Publications

Publications

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

There were a total of 2606 results for your search.

Abstract

Swine vesicular disease virus (SVDV) is an enterovirus that is both genetically and antigenically closely related to human coxsackievirus B5 within the Picornaviridae family. SVDV is the causative agent of a highly contagious (though rarely fatal) vesicular disease in pigs. We report a rapid method that is suitable for sequencing the complete protein-encoding sequences of SVDV isolates in which the RNA is relatively intact. The approach couples a single PCR amplification reaction, using only a single PCR primer set to amplify the near-complete SVDV genome, with deep-sequencing using a small fraction of the capacity of a Roche GS FLX sequencing platform. Sequences were initially verified through one of two criteria; either a match between a de novo assembly and a reference mapping, or a match between all of five different reference mappings performed against a fixed set of starting reference genomes with significant genetic distances within the same species of viruses. All reference mappings used an iterative method to avoid bias. Further verification was achieved through phylogenetic analysis against published SVDV genomes and additional Enterovirus B sequences. This approach allows high confidence in the obtained consensus sequences, as well as provides sufficiently high and evenly dispersed sequence coverage to allow future studies of intra-host variation.

Abstract

Monoclonal-antibody (MAb)-resistant mutants were used to map antigenic sites on foot-and-mouth disease virus (FMDV), which resulted in the identification of neutralizing epitopes in the flexible ?G-?H loop in VP1. For FMDV SAT2 viruses, studies have shown that at least two antigenic sites exist. By use of an infectious SAT2 cDNA clone, 10 structurally exposed and highly variable loops were identified as putative antigenic sites on the VP1, VP2, and VP3 capsid proteins of SAT2/Zimbabwe (ZIM)/7/83 (topotype II) and replaced with the corresponding regions of SAT2/Kruger National Park (KNP)/19/89 (topotype I). Virus neutralization assays using convalescent-phase antisera raised against the parental virus, SAT2/ZIM/7/83, indicated that the mutant virus containing the TQQS-to-ETPV mutation in the N-terminal part of the ?G-?H loop of VP1 showed not only a significant increase in the neutralization titer but also an increase in the index of avidity to the convalescent-phase antisera. Furthermore, antigenic profiling of the epitope-replaced and parental viruses with nonneutralizing SAT2-specific MAbs led to the identification of two nonneutralizing antigenic regions. Both regions were mapped to incorporate residues 71 to 72 of VP2 as the major contact point. The binding footprint of one of the antigenic regions encompasses residues 71 to 72 and 133 to 134 of VP2 and residues 48 to 50 of VP1, and the second antigenic region encompasses residues 71 to 72 and 133 to 134 of VP2 and residues 84 to 86 and 109 to 11 of VP1. This is the first time that antigenic regions encompassing residues 71 to 72 of VP2 have been identified on the capsid of a SAT2 FMDV.
Ortego J, Mertens P P (2014)

Bluetongue virus revisited

Virus Research 182, 1-2

Abstract

Bluetongue (BT) is a vector-borne viral disease of ruminants that causes high socio-economic and sanitary consequences. Bluetongue virus (BTV) is a member of the genus Orbivirus of the family Reoviridae and so far 26 serotypes have been described. The disease has been known to the South African sheep farmers since at least the early years of the 19th century. From this date, more than 2000 articles have been published about BTV and around 800 of them have appeared in the last ten years. This high number of publications in recent years reflects an important and fast advance in the understanding of this virus, especially since 2006, when an outbreak of BTV-8 was detected in Northern Europe. This special issue of Virus Research reviews the work that has been done on BTV in the last few years. It contains a brief introduction and nine review articles from leading experts in the field. This issue highlights the recent achievements in the field and shows the future directions in bluetongue virus research.

Abstract

Human rhinovirus (HRV) is a non-enveloped virus of the picornavirus family and is responsible for respiratory infections (common colds) costing billions of dollars ($) annually. There remains no vaccine or licensed drug to prevent or reduce infection. Related members of the picornavirus family include significant pathogens such as poliovirus, enterovirus 71 and foot-and-mouth disease virus, for which improved control measures are also required. A fundamental step in virus infection is the delivery of the viral genetic material through the barrier of the cellular membrane. Viruses such as HIV and influenza are enveloped in an outer membrane which can fuse with the host cell membrane to allow the viral genome to penetrate into the cytoplasm. However, non-enveloped viruses such as picornaviruses lack a membrane and the mechanisms for penetration of the membrane by these viruses remain poorly understood. The capsid protein VP4 has previously been implicated in the delivery of the picornavirus genome. In this study we demonstrate that HRV VP4 interacts with membranes to make them permeable by the formation of multimeric, size-selective membrane pores with properties consistent with the transport of viral genome through the membrane. This function of VP4 provides a novel antiviral target for this family of viruses.

Abstract

Ligands for Toll-like receptors (TLRs) are known to stimulate immune responses, leading to protection against bacterial and viral pathogens. Here, we aimed to examine the effects of various TLR ligands on the development of Marek's disease in chickens. Specific-pathogen free chickens were treated with a series of TLR ligands that interact with TLR3, TLR9 and TLR21. In a pilot study, it was determined that TLR4 and TLR21 ligands are efficacious, in that they could reduce the incidence of Marek's disease tumors in infected birds. Hence, in a subsequent study, chickens were treated with lipopolysaccharide (LPS) as a TLR4 and CpG oligodeoxynucleotides (ODN) as TLR21 agonists before being challenged with the RB1B strain of Marek's disease virus (MDV) via the respiratory route. The results demonstrated that the administration of LPS or CpG ODN, but not PBS or non-CpG ODN, delayed disease onset and reduced MDV genome copy number in the spleens of infected chickens. Taken together, our data demonstrate that TLR4 and 21 agonists modulate anti-virus innate immunity including cytokine responses in MD-infected chicken and this response can only delay, but not inhibit, disease progression.

Abstract

To eliminate incursions of foot-and-mouth disease (FMD) quickly, a combination of measures, including emergency vaccination, can help block the spread of infection. For the earliest recovery of the FMD-free status for trade, without the slaughter of uninfected vaccinated animals, a serosurvey for antibodies to FMD virus non-structural proteins (NSP) must be used to substantiate absence of occult virus infections. Areas of doubt over requirements for post-vaccination serosurveillance and its feasibility include the required and achievable confidence, the amount of sampling necessary, and the appropriate responses to and consequences of different seropositive findings. This derives largely from uncertainty over the extent of localised pockets of virus infection that may remain within vaccinated populations and the circumstances that permit this. The question therefore remains whether tests are sufficiently sensitive and specific to detect and eliminate infected animals, without excessive culling of uninfected animals, before vaccinated animals mix with non-vaccinated livestock when movement restrictions are lifted. It is recommended to change the rationale for serosurveillance after emergency vaccination. Only when emergency vaccination is used in limited outbreaks is it possible to test and cull comprehensively, an approach compatible with a three-month minimum period to recover the FMD-free status. In other situations, where emergency vaccination is used, such as dealing with large outbreaks in animal-dense regions and where the onset of vaccination has been delayed, post-vaccination serosurveys should be targeted and focus on providing an assurance to detect higher levels of infection, in case of inadequate control measures. As this provides less assurance of absence of infection, the approach would be compatible with a six-month waiting period for free-status recovery and should be complemented by other methods to provide evidence that vaccination and control measures have been effectively implemented, as these are the best guarantee against continuing virus transmission.
Perez de Diego A C, Sanchez-Cordon P J, Sanchez-Vizcaino J M (2014)

Bluetongue in Spain: from the first outbreak to 2012

Transboundary and Emerging Diseases 61 (6), e1-e11

Abstract

Outbreaks of bluetongue disease have occurred in Spain six times and have been caused by the following serotypes of bluetongue virus (BTV), in chronological order: BTV10, BTV2, BTV4, BTV1 and BTV8. Serotypes BTV1, BTV2 and BTV4 may have entered the country in Culicoides transported by wind; BTV8 via infected animal movements; and BTV10 across the Portuguese border. The evolution of each serotype has been different: BTV1, BTV4 and BTV10 spread throughout mainland Spain; BTV2 did not spread from the Balearic Islands to the Iberian Peninsula; and BTV8 has proven very poor at spreading throughout mainland Spain. The significant economic impact of the disease has led authorities to adopt control and eradication measures, which have evolved as new diagnostic tools and vaccines have become available. This review describes BTV infection in Spain, and it focuses on the clinical disease produced by each serotype, the Culicoides species which were present at what time, the origin of the virus and the control measures adopted. In the field, it has proven necessary to vaccinate livestock against each new BTV serotype as it arrived. Therefore, future eradication strategies should focus on developing polyvalent vaccines and vaccines that allow the differentiation of infected and vaccinated animals. As of 1 January 2013, the Iberian Peninsula is considered a restricted area for BTV1, and a small zone in southern Spain is a restricted area for BTV4, which includes the little BTV8 restricted area. Serotypes BTV1 and BTV4 were detected in sentinel animals in January and November and in March 2012, respectively. The last BTV8 positive animal was detected in November 2010, which implies that in the coming months, Spain may be declared free of BTV8.

Abstract

The aim of this study was to compare and correlate antibody titres against porcine circovirus type 2 (PCV2) in porcine sera (n=1270) obtained by immunoperoxidase monolayer assay (IPMA) with the results of three commercial ELISAs (designated E1, E2 and E3). The correlation between IPMA and ELISA results was excellent (r(2) >= 0.90). Compared to IPMA, E2 had the highest sensitivity (93.0%), followed by E3 (90.1%) and E1 (85.0%); the specificity was 100% for all tests. All three commercial ELIsAs had predictive values similar to those of IPMA and could be used to monitor antibody responses against PCV2 infection and/or vaccination.
Reid A J, Blake D P, Ansari H R, Billington K, Browne H P, Bryant J, Dunn M, Hung S S, Kawahara F, Miranda-Saavedra D, Malas T B, Mourier T, Naghra H, Nair M, Otto T D, Rawlings N D, Rivailler P, Sanchez-Flores A, Sanders M, Subramaniam C, Tay Y L, Woo Y, Wu X K, Barrell B, Dear P H, Doerig C, Gruber A, Ivens A C, Parkinson J, Rajandream M A, Shirley M W, Wan K L, Berriman M, Tomley F M, Pain A (2014)

Genomic analysis of the causative agents of coccidiosis in domestic chickens

Genome Research 24 (10), 1676-1685

Abstract

Global production of chickens has trebled in the past two decades and they are now the most important source of dietary animal protein worldwide. Chickens are subject to many infectious diseases that reduce their performance and productivity. Coccidiosis, caused by apicomplexan protozoa of the genus Eimeria, is one of the most important poultry diseases. Understanding the biology of Eimeria parasites underpins development of new drugs and vaccines needed to improve global food security. We have produced annotated genome sequences of all seven species of Eimeria that infect domestic chickens, which reveal the full extent of previously described repeat-rich and repeat-poor regions and show that these parasites possess the most repeat-rich proteomes ever described. Furthermore, while no other apicomplexan has been found to possess retrotransposons, Eimeria is home to a family of chromoviruses. Analysis of Eimeria genes involved in basic biology and host-parasite interaction highlights adaptations to a relatively simple developmental life cycle and a complex array of co-expressed surface proteins involved in host cell binding.

Barbknecht M, Sepsenwol S, Leis E, Tuttle-Lau M, Gaikowski M, Knowles N J, Lasee B, Hoffman M A (2014)

Characterization of a new picornavirus isolated from the freshwater fish Lepomis macrochirus

Journal of General Virology 95 (3), 601-613

Abstract

The freshwater fish Lepomis macrochirus (bluegill) is common to North American waters, and important both ecologically and as a sport fish. In 2001 an unknown virus was isolated from bluegills following a bluegill fish kill. This virus was identified as a picornavirus [termed bluegill picornavirus (BGPV)] and a diagnostic reverse transcriptase PCR was developed. A survey of bluegills in Wisconsin waters showed the presence of BGPV in 5 of 17 waters sampled, suggesting the virus is widespread in bluegill populations. Experimental infections of bluegills confirmed that BGPV can cause morbidity and mortality in bluegills. Molecular characterization of BGPV revealed several distinct genome characteristics, the most unusual of which is the presence of a short poly(C) tract in the 3? UTR. Additionally, the genome encodes a polyprotein lacking a leader peptide and a VP0 maturation cleavage site, and is predicted to encode two distinct 2A proteins. Sequence comparison showed that the virus is most closely related to a phylogenetic cluster of picornaviruses that includes the genera Aquamavirus, Avihepatovirus and Parechovirus. However, it is distinct enough, for example sharing only about 38?% sequence identity to the parechoviruses in the 3D region, that it may represent a new genus in the family Picornaviridae.

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