The Bunyaviridae family is one of the largest among RNA viruses, comprising more than 350 serologically distinct viruses. The family is classified into five genera, Orthobunyavirus, Hantavirus, Nairovirus, Phlebovirus, and Tospovirus. Orthobunyaviruses, nairoviruses and phleboviruses are maintained in nature by a propagative cycle involving blood-feeding arthropods and susceptible vertebrate hosts. Like most arthropod-borne viruses, bunyavirus replication causes little damage to the vector, whereas infection of the mammalian host may lead to death. This situation is mimicked in the laboratory: in cultured mosquito cells no cytopathology is observed and a persistent infection is established, whereas in cultured mammalian cells orthobunyavirus infection is lytic and leads to cell death. Bunyaviruses encode four common structural proteins: an RNA-dependent RNA polymerase, two glycoproteins (Gc and Gn), and a nucleoprotein N. Some viruses also code for nonstructural proteins called NSm and NSs. The NSs protein of the prototype bunyavirus, Bunyamwera virus, seems to be one of the factors responsible for the different outcomes of infection in mammalian and mosquito cell lines. However, only limited information is available on the growth of bunyaviruses in cultured mosquito cell lines other than Aedes albopictus C6/36 cells. Here, I compared the replication of Bunyamwera virus in two additional Aedes albopictus cell clones, C7-10 and U4.4, and two Aedes aegypti cell clones, Ae and A20, and investigated the impact of virus replication on cell function. In addition, whereas the vertebrate innate immune response to arbovirus infection is well studied, relatively little is known about mosquitoes’ reaction to these infections. I investigated the immune responses of the different mosquito cells to Bunyamwera virus infection, in particular antimicrobial signaling pathways (Toll and IMD) and RNA interference (RNAi). The data obtained in U4.4 cells suggest that NSs plays an important role in the infection of mosquitoes. Moreover infection of U4.4 cells more closely resembles infection in Ae and A20 cells and live Aedes aegypti mosquitoes. My data showed that the investigated cell lines have various properties, and therefore they can be used to study different aspects of mosquito-virus interactions.

Interferon (IFN) and phosphatidylinositol 3-kinase (PI3K) are apoptosis regulators that are targeted by viruses to promote survival of infected cells. Significant crosstalk exists between IFN and PI3K, and this study sought to investigate the relationships between IFN, PI3K and apoptosis during virus infection. Parainfluenza virus 5 (PIV5) and influenza A virus (IAV) are both negative-sense single-stranded RNA viruses that encode multifunctional proteins in order to maximise their genome coding capacity. The PIV5 V and IAV NS1 proteins are well-studied as IFN antagonists and, in addition, both are reported to modulate PI3K signalling. Less well-studied is the role of these proteins in apoptosis regulation; the ability of V and NS1 to inhibit apoptosis was therefore investigated. PIV5/V was found to limit cell death in response to a number of apoptosis inducers in a manner that required its STAT1- degradative activity and also inhibited activation of the PI3K downstream target, Akt. IAV/NS1 binds directly to PI3K to stimulate its activity, and this is reported to mediate anti-apoptotic signalling during IAV infection. However, a virus expressing an NS1 unable to bind PI3K did not induce more apoptosis than wt virus. NS1 expression, either in a stable cell-line or during virus infection, was also unable to protect cells from pro-apoptotic stimuli. NS1-mediated PI3K activation similarly had no effect on IFN production or ISG expression in infected cells. In contrast, other NS1 mutant viruses induced large amounts of apoptosis. These viruses also induced significant levels of IFN and were unable to cause apoptosis in IFN-deficient cells, indicating that NS1 limits apoptosis induction through its IFN antagonist functions. The implications of this work for anti-cancer and anti-viral therapies are discussed.

Retroviruses possess several biological features that differentiate them from all other infectious agents. The obligatory integration step of the retrovirus genome into the host genome has allowed these viruses to associate, modulate and alter the biology of the cell with a variety of unique mechanisms. Integration of retroviruses into the germ line of the host results in the formation of vertically transmitted “endogenous” retroviruses (ERVs). It is now becoming apparent that ERVs have often been selected as they provided evolutionary advantages to the host. Sheep Betaretroviruses provide a unique biological system to study the complex interaction between retroviruses and their hosts. Jaagsiekte sheep retrovirus (JSRV) is the causative agent of ovine pulmonary adenocarcinoma (OPA), a naturally occurring lung cancer of sheep. The JSRV Env glycoprotein is a dominant oncoprotein and its expression is sufficient to induce cell transformation in vitro and in vivo. Thus, OPA is a unique large animal model for the study of lung carcinogenesis. The sheep genome harbours at least 27 copies of ERVs highly related to JSRV (enJSRVs). Studies on enJSRVs have provided evidence supporting the idea that ERVs, exogenous retroviruses and the host have coevolved through a dynamic process throughout evolution. enJSRVs play a critical role in conceptus development and placental morphogenesis, and can block JSRV replication in vitro at both early and late stages of the replication cycle. The work presented here focuses on the study of the exogenous and endogenous JSRV Envs and their role in cell transformation and trophoblast differentiation respectively. We were able to show that: I) the JSRV Env transforms epithelial cells in vitro independently from its cellular receptor; II) both the exogenous and endogenous JSRV Envs interact with the receptor tyrosine kinase RON and that the cytoplasmic tail of the Env is the major determinant modulating the biological effects of the Env-RON interaction; III) the molecular chaperone Hsp90 regulates JSRV Env induced cell transformation, in part by downregulating Akt; and IV) OPA is a useful large animal model for the evaluation of new anti-cancer therapeutic agents. Moreover, we characterized the transforming properties, receptor usage and fusogenic activity of enJSRVs Envs to gain insight into their role in placental morphogenesis. The studies described in this thesis contributed to the understanding of JSRV induced cell transformation and the biology of enJSRVs.

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.

Marine vibrio MV-1 is a magnetotactic bacterium capable of aligning its cell in response to the Earth’s magnetic field. This ability is due to the presence of chainlike structures comprising magnetosomes, magnetite particles enclosed in a lipid membrane with associated proteins. Strain MV-1 differs from other, bettercharacterized strains of magnetotactic bacteria as the cells produce higher amounts of biomagnetite per litre of culture and its magnetosomes are unique in shape. This study investigates the presence and organisation of a gene cluster termed a “magnetosome island” within the genome of MV-1. In other magnetotactic bacteria this genomic region has been shown to contain many of the genes associated with magnetosome formation but has not been previously investigated for MV-1. One of the conserved fragments of this region was amplified using degenerate primers followed by extension of the known sequence using inverse PCR based technique and constructing plasmid libraries. Sequencing of the genome of strain MV-1 was accomplished as a part of this study. Significant work was done on comparison of the sequence quality obtained from SOLEXA, 454 and Sanger sequencing technologies. A number of obtained contigs were joined manually and the resulting sequence was automatically annotated using RAST. The obtained genome sequence of 3.6 Mb with a G+C content of 54.3 % was preliminarily analysed and used to search for magnetosome related genes. This study also analysed proteins associated with the magnetosomes of strain MV-1 using MALDI-TOF, LC-MS and Orbitrap mass spectrometry. These approaches allowed the identification of a number of proteins in the isolated magnetosome membrane fraction. Some of these proteins have very low similarity with other characterized proteins (either in magnetotactic bacteria or in other organisms). Another significant point is that genes that code for proteins such as MamR, MamK and MmsF were found to be present in several homologous copies within the “magnetosome island” of MV-1. Interestingly, this study shows that all homologous copies of these proteins were identified in the magnetosome membrane fraction. Generation of knock-out mutants of several specific genes from the “magnetosome island” of strain MV-1 was attempted; constructs were made based on suicide plasmids carrying the cre-lox or I-SceI systems. Despite altering numerous experimental conditions it was not possible to obtain conclusive evidence of the isolation of MV-1 transconjugants containing the integrated constructs. In order to investigate the cell localization of the magnetosome associated protein CAV30779.1, an enhanced green fluorescent protein (EGFP) fusion based construct was generated and transferred into MV-1 cells. The EGFP fluorescent protein fusions within the cells were detected by microscopy. This study reveals novel information about magnetosome formation in marine vibrio MV-1. The obtained results provide an important foundation for further investigation of this organism and contribute towards broadening the knowledge of the complex process of magnetosome formation in bacteria.

No description available.

Foot-and-mouth disease (FMD) is a highly infectious disease of wild and domestic cloven–hoofed animals such as cattle, swine and deer. It is caused by one of the most contagious animal diseases known; FMD virus (FMDV). Since the disease is endemic in many countries, transmission by international travel/trade presents an on-going potential threat to the UK. Very little is known at the molecular level about how FMDV replicates within host cells. In this study, FMDV replicons have been used to investigate FMDV RNA replication and to improve our understanding of the viral life cycle: a process which will aid in the production of a new generation of live-attenuated vaccine candidate strains. Sequences encoding the capsid coding region of the genome have been replaced with green fluorescent protein (GFP) such that replication can be monitored in live cells via GFP fluorescence. This provides a rapid, non-invasive screen for replicative fitness that can be used outwith high disease security facilities. Differences between replicating and non-replicating forms could easily be distinguished, highlighting the potential of this system to screen for attenuated genomes. The FMDV replicon system was improved through a series of construct modifications until an optimal system was produced. A range of different methods were used to attenuate the replication of these genomes. Of major significance is the finding that increasing dinucleotide frequencies were shown to decrease growth kinetics of Echovirus 7 – as opposed to altering the codon-pair bias - and the application of this finding to construction of further replicon systems (and RNA viruses in general) is described.

L’analyse par spectrométrie de masse des protéines qu’interagies avec Dicer-2, R2D2 a identifié six sur huit composés du complexe chaperon TRiC / CCT. L’élimination de l'un des six composants du complexe TRiC / CCT identifiés par spectrométrie de masse a conduit à une réplication virale accrue d'au moins un des trois virus testés. L’ensemble des mes résultats suggèrent un rôle nouveau pour le complexe TRiC / CCT dans l'ARNi antiviral. Mes résultats soulèvent la question de savoir pourquoi le GRR d’AGO2 semble être nécessaire dans le contexte d'une réponse antivirale. Mes résultats indiquent que le complexe TRiC / CCT participe à l’étape de dissociation et à la relocalisation dynamique d'AGO2-L pendant l’infection virale. / The mass spectrometry analysis of the complexes associating with Dicer-2, R2D2, and AGO2 identified six out of the eight subunits forming the TRiC/CCT complex. Knockdown of one of the six subunits identified is sufficient to increase the replication of DCV (DrosophilaC Virus). My results identify an interaction between the TRiC/CCT complex and the antiviral RNA interference. This interaction raises the question of how the GRR region of AGO2 is necessary for the antiviral response. My results suggest that the TRiC/CCT complex is involved in the dynamic dissociation and relocalization of AGO2 during viral infection.

Enigmatic amphibian declines are strongly associated with infectious diseases, including chytridiomycosis, caused by the fungus 'Batrachochytrium dendrobatidis' (Bd), and ranaviral disease induced by ranaviruses. A series of data analyses, field sampling, laboratory experimentation and molecular techniques were utilized to test the hypothesis that the international live animal trade is contributing to the spread of these amphibian pathogens. Regions sampled included specific locations in North America, South America and Asia. The magnitude of the live importation of amphibians into the United States (U.S.) was calculated in the millions of animals per year. Batrachochytrium dendrobatidis and ranavirus infections were identified in live food animals in: (a) U.S. wet markets (in 'Lithobates catesbeianus', the North American bullfrog); (b) frog farms in Taiwan (in 'L. catesbeianus'); and (c) wet markets in Taiwan (in 'Rana tigrina', the Chinese bullfrog). 'Batrachochytrium dendrobatidis' infections were also identified in 'L. catesbeianus' farmed in Brazil and in 8 species of amphibians in the U.S. pet trade (in captive bred and directly imported animals). Detection of Bd in individuals upon initial entry into the U.S. demonstrated definitively the trans-continental movement of this potentially lethal amphibian pathogen. Laboratory experimentation illustrated transmission of Bd from a highly traded carrier host ('L. catesbeianus') to frogs of the same species, and to a known susceptible frog species ('Litoria caerulea', White's tree-frog). Molecular data linked U.S. market frogs and their associated ranaviral infections to origins in Asia and South America. Genotyping of pure, cultured isolates of Bd from farmed 'L. catesbeianus' in Brazil showed that they were most similar to isolates from native amphibians in Latin America when compared to a global dataset, providing evidence for transmission between wild and farmed amphibians. Analysis of isolates from market 'L. catesbeianus' led to the discovery of a novel genotype of Bd in Ypsilanti, Michigan that appeared to have a disparate lineage compared with the previously identified panzootic genotypes. DNA sequence analysis from the Ypsilanti frog indicated its origin in Brazil, where the novel genotype was also discovered in native Brazilian frog populations. The demonstration of amphibian pathogens on frog farms, in live wet markets and at border crossings, the evidence of inter- and intra-species transmission, and the existence of a novel genotype in traded anurans, all indicate that international transport of amphibians and their pathogens could produce not only mixing of pathogen genotypes, but the inadvertent spread of strains of unknown virulence that could negatively impact amphibian health. In 2008, data from research contained in this thesis were instrumental in the decision to list both Bd and ranaviral disease in the World Organization for Animal Health Aquatic Animal Health Code, providing guidelines (such as quarantine procedures) to limit the spread of these pathogens through the trade. The evidence provided in this work re-enforces the need for urgent action to minimize the potential spread of amphibian diseases through international trade routes, for the benefit of amphibian populations throughout the world.

Background Shiga toxin producing Escherichia coli (STEC) O157 causes severe gastrointestinal disease and haemolytic uremic syndrome, and has a major impact on public health worldwide with regular outbreaks and sporadic infection. Phage typing, i.e. the susceptibility of STEC O157 strains to a bank of 16 bacteriophages, has been used in the UK to differentiate STEC O157 for the past 25 years and the phage type (PT) can be an epidemiological marker of strains associated with severe disease or associated with cases that occur from foreign travel. However, little is known about the molecular interactions between the typing phages (TP) and STEC O157. The aims of this thesis were to use whole genome sequencing to elucidate the genetic basis for phage typing of STEC O157 and through this understand genetic differences between strains relevant to disease severity and epidemiology. Results Sequencing the STEC O157 TPs revealed that they were clustered into 4 groups based on sequence similarity that corresponded with their infectivity. Long read sequencing revealed microevolutionary events occuring in STEC O157 genomes over a short time period (approximately 1 year), evidenced by the loss and gain of prophage regions and plasmids. An IncHI2 plasmid was found responsible for a change in Phage Type (PT) from PT8 to PT54 during two related outbreaks at the same restaurant. These changes resulted in a strain (PT54) that was fitter under certain growth conditions and associated with a much larger outbreak (140 as opposed to 4 cases). TraDIS (Transposon directed Insertion site sequencing) was used to identify 114 genes associated with phage sensitivity and 44 genes involved in phage resistance, emphasising the complex nature of identifying specific genetic markers of phage susceptibility or resistance. Further work is required to prove their phage-related functions but several are likely to encode novel phage receptors. Deletion of a Stx2a prophage from a PT21/28 strain led to a strain that typed as PT32, supporting the concept that the highly pathogenic PT21/28 lineage I strains emerged from Stx2c+ PT32 strains in the last two decades by acquisition of Stx2a-encoding prophages. Conclusions This body of work has highlighted the complexity of bacteriophage interaction and investigated the genetic basis for susceptibility and resistance in E. coli. The grouping of the TPs showed that resistance or susceptibility to all members of a typing group was likely to be caused by one mechanism. IncHI2 was identified as one of the markers for the PT54 phenotype. The Stx2a prophage region was associated with the switch from PT32 to PT21/28, although PT32 strains containing both Stx2a and Stx2c-encoding prophages have been isolated and can provide insights into phage variation underpinning the susceptibility to the relevant typing phages. The TraDIS results indicated that susceptibility or resistance was governed by multiple genetic factors and not controlled by a single gene. The significance of LPS for initial protection from phage adsorption was evident and a number of novel genes controlling phage susceptibility and resistance identified including the Sap operon and stringent starvation protein A respectively. While SNP-based typing provides an excellent indication of the evolution and relatedness of strains, phage typing can provide real insights into short term evolution of the bacteria as PTs can be altered by mobile elements such as prophages and plasmids. This study has shown that, although complex, genetic determinants for PT can be mined from the genome and allow us to understand the evolution of this zoonotic pathogen between host species and during outbreaks.