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The Pirbright Institute publication directory contains details of selected publications written by our researchers.

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Dawson H D, Loveland J E, Pascal G, Gilbert J G, Uenishi H, Mann K M, Sang Y, Zhang J, Carvalho-Silva D, Hunt T, Hardy M, Hu Z, Zhao S H, Anselmo A, Shinkai H, Chen C, Badaoui B, Berman D, Amid C, Kay M, Lloyd D, Snow C, Morozumi T, Cheng R P, Bystrom M, Kapetanovic R, Schwartz J C, Kataria R, Astley M, Fritz E, Steward C, Thomas M, Wilming L, Toki D, Archibald A L, Bed'Hom B, Beraldi D, Huang T H, Ait-Ali T, Blecha F, Botti S, Freeman T C, Giuffra E, Hume D A, Lunney J K, Murtaugh M P, Reecy J M, Harrow J L, Rogel-Gaillard C, Tuggle C K (2013)

Structural and functional annotation of the porcine immunome

BMC Genomics 14, 332
Publisher’s version: http://dx.doi.org/10.1186/1471-2164-14-332

Abstract

BACKGROUND: The domestic pig is known as an excellent model for human immunology and the two species share many pathogens. Susceptibility to infectious disease is one of the major constraints on swine performance, yet the structure and function of genes comprising the pig immunome are not well-characterized. The completion of the pig genome provides the opportunity to annotate the pig immunome, and compare and contrast pig and human immune systems. RESULTS: The Immune Response Annotation Group (IRAG) used computational curation and manual annotation of the swine genome assembly 10.2 (Sscrofa10.2) to refine the currently available automated annotation of 1,369 immunity-related genes through sequence-based comparison to genes in other species. Within these genes, we annotated 3,472 transcripts. Annotation provided evidence for gene expansions in several immune response families, and identified artiodactyl-specific expansions in the cathelicidin and type 1 Interferon families. We found gene duplications for 18 genes, including 13 immune response genes and five non-immune response genes discovered in the annotation process. Manual annotation provided evidence for many new alternative splice variants and 8 gene duplications. Over 1,100 transcripts without porcine sequence evidence were detected using cross-species annotation. We used a functional approach to discover and accurately annotate porcine immune response genes. A co-expression clustering analysis of transcriptomic data from selected experimental infections or immune stimulations of blood, macrophages or lymph nodes identified a large cluster of genes that exhibited a correlated positive response upon infection across multiple pathogens or immune stimuli. Interestingly, this gene cluster (cluster 4) is enriched for known general human immune response genes, yet contains many un-annotated porcine genes. A phylogenetic analysis of the encoded proteins of cluster 4 genes showed that 15% exhibited an accelerated evolution as compared to 4.1% across the entire genome. CONCLUSIONS: This extensive annotation dramatically extends the genome-based knowledge of the molecular genetics and structure of a major portion of the porcine immunome. Our complementary functional approach using co-expression during immune response has provided new putative immune response annotation for over 500 porcine genes. Our phylogenetic analysis of this core immunome cluster confirms rapid evolutionary change in this set of genes, and that, as in other species, such genes are important components of the pig's adaptation to pathogen challenge over evolutionary time. These comprehensive and integrated analyses increase the value of the porcine genome sequence and provide important tools for global analyses and data-mining of the porcine immune response.
de la Poza F, Calvo-Pinilla E, Lopez-Gil E, Marin-Lopez A, Mateos F, Castillo-Olivares J, Lorenzo G, Ortego J (2013)

Ns1 is a key protein in the vaccine composition to protect IFNAR(-/-) mice against infection with multiple serotypes of African horse sickness virus

PLoS ONE 8 (7), e70197
Publisher’s version: http://dx.doi.org/10.1371/journal.pone.0070197

Abstract

African horse sickness virus (AHSV) belongs to the genus Orbivirus. We have now engineered naked DNAs and recombinant modified vaccinia virus Ankara (rMVA) expressing VP2 and NS1 proteins from AHSV-4. IFNAR((-/-)) mice inoculated with DNA/rMVA-VP2,-NS1 from AHSV-4 in an heterologous prime-boost vaccination strategy generated significant levels of neutralizing antibodies specific of AHSV-4. In addition, vaccination stimulated specific T cell responses against the virus. The vaccine elicited partial protection against an homologous AHSV-4 infection and induced cross-protection against the heterologous AHSV-9. Similarly, IFNAR((-/-)) mice vaccinated with an homologous prime-boost strategy with rMVA-VP2-NS1 from AHSV-4 developed neutralizing antibodies and protective immunity against AHSV-4. Furthermore, the levels of immunity were very high since none of vaccinated animals presented viraemia when they were challenged against the homologous AHSV-4 and very low levels when they were challenged against the heterologous virus AHSV-9. These data suggest that the immunization with rMVA/rMVA was more efficient in protection against a virulent challenge with AHSV-4 and both strategies, DNA/rMVA and rMVA/rMVA, protected against the infection with AHSV-9. The inclusion of the protein NS1 in the vaccine formulations targeting AHSV generates promising multiserotype vaccines.
Dixon L K, Abrams C C, Chapman D D, Goatley L C, Netherton C L, Taylor G, Takamatsu H H (2013)

Prospects for development of African swine fever virus vaccines

Developments in Biologicals 135, 147-157
Publisher’s version: http://dx.doi.org/10.1159/000170936

Abstract

African swine fever virus is a large DNA virus which can cause an acute haemorrhagic fever in pigs resulting in high mortality. No vaccine is available, limiting options for control. The virus encodes up to 165 genes and virus particles are multi-layered and contain more than 50 proteins. Pigs immunised with natural low virulence isolates or attenuated viruses produced by passage in tissue culture and by targeted gene deletions can be protected against challenge with virulent viruses. CD8+ cells are required for protection induced by attenuated strain OURT88/3. Passive transfer of antibodies from immune to naïve pigs can also induce protection. Knowledge of the genome sequences of attenuated and virulent strains and targeted gene deletions from virulent strains have identified a number of virus genes involved in virulence and immune evasion. This information can be used to produce rationally attenuated vaccine strains. Virus antigens that are targets for neutralising antibodies have been identified and immunisation with these recombinant proteins has been shown to induce partial protection. However knowledge of antigens which encode the dominant protective epitopes recognised by CD8+ T cells is lacking.
Dixon L K, Chapman D A G, Netherton C L, Upton C (2013)

African swine fever virus replication and genomics

Virus Research 173 (1), 3-14
Publisher’s version: http://dx.doi.org/10.1016/j.virusres.2012.10.020

Abstract

African swine fever virus (ASFV) is a large icosahedral DNA virus which replicates predominantly in the cytoplasm of infected cells. The ASFV double-stranded DNA genome varies in length from about 170 to 193 kbp depending on the isolate and contains between 150 and 167 open reading frames. These are closely spaced and read from both DNA strands. The virus genome termini are covalently closed by imperfectly base-paired hairpin loops that are present in two forms that are complimentary and inverted with respect to each other. Adjacent to the termini are inverted arrays of different tandem repeats. Head to head concatemeric genome replication intermediates have been described. A similar mechanism of replication to Poxviruses has been proposed for ASFV. Virus genome transcription occurs independently of the host RNA polymerase II and virus particles contain all of the enzymes and factors required for early gene transcription. DNA replication begins in perinuclear factory areas about 6 h post-infection although an earlier stage of nuclear DNA synthesis has been reported. The virus genome encodes enzymes required for transcription and replication of the virus genome and virion structural proteins. Enzymes that are involved in a base excision repair pathway may be an adaptation to enable virus replication in the oxidative environment of the macrophage cytoplasm. Other ASFV genes encode factors involved in evading host defence systems and modulating host cell function. Variation between the genomes of different ASFV isolates is most commonly due to gain or loss of members of multigene families, MGFs 100, 110, 300, 360, 505/530 and family p22. These are located within the left terminal 40 kbp and right terminal 20 kbp. ASFV is the only member of the Asfarviridae, which is one of the families within the nucleocytoplasmic large DNA virus superfamily.
Dyachenko V, Geiger C, Pantchev N, Majzoub M, Bell-Sakyi L, Krupka I, Straubinger R K (2013)

Isolation of canine Anaplasma phagocytophilum strains from clinical blood samples using the Ixodes ricinus cell line IRE/CTVM20

Veterinary Microbiology 162 (2–4), 980-986
Publisher’s version: http://dx.doi.org/10.1016/j.vetmic.2012.10.021

Abstract

Anaplasma phagocytophilum is an intracellular tick-borne rickettsial pathogen, which causes granulocytic anaplasmosis in various species of livestock and companion animals and also in humans. Previously A. phagocytophilum has been isolated and propagated in cell lines derived from the tick Ixodes scapularis and in the human promyelocytic cell line HL60. In this study we used the Ixodes ricinus-derived cell line IRE/CTVM20 to isolate and propagate two new canine strains of A. phagocytophilum. Blood samples were collected by veterinarians from two dogs, one from Germany and the other from Austria. Suspicion of clinical canine granulocytic anaplasmosis was raised by the treating veterinarians and after confirmation of A. phagocytophilum infection by real-time PCR, buffy coat cells were isolated and co-cultivated with IRE/CTVM20 cells maintained at 28 °C in L15/L15B medium. In the tick cells, rickettsial inclusions were first recognised after 86 days of incubation. Electron microscopic examination of tick cells infected with one of the isolates revealed cytoplasmic vacuoles containing pleomorphic organisms with individual bacteria enveloped by a bilayer membrane. Sequencing of 16S rRNA genes confirmed the isolation of A. phagocytophilum and showed the highest identity to the A. phagocytophilum human HZ strain. The two A. phagocytophilum isolates were passaged several times in IRE/CTVM20 cells and transferred to the I. scapularis cell line ISE6. This confirms for the first time the successful establishment and continuous cultivation of this pathogen in I. ricinus cells as well as infectivity of these canine strains for I. scapularis cells.
Dziva F, Hauser H, Connor T R, van Diemen P M, Prescott G, Langridge G C, Eckert S, Chaudhuri R R, Ewers C, Mellata M, Mukhopadhyay S, Curtiss R, Dougan G, Wieler L H, Thomson N R, Pickard D J, Stevens M P (2013)

Sequencing and functional annotation of avian pathogenic Escherichia coli serogroup O78 strains reveal the evolution of E. coli lineages pathogenic for poultry via distinct mechanisms

Infection and Immunity 81 (3), 838-849
Publisher’s version: http://dx.doi.org/10.1128/iai.00585-12

Abstract

Avian pathogenic Escherichia coli (APEC) causes respiratory and systemic disease in poultry. Sequencing of a multilocus sequence type 95 (ST95) serogroup O1 strain previously indicated that APEC resembles E. coli causing extraintestinal human diseases. We sequenced the genomes of two strains of another dominant APEC lineage (ST23 serogroup O78 strains ?7122 and IMT2125) and compared them to each other and to the reannotated APEC O1 sequence. For comparison, we also sequenced a human enterotoxigenic E. coli (ETEC) strain of the same ST23 serogroup O78 lineage. Phylogenetic analysis indicated that the APEC O78 strains were more closely related to human ST23 ETEC than to APEC O1, indicating that separation of pathotypes on the basis of their extraintestinal or diarrheagenic nature is not supported by their phylogeny. The accessory genome of APEC ST23 strains exhibited limited conservation of APEC O1 genomic islands and a distinct repertoire of virulence-associated loci. In light of this diversity, we surveyed the phenotype of 2,185 signature-tagged transposon mutants of ?7122 following intra-air sac inoculation of turkeys. This procedure identified novel APEC ST23 genes that play strain- and tissue-specific roles during infection. For example, genes mediating group 4 capsule synthesis were required for the virulence of ?7122 and were conserved in IMT2125 but absent from APEC O1. Our data reveal the genetic diversity of E. coli strains adapted to cause the same avian disease and indicate that the core genome of the ST23 lineage serves as a chassis for the evolution of E. coli strains adapted to cause avian or human disease via acquisition of distinct virulence genes.
Elnekave E, Li Y, Zamir L, Even-Tov B, Hamblin P, Gelman B, Hammond J, Klement E (2013)

The field effectiveness of routine and emergency vaccination with an inactivated vaccine against foot and mouth disease

Vaccine 31 (6), 879-885
Publisher’s version: http://dx.doi.org/10.1016/j.vaccine.2012.12.011

Abstract

High potency, inactivated foot and mouth disease (FMD) vaccines may be used in non endemic countries for emergency vaccination during outbreaks in order to prevent virus spread. In endemic countries either standard or high potency vaccines are used for routine vaccination. Despite their wide use there is a shortage of data on the field effectiveness of inactivated FMD vaccines. Epidemics of FMD caused by viruses of serotype O occur frequently in Israel, where a high potency (>= 6PD(50)) vaccine is used for both routine and emergency vaccination. We investigated an outbreak of FMD caused by a virus of serotype 0, which took place during 2011 in a feedlot and an adjacent dairy herd. Post outbreak testing of antibodies against non-structural protein demonstrated that infection occurred in 96% of the calves that received two doses of vaccine at least three months prior to the outbreak and more than 50% showed clinical signs consistent with FMD. Replacement heifers that had been vaccinated 3-5 times with the last vaccination administered 7 months prior to the outbreak were all infected and 18% showed clinical signs. Testing of cattle sera of the same vaccination status as the affected cattle demonstrated low neutralizing antibody (NA) titers against the field virus strain and an r(1) value of 0.37 compared to the vaccine strain. In contrast, cattle vaccinated only once but up to two weeks before the outbreak, were almost all protected from clinical disease and to a lesser extent, protected from FMD virus infection, despite low NA titers. We conclude that emergency vaccination was highly effective due to a mechanism not associated with NA, whereas routine vaccination with the same vaccine formulation provided only limited protection due to poor longevity of the elicited immunity and low matching with the field strain (despite an r(1) higher than 0.3).
Emmott E, Munday D, Bickerton E, Britton P, Rodgers M A, Whitehouse A, Zhou E-M, Hiscox J A (2013)

The cellular interactome of the coronavirus infectious bronchitis virus nucleocapsid protein and functional implications for virus biology

Journal of Virology 87 (17), 9486-9500
Publisher’s version: http://dx.doi.org/10.1128/jvi.00321-13

Abstract

The coronavirus nucleocapsid (N) protein plays a multifunctional role in the virus life cycle, from regulation of replication and transcription and genome packaging to modulation of host cell processes. These functions are likely to be facilitated by interactions with host cell proteins. The potential interactome of the infectious bronchitis virus (IBV) N protein was mapped using stable isotope labeling with amino acids in cell culture (SILAC) coupled to a green fluorescent protein-nanotrap pulldown methodology and liquid chromatography-tandem mass spectrometry. The addition of the SILAC label allowed discrimination of proteins that were likely to specifically bind to the N protein over background binding. Overall, 142 cellular proteins were selected as potentially binding to the N protein, many as part of larger possible complexes. These included ribosomal proteins, nucleolar proteins, translation initiation factors, helicases, and hnRNPs. The association of selected cellular proteins with IBV N protein was confirmed by immunoblotting, cosedimentation, and confocal microscopy. Further, the localization of selected proteins in IBV-infected cells as well as their activity during virus infection was assessed by small interfering RNA-mediated depletion, demonstrating the functional importance of cellular proteins in the biology of IBV. This interactome not only confirms previous observations made with other coronavirus and IBV N proteins with both overexpressed proteins and infectious virus but also provides novel data that can be exploited to understand the interaction between the virus and the host cell.
Engler O, Savini G, Papa A, Figuerola J, Groschup M H, Kampen H, Medlock J, Vaux A, Wilson A J, Werner D, Joest H, Goffredo M, Capelli G, Federici V, Tonolla M, Patocchi N, Flacio E, Portmann J, Rossi-Pedruzzi A, Mourelatos S, Ruiz S, Vazquez A, Calzolari M, Bonilauri P, Dottori M, Schaffner F, Mathis A, Johnson N (2013)

European surveillance for West Nile virus in mosquito populations

International Journal of Environmental Research and Public Health 10 (10), 4869-4895
Publisher’s version: http://dx.doi.org/10.3390/ijerph10104869

Abstract

A wide range of arthropod-borne viruses threaten both human and animal health either through their presence in Europe or through risk of introduction. Prominent among these is West Nile virus (WNV), primarily an avian virus, which has caused multiple outbreaks associated with human and equine mortality. Endemic outbreaks of West Nile fever have been reported in Italy, Greece, France, Romania, Hungary, Russia and Spain, with further spread expected. Most outbreaks in Western Europe have been due to infection with WNV Lineage 1. In Eastern Europe WNV Lineage 2 has been responsible for human and bird mortality, particularly in Greece, which has experienced extensive outbreaks over three consecutive years. Italy has experienced co-circulation with both virus lineages. The ability to manage this threat in a cost-effective way is dependent on early detection. Targeted surveillance for pathogens within mosquito populations offers the ability to detect viruses prior to their emergence in livestock, equine species or human populations. In addition, it can establish a baseline of mosquito-borne virus activity and allow monitoring of change to this over time. Early detection offers the opportunity to raise disease awareness, initiate vector control and preventative vaccination, now available for horses, and encourage personal protection against mosquito bites. This would have major benefits through financial savings and reduction in equid morbidity/mortality. However, effective surveillance that predicts virus outbreaks is challenged by a range of factors including limited resources, variation in mosquito capture rates (too few or too many), difficulties in mosquito identification, often reliant on specialist entomologists, and the sensitive, rapid detection of viruses in mosquito pools. Surveillance for WNV and other arboviruses within mosquito populations varies between European countries in the extent and focus of the surveillance. This study reviews the current status of WNV in mosquito populations across Europe and how this is informing our understanding of virus epidemiology. Key findings such as detection of virus, presence of vector species and invasive mosquito species are summarized, and some of the difficulties encountered when applying a cost-effective surveillance programme are highlighted.
Ferguson K J, Cleaveland S, Haydon D T, Caron A, Kock R A, Lembo T, Hopcraft J G C, Chardonnet B, Nyariki T, Keyyu J, Paton D J, Kivaria F M (2013)

Evaluating the potential for the environmentally sustainable control of foot and mouth disease in Sub-Saharan Africa

EcoHealth 10 (3), 314-322
Publisher’s version: http://dx.doi.org/10.1007/s10393-013-0850-6

Abstract

Strategies to control transboundary diseases have in the past generated unintended negative consequences for both the environment and local human populations. Integrating perspectives from across disciplines, including livestock, veterinary and conservation sectors, is necessary for identifying disease control strategies that optimise environmental goods and services at the wildlife-livestock interface. Prompted by the recent development of a global strategy for the control and elimination of foot-and-mouth disease (FMD), this paper seeks insight into the consequences of, and rational options for potential FMD control measures in relation to environmental, conservation and human poverty considerations in Africa. We suggest a more environmentally nuanced process of FMD control that safe-guards the integrity of wild populations and the ecosystem dynamics on which human livelihoods depend while simultaneously improving socio-economic conditions of rural people. In particular, we outline five major issues that need to be considered: 1) improved understanding of the different FMD viral strains and how they circulate between domestic and wildlife populations; 2) an appreciation for the economic value of wildlife for many African countries whose presence might preclude the country from ever achieving an FMD-free status; 3) exploring ways in which livestock production can be improved without compromising wildlife such as implementing commodity-based trading schemes; 4) introducing a participatory approach involving local farmers and the national veterinary services in the control of FMD; and 5) finally the possibility that transfrontier conservation might offer new hope of integrating decision-making at the wildlife-livestock interface.

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