Relationship between clinical signs and transmission of an infectious disease and the implications for control

Phylodynamic analysis of foot-and-mouth disease virus evolution in Mar Chiquita, Argentina

Foot-and-mouth disease is a highly contagious disease affecting cloven-hoofed animals, resulting in considerable economic losses. Its causal agent is foot-and-mouth disease virus (FMDV), a picornavirus. Due to its error-prone replication and rapid evolution, the transmission and evolutionary dynamics of FMDV can be studied using genomic epidemiological approaches. To analyze FMDV evolution and identify possible transmission routes in an Argentinean region, field samples that tested positive for FMDV by PCR were obtained from 21 farms located in the Mar Chiquita district. Whole FMDV genome sequences were obtained by PCR amplification in seven fragments and sequencing using the Sanger technique. The genome sequences obtained from these samples were then analyzed using phylogenetic, phylogeographic, and evolutionary approaches. Three local transmission clusters were detected among the sampled viruses. The dataset was analyzed using Bayesian phylodynamic methods with appropriate coalescent and relaxed molecular clock models. The estimated mean viral evolutionary rate was 1.17 × 10- 2 substitutions/site/year. No significant differences in the rate of viral evolution were observed between farms with vaccinated animals and those with unvaccinated animals. The most recent common ancestor of the sampled sequences was dated to approximately one month before the first reported case in the outbreak. Virus transmission started in the south of the district and later dispersed to the west, and finally arrived in the east. Different transmission routes among the studied herds, such as non-replicating vectors and close contact contagion (i.e., aerosols), may be responsible for viral spread.

Spatio-temporal ditribution and transmission dynamics of sheep pox and goat pox diseases in South Wollo zone north East Ethiopia

Sheep pox (SP) and goat pox diseases (GP) are highly transmittable, malignant systemic and economically significant caused by the genus Capripoxvirus. using The spatio-temporal distribution of SP and GP outbreaks in South Wollo zone from September 2013 to December 2019 was determined retrospectively using SP and GP outbreaks report Kombolcha regional laboratory. A follow up study was also conducted from December 2019 to March 2021 to estimate the transmission parameter of SP and GP outbreaks in South Wollo zone of Kutaber district, Amhara region. Tissue samples from outbreaks in Kundi and Haroye kebele of Kutaber district were taken to confirm the outbreak by conventional polymerase chain reaction (PCR). The transmission parameters were estimated using Generalized linear model (GLM) based on stochastic Susceptible Infected and Recovered (SIR) model. In South Wollo zone, 249 SGP outbreaks were reported from 2013 to 2019. The incidence differed between months, with a highest peak in October and November and a lowest peak in February. The basic reproduction ratios (R0) of the SGP disease outbreaks were 1.84 and 3 for Haroye and Kundi kebele outbreaks, respectively. The disease is distributed throughout the zone and the investigated active outbreaks had moderate transmission between animals. Hence, it needs a great effort which focuses on the application of control measures that reduce the transmission of the disease.

Inferring transmission routes for foot-and-mouth disease virus within a cattle herd using approximate Bayesian computation

To control an outbreak of an infectious disease it is essential to understand the different routes of transmission and how they contribute to the overall spread of the pathogen. With this information, policy makers can choose the most efficient methods of detection and control during an outbreak. Here we assess the contributions of direct contact and environmental contamination to the transmission of foot-and-mouth disease virus (FMDV) in a cattle herd using an individual-based model that includes both routes. Model parameters are inferred using approximate Bayesian computation with sequential Monte Carlo sampling (ABC-SMC) applied to data from transmission experiments and the 2007 epidemic in Great Britain. This demonstrates that the parameters derived from transmission experiments are applicable to outbreaks in the field, at least for closely related strains. Under the assumptions made in the model we show that environmental transmission likely contributes a majority of infections within a herd during an outbreak, although there is a lot of variation between simulated outbreaks. The accumulation of environmental contamination not only causes infections within a farm, but also has the potential to spread between farms via fomites. We also demonstrate the importance and effectiveness of rapid detection of infected farms in reducing transmission between farms, whether via direct contact or the environment.

Quantifying the relationship between within-host dynamics and transmission for viral diseases of livestock

Understanding the population dynamics of an infectious disease requires linking within-host dynamics and between-host transmission in a quantitative manner, but this is seldom done in practice. Here a simple phenomenological model for viral dynamics within a host is linked to between-host transmission by assuming that the probability of transmission is related to log viral titre. Data from transmission experiments for two viral diseases of livestock, foot-and-mouth disease virus in cattle and swine influenza virus in pigs, are used to parametrize the model and, importantly, test the underlying assumptions. The model allows the relationship between within-host parameters and transmission to be determined explicitly through their influence on the reproduction number and generation time. Furthermore, these critical within-host parameters (time and level of peak titre, viral growth and clearance rates) can be computed from more complex within-host models, raising the possibility of assessing the impact of within-host processes on between-host transmission in a more detailed quantitative manner.

Laboratory testing and on-site storage are successful at mitigating the risk of release of foot-and-mouth disease virus via production of bull semen in the USA

Thousands of frozen bovine semen doses are produced daily in the US for domestic use. An incursion of foot-and-mouth disease (FMD) in the country would pose strong challenges to the movements of animals and animal products between premises. Secure supply plans require an estimation of the risk associated with target commodities and the effectiveness of mitigation measures. This study presents the results of a quantitative assessment of the risk of release of FMD virus from five of the largest commercial bull studs in the US via contaminated frozen processed semen. The methodology from a previous study was adapted to better fit the US production system and includes more recent data. Two models were combined, a deterministic compartmental model of FMD transmission and a stochastic risk assessment model. The compartmental model simulated an FMD outbreak within a collection facility, following the introduction of a latent-infected bull. The risk of release was defined as the annual likelihood of releasing at least one frozen semen batch, defined as the total amount of semen collected from a single bull on a given collection day, containing viable FMD virus. A scenario tree was built using nine steps leading from the collection to the release of a contaminated batch from a given facility. The first step, the annual probability of an FMD outbreak in a given facility, was modeled using an empirical distribution fitted to incidence data predicted by five models published between 2012 and 2022. An extra step was added to the previously published risk pathway, to account for routine serological or virological surveillance within facilities. The results showed that the mitigation measures included in the assessment were effective at reducing the risk of release. The median annual risk of release from the five facilities was estimated at less than 2 in 10 billion (1.5 x 10-10) in the scenario including a 30-day storage, routine genome detection assays performed every two weeks and RT-PCR testing of the semen. In this scenario, there was a 95% chance that the risk of release would be lower than 0.00041. This work provides strong support to the industry for improving their response plans to an incursion of FMD virus in the US.

The heterogeneous herd: Drivers of close-contact variation in African buffalo and implications for pathogen invasion

Many infectious pathogens are shared through social interactions, and examining host connectivity has offered valuable insights for understanding patterns of pathogen transmission across wildlife species. African buffalo are social ungulates and important reservoirs of directly-transmitted pathogens that impact numerous wildlife and livestock species. Here, we analyzed African buffalo social networks to quantify variation in close contacts, examined drivers of contact heterogeneity, and investigated how the observed contact patterns affect pathogen invasion likelihoods for a wild social ungulate. We collected continuous association data using proximity collars and sampled host traits approximately every 2 months during a 15-month study period in Kruger National Park, South Africa. Although the observed herd was well connected, with most individuals contacting each other during each bimonthly interval, our analyses revealed striking heterogeneity in close-contact associations among herd members. Network analysis showed that individual connectivity was stable over time and that individual age, sex, reproductive status, and pairwise genetic relatedness were important predictors of buffalo connectivity. Calves were the most connected members of the herd, and adult males were the least connected. These findings highlight the role susceptible calves may play in the transmission of pathogens within the herd. We also demonstrate that, at time scales relevant to infectious pathogens found in nature, the observed level of connectivity affects pathogen invasion likelihoods for a wide range of infectious periods and transmissibilities. Ultimately, our study identifies key predictors of social connectivity in a social ungulate and illustrates how contact heterogeneity, even within a highly connected herd, can shape pathogen invasion likelihoods.

An exploration of within-herd dynamics of a transboundary livestock disease: A foot and mouth disease case study

Transboundary livestock diseases are a high priority for policy makers because of the serious economic burdens associated with infection. In order to make well informed preparedness and response plans, policy makers often utilize mathematical models to understand possible outcomes of different control strategies and outbreak scenarios. Many of these models focus on the transmission between herds and the overall trajectory of the outbreak. While the course of infection within herds has not been the focus of the majority of models, a thorough understanding of within-herd dynamics can provide valuable insight into a disease system by providing information on herd-level biological properties of the infection, which can be used to inform decision making in both endemic and outbreak settings and to inform larger between-herd models. In this study, we develop three stochastic simulation models to study within-herd foot and mouth disease dynamics and the implications of different empirical data-based assumptions about the timing of the onset of infectiousness and clinical signs. We also study the influence of herd size and the proportion of the herd that is initially infected on the outcome of the infection. We find that increasing herd size increases the duration of infectiousness and that the size of the herd plays a more significant role in determining this duration than the number of initially infected cattle in that herd. We also find that the assumptions made regarding the onset of infectiousness and clinical signs, which are based on contradictory empirical findings, can result in the predictions about when infection would be detectable differing by several days. Therefore, the disease progression used to characterize the course of infection in a single bovine host could have significant implications for determining when herds can be detected and subsequently controlled; the timing of which could influence the overall predicted trajectory of outbreaks.

Decision tree risk analysis for FMD outbreak prevention in Egyptian feedlots

Foot and Mouth Disease (FMD) is one of the most contagious and economically influential viral diseases on animal health and productivity. Introduction of newly purchased animals to beef farms constitutes a greater risk for the FMD outbreaks in endemic countries. Physical examination of newly purchased animals in live animal markets and/or at the receiving farm, and the timing of preventative FMD vaccination may reduce the risk of FMD outbreaks under endemic conditions. Small (< 50 animals) and medium (50-500 animals) sized beef farms in Egypt constitute more than 60% of the country's beef industry where protocols for receiving newly purchased animals vary widely between farms. The current risk analysis aimed to build a decision tree model to reduce FMD outbreaks associated with introduction of replacement cattle on Egypt's medium sized beef farms. Management practices explored were the use of physical examinations and FMD vaccination and their timing for replacements with the goal of reducing losses due to FMD outbreaks. A producer survey revealed that more than 50% of the study herds relied on live animal markets as a source for replacements and reported more FMD outbreaks (P-value=0.09), FMD herd morbidity > 50% (p-value=0.05), and weight loss > 15 kg/animal in FMD clinical cases (P-value=0.01) in comparison to herds that received replacements from other farms, imported, or purchased from small stakeholders. More than 70% of the surveyed farms received replacements ≤ 1year old and reported significantly higher FMD outbreaks (P-value=0.02) in comparison to farms that received older animals. More than 80% of the surveyed farms performed physical examination of newly purchased animals before arrival at their premises. Of the surveyed farms, 73% reported FMD outbreaks with 67% of the outbreaks being reported during the Fall and Winter seasons. The decision tree identified physical examination of newly purchased animals prior to arrival and mixing with a premises beef herd followed by vaccination against FMD upon arrival as the intervention resulting in the lowest probability of FMD outbreak (8.9%). In contrast, herds that did not perform physical examination and delay the FMD vaccination for two or more weeks had the highest probability of FMD outbreaks (33.5%).

Silver nanoparticles inhibit goatpox virus replication

No effective drugs against goatpox virus (GTPV) exist despite the high morbidity and mortality (up to 100%) caused by this virus. In this study, the antiviral activity of silver nanoparticles (AgNPs) against GTPV, a member of the genus Capripoxvirus, was evaluated. Piper betle leaf extract was used as a reducing agent during the biological synthesis of AgNPs from silver nitrate. The AgNPs were characterized using ultraviolet/visible (UV/vis) absorption spectroscopy, X-ray diffraction (XRD), Fourier transform infrared spectroscopy (FTIR), and transmission electron microscopy (TEM). AgNPs were tested at different concentrations as antiviral agents against GTPV, and the reduction in the median tissue culture infectious dose (TCID₅₀/mL) was used to quantitate antiviral activity. AgNPs caused significant inhibition of GTPV replication by preventing virus entry into the host cell. Pre-treatment of cells with AgNPs caused a slight reduction in infectivity, but this did not significantly correlate with the effect on virus attachment. AgNPs also appeared to significantly reduce the viral genome copy number. This study demonstrates that the AgNPs are capable of inhibiting GTPV replication in vitro.

Viral dynamics and immune responses to foot-and-mouth disease virus in African buffalo (Syncerus caffer)

Foot-and-mouth disease (FMD) is one of the most important livestock diseases restricting international trade. While African buffalo (Syncerus caffer) act as the main wildlife reservoir, viral and immune response dynamics during FMD virus acute infection have not been described before in this species. We used experimental needle inoculation and contact infections with three Southern African Territories serotypes to assess clinical, virological and immunological dynamics for thirty days post infection. Clinical FMD in the needle inoculated buffalo was mild and characterised by pyrexia. Despite the absence of generalised vesicles, all contact animals were readily infected with their respective serotypes within the first two to nine days after being mixed with needle challenged buffalo. Irrespective of the route of infection or serotype, there were positive associations between the viral loads in blood and the induction of host innate pro-inflammatory cytokines and acute phase proteins. Viral loads in blood and tonsil swabs were tightly correlated during the acute phase of the infection, however, viraemia significantly declined after a peak at four days post-infection (dpi), which correlated with the presence of detectable neutralising antibodies. In contrast, infectious virus was isolated in the tonsil swabs until the last sampling point (30 dpi) in most animals. The pattern of virus detection in serum and tonsil swabs was similar for all three serotypes in the direct challenged and contact challenged animals. We have demonstrated for the first time that African buffalo are indeed systemically affected by FMD virus and clinical FMD in buffalo is characterized by a transient pyrexia. Despite the lack of FMD lesions, infection of African buffalo was characterised by high viral loads in blood and oropharynx, rapid and strong host innate and adaptive immune responses and high transmissibility.

Carboxamide and N-alkylcarboxamide additives can greatly reduce non specific amplification in Loop-Mediated Isothermal Amplification for Foot-and-Mouth disease Virus (FMDV) using Bst 3.0 polymerase

Foot-and-Mouth disease Virus (FMDV) is a highly infectious RNA virus that causes severe economic losses in cloven-hoofed animals. Early detection is needed to control epidemics, and loop-mediated isothermal amplification (LAMP) can be performed using inexpensive and commonly available equipment with a short processing time, but existing assays for FMDV still require an additional reverse transcriptase enzyme to convert RNA to cDNA prior to amplification. We sought to develop a novel RT-LAMP assay for FMDV with carboxamide and N-alkylcarboxamide additives to reduce non-specific amplification in combination with an improved commercially available polymerase (Bst 3.0) with efficient reverse transcriptase activity. SYBR Green I dye was used for sensitive visual detection of amplification products from our LAMP assay within 15 min without the need for a colorimeter. In the presence of a carefully titrated mixture of carboxamide and N-alkylcarboxamide additives, longer reactions of up to 1 h were also possible on both RNA and cDNA without the appearance of non-specific amplification products, thereby increasing the potential robustness of the assay by allowing a greater window of time in which to detect weak positives.

shRNA transgenic swine display resistance to infection with the foot-and-mouth disease virus

Foot-and-mouth disease virus (FMDV) is one of the most important animal pathogens in the world. FMDV naturally infects swine, cattle, and other cloven-hoofed animals. FMD is not adequately controlled by vaccination. An alternative strategy is to develop swine that are genetically resistant to infection. Here, we generated FMDV-specific shRNA transgenic cells targeting either nonstructural protein 2B or polymerase 3D of FMDV. The shRNA-positive transgenic cells displayed significantly lower viral production than that of the control cells after infection with FMDV (P < 0.05). Twenty-three transgenic cloned swine (TGCS) and nine non-transgenic cloned swine (Non-TGCS) were produced by somatic cell nuclear transfer (SCNT). In the FMDV challenge study, one TGCS was completely protected, no clinical signs, no viremia and no viral RNA in the tissues, no non-structural antibody response, another one TGCS swine recovered after showing clinical signs for two days, whereas all of the normal control swine (NS) and Non-TGCS developed typical clinical signs, viremia and viral RNA was determined in the tissues, the non-structural antibody was determined, and one Non-TGCS swine died. The viral RNA load in the blood and tissues of the TGCS was reduced in both challenge doses. These results indicated that the TGCS displayed resistance to the FMDV infection. Immune cells, including CD3⁺, CD4⁺, CD8⁺, CD21⁺, and CD172⁺ cells, and the production of IFN-γ were analyzed, there were no significant differences observed between the TGCS and NS or Non-TGCS, suggesting that the FMDV resistance may be mainly derived from the RNAi-based antiviral pathway. Our work provides a foundation for a breeding approach to preventing infectious disease in swine.

Temporal-spatial analysis of an age-space structured foot-and-mouth disease model with Dirichlet boundary condition

Foot-and-mouth disease is a highly contagious and economically devastating disease of cloven-hoofed animals. The historic occurrences of foot-and-mouth diseases led to huge economic losses and seriously threatened the livestock food security. In this paper, a novel age-space diffusive foot-and-mouth disease model with a Dirichlet boundary condition, coupling the virus-to-animals and animals-to-animals transmission routes, has been proposed. The basic reproduction number R₀ is defined as the spectral radius of a next generation operator K, which is calculated in an explicit form, and it serves as a vital value determining whether or not the disease persists. The existence of a unique trivial nonconstant steady state and at least one nonconstant endemic steady state of the system is established by a smart Lyapunov functional and the Kronoselskii fixed point theorem. An application to a foot-and-mouth outbreak in China is presented. The findings suggest that increasing the movements and disinfection of the environment for animals apparently reduce the risk of a foot-and-mouth infection.

Interventions targeting non-symptomatic cases can be important to prevent local outbreaks: SARS-CoV-2 as a case study

During infectious disease epidemics, an important question is whether cases travelling to new locations will trigger local outbreaks. The risk of this occurring depends on the transmissibility of the pathogen, the susceptibility of the host population and, crucially, the effectiveness of surveillance in detecting cases and preventing onward spread. For many pathogens, transmission from pre-symptomatic and/or asymptomatic (together referred to as non-symptomatic) infectious hosts can occur, making effective surveillance challenging. Here, by using SARS-CoV-2 as a case study, we show how the risk of local outbreaks can be assessed when non-symptomatic transmission can occur. We construct a branching process model that includes non-symptomatic transmission and explore the effects of interventions targeting non-symptomatic or symptomatic hosts when surveillance resources are limited. We consider whether the greatest reductions in local outbreak risks are achieved by increasing surveillance and control targeting non-symptomatic or symptomatic cases, or a combination of both. We find that seeking to increase surveillance of symptomatic hosts alone is typically not the optimal strategy for reducing outbreak risks. Adopting a strategy that combines an enhancement of surveillance of symptomatic cases with efforts to find and isolate non-symptomatic infected hosts leads to the largest reduction in the probability that imported cases will initiate a local outbreak.

Quantifying and Modeling the Acquisition and Retention of Lumpy Skin Disease Virus by Hematophagus Insects Reveals Clinically but Not Subclinically Affected Cattle Are Promoters of Viral Transmission and Key Targets for Control of Disease Outbreaks

Lumpy skin disease virus (LSDV) causes a severe systemic disease characterized by cutaneous nodules in cattle. LSDV is a rapidly emerging pathogen, having spread since 2012 into Europe and Russia and across Asia.

Lumpy skin disease virus (LSDV) is a vector-transmitted poxvirus that causes disease in cattle. Vector species involved in LSDV transmission and their ability to acquire and transmit the virus are poorly characterized. Using a highly representative bovine experimental model of lumpy skin disease, we fed four model vector species (Aedes aegypti, Culex quinquefasciatus, Stomoxys calcitrans, and Culicoides nubeculosus) on LSDV-inoculated cattle in order to examine their acquisition and retention of LSDV. Subclinical disease was a more common outcome than clinical disease in the inoculated cattle. Importantly, the probability of vectors acquiring LSDV from a subclinical animal (0.006) was very low compared with that from a clinical animal (0.23), meaning an insect feeding on a subclinical animal was 97% less likely to acquire LSDV than one feeding on a clinical animal. All four potential vector species studied acquired LSDV from the host at a similar rate, but Aedes aegypti and Stomoxys calcitrans retained the virus for a longer time, up to 8 days. There was no evidence of virus replication in the vector, consistent with mechanical rather than biological transmission. The parameters obtained in this study were combined with data from studies of LSDV transmission and vector life history parameters to determine the basic reproduction number of LSDV in cattle mediated by each of the model species. This reproduction number was highest for Stomoxys calcitrans (19.1), followed by C. nubeculosus (7.1) and Ae. aegypti (2.4), indicating that these three species are potentially efficient transmitters of LSDV; this information can be used to inform LSD control programs.

IMPORTANCE Lumpy skin disease virus (LSDV) causes a severe systemic disease characterized by cutaneous nodules in cattle. LSDV is a rapidly emerging pathogen, having spread since 2012 into Europe and Russia and across Asia. The vector-borne nature of LSDV transmission is believed to have promoted this rapid geographic spread of the virus; however, a lack of quantitative evidence about LSDV transmission has hampered effective control of the disease during the current epidemic. Our research shows subclinical cattle play little part in virus transmission relative to clinical cattle and reveals a low probability of virus acquisition by insects at the preclinical stage. We have also calculated the reproductive number of different insect species, therefore identifying efficient transmitters of LSDV. This information is of utmost importance, as it will help to define epidemiological control measures during LSDV epidemics and of particular consequence in resource-poor regions where LSD vaccination may be less than adequate.

The economics of the COVID-19 pandemic: an assessment

The COVID-19 pandemic has created both a medical crisis and an economic crisis. As others have noted, we face challenges just as big as those in the Spanish Flu Pandemic and the Great Depression—all at once. The tasks facing policy-makers are extraordinary. Many new kinds of intervention are urgently required. This issue of the Oxford Review of Economic Policy has two objectives. The first is to explore these new interventions: evaluating their use, suggesting how they might be improved, and proposing alternatives. The second is to show that the challenges facing us are global and will require international cooperation if they are to be dealt with effectively. This short introductory essay positions the papers in the issue within an overall conceptual framework, with the aim of telling an overarching story about the pandemic.

Quantifying the Transmission of Foot-and-Mouth Disease Virus in Cattle via a Contaminated Environment

Effective control of a disease relies on comprehensive understanding of how transmission occurs, in order to design and apply effective control measures. Foot-and-mouth disease virus (FMDV) is primarily spread by direct contact between infected and naive individuals, although the high levels of virus shed by infected animals mean that virus can also be spread through contact with contaminated environments. Using a series of transmission experiments, we demonstrate that environmental transmission alone would be sufficient to sustain an outbreak. Key observations include that a risk of transmission exists before clinical signs of foot-and-mouth disease (FMD) are apparent in cattle and that survival of virus in the environment extends the transmission risk period. This study highlights the role a contaminated environment can play in the transmission of FMDV and presents approaches that can also be applied to study the transmission of other pathogens that are able to survive in the environment.

Indirect transmission via a contaminated environment can occur for a number of pathogens, even those typically thought of as being directly transmitted, such as influenza virus, norovirus, bovine tuberculosis, or foot-and-mouth disease virus (FMDV). Indirect transmission facilitates spread from multiple sources beyond the infectious host, complicating the epidemiology and control of these diseases. This study carried out a series of transmission experiments to determine the dose-response relationship between environmental contamination and transmission of FMDV in cattle from measurements of viral shedding and rates of environmental contamination and survival. Seven out of ten indirect exposures resulted in successful transmission. The basic reproduction number for environmental transmission of FMDV in this experimental setting was estimated at 1.65, indicating that environmental transmission alone could sustain an outbreak. Importantly, detection of virus in the environment prior to the appearance of clinical signs in infected cattle and successful transmission from these environments highlights there is a risk of environmental transmission even before foot-and-mouth disease (FMD) is clinically apparent in cattle. Estimated viral decay rates suggest that FMDV remained viable in this environment for up to 14 days, emphasizing the requirement for stringent biosecurity procedures following outbreaks of FMD and the design of control measures that reflect the biology of a pathogen.

Transmission network reconstruction for foot-and-mouth disease outbreaks incorporating farm-level covariates

Transmission network modelling to infer ‘who infected whom’ in infectious disease outbreaks is a highly active area of research. Outbreaks of foot-and-mouth disease have been a key focus of transmission network models that integrate genomic and epidemiological data. The aim of this study was to extend Lau’s systematic Bayesian inference framework to incorporate additional parameters representing predominant species and numbers of animals held on a farm. Lau’s Bayesian Markov chain Monte Carlo algorithm was reformulated, verified and pseudo-validated on 100 simulated outbreaks populated with demographic data Japan and Australia. The modified model was then implemented on genomic and epidemiological data from the 2010 outbreak of foot-and-mouth disease in Japan, and outputs compared to those from the SCOTTI model implemented in BEAST2. The modified model achieved improvements in overall accuracy when tested on the simulated outbreaks. When implemented on the actual outbreak data from Japan, infected farms that held predominantly pigs were estimated to have five times the transmissibility of infected cattle farms and be 49% less susceptible. The farm-level incubation period was 1 day shorter than the latent period, the timing of the seeding of the outbreak in Japan was inferred, as were key linkages between clusters and features of farms involved in widespread dissemination of this outbreak. To improve accessibility the modified model has been implemented as the R package ‘BORIS’ for use in future outbreaks.

Duration of Contagion of Foot-And-Mouth Disease Virus in Infected Live Pigs and Carcasses

Data-driven modeling of incursions of high-consequence, transboundary pathogens of animals is a critical component of veterinary preparedness. However, simplifying assumptions and excessive use of proxy measures to compensate for gaps in available data may compromise modeled outcomes. The current investigation was prospectively designed to address two major gaps in current knowledge of foot-and-mouth disease virus (FMDV) pathogenesis in pigs: the end (duration) of the infectious period and the viability of FMDV in decaying carcasses. By serial exposure of sentinel groups of pigs to the same group of donor pigs infected by FMDV A24 Cruzeiro, it was demonstrated that infected pigs transmitted disease at 10 days post infection (dpi), but not at 15 dpi. Assuming a latent period of 1 day, this would result in a conservative estimate of an infectious duration of 9 days, which is considerably longer than suggested by a previous report from an experiment performed in cattle. Airborne contagion was diminished within two days of removal of infected pigs from isolation rooms. FMDV in muscle was inactivated within 7 days in carcasses stored at 4^oC. By contrast, FMDV infectivity in vesicle epithelium harvested from intact carcasses stored under similar conditions remained remarkably high until the study termination at 11 weeks post mortem. The output from this study consists of experimentally determined data on contagion associated with FMDV-infected pigs. This information may be utilized to update parameterization of models used for foot-and-mouth disease outbreak simulations involving areas of substantial pig production.

Linking longitudinal and cross-sectional biomarker data to understand host-pathogen dynamics: Leptospira in California sea lions (Zalophus californianus) as a case study

Confronted with the challenge of understanding population-level processes, disease ecologists and epidemiologists often simplify quantitative data into distinct physiological states (e.g. susceptible, exposed, infected, recovered). However, data defining these states often fall along a spectrum rather than into clear categories. Hence, the host-pathogen relationship is more accurately defined using quantitative data, often integrating multiple diagnostic measures, just as clinicians do to assess their patients. We use quantitative data on a major neglected tropical disease (Leptospira interrogans) in California sea lions (Zalophus californianus) to improve individual-level and population-level understanding of this Leptospira reservoir system. We create a "host-pathogen space" by mapping multiple biomarkers of infection (e.g. serum antibodies, pathogen DNA) and disease state (e.g. serum chemistry values) from 13 longitudinally sampled, severely ill individuals to characterize changes in these values through time. Data from these individuals describe a clear, unidirectional trajectory of disease and recovery within this host-pathogen space. Remarkably, this trajectory also captures the broad patterns in larger cross-sectional datasets of 1456 wild sea lions in all states of health but sampled only once. Our framework enables us to determine an individual's location in their time-course since initial infection, and to visualize the full range of clinical states and antibody responses induced by pathogen exposure. We identify predictive relationships between biomarkers and outcomes such as survival and pathogen shedding, and use these to impute values for missing data, thus increasing the size of the useable dataset. Mapping the host-pathogen space using quantitative biomarker data enables more nuanced understanding of an individual's time course of infection, duration of immunity, and probability of being infectious. Such maps also make efficient use of limited data for rare or poorly understood diseases, by providing a means to rapidly assess the range and extent of potential clinical and immunological profiles. These approaches yield benefits for clinicians needing to triage patients, prevent transmission, and assess immunity, and for disease ecologists or epidemiologists working to develop appropriate risk management strategies to reduce transmission risk on a population scale (e.g. model parameterization using more accurate estimates of duration of immunity and infectiousness) and to assess health impacts on a population scale.

Transmission dynamics of foot and mouth disease in selected outbreak areas of northwest Ethiopia

Foot and mouth disease (FMD) is a highly contagious and economically important disease of cloven-hoofed animals, which is endemic in Ethiopia. An outbreak follow-up study was undertaken to quantify the transmission parameters of FMD in the crop-livestock mixed (CLM) system and commercial dairy farms in selected areas of northwest Ethiopia. The transmission parameters were quantified using a generalised linear model (GLM) based on a susceptible-infectious-recovered (SIR) epidemic model. The per day average transmission rate between animals was 0.26 (95% CI 0.22-0.32) and 0.33 (95% CI 0.21-0.57) in the CLM system and in the commercial dairy farms, respectively. The average basic reproduction ratio of FMD was 1.68 (95% CI 1.42-2.07) in the CLM system and 1.98 (95% CI 1.26-3.42) in the commercial dairy farms. The medium per day transmission rate and moderate basic reproduction ratio observed in this study indicated that a vaccination coverage needed to stop transmission of the disease in these populations might not be very high.

Into the Deep (Sequence) of the Foot-and-Mouth Disease Virus Gene Pool: Bottlenecks and Adaptation during Infection in Naïve and Vaccinated Cattle

Foot-and-mouth disease virus (FMDV) infects hosts as a population of closely related viruses referred to as a quasispecies. The behavior of this quasispecies has not been described in detail in natural host species. In this study, virus samples collected from vaccinated and non-vaccinated cattle up to 35 days post-experimental infection with FMDV A24-Cruzeiro were analyzed by deep-sequencing. Vaccination induced significant differences compared to viruses from non-vaccinated cattle in substitution rates, entropy, and evidence for adaptation. Genomic variation detected during early infection reflected the diversity inherited from the source virus (inoculum), whereas by 12 days post infection, dominant viruses were defined by newly acquired mutations. Mutations conferring recognized fitness gain occurred and were associated with selective sweeps. Persistent infections always included multiple FMDV subpopulations, suggesting distinct foci of infection within the nasopharyngeal mucosa. Subclinical infection in vaccinated cattle included very early bottlenecks associated with reduced diversity within virus populations. Viruses from both animal cohorts contained putative antigenic escape mutations. However, these mutations occurred during later stages of infection, at which time transmission is less likely to occur. This study improves upon previously published work by analyzing deep sequences of samples, allowing for detailed characterization of FMDV populations over time within multiple hosts.

The Carrier Conundrum; A Review of Recent Advances and Persistent Gaps Regarding the Carrier State of Foot-and-Mouth Disease Virus

The existence of a prolonged, subclinical phase of foot-and-mouth disease virus (FMDV) infection in cattle was first recognized in the 1950s. Since then, the FMDV carrier state has been a subject of controversy amongst scientists and policymakers. A fundamental conundrum remains in the discordance between the detection of infectious FMDV in carriers and the apparent lack of contagiousness to in-contact animals. Although substantial progress has been made in elucidating the causal mechanisms of persistent FMDV infection, there are still critical knowledge gaps that need to be addressed in order to elucidate, predict, prevent, and model the risks associated with the carrier state. This is further complicated by the occurrence of a distinct form of neoteric subclinical infection, which is indistinguishable from the carrier state in field scenarios, but may have substantially different epidemiological properties. This review summarizes the current state of knowledge of the FMDV carrier state and identifies specific areas of research in need of further attention. Findings from experimental investigations of FMDV pathogenesis are discussed in relation to experience gained from field studies of foot-and-mouth disease.

Polyalthia longifolia leaves methanolic extract targets entry and budding of viruses-an in vitro experimental study against paramyxoviruses

ETHNOPHARMACOLOGICAL RELEVANCE

Synthetic antiviral drugs have several limitations including high cost. Thus research on antiviral property of medicinal plants is continuously gaining importance. Polyalthia longifolia possesses several medicinal properties and has been used in traditional ayurvedic medicine for treatment of dermatological ailments as kushta, visarpa/herpes virus infection and also to treat pyrexia of unknown origin as mentioned in Visarpa Chikitsa.

AIM OF THE STUDY

Keeping in view the cytotoxic, anti-cancer activity and antiviral efficacy of Polyalthia longifolia against herpes, present study was undertaken to evaluate the in vitro antiviral activity of methanolic extract of Polyalthia longifolia leaves, if any, and to unravel the possible target(s)/mechanism of action.

MATERIAL AND METHODS

Antiviral activity of Polyalthia longifolia methanolic extract was studied using Vero cell lines against paramyxoviruses, namely-peste des petits ruminants virus (PPRV) and Newcastle disease virus (NDV). Cytotoxicity of the test extract was evaluated employing MTT assay. Virucidal activity, and viral-attachment, virus entry and release assays were determined in Vero cells using standard experimental protocols. The viral RNA in the virus-infected cells was quantified by qRT-PCR.

RESULTS

At non-cytotoxic concentration, methanolic extract of Polyalthia longifolia leaves was found to inhibit the replication of PPRV and NDV at viral entry and budding level, whereas other steps of viral life cycle such as attachment and RNA synthesis remained unaffected.

CONCLUSIONS

Polyalthia longifolia leaves extract possesses promising antiviral activity against paramyxoviruses and acts by inhibiting the entry and budding of viruses; and this plant extract evidently possesses excellent and promising potential for development of effective herbal antiviral drug.

Identification of the relative timing of infectiousness and symptom onset for outbreak control

In an outbreak of an emerging disease the epidemiological characteristics of the pathogen may be largely unknown. A key determinant of ability to control the outbreak is the relative timing of infectiousness and symptom onset. We provide a method for identifying this relationship with high accuracy based on data from simulated household-stratified symptom-onset data. Further, this can be achieved with observations taken on only a few specific days, chosen optimally, within each household. The information provided by this method may inform decision making processes for outbreak response. An accurate and computationally-efficient heuristic for determining the optimal surveillance scheme is introduced. This heuristic provides a novel approach to optimal design for Bayesian model discrimination.

Modeling the Transmission of Foot and Mouth Disease to Inform Transportation of Infected Carcasses to a Disposal Site During an Outbreak Event

In the event of a Food and Mouth Disease (FMD) outbreak in the United States, an infected livestock premises is likely to result in a high number of carcasses (swine and/or cattle) as a result of depopulation. If relocating infected carcasses to an off-site disposal site is allowed, the virus may have increased opportunity to spread to uninfected premises and result in exposure of susceptible livestock. A stochastic within-herd disease spread model was used to predict the time to detect the disease by observation of clinical signs within the herd, and the number of animals in different disease stages over time. Expert opinion was elicited to estimate depopulation parameters in various scenarios. Disease detection was assumed when 5% of the population showed clinical signs by direct observation. Time to detection (5 and 95th percentile values) was estimated for all swine farm sizes (500-10,000 head) ranged from 102 to 282 h, from 42 to 216 h for all dairy cattle premises sizes (100-2,000 head) and from 66 to 240 h for all beef cattle premises sizes (5,000-50,000 head). Total time from infection to beginning depopulation (including disease detection and confirmation) for the first FMD infected case was estimated between 8.5-14.3 days for swine, 6-12.8 days for dairy or beef cattle premises. Total time estimated for subsequent FMD cases was between 6.8-12.3 days for swine, 4.3-10.8 days for dairy and 4.5-10.5 days for beef cattle premises. On an average sized operation, a sizable proportion of animals in the herd (34-56% of swine, 48-60% of dairy cattle, and 47-60% of beef cattle for the first case and 49-60% of swine, 55-60% of dairy cattle, 56-59% of beef cattle for subsequent cases) would be viremic at the time of beginning depopulation. A very small fraction of body fluids from the carcasses (i.e., 1 mL) would contain virus that greatly exceeds the minimum infectious dose by oral (4-7x) or inhalation (7-13x) route for pigs and cattle.

Multi-scale dynamics of infectious diseases

To address the challenge of multiscale dynamics of infectious diseases, the Mathematical Biosciences Institute organized a workshop at The Ohio State University to bring together scientists from a variety of disciplines to share expertise gained through looking at infectious diseases across different scales. The researchers at the workshop, held in April 2018, were specifically looking at three model systems: foot-and-mouth disease, vector-borne diseases and enteric diseases. Although every multiscale model must be necessarily derived from a multiscale system, not every multiscale system has to lead to multiscale models. These three model systems seem to have produced a variety of both multiscale and integrated single-scale mechanistic models that have developed their own strengths and particular challenges. Here, we present papers from some of the workshop participants to show the breadth of the field.

Estimating viral bottleneck sizes for FMDV transmission within and between hosts and implications for the rate of viral evolution

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.

Effects of regional differences and demography in modelling foot-and-mouth disease in cattle at the national scale

Foot-and-mouth disease (FMD) is a fast-spreading viral infection that can produce large and costly outbreaks in livestock populations. Transmission occurs at multiple spatial scales, as can the actions used to control outbreaks. The US cattle industry is spatially expansive, with heterogeneous distributions of animals and infrastructure. We have developed a model that incorporates the effects of scale for both disease transmission and control actions, applied here in simulating FMD outbreaks in US cattle. We simulated infection initiating in each of the 3049 counties in the contiguous US, 100 times per county. When initial infection was located in specific regions, large outbreaks were more likely to occur, driven by infrastructure and other demographic attributes such as premises clustering and number of cattle on premises. Sensitivity analyses suggest these attributes had more impact on outbreak metrics than the ranges of estimated disease parameter values. Additionally, although shipping accounted for a small percentage of overall transmission, areas receiving the most animal shipments tended to have other attributes that increase the probability of large outbreaks. The importance of including spatial and demographic heterogeneity in modelling outbreak trajectories and control actions is illustrated by specific regions consistently producing larger outbreaks than others.

Endemic foot and mouth disease: pastoral in-herd disease dynamics in sub-Saharan Africa

Foot and mouth disease (FMD) burden disproportionally affects Africa where it is considered endemic. Smallholder livestock keepers experience significant losses due to disease, but the dynamics and mechanisms underlying persistence at the herd-level and beyond remain poorly understood. We address this knowledge gap using stochastic, compartmental modelling to explore FMD virus (FMDV) persistence, outbreak dynamics and disease burden in individual cattle herds within an endemic setting. Our analysis suggests repeated introduction of virus from outside the herd is required for long-term viral persistence, irrespective of carrier presence. Risk of new disease exposures resulting in significant secondary outbreaks is reduced by the presence of immune individuals giving rise to a period of reduced risk, the predicted duration of which suggests that multiple strains of FMDV are responsible for observed yearly herd-level outbreaks. Our analysis suggests management of population turnover could potentially reduce disease burden and deliberate infection of cattle, practiced by local livestock keepers in parts of Africa, has little effect on the duration of the reduced risk period but increases disease burden. This work suggests that FMD control should be implemented beyond individual herds but, in the interim, herd management may be used to reduced FMD impact to livestock keepers.

Soluble FMDV VP1 proteins fused with calreticulin expressed in Escherichia coli under the assist of trigger factor16 (Tf16) formed into high immunogenic polymers

Foot and mouth disease virus (FMDV) is a highly contagious pathogen propagating among cloven-hoofed animals. As a major immunogenic protein, VP1 plays a pivotal role in the induction of neutralizing antibodies, which therefore is an ideal target for developing subunit vaccines. In current study, four prokaryotic expression clones (rV4C, rC4V, rV5F and rF5V) were constructed by fusing truncated calreticulin (CRT) (120-250 aa or 120-308 aa) at the N/C terminal of vp1 gene, and co-expressed with chaperone trigger factor 16 (Tf16) in E.coli, respectively. The soluble recombinant CRT-fused VP1 proteins could form into homogeneous reactive polymers with average hydrodynamic diameters around 100 nm according to the dynamic light scattering (DLS) data. Immunization of guinea pigs with 10 μg purified CRT-fused VP1 proteins induced high levels of antibodies against naked-VP1 through indirect ELISA. Sandwich ELISA showed that only rC4V could elicit the same level of antibody against FMD virus as commercial inactivated vaccine after booster. The lymphocyte cytokines secretion of immunized rC4V was higher than the other CRT-fused VP1 proteins in guinea pigs. These results showed that the soluble CRT-fused VP1 proteins, especially rC4V, expressed with Tf16 in E. coli might have potential to be used as subunit vaccine candidate against FMDV.

The Risk of Foot and Mouth Disease Transmission Posed by Public Access to the Countryside During an Outbreak

During the 2001 UK FMD outbreak, local authorities restricted rural access to try to prevent further disease spread by people and animals, which had major socio-economic consequences for rural communities. This study describes the results of qualitative veterinary risk assessments to assess the likelihood of different recreational activities causing new outbreaks of foot and mouth disease, as part of contingency planning for future outbreaks. For most activities, the likelihood of causing new outbreaks of foot and mouth disease is considered to vary from very low to medium depending on the control zone (which is based on distance to the nearest infected premises), assuming compliance with specified mitigation strategies. The likelihood of new outbreaks associated with hunting, shooting, stalking, and equestrian activities is considered to be greater. There are areas of significant uncertainty associated with data paucity, particularly regarding the likelihood of transmission via fomites. This study provides scientific evidence to underpin refinement of rural access management plans and inform decision-making in future disease outbreaks.

Horizontal transmission of foot-and-mouth disease virus O/JPN/2010 among different animal species by direct contact

Foot-and-mouth disease (FMD) is highly contagious and easily transmitted among species of cloven-hoofed animals. To investigate the transmission of FMD virus (FMDV) among different animal species, experimental infections using the O/JPN/2010 strain were performed in cows, goats and pigs. One cow or two goats/pigs were housed with a different species of inoculated animals, and clinical observations, virus shedding and antibody responses were analysed daily. Whilst all cows and goats were infected horizontally by contact with inoculated pigs, transmission from cows to goats/pigs and from goats to cows/pigs was not observed in all in-contact animals. In particular, no pigs were infected horizontally by contact with inoculated goats. Comparison with our previous study on experimental infections among animals of the same species indicates that horizontal transmission occurred more easily between animals of the same species than between those of the different species. These findings will be useful for establishing and performing species-specific countermeasures in farms and regions where multiple species of animals coexist in potential future outbreaks.

African Swine Fever: Fast and Furious or Slow and Steady?

Since the introduction of African swine fever (ASF) into Georgia in 2007, the disease has been spreading in an unprecedented way. Many countries that are still free from the disease fear the emergence of ASF in their territory either in domestic pigs or in wild boar. In the past, ASF was often described as being a highly contagious disease with mortality often up to 100%. However, the belief that the disease might enter a naïve population and rapidly affect the entire susceptible population needs to be critically reviewed. The current ASF epidemic in wild boar, but also the course of ASF within outbreaks in domestic pig holdings, suggest a constant, but relatively slow spread. Moreover, the results of several experimental and field studies support the impression that the spread of ASF is not always fast. ASF spread and its speed depend on various factors concerning the host, the virus, and also the environment. Many of these factors and their effects are not fully understood. For this review, we collated published information regarding the spreading speed of ASF and the factors that are deemed to influence the speed of ASF spread and tried to clarify some issues and open questions in this respect.

Parameterization of the Durations of Phases of Foot-And-Mouth Disease in Cattle

The objective of the current study was to update parameterization of mathematical simulation models for foot-and-mouth disease (FMD) spread in cattle utilizing recent knowledge of FMD virus (FMDV) pathogenesis and infection dynamics to estimate the duration of distinct phases of FMD. Specifically, the durations of incubation, latent, and infectious periods were estimated for 3 serotypes (O, Asia1, and A) of FMDV, individually and collectively (pan-serotypic). Animal-level data were used in Accelerated Failure Time (AFT) models to estimate the duration of the defined phases of infection, while also investigating the influence of factors related to the experimental design (exposure methods) and virus serotype on disease progression. Substantial influences upon the estimated duration of distinct phases of FMD included the quantity of viral shedding used as a proxy for the onset of infectiousness, virus serotypes, and experimental exposure methods. The use of detection of any viral RNA in nasal secretions as a proxy of infectiousness lengthened the total infectious period compared to use of threshold-based detection. Additionally, the experimental system used to infect the animals also had significant effects on the duration of distinct phases of disease. Overall, the mean [95% Confidence Interval (CI)] durations of pan-serotype disease phases in cattle were estimated to be: incubation phase = 3.6 days (2.7–4.8), latent phase = 1.5 days (1.1–2.1), subclinical infectious phase = 2.2 days (1.5–3.5), clinical infectious phase = 8.5 days (6.2–11.6), and total infectious phase = 10.8 days (8.2–14.2). This study highlights the importance of identifying appropriate proxy measures to define the onset and duration of infectiousness in FMDV-infected cattle in the absence of actual transmission data. Additionally, it is demonstrated herein that factors associated with experimental design, such as virus exposure methods, may significantly affect disease progression in individual animals and should be considered when data is extrapolated from experimental studies. Given limitations in experimental data availability, pan-serotypic parameters which include all routes of exposure and a threshold-defined onset of infectiousness may be the most robust parameters for exploratory disease spread modeling approaches, when information on the specific virus of interest is not available.

The Inclusive Behavioral Immune System

Although living in social groups offers many advantages, it comes at a cost of increased transmissible disease. The behavioral immune system (BIS) is thought to have evolved as a first line of defense against such infections. It acts by minimizing the contact of yet uninfected hosts with potential pathogens. The BIS has been observed in a wide range of animals including insects, amphibians and mammals, but most research has focused on humans where the BIS is guided by complex cognitive and emotional processing. When researchers discuss the evolutionary origin of the BIS, they assess how it raises individual fitness. What would happen though if we shift our attention to the evolutionary unit of selection – the gene? Success would be measured as the change in the gene’s prevalence in the entire population, and additional behaviors would come to our attention – those that benefit relatives, i.e., behaviors that raise inclusive fitness. One widely-recognized example of the inclusive BIS is social immunity, which is prevalent among eusocial organisms such as bees and ants. Their colonies engage in a collaborative protective behavior such as grooming and the removal of infected members from the nest. Another example may be sickness behavior, which includes the behavioral, cognitive and emotional symptoms that accompany infection, such as fatigue, and loss of appetite and social interest. My colleague and I recently suggested that sickness behavior has evolved because it reduces the direct and indirect contact between an infected host and its healthy kin – improving inclusive fitness. These additional behaviors are not carried out by the healthy individuals, but rather by whole communities in the first case, and by already infected individuals in the second. Since they step beyond the classical definition of BIS, it may be useful to broaden the term to the inclusive behavioral immune system.

The evolution of a super-swarm of foot-and-mouth disease virus in cattle

Foot-and-mouth disease (FMD) is a highly contagious viral disease that severely impacts global food security and is one of the greatest constraints on international trade of animal products. Extensive viral population diversity and rapid, continuous mutation of circulating FMD viruses (FMDVs) pose significant obstacles to the control and ultimate eradication of this important transboundary pathogen. The current study investigated mechanisms contributing to within-host evolution of FMDV in a natural host species (cattle). Specifically, vaccinated and non-vaccinated cattle were infected with FMDV under controlled, experimental conditions and subsequently sampled for up to 35 days to monitor viral genomic changes as related to phases of disease and experimental cohorts. Consensus-level genomic changes across the entire FMDV coding region were characterized through three previously defined stages of infection: early, transitional, and persistent. The overall conclusion was that viral evolution occurred via a combination of two mechanisms: emergence of full-genomic minority haplotypes from within the inoculum super-swarm, and concurrent continuous point mutations. Phylogenetic analysis indicated that individuals were infected with multiple distinct haplogroups that were pre-existent within the ancestral inoculum used to infect all animals. Multiple shifts of dominant viral haplotype took place during the early and transitional phases of infection, whereas few shifts occurred during persistent infection. Overall, this work suggests that the establishment of the carrier state is not associated with specific viral genomic characteristics. These insights into FMDV population dynamics have important implications for virus sampling methodology and molecular epidemiology.

Quantitative impacts of incubation phase transmission of foot-and-mouth disease virus

The current investigation applied a Bayesian modeling approach to a unique experimental transmission study to estimate the occurrence of transmission of foot-and-mouth disease (FMD) during the incubation phase amongst group-housed pigs. The primary outcome was that transmission occurred approximately one day prior to development of visible signs of disease (posterior median 21 hours, 95% CI: 1.1-45.0). Updated disease state durations were incorporated into a simulation model to examine the importance of addressing preclinical transmission in the face of robust response measures. Simulation of FMD outbreaks in the US pig production sector demonstrated that including a preclinical infectious period of one day would result in a 40% increase in the median number of farms affected (166 additional farms and 664,912 pigs euthanized) compared to the scenario of no preclinical transmission, assuming suboptimal outbreak response. These findings emphasize the importance of considering transmission of FMD during the incubation phase in modeling and response planning.

The evolution of a super-swarm of foot-and-mouth disease virus in cattle

Foot-and-mouth disease (FMD) is a highly contagious viral disease that severely impacts global food security and is one of the greatest constraints on international trade of animal products. Extensive viral population diversity and rapid, continuous mutation of circulating FMD viruses (FMDVs) pose significant obstacles to the control and ultimate eradication of this important transboundary pathogen. The current study investigated mechanisms contributing to within-host evolution of FMDV in a natural host species (cattle). Specifically, vaccinated and non-vaccinated cattle were infected with FMDV under controlled, experimental conditions and subsequently sampled for up to 35 days to monitor viral genomic changes as related to phases of disease and experimental cohorts. Consensus-level genomic changes across the entire FMDV coding region were characterized through three previously defined stages of infection: early, transitional, and persistent. The overall conclusion was that viral evolution occurred via a combination of two mechanisms: emergence of full-genomic minority haplotypes from within the inoculum super-swarm, and concurrent continuous point mutations. Phylogenetic analysis indicated that individuals were infected with multiple distinct haplogroups that were pre-existent within the ancestral inoculum used to infect all animals. Multiple shifts of dominant viral haplotype took place during the early and transitional phases of infection, whereas few shifts occurred during persistent infection. Overall, this work suggests that the establishment of the carrier state is not associated with specific viral genomic characteristics. These insights into FMDV population dynamics have important implications for virus sampling methodology and molecular epidemiology.

Review of epidemiological risk models for foot-and-mouth disease: Implications for prevention strategies with a focus on Africa

Foot-and-mouth disease (FMD) is a highly infectious transboundary disease that affects domestic and wild cloven-hoofed animal species. The aim of this review was to identify and critically assess some modelling techniques for FMD that are well supported by scientific evidence from the literature with a focus on their use in African countries where the disease remains enzootic. In particular, this study attempted to provide a synopsis of the relative strengths and weaknesses of these models and their relevance to FMD prevention policies. A literature search was conducted to identify quantitative and qualitative risk assessments for FMD, including studies that describe FMD risk factor modelling and spatiotemporal analysis. A description of retrieved papers and a critical assessment of the modelling methods, main findings and their limitations were performed. Different types of models have been used depending on the purpose of the study and the nature of available data. The most frequently identified factors associated with the risk of FMD occurrence were the movement (especially uncontrolled animal movement) and the mixing of animals around water and grazing points. Based on the qualitative and quantitative risk assessment studies, the critical pathway analysis showed that the overall risk of FMDV entering a given country is low. However, in some cases, this risk can be elevated, especially when illegal importation of meat and the movement of terrestrial livestock are involved. Depending on the approach used, these studies highlight shortcomings associated with the application of models and the lack of reliable data from endemic settings. Therefore, the development and application of specific models for use in FMD endemic countries including Africa is encouraged.

Development and evaluation of serotype-specific recombinase polymerase amplification combined with lateral flow dipstick assays for the diagnosis of foot-and-mouth disease virus serotype A, O and Asia1

Background

Foot-and-mouth disease (FMD) caused by foot-and-mouth disease virus (FMDV) is one of the most highly infectious diseases in livestock, and leads to huge economic losses. Early diagnosis and rapid differentiation of FMDV serotype is therefore integral to the prevention and control of FMD. In this study, a series of serotype-specific reverse transcription recombinase polymerase amplification assays combined with lateral flow dipstick (RPA-LFD) were establish to differentiate FMDV serotypes A, O or Asia 1, respectively.

Results

The serotype-specific primers and probes of RPA-LFD were designed to target conserved regions of the FMDV VP1 gene sequence, and three primer and probe sets of serotype-specific RPA-LFD were selected for amplification of FMDV serotypes A, O or Asia 1, respectively. Following incubation at 38 °C for 20 min, the RPA amplification products could be visualized by LFD. Analytical sensitivity of the RPA assay was then determined with ten-fold serial dilutions of RNA of VP1 gene and the recombinant vector respectively containing VP1 gene from FMDV serotypes A, O or Asia1, the detection limits of these assays were 3 copies of plasmid DNA or 50 copies of viral RNA per reaction. Moreover, the specificity of the assay was assessed, and there was no cross reactions with other viruses leading to bovine vesicular lesions. Furthermore, 126 clinical samples were respectively detected with RPA-LFD and real-time PCR (rPCR), there was 98.41% concordance between the two assays, and two samples were positive by RPA-LFD but negative in rPCR, these were confirmed as FMDV-positive through viral isolation in BHK-21 cells. It showed that RPA-LFD assay was more sensitive than the rPCR method in this study.

Conclusion

The development of serotype-specific RPA-LFD assay provides a rapid, sensitive, and specific method for differentiation of FMDV serotype A, O or Asia1, respectively. It is possible that the serotype-specific RPA-LFD assay may be used as a integral protocol for field detection of FMDV.

Efficacy of an adenovirus-vectored foot-and-mouth disease virus serotype A subunit vaccine in cattle using a direct contact transmission model

Background

A direct contact transmission challenge model was used to simulate natural foot-and-mouth disease virus (FMDV) spread from FMDV A24/Cruzeiro/BRA/55 infected ‘seeder’ steers to naïve or vaccinated steers previously immunized with a replication-deficient human adenovirus-vectored FMDV A24/Cruzeiro/BRA/55 capsid-based subunit vaccine (AdtA24). In two independent vaccine efficacy trials, AdtA24 was administered once intramuscularly in the neck 7 days prior to contact with FMDV A24/Cruzeiro/BRA/55-infected seeder steers.

Results

In Efficacy Study 1, we evaluated three doses of AdtA24 to estimate the 50%/90% bovine protective dose (BPD_50/90) for prevention of clinical FMD. In vaccinated, contact-challenged steers, the BPD_50/90 was 3.1 × 10¹⁰ / 5.5 × 10¹⁰ AdtA24 particles formulated without adjuvant. In Efficacy Study 2, steers vaccinated with 5 × 10¹⁰ AdtA24 particles, exposed to FMDV A24/Cruzeiro/BRA/55-infected seeder steers, did not develop clinical FMD or transmit FMDV to other vaccinated or naïve, non-vaccinated steers. In contrast, naïve, non-vaccinated steers that were subsequently exposed to FMDV A24/Cruzeiro/BRA/55-infected seeder steers developed clinical FMD and transmitted FMDV by contact to additional naïve, non-vaccinated steers. The AdtA24 vaccine differentiated infected from vaccinated animals (DIVA) because no antibodies to FMDV nonstructural proteins were detected prior to FMDV exposure.

Conclusions

A single dose of the AdtA24 non-adjuvanted vaccine conferred protection against clinical FMD at 7 days post-vaccination following direct contact transmission from FMDV-infected, naïve, non-vaccinated steers. The AdtA24 vaccine was effective in preventing FMDV transmission from homologous challenged, contact-exposed, AdtA24-vaccinated, protected steers to co-mingled, susceptible steers, suggesting that the vaccine may be beneficial in reducing both the magnitude and duration of a FMDV outbreak in a commercial cattle production setting.

Transmission risk predicts avoidance of infected conspecifics in Trinidadian guppies

Associating with conspecifics afflicted with infectious diseases increases the risk of becoming infected, but engaging in avoidance behaviour incurs the cost of lost social benefits. Across systems, infected individuals vary in the transmission risk they pose, so natural selection should favour risk-sensitive avoidance behaviour that optimally balances the costs and benefits of sociality. Here, we use the guppy Poecilia reticulata-Gyrodactylus turnbulli host-parasite system to test the prediction that individuals avoid infected conspecifics in proportion to the transmission risk they pose. In dichotomous choice tests, uninfected fish avoided both the chemical and visual cues, presented separately, of infected conspecifics only in the later stages of infection. A transmission experiment indicated that this avoidance behaviour accurately tracked transmission risk (quantified as both the speed at which transmission occurs and the number of parasites transmitting) through the course of infection. Together, these findings reveal that uninfected hosts can use redundant cues across sensory systems to inform dynamic risk-sensitive avoidance behaviour. This correlation between the transmission risk posed by infected individuals and the avoidance response they elicit has implications for the evolutionary ecology of infectious disease, and its explicit inclusion may improve the ability of epidemic models to predict disease spread.

Quantifying Transmission

Transmissibility is the defining characteristic of infectious diseases. Quantifying transmission matters for understanding infectious disease epidemiology and designing evidence-based disease control programs. Tracing individual transmission events can be achieved by epidemiological investigation coupled with pathogen typing or genome sequencing. Individual infectiousness can be estimated by measuring pathogen loads, but few studies have directly estimated the ability of infected hosts to transmit to uninfected hosts. Individuals' opportunities to transmit infection are dependent on behavioral and other risk factors relevant given the transmission route of the pathogen concerned. Transmission at the population level can be quantified through knowledge of risk factors in the population or phylogeographic analysis of pathogen sequence data. Mathematical model-based approaches require estimation of the per capita transmission rate and basic reproduction number, obtained by fitting models to case data and/or analysis of pathogen sequence data. Heterogeneities in infectiousness, contact behavior, and susceptibility can have substantial effects on the epidemiology of an infectious disease, so estimates of only mean values may be insufficient. For some pathogens, super-shedders (infected individuals who are highly infectious) and super-spreaders (individuals with more opportunities to transmit infection) may be important. Future work on quantifying transmission should involve integrated analyses of multiple data sources.

Efficacy of a high-potency multivalent foot-and-mouth disease virus vaccine in cattle against heterologous challenge with a field virus from the emerging A/ASIA/G-VII lineage

In 2015, outbreaks of foot-and-mouth disease (FMD) in the Middle East were discovered to be caused by a viral lineage (A/ASIA/G-VII), which has recently emerged from the Indian sub-continent. In vitro vaccine matching data generated by the World Reference Laboratory (WRLFMD) indicated that A/ASIA/G-VII field viruses were poorly matched with vaccines (A-SAU-95, A22 IRQ and A-IRN-05) that are already used in the region. In order to assess the likely performance of one of these commercially available FMD vaccines, sixteen cattle were vaccinated with a polyvalent vaccine which contained two serotype A components (A-SAU-95 and A-IRN-05) with a homologous potency of at least 6PD50, and two cattle were left unvaccinated as controls. Twenty-one days later, all 18 cattle were challenged by tongue inoculation with an FMDV field isolate A/IRN/22/2015 from the A/ASIA/G-VII lineage, in line with the European Pharmacopeia PPG test conditions. The two control animals developed generalised FMD, and 7/16 vaccinated animals developed at least one foot lesion, thus only 56.3% were defined as protected. For the vaccine components, there was a significant increase in the probability of protection with increasing serological titres for A-SAU-95 (p = 0.03), but not for A-IRN-05 (p = 0.42). Analysis of FMDV in blood and nasal swabs suggested that vaccination reduced shedding and potential onward spread of FMD virus even if the animal developed foot lesions. In summary, the results from this study suggest that whilst this vaccine would not be appropriate for use in an emergency situation (in previously FMD-free countries), it may be partially effective in the field in endemic countries where repeat prophylactic vaccination is practiced. For emergency reactive vaccination, the findings from this study support the idea that a new vaccine strain should be developed that is tailored to the A/ASIA/G-VII lineage.

Invited review: Genetic and genomic mouse models for livestock research

Abstract. Knowledge about the function and functioning of single or multiple interacting genes is of the utmost significance for understanding the organism as a whole and for accurate livestock improvement through genomic selection. This includes, but is not limited to, understanding the ontogenetic and environmentally driven regulation of gene action contributing to simple and complex traits. Genetically modified mice, in which the functions of single genes are annotated; mice with reduced genetic complexity; and simplified structured populations are tools to gain fundamental knowledge of inheritance patterns and whole system genetics and genomics. In this review, we briefly describe existing mouse resources and discuss their value for fundamental and applied research in livestock.

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

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.

Foot-and-mouth disease virus transmission dynamics and persistence in a herd of vaccinated dairy cattle in India

Foot-and-mouth disease (FMD) is an important transboundary disease with substantial economic impacts. Although between-herd transmission of the disease has been well studied, studies focusing on within-herd transmission using farm-level outbreak data are rare. The aim of this study was to estimate parameters associated with within-herd transmission, host physiological factors and FMD virus (FMDV) persistence using data collected from an outbreak that occurred at a large, organized dairy farm in India. Of 1,836 regularly vaccinated, adult dairy cattle, 222 had clinical signs of FMD over a 39-day period. Assuming homogenous mixing, a frequency-dependent compartmental model of disease transmission was built. The transmission coefficient and basic reproductive number were estimated to be between 16.2-18.4 and 67-88, respectively. Non-pregnant animals were more likely to manifest clinical signs of FMD as compared to pregnant cattle. Based on oropharyngeal fluid (probang) sampling and FMDV-specific RT-PCR, four of 36 longitudinally sampled animals (14%) were persistently infected carriers 10.5 months post-outbreak. There was no statistical difference between subclinical and clinically infected animals in the duration of the carrier state. However, prevalence of NSP-ELISA antibodies differed significantly between subclinical and clinically infected animals 12 months after the outbreak with 83% seroprevalence amongst clinically infected cattle compared to 69% of subclinical animals. This study further elucidates within-herd FMD transmission dynamics during the acute-phase and characterizes duration of FMDV persistence and seroprevalence of FMD under natural conditions in an endemic setting.

Bayesian inference of epidemiological parameters from transmission experiments

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.

Bayesian uncertainty quantification for transmissibility of influenza, norovirus and Ebola using information geometry

Infectious diseases exert a large and in many contexts growing burden on human health, but violate most of the assumptions of classical epidemiological statistics and hence require a mathematically sophisticated approach. Viral shedding data are collected during human studies—either where volunteers are infected with a disease or where existing cases are recruited—in which the levels of live virus produced over time are measured. These have traditionally been difficult to analyse due to strong, complex correlations between parameters. Here, we show how a Bayesian approach to the inverse problem together with modern Markov chain Monte Carlo algorithms based on information geometry can overcome these difficulties and yield insights into the disease dynamics of two of the most prevalent human pathogens—influenza and norovirus—as well as Ebola virus disease.