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

There were a total of 1662 results for your search.
Limon G, Fournié G, Lewis E G, Dominguez-Salas P, Leyton-Michovich D, Gonzales-Gustavson E A, Gonzalez A E, Cabezas A H, Pinto J, Rushton J, Guitian J (2017)

Using mixed methods to assess food security and coping strategies: a case study among smallholders in the Andean region

Food Security 9 (5), 1019-1040


International organizations and national governments in resource-scarce settings regularly support programs for the control of animal diseases with the aim of improving smallholder food security. However, the impact of such disease control programs on smallholder food security remains unclear. Mixed methods designs that integrate the collection, analysis and interpretation of qualitative and quantitative data in a single study, are increasingly being used to achieve deeper explorations of complex topics. We propose a mixed methods design to assess the four pillars of food security and coping strategies among smallholders. The methodology is illustrated with a case study in the context of a transnational program for the control of Foot and Mouth Disease (FMD) in the Andean region, involving interviews with 632 smallholders in three countries. Quantitative data were analysed using multivariate analysis to describe smallholders’ profiles. Food Consumption Score (FCS) was calculated for each household. The qualitative phase involved developing themes to characterise these smallholders’ experiences using Thematic Analysis. Food acquisition capacity and coping strategies varied greatly across smallholders. Only nine (1.4%) of households had a FCS below the acceptable threshold, however, food stability was compromised across study areas. Household production, financial capacity, household demographics and food prices were the main factors influencing variation in food consumption. The case study presented here illustrates the use of a mixed methods approach to assess the four dimensions of food security and categorise key differences across smallholders during a single visit.

Meng X Y, Luo Y Z, Anwar M N, Sun Y, Gao Y, Zhang H W, Munir M, Qiu H J (2017)

Long non-coding RNAs: emerging and versatile regulators in host-virus interactions

Frontiers in Immunology 8, 1663


Long non-coding RNAs (lncRNAs) are a class of non-protein-coding RNA molecules, which are involved in various biological processes, including chromatin modification, cell differentiation, pre-mRNA transcription and splicing, protein translation, etc. During the last decade, increasing evidence has suggested the involvement of lncRNAs in both immune and antiviral responses as positive or negative regulators. The immunity-associated lncRNAs modulate diverse and multilayered immune checkpoints, including activation or repression of innate immune signaling components, such as interleukin (IL)-8, IL-10, retinoic acid inducible gene I, toll-like receptors 1, 3, and 8, and interferon (IFN) regulatory factor 7, transcriptional regulation of various IFN-stimulated genes, and initiation of the cell apoptosis pathways. Additionally, some virus-encoded lncRNAs facilitate viral replication through individually or synergistically inhibiting the host antiviral responses or regulating multiple steps of the virus life cycle. Moreover, some viruses are reported to hijack host-encoded lncRNAs to establish persistent infections. Based on these amazing discoveries, lncRNAs are an emerging hotspot in host-virus interactions. In this review, we summarized the current findings of the hostor virus-encoded lncRNAs and the underlying mechanisms, discussed their impacts on immune responses and viral replication, and highlighted their critical roles in host-virus interactions.

Hu B, Gonzales J L, Gubbins S (2017)

Bayesian inference of epidemiological parameters from transmission experiments

Scientific Reports 7 (1), 16774


Epidemiological parameters for livestock diseases are often inferred from transmission experiments. However, there are several limitations inherent to the design of such experiments that limits the precision of parameter estimates. In particular, infection times and latent periods cannot be directly observed and infectious periods may also be censored. We present a Bayesian framework accounting for these features directly and employ Markov chain Monte Carlo techniques to provide robust inferences and quantify the uncertainty in our estimates. We describe the transmission dynamics using a susceptible-exposed-infectious-removed compartmental model, with gamma-distributed transition times. We then fit the model to published data from transmission experiments for foot-and-mouth disease virus (FMDV) and African swine fever virus (ASFV). Where the previous analyses of these data made various assumptions on the unobserved processes in order to draw inferences, our Bayesian approach includes the unobserved infection times and latent periods and quantifies them along with all other model parameters. Drawing inferences about infection times helps identify who infected whom and can also provide insights into transmission mechanisms. Furthermore, we are able to use our models to measure the difference between the latent periods of inoculated and contact-challenged animals and to quantify the effect vaccination has on transmission.

Gordon S J G, Bolwell C, Rogers C W, Musuka G, Kelly P, Guthrie A, Mellor P S, Hamblin C (2017)

A serosurvey of bluetongue and epizootic haemorrhagic disease in a convenience sample of sheep and cattle herds in Zimbabwe

Onderstepoort Journal of Veterinary Research 84 (1), a1505


A convenience sample of sheep and cattle herds around the cities of Harare, Kwekwe and Bulawayo, located in the Highveld region of Zimbabwe, was used to estimate the sero-prevalence and sero-incidence of bluetongue virus (BTV) and epizootic haemorrhagic disease virus (EHDV) antibodies. A competitive enzyme-linked immunosorbent assay was used to identify serum antibodies against BTV and EHDV across three rainy seasons. The median sero-prevalence of BTV and EHDV antibodies in cattle was 62% (interquartile range [IQR]: 30-89) and 56% (IQR: 5-77), respectively. In sheep, the median sero-prevalence of BTV and EHDV was 41% (IQR: 19-63) and 0% (IQR: 0-21), respectively. Median sero-incidences of BTV and EHDV antibodies in cattle of 43% (IQR: 22-67) and 27% (IQR: 9-57) respectively were recorded. The median sero-incidence of BTV in sheep was 14% (IQR: 6-23). Based on these preliminary findings, animal health workers in Zimbabwe should continue to monitor the exposure rates of cattle and sheep to BTV and consider the possibility of strains emerging with increased pathogenicity. There are no previous published reports of antibodies against EHDV in Zimbabwe so the possibility of epizootic haemorrhagic disease existing in domestic livestock should now be considered by Zimbabwean animal health officials. Seroconversions to BTV and EHDV occurred predominantly at the end of each rainy season (March and April), which generally corresponds to high numbers of the Culicoides vectors. BTV isolations were made from three individual cows in two of the sentinel herds and all three were identified as serotype 3. This is the first time BTV serotype 3 has been recorded in Zimbabwe, although its presence in neighbouring South Africa is well documented.

Ahmed Z, Pauszek S J, Ludi A, LaRocco M, Khan E-u-H, Afzal M, Arshed M J, Farooq U, Arzt J, Bertram M, Brito B, Naeem K, Abubakar M, Rodriguez L L (2017)

Genetic diversity and comparison of diagnostic tests for characterization of foot-and-mouth disease virus strains from Pakistan 2008 - 2012

Transboundary and Emerging Diseases early view,


We report the laboratory analysis of 125 clinical samples from suspected cases of foot-and-mouth disease (FMD) in cattle and Asian buffalo collected in Pakistan between 2008 and 2012. Of these samples, 89 were found to contain viral RNA by rRT-PCR, of which 88 were also found to contain infectious FMD virus (FMDV) by virus isolation (VI), with strong correlation between these tests (? = 0.96). Samples that were VI-positive were serotyped by antigen detection ELISA (Ag-ELISA) and VP1 sequence acquisition and analysis. Sequence data identified FMDV serotypes A (n = 13), O (n = 36) and Asia-1 (n = 41), including three samples from which both serotypes Asia-1 and O were detected. Serotype A viruses were classified within three different Iran-05 sublineages: HER-10, FAR-11 and ESF-10. All serotype Asia-1 were within Group VII (Sindh-08 lineage), in a genetic clade that differs from viruses isolated prior to 2010. All serotypes O were classified as PanAsia-2 within two different sublineages: ANT-10 and BAL-09. Using VP1 sequencing as the gold standard for serotype determination, the overall sensitivity of Ag-ELISA to correctly determine serotype was 74%, and serotype-specific sensitivity was 8% for serotype A, 88% for Asia-1 and 89% for O. Serotype-specific specificity was 100% for serotype A, 93% for Asia-1 and 94% for O. Interestingly, 12 of 13 serotype A viruses were not detected by Ag-ELISA. This study confirms earlier accounts of regional genetic diversity of FMDV in Pakistan and highlights the importance of continued validation of diagnostic tests for rapidly evolving pathogens such as FMDV.

Rao P P, Hegde N R, Singh K P, Putty K, Hemadri D, Maan N S, Reddy Y N, Maan S, Mertens P P C (2017)

Bluetongue: Aetiology, Epidemiology, Pathogenesis, Diagnosis and Control (chapter 1)

In: Bayry, J (ed.) Emerging and Re-emerging Infectious Diseases of Livestock, Springer , 3-54


Bluetongue (BT) is an emerging and re-emerging vector-borne viral disease of domestic and wild ruminants, caused by viruses classified within the species bluetongue virus (BTV), genus Orbivirus, family Reoviridae. There are 27 recognized serotypes of BTV (with two more recently discovered ‘putative’ serotypes) as well as multiple geographic variants (topotypes) and many different strains and genotypes, most of which are transmitted between their vertebrate hosts by certain ‘vector-competent’ biting midges of the genus Culicoides. Bluetongue is an economically important transboundary disease that is listed by the World Organisation for Animal Health, reflecting the ability of BTV to (a) infect all ruminants, including important domesticated species; (b) cause severe disease, with high fatality rates in sheep and certain species of deer; and (c) cause large economic losses due to fatalities, reduced productivity and reproductive performance, animal movement and trade restrictions and surveillance and control strategies (including vaccination). The plurality of BTV serotypes and strains, the involvement of multiple host and vector species and the potential for (re)introduction of exotic BTV strains make the control and eradication of BT very complex and difficult to achieve. In this chapter, we review the current understanding of BTV biology, bluetongue epidemiology, pathogenesis and pathology, laboratory techniques to diagnose the disease and identify the virus, experimental animal models to study the disease and to evaluate vaccines and methods for the control and/or eradication of bluetongue.

Howson E L A, Soldan A, Webster K, Beer M, Zientara S, Belák S, Sánchez-Vizcaíno J M, Van Borm S, King D P, Fowler V L (2017)

Technological advances in veterinary diagnostics: opportunities to deploy rapid decentralised tests to detect pathogens affecting livestock.

Revue Scientifique et Technique 36 (2), 479-498
Publisher’s version:


Sustainable food production capable of feeding a growing human population is a significant global challenge, and is a priority encompassed within the United Nations Millennium Development Goals to ‘eradicate extreme poverty and hunger’. Infectious diseases reduce the productivity of farm animals, and the globalised trade of animals and their products increases the threat of disease incursion. Accurate and rapid diagnostic tests are an essential component of contingency plans to detect, control and eradicate such diseases. Diagnosis involves a ‘pipeline’ that normally starts with clinical suspicion, followed by collecting samples, transporting specimens to a centralised laboratory setting (e.g. national/international Reference Laboratories), analysing these samples using a range of diagnostic tests and reporting the results. However, the transport of specimens from the field to the laboratory can be a lengthy process that can delay critical decision-making and severely affect the quality of the samples. This important limitation of centralised diagnostic testing has motivated the development of tools for rapid, simple detection of livestock pathogens. Recent advances in the development of technologies for personalised human medicine have motivated the development of prototype diagnostic tests for a wide selection of diseases of livestock. However, many of these tests are not yet used routinely or are commercially available. This paper critically reviews the most promising examples of such assays, and highlights the challenges that remain to transition these tests from applied research and development into routine use.

Newman J, Asfor A S, Berryman S, Jackson T, Curry S, Tuthill T J (2017)

The cellular chaperone heat shock protein 90 is required for foot-and-mouth disease virus capsid precursor processing and assembly of capsid pentamers

Journal of Virology early view,


Productive picornavirus infection requires the hijack of host cell pathways to aid with the different stages of virus entry, synthesis of the viral polyprotein and viral genome replication. Many picornaviruses, including foot-and-mouth disease virus (FMDV), assemble capsids via the multimerisation of several copies of a single capsid precursor protein into a pentameric subunit which further encapsidates the RNA. Pentamer formation is preceded by co- and post-translational modification of the capsid precursor (P1-2A) by viral and cellular enzymes, and the subsequent rearrangement of P1-2A into a structure amenable to pentamer formation. We have developed a cell-free system to study FMDV pentamer assembly using recombinantly expressed FMDV capsid precursor and 3C protease. Using this assay, we have shown that two structurally different inhibitors of the cellular chaperone heat shock protein 90 (hsp90), impeded FMDV capsid precursor processing and subsequent pentamer formation. Treatment of FMDV permissive cells with the hsp90 inhibitor prior to infection reduced the endpoint titre by more than ten-fold while not affecting the activity of a sub-genomic replicon indicating that translation and replication of viral RNA were unaffected by the drug.IMPORTANCE Foot-and-mouth disease virus (FMDV), of the Picornaviridae family is a pathogen of huge economic importance to the livestock industry due to its effect on the restriction of livestock movement and necessary control measures required following an outbreak. The study of FMDV capsid assembly, and picornavirus capsid assembly more generally, has tended to be focused upon the formation of capsids from pentameric intermediates, or the immediate co-translational modification of the capsid precursor protein. Here we describe a system to analyse the early stages of FMDV pentameric capsid intermediate assembly and demonstrate a novel requirement for the cellular chaperone hsp90 in the formation of these pentameric intermediates. We show the added complexity involved for this process to occur which could be the bases for a novel antiviral control mechanism for FMDV.

Shabbir M Z, Sohail M U, Chaudhary U N, Yaqub W, Rashid I, Saleem M H, Munir M (2017)

Genetic characterization of canine parvovirus from dogs in Pakistan

Acta Virologica 61 (2), 175-182


Canine parvoviruses (CPV) exist as antigenic variants with varying frequencies and genetic variabilities across the globe. Given the endemicity and high prevalence in Pakistan, we characterized the CPVs originating from dogs-population to elucidate viral diversity and evolution. Fecal samples from clinically diseased pups (n = 17) of different breeds and age (2-6 months) were processed for hemagglutination assay (HA), and later for partial amplification of VP2 gene sequence and amino acid analysis. A total of 11 samples (64.71%) were found positive both in hemagglutination and PCR assays. Phylogenetic and evolutionary analysis demonstrated higher genetic heterogeneity in studied strains and constituted seven clusters within the CPV-2a group, however, they shared high level of identity with Chinese strains. Further studies are necessary to elucidate genetic analysis and epidemiology of CPV variants across a wide geographical area of the country.

Mahapatra M, Upadhyaya S, Aviso S, Babu A, Hutchings G, Parida S (2017)

Selection of vaccine strains for serotype O foot-and-mouth disease viruses (2007-2012) circulating in Southeast Asia, East Asia and Far East

Vaccine 35 (51), 7147-7153


Foot-and-mouth disease (FMD) is endemic in Southeast Asia (SEA) and East Asia with circulation of multiple serotypes and multiple genotypes within each serotype of the virus. Although countries like Japan and South Korea in the Far East were free of FMD, in 2010 FMD serotype O (O/Mya-98) outbreaks were recorded and since then South Korea has experienced several FMD outbreaks despite regular vaccination. In this study a total of 85 serotype O FMD viruses (FMDV) isolated from 2007 to 2012 from SEA, East Asia and Far East were characterized by virus neutralisation tests using antisera to four existing (O/HKN/6/83, O/IND/R2/75, O/SKR/2010 and O/PanAsia-2) and one putative (O/MYA/2009) vaccine strains, and by full capsid sequencing. Serological studies revealed broad cross-reactivity with the vaccine strains; O/PanAsia-2 exhibited a good match with 95.3%, O/HKN/6/83 with 91.8%, O/IND/R2/75 with 80%, and the putative strain O/MYA/2009 with 89.4% isolates employed in this study. Similarly O/PanAsia-2 and O/IND/R2/75 vaccines showed a good match with all eight viruses belonging to O-Ind-2001d sublineage whereas the vaccines of O/Mya-98 lineage, O/MYA/2009 and O/SKR/2010 exhibited the lowest match indicating their unsuitability to protect infections from O-Ind-2001d viruses. A Bayesian analysis of the capsid sequence data indicated these circulating viruses (n?=?85) to be of either SEA or Middle East-South Asian (ME-SA) topotype. The ME-SA topotype viruses were mainly detected in Lao PDR, Vietnam, Myanmar and Thailand reflecting the trade links with the Indian subcontinent, and also within the SEA countries. Implications of these results in the context of FMD control in SEA and East Asian countries are discussed.


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