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

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Pruvot M, Fine A E, Hollinger C, Strindberg S, Damdinjav B, Buuveibaatar B, Chimeddorj B, Bayandonoi G, Khishgee B, Sandag B, Narmandakh J, Jargalsaikhan T, Bataa B, McAloose D, Shatar M, Basan G, Mahapatra M, Selvaraj M, Parida S, Njeumi F, Kock R, Shiilegdamba E (2020)

Outbreak of peste des petits ruminants among critically endangered mongolian saiga and other wild ungulates, Mongolia, 2016-2017

Emerging Infectious Diseases 26 (1), 51-62


The 2016-2017 introduction of peste des petits ruminants virus (PPRV) into livestock in Mongolia was followed by mass mortality of the critically endangered Mongolian saiga antelope and other rare wild ungulates. To assess the nature and population effects of this outbreak among wild ungulates, we collected clinical, histopathologic, epidemiologic, and ecological evidence. Molecular characterization confirmed that the causative agent was PPRV lineage IV. The spatiotemporal patterns of cases among wildlife were similar to those among livestock affected by the PPRV outbreak, suggesting spillover of virus from livestock at multiple locations and time points and subsequent spread among wild ungulates. Estimates of saiga abundance suggested a population decline of 80%, raising substantial concerns for the species' survival. Consideration of the entire ungulate community (wild and domestic) is essential for elucidating the epidemiology of PPRV in Mongolia, addressing the threats to wild ungulate conservation, and achieving global PPRV eradication.


RNA viruses exist as populations of closely related genomes, characterized by a high diversity of low-frequency variants. As viral genomes from one population disperse to establish new sites of replication, the fate of these low-frequency variants depends to a large extent on the size of the founding population. Focusing on foot-and-mouth disease virus (FMDV) we conjecture that variants are more likely to be transmitted through wide bottlenecks, but more likely to approach fixation in new populations following narrow bottlenecks; therefore, the longer-term rate of accumulation of 'nearly neutral' variants at high frequencies is likely to be inversely related to the bottleneck size. We examine this conjecture in vivo by estimating bottleneck sizes relating 'parent' and 'daughter' populations observed at different scales ranging from within host to between host (within the same herd, and in different herds) using a previously established method. Within hosts, we find bottleneck sizes to range from 5 to 20 viral genomes between populations transmitted from the pharynx to the serum, and from 4 to 54 between serum and lesion populations. Between hosts, we find bottleneck sizes to range from 2 to 39, suggesting inter-host bottlenecks are of a similar size to intra-host bottlenecks. We establish a statistically significant negative relationship between the probability of genomic consensus level change and bottleneck size, and present a simple sampling model that captures this empirical relationship. We also present a novel in vitro experiment to investigate the impact of bottleneck size on the frequency of mutations within FMDV populations, demonstrate that variant frequency in a population increases more rapidly during small population passages, and provide evidence for positive selection during the passage of large populations.


There are 7 serotypes of Foot-and-Mouth Disease Virus and multiple strains of each serotype. The emergence of new strains can result in widespread outbreaks of disease and requires new vaccines to be developed. The major mechanisms driving variation are thought to be substitutions in the viral genome. Recombination in the capsid-coding region of the virus genome has been described at phylogenetic scales but not thought to play a major role in generating variants. In the current experiment, a co-infection of African buffaloes with closely related sub-populations of viruses allowed us to detect recombination events. For structural protein-coding sequences, the genetic composition of the population is driven by extensive within-host recombination. During the acute infection phase the intra-host recombination rates of 0.1 per base per year are comparable to the typical mutation rates of the virus. The recombination map reveals two strongly linked regions within the VP1 protein-coding sequence. Epistatic interactions between co-evolved mutations in VP1 are caused by intra-host selection at the RNA and protein level and are present both within and between the two regions. Our findings in this experimental setting support a major role for recombination and epistasis in the intra-host evolution of FMDV.


Recent data suggest that porcine gammadelta T cells exhibit a similar degree of functional plasticity as human and murine gammadelta T cells. Due to the high frequency of TCR-gammadelta+ cells in blood and secondary lymphatic organs, the pig is an attractive model to study these cells, especially their combined features of the innate and the adaptive immune system. Using a 5' RACE-like approach, we translated a human/murine NGS library preparation strategy to capture full-length V-(D)-J TRG and TRD clonotypes in swine. After oligo(dT) primed conversion of input RNA, the cDNA population was enriched for full-length V(D)J TCR transcripts with porcine-specific primers including Illumina adaptor sequences as overhangs for Illumina MiSeq analysis. After quality control and processing by FastQC and ea-utils, porcine TRG and TRD sequences were mapped against the human IMGT reference directory. Porcine blood-derived CD2+ and CD2- TCR-gammadelta+ cells exhibited two distinct clonotypes Vgamma11JgammaP1 (74.6%) and Vgamma10JgammaP1 (57.7%), respectively. Despite the high TCR-delta diversity among CD2+ cells (39 clonotypes), both subsets shared the same abundant Vdelta1DdeltaxJdelta4 clonotype at approximately identically frequencies (CD2+: 31.2%; CD2- : 37.0%). The flexible nature of this approach will facilitate the assessment of organ-specific phenotypes of gammadelta T cell subsets alongside with their respective TCR diversity at single cell resolution.                       


Vaccination is the main tool for control of peste des petits ruminants (PPR) because of the availability of effective and safe vaccines that provide long lasting protection. However vaccination campaigns may not always provide sufficient herd immunity needed to prevent disease outbreaks because of logistic problems with vaccination such as inappropriate cold chain and vaccine delivery methods, and the rapid population turnover of small ruminants. This study was carried out to assess post-vaccination herd immunity against PPR and inter-vaccination population turnover in small ruminant flocks in Metema district, northwest Ethiopia where frequent PPR outbreaks occur despite regular vaccination. A total of 412 serum samples were collected from selected small ruminants in 72 flocks (average flock size of 33.4 and standard deviation of 30) above three months of age in three kebeles immediately before a vaccination program. One month after the vaccination using freeze dried live attenuated vaccine, 359 serum samples were collected from randomly selected small ruminants in the same flocks. The collected serum samples were analyzed to determine the seropositivity using a monoclonal antibody-based C-ELISA. The pre-vaccination seropositivity of 72.3% (95% CI: 67.8-76.4) increased to 93.9% (95% CI: 90.9-95.9) post-vaccination (P<0.001). The observed seropositivity following vaccination was above the recommended herd immunity threshold (80%) required to reduce the transmission of infection in the population sufficient to eliminate virus. A survey of sampled flocks six months post-sampling indicated only 68% of animals were still present in these flocks. This population turnover reduces the herd immunity to about 64% which is below the required threshold for control. The high level of herd immunity achieved post-vaccination indicates good vaccine quality, cold chain maintenance and effective vaccine delivery in the district's vaccination campaigns. The decrease in herd immunity associated with population turnover and annual vaccination intervals represents a challenge to effective control and suggests changes to the timing or frequency of the vaccination is required.


In the present study, we determined the in vitro characteristics and binding interactions of chicken PD-1 (chPD-1) and PD-L1 (chPD-L1) and developed a panel of specific monoclonal antibodies against the two proteins. ChPD-1 and chPD-L1 sequence identities and similarities were lower compared with those of humans and other mammalian species. Furthermore, in phylogenetic analysis, chPD-1 and chPD-L1 were grouped separately from the mammalian PD-1 and PD-L1 sequences. As in other species, chPD-1 and chPD-L1 sequences showed signal peptide, extracellular domain, a transmembrane domain and intracellular domain. Based on the three dimensional (3D) structural homology, chPD-1, and chPD-L1 were similar to 3D structures of mammalian PD-1 and PD-L1. Further, Ig V domain of chPD-1 and the Ig V and Ig C domains of chPD-L1 were highly conserved with the mammalian counterparts. In vitro binding interaction studies using Superparamagnetic Dynabeads® confirmed that recombinant soluble chPD-1/PD-L1 fusion proteins and surface chPD-1/PD-L1 proteins interacted with each other on COS cells. Two monoclonal antibodies specific against chPD-1 and five antibodies against chPD-L1 were developed and their specific binding characteristics confirmed by immunofluorescence staining and Western blotting.


Foot-and-mouth disease (FMD) affects the livestock industry in a transboundary manner. It is essential to understand the FMD phylodynamics to assist in the disease-eradication. FMD critically affects the Sri Lankan cattle industry causing substantial economic losses. Even though many studies have covered the serotyping and genotyping of FMD virus (FMDV) in Sri Lanka, there is a significant knowledge gap exists in understanding the FMDV phylodynamics in the country. In the present study, the VP1 genomic region of FMD viral isolates belonging to serotype C from Sri Lanka and other South Asian countries were sequenced. All the published VPI sequences of serotype C and most of the published VP1 sequences for lineage ME-SA/Ind-2001d of serotype O from Sri Lanka, India, and other South Asian countries were retrieved. The datasets of serotype C and serotype O were separately analyzed using Bayesian, maximum likelihood, and phylogenetic networking methods to infer the transboundary movements and evolutionary aspects of the FMDV incursions in Sri Lanka. A model-based approach was used to detect any possible recombination events of FMDV incursions. Our results revealed that the invasions of the topotype ASIA of serotype C and the lineage ME-SA/Ind-2001d have a similar pattern of transboundary movement and evolution. The haplotype networks and phylogenies developed in the present study confirmed that FMDV incursions in Sri Lanka mainly originate from the Indian subcontinent, remain quiet after migration, and then cause outbreaks in a subsequent year. Since there are no recombination events detected among the different viral strains across serotypes and topotypes, we can assume that the incursions tend to show the independent evolution compared to the ancestral viral populations. Thus, we highlight the need for thorough surveillance of cattle/ruminants and associated product-movement into Sri Lanka from other regions to prevent the transboundary movement of FMDV.

Opsteegh M, Spano F, Aubert D, Balea A, Burrells A, Cherchi S, Cornelissen J, Dam-Deisz C, Guitian J, Gyorke A, Innes E A, Katzer F, Limon G, Possenti A, Pozio E, Schares G, Villena I, Wisselink H J, van der Giessen J W B (2019)

The relationship between the presence of antibodies and direct detection of Toxoplasma gondii in slaughtered calves and cattle in four European countries

International Journal of Parasitology 49 (7), 515-522


In cattle, antibodies to Toxoplasma gondii infection are frequently detected, but evidence for the presence of T. gondii tissue cysts in cattle is limited. To study the concordance between the presence of anti-T. gondii IgG and viable tissue cysts of T. gondii in cattle, serum, liver and diaphragm samples of 167 veal calves and 235 adult cattle were collected in Italy, the Netherlands, Romania and the United Kingdom. Serum samples were tested for anti-T. gondii IgG by the modified agglutination test and p30 immunoblot. Samples from liver were analyzed by mouse bioassay and PCR after trypsin digestion. In addition, all diaphragms of cattle that had tested T. gondii-positive (either in bioassay, by PCR on trypsin-digested liver or serologically by MAT) and a selection of diaphragms from cattle that had tested negative were analyzed by magnetic capture quantitative PCR (MC-PCR). Overall, 13 animals were considered positive by a direct detection method: seven out of 151 (4.6%) by MC-PCR and six out of 385 (1.6%) by bioassay, indicating the presence of viable parasites. As cattle that tested positive in the bioassay tested negative by MC-PCR and vice-versa, these results demonstrate a lack of concordance between the presence of viable parasites in liver and the detection of T. gondii DNA in diaphragm. In addition, the probability to detect T. gondii parasites or DNA in seropositive and seronegative cattle was comparable, demonstrating that serological testing by MAT or p30 immunoblot does not provide information about the presence of T. gondii parasites or DNA in cattle and therefore is not a reliable indicator of the risk for consumers.


Increasing access to next-generation sequencing (NGS) technologies is revolutionizing the life sciences. In disease ecology, NGS-based methods have the potential to provide higher-resolution data on communities of parasites found in individual hosts as well as host populations. Here, we demonstrate how a novel analytical method, utilizing high-throughput sequencing of PCR amplicons, can be used to explore variation in blood-borne parasite (Theileria—Apicomplexa: Piroplasmida) communities of African buffalo at higher resolutions than has been obtained with conventional molecular tools. Results reveal temporal patterns of synchronized and opposite fluctuations of prevalence and relative abundance of Theileria spp. within the host population, suggesting heterogeneous transmission across taxa. Furthermore, we show that the community composition of Theileria spp. and their subtypes varies considerably between buffalo, with differences in composition reflected in mean and variance of overall parasitemia, thereby showing potential to elucidate previously unexplained contrasts in infection outcomes for host individuals. Importantly, our methods are generalizable as they can be utilized to describe blood-borne parasite communities in any host species. Furthermore, our methodological framework can be adapted to any parasite system given the appropriate genetic marker. The findings of this study demonstrate how a novel NGS-based analytical approach can provide fine-scale, quantitative data, unlocking opportunities for discovery in disease ecology.


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