Eliminating bovine tuberculosis in cattle and badgers: insight from a dynamic model.

Bovine tuberculosis (BTB) is a multi-species infection that commonly affects cattle and badgers in Great Britain. Despite years of study, the impact of badgers on BTB incidence in cattle is poorly understood. Using a two-host transmission model of BTB in cattle and badgers, we find that published data and parameter estimates are most consistent with a system at the threshold of control. The most consistent explanation for data obtained from cattle and badger populations includes within-host reproduction numbers close to 1 and between-host reproduction numbers of approximately 0.05. In terms of controlling infection in cattle, reducing cattle-to-cattle transmission is essential. In some regions, even large reductions in badger prevalence can have a modest impact on cattle infection and a multi-stranded approach is necessary that also targets badger-to-cattle transmission directly. The new perspective highlighted by this two-host approach provides insight into the control of BTB in Great Britain.The work and E.B.-P.’s fellowship was funded by the EPSRC (EP/H027270/1). J.L.N.W. is supported by the Alborada Trust, the RAPIDD program of the Science & Technology Directorate, US Department of Homeland Security, the Fogarty International Center, US National Institutes of Health, the European Union FP7 project ANTIGONE (contract number 278976) and by BBSRC grant BB/I012192/1.This is the final version. It was first published by Royal Society Publishing at http://rspb.royalsocietypublishing.org/content/282/1808/20150374

Nine challenges in modelling the emergence of novel pathogens.

Studying the emergence of novel infectious agents involves many processes spanning host species, spatial scales, and scientific disciplines. Mathematical models play an essential role in combining insights from these investigations and drawing robust inferences from field and experimental data. We describe nine challenges in modelling the emergence of novel pathogens, emphasizing the interface between models and data.We acknowledge support from the Research and Policy for Infectious Disease Dynamics (RAPIDD) programme of the Science and Technology Directory, Department of Homeland Security, and Fogarty International Center, National Institutes of Health. JLS was also supported by the National Science Foundation (EF-0928987 and OCE-1335657) and the De Logi Chair in Biological Sciences. SF was supported by a UK Medical Research Council Career Development Award in Biostatistics. SR was supported by: Wellcome Trust Project Award 093488/Z/10/Z; R01 TW008246-01 from Fogarty International Centre; and The Medical Research Council (UK, Project Grant MR/J008761/1). JLNW was also supported by the Alborada Trust and the European Union FP7 project ANTIGONE (contract number 278976).This is the final version of the article. It first appeared from Elsevier via http://dx.doi.org/10.1016/j.epidem.2014.09.00

New methodologies for the estimation of population vulnerability to diseases: a case study of Lassa fever and Ebola in Nigeria and Sierra Leone.

Public health practitioners require measures to evaluate how vulnerable populations are to diseases, especially for zoonoses (i.e. diseases transmitted from animals to humans) given their pandemic potential. These measures would be valuable to support strategic and operational decision making and allocation of resources. Although vulnerability is well defined for natural hazards, for public health threats the concept remains undetermined. Here, we develop new methodologies to: (i) quantify the impact of zoonotic diseases and the capacity of countries to cope with these diseases, and (ii) combine these two measures (impact and capacity) into one overall vulnerability indicator. The adaptive capacity is calculated from estimations of disease mortality, although the method can be adapted for diseases with no or low mortality but high morbidity. As an example, we focused on the vulnerability of Nigeria and Sierra Leone to Lassa Fever and Ebola. We develop a simple analytical form that can be used to estimate vulnerability scores for different spatial units of interest, e.g. countries or regions. We show how some populations can be highly vulnerable despite low impact threats. We finally outline future research to more comprehensively inform vulnerability with the incorporation of relevant factors depicting local heterogeneities (e.g. bio-physical and socio-economic factors). This article is part of the theme issue 'Modelling infectious disease outbreaks in humans, animals and plants: epidemic forecasting and control'. This theme issue is linked with the earlier issue 'Modelling infectious disease outbreaks in humans, animals and plants: approaches and important themes'.FRSF Pump Prime Gran

A Longitudinal Study of Cattle Productivity in Intensive Dairy Farms in Central Ethiopia.

Ethiopia is witnessing an emergence of intensive urban dairy farming. The aims of this study were to capture cattle productivity parameters in selected intensive dairy farms in and around Addis Ababa (Central Ethiopia). The study is a pre-requisite and baseline for further economic analysis of diseases such as bovine tuberculosis (BTB) and to assess some of the current challenges faced by farm owners for optimal animal performances. Hence, a 3-year longitudinal observational study was conducted for the first time in Ethiopia, in 24 dairy farms with intensive husbandry, including a total of 1,705 dairy animals. Herd characteristics, animal movement, and productivity parameters (fertility, morbidity, mortality) were recorded in a herd-book. Whereas, half the farms saw their animals increase in number over the 3 years, 37.5% (mainly large farms) saw their herd size decrease. Offtakes accounted for 76.6% of all animal exits. One hundred and ninety (11.1%) animals died of natural causes. Highest mortality was observed in young stock (13.9%). Overall, diseases were the leading cause for death (57.5%). The majority of calves (69%) that died, did so within the first week of life. Mean calving interval (CI) was 483.2 days. Successful conception after artificial insemination (AI) was 66.1% with Addis Ababa and smaller farms faring worst. Mean time interval from calving to first service was 152 days. Date of birth to first service was 592.2 days and date of birth to first calving was 794.7 days. In conclusion, the study showed sub-optimal productivity performances in intensive dairy cattle and highlighted some of the current gaps and challenges in urban dairy productivity

Risk factors and variations in detection of new bovine tuberculosis breakdowns via slaughterhouse surveillance in Great Britain.

Slaughterhouse surveillance through post-mortem meat inspection provides an important mechanism for detecting bovine tuberculosis (bTB) infections in cattle herds in Great Britain (GB), complementary to the live animal skin test based programme. We explore patterns in the numbers of herd breakdowns detected through slaughterhouse surveillance and develop a Bayesian hierarchical regression model to assess the associations of animal-level factors with the odds of an infected animal being detected in the slaughterhouse, allowing us to highlight slaughterhouses that show atypical patterns of detection. The analyses demonstrate that the numbers and proportions of breakdowns detected in slaughterhouses increased in GB over the period of study (1998-2013). The odds of an animal being a slaughterhouse case was strongly associated with the region of the country that the animal spent most of its life, with animals living in high-frequency testing areas of England having on average 21 times the odds of detection compared to animals living in Scotland. There was also a strong effect of age, with animals slaughtered at > 60 months of age having 5.3 times the odds of detection compared to animals slaughtered between 0-18 months of age. Smaller effects were observed for cattle having spent time on farms with a history of bTB, quarter of the year that the animal was slaughtered, movement and test history. Over-and-above these risks, the odds of detection increased by a factor of 1.1 for each year of the study. After adjustment for these variables, there were additional variations in risk between slaughterhouses and breed. Our framework has been adopted into the routine annual surveillance reporting carried out by the Animal Plant Health Agency and may be used to target more detailed investigation of meat inspection practices.Defra Project SE3133. (Department of Environment and Rural Affairs, UK Government

Persistence of Multiple Paramyxoviruses in a Closed Captive Colony of Fruit Bats (Eidolon helvum).

Bats have been identified as the natural hosts of several emerging zoonotic viruses, including paramyxoviruses, such as Hendra and Nipah viruses, that can cause fatal disease in humans. Recently, African fruit bats with populations that roost in or near urban areas have been shown to harbour a great diversity of paramyxoviruses, posing potential spillover risks to public health. Understanding the circulation of these viruses in their reservoir populations is essential to predict and prevent future emerging diseases. Here, we identify a high incidence of multiple paramyxoviruses in urine samples collected from a closed captive colony of circa 115 straw-coloured fruit bats (Eidolon helvum). The sequences detected have high nucleotide identities with those derived from free ranging African fruit bats and form phylogenetic clusters with the Henipavirus genus, Pararubulavirus genus and other unclassified paramyxoviruses. As this colony had been closed for 5 years prior to this study, these results indicate that within-host paramyxoviral persistence underlies the role of bats as reservoirs of these viruses.This research was funded by Research England, the Royal Veterinary College, the Medical Research Council (grant number MR/P025226/1) and the Defense Advanced Research Projects Agency (DARPA) administered through Cooperative Agreement #D18AC00031-PREEMPT. JLNW and OR are funded by The Alborada Trust. AAC was part-funded by a Royal Society Wolfson Research Merit award

High turnover drives prolonged persistence of influenza in managed pig herds.

Pigs have long been hypothesized to play a central role in the emergence of novel human influenza A virus (IAV) strains, by serving as mixing vessels for mammalian and avian variants. However, the key issue of viral persistence in swine populations at different scales is ill understood. We address this gap using epidemiological models calibrated against seroprevalence data from Dutch finishing pigs to estimate the 'critical herd size' (CHS) for IAV persistence. We then examine the viral phylogenetic evidence for persistence by comparing human and swine IAV. Models suggest a CHS of approximately 3000 pigs above which influenza was likely to persist, i.e. orders of magnitude lower than persistence thresholds for IAV and other acute viruses in humans. At national and regional scales, we found much stronger empirical signatures of prolonged persistence of IAV in swine compared with human populations. These striking levels of persistence in small populations are driven by the high recruitment rate of susceptible piglets, and have significant implications for management of swine and for overall patterns of genetic diversity of IAV.This work was supported by the RAPIDD program of the Science and Technology Directorate, Department of Homeland Security, and the Fogarty International Center, National Institutes of Health (V.E.P., S.R., J.L.N.W. and B.T.G.) and the Bill & Melinda Gates Foundation (V.E.P. and B.T.G.). J.L.N.W. is also supported by the Alborada Trust, the European Union FP7 project ANTIGONE (contract no. 278976) and by Biotechnology and Biological Sciences Research Council sLOLA BB/L001330/1.This is the final version of the article. It first appeared from Royal Society Publishing via http://dx.doi.org/10.1098/rsif.2016.013

Environmental limits of Rift Valley fever revealed using ecoepidemiological mechanistic models.

Vector-borne diseases (VBDs) of humans and domestic animals are a significant component of the global burden of disease and a key driver of poverty. The transmission cycles of VBDs are often strongly mediated by the ecological requirements of the vectors, resulting in complex transmission dynamics, including intermittent epidemics and an unclear link between environmental conditions and disease persistence. An important broader concern is the extent to which theoretical models are reliable at forecasting VBDs; infection dynamics can be complex, and the resulting systems are highly unstable. Here, we examine these problems in detail using a case study of Rift Valley fever (RVF), a high-burden disease endemic to Africa. We develop an ecoepidemiological, compartmental, mathematical model coupled to the dynamics of ambient temperature and water availability and apply it to a realistic setting using empirical environmental data from Kenya. Importantly, we identify the range of seasonally varying ambient temperatures and water-body availability that leads to either the extinction of mosquito populations and/or RVF (nonpersistent regimens) or the establishment of long-term mosquito populations and consequently, the endemicity of the RVF infection (persistent regimens). Instabilities arise when the range of the environmental variables overlaps with the threshold of persistence. The model captures the intermittent nature of RVF occurrence, which is explained as low-level circulation under the threshold of detection, with intermittent emergence sometimes after long periods. Using the approach developed here opens up the ability to improve predictions of the emergence and behaviors of epidemics of many other important VBDs.The work was partially supported by the National Institute for Health Research (NIHR) Health Protection Research Unit in Environmental Change and Health at the London School of Hygiene and Tropical Medicine in partnership with Public Health England (PHE) and in collaboration with the University of Exeter, University College London, and the Met Office. European Union FP7 Project ANTIGONE (Contract 278976). Royal Society Wolfson Research Merit Award. The Alborada Trust

Characteristics and Risk Perceptions of Ghanaians Potentially Exposed to Bat-Borne Zoonoses through Bushmeat.

Emerging zoonotic pathogens from wildlife pose increasing public health threats globally. Bats, in particular, host an array of zoonotic pathogens, yet there is little research on how bats and humans interact, how people perceive bats and their accompanying disease risk, or who is most at risk. Eidolon helvum, the largest and most abundant African fruit bat species, is widely hunted and eaten in Ghana and also carries potentially zoonotic pathogens. This combination raises concerns, as hunting and butchering bushmeat are common sources of zoonotic transmission. Through a combination of interviews with 577 Ghanaians across southern Ghana, we identified the characteristics of people involved in the bat-bushmeat trade and we explored their perceptions of risk. Bat hunting, selling and consumption are widely distributed across regional and ethnic lines, with hotspots in certain localities, while butchering is predominantly done by women and active hunters. Interviewees held little belief of disease risk from bats, saw no ecological value in fruit bats and associated the consumption of bats with specific tribes. These data can be used to inform disease and conservation management plans, drawing on social contexts and ensuring that local voices are heard within the larger global effort to study and mitigate outbreaks.This is the final version. It was first published by Springer in EcoHealth at http://link.springer.com/article/10.1007%2Fs10393-014-0977-0