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Magalhães ES, Zhang D, Moura CAA, Trevisan G, Holtkamp DJ, López WA, Wang C, Linhares DCL, Silva GS. Development of a pig wean-quality score using machine-learning algorithms to characterize and classify groups with high mortality risk under field conditions. Prev Vet Med 2024; 232:106327. [PMID: 39216328 DOI: 10.1016/j.prevetmed.2024.106327] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Revised: 07/15/2024] [Accepted: 08/22/2024] [Indexed: 09/04/2024]
Abstract
Mortality during the post-weaning phase is a critical indicator of swine production system performance, influenced by a complex interaction of multiple factors of the epidemiological triad. This study leveraged retrospective data from 1723 groups of pigs marketed within a US swine production system to develop a Wean-Quality Score (WQS) using machine learning techniques. The study evaluated three machine learning models, Random Forest, Support Vector Machine, and Gradient Boosting Machine, to classify groups having high or low 60-day mortality, where high mortality groups represented 25 % of the groups among the study population with the highest mortality values (n=431; 60-day mortality=9.98 %), and the remaining 75 % of the groups were of low mortality (n=1292; 60-day mortality=2.75 %). The best-performing model, Random Forest (RF), outperformed the other ML models in terms of accuracy (0.90), sensitivity (0.84), and specificity (0.92) metrics, and was then selected for further analysis, which consisted of creating the WQS and ranking the most important factors for classifying groups as high or low mortality. The most important factors ranked through the RF model to classify groups with high mortality were pre-weaning mortality, weaning age, average parity of litters in sow farms, and PRRS status. Additionally, stocking conditions such as stocking density and time to fill the barn were important predictors of high mortality. The WQS was developed and correlated (r = 0.74) with the actual 60-day mortality of the groups, offering a valuable tool for assessing post-weaning survivability in swine production systems before weaning. This study highlights the potential of machine learning and comprehensive data utilization to improve the assessment and management of weaned pig quality in commercial swine production, which producers can utilize to identify and intervene in groups, according to the WQS.
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Affiliation(s)
- Edison S Magalhães
- Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA, USA
| | - Danyang Zhang
- Department of Statistics, College of Liberal Arts and Sciences, Iowa State University, Ames, IA, USA
| | | | - Giovani Trevisan
- Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA, USA
| | - Derald J Holtkamp
- Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA, USA
| | - Will A López
- Pig Improvement Company (PIC), Hendersonville, TN, USA
| | - Chong Wang
- Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA, USA; Department of Statistics, College of Liberal Arts and Sciences, Iowa State University, Ames, IA, USA
| | - Daniel C L Linhares
- Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA, USA
| | - Gustavo S Silva
- Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA, USA.
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2
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García-Vázquez FA. Artificial intelligence and porcine breeding. Anim Reprod Sci 2024:107538. [PMID: 38926001 DOI: 10.1016/j.anireprosci.2024.107538] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2024] [Revised: 06/13/2024] [Accepted: 06/14/2024] [Indexed: 06/28/2024]
Abstract
Livestock management is evolving into a new era, characterized by the analysis of vast quantities of data (Big Data) collected from both traditional breeding methods and new technologies such as sensors, automated monitoring system, and advanced analytics. Artificial intelligence (A-In), which refers to the capability of machines to mimic human intelligence, including subfields like machine learning and deep learning, is playing a pivotal role in this transformation. A wide array of A-In techniques, successfully employed in various industrial and scientific contexts, are now being integrated into mainstream livestock management practices. In the case of swine breeding, while traditional methods have yielded considerable success, the increasing amount of information requires the adoption of new technologies such as A-In to drive productivity, enhance animal welfare, and reduce environmental impact. Current findings suggest that these techniques have the potential to match or exceed the performance of traditional methods, often being more scalable in terms of efficiency and sustainability within the breeding industry. This review provides insights into the application of A-In in porcine breeding, from the perspectives of both sows (including welfare and reproductive management) and boars (including semen quality and health), and explores new approaches which are already being applied in other species.
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Affiliation(s)
- Francisco A García-Vázquez
- Departamento de Fisiología, Facultad de Veterinaria, Campus de Excelencia Mare Nostrum, Universidad de Murcia, Murcia 30100, Spain; Instituto Murciano de Investigación Biosanitaria (IMIB-Arrixaca), Murcia, Spain.
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3
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Halev A, Martínez-López B, Clavijo M, Gonzalez-Crespo C, Kim J, Huang C, Krantz S, Robbins R, Liu X. Infection prediction in swine populations with machine learning. Sci Rep 2023; 13:17738. [PMID: 37853003 PMCID: PMC10584972 DOI: 10.1038/s41598-023-43472-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Accepted: 09/24/2023] [Indexed: 10/20/2023] Open
Abstract
The pork industry is an essential part of the global food system, providing a significant source of protein for people around the world. A major factor restraining productivity and compromising animal wellbeing in the pork industry is disease outbreaks in pigs throughout the production process: widespread outbreaks can lead to losses as high as 10% of the U.S. pig population in extreme years. In this study, we present a machine learning model to predict the emergence of infection in swine production systems throughout the production process on a daily basis, a potential precursor to outbreaks whose detection is vital for disease prevention and mitigation. We determine features that provide the most value in predicting infection, which include nearby farm density, historical test rates, piglet inventory, feed consumption during the gestation period, and wind speed and direction. We utilize these features to produce a generalizable machine learning model, evaluate the model's ability to predict outbreaks both seven and 30 days in advance, allowing for early warning of disease infection, and evaluate our model on two swine production systems and analyze the effects of data availability and data granularity in the context of our two swine systems with different volumes of data. Our results demonstrate good ability to predict infection in both systems with a balanced accuracy of [Formula: see text] on any disease in the first system and balanced accuracies (average prediction accuracy on positive and negative samples) of [Formula: see text], [Formula: see text], [Formula: see text] and [Formula: see text] on porcine reproductive and respiratory syndrome, porcine epidemic diarrhea virus, influenza A virus, and Mycoplasma hyopneumoniae in the second system, respectively, using the six most important predictors in all cases. These models provide daily infection probabilities that can be used by veterinarians and other stakeholders as a benchmark to more timely support preventive and control strategies on farms.
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Affiliation(s)
- Avishai Halev
- Department of Mathematics, University of California, Davis, Davis, CA, USA
| | - Beatriz Martínez-López
- Department of Medicine and Epidemiology, Center for Animal Disease Modeling and Surveillance (CADMS), School of Veterinary Medicine, University of California, Davis, Davis, CA, USA.
| | - Maria Clavijo
- Department of Veterinary Diagnostic & Production Animal Medicine (VDPAM), Iowa State University, Ames, IA, USA
| | - Carlos Gonzalez-Crespo
- Department of Medicine and Epidemiology, Center for Animal Disease Modeling and Surveillance (CADMS), School of Veterinary Medicine, University of California, Davis, Davis, CA, USA
| | - Jeonghoon Kim
- Department of Mathematics, University of California, Davis, Davis, CA, USA
| | - Chao Huang
- Department of Computer Science, University of California, Davis, Davis, CA, USA
| | | | | | - Xin Liu
- Department of Computer Science, University of California, Davis, Davis, CA, USA
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4
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Harding AB, Ramirez MR, Ryan AD, Xiong BN, Rosebush CE, Woods-Jaeger B. Impacts of COVID-19 on Stress in Middle School Teachers and Staff in Minnesota: An Exploratory Study Using Random Forest Analysis. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2023; 20:6698. [PMID: 37681838 PMCID: PMC10487626 DOI: 10.3390/ijerph20176698] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 08/26/2023] [Accepted: 08/29/2023] [Indexed: 09/09/2023]
Abstract
While the COVID-19 pandemic has negatively impacted many occupations, teachers and school staff have faced unique challenges related to remote and hybrid teaching, less contact with students, and general uncertainty. This study aimed to measure the associations between specific impacts of the COVID-19 pandemic and stress levels in Minnesota educators. A total of 296 teachers and staff members from eight middle schools completed online surveys between May and July of 2020. The Epidemic Pandemic Impacts Inventory (EPII) measured the effects of the COVID-19 pandemic according to nine domains (i.e., Economic, Home Life). The Kessler-6 scale measured non-specific stress (range: 0-24), with higher scores indicating greater levels of stress. Random forest analysis determined which items of the EPII were predictive of stress. The average Kessler-6 score was 6.8, indicating moderate stress. Three EPII items explained the largest amount of variation in the Kessler-6 score: increase in mental health problems or symptoms, hard time making the transition to working from home, and increase in sleep problems or poor sleep quality. These findings indicate potential areas for intervention to reduce employee stress in the event of future disruptions to in-person teaching or other major transitions during dynamic times.
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Affiliation(s)
- Alyson B. Harding
- Division of Environmental Health Sciences, School of Public Health, University of Minnesota, Minneapolis, MN 55455, USA; (M.R.R.); (A.D.R.); (B.N.X.)
| | - Marizen R. Ramirez
- Division of Environmental Health Sciences, School of Public Health, University of Minnesota, Minneapolis, MN 55455, USA; (M.R.R.); (A.D.R.); (B.N.X.)
- Department of Environmental and Occupational Health, Program of Public Health, University of California at Irvine, Irvina, CA 92697, USA
| | - Andrew D. Ryan
- Division of Environmental Health Sciences, School of Public Health, University of Minnesota, Minneapolis, MN 55455, USA; (M.R.R.); (A.D.R.); (B.N.X.)
| | - Bao Nhia Xiong
- Division of Environmental Health Sciences, School of Public Health, University of Minnesota, Minneapolis, MN 55455, USA; (M.R.R.); (A.D.R.); (B.N.X.)
| | - Christina E. Rosebush
- Division of Environmental Health Sciences, School of Public Health, University of Minnesota, Minneapolis, MN 55455, USA; (M.R.R.); (A.D.R.); (B.N.X.)
| | - Briana Woods-Jaeger
- Department of Behavioral, Social and Health Education Sciences, Rollins School of Public Health, Emory University, Atlanta, GA 30322, USA;
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Sanchez F, Galvis JA, Cardenas NC, Corzo C, Jones C, Machado G. Spatiotemporal relative risk distribution of porcine reproductive and respiratory syndrome virus in the United States. Front Vet Sci 2023; 10:1158306. [PMID: 37456959 PMCID: PMC10340085 DOI: 10.3389/fvets.2023.1158306] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Accepted: 06/12/2023] [Indexed: 07/18/2023] Open
Abstract
Porcine reproductive and respiratory syndrome virus (PRRSV) remains widely distributed across the U.S. swine industry. Between-farm movements of animals and transportation vehicles, along with local transmission are the primary routes by which PRRSV is spread. Given the farm-to-farm proximity in high pig production areas, local transmission is an important pathway in the spread of PRRSV; however, there is limited understanding of the role local transmission plays in the dissemination of PRRSV, specifically, the distance at which there is increased risk for transmission from infected to susceptible farms. We used a spatial and spatiotemporal kernel density approach to estimate PRRSV relative risk and utilized a Bayesian spatiotemporal hierarchical model to assess the effects of environmental variables, between-farm movement data and on-farm biosecurity features on PRRSV outbreaks. The maximum spatial distance calculated through the kernel density approach was 15.3 km in 2018, 17.6 km in 2019, and 18 km in 2020. Spatiotemporal analysis revealed greater variability throughout the study period, with significant differences between the different farm types. We found that downstream farms (i.e., finisher and nursery farms) were located in areas of significant-high relative risk of PRRSV. Factors associated with PRRSV outbreaks were farms with higher number of access points to barns, higher numbers of outgoing movements of pigs, and higher number of days where temperatures were between 4°C and 10°C. Results obtained from this study may be used to guide the reinforcement of biosecurity and surveillance strategies to farms and areas within the distance threshold of PRRSV positive farms.
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Affiliation(s)
- Felipe Sanchez
- Department of Population Health and Pathobiology, College of Veterinary Medicine, North Carolina State University, Raleigh, NC, United States
- Center for Geospatial Analytics, North Carolina State University, Raleigh, NC, United States
| | - Jason A. Galvis
- Department of Population Health and Pathobiology, College of Veterinary Medicine, North Carolina State University, Raleigh, NC, United States
| | - Nicolas C. Cardenas
- Department of Population Health and Pathobiology, College of Veterinary Medicine, North Carolina State University, Raleigh, NC, United States
| | - Cesar Corzo
- Veterinary Population Medicine Department, College of Veterinary Medicine, University of Minnesota, Saint Paul, MN, United States
| | - Christopher Jones
- Center for Geospatial Analytics, North Carolina State University, Raleigh, NC, United States
| | - Gustavo Machado
- Department of Population Health and Pathobiology, College of Veterinary Medicine, North Carolina State University, Raleigh, NC, United States
- Center for Geospatial Analytics, North Carolina State University, Raleigh, NC, United States
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6
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Desrosiers R, Cousin V. Air filtration to prevent porcine reproductive and respiratory syndrome virus infection. JOURNAL OF SWINE HEALTH AND PRODUCTION 2023. [DOI: 10.54846/jshap/1303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/06/2023]
Abstract
This commentary reviews results obtained in France and North America with different air filtration systems to prevent porcine reproductive and respiratory syndrome virus (PRRSV) infection. Most systems installed in France use high-efficiency particulate air (HEPA) filters and positive-pressure ventilation systems, while those in North America initially used mainly negative-pressure ventilation systems and filters with minimum efficiency rating values of 14 to 16. Major reductions in PRRSV cases were observed in most studies where the latter were used. Installing HEPA filters resulted in an almost complete elimination of PRRSV cases. No cases were recorded in 95% of farms where they were used.
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Havas KA, Brands L, Cochrane R, Spronk GD, Nerem J, Dee SA. An assessment of enhanced biosecurity interventions and their impact on porcine reproductive and respiratory syndrome virus outbreaks within a managed group of farrow-to-wean farms, 2020-2021. Front Vet Sci 2023; 9:952383. [PMID: 36713879 PMCID: PMC9879578 DOI: 10.3389/fvets.2022.952383] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Accepted: 12/21/2022] [Indexed: 01/14/2023] Open
Abstract
Introduction Porcine reproductive and respiratory syndrome virus (PRRSV) has been a challenge for the U.S. swine industry for over 30 years, costing producers more than $600 million annually through reproductive disease in sows and respiratory disease in growing pigs. In this study, the impact of enhanced biosecurity practices of site location, air filtration, and feed mitigation was assessed on farrow-to-wean sites managed by a large swine production management company in the Midwest United States. Those three factors varied in the system that otherwise had implemented a stringent biosecurity protocol on farrow-to-wean sites. The routine biosecurity followed commonplace activities for farrow-to-wean sites that included but were not limited to visitor registration, transport disinfection, shower-in/shower-out procedures, and decontamination and disinfection of delivered items and were audited. Methods Logistic regression was used to evaluate PRRSV infection by site based on the state where the site is located and air filtration use while controlling for other variables such as vaccine status, herd size, and pen vs. stall. A descriptive analysis was used to evaluate the impact of feed mitigation stratified by air filtration use. Results Sites that used feed mitigates as additives in the diets, air filtration of barns, and that were in less swine-dense areas appeared to experience fewer outbreaks associated with PRRSV infection. Specifically, 23.1% of farms that utilized a feed mitigation program experienced PRRSV outbreaks, in contrast to 100% of those that did not. Sites that did not use air filtration had 20 times greater odds of having a PRRSV outbreak. The strongest protective effect was found when both air filtration and feed mitigation were used. Locations outside of Minnesota and Iowa had 98.5-99% lesser odds of infection as well. Discussion Enhanced biosecurity practices may yield significant protective effects and should be considered for producers in swine-dense areas or when the site contains valuable genetics or many pigs.
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Affiliation(s)
- Karyn A. Havas
- Pipestone Research, Pipestone Holdings, Pipestone, MN, United States,*Correspondence: Karyn A. Havas ✉
| | - Lisa Brands
- Pipestone Research, Pipestone Holdings, Pipestone, MN, United States
| | - Roger Cochrane
- Pipestone Nutrition, Pipestone Holdings, Pipestone, MN, United States
| | - Gordon D. Spronk
- Pipestone Veterinary Services, Pipestone Holdings, Pipestone, MN, United States
| | - Joel Nerem
- Pipestone Veterinary Services, Pipestone Holdings, Pipestone, MN, United States
| | - Scott A. Dee
- Pipestone Research, Pipestone Holdings, Pipestone, MN, United States
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Trostle P, Corzo CA, Reich BJ, Machado G. A discrete-time survival model for porcine epidemic diarrhoea virus. Transbound Emerg Dis 2022; 69:3693-3703. [PMID: 36217910 PMCID: PMC10369857 DOI: 10.1111/tbed.14739] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2022] [Revised: 09/30/2022] [Accepted: 10/03/2022] [Indexed: 02/07/2023]
Abstract
Since the arrival of porcine epidemic diarrhea virus (PEDV) in the United States in 2013, elimination and control programmes have had partial success. The dynamics of its spread are hard to quantify, though previous work has shown that local transmission and the transfer of pigs within production systems are most associated with the spread of PEDV. Our work relies on the history of PEDV infections in a region of the southeastern United States. This infection data is complemented by farm-level features and extensive industry data on the movement of both pigs and vehicles. We implement a discrete-time survival model and evaluate different approaches to modelling the local-transmission and network effects. We find strong evidence in that the local-transmission and pig-movement effects are associated with the spread of PEDV, even while controlling for seasonality, farm-level features and the possible spread of disease by vehicles. Our fully Bayesian model permits full uncertainty quantification of these effects. Our farm-level out-of-sample predictions have a receiver-operating characteristic area under the curve (AUC) of 0.779 and a precision-recall AUC of 0.097. The quantification of these effects in a comprehensive model allows stakeholders to make more informed decisions about disease prevention efforts.
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Affiliation(s)
- Parker Trostle
- Department of Statistics, North Carolina State University, Raleigh, North Carolina, USA
| | - Cesar A Corzo
- Veterinary Population Medicine Department, College of Veterinary Medicine, University of Minnesota, Saint Paul, Minnesota, USA
| | - Brian J Reich
- Department of Statistics, North Carolina State University, Raleigh, North Carolina, USA
| | - Gustavo Machado
- Department of Population Health and Pathobiology, College of Veterinary Medicine, North Carolina State University, Raleigh, North Carolina, USA
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9
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Galvis JA, Corzo CA, Machado G. Modelling and assessing additional transmission routes for porcine reproductive and respiratory syndrome virus: Vehicle movements and feed ingredients. Transbound Emerg Dis 2022; 69:e1549-e1560. [PMID: 35188711 PMCID: PMC9790477 DOI: 10.1111/tbed.14488] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Revised: 02/02/2022] [Accepted: 02/13/2022] [Indexed: 12/30/2022]
Abstract
Accounting for multiple modes of livestock disease dissemination in epidemiological models remains a challenge. We developed and calibrated a mathematical model for transmission of porcine reproductive and respiratory syndrome virus (PRRSV), tailored to fit nine modes of between-farm transmission pathways including: farm-to-farm proximity (local transmission), contact network of batches of pigs transferred between farms (pig movements), re-break probabilities for farms with previous PRRSV outbreaks, with the addition of four different contact networks of transportation vehicles (vehicles to transport pigs to farms, pigs to markets, feed and crew) and the amount of animal by-products within feed ingredients (e.g., animal fat or meat and bone meal). The model was calibrated on weekly PRRSV outbreaks data. We assessed the role of each transmission pathway considering the dynamics of specific types of production (i.e., sow, nursery). Although our results estimated that the networks formed by transportation vehicles were more densely connected than the network of pigs transported between farms, pig movements and farm proximity were the main PRRSV transmission routes regardless of farm types. Among the four vehicle networks, vehicles transporting pigs to farms explained a large proportion of infections, sow = 20.9%; nursery = 15%; and finisher = 20.6%. The animal by-products showed a limited association with PRRSV outbreaks through descriptive analysis, and our model results showed that the contribution of animal fat contributed only 2.5% and meat and bone meal only .03% of the infected sow farms. Our work demonstrated the contribution of multiple routes of PRRSV dissemination, which has not been deeply explored before. It also provides strong evidence to support the need for cautious, measured PRRSV control strategies for transportation vehicles and further research for feed by-products modelling. Finally, this study provides valuable information and opportunities for the swine industry to focus effort on the most relevant modes of PRRSV between-farm transmission.
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Affiliation(s)
- Jason A. Galvis
- Department of Population Health and PathobiologyCollege of Veterinary MedicineNorth Carolina State UniversityRaleighNorth CarolinaUSA
| | - Cesar A. Corzo
- Veterinary Population Medicine DepartmentCollege of Veterinary MedicineUniversity of MinnesotaSt PaulMinnesotaUSA
| | - Gustavo Machado
- Department of Population Health and PathobiologyCollege of Veterinary MedicineNorth Carolina State UniversityRaleighNorth CarolinaUSA
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10
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Radmehr M, Adebayo TS. Does health expenditure matter for life expectancy in Mediterranean countries? ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2022; 29:60314-60326. [PMID: 35420335 PMCID: PMC9008298 DOI: 10.1007/s11356-022-19992-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Accepted: 03/26/2022] [Indexed: 06/14/2023]
Abstract
This research assesses the effect of health expenditure and sanitation on life expectancy in Mediterranean countries. We also consider other drivers of life expectancy, such as CO2 emissions and economic growth. The study covers the period 2000-2018, and the recently developed method of moments quantile regression (MMQR) approach was utilised to assess these interconnections. This method is immune to outliers and creates an asymmetric interrelationship between variables. The outcomes from the MMQR unveiled that economic growth, health expenditure, and sanitation enhanced life expectancy in all quantiles (0.1-0.90). Furthermore, in all quantiles (0.1-0.90), the effect of CO2 emissions on life expectancy was negative. Moreover, as a robustness check, the FMOLS, DOLS, and FE-OLS long-run estimators were applied, and the outcomes validated the MMQR outcomes. Based on the results generated, policymakers in these nations should implement effective environmental and public health measures that will pay off in the long run through improved health as a result of lower emissions of CO2, as well as increased economic expansion and productivity.
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Affiliation(s)
- Mehrshad Radmehr
- Faculty of Economics and Administrative Science, Department of Business Administration, Cyprus International University, Mersin 10, Nicosia, Northern Cyprus Turkey
| | - Tomiwa Sunday Adebayo
- Faculty of Economics and Administrative Science, Department of Business Administration, Cyprus International University, Mersin 10, Nicosia, Northern Cyprus Turkey
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11
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Sánchez J, Matas M, Ibáñez-López FJ, Hernández I, Sotillo J, Gutiérrez AM. The Connection Between Stress and Immune Status in Pigs: A First Salivary Analytical Panel for Disease Differentiation. Front Vet Sci 2022; 9:881435. [PMID: 35782547 PMCID: PMC9244398 DOI: 10.3389/fvets.2022.881435] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Accepted: 05/17/2022] [Indexed: 11/13/2022] Open
Abstract
This paper analyzes the association between stress and immune response activations in different diseases, based on the salivary analytics. Moreover, a first attempt to discriminate between diseases was performed by principal component analysis. The salivary analytics consisted of the measurement of psychosocial stress (cortisol and salivary alpha-amylase) indicators, innate (acute phase proteins: C-reactive protein and haptoglobin), and adaptive immune (adenosine deaminase, Cu and Zn) markers and oxidative stress parameters (antioxidant capacity and oxidative status). A total of 107 commercial growing pigs in the field were divided into six groups according to the signs of disease after proper veterinary clinical examination, especially, healthy pigs, pigs with rectal prolapse, tail-biting lesions, diarrhea, lameness, or dyspnea. Associations between stress and immune markers were observed with different intensities. High associations (r = 0.61) were observed between oxidative stress markers and adaptive immune markers. On the other hand, moderate associations (r = 0.31–0.48) between psychosocial stress markers with both innate and adaptive immune markers were observed. All pathological conditions showed statistically significant differences in at least 4 out of the 11 salivary markers studied, with no individual marker dysregulated in all the diseases. Moreover, each disease condition showed differences in the degree of activation of the analyzed systems which could be used to create different salivary profiles. A total of two dimensions were selected through the principal component analysis to explain the 48.3% of the variance of our data. Lameness and rectal prolapse were the two pathological conditions most distant from the healthy condition followed by dyspnea. Tail-biting lesions and diarrhea were also far from the other diseases but near to healthy animals. There is still room for improvements, but these preliminary results displayed a great potential for disease detection and characterization using salivary biomarkers profiling in the near future.
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Affiliation(s)
- J. Sánchez
- BioVetMed Research Group, Department of Animal Medicine and Surgery, Veterinary School, CEIR Campus Mare Nostrum (CMN), University of Murcia, Murcia, Spain
- Cefu SA, Murcia, Spain
| | - M. Matas
- BioVetMed Research Group, Department of Animal Medicine and Surgery, Veterinary School, CEIR Campus Mare Nostrum (CMN), University of Murcia, Murcia, Spain
| | - F. J. Ibáñez-López
- Statistical Support Service (SAE), Scientific and Technological Research Area (ACTI), CEIR Campus Mare Nostrum (CMN), University of Murcia, Murcia, Spain
| | - I. Hernández
- Statistical Support Service (SAE), Scientific and Technological Research Area (ACTI), CEIR Campus Mare Nostrum (CMN), University of Murcia, Murcia, Spain
| | - J. Sotillo
- BioVetMed Research Group, Department of Animal Medicine and Surgery, Veterinary School, CEIR Campus Mare Nostrum (CMN), University of Murcia, Murcia, Spain
| | - A. M. Gutiérrez
- BioVetMed Research Group, Department of Animal Medicine and Surgery, Veterinary School, CEIR Campus Mare Nostrum (CMN), University of Murcia, Murcia, Spain
- *Correspondence: A. M. Gutiérrez
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12
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Magalhães ES, Zimmerman JJ, Holtkamp DJ, Classen DM, Groth DD, Glowzenski L, Philips R, Silva GS, Linhares DCL. Next Generation of Voluntary PRRS Virus Regional Control Programs. Front Vet Sci 2021; 8:769312. [PMID: 34805344 PMCID: PMC8602550 DOI: 10.3389/fvets.2021.769312] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Accepted: 10/11/2021] [Indexed: 11/13/2022] Open
Abstract
Porcine reproductive and respiratory syndrome virus (PRRSV) became pandemic in the 1980's and today remains one of the most significant pathogens of the global swine industry. At the herd level, control of PRRSV is complicated by its extreme genetic diversity and its ability to persist in pigs, despite an active immune response. Ultimately, PRRSV control or elimination requires the coordination and active cooperation of producers and veterinarians at the regional level. Early voluntary PRRSV regional control programs focused on routine diagnostic testing and voluntary data-sharing regarding the PRRSV status of participants' herds, but no pre-defined action plans or decision trees were developed to secure project successes (or recover from failures). Given that control of PRRSV is paramount to producer profitability, we propose a coordinated approach for detecting, controlling, and ultimately eliminating wild-type PRRSV from herds participating in regional projects. Fundamental to project success is real-time, multi-platform communication of all data, information, and events that concern the regional project and project participants. New to this approach is the concept of agreed-upon action plans to be implemented by project participants in response to specific events or situations. The simultaneous and coordinated implementation of these strategies allows for early detection of wild-type PRRSV virus introductions and rapid intervention based on agreed-upon response plans. An example is given of a project in progress in the Midwest USA.
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Affiliation(s)
- Edison S Magalhães
- Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA, United States
| | - Jeffrey J Zimmerman
- Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA, United States
| | - Derald J Holtkamp
- Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA, United States
| | | | - Douglas D Groth
- Carthage Veterinary Service, Ltd., Carthage, IL, United States
| | | | - Reid Philips
- Boehringer Ingelheim Animal Health USA Inc., Atlanta, GA, United States
| | - Gustavo S Silva
- Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA, United States
| | - Daniel C L Linhares
- Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA, United States
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Sykes AL, Silva GS, Holtkamp DJ, Mauch BW, Osemeke O, Linhares DCL, Machado G. Interpretable machine learning applied to on-farm biosecurity and porcine reproductive and respiratory syndrome virus. Transbound Emerg Dis 2021; 69:e916-e930. [PMID: 34719136 DOI: 10.1111/tbed.14369] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Revised: 09/22/2021] [Accepted: 10/24/2021] [Indexed: 11/28/2022]
Abstract
Effective biosecurity practices in swine production are key in preventing the introduction and dissemination of infectious pathogens. Ideally, on-farm biosecurity practices should be chosen by their impact on bio-containment and bio-exclusion; however, quantitative supporting evidence is often unavailable. Therefore, the development of methodologies capable of quantifying and ranking biosecurity practices according to their efficacy in reducing disease risk has the potential to facilitate better-informed choices of biosecurity practices. Using survey data on biosecurity practices, farm demographics, and previous outbreaks from 139 herds, a set of machine learning algorithms were trained to classify farms by porcine reproductive and respiratory syndrome virus status, depending on their biosecurity practices and farm demographics, to produce a predicted outbreak risk. A novel interpretable machine learning toolkit, MrIML-biosecurity, was developed to benchmark farms and production systems by predicted risk and quantify the impact of biosecurity practices on disease risk at individual farms. By quantifying the variable impact on predicted risk, 50% of 42 variables were associated with fomite spread while 31% were associated with local transmission. Results from machine learning interpretations identified similar results, finding substantial contribution to predicted outbreak risk from biosecurity practices relating to the turnover and number of employees, the surrounding density of swine premises and pigs, the sharing of haul trailers, distance from the public road and farm production type. In addition, the development of individualized biosecurity assessments provides the opportunity to better guide biosecurity implementation on a case-by-case basis. Finally, the flexibility of the MrIML-biosecurity toolkit gives it the potential to be applied to wider areas of biosecurity benchmarking, to address biosecurity weaknesses in other livestock systems and industry-relevant diseases.
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Affiliation(s)
- Abagael L Sykes
- Department of Population Health and Pathobiology, College of Veterinary Medicine, North Carolina State University, Raleigh, North Carolina, USA
| | - Gustavo S Silva
- Veterinary Diagnostic and Production Animal Medicine Department, College of Veterinary Medicine, Iowa State University, Ames, Iowa, USA
| | - Derald J Holtkamp
- Veterinary Diagnostic and Production Animal Medicine Department, College of Veterinary Medicine, Iowa State University, Ames, Iowa, USA
| | - Broc W Mauch
- Veterinary Diagnostic and Production Animal Medicine Department, College of Veterinary Medicine, Iowa State University, Ames, Iowa, USA
| | - Onyekachukwu Osemeke
- Veterinary Diagnostic and Production Animal Medicine Department, College of Veterinary Medicine, Iowa State University, Ames, Iowa, USA
| | - Daniel C L Linhares
- Veterinary Diagnostic and Production Animal Medicine Department, College of Veterinary Medicine, Iowa State University, Ames, Iowa, USA
| | - Gustavo Machado
- Department of Population Health and Pathobiology, College of Veterinary Medicine, North Carolina State University, Raleigh, North Carolina, USA
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Makau DN, Alkhamis MA, Paploski IAD, Corzo CA, Lycett S, VanderWaal K. Integrating animal movements with phylogeography to model the spread of PRRSV in the USA. Virus Evol 2021; 7:veab060. [PMID: 34532062 PMCID: PMC8438914 DOI: 10.1093/ve/veab060] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Revised: 05/22/2021] [Accepted: 06/14/2021] [Indexed: 12/17/2022] Open
Abstract
Viral sequence data coupled with phylodynamic models have become instrumental in investigating the outbreaks of human and animal diseases, and the incorporation of the hypothesized drivers of pathogen spread can enhance the interpretation from phylodynamic inference. Integrating animal movement data with phylodynamics allows us to quantify the extent to which the spatial diffusion of a pathogen is influenced by animal movements and contrast the relative importance of different types of movements in shaping pathogen distribution. We combine animal movement, spatial, and environmental data in a Bayesian phylodynamic framework to explain the spatial diffusion and evolutionary trends of a rapidly spreading sub-lineage (denoted L1A) of porcine reproductive and respiratory syndrome virus (PRRSV) Type 2 from 2014 to 2017. PRRSV is the most important endemic pathogen affecting pigs in the USA, and this particular virulent sub-lineage emerged in 2014 and continues to be the dominant lineage in the US swine industry to date. Data included 984 open reading frame 5 (ORF5) PRRSV L1A sequences obtained from two production systems in a swine-dense production region (∼85,000 mi2) in the USA between 2014 and 2017. The study area was divided into sectors for which model covariates were summarized, and animal movement data between each sector were summarized by age class (wean: 3–4 weeks; feeder: 8–25 weeks; breeding: ≥21 weeks). We implemented a discrete-space phylogeographic generalized linear model using Bayesian evolutionary analysis by sampling trees (BEAST) to infer factors associated with variability in between-sector diffusion rates of PRRSV L1A. We found that between-sector spread was enhanced by the movement of feeder pigs, spatial adjacency of sectors, and farm density in the destination sector. The PRRSV L1A strain was introduced in the study area in early 2013, and genetic diversity and effective population size peaked in 2015 before fluctuating seasonally (peaking during the summer months). Our study underscores the importance of animal movements and shows, for the first time, that the movement of feeder pigs (8–25 weeks old) shaped the spatial patterns of PRRSV spread much more strongly than the movements of other age classes of pigs. The inclusion of movement data into phylodynamic models as done in this analysis may enhance our ability to identify crucial pathways of disease spread that can be targeted to mitigate the spatial spread of infectious human and animal pathogens.
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Affiliation(s)
- Dennis N Makau
- Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, Minneapolis, 1365 Gortner Avenue, St. Paul, MN, 55108, USA
| | - Moh A Alkhamis
- Department of Epidemiology and Biostatistics, Faculty of Public Health, Health Sciences Center, Kuwait University, Kuwait City, 24923, Safat 13110, Kuwait
| | - Igor A D Paploski
- Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, Minneapolis, 1365 Gortner Avenue, St. Paul, MN, 55108, USA
| | - Cesar A Corzo
- Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, Minneapolis, 1365 Gortner Avenue, St. Paul, MN, 55108, USA
| | - Samantha Lycett
- Roslin Institute, University of Edinburgh, Edinburgh, Midlothian, EH25 9RG, UK
| | - Kimberly VanderWaal
- Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, Minneapolis, 1365 Gortner Avenue, St. Paul, MN, 55108, USA
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15
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Galvis JA, Corzo CA, Prada JM, Machado G. Modelling the transmission and vaccination strategy for porcine reproductive and respiratory syndrome virus. Transbound Emerg Dis 2021; 69:485-500. [PMID: 33506620 DOI: 10.1111/tbed.14007] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2020] [Revised: 01/22/2021] [Accepted: 01/25/2021] [Indexed: 12/15/2022]
Abstract
Many aspects of the porcine reproductive and respiratory syndrome virus (PRRSV) between-farm transmission dynamics have been investigated, but uncertainty remains about the significance of farm type and different transmission routes on PRRSV spread. We developed a stochastic epidemiological model calibrated on weekly PRRSV outbreaks accounting for the population dynamics in different pig production phases, breeding herds, gilt development units, nurseries and finisher farms, of three hog producer companies. Our model accounted for indirect contacts by the close distance between farms (local transmission), between-farm animal movements (pig flow) and reinfection of sow farms (re-break). The fitted model was used to examine the effectiveness of vaccination strategies and complementary interventions such as enhanced PRRSV detection and vaccination delays and forecast the spatial distribution of PRRSV outbreak. The results of our analysis indicated that for sow farms, 59% of the simulated infections were related to local transmission (e.g. airborne, feed deliveries, shared equipment) whereas 36% and 5% were related to animal movements and re-break, respectively. For nursery farms, 80% of infections were related to animal movements and 20% to local transmission; while at finisher farms, it was split between local transmission and animal movements. Assuming that the current vaccines are 1% effective in mitigating between-farm PRRSV transmission, weaned pigs vaccination would reduce the incidence of PRRSV outbreaks by 3%, indeed under any scenario vaccination alone was insufficient for completely controlling PRRSV spread. Our results also showed that intensifying PRRSV detection and/or vaccination pigs at placement increased the effectiveness of all simulated vaccination strategies. Our model reproduced the incidence and PRRSV spatial distribution; therefore, this model could also be used to map current and future farms at-risk. Finally, this model could be a useful tool for veterinarians, allowing them to identify the effect of transmission routes and different vaccination interventions to control PRRSV spread.
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Affiliation(s)
- Jason A Galvis
- Department of Population Health and Pathobiology, College of Veterinary Medicine, Raleigh, NC, USA
| | - Cesar A Corzo
- Veterinary Population Medicine Department, College of Veterinary Medicine, University of Minnesota, St Paul, MN, USA
| | - Joaquin M Prada
- School of Veterinary Medicine, Faculty of Health and Medical Sciences, University of Surrey, Guildford, UK
| | - Gustavo Machado
- Department of Population Health and Pathobiology, College of Veterinary Medicine, Raleigh, NC, USA
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16
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Alarcón LV, Allepuz A, Mateu E. Biosecurity in pig farms: a review. Porcine Health Manag 2021; 7:5. [PMID: 33397483 PMCID: PMC7780598 DOI: 10.1186/s40813-020-00181-z] [Citation(s) in RCA: 66] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Accepted: 12/01/2020] [Indexed: 12/29/2022] Open
Abstract
The perception of the importance of animal health and its relationship with biosecurity has increased in recent years with the emergence and re-emergence of several diseases difficult to control. This is particularly evident in the case of pig farming as shown by the recent episodes of African swine fever or porcine epidemic diarrhoea. Moreover, a better biosecurity may help to improve productivity and may contribute to reducing the use of antibiotics. Biosecurity can be defined as the application of measures aimed to reduce the probability of the introduction (external biosecurity) and further spread of pathogens within the farm (internal biosecurity). Thus, the key idea is to avoid transmission, either between farms or within the farm. This implies knowledge of the epidemiology of the diseases to be avoided that is not always available, but since ways of transmission of pathogens are limited to a few, it is possible to implement effective actions even with some gaps in our knowledge on a given disease. For the effective design of a biosecurity program, veterinarians must know how diseases are transmitted, the risks and their importance, which mitigation measures are thought to be more effective and how to evaluate the biosecurity and its improvements. This review provides a source of information on external and internal biosecurity measures that reduce risks in swine production and the relationship between these measures and the epidemiology of the main diseases, as well as a description of some systems available for risk analysis and the assessment of biosecurity. Also, it reviews the factors affecting the successful application of a biosecurity plan in a pig farm.
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Affiliation(s)
- Laura Valeria Alarcón
- Facultad de Ciencias Veterinarias, Universidad Nacional de La Plata, Calle 60 y 118, La Plata, Buenos Aires, Argentina.
| | - Alberto Allepuz
- Departament de Sanitat i Anatomia Animals, Facultat de Veterinària, Universitat Autònoma de Barcelona, Travessera dels Turons s/n, 08193 Cerdanyola del Vallès, Barcelona, Spain.,Centre de Recerca en Sanitat Animal (CreSA-IRTA-UAB), campus UAB, 08193 Cerdanyola del Vallès, Barcelona, Spain
| | - Enric Mateu
- Departament de Sanitat i Anatomia Animals, Facultat de Veterinària, Universitat Autònoma de Barcelona, Travessera dels Turons s/n, 08193 Cerdanyola del Vallès, Barcelona, Spain.,Centre de Recerca en Sanitat Animal (CreSA-IRTA-UAB), campus UAB, 08193 Cerdanyola del Vallès, Barcelona, Spain
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17
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Saegerman C, Bianchini J, Snoeck CJ, Moreno A, Chiapponi C, Zohari S, Ducatez MF. First expert elicitation of knowledge on drivers of emergence of influenza D in Europe. Transbound Emerg Dis 2020; 68:3349-3359. [PMID: 33249766 DOI: 10.1111/tbed.13938] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Revised: 11/23/2020] [Accepted: 11/23/2020] [Indexed: 10/22/2022]
Abstract
The influenza D virus (IDV) was first identified and characterized in 2011. Considering the virus' zoonotic potential, its genome nature (segmented RNA virus), its worldwide circulation in livestock and its role in bovine respiratory disease, an increased interest is given to IDV. However, few data are available on drivers of emergence of IDV. We first listed fifty possible drivers of emergence of IDV in ruminants and swine. As recently carried out for COVID-19 in pets (Transboundary and Emerging Diseases, 2020), a scoring system was developed per driver and scientific experts (N = 28) were elicited to (a) allocate a score to each driver, (b) weight the drivers' scores within each domain and (c) weight the different domains among themselves. An overall weighted score was calculated per driver, and drivers were ranked in decreasing order. Drivers with comparable likelihoods to play a role in the emergence of IDV in ruminants and swine in Europe were grouped using a regression tree analysis. Finally, the robustness of the expert elicitation was verified. Eight drivers were ranked with the highest probability to play a key role in the emergence of IDV: current species specificity of the causing agent of the disease; influence of (il)legal movements of live animals (ruminants, swine) from neighbouring/European Union member states and from third countries for the disease to (re-)emerge in a given country; detection of emergence; current knowledge of the pathogen; vaccine availability; animal density; and transport vehicles of live animals. As there is still limited scientific knowledge on the topic, expert elicitation of knowledge and multi-criteria decision analysis, in addition to clustering and sensitivity analyses, are very important to prioritize future studies, starting from the top eight drivers. The present methodology could be applied to other emerging animal diseases.
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Affiliation(s)
- Claude Saegerman
- Fundamental and Applied Research for Animal and Health (FARAH) Center, University of Liège, Liège, Belgium
| | - Juana Bianchini
- Fundamental and Applied Research for Animal and Health (FARAH) Center, University of Liège, Liège, Belgium
| | - Chantal J Snoeck
- Clinical and Applied Virology group, Department of Infection and Immunity, Luxembourg Institute of Health, Esch-sur-Alzette, Luxembourg
| | - Ana Moreno
- Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia Romagna 'Bruno Ubertini', Brescia, Italy
| | - Chiara Chiapponi
- Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia Romagna 'Bruno Ubertini', Brescia, Italy
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18
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Machado G, Galvis JA, Lopes FPN, Voges J, Medeiros AAR, Cárdenas NC. Quantifying the dynamics of pig movements improves targeted disease surveillance and control plans. Transbound Emerg Dis 2020; 68:1663-1675. [PMID: 32965771 DOI: 10.1111/tbed.13841] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Revised: 08/27/2020] [Accepted: 09/12/2020] [Indexed: 12/11/2022]
Abstract
Tracking animal movements over time may fundamentally determine the success of disease control interventions. In commercial pig production growth stages determine animal transportation schedule, thus it generates time-varying contact networks showed to influence the dynamics of disease spread. In this study, we reconstructed pig networks of one Brazilian state from 2017 to 2018, comprising 351,519 movements and 48 million transported pigs. The static networks view did not capture time-respecting movement pathways. For this reason, we propose a time-dependent network approach. A susceptible-infected model was used to spread an epidemic over the pig network globally through the temporal between-farm networks, and locally by a stochastic model to account for within-farm dynamics. We propagated disease to calculate the cumulative contacts as a proxy of epidemic sizes and evaluate the impact of network-based disease control strategies in the absence of other intervention alternatives. The results show that targeting 1,000 farms ranked by degree would be sufficient and feasible to diminish disease spread considerably. Our modelling results indicated that independently from where initial infections were seeded (i.e. independent, commercial farms), the epidemic sizes and the number of farms needed to be targeted to effectively control disease spread were quite similar; indeed, this finding can be explained by the presence of contact among all pig operation types The proposed strategy limited the transmission the total number of secondarily infected farms to 29, over two simulated years. The identified 1,000 farms would benefit from enhanced biosecurity plans and improved targeted surveillance. Overall, the modelling framework provides a parsimonious solution for targeted disease surveillance when temporal movement data are available.
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Affiliation(s)
- Gustavo Machado
- Department of Population Health and Pathobiology, College of Veterinary Medicine, Raleigh, North Carolina, USA
| | - Jason Ardila Galvis
- Department of Population Health and Pathobiology, College of Veterinary Medicine, Raleigh, North Carolina, USA
| | - Francisco Paulo Nunes Lopes
- Departamento de Defesa Agropecuária, Secretaria da Agricultura, Pecuária e Desenvolvimento Rural (SEAPDR), Porto Alegre, Brazil
| | - Joana Voges
- Departamento de Defesa Agropecuária, Secretaria da Agricultura, Pecuária e Desenvolvimento Rural (SEAPDR), Porto Alegre, Brazil
| | - Antônio Augusto Rosa Medeiros
- Departamento de Defesa Agropecuária, Secretaria da Agricultura, Pecuária e Desenvolvimento Rural (SEAPDR), Porto Alegre, Brazil
| | - Nicolás Céspedes Cárdenas
- Department of Preventive Veterinary Medicine and Animal Health, School of Veterinary Medicine and Animal Science, University of São Paulo, São Paulo, Brazil
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Jara M, Rasmussen DA, Corzo CA, Machado G. Porcine reproductive and respiratory syndrome virus dissemination across pig production systems in the United States. Transbound Emerg Dis 2020; 68:667-683. [PMID: 32657491 DOI: 10.1111/tbed.13728] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Revised: 06/25/2020] [Accepted: 07/08/2020] [Indexed: 12/16/2022]
Abstract
Porcine reproductive and respiratory syndrome virus (PRRSV) remains widespread in the North American pig population. Despite improvements in virus characterization, it is unclear whether PRRSV infections are a product of viral circulation within production systems (local) or across production systems (external). Here, we examined the local and external dissemination dynamics of PRRSV and the processes facilitating its spread in three production systems. Overall, PRRSV genetic diversity has declined since 2018, while phylodynamic results support frequent external transmission. We found that PRRSV dissemination predominantly occurred mostly through transmission between farms of different production companies for several months, especially from November until May, a timeframe already established as PRRSV season. Although local PRRSV dissemination occurred mainly through regular pig flow (from sow to nursery and then to finisher farms), an important flux of PRRSV dissemination also occurred in the opposite direction, from finisher to sow and nursery farms, highlighting the importance of downstream farms as sources of the virus. Our results also showed that farms with pig densities of 500 to 1,000 pig/km2 and farms located at a range within 0.5 km and 0.7 km from major roads were more likely to be infected by PRRSV, whereas farms at an elevation of 41 to 61 meters and surrounded by denser vegetation were less likely to be infected, indicating their role as dissemination barriers. In conclusion, our results demonstrate that external dissemination was intense, and reinforce the importance of farm proximity on PRRSV spread. Thus, consideration of farm location, geographic characteristics and animal densities across production systems may help to forecast PRRSV collateral dissemination.
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Affiliation(s)
- Manuel Jara
- Department of Population Health and Pathobiology, College of Veterinary Medicine, North Carolina State University, Raleigh, NC, USA
| | - David A Rasmussen
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC, USA.,Bioinformatics Research Center, North Carolina State University, Raleigh, NC, USA
| | - Cesar A Corzo
- Veterinary Population Medicine Department, College of Veterinary Medicine, University of Minnesota, St Paul, MN, USA
| | - Gustavo Machado
- Department of Population Health and Pathobiology, College of Veterinary Medicine, North Carolina State University, Raleigh, NC, USA
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