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

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Bakshy K, Heimeier D, Schwartz J C, Glass E J, Wilkinson S, Skuce R A, Allen A R, Young J, McClure J C, Cole J B, Null D J, Hammond J A, Smith T P L, Bickhart D M (2021)

Development of polymorphic markers in the immune gene complex loci of cattle

Journal of Dairy Science 104 (5)


The addition of cattle health and immunity traits to genomic selection indices holds promise to increase individual animal longevity and productivity, and decrease economic losses from disease. However, highly variable genomic loci that contain multiple immune-related genes were poorly assembled in the first iterations of the cattle reference genome assembly and underrepresented during the development of most commercial genotyping platforms. As a consequence, there is a paucity of genetic markers within these loci that may track haplotypes related to disease susceptibility. By using hierarchical assembly of bacterial artificial chromosome inserts spanning 3 of these immune-related gene regions, we were able to assemble multiple full-length haplotypes of the major histocompatibility complex, the leukocyte receptor complex, and the natural killer cell complex. Using these new assemblies and the recently released ARS-UCD1.2 reference, we aligned whole-genome shotgun reads from 125 sequenced Holstein bulls to discover candidate variants for genetic marker development. We selected 124 SNPs, using heuristic and statistical models to develop a custom genotyping panel. In a proof-of-principle study, we used this custom panel to genotype 1,797 Holstein cows exposed to bovine tuberculosis (bTB) that were the subject of a previous GWAS study using the Illumina BovineHD array. Although we did not identify any significant association of bTB phenotypes with these new genetic markers, 2 markers exhibited substantial effects on bTB phenotypic prediction. The models and parameters trained in this study serve as a guide for future marker discovery surveys particularly in previously unassembled regions of the cattle genome.

Cockerill G S, Angell R M, Bedernjak A, Chuckowree I, Fraser I a, Gascon-Simorte J, Gilman M S A, Good J A D, Harland R, Johnson S M, Ludes-Meyers J H, Littler E, Lumley J, Lunn G, Mathews N, McLellan J S, Paradowski M, Peeples M E, Scott C, Tait D, Taylor G, Thom M, Thomas E, Villalonga Barber C, Ward S E, Watterson D, Williams G, Young P, Powell K (2021)

Discovery of Sisunatovir (RV521), an inhibitor of respiratory syncytial virus fusion

Journal of Medicinal Chemistry early view


RV521 is an orally bioavailable inhibitor of respiratory syncytial virus (RSV) fusion that was identified after a lead optimization process based upon hits that originated from a physical property directed hit profiling exercise at Reviral. This exercise encompassed collaborations with a number of contract organizations with collaborative medicinal chemistry and virology during the optimization phase in addition to those utilized as the compound proceeded through preclinical and clinical evaluation. RV521 exhibited a mean IC50 of 1.2 nM against a panel of RSV A and B laboratory strains and clinical isolates with antiviral efficacy in the Balb/C mouse model of RSV infection. Oral bioavailability in preclinical species ranged from 42 to >100% with evidence of highly efficient penetration into lung tissue. In healthy adult human volunteers experimentally infected with RSV, a potent antiviral effect was observed with a significant reduction in viral load and symptoms compared to placebo.


Interpreting the interplay between politics, social demographics and epidemiology is essential for understanding how a disease's occurrence and control evolve over time. Foot-and-mouth disease (FMD) virus was first detected in Kenya in 1915 and serotyped in 1932. This review aims to describe and appraise initiatives to control FMD in Kenya since its independence from British rule in 1964, using information from the scientific literature. We describe the historical dynamics of FMD epidemiology in the country and determine socio-political factors that have shaped the control strategies used. PubMed, Scopus, CAB abstracts, Science Direct, Web of Science and Google Scholar were used to search and retrieve papers, using predetermined search criteria encompassing FMD, Kenya and disease control programme descriptors. In total 1234 papers were identified and screened for relevance using the World Health Organization's guidelines for rapid review. Ultimately 69 references from this search were included, and information extracted and consolidated. These papers highlight that following independence, there was a structured effort to control FMD consisting of a compulsory subsidised vaccination programme in the Rift Valley with movement controls and quarantine when outbreaks occurred. This programme led to an initial decrease in recorded FMD outbreaks. However, endemic circulation continued and this programme was discontinued due to multiple factors, including political deprioritisation and changes in the structure of veterinary services. Only low levels of active surveillance have been applied since 1964; most surveillance is passive and relies on outbreak reports. Currently control focuses on outbreak management and a mixture of public- and privately-funded vaccination. This review highlights critical drivers influencing disease control programme implementation including veterinary service structure, the active participation of stakeholders with farming systems and availability of affordable and matched FMD vaccine. Additionally, it appraises the availability of historical information and draws attention to gaps in the historical record.

Dascalu S, Geambasu O, Covaciu O, Chereches R M, Diaconu G, Dumitra G G, Gheorghita V, Popovici E D (2021)

Prospects of COVID-19 vaccination in Romania: challenges and potential solutions

Frontiers in Public Health 9, 644538


The rapid advancement in vaccine development represents a critical milestone that will help humanity tackle the COVID-19 pandemic. However, the success of these efforts is not guaranteed, as it relies on the outcomes of national and international vaccination strategies. In this article, we highlight some of the challenges that Romania will face and propose a set of solutions to overcome them. With this in mind, we discuss issues such as the infrastructure of vaccine storage and delivery, the deployment and administration of immunisations, and the public acceptance of vaccines. The ways in which Romanian society will respond to a national COVID-19 vaccination campaign will be contingent on appropriate and timely actions. As many of the problems encountered in Romania are not unique, the proposed recommendations could be adapted and implemented in other countries that face similar issues, thereby informing better practices in the management of the COVID-19 pandemic.

Edmans M D, Connelley T K, Jayaraman S, Vrettou C, Vordermeier M, Mak J Y W, Liu L, Fairlie D P, Maze E A, Chrun T, Klenerman P, Eckle S B G, Tchilian E, Benedictus L (2021)

Identification and phenotype of MAIT cells in cattle and their response to bacterial infections

Frontiers in Immunology 12, 627173


Mucosal-associated invariant T (MAIT) cells are a population of innate-like T cells that utilize a semi-invariant T cell receptor (TCR) α chain and are restricted by the highly conserved antigen presenting molecule MR1. MR1 presents microbial riboflavin biosynthesis derived metabolites produced by bacteria and fungi. Consistent with their ability to sense ligands derived from bacterial sources, MAIT cells have been associated with the immune response to a variety of bacterial infections, such as Mycobacterium spp., Salmonella spp. and Escherichia coli. To date, MAIT cells have been studied in humans, non-human primates and mice. However, they have only been putatively identified in cattle by PCR based methods; no phenotypic or functional analyses have been performed. Here, we identified a MAIT cell population in cattle utilizing MR1 tetramers and high-throughput TCR sequencing. Phenotypic analysis of cattle MAIT cells revealed features highly analogous to those of MAIT cells in humans and mice, including expression of an orthologous TRAV1-TRAJ33 TCR α chain, an effector memory phenotype irrespective of tissue localization, and expression of the transcription factors PLZF and EOMES. We determined the frequency of MAIT cells in peripheral blood and multiple tissues, finding that cattle MAIT cells are enriched in mucosal tissues as well as in the mesenteric lymph node. Cattle MAIT cells were responsive to stimulation by 5-OP-RU and riboflavin biosynthesis competent bacteria in vitro. Furthermore, MAIT cells in milk increased in frequency in cows with mastitis. Following challenge with virulent Mycobacterium bovis, a causative agent of bovine tuberculosis and a zoonosis, peripheral blood MAIT cells expressed higher levels of perforin. Thus, MAIT cells are implicated in the immune response to two major bacterial infections in cattle. These data suggest that MAIT cells are functionally highly conserved and that cattle are an excellent large animal model to study the role of MAIT cells in important zoonotic infections.


The enveloped morbilliviruses utilise conserved proteinaceous receptors to enter host cells: SLAMF1 or Nectin-4. Receptor binding is initiated by the viral attachment protein Haemagglutinin (H), with the viral Fusion protein (F) driving membrane fusion. Crystal structures of the prototypic morbillivirus measles virus H with either SLAMF1 or Nectin-4 are available and have served as the basis for improved understanding of this interaction. However, whether these interactions remain conserved throughout the morbillivirus genus requires further characterisation. Using a random mutagenesis approach, based on error-prone PCR, we targeted the putative receptor binding site for SLAMF1 interaction on peste des petits ruminants virus (PPRV) H, identifying mutations that inhibited virus-induced cell-cell fusion. These data, combined with structural modelling of the PPRV H and ovine SLAMF1 interaction, indicate this region is functionally conserved across all morbilliviruses. Error-prone PCR provides a powerful tool for functionally characterising functional domains within viral proteins.


BACKGROUND: Previous genetic pest management (GPM) systems in diamondback moth (DBM) have relied on expressing lethal proteins ('effectors') that are 'cell-autonomous', that is, they do not leave the cell in which they are expressed. To increase the flexibility of future GPM systems in DBM, we aimed to assess the use of a non-cell-autonomous, invertebrate-specific, neurotoxic effector - the scorpion toxin AaHIT. This AaHIT effector was designed to be secreted by expressing cells, potentially leading to effects on distant cells, specifically neuromuscular junctions.

RESULTS: Expression of AaHIT caused a 'shaking/quivering' phenotype that could be repressed by provision of an antidote (tetracycline): a phenotype consistent with the AaHIT mode-of-action. This effect was more pronounced when AaHIT expression was driven by the Hr5/ie1 promoter (82.44% of males, 65.14% of females) rather than Op/ie2 (57.35% of males, 48.39% of females). Contrary to expectations, the shaking phenotype and observed fitness costs were limited to adults in which they caused severe reductions in mean longevity (-81%) and median female fecundity (-93%). Quantitative polymerase chain reactions of AaHIT expression patterns and analysis of piggyBac-mediated transgene insertion sites suggest that restriction of the observed effects to the adult stages may be due to the influence of the local genomic environment on the tetO-AaHIT transgene.

CONCLUSION: We demonstrated the feasibility of using non-cell-autonomous effectors within a GPM context for the first time in Lepidoptera, one of the most economically damaging orders of insects. These findings provide a framework for extending this system to other pest Lepidoptera and to other secreted effectors.

Holzer B, Rijal P, McNee A, Paudyal B, Martini V, Clark B, Manjegowda T, Salguero F J, Bessell E, Schwartz J C, Moffat K, Pedrera M, Graham S P, Noble A, Bonnet-Di Placido M, La Ragione R M, Mwangi W, Beverley P, McCauley J W, Daniels R S, Hammond J A, Townsend A R, Tchilian E (2021)

Protective porcine influenza virus-specific monoclonal antibodies recognize similar haemagglutinin epitopes as humans

PloS Pathogens 17 (3), e1009330


Pigs are natural hosts for the same subtypes of influenza A viruses as humans and integrally involved in virus evolution with frequent interspecies transmissions in both directions. The emergence of the 2009 pandemic H1N1 virus illustrates the importance of pigs in evolution of zoonotic strains. Here we generated pig influenza-specific monoclonal antibodies (mAbs) from H1N1pdm09 infected pigs. The mAbs recognized the same two major immunodominant haemagglutinin (HA) epitopes targeted by humans, one of which is not recognized by post-infection ferret antisera that are commonly used to monitor virus evolution. Neutralizing activity of the pig mAbs was comparable to that of potent human anti-HA mAbs. Further, prophylactic administration of a selected porcine mAb to pigs abolished lung viral load and greatly reduced lung pathology but did not eliminate nasal shedding of virus after H1N1pdm09 challenge. Hence mAbs from pigs, which target HA can significantly reduce disease severity. These results, together with the comparable sizes of pigs and humans, indicate that the pig is a valuable model for understanding how best to apply mAbs as therapy in humans and for monitoring antigenic drift of influenza viruses in humans, thereby providing information highly relevant to making influenza vaccine recommendations.


Much of our understanding of proteins and proteomes comes from the traditional protein structure-function paradigm. However, in the last 2 decades, both computational and experimental studies have provided evidence that a large fraction of functional proteomes across different domains of life consists of intrinsically disordered proteins, thus triggering a quest to unravel and decipher protein intrinsic disorder. Unlike structured/ordered proteins, intrinsically disordered proteins/regions (IDPs/IDRs) do not possess a well-defined structure under physiological conditions and exist as highly dynamic conformational ensembles. In spite of this peculiarity, these proteins have crucial roles in cell signaling and regulation. To date, studies on the abundance and function of IDPs/IDRs in viruses are rather limited. To fill this gap, we carried out an extensive and thorough bioinformatics analysis of 283000 proteins from 6108 reference viral proteomes. We analyzed protein intrinsic disorder from multiple perspectives, such as abundance of IDPs/IDRs across diverse virus types, their functional annotations, and subcellular localization in taxonomically divergent hosts. We show that the content of IDPs/IDRs in viral proteomes varies broadly as a function of virus genome types and taxonomically divergent hosts. We have combined the two most commonly used and accurate IDP predictors' results with charge-hydropathy (CH) versus cumulative distribution function (CDF) plots to categorize the viral proteins according to their IDR content and physicochemical properties. Mapping of gene ontology on the disorder content of viral proteins reveals that IDPs are primarily involved in key virus-host interactions and host antiviral immune response downregulation, which are reinforced by the post-translational modifications tied to disorder-enriched viral proteins. The present study offers detailed insights into the prevalence of the intrinsic disorder in viral proteomes and provides appealing targets for the design of novel therapeutics.


Dendritic cells (DCs) are the most potent antigen presenting cells (APCs). Because of the difficulty in obtaining these cells directly from tissues, different sources of DCs are frequently used for in vitro experimentation and many of their biological and functional characteristics were studied using these systems. Until recently, it was assumed that specific culture conditions polarized the differentiation of either DCs or macrophages (Macs); however, it was shown that some DC culture systems in other species generate heterogeneous cell populations that can be identified according to their CD11c and MHC class II (MHC-II) expression. Following this approach, porcine DCs were directly isolated from peripheral blood or differentiated in vitro by culturing bone marrow (BM) progenitor cells or blood monocytes treated with growth factors. Mostly homogeneous monocyte-derived DCs (MoDCs) were obtained with similar phenotype and phagocytic characteristics to that of blood DCs. On the contrary, BM-derived DC (BMDC) cultures generated two distinct heterogeneous populations identified as MHC-II+ and MHC-II++ cells. BMDCs MHC-II+ had similar phenotypic and phagocytic characteristics to those of MoDCs and blood DCs. However, BMDCs MHC-II++ population expressed a higher amount of surface markers and transcribed genes associated with Macs-lineage exhibiting a higher phagocytic capacity than all the other cells. Noteworthy, every cell system expressed different genetic signatures. These results will help interpreting and re-interpreting data obtained using in vitro systems.


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