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

There were a total of 1662 results for your search.
Erickson A, Fisher M, Furukawa-Stoffer T, Ambagala A, Hodko D, Pasick J, King D P, Nfon C, Ortega Polo R, Lung O (2018)

A multiplex reverse transcription PCR and automated electronic microarray assay for detection and differentiation of seven viruses affecting swine

Transboundary and Emerging Diseases early view,


Microarray technology can be useful for pathogen detection as it allows simultaneous interrogation of the presence or absence of a large number of genetic signatures. However, most microarray assays are labour-intensive and time-consuming to perform. This study describes the development and initial evaluation of a multiplex reverse transcription (RT)-PCR and novel accompanying automated electronic microarray assay for simultaneous detection and differentiation of seven important viruses that affect swine (foot-and-mouth disease virus [FMDV], swine vesicular disease virus [SVDV], vesicular exanthema of swine virus [VESV], African swine fever virus [ASFV], classical swine fever virus [CSFV], porcine respiratory and reproductive syndrome virus [PRRSV] and porcine circovirus type 2 [PCV2]). The novel electronic microarray assay utilizes a single, user-friendly instrument that integrates and automates capture probe printing, hybridization, washing and reporting on a disposable electronic microarray cartridge with 400 features. This assay accurately detected and identified a total of 68 isolates of the seven targeted virus species including 23 samples of FMDV, representing all seven serotypes, and 10 CSFV strains, representing all three genotypes. The assay successfully detected viruses in clinical samples from the field, experimentally infected animals (as early as 1 day post-infection (dpi) for FMDV and SVDV, 4 dpi for ASFV, 5 dpi for CSFV), as well as in biological material that were spiked with target viruses. The limit of detection was 10 copies/μl for ASFV, PCV2 and PRRSV, 100 copies/μl for SVDV, CSFV, VESV and 1,000 copies/μl for FMDV. The electronic microarray component had reduced analytical sensitivity for several of the target viruses when compared with the multiplex RT-PCR. The integration of capture probe printing allows custom onsite array printing as needed, while electrophoretically driven hybridization generates results faster than conventional microarrays that rely on passive hybridization. With further refinement, this novel, rapid, highly automated microarray technology has potential applications in multipathogen surveillance of livestock diseases.

Paton D J, Gubbins S, King D P (2018)

Understanding the transmission of foot-and-mouth disease virus at different scales

Current Opinion in Virology 28, 85-91


Foot-and-mouth disease (FMD) is highly infectious, but despite the large quantities of FMD virus released into the environment and the extreme susceptibility of host species to infection, transmission is not always predictable. Whereas virus spread in endemic settings is characterised by frequent direct and indirect animal contacts, incursions into FMD-free countries may be seeded by low-probability events such as fomite or wind-borne aerosol routes. There remains a void between data generated from small-scale experimental studies and our ability to reliably reconstruct transmission routes at different scales between farms, countries and regions. This review outlines recent transmission studies in susceptible host species, and considers new approaches that integrate virus genomics and epidemiological data to recreate and understand the spread of FMD.
Sánchez-Cordón P J, Jabbar T, Berrezaie M, Chapman D, Reis A, Sastre P, Rueda P, Goatley L, Dixon L K (2018)

Evaluation of protection induced by immunisation of domestic pigs with deletion mutant African swine fever virus Benin∆MGF by different doses and routes

Vaccine 36 (5), 707-715


A live attenuated African swine fever virus (ASFV) vaccine candidate, produced by deletion of several genes belonging to multi-gene families MGF360 and 505 from virulent Benin 97/1 strain (BeninΔMGF), induces protection in pigs against parental virulent strain. In order to better define the safety and efficacy of this attenuated vaccine candidate and to understand protective mechanisms, we extended previous studies by intramuscular immunisation of pigs with the deletion mutant BeninΔMFG at different doses (102, 103, 104 TCID50), together with intranasal immunisation at the 103 dose. Results demonstrated a strong correlation between both doses and routes of immunisation of BeninΔMFG and the percentage of protection achieved, the onset of clinical signs, the viremia levels reached and the onset of death in non-protected pigs. The results show that the intramuscular route using high doses (104 TCID50) is the best option for immunisation. Only transient increase in temperature associated with a peak of virus genome levels was observed in most pigs after immunisation. Then, virus genome levels progressively decreased throughout the experiment until reaching low or undetectable levels in those protected pigs that survived after challenge. The IgM antibody responses following immunisation were detected between day 7–10 post-immunisation and remained at elevated levels for 10–18 days in most pigs before dropping. IgG was detected from day 15 to 21 post-immunisation and maintained at increased levels for the remainder of the experiment in most pigs. Induction of IFNγ and IL-10 was detected by ELISA in sera from some pigs immunised with 103 TCID50 by intramuscular or intranasal route at early times post-immunisation. IL-10 was also detected in serum from some non-protected pigs included in these groups after challenge.

Smith L P, Petheridge L, Nair V, Wood A, Welchman D (2018)

Avian leukosis virus subgroup J-associated myelocytoma in a hobby chicken

Veterinary Record 182 (1), 23


The avian leukosis viruses (ALVs) are a major group of retroviruses associated with neoplastic diseases in poultry. The ALV-J strain was identified as a cause of myelocytomas in broiler breeder and broiler chickens in the UK in the 1980s; however, following eradication of the virus,commercial broilers have remained free of infection since the early 2000s. A pet chicken was submitted to Animal and Plant Health Agency (APHA) in 2013 with a history of croaking respirations, abnormality of the left eye and apparent paralysis. Postmortem examination of the bird showed widespread tumour-like infiltration of many organs, including the pectoral muscles, internal organs, sternum and ribs. Histopathological examination of the affected tissues revealed myelocytoma formation typical of the lesions associated with ALV-J, and the virus was confirmed by PCR testing and sequencing. Virus was not detected in blood samples in the other five chickens remaining in the flock. The source of infection was not established. This was the first time ALV-J had been seen in the UK since its eradicationand the case highlights the importance of continued surveillance of backyard and hobby chickens to detect potential new and re-emerging disease threats, such as ALV-J, which may be of significance to the wider poultry population.

Farhanah M I, Yasmin A R, Mat Isa N, Hair-Bejo M, Ideris A, Powers C, Oladapo O, Nair V, Khoo J-S, Ghazali A-K, Yee W-Y, Omar A R (2018)

Bursal transcriptome profiling of different inbred chicken lines reveals key differentially expressed genes at 3 days post-infection with very virulent infectious bursal disease virus

Journal of General Virology 99 (1), 21-35


Infectious bursal disease is a highly contagious disease in the poultry industry and causes immunosuppression in chickens. Genome-wide regulations of immune response genes of inbred chickens with different genetic backgrounds, following very virulent infectious bursal disease virus (vvIBDV) infection are poorly characterized. Therefore, this study aims to analyse the bursal tissue transcriptome of six inbred chicken lines 6, 7, 15, N, O and P following infection with vvIBDV strain UK661 using strand-specific next-generation sequencing, by highlighting important genes and pathways involved in the infected chicken during peak infection at 3?days post-infection. All infected chickens succumbed to the infection without major variations among the different lines. However, based on the viral loads and bursal lesion scoring, lines P and 6 can be considered as the most susceptible lines, while lines 15 and N were regarded as the least affected lines. Transcriptome profiling of the bursa identified 4588 genes to be differentially expressed, with 2985 upregulated and 1642 downregulated genes, in which these genes were commonly or uniquely detected in all or several infected lines. Genes that were upregulated are primarily pro-inflammatory cytokines, chemokines and IFN-related. Various genes that are associated with B-cell functions and genes related to apoptosis were downregulated, together with the genes involved in p53 signalling. In conclusion, bursal transcriptome profiles of different inbred lines showed differential expressions of pro-inflammatory cytokines and chemokines, Th1 cytokines, JAK-STAT signalling genes, MAPK signalling genes, and their related pathways following vvIBDV infection.

Howson E L A, Armson B, Lyons N A, Chepkwony E, Kasanga C J, Kandusi S, Ndusilo N, Yamazaki W, Gizaw D, Cleaveland S, Lembo T, Rauh R, Nelson W M, Wood B A, Mioulet V, King D P, Fowler V L (2018)

Direct detection and characterisation of foot-and-mouth disease virus in East Africa using a field-ready real-time PCR platform

Transboundary and Emerging Diseases 65 (1), 221-231


Effective control and monitoring of foot-and-mouth disease (FMD) relies upon rapid and accurate disease confirmation. Currently, clinical samples are usually tested in reference laboratories using standardized assays recommended by The World Organisation for Animal Health (OIE). However, the requirements for prompt and serotype-specific diagnosis during FMD outbreaks, and the need to establish robust laboratory testing capacity in FMD-endemic countries have motivated the development of simple diagnostic platforms to support local decision-making. Using a portable thermocycler, the T-COR™ 8, this study describes the laboratory and field evaluation of a commercially available, lyophilized pan-serotype-specific real-time RT-PCR (rRT-PCR) assay and a newly available FMD virus (FMDV) typing assay (East Africa-specific for serotypes: O, A, Southern African Territories [SAT] 1 and 2). Analytical sensitivity, diagnostic sensitivity and specificity of the pan-serotype-specific lyophilized assay were comparable to that of an OIE-recommended laboratory-based rRT-PCR (determined using a panel of 57 FMDV-positive samples and six non-FMDV vesicular disease samples for differential diagnosis). The FMDV-typing assay was able to correctly identify the serotype of 33/36 FMDV-positive samples (no cross-reactivity between serotypes was evident). Furthermore, the assays were able to accurately detect and type FMDV RNA in multiple sample types, including epithelial tissue suspensions, serum, oesophageal–pharyngeal (OP) fluid and oral swabs, both with and without the use of nucleic acid extraction. When deployed in laboratory and field settings in Tanzania, Kenya and Ethiopia, both assays reliably detected and serotyped FMDV RNA in samples (n = 144) collected from pre-clinical, clinical and clinically recovered cattle. These data support the use of field-ready rRT-PCR platforms in endemic settings for simple, highly sensitive and rapid detection and/or characterization of FMDV.

Souley Kouato B, Elliot F M, King D P, Hyera J, Knowles N J, Ludi A B, Mioulet V, Matlho G, De Clercq K, Thys E, Marichatou H, Issa S, Saegerman C (2018)

Outbreak investigations and molecular characterization of foot-and-mouth disease viruses circulating in south-west Niger

Transboundary and Emerging Diseases 65 (1), 146-157


In Niger, the epidemiological situation regarding foot-and-mouth disease is unclear as many outbreaks are unreported. This study aimed (i) to identify Foot-and-mouth disease virus (FMDV) strains currently circulating in cattle herds, and (ii) to identify risk factors associated with Foot-and-mouth disease (FMD)-seropositive animals in clinical outbreaks. Epithelial tissues (n = 25) and sera (n = 227) were collected from cattle in eight districts of the south-western part of Niger. Testing of clinical material revealed the presence of FMDV serotype O that was characterized within the O/WEST AFRICA topotype. The antigenic relationship between one of the FMDV isolates from Niger (O/NGR/4/2015) and three reference vaccine strains was determined by the two-dimensional virus neutralization test (2dmVNT), revealing a close antigenic match between the field isolate from Niger and three FMDV serotype O vaccine strains. Serological analyses using a non-structural protein (NSP) test provided evidence for previous FMDV infection in 70% (158/227) of the sera tested. Multivariate logistic regression analysis revealed that only the herd composition (presence of both cattle and small ruminants) was significantly associated with FMDV seropositivity as defined by NSP-positive results (p-value = .006). Of these positive sera, subsequent testing by liquid-phase blocking ELISA (LPBE) showed that 86% (136/158) were positive for one (or more) of four FMDV serotypes (A, O, Southern African Territories (SAT) 1 and SAT 2). This study provides epidemiological information about FMD in the south-western part of Niger and highlights the complex transboundary nature of FMD in Africa. These findings may help to develop effective control and preventive strategies for FMD in Niger as well, as other countries in West Africa.

Ahmed Mahgoub H, Elnaggar A, Sadeyen J-R (2017)

Implementation of tissue histopathology and parasitic morphometric analysis in the diagnosis of Myxobolus fomenai infection in the skeletal muscles Nile tilapia

American Journal of Infectious Diseases and Microbiology 5 (4), 137-142
Publisher’s version:


Class Myxosporea includes Myxobolus parasite. Myxosporean species could infect the skeletal muscles of freshwater fish, including Nile tilapia. In this study, four Nile tilapia fish, collected from a fish farm in Dakahleya province, died and showed gross lesions of haemorrhage on the outer surface (external skeletal muscles and fins). Fish was necropsied and samples were collected for both histopathological examination and quantitative analysis of the transcriptional level of interleukin-8 and tumour necrosis factor-α mRNA in selected tissues. Careful examination revealed the residence of myxospore-producing plasmodia in the affected skeletal muscles of Nile tilapia. The morphometric analysis revealed approximate morphometric results to Myxobolus fomenai. The plasmodia were detected in the skeletal muscles, focally replacing the muscle tissue and containing various developmental stages. The parasite was either surrounded with polymorphnuclear and mononuclear cells and few erythrocytes (haemorrhage), together with necrosis of the adjacent myocytes, or it was seen with sparse or without inflammatory reaction. Transcriptional analysis of interleukin-8 and tumour necrosis factor-α in the skeletal muscles, fins, spleen, and head-kidney revealed the slight down-regulation of interleukin-8 and tumour necrosis factor-α mRNA in the skeletal muscles and their slight up-regulation in the fins of infected fish. However, their mRNA levels in the spleen and head-kidney remained unaffected by infection. Careful future histopathological examination is required to reveal the possibility of Myxobolus fomenai infection in other organs of Nile tilapia. In addition, further immunological investigation needs to be accomplished in relation to such parasitological infestation.

Gurung A, Kamble N, Kaufer B B, Pathan A, Behboudi S (2017)

Association of Marek's disease induced immunosuppression with activation of a novel regulatory T cell

PLOS Pathogens 13 (12), e1006745


Marek's Disease Virus (MDV) is an alphaherpesvirus that infects chickens, transforms CD4+ T cells and causes deadly lymphomas. In addition, MDV induces immunosuppression early during infection by inducing cell death of the infected lymphocytes, and potentially due to activation of regulatory T (Treg)-cells. Furthermore, immunosuppression also occurs during the transformation phase of the disease; however, it is still unknown how the disease can suppress immune response prior or after lymphoma formation. Here, we demonstrated that chicken TGF-beta+ Treg cells are found in different lymphoid tissues, with the highest levels found in the gut-associated lymphoid tissue (cecal tonsil: CT), fostering an immune-privileged microenvironment exerted by TGF-beta. Surprisingly, significantly higher frequencies of TGF-beta+ Treg cells are found in the spleens of MDV-susceptible chicken lines compared to the resistant line, suggesting an association between TGF-beta+ Treg cells and host susceptibility to lymphoma formation. Experimental infection with a virulent MDV elevated the levels of TGF-beta+ Treg cells in the lungs as early as 4 days post infection, and during the transformation phase of the disease in the spleens. In contrast to TGF-beta+ Treg cells, the levels of CD4+CD25+ T cells remained unchanged during the infection and transformation phase of the disease. Furthermore, our results demonstrate that the induction of TGF-beta+ Treg cells is associated with pathogenesis of the disease, as the vaccine strain of MDV did not induce TGF-beta+ Treg cells. Similar to human haematopoietic malignant cells, MDV-induced lymphoma cells expressed high levels of TGF-beta but very low levels of TGF-beta receptor I and II genes. The results confirm that COX-2/ PGE2 pathway is involved in immunosuppression induced by MDV-lymphoma cells. Taken together, our results revealed a novel TGF-beta+ Treg subset in chickens that is activated during MDV infection and tumour formation.

Reeman S, Gates A J, Pulford D J, Krieg A, Ulaeto D O (2017)

Protection of mice from lethal vaccinia virus infection by vaccinia virus protein subunits with a CpG Adjuvant

Viruses 9 (12), 378
Publisher’s version:


Smallpox vaccination carries a high risk of adverse events in recipients with a variety of contra-indications for live vaccines. Although alternative non-replicating vaccines have been described in the form of replication-deficient vaccine viruses, DNA vaccines, and subunit vaccines, these are less efficacious than replicating vaccines in animal models. DNA and subunit vaccines in particular have not been shown to give equivalent protection to the traditional replicating smallpox vaccine. We show here that combinations of the orthopoxvirus A27, A33, B5 and L1 proteins give differing levels of protection when administered in different combinations with different adjuvants. In particular, the combination of B5 and A27 proteins adjuvanted with CpG oligodeoxynucleotides (ODN) gives a level of protection in mice that is equivalent to the Lister traditional vaccine in a lethal vaccinia virus challenge model.


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