Investigating poultry trade patterns to guide avian influenza surveillance and control: a case study in Vietnam

Live bird markets are often the focus of surveillance activities monitoring avian influenza viruses (AIV) circulating in poultry. However, in order to ensure a high sensitivity of virus detection and effectiveness of management actions, poultry management practices features influencing AIV dynamics need to be accounted for in the design of surveillance programmes. In order to address this knowledge gap, a cross-sectional survey was conducted through interviews with 791 traders in 18 Vietnamese live bird markets. Markets greatly differed according to the sources from which poultry was obtained, and their connections to other markets through the movements of their traders. These features, which could be informed based on indicators that are easy to measure, suggest that markets could be used as sentinels for monitoring virus strains circulating in specific segments of the poultry production sector. AIV spread within markets was modelled. Due to the high turn-over of poultry, viral amplification was likely to be minimal in most of the largest markets. However, due to the large number of birds being introduced each day, and challenges related to cleaning and disinfection, environmental accumulation of viruses at markets may take place, posing a threat to the poultry production sector and to public health.

Modelling African swine fever presence and reported abundance in the Russian Federation using national surveillance data from 2007 to 2014

African swine fever (ASF) is a viral disease of swine that has been present in the Russian Federation since 2007. Counts of ASF outbreaks reported in the Southern regions of the country (2007-2014) were aggregated to a grid of hexagons, and a zero-inflated Poisson model accounting for spatial dependence between hexagons was used to identify factors associated with the presence of ASF outbreaks and factors associated with the number of ASF reports in affected hexagons. Increasing density of pigs raised on low biosecurity farms was found to be positively associated with the probability of occurrence of at least one ASF outbreak in a hexagon and with the average number of reported ASF outbreaks amongst affected hexagons. Increasing human population density and increasing distance from the closest diagnostic laboratory were additional variables associated with number of reported ASF outbreaks amongst affected hexagons. The model was shown to have good predictive ability.

Spatial analysis and identification of environmental risk factors affecting the distribution of Indoplanorbis and Lymnaea species in semi-arid and irrigated areas of Haryana, India

Fasciolosis, amphistomosis and schistosomosis, transmitted by the freshwater snail species Indoplanorbis and Lymnaea, are important snail-borne diseases in India as they affect the entire spectrum of domestic animals causing substantial mortality and economic loss. Identifying any heterogeneity in the spatial distribution of these snail-borne diseases will allow for targeted disease control and efficient use of resources. The objectives of this study were threefold: (i) to describe and explore the spatial distribution of Indoplanorbis and Lymnaea in Rohtak and Jhajjar districts of Haryana, India (ii) to identify factors associated with occurrence of these freshwater snail species and (iii) to produce a map showing the predicted risk of occurrence of Lymnaea and Indoplanorbis spp. in the study area. Snails were collected from water bodies of 99 settlements out of a total of 453 in the study area. Kernel smoothing was used to generate a kernel ratio map while Kulldorff's spatial scan statistic was used to detect clusters of settlements with a high/low risk. Multivariable logistic regression showed that snails were almost ten times more likely to be present in rice-growing areas than in those not growing rice (OR 9.24) and that snails were less likely to be present with each 1 km increase in distance from a canal (OR 0.86). The regression model was used to produce a map illustrating the predicted risk of snail occurrence. Since the distribution of vector snails mirrors the distribution of snail-borne parasitic diseases, such spatial analysis helps to determine the relative risk of snail-infestation as well as snail-borne diseases' distribution and planning of control activities.

Modelling the within-herd transmission of Mycoplasma hyopneumoniae in closed pig herds

Background

A discrete time, stochastic, compartmental model simulating the spread of Mycoplasma hyopneumoniae within a batch of industrially raised pigs was developed to understand infection dynamics and to assess the impact of a range of husbandry practices. A ‘disease severity’ index was calculated based on the ratio between the cumulative numbers of acutely and chronically diseased and infectious pigs per day in each age category, divided by the length of time that pigs spent in this age category. This is equal to the number of pigs per day, either acutely or chronically infectious and diseased, divided by the number of all pigs per all days in the model. The impact of risk and protective factors at batch level was examined by adjusting ‘acclimatisation of gilts’, ‘length of suckling period’, ‘vaccination of suckling pigs against M. hyopneumoniae’, ‘contact between fattening pigs of different age during restocking of compartments’ and ‘co-infections in fattening pigs’.

Results

The highest ‘disease severity’ was predicted, when gilts do not have contact with live animals during their acclimatisation, suckling period is 28 days, no vaccine is applied, fatteners have contact with pigs of other ages and are suffering from co-infections. Pigs in this scenario become diseased/infectious for 26.1 % of their lifetime. Logistic regression showed that vaccination of suckling pigs was influential for ‘disease severity’ in growers and finishers, but not in suckling and nursery pigs. Lack of contact between gilts and other live pigs during the acclimatisation significantly influenced the ‘disease severity’ in suckling pigs but had less impact in growing and finishing pigs. The length of the suckling period equally affected the severity of the disease in all age groups with the strongest association in nursery pigs. The contact between fatteners of different groups influenced the course of infection among finishers, but not among other pigs. Finally, presence of co-infections was relevant in growers and finishers, but not in younger pigs.

Conclusion

The developed model allows comparison of different prevention programmes and strategies for controlling transmission of M. hyopneumoniae.

Electronic supplementary material

The online version of this article (doi:10.1186/s40813-016-0026-1) contains supplementary material, which is available to authorized users.

Who Is Spreading Avian Influenza in the Moving Duck Flock Farming Network of Indonesia?

Duck populations are considered to be a reservoir of Highly pathogenic avian influenza (HPAI) virus H5N1 in some agricultural production systems, as they are able to shed the virus for several days without clinical signs. Countries endemically affected with HPAI in Asia are characterised by production systems where ducks are fed on post-harvest spilled rice. During this scavenging process it is common for ducks to come into contact with other duck flocks or wild birds, thereby providing opportunities for virus spread. Effective risk management for HPAI has been significantly compromised by a limited understanding of management of moving duck flocks in these countries, despite of a small number of recent investigations. Here, for the first time, we described the management of moving duck flocks and the structure of the moving duck flock network in quantitative terms so that factors influencing the risk of HPAIV transmission can be identified. By following moving duck flock farmers over a period of 6 months in Java, Indonesia, we were able to describe the movement of flocks and to characterise the network of various types of actors associated with the production system. We used these data to estimate the basic reproductive number for HPAI virus spread. Our results suggest that focussing HPAI prevention measures on duck flocks alone will not be sufficient. Instead, the role of transporters of moving duck flocks, hatcheries and rice paddy owners, in the spread of the HPAI virus needs to be recognised.

Transmission routes of African swine fever virus to domestic pigs: current knowledge and future research directions

African swine fever (ASF) is a major threat to the pig industry in Europe. Since 2007, ASF outbreaks have been ongoing in the Caucasus, Eastern Europe and the Baltic countries, causing severe economic losses for many pig farmers and pork producers. In addition, the number of ASF cases in wild boar populations has dramatically increased over the past few years. Evidence supports direct contact with infectious domestic pigs and wild boars, and consumption of contaminated feed, as the main transmission routes of ASF virus (ASFV) to domestic pigs. However, significant knowledge gaps highlight the urgent need for research to investigate the dynamics of indirect transmission via the environment, the minimal infective doses for contaminated feed ingestion, the probability of effective contacts between infectious wild boars and domestic pigs, the potential for recovered animals to become carriers and a reservoir for transmission, the potential virus persistence within wild boar populations and the influence of human behaviour for the spread of ASFV. This will provide an improved scientific basis to optimise current interventions and develop new tools and strategies to reduce the risk of ASFV transmission to domestic pigs.

Statistical Exploration of Local Transmission Routes for African Swine Fever in Pigs in the Russian Federation, 2007-2014

African swine fever (ASF) is a devastating viral disease of swine that is present in both pigs and wild boar in the western part of the Russian Federation and the eastern part of the European Union. It represents a significant threat for the European pig production industry as neither treatment nor vaccine is available. This study analysed the spatial and spatio-temporal distributions of ASF cases that were reported in domestic pigs and wild boar for assessing the likelihood of wild boar-to-domestic pig and farm-to-farm transmission routes in the epidemic that occurred from 2007 to 2014 in the Krasnodar and the Tver regions, two of the most affected areas of the Russian Federation. Results suggest that in both regions, the spatial proximity to an infectious farm was a strong risk factor for infection of a susceptible farm. In the Krasnodar region, the results of the statistical analysis suggest that the epidemics in wild boar and in domestic pigs were independent from each other. In contrast, there seemed to be a dependence between the two epidemics in the Tver region. But because outbreaks in domestic pigs were not statistically significantly clustered around wild boar cases, the joint spatial distribution of wild boar cases and of outbreaks in domestic pigs in the Tver region may be explained by regular spillovers from the domestic pig to the wild boar population. These findings confirm the need to maintain high biosecurity standards on pig farms and justify strict control measures targeted at domestic pig production such as culling of infected herds and local movement restrictions.

A Spatial Analysis of Rift Valley Fever Virus Seropositivity in Domestic Ruminants in Tanzania

Rift Valley fever (RVF) is an acute arthropod-borne viral zoonotic disease primarily occurring in Africa. Since RVF-like disease was reported in Tanzania in 1930, outbreaks of the disease have been reported mainly from the eastern ecosystem of the Great Rift Valley. This cross-sectional study was carried out to describe the variation in RVF virus (RVFV) seropositivity in domestic ruminants between selected villages in the eastern and western Rift Valley ecosystems in Tanzania, and identify potential risk factors. Three study villages were purposively selected from each of the two Rift Valley ecosystems. Serum samples from randomly selected domestic ruminants (n = 1,435) were tested for the presence of specific immunoglobulin G (IgG) and M (IgM), using RVF enzyme-linked immunosorbent assay methods. Mixed effects logistic regression modelling was used to investigate the association between potential risk factors and RVFV seropositivity. The overall RVFV seroprevalence (n = 1,435) in domestic ruminants was 25.8% and species specific seroprevalence was 29.7%, 27.7% and 22.0% in sheep (n = 148), cattle (n = 756) and goats (n = 531), respectively. The odds of seropositivity were significantly higher in animals sampled from the villages in the eastern than those in the western Rift Valley ecosystem (OR = 1.88, CI: 1.41, 2.51; p<0.001), in animals sampled from villages with soils of good than those with soils of poor water holding capacity (OR = 1.97; 95% CI: 1.58, 3.02; p< 0.001), and in animals which had been introduced than in animals born within the herd (OR = 5.08, CI: 2.74, 9.44; p< 0.001). Compared with animals aged 1-2 years, those aged 3 and 4-5 years had 3.40 (CI: 2.49, 4.64; p< 0.001) and 3.31 (CI: 2.27, 4.82, p< 0.001) times the odds of seropositivity. The findings confirm exposure to RVFV in all the study villages, but with a higher prevalence in the study villages from the eastern Rift Valley ecosystem.

Systematic review of surveillance systems and methods for early detection of exotic, new and re-emerging diseases in animal populations

In this globalized world, the spread of new, exotic and re-emerging diseases has become one of the most important threats to animal production and public health. This systematic review analyses conventional and novel early detection methods applied to surveillance. In all, 125 scientific documents were considered for this study. Exotic (n = 49) and re-emerging (n = 27) diseases constituted the most frequently represented health threats. In addition, the majority of studies were related to zoonoses (n = 66). The approaches found in the review could be divided in surveillance modalities, both active (n = 23) and passive (n = 5); and tools and methodologies that support surveillance activities (n = 57). Combinations of surveillance modalities and tools (n = 40) were also found. Risk-based approaches were very common (n = 60), especially in the papers describing tools and methodologies (n = 50). The main applications, benefits and limitations of each approach were extracted from the papers. This information will be very useful for informing the development of tools to facilitate the design of cost-effective surveillance strategies. Thus, the current literature review provides key information about the advantages, disadvantages, limitations and potential application of methodologies for the early detection of new, exotic and re-emerging diseases.

From risk analysis to risk governance - Adapting to an ever more complex future

Risk analysis is now widely accepted amongst veterinary authorities and other stakeholders around the world as a conceptual framework for integrating scientific evidence into animal health decision making. The resulting risk management for most diseases primarily involves linking epidemiological understanding with diagnostics and/or vaccines. Recent disease outbreaks such as Nipah virus, SARS, avian influenza H5N1, bluetongue serotype 8 and Schmallenberg virus have led to realising that we need to explicitly take into account the underlying complex interactions between environmental, epidemiological and social factors which are often also spatially and temporally heterogeneous as well as interconnected across affected regions and beyond. A particular challenge is to obtain adequate understanding of the influence of human behaviour and to translate this into effective mechanisms leading to appropriate behaviour change where necessary. Both, the One Health and the ecohealth approaches reflect the need for such a holistic systems perspective, however the current implementation of risk analysis frameworks for animal health and food safety is still dominated by a natural or biomedical perspective of science as is the implementation of control and prevention policies. This article proposes to integrate the risk analysis approach with a risk governance framework which explicitly adds the socio-economic context to policy development and emphasizes the need for organisational change and stakeholder engagement.

Spatial and temporal epidemiological analysis in the Big Data era

Concurrent with global economic development in the last 50 years, the opportunities for the spread of existing diseases and emergence of new infectious pathogens, have increased substantially. The activities associated with the enormously intensified global connectivity have resulted in large amounts of data being generated, which in turn provides opportunities for generating knowledge that will allow more effective management of animal and human health risks. This so-called Big Data has, more recently, been accompanied by the Internet of Things which highlights the increasing presence of a wide range of sensors, interconnected via the Internet. Analysis of this data needs to exploit its complexity, accommodate variation in data quality and should take advantage of its spatial and temporal dimensions, where available. Apart from the development of hardware technologies and networking/communication infrastructure, it is necessary to develop appropriate data management tools that make this data accessible for analysis. This includes relational databases, geographical information systems and most recently, cloud-based data storage such as Hadoop distributed file systems. While the development in analytical methodologies has not quite caught up with the data deluge, important advances have been made in a number of areas, including spatial and temporal data analysis where the spectrum of analytical methods ranges from visualisation and exploratory analysis, to modelling. While there used to be a primary focus on statistical science in terms of methodological development for data analysis, the newly emerged discipline of data science is a reflection of the challenges presented by the need to integrate diverse data sources and exploit them using novel data- and knowledge-driven modelling methods while simultaneously recognising the value of quantitative as well as qualitative analytical approaches. Machine learning regression methods, which are more robust and can handle large datasets faster than classical regression approaches, are now also used to analyse spatial and spatio-temporal data. Multi-criteria decision analysis methods have gained greater acceptance, due in part, to the need to increasingly combine data from diverse sources including published scientific information and expert opinion in an attempt to fill important knowledge gaps. The opportunities for more effective prevention, detection and control of animal health threats arising from these developments are immense, but not without risks given the different types, and much higher frequency, of biases associated with these data.

Sources of spatial animal and human health data: Casting the net wide to deal more effectively with increasingly complex disease problems

During the last 30years it has become commonplace for epidemiological studies to collect locational attributes of disease data. Although this advancement was driven largely by the introduction of handheld global positioning systems (GPS), and more recently, smartphones and tablets with built-in GPS, the collection of georeferenced disease data has moved beyond the use of handheld GPS devices and there now exist numerous sources of crowdsourced georeferenced disease data such as that available from georeferencing of Google search queries or Twitter messages. In addition, cartography has moved beyond the realm of professionals to crowdsourced mapping projects that play a crucial role in disease control and surveillance of outbreaks such as the 2014 West Africa Ebola epidemic. This paper provides a comprehensive review of a range of innovative sources of spatial animal and human health data including data warehouses, mHealth, Google Earth, volunteered geographic information and mining of internet-based big data sources such as Google and Twitter. We discuss the advantages, limitations and applications of each, and highlight studies where they have been used effectively.

Randomised field trial to evaluate serological response after foot-and-mouth disease vaccination in Turkey

Despite years of biannual mass vaccination of cattle, foot-and-mouth disease (FMD) remains uncontrolled in Anatolian Turkey. To evaluate protection after mass vaccination we measured post-vaccination antibodies in a cohort of cattle (serotypes O, A and Asia-1). To obtain results reflecting typical field protection, participants were randomly sampled from across Central and Western Turkey after routine vaccination. Giving two-doses one month apart is recommended when cattle are first vaccinated against FMD. However, due to cost and logistics, this is not routinely performed in Turkey, and elsewhere. Nested within the cohort, we conducted a randomised trial comparing post-vaccination antibodies after a single-dose versus a two-dose primary vaccination course. Four to five months after vaccination, only a third of single-vaccinated cattle had antibody levels above a threshold associated with protection. A third never reached this threshold, even at peak response one month after vaccination. It was not until animals had received three vaccine doses in their lifetime, vaccinating every six months, that most (64% to 86% depending on serotype) maintained antibody levels above this threshold. By this time cattle would be >20 months old with almost half the population below this age. Consequently, many vaccinated animals will be unprotected for much of the year. Compared to a single-dose, a primary vaccination course of two-doses greatly improved the level and duration of immunity. We concluded that the FMD vaccination programme in Anatolian Turkey did not produce the high levels of immunity required. Higher potency vaccines are now used throughout Turkey, with a two-dose primary course in certain areas. Monitoring post-vaccination serology is an important component of evaluation for FMD vaccination programmes. However, consideration must be given to which antigens are present in the test, the vaccine and the field virus. Differences between these antigens affect the relationship between antibody titre and protection.

Dynamics of African swine fever virus shedding and excretion in domestic pigs infected by intramuscular inoculation and contact transmission

African swine fever virus (ASFV) is a highly virulent swine pathogen that has spread across Eastern Europe since 2007 and for which there is no effective vaccine or treatment available. The dynamics of shedding and excretion is not well known for this currently circulating ASFV strain. Therefore, susceptible pigs were exposed to pigs intramuscularly infected with the Georgia 2007/1 ASFV strain to measure those dynamics through within- and between-pen transmission scenarios. Blood, oral, nasal and rectal fluid samples were tested for the presence of ASFV by virus titration (VT) and quantitative real-time polymerase chain reaction (qPCR). Serum was tested for the presence of ASFV-specific antibodies. Both intramuscular inoculation and contact transmission resulted in development of acute disease in all pigs although the experiments indicated that the pathogenesis of the disease might be different, depending on the route of infection. Infectious ASFV was first isolated in blood among the inoculated pigs by day 3, and then chronologically among the direct and indirect contact pigs, by day 10 and 13, respectively. Close to the onset of clinical signs, higher ASFV titres were found in blood compared with nasal and rectal fluid samples among all pigs. No infectious ASFV was isolated in oral fluid samples although ASFV genome copies were detected. Only one animal developed antibodies starting after 12 days post-inoculation. The results provide quantitative data on shedding and excretion of the Georgia 2007/1 ASFV strain among domestic pigs and suggest a limited potential of this isolate to cause persistent infection.

Epidemiology caught in the causal web of bovine tuberculosis

Bovine tuberculosis in domestic cattle in the presence of significant infection levels in wild animal species represents a major challenge for disease control. The use of wild animal population density reduction as part of risk management policies is highly controversial from the perspectives of scientific effectiveness and societal acceptability. The experience in Great Britain in dealing with this problem over the last 20 years demonstrates the need to engage in an integrated approach towards risk governance to more effectively deal with such a complex and contentious multifactorial animal disease problem. As part of this process, the traditional emphasis on bioscientific, in particular epidemiological, research needs to be complemented by relevant social science approaches. In addition, the risk assessment as well as the risk management should have effective participatory elements.

Modular framework to assess the risk of African swine fever virus entry into the European Union

Background

The recent occurrence and spread of African swine fever (ASF) in Eastern Europe is perceived as a serious risk for the pig industry in the European Union (EU). In order to estimate the potential risk of ASF virus (ASFV) entering the EU, several pathways of introduction were previously assessed separately. The present work aimed to integrate five of these assessments (legal imports of pigs, legal imports of products, illegal imports of products, fomites associated with transport and wild boar movements) into a modular tool that facilitates the visualization and comprehension of the relative risk of ASFV introduction into the EU by each analyzed pathway.

Results

The framework’s results indicate that 48% of EU countries are at relatively high risk (risk score 4 or 5 out of 5) for ASFV entry for at least one analyzed pathway. Four of these countries obtained the maximum risk score for one pathway: Bulgaria for legally imported products during the high risk period (HRP); Finland for wild boar; Slovenia and Sweden for legally imported pigs during the HRP. Distribution of risk considerably differed from one pathway to another; for some pathways, the risk was concentrated in a few countries (e.g., transport fomites), whereas other pathways incurred a high risk for 4 or 5 countries (legal pigs, illegal imports and wild boar).

Conclusions

The modular framework, developed to estimate the risk of ASFV entry into the EU, is available in a public domain, and is a transparent, easy-to-interpret tool that can be updated and adapted if required. The model’s results determine the EU countries at higher risk for each ASFV introduction route, and provide a useful basis to develop a global coordinated program to improve ASFV prevention in the EU.

Foot and mouth disease in Zambia: Spatial and temporal distributions of outbreaks, assessment of clusters and implications for control

Zambia has been experiencing low livestock productivity as well as trade restrictions owing to the occurrence of foot and mouth disease (FMD), but little is known about the epidemiology of the disease in these endemic settings. The fundamental questions relate to the spatio-temporal distribution of FMD cases and what determines their occurrence. A retrospective review of FMD cases in Zambia from 1981 to 2012 was conducted using geographical information systems and the SaTScan software package. Information was collected from peer-reviewed journal articles, conference proceedings, laboratory reports, unpublished scientific reports and grey literature. A space–time permutation probability model using a varying time window of one year was used to scan for areas with high infection rates. The spatial scan statistic detected a significant purely spatial cluster around the Mbala–Isoka area between 2009 and 2012, with secondary clusters in Sesheke–Kazungula in 2007 and 2008, the Kafue flats in 2004 and 2005 and Livingstone in 2012. This study provides evidence of the existence of statistically significant FMD clusters and an increase in occurrence in Zambia between 2004 and 2012. The identified clusters agree with areas known to be at high risk of FMD. The FMD virus transmission dynamics and the heterogeneous variability in risk within these locations may need further investigation.

Spatial and temporal pattern of Rift Valley fever outbreaks in Tanzania; 1930 to 2007

BACKGROUND

Rift Valley fever (RVF)-like disease was first reported in Tanzania more than eight decades ago and the last large outbreak of the disease occurred in 2006-07. This study investigates the spatial and temporal pattern of RVF outbreaks in Tanzania over the past 80 years in order to guide prevention and control strategies.

MATERIALS AND METHODS

A retrospective study was carried out based on disease reporting data from Tanzania at district or village level. The data were sourced from the Ministries responsible for livestock and human health, Tanzania Meteorological Agency and research institutions involved in RVF surveillance and diagnosis. The spatial distribution of outbreaks was mapped using ArcGIS 10. The space-time permutation model was applied to identify clusters of cases, and a multivariable logistic regression model was used to identify risk factors associated with the occurrence of outbreaks in the district.

PRINCIPAL FINDINGS

RVF outbreaks were reported between December and June in 1930, 1947, 1957, 1960, 1963, 1968, 1977-79, 1989, 1997-98 and 2006-07 in 39.2% of the districts in Tanzania. There was statistically significant spatio-temporal clustering of outbreaks. RVF occurrence was associated with the eastern Rift Valley ecosystem (OR = 6.14, CI: 1.96, 19.28), total amount of rainfall of >405.4 mm (OR = 12.36, CI: 3.06, 49.88), soil texture (clay [OR = 8.76, CI: 2.52, 30.50], and loam [OR = 8.79, CI: 2.04, 37.82]).

CONCLUSION/SIGNIFICANCE

RVF outbreaks were found to be distributed heterogeneously and transmission dynamics appeared to vary between areas. The sequence of outbreak waves, continuously cover more parts of the country. Whenever infection has been introduced into an area, it is likely to be involved in future outbreaks. The cases were more likely to be reported from the eastern Rift Valley than from the western Rift Valley ecosystem and from areas with clay and loam rather than sandy soil texture.

Spatial multi-criteria decision analysis to predict suitability for African swine fever endemicity in Africa

Background

African swine fever (ASF) is endemic in several countries of Africa and may pose a risk to all pig producing areas on the continent. Official ASF reporting is often rare and there remains limited awareness of the continent-wide distribution of the disease.

In the absence of accurate ASF outbreak data and few quantitative studies on the epidemiology of the disease in Africa, we used spatial multi-criteria decision analysis (MCDA) to derive predictions of the continental distribution of suitability for ASF persistence in domestic pig populations as part of sylvatic or domestic transmission cycles. In order to incorporate the uncertainty in the relative importance of different criteria in defining suitability, we modelled decisions within the MCDA framework using a stochastic approach. The predictive performance of suitability estimates was assessed via a partial ROC analysis using ASF outbreak data reported to the OIE since 2005.

Results

Outputs from the spatial MCDA indicate that large areas of sub-Saharan Africa may be suitable for ASF persistence as part of either domestic or sylvatic transmission cycles. Areas with high suitability for pig to pig transmission (‘domestic cycles’) were estimated to occur throughout sub-Saharan Africa, whilst areas with high suitability for introduction from wildlife reservoirs (‘sylvatic cycles’) were found predominantly in East, Central and Southern Africa. Based on average AUC ratios from the partial ROC analysis, the predictive ability of suitability estimates for domestic cycles alone was considerably higher than suitability estimates for sylvatic cycles alone, or domestic and sylvatic cycles in combination.

Conclusions

This study provides the first standardised estimates of the distribution of suitability for ASF transmission associated with domestic and sylvatic cycles in Africa. We provide further evidence for the utility of knowledge-driven risk mapping in animal health, particularly in data-sparse environments.

Calf-level factors associated with bovine neonatal pancytopenia--a multi-country case-control study

Bovine neonatal pancytopenia (BNP), a high fatality condition causing haemorrhages in calves aged less than 4 weeks, was first reported in 2007 in Germany and subsequently observed at low incidence in other European countries and New Zealand. A multi-country matched case-control study was conducted in 2011 to identify calf-level risk factors for BNP. 405 BNP cases were recruited from 330 farms in Belgium, France, Germany and the Netherlands by laboratory confirmation of farmer-reported cases. Up to four calves of similar age from the same farm were selected as controls (1154 calves). Risk factor data were collected by questionnaire. Multivariable modelling using conditional logistic regression indicated that PregSure®BVD (PregSure, Pfizer Animal Health) vaccination of the dam was strongly associated with BNP cases (adjusted matched Odds Ratio - amOR 17.8 first lactation dams; 95% confidence interval – ci 2.4, 134.4; p = 0.005), and second or more lactation PregSure-vaccinated dams were more likely to have a case than first lactation vaccinated dams (amOR 2.2 second lactation; ci 1.1, 4.3; p = 0.024; amOR 5.3 third or more lactation; ci 2.9, 9.8; p = <0.001). Feeding colostrum from other cows was strongly associated with BNP if the dam was not PregSure-vaccinated (amOR 30.5; ci 2.1, 440.5; p = 0.012), but the effect was less if the dam was PregSure-vaccinated (amOR 2.1; ci 1.1, 4.0; p = 0.024). Feeding exclusively dam’s milk was a higher risk than other types of milk (amOR 3.4; ci 1.6, 7.5; p = 0.002). The population attributable fractions were 0.84 (ci 0.68, 0.92) for PregSure vaccination, 0.13 (ci 0.06, 0.19) for feeding other cows’ colostrum, and 0.15 (ci 0.08, 0.22) for feeding dam’s milk. No other calf-level factors were identified, suggesting that there are other important factors that are outside the scope of this study, such as genetics, which explain why BNP develops in some PregSure-colostrum-exposed calves but not in others.

Modelling the expected rate of laboratory biosafety breakdowns involving rinderpest virus in the post-eradication era

Now that we are in the rinderpest post-eradication era, attention is focused on the risk of re-introduction. A semi-quantitative risk assessment identified accidental use of rinderpest virus in laboratories as the most likely cause of re-introduction. However there is little data available on the rates of laboratory biosafety breakdowns in general. In addition, any predictions based on past events are subject to various uncertainties. The aims of this study were therefore to investigate the potential usefulness of historical data for predicting the future risk of rinderpest release via laboratory biosafety breakdowns, and to investigate the impacts of the various uncertainties on these predictions. Data were collected using a worldwide online survey of laboratories, a structured search of ProMED reports and discussion with experts. A stochastic model was constructed to predict the number of laboratory biosafety breakdowns involving rinderpest that will occur over the next 10 years, based on: (1) the historical rate of biosafety breakdowns; and (2) the change in the number of laboratories that will have rinderpest virus in the next 10 years compared to historically. The search identified five breakdowns, all of which occurred during 1970-2000 and all of which were identified via discussions with experts. Assuming that our search for historical events had a sensitivity of over 60% and there has been at least a 40% reduction in the underlying risk (attributable to decreased laboratory activity post eradication) the most likely number of biosafety events worldwide was estimated to be zero over a 10 year period. However, the risk of at least one biosafety breakdown remains greater than 1 in 10,000 unless the sensitivity was at least 99% or the number of laboratories has decreased by at least 99% (based on 2000-2010 during which there were no biosafety breakdowns).

Transmission potential of Rift Valley fever virus over the course of the 2010 epidemic in South Africa

A Rift Valley fever (RVF) epidemic affecting animals on domestic livestock farms was reported in South Africa during January-August 2010. The first cases occurred after heavy rainfall, and the virus subsequently spread countrywide. To determine the possible effect of environmental conditions and vaccination on RVF virus transmissibility, we estimated the effective reproduction number (Re) for the virus over the course of the epidemic by extending the Wallinga and Teunis algorithm with spatial information. Re reached its highest value in mid-February and fell below unity around mid-March, when vaccination coverage was 7.5%-45.7% and vector-suitable environmental conditions were maintained. The epidemic fade-out likely resulted first from the immunization of animals following natural infection or vaccination. The decline in vector-suitable environmental conditions from April onwards and further vaccination helped maintain Re below unity. Increased availability of vaccine use data would enable evaluation of the effect of RVF vaccination campaigns.