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

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Bachanek-Bankowska K, Wadsworth J, Henry E, Ludi A B, Bin-Tarif A, Statham B, King D P, Afzal M, Hussain M, Manzoor S, Abubakar M, Knowles N J (2019)

Genome sequences of antigenically distinct serotype O foot-and-mouth disease viruses from Pakistan

Microbiology Resource Announcements 8 (3), e01397-18


The genome sequences of three serotype O foot-and-mouth disease viruses (FMDVs) isolated from outbreaks in Pakistan in 2016 and 2017 are described. Despite all three isolates being classified in the same FMDV genetic sublineage, two of them displayed a distinct antigenic phenotype against commonly used vaccine strains.

Flannery J, Sanz-Bernardo B, Ashby M, Brown H, Carpenter S, Cooke L, Corla A, Frost L, Gubbins S, Hicks H, Qureshi M, Rajko-Nenow P, Sanders C, Tully M, Bréard E, Sailleau C, Zientara S, Darpel K, Batten C (2019)

Evidence of reduced viremia, pathogenicity and vector competence in a re-emerging European strain of bluetongue virus serotype 8 in sheep

Transboundary and Emerging Diseases early view,
Publisher’s version:


The outbreak of bluetongue virus (BTV) serotype 8 (BTV-8) during 2006-2009 in Europe was the most costly epidemic of the virus in recorded history. In 2015, a BTV-8 strain re-emerged in France which has continued to circulate since then. To examine anecdotal reports of reduced pathogenicity and transmission efficiency, we investigated the infection kinetics of a 2007 UK BTV-8 strain alongside the re-emerging BTV-8 strain isolated from France in 2017. Two groups of eight BTV-naïve British mule sheep were inoculated with 5.75 log10TCID50 ml?1 of either BTV-8 strain. BTV RNA was detected by 2 dpi in both groups with peak viremia occurring between 5-9 dpi. A significantly greater amount of BTV RNA was detected in sheep infected with the 2007 strain (6.0-8.8 log10 genome copies mL-1) than the re-emerging BTV-8 strain (2.9-7.9 log10 genome copies mL?1). All infected sheep developed BTV-specific antibodies by 9 dpi. BTV was isolated from 2 dpi to 12 dpi for 2007 BTV-8-inoculated sheep and from 5 to 10 dpi for sheep inoculated with the remerging BTV-8. In Culicoides sonorensis feeding on the sheep over the period 7-12 dpi, vector competence was significantly higher for the 2007 strain than the re-emerging strain. Both the proportion of animals showing moderate (as opposed to mild or no) clinical disease (6/8 vs 1/8) and the overall clinical scores (median 5.25 vs 3) were significantly higher in sheep infected with the 2007 strain, compared to those infected with the re-emerging strain. However, one sheep infected with the re-emerging strain was euthanized at 16 dpi having developed severe lameness. This highlights the potential of the re-emerging BTV-8 to still cause illness in naïve ruminants with concurrent costs to the livestock industry.

Sabaratnam K, Renner M, Paesen G, Harlos K, Nair V, Owens R J, Grimes J M (2019)

Insights from the crystal structure of the chicken CREB3 bZIP suggest members of the CREB3 subfamily transcription factors may be activated in response to oxidative stress

Protein Science early view,
Publisher’s version:


cAMP response element binding protein 3 (CREB3) is an endoplasmic reticulum (ER) membrane-bound transcription factor, which belongs to the basic leucine zipper (bZIP) superfamily of eukaryotic transcription factors. CREB3 plays a role in the ER-stress induced unfolded protein response (UPR) and is a multifunctional cellular factor implicated in a number of biological processes including cell proliferation and migration, tumour suppression, and immune-related gene expression. To gain structural insights into the transcription factor, we determined the crystal structure of the conserved bZIP domain of chicken CREB3 (chCREB3) to a resolution of 3.95Å. The X-ray structure provides evidence that chCREB3 can form a stable homodimer. The chCREB3 bZIP has a structured, pre-formed DNA binding region, even in the absence of DNA, a feature that could potentially enhance both the DNA binding specificity and affinity of chCREB3. Significantly, the homodimeric bZIP possesses an intermolecular disulphide bond that connects equivalent cysteine residues of the parallel helices in the leucine zipper region. This disulphide bond in the hydrophobic core of the bZIP may increase the stability of the homodimer under oxidising conditions. Moreover, sequence alignment of bZIP sequences from chicken, human and mouse reveals only members of the CREB3 subfamily contain this cysteine residue, indicating it could act as a redox-sensor. Taken together, these results suggest activity of these transcription factors may be redox-regulated and they may be activated in response to oxidative stress.

Zhu M, Zhou J, Ma X, Li G, He S, Tang H, Yao Y, Cheng Z (2019)

CCCH-type zinc finger antiviral protein is specifically overexpressed in spleen in response to subgroup J avian leukosis virus infection in chicken

Research in Veterinary Science 123, 65-70


The CCCH-type zinc finger antiviral protein (ZAP), a host antiviral factor, plays an important role in innate defenses. Although the anti-viral mechanism of ZAP has been elucidated, however, the tissue specificity and the viral infection correlativity have not been fully understood. Here, we tested the dynamic distribution and localization of chicken ZAP (chZAP) before and after avian leukosis virus subgroup J (ALV-J) infection. The results showed that chZAP was highly expressed in adrenal gland and testis before ALV-J infection, and significantly upregulated in liver, kidney and bursa of Fabricius, and extremely overexpressed in spleen after ALV-J infection. The results indicated that chZAP is an inducible protein and showed specific overexpression in spleen after ALV-J infection. Furthermore, we demonstrated that chZAP, as a host intracytoplasmic factor, accumulated and migrated to the periphery of nucleus in DF-1 cells post-infection with ALV-J. Taken together, chZAP characterized as an inducible antiviral protein and specifically overexpressed in spleen after ALV-J infection.

Tang N, Zhang Y, Pedrera M, Chang P, Baigent S, Moffat K, Shen Z, Nair V, Yao Y (2019)

Generating recombinant avian herpesvirus vectors with CRISPR/Cas9 gene editing

Journal of Visualized Experiments 143, e58193


Herpesvirus of turkeys (HVT) is an ideal viral vector for the generation of recombinant vaccines against a number of avian diseases, such as avian influenza (AI), Newcastle disease (ND), and infectious bursal disease (IBD), using bacterial artificial chromosome (BAC) mutagenesis or conventional recombination methods. The clustered regularly interspaced palindromic repeats (CRISPR)/Cas9 system has been successfully used in many settings for gene editing, including the manipulation of several large DNA virus genomes. We have developed a rapid and efficient CRISPR/Cas9-mediated genome editing pipeline to generate recombinant HVT. To maximize the potential use of this method, we present here detailed information about the methodology of generating recombinant HVT expressing the VP2 protein of IBDV. The VP2 expression cassette is inserted into the HVT genome via an NHEJ (nonhomologous end-joining)-dependent repair pathway. A green fluorescence protein (GFP) expression cassette is first attached to the insert for easy visualization and then removed via the Cre-LoxP system. This approach offers an efficient way to introduce other viral antigens into the HVT genome for the rapid development of recombinant vaccines.

Lyons N A, Jemberu W T, Chaka H, Salt J S, Rushton J (2019)

Field-derived estimates of costs for peste des petits ruminants vaccination in Ethiopia

Preventive Veterinary Medicine 163, 37-43


In 2015, the OIE and FAO launched a global eradication programme for Peste des Petits Ruminants (PPR). Vaccination is a major component of this strategy yet the costs of implementing a campaign are unknown or based on assumptions without field-based verification necessary for effective economic planning. This study used experiences of attending four PPR vaccination campaigns in Ethiopia to estimate various cost components in pastoral and mixed-crop livestock systems. These components included: cost of vaccine; vaccine transport from the producer to the local storage facility; storage of vaccine at the local facility; delivery and administration of vaccine in the field; opportunity cost of farmer’s time to attend the vaccination; co-ordination of vaccination campaign; publicity and mobilisation costs; vaccine wastage from missed shots and vaccine discard. The overall cost of vaccination was approximately 6 Ethiopian birr (ETB) or US$0.2 per animal in the mixed-crop livestock system compared to approximately 3ETB or US$0.1 in pastoral areas. The relative importance of cost components varied in the two systems with farmer time being the largest contributor in the mixed-crop livestock system while field delivery was the main cost in pastoral areas. Notable vaccine wastage was observed particularly through missed shots that were typically between 0 and 10% but as high as 33%. At the national level, the output of the stochastic model showed the cost of vaccination to be highly variable particularly in the mixed-crop livestock system. These results highlight the importance of doing economic assessments of vaccination campaigns and issues that may be compromising efficiency of delivery and vaccine coverage. It is recommended that the framework be used for further economic evaluations of vaccination for PPR and other livestock diseases particularly when limited public or donor funds are being used, and that the approach be expanded to other countries and regions.

Gubbins S, Stegeman A, Klement E, Pite L, Broglia A, Cortiñas Abrahantes J (2019)

Inferences about the transmission of lumpy skin disease virus between herds from outbreaks in Albania in 2016

Preventive Veterinary Medicine early view,


Lumpy skin disease has recently emerged as a major threat to cattle populations outside of Africa, where it is endemic. In 2015 the first ever European outbreaks occurred in Greece, which were followed by spread across much of the Balkans in 2016. Here we use a simple mathematical model for the transmission of lumpy skin disease virus (LSDV) between herds to explore factors influencing its spread by fitting it to data on outbreaks in Albania in 2016. We show that most transmission occurs over short distances (<5 km), but with an appreciable probability of transmission at longer distances. We also show that there is evidence for seasonal variation in the force of infection associated with temperature, possibly through its influence on the relative abundance of the stable fly, Stomoxys calcitrans. These two results together are consistent with LSDV being transmitted by the bites of blood-feeding insects, though further work is required to incriminate specific species as vectors. Finally, we show that vaccination has a significant impact on spread and estimate the vaccine effectiveness to be 76%.

Brown-Joseph T, Rajko-Nenow P, Hicks H, Sahadeo N, Harrup L E, Carrington C V, Batten C, Oura C A L (2019)

Identification and characterization of epizootic hemorrhagic disease virus serotype 6 in cattle co-infected with bluetongue virus in Trinidad, West Indies

Veterinary Microbiology 229,


Epizootic hemorrhagic disease virus (EHDV) is an economically important virus that can cause severe clinical disease in deer and to a lesser extent cattle. This study set out to determine and characterize which EHDV serotypes were circulating in Trinidad. Serum and whole blood samples were collected monthly for six months from a cohort of cattle imported to Trinidad from the USA. Results revealed that all the cattle seroconverted to EHDV within six months of their arrival, with EHDV RNA being detected in the samples just prior to antibodies, as expected. Serotyping assays revealed that a single serotype (EHDV-6) was circulating in the cattle. Sequencing of the surface viral protein (VP2) of EHDV-6, followed by phylogenetic analysis, revealed that the Trinidad EHDV-6 strain was closely related to EHDV-6 viruses found in Guadeloupe (2010), Martinique (2010) and USA (2006), with 96–97.2% nucleotide identity. The Trinidad EHDV-6 VP-2 shared 97.2% identity with the Australian EHDV-6 prototype strain, classifying it within the eastern topotype clade. Bayesian coalescent analysis support Australia as the most probable source for the EHDV-6 VP2 sequences in the Americas and Caribbean region and suggests that the they diverged from the Australian prototype strain around 1966 (95% HPD 1941–1979).

Bo L L, Lwin K S, Ungvanijban S, Knowles N J, Wadsworth J, King D P, Abila R, Qiu Y (2019)

Foot-and-mouth disease outbreaks due to an exotic serotype Asia 1 virus in Myanmar in 2017

Transboundary and Emerging Diseases early view,
Publisher’s version:


In January 2017, two villages located in Rakhine State of Myanmar reported clinical signs in cattle suggestive of foot-and-mouth disease virus (FMDV) infection. Laboratory analysis identified the outbreak virus as FMDV serotype Asia 1, which represented the first detection of this serotype in Myanmar since 2005 and in the region of South-East Asia (SEA) since 2007. Genetic analysis revealed that the outbreak virus was different from historical viruses from Myanmar and was more closely related to viruses circulating in Bangladesh and India during 2012-2013, indicating a novel viral introduction had occurred. The precise origin of the outbreaks was not clear, but frequent informal livestock trade with Bangladesh was reported. Responses to the outbreaks involved disinfection, quarantine and animal movement restrictions; no further outbreaks were detected under the present passive surveillance system. Detection of serotype Asia 1 highlights the complex and dynamic nature of FMDV in SEA. Active surveillance is needed to assess the extent and distribution of this exotic Asia 1 strain and continued vigilance to timely detect the occurrence of emerging and re-emerging FMDV strains is essential.

Muzaffar A, Tahir Y, Mukhtar N, Imran M, Ghafoor A, Shahid MF, N Muhammad, Iqbal M, Smith GJD, Su Y. (2019)

Avian influenza A(H9N2) virus in poultry worker, Pakistan, 2015

Emerging Infectious Diseases 25 (1), 136-139


Avian influenza A(H9N2) virus isolated from a poultry worker in Pakistan in 2015 was closely related to viruses detected in poultry farms. Observed mutations in the hemagglutinin related to receptor-binding affinity and antigenicity could affect cross-reactivity with prepandemic H9N2 vaccine strains.


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