh-bands as a tool to investigate the effect of parasitism on the host was also examined. In year one of the study, the six farms were visited on four occasions throughout the grazing season where fifteen first season grazers on each farm had their liveweight measured (weigh-band or weigh-scale), a faecal egg count (FEC) recorded and plasma pepsinogen, plasma fructosamine and Ostertagia ostertagi antibody concentrations measured. Knowledge of the epidemiology and pathophysiology of gastrointestinal nematode infestation has led to the identification of parasitic biomarkers for use either as a diagnostic tool or for providing a threshold for anthelmintic treatment. Faecal egg counts (FEC) are the most widely used parameter, both clinically and in studies on gastrointestinal nematode infections of ruminants, because of their relative convenience and low cost. Organic producers are encouraged to use faecal egg counts in order to direct anthelmintic treatment to calves, or groups of calves, that have counts of 200 eggs per gram or more (Soil Association, 2010). The recent launch of COWS (Control of Worms Sustainably in Cattle) in May 2010 - an initiative to prevent widespread anthelmintic resistance and to use anthelmintics appropriately in cattle in the UK - has also seen conventional farmers encouraged to use faecal egg counts in the same manner as their organic counterparts (Taylor, 2010i). None of the biomarkers, including FEC, investigated in the study reflected liveweight gain adequately to use in a targeted selective anthelmintic treatment programme. An ideal biomarker would give indication of calves that would most benefit from anthelmintic treatment before liveweight gain was affected. The biomarkers in this study indicated presence of gastrointestinal parasitism but could not target the animals that had poor liveweight gains. The emphasis on FEC in advice to farmers regarding the need for anthelmintic treatment requires re-evaluation. The data from year one showed that the conventionally farmed first season grazers (FSG) had significantly higher liveweight gains than the organically farmed calves. Anthelmintic treatment was applied to the organic calves in the study when the calves were known to be harbouring gastrointestinal parasite infection from positive faecal egg counts. The organically farmed first season grazers in this study had high gastrointestinal parasite challenge, indicated by parasite-based markers such as FEC and plasma pepsinogen concentration. The conventional producers in this study exposed FSG to 652% more days of anthelmintic than the organic producers and gained superior liveweight gains over the grazing season. Essentially, the organic producers fulfilled the ethos of organic production, reducing anthelmintic usage and showing necessity of anthelmintic treatment. However, subclinical and clinical parasitic gastroenteritis reduces animal welfare, the essence of the organic ethos. The organic industry needs to investigate whether there is a superior alternative to FEC that still promotes the organic ethos and reduces subclinical and clinical parasitic gastroenteritis. The possibility of using liveweight gain as a marker for anthelmintic treatment was investigated. An accurate assessment of liveweight is necessary if calf liveweight gain is to be calculated accurately and used as a threshold for anthelmintic treatment. Cattle weigh-scales are expensive and often not available on farm, particularly where youngstock may be grazing at pasture and gathered in the field for handling. With this in mind, cattle weigh-bands, which measure heart girth and relate this to liveweight, have been devised and used in practice in order to estimate cattle liveweight. Realistically, if a liveweight gain threshold were to be recommended for use on farms in the UK, the weigh-band must estimate liveweight and hence liveweight gain accurately. Given that many farmers do not possess weigh-scales on farm, use of heart-girth measurements to estimate liveweight gain is the best option available to farmers currently. Year two involved the implementation of a targeted selective anthelmintic treatment (TST) programme on two organic farms and one conventional farm; all were previously involved in the year one study. Anthelmintic treatment was applied only to FSG calves growing at <0.75kg/day at two points in the grazing season. Organic Farm 1 (O1) and Organic Farm 2 (O2) increased the liveweight gain of the FSG in year two by 50% and 44% respectively. Farm O2 exposed the FSG to 1160% more days of anthelmintic than in 2009; however, approximately 10% of the group were left untreated. Conventional FSG showed reduced liveweight gain from the previous year by 19%. However, respiratory disease was present on-farm also and may have confounded findings. Applying a performance-based targeted anthelmintic regime treatment in the field is possible and using it on farms where anthelmintic treatment was already minimal, such as organic farms, increased liveweight gain in first season grazers without significantly increasing anthelmintic treatment. Applying a TST regime to a conventional farm where previously a suppressive anthelmintic treatment had been applied may have reduced liveweight gain in the first season grazers (FSG) but maintained it at an acceptable level. The acceptance by farmers of TST strategies, and their implementation, may require a high level of input and education to the farming community.

Worldwide, an estimated 9.1 billion birds may need to be killed on farm each year. As of January 2013 the use of manual cervical dislocation (MCD) as a killing method for poultry on-farm has been heavily restricted through new EU legislation (EC 1099/2009) on the Welfare of Animals at the Time of Killing, following reported welfare concerns. The method by which birds are killed on farm is crucial to poultry welfare on a large scale. The overall aim of this project was to design a mechanical device conforming to the new legislation to kill poultry humanely on-farm and provide a competitive replacement for MCD. Following a survey and a literature review, four mechanical devices were designed and prototyped: Modified Armadillo (MARM); Modified Pliers (MPLI); Modified Rabbit Zinger (MZIN) and a Novel mechanical cervical dislocation glove (NMCD). The devices were tested for killing efficacy in three laboratory experiments, assessing their performance in poultry cadavers (Study 1), anaesthetised birds (Study 2) and live conscious birds (Study 3). The reliability and welfare impact of the devices, along with comparisons with a control method (MCD) were evaluated via post-mortem analysis, reflex and behaviour durations, and characteristics of electroencephalography (EEG) analysis. Due to consistently high kill success rates and rapid loss of reflexes, as well as short durations of EEG activity indicating consciousness across three laboratory experiments, the NMCD device was shown to have the most promise as a mechanical device to be used as an alternative to MCD for poultry stock-workers and keepers. The final experiment explored the user-reliability and practicality of the NMCD device in two relevant commercial environments (a layer hen farm and a broiler farm). When applied by multiple users, the NMCD device did not match the killing performance of MCD, however it did show promise and the study highlighted the need for further refinement in the training protocol in order to encompass the wide variation in MCD techniques and experience. The result of this project is a novel on-farm mechanical killing device, which shows great potential in laboratory experiments and competed with the traditional MCD method in commercial environments. Further training refinements are required in order to develop the device into a marketable product which any individual could purchase and use as a humane method for killing poultry.

Animal trypanosomiasis is a major hinderance to the growth of livestock farming in sub-Saharan Africa. Chemotherapy using isometamidium, diminazene and ethidium bromide has been the main control method in the absence of a vaccine against this disease. The effectiveness of these few trypanocides is severely threatened by the widespread development of resistance. Therefore, an understanding of the mechanism(s) involved in the development of resistance will assist in the development of screening protocols for easy identification of resistant cases prior to treatment, and also in finding ways to reverse the resistance. We studied the mechanism of resistance to isometamidium in bloodstream forms of Trypanosoma brucei. Resistance to isometamidium in Trypanosoma brucei was found to be composed of a reduced uptake of the drug and the modification of the F1F0 ATPase complex; active drug efflux by ABC transporters was not involved in the resistance mechanism, although efflux of ISM could be observed in both wild-type and resistant lines. Expression of the transporter gene TbAT1, as well as of TbAT-E and TbAT-A, in yeast, each resulted in increased ISM uptake. In addition, the Vmax for the LAPT1 drug transport activity (Low Affinity Pentamidine Transporter) in ISM-resistant trypanosomes (clone ISMR1) was significantly reduced (P<0.05; Student’s t-test) compared to the wild type control. Also, two point mutations, namely G37A and C851A were found in the ATP synthase gamma subunit of the F1F0 ATPase complex of isometamidium-resistant trypanosomes. The resistant clones also lost their mitochondrial DNA and mitochondrial membrane potential and displayed various levels of cross-resistance to ethidium, diminazene, pentamidine and oligomycin. The C851A mutation introduced a stop codon in the open reading frame of the ATP synthase gamma gene. This mutation, when introduced into the wild type Tb427, produced resistance to isometamidium, and cross resistance to diminazene, ethidium, pentamidine and oligomycin. C851A-ATP synthase gamma proves to be a dominant mutation that allows the rapid loss of mitochondrial DNA after just three days exposure of the parasites to 20 nM ISM or ethidium bromide. Finally, following a recent genome-wide loss-of-function RNAi screen that linked TbAQP2 with pentamidine and melarsoprol cross resistance, we were able to demonstrate that TbAQP2 encodes the HAPT1 in T. brucei, thus leaving us with the LAPT1 as the only known T. b. brucei drug transporter of unknown genetic origin. We however identified specific inhibitors for this transporter (LAPT1) that will be of use in its further characterization.

In this thesis, I focus on methodological concepts of studying infectious disease transmission between agricultural premises. I used different disease systems as exemplars for spatial and network methods to investigate transmission patterns. Infectious diseases cause tangible economic threat to the farming industry worldwide by damaging livestock populations, reducing farm productivity and causing trade restriction. This implies the importance of veterinary epidemiological studies in control and eradication of pathogens. Recent increase in availability of data and computational power allowed for more opportunities to study mechanisms of pathogenic transmission. Nowadays, the bottleneck is primarily associated with efficient methods that can analyse vast amounts of high-resolution data. Here I address two livestock pathogens that differ in their epidemiology: bacteria Streptococcus agalactiae and foot-and-mouth disease (FMD) virus. Streptococcus agalactiae is a contagious pathogen that causes mastitis in cattle, and thus possesses a substantial economic burden to the dairy industry. Known transmission routes between cattle are restricted to those via milking machines, milkers’ hands and fomites during milking process. Additionally, recent studies suggested potential introductions from other host species: primarily, humans. However, strain typing data showed discrepancies in strain compositions of bacteria isolated from humans and bovines. In this thesis, strain-specific features of between-herd transmission of Streptococcus agalactiae within dairy cattle population in Denmark are investigated. Foot-and-mouth disease (FMD) is a viral infection that affects cloven-hoofed animals and is of big importance mainly because of the trade restrictions against infected regions and countries. Control programmes against FMD usually include vaccination and culling of animals. However, the debate on the optimal control for FMD is still ongoing. In this thesis, I address questions on identification of the routes of infection and on requirements for movement recording systems to be used for efficient contact tracing during an FMD outbreak. This thesis reveals several interesting findings. Firstly, the increased understanding of strain-specific transmission characteristics of Streptococcus agalactiae. One of the observed strains (ST103) showed significant and consistent spatial clustering of its cases among Danish dairy cattle herds in 2009–2011. Secondly, the network analysis of cattle movements and affiliations with veterinary practices showed that veterinary practices were exclusively associated with transmission of ST103 of Streptococcus agalactiae. Contrastingly, movement networks appeared to be important for all the three predominant bacterial strains (ST1, ST23 and ST103). Fourthly, the new extended approach that allows estimation of the whole transmission tree at once was proposed and tested for the Darlington cluster within the 2001 FMD UK epidemic. Finally, in chapter 6, it was shown that mathematical modelling did not suggest any advantages of ensuring smaller delays in the post-silent control of FMD-like pathogens.

Feline immunodeficiency virus (FIV) is an important pathogen of domestic cats which in some cases can lead to feline AIDS. It shares many similarities with its human counterpart and is studied to understand correlates of immune-protection and mechanisms of disease progression in cats, both to improve the welfare of infected cats and as an animal model for the pathogenesis of HIV infection in humans. FIV is believed to evolve during the course of infection as a result of the error prone nature of reverse transcriptase and recombination between viral variants, but relatively little is known about this process in naturally occurring infection. Ultimately, it remains unknown why some infected cats remain healthy while others progress to AIDS rapidly. The studies reported in this thesis addressed this lack of knowledge by examining sequential blood samples obtained during the course of natural FIV infection in a population of 44 privately owned domestic cats. Employing Bayesian coalescent framework, it was demonstrated that the FIV env gene is relatively stable genetically. Although not necessary a prerequisite, this is likely to explain why many naturally infected cats can remain healthy and do not progress to AIDS. By determining the cell tropism of isolated viral variants, it was shown that sick cats were more likely to harbour viruses of the “late” phenotype than healthy animals, similar to the co-receptor switch observed during the progression of HIV infection. Intra-host diversity analyses highlighted a likely role for the leader region of the env gene in viral pathogenesis. Furthermore, recombination was demonstrated to be abundant in natural infection, indicating a requirement for the current phylogenetic classification of FIV to be revised. By assessing the strength and breadth of neutralising antibodies (NAbs), it was shown that NAbs did not appear to influence the course of natural FIV infection, arguing against a role in controlling infection and disease progression. Following an examination of samples collected from a group of privately owned Australian vaccinates, it was shown that the Fel-O-Vax FIV vaccine did not induce cross-reactive neutralising antibodies. Furthermore, in the country where commercial FIV vaccine is licenced, we identified and characterised the virus strain which was likely able to establish infection in vaccinated cat and raised concerns of vaccine’s efficacy. Overall this study broadens our understanding of natural FIV infection, and highlights that much can be learned, not from the similarities but rather by studying the differences between the feline and human lentiviruses. Such comparative studies are likely to contribute to design of highly desirable, safe and fully efficacious lentiviral vaccines.