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.

Simultaneous evaluation of diagnostic marker utility for enzootic bovine leukosis.

BACKGROUND: Enzootic bovine leukosis (EBL) is a disease of cattle caused by bovine leukemia virus (BLV). More than 60% of BLV-infected cattle remain subclinical and are thus referred to as aleukemic (AL) cattle. Approximately 30% of infected cattle show a relatively stable increase in the number of B lymphocytes; these cattle are termed persistent lymphocytosis (PL) cattle. A small percentage of infected cattle develop BLV-induced B cell lymphoma (EBL) and are called EBL cattle. Due to the increase in the number of BLV-infected cattle, the number of EBL cattle has featured a corresponding increase over recent years in Japan. Several diagnostic criteria for EBL (e.g., enlarged superficial lymph nodes, protrusion of the eye, increased peripheral blood lymphocyte, etc.) are used for on-farm diagnosis and antemortem tests at slaughterhouses. Since the slaughter of EBL cattle for human consumption is not allowed, on-farm detection of EBL cattle is important for reducing the economic loss incurred by farms. Therefore, establishing new diagnostic markers to improve the efficiency and accuracy of the antemortem detection of EBL cattle is a critical, unmet need. To simultaneously evaluate the utility of candidate markers, this study measured the values of each marker using the blood samples of 687 cattle with various clinical statuses of BLV infection (EBL, PL, AL and non-infected cattle). RESULTS: Sensitivity (Se) and specificity (Sp) were highest for the serum thymidine kinase (TK) followed by the serum lactate dehydrogenase (LDH) isozyme 2. The number of peripheral blood lymphocytes and proviral load in peripheral blood had the lowest Se and Sp. The values of all markers other than TK were influenced by the sex of the tested cattle. CONCLUSIONS: Although tLDH and its isozymes (LDHs) may be influenced by the sex of the tested cattle, the high accuracy of TK and LDH2 as well as accessibility and simplicity of the protocol used to measure these enzymes recommend the utility of TK and LDHs for EBL cattle detection. Using these markers for screening followed by the application of existing diagnostic criteria may improve the efficiency and accuracy of EBL cattle detection on farms, thereby contributing to the reduction of economic losses in farms.

Wild boars: A potential source of Erysipelothrix rhusiopathiae infection in Japan.

The potential role of wild boars as a source of erysipelas infection was investigated. An ELISA test of wild boar serum samples from 41 prefectures in Japan revealed that proportions of the Erysipelothrix rhusiopathiae-positive samples were very high in all the prefectures, and the mean positive rate was 95.6% (1312/1372). Serovars of E. rhusiopathiae isolates from wild boars were similar to those of previously reported swine isolates, and all serovar isolates tested were found to be pathogenic to mice. These results suggest that wild boars in Japan constitute a reservoir of E. rhusiopathiae and may pose risks to other animals.

Surveillance of Culicoides biting midges in northern Honshu, Japan, during the period of Akabane virus spread.

A surveillance of Culicoides biting midges with light suction traps was conducted in the northern region of Honshu, main island of Japan, during the summers and autumns of 2009 and 2010. A total of 106 trap collections across 37 cattle farms were investigated for the structure and distribution of Culicoides species. Forty-thousand and one hundred forty-nine specimens of Culicoides biting midges were identified at the species level, and ≥19 species were included in the specimens. Culicoides oxystoma, which is a known major vector of Akabane virus (AKAV), appeared not to have expanded in northern Honshu during the surveillance. Of the potential AKAV vectors suggested by a previous laboratory experiment, C. tainanus and C. punctatus widely infested cowsheds across northern Honshu. The AKAV circulation was confirmed by serological surveillance of sentinel cattle in northern Honshu during the summer and autumn of 2010 and, consequently, >200 calves affected by the virus were identified as of spring 2011. Our surveillance demonstrated that C. tainanus and C. punctatus were widely spread and often dominated at cattle farms in/around the seroconverted regions, and our results thus suggest that these species played a critical role in the AKAV transmission in 2010. Because the distribution ranges of C. tainanus and C. punctatus cover almost all of mainland Japan, a potential risk of AKAV transmission might be expected even in areas outside the range of C. oxystoma.

Reconstructing a transmission network and identifying risk factors of secondary transmissions in the 2010 foot-and-mouth disease outbreak in Japan.

Research aimed at understanding transmission networks, representing a network of "who infected whom" for an infectious disease outbreak, have been actively conducted in recent years. Transmission network models incorporating epidemiological and genetic data are valuable for elucidating disease transmission pathways. In this study, we reconstructed the transmission network of the foot-and-mouth disease (FMD) epidemic in Japan in 2010, and explored farm-level risk factors associated with increased risk of secondary transmission. A published, systematic Bayesian transmission network model was applied to epidemiological data of 292 infected farms and whole genome sequence data of 104 of the infected farms. This model can make inferences for known infected farms even lacking genetic data. After estimating the consensus network, the accuracy of the network was examined by comparison with epidemiological data. Then, risk factors inferred to have been sources of secondary transmission were explored using zero-inflated Poisson regression model. As far as we are aware, this study represents the largest FMD outbreak transmission network to be published by such means combining epidemiological and genetic data. The consensus network reasonably generated the epidemiological links, which were estimated from the actual epidemiological investigation. Among 292 farms, 101 farms (35%) were inferred to have been the sources of secondary transmission, and amongst these farms, the median number of secondary cases was 2 (min:1-max:18) farms. The farm-type (small and large -sized pig farms), the number of days from onset to notification, and the number of susceptible farms within a 1-km radius were significantly associated with secondary transmission. Transmission network modelling enabled inference of the connections between infected farms during the FMD epidemic and identified important factors for controlling the risk of secondary transmission. This study demonstrated that the predominant susceptible species held on a farm, farm size, and animal density were associated with increased onwards transmission.

A Case of Spontaneous Spinal Subdural Hematoma Complicated by Cranial Subarachnoid Hemorrhage and Spinal Adhesive Arachnoiditis.

A 76-year-old woman with a spinal subdural hematoma (SDH) was presented with severe back pain without headache. Magnetic resonance imaging (MRI) performed 4 days after onset showed SDH extending from Th2 to L3. She was diagnosed with spontaneous SDH without neurological manifestation, and conservative treatment was selected. Transient disturbance of orientation appeared 7 days after onset. Small subarachnoid hemorrhage (SAH) was detected on head CT, and strict antihypertensive therapy was started. Symptoms changed for the better. Back pain disappeared 4 weeks after onset. On follow-up MRI at 6 months after onset, the SDH had been resolved spontaneously. Although adhesive arachnoiditis was observed at Th4-6, the recurrence of clinical symptoms was not observed at one year and a half after onset. Spinal subdural space is almost avascular; a hematoma in a subdural space is considered to come from a subarachnoid space when it is a lot. A hemorrhage in subarachnoid space was flushed by cerebral spinal fluid; hematoma or arachnoiditis was not formed in general. In our case, hemorrhage was a lot and expansion of SDH was large enough to cause cranial SAH and arachnoiditis. But longitudinally expanded SDH did not show neurological manifestation and resolved spontaneously in our case.

Reconstructing foot-and-mouth disease outbreaks: a methods comparison of transmission network models.

A number of transmission network models are available that combine genomic and epidemiological data to reconstruct networks of who infected whom during infectious disease outbreaks. For such models to reliably inform decision-making they must be transparently validated, robust, and capable of producing accurate predictions within the short data collection and inference timeframes typical of outbreak responses. A lack of transparent multi-model comparisons reduces confidence in the accuracy of transmission network model outputs, negatively impacting on their more widespread use as decision-support tools. We undertook a formal comparison of the performance of nine published transmission network models based on a set of foot-and-mouth disease outbreaks simulated in a previously free country, with corresponding simulated phylogenies and genomic samples from animals on infected premises. Of the transmission network models tested, Lau's systematic Bayesian integration framework was found to be the most accurate for inferring the transmission network and timing of exposures, correctly identifying the source of 73% of the infected premises (with 91% accuracy for sources with model support >0.80). The Structured COalescent Transmission Tree Inference provided the most accurate inference of molecular clock rates. This validation study points to which models might be reliably used to reconstruct similar future outbreaks and how to interpret the outputs to inform control. Further research could involve extending the best-performing models to explicitly represent within-host diversity so they can handle next-generation sequencing data, incorporating additional animal and farm-level covariates and combining predictions using Ensemble methods and other approaches.

Matched case-control study of the influence of inland waters surrounding poultry farms on avian influenza outbreaks in Japan.

To successfully control highly pathogenic avian influenza (HPAI), understanding the risk factors related to the incursion of the virus into poultry farms is essential. In this study, we focused on the presence of inland waters surrounding poultry farms as a potential risk factor of incursion of the virus. To evaluate the influence of inland waters surrounding poultry farms on HPAI outbreaks in Japan, a simple matched case-control study was conducted. The results of the conditional regression analyses indicated that the number of farms with neighbouring inland waters was significantly high among the affected farms during the 2016-2017 outbreak period. These results provide good grounds for strengthening biosecurity management at farms located near inland waters.

Mathematical modeling of porcine epidemic diarrhea virus dynamics within a farrow-to-finish swine farm to investigate the effects of control measures.

Porcine epidemic diarrhea (PED) is a highly contagious enteric disease in swine that can cause devastating economic damage to pig producers. Japan was severely affected by PED epidemics from 2013 through 2015, with over 1000 farms were affected during this period. Although many studies have unraveled pathological and molecular characteristics of PED virus (PEDV), the mechanism for within-farm spread is largely unknown. Here, we constructed a deterministic compartmental model to quantitatively describe the infection dynamics in a farm setting and to investigate effective control measures. The model consisted of three separate houses and four swine populations framed in a standard commercial farrow-to-finish swine operation in Japan, with a special focus on the role of indirect transmission via the on-farm environment contaminated by feces of infected pigs. Some model parameters were estimated using the Japanese empirical outbreak data. Model outputs over a 90-day period showed that the number of infected sows in a dry sow house peaked within a week after disease introduction, and PEDV was retained on the farm. In the farrowing house, the number of infected sows also peaked within a week followed by a tentative disappearance of infected pigs, whereas the number of infected piglets in the farrowing house spiked and the number of neonatal deaths increased rapidly until around Day 21 followed by a continued increase at a slower pace. In the fattening house, the number of infected pigs reached an equilibrium at around Day 25 and approximately 15% of pigs continued to be infected thereafter. Herd size was not found to have a significant influence on the overall trend in our model output. Among the control measures examined using our model, the application of effective vaccination was considered to be the most promising. Activities such as performing more thorough cleanings to remove residual virus or implementing stricter on-farm biosecurity to cease between-house virus transfer demonstrated little effectiveness for the control of PED. These results may imply that preventing PEDV incursion on a swine farm by elevated farm biosecurity measures is critically important, and that further research is necessary to prepare for future outbreaks, particularly research related to development of an effective vaccine that can prevent infection, and/or reduction of piglet mortality.

Evaluation of fecal shedding and antibody response in dairy cattle infected with paratuberculosis using national surveillance data in Japan.

Paratuberculosis or Johne's disease (JD), is a chronic infectious disease causing intractable diarrhea in cattle, which leads to less productivity, such as decreased milk yield, and lower daily weight gain. As a control measure against JD in cattle, national serological surveillance has been conducted in Japan since 1998. To conduct modeling studies that are useful to evaluate the effectiveness of control measures against JD, reliable parameter values, such as length of time from infection to the start of fecal shedding or antibody expression, are especially important. These parameters in the Japanese cattle population are assumed to be different from those in other countries with a higher prevalence of JD or in experimental infection settings; therefore, they must be estimated for the cattle population in Japan. Data from national surveillance conducted in Tokachi District, Hokkaido Prefecture, were used for this study. Using data from JD diagnostic tests for all cattle in Tokachi District between 1998 and 2014, all testing histories for infected animals were estimated as the number of tested cattle and positive cattle at each age of month for both fecal and antibody tests. A deterministic mathematical model for JD development, from infection to fecal shedding and antibody expression in infected cattle, was constructed to obtain the probability of testing positive when applied to both fecal and antibody tests at a given age. Likelihood was obtained from these estimated test results and best values for parameters were obtained using the Markov Chain Monte-Carlo method. Fifty-five percent of infected cattle were projected to have a transient shedding period, which was estimated to start 12 months after infection and last for 4 months. Persistent shedding was projected to occur in all infected cattle, and estimated to begin 7-84 months from infection. Following persistent shedding, antibody expression was estimated to start 7 months later. These values are useful for developing models to evaluate the status of JD infection and the effectiveness of control measures in the Japanese cattle population.

Meteorological factors affecting seroconversion of Akabane disease in sentinel calves in the subtropical Okinawa Islands of Japan.

Akabane virus, the pathogen-causing Akabane disease, is an arthropod-borne virus (arbovirus) transmitted by the Culicoides biting midge. A nationwide serological surveillance program for bovine arboviral diseases, including Akabane disease, has been established in Japan to monitor the circulation of arboviruses by targeting sentinel calves. Okinawa, which is located in the southwestern-most region of Japan, is a high-risk area for incursion of arboviruses. The aim of the present study was to identify the meteorological factors related to farm-level seroconversion of Akabane virus by analyzing the serological surveillance data for sentinel calves collected in Okinawa between 2007 and 2015. Rainfall in winter, spring, and autumn was positively associated with seroconversion. Adequate rainfall seems to keep the soil in a suitably moist state for growth and survival of biting midges. Maximum temperature in winter was also positively associated with seroconversion in sentinel calves. The warmer temperatures in winter may provide conditions suitable for shortening the larval development cycle and increase production of adult midges. Our findings indicate that meteorological factors such as temperature and rainfall may be important factors that produce circumstances conducive to effective transmission of the virus between vectors and the host. The results of this study provide a better understanding of the circulation of arboviruses and offer suggestions for developing better surveillance and measures to prevent arboviral disease.

Competencies for government veterinary services of the future: Summary of ISVEE 14 Yucatan 2015 roundtable discussion.

This short communication summarizes the strengths and weaknesses of current organisational structures in government veterinary services, as well as future technical, financial and societal challenges and related necessary competencies for government veterinary services of the future as discussed by an expert panel at ISVEE2015. First, participating representatives of veterinary services of diverse geographical backgrounds and statements from the audience confirmed that non-technical skills such as ability to work in teams, adaptability to new environments and situations, social and communication skills are increasingly seen as important. The second challenge faced by veterinary services is related to capacity issues, i.e. to have enough manpower to plan and deliver according to legislation in a period of shrinking budgets. New and emerging diseases can result in sudden, massive increases in the workload of veterinary services. Technical complexity has also increased for some hazards. Staff skills in veterinary services therefore need to be continuously updated, and it is essential to establish cross technical collaboration with other sectors including food safety, public health and environment. ISVEE conferences were seen as an opportunity to provide a global platform to develop skills needed by veterinary services, now and in the future.

A Large-Scale Survey of Trichinella spp. Infection in Japanese Wild Boars.

This study presents the results of a large-scale, one-year survey of Trichinella spp. in Japanese wild boars (Sus scrofa). We analyzed the tongues of 1,168 wild boars captured by hunters in 30 prefectures of Japan, most of which were boar habitats, from October 2014 to January 2015. The samples were digested, and the prevalence of Trichinella spp. muscle larvae was examined. Examination of pooled samples from 10 individuals (15 g per head) or 117 randomly selected samples (10% of the total number of samples) that were individually processed showed no larval infection. Thus, our data suggests that Japanese wild boars do not play a major role in the sylvatic cycle of Trichinella parasites.

Survey for detecting persistently infected cattle with bovine viral diarrhea in Japan.

To establish effective and efficient control measures for bovine viral diarrhea (BVD) in Japan, a pilot survey on persistently infected (PI) animals in dairy farms was conducted. A total of 5,949 cattle from 79 farms in 11 prefectures were tested; seven cattle in six farms were identified as PI animals. The proportion of farms with PI animals in Japan was calculated as 7.6% (95% confidence interval: 3.1-16.4%), and proportion of cattle tested as PI animals was 0.12% (95% confidence interval: 0.05-0.25%). The presence of only one or two animals in PI positive farms suggested the application of screening tests covering almost all cattle in each farm using pooled serum or bulk milk could be effective for implementing a large-scale survey for detecting PI animals.

Epidemiological analysis of bovine ephemeral fever in 2012-2013 in the subtropical islands of Japan.

BACKGROUND: Bovine ephemeral fever (BEF) is a febrile disease of cattle that is transmitted by arthropod vectors such as mosquitoes and Culicoides biting midges. An outbreak of BEF recently occurred in Ishigaki Island and surrounding islands that are located southwest of Japan. In this study, an epidemiological analysis was conducted to understand the temporal and spatial characteristics of the outbreak. Factors associated with the disease spread within Ishigaki Island were investigated by hierarchical Bayesian models. The possibility of between-island transmission by windborne vectors and transmission by long-distance migration of infected vectors were examined using atmospheric dispersion models. RESULTS: In September 2012, the first case of the disease was detected in the western part of Ishigaki Island. In 1 month, it had rapidly spread to the southern part of the island and to surrounding islands, and led to 225 suspected cases of BEF during the outbreak. The dispersion model demonstrated the high possibility of between-island transmission by wind. Spatial analysis showed that paddy fields, farmlands, and slope gradients had a significant impact on the 1-km cell-level incidence risk. These factors may have influenced the habitats and movements of the vectors with regard to the spread of BEF. A plausible incursion event of infected vectors from Southeast Asia to Ishigaki Island was estimated to have occurred at the end of August. CONCLUSION: This study revealed that the condition of a terrain and land use significantly influenced disease transmission. These factors are important in assessing favorable environments for related vectors. The results of the dispersion model indicated the likely transmission of the infected vectors by wind on the local scale and on the long-distance scale. These findings would be helpful for developing a surveillance program and developing preventive measures against BEF.

Spatial epidemiological analysis of bovine encephalomyelitis outbreaks caused by Akabane virus infection in western Japan in 2011.

Akabane disease, which is distributed in temperate and tropical regions in the world, is a vector-borne disease of ruminants caused by the Akabane virus, transmitted by Culicoides biting midges. In 2011, outbreaks of Akabane viral encephalomyelitis occurred in the Shimane Prefecture in western Japan. In this study, a spatial epidemiological analysis was conducted to understand environmental factors associated with the spread of Akabane disease. By applying a conditional autoregressive model, the relationship between infection and environmental variables was explored. The results showed that the dominance of farmlands and the presence of infected farms within a 3-km radius had a significant effect on infection. This result implies that land use, which would relate with the vector habitat, and the presence of neighboring infected farms as a source of infection may have influenced the spread of the disease in this region. These findings provide basic insights into the spread of Akabane disease and useful suggestions for developing a surveillance program and preventive measures against the disease.

Genomic Motifs as a Novel Indicator of the Relationship between Strains Isolated from the Epidemic of Porcine Epidemic Diarrhea in 2013-2014.

Porcine epidemic diarrhea virus (PEDV) is a positive-sense RNA virus that causes infectious gastroenteritis in pigs. Following a PED outbreak that occurred in China in 2010, the disease was identified for the first time in the United States in April 2013, and was reported in many other countries worldwide from 2013 to 2014. As a novel approach to elucidate the epidemiological relationship between PEDV strains, we explored their genome sequences to identify the motifs that were shared within related strains. Of PED outbreaks reported in many countries during 2013-2014, 119 PEDV strains in Japan, USA, Canada, Mexico, Germany, and Korea were selected and used in this study. We developed a motif mining program, which aimed to identify a specific region of the genome that was exclusively shared by a group of PEDV strains. Eight motifs were identified (M1-M8) and they were observed in 41, 9, 18, 6, 10, 14, 2, and 2 strains, respectively. Motifs M1-M6 were shared by strains from more than two countries, and seemed to originate from one PEDV strain, Indiana12.83/USA/2013, among the 119 strains studied. BLAST search for motifs M1-M6 revealed that M3-M5 were almost identical to the strain ZMDZY identified in 2011 in China, while M1 and M2 were similar to other Chinese strains isolated in 2011-2012. Consequently, the PED outbreaks in these six countries may be closely related, and multiple transmissions of PEDV strains between these countries may have occurred during 2013-2014. Although tools such as phylogenetic tree analysis with whole genome sequences are increasingly applied to reveal the connection between isolates, its interpretation is sometimes inconclusive. Application of motifs as a tool to examine the whole genome sequences of causative agents will be more objective and will be an explicit indicator of their relationship.

Fraction of bovine leukemia virus-infected dairy cattle developing enzootic bovine leukosis.

Enzootic bovine leucosis (EBL) is a transmissible disease caused by the bovine leukemia virus that is prevalent in cattle herds in many countries. Only a small fraction of infected animals develops clinical symptoms, such as malignant lymphosarcoma, after a long incubation period. In the present study, we aimed to determine the fraction of EBL-infected dairy cattle that develop lymphosarcoma and the length of the incubation period before clinical symptoms emerge. These parameters were determined by a mathematical modeling approach based on the maximum-likelihood estimation method, using the results of a nationwide serological survey of prevalence in cattle and passive surveillance records. The best-fit distribution to estimate the disease incubation period was determined to be the Weibull distribution, with a median and average incubation period of 7.0 years. The fraction of infected animals developing clinical disease was estimated to be 1.4% with a 95% confidence interval of 1.2-1.6%. The parameters estimated here contribute to an examination of efficient control strategies making quantitative evaluation available.

Potential impact of species and livestock density on the epidemic size and effectiveness of control measures for foot-and-mouth disease in Japan.

The characteristics of a livestock area, including farm density and animal species, influence the spread of foot-and-mouth disease (FMD). In this study, the impact of livestock area on FMD epidemics was examined using an FMD transmission model. For this simulation, three major livestock areas were selected: the 2010 FMD epidemic area in Japan as the baseline area (BS), a cattle and pig mixed production area (CP) and a cattle production area (C). Simulation results demonstrated that under the 24-hr culling policy, only 12% of epidemics among 1,000 simulations were abated within 100 days in the CP area, whereas 90% of the epidemics ceased in the BS area. In the C area, all epidemics were successfully contained within 100 days. Evaluation of additional control measures in the CP area showed that the 0.5-km pre-emptive culling, even when only targeting pig farms, raised the potential for successful containment to 94%. A 10-km vaccination on day 7 or 14 after initial detection was also effective in halting the epidemics (80%), but accompanied a large number of culled or vaccinated farms. The combined strategy of 10-km vaccination and 0.5-km pre-emptive culling targeting pig farms succeeded in containing all epidemics within 100 days. The present study suggests the importance of preparedness for the 24-hr culling policy and additional control measures when an FMD outbreak occurs in a densely populated area. Considering the characteristics of the livestock area is important in planning FMD control strategies.

Serological survey of caprine arthritis-encephalitis virus infection in Japan.

A serological survey of caprine arthritis-encephalitis virus (CAEV) infection was conducted from September 2006 to February 2007 in Japan. A total of 857 serum samples were collected from 113 herds in 28 prefectures and were analyzed for the presence of CAEV antibodies using agar gel immunodiffusion test. The seroprevalence of CAEV infection at the herd and animal levels was 15.0% (17/113) and 10.0% (86/857), respectively. Large farms with more than 10 goats and with animals for dairy and breeding purposes had higher seroprevalence (P<0.05). The results of this study provide useful information to consider effective control programs against CAEV infection in Japan.