1
|
Conteddu K, English HM, Byrne AW, Amin B, Griffin LL, Kaur P, Morera-Pujol V, Murphy KJ, Salter-Townshend M, Smith AF, Ciuti S. A scoping review on bovine tuberculosis highlights the need for novel data streams and analytical approaches to curb zoonotic diseases. Vet Res 2024; 55:64. [PMID: 38773649 PMCID: PMC11110237 DOI: 10.1186/s13567-024-01314-w] [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: 05/09/2023] [Accepted: 03/20/2024] [Indexed: 05/24/2024] Open
Abstract
Zoonotic diseases represent a significant societal challenge in terms of their health and economic impacts. One Health approaches to managing zoonotic diseases are becoming more prevalent, but require novel thinking, tools and cross-disciplinary collaboration. Bovine tuberculosis (bTB) is one example of a costly One Health challenge with a complex epidemiology involving humans, domestic animals, wildlife and environmental factors, which require sophisticated collaborative approaches. We undertook a scoping review of multi-host bTB epidemiology to identify trends in species publication focus, methodologies, and One Health approaches. We aimed to identify knowledge gaps where novel research could provide insights to inform control policy, for bTB and other zoonoses. The review included 532 articles. We found different levels of research attention across episystems, with a significant proportion of the literature focusing on the badger-cattle-TB episystem, with far less attention given to tropical multi-host episystems. We found a limited number of studies focusing on management solutions and their efficacy, with very few studies looking at modelling exit strategies. Only a small number of studies looked at the effect of human disturbances on the spread of bTB involving wildlife hosts. Most of the studies we reviewed focused on the effect of badger vaccination and culling on bTB dynamics with few looking at how roads, human perturbations and habitat change may affect wildlife movement and disease spread. Finally, we observed a lack of studies considering the effect of weather variables on bTB spread, which is particularly relevant when studying zoonoses under climate change scenarios. Significant technological and methodological advances have been applied to bTB episystems, providing explicit insights into its spread and maintenance across populations. We identified a prominent bias towards certain species and locations. Generating more high-quality empirical data on wildlife host distribution and abundance, high-resolution individual behaviours and greater use of mathematical models and simulations are key areas for future research. Integrating data sources across disciplines, and a "virtuous cycle" of well-designed empirical data collection linked with mathematical and simulation modelling could provide additional gains for policy-makers and managers, enabling optimised bTB management with broader insights for other zoonoses.
Collapse
Affiliation(s)
- Kimberly Conteddu
- Laboratory of Wildlife Ecology and Behaviour, School of Biology and Environmental Science, University College Dublin, Dublin, Ireland.
| | - Holly M English
- Laboratory of Wildlife Ecology and Behaviour, School of Biology and Environmental Science, University College Dublin, Dublin, Ireland
| | - Andrew W Byrne
- Department of Agriculture, Food and the Marine, One Health Scientific Support Unit, Dublin, Ireland
| | - Bawan Amin
- Laboratory of Wildlife Ecology and Behaviour, School of Biology and Environmental Science, University College Dublin, Dublin, Ireland
| | - Laura L Griffin
- Laboratory of Wildlife Ecology and Behaviour, School of Biology and Environmental Science, University College Dublin, Dublin, Ireland
| | - Prabhleen Kaur
- School of Mathematics and Statistics, University College Dublin, Dublin, Ireland
| | - Virginia Morera-Pujol
- Laboratory of Wildlife Ecology and Behaviour, School of Biology and Environmental Science, University College Dublin, Dublin, Ireland
| | - Kilian J Murphy
- Laboratory of Wildlife Ecology and Behaviour, School of Biology and Environmental Science, University College Dublin, Dublin, Ireland
| | | | - Adam F Smith
- Department of Wildlife Ecology and Management, Faculty of Environment and Natural Resources, University of Freiburg, Freiburg, Germany
- The Frankfurt Zoological Society, Frankfurt, Germany
- Department of National Park Monitoring and Animal Management, Bavarian Forest National Park, Grafenau, Germany
| | - Simone Ciuti
- Laboratory of Wildlife Ecology and Behaviour, School of Biology and Environmental Science, University College Dublin, Dublin, Ireland
| |
Collapse
|
2
|
Lizarraga AJ, Hart L, Wright RM, Williams LR, Glavy JS. Incidents of snake fungal disease caused by the fungal pathogen Ophidiomyces ophidiicola in Texas. FRONTIERS IN FUNGAL BIOLOGY 2023; 4:1064939. [PMID: 37746129 PMCID: PMC10512329 DOI: 10.3389/ffunb.2023.1064939] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/08/2022] [Accepted: 02/08/2023] [Indexed: 09/26/2023]
Abstract
The pathogen Ophidiomyces ophidiicola, widely known as the primary cause of snake fungal disease (SFD) has been detected in Texas's naïve snakes. Our team set out to characterize O. ophidiicola's spread in eastern Texas. From December 2018 until November 2021, we sampled and screened with ultraviolet (UV) light, 176 snakes across eastern Texas and detected 27. O. ophidiicola's positive snakes using qPCR and one snake in which SFD was confirmed via additional histological examination. Upon finding the ribbon snake with clear clinical display, we isolated and cultured what we believe to be the first culture from Texas. This cultured O. ophidiicola TX displays a ring halo formation when grown on a solid medium as well as cellular autofluorescence as expected. Imaging reveals individual cells within the septated hyphae branches contain a distinct nucleus separation from neighboring cells. Overall, we have found over 1/10 snakes that may be infected in East Texas, gives credence to the onset of SFD in Texas. These results add to the progress of the disease across the continental United States.
Collapse
Affiliation(s)
- Alan J. Lizarraga
- Biology Department, The University of Texas at Tyler, Tyler, TX, United States
| | - Lezley Hart
- Biology Department, The University of Texas at Tyler, Tyler, TX, United States
| | - R. Michele Wright
- Biology Department, The University of Texas at Tyler, Tyler, TX, United States
- The Department of Pharmaceutical Sciences, Fisch College of Pharmacy, The University of Texas at Tyler, Tyler, TX, United States
| | - Lance R. Williams
- Biology Department, The University of Texas at Tyler, Tyler, TX, United States
| | - Joseph S. Glavy
- Biology Department, The University of Texas at Tyler, Tyler, TX, United States
- The Department of Pharmaceutical Sciences, Fisch College of Pharmacy, The University of Texas at Tyler, Tyler, TX, United States
| |
Collapse
|
3
|
Global Dynamics of a Reaction-Diffusion Model of Zika Virus Transmission with Seasonality. Bull Math Biol 2021; 83:43. [PMID: 33743086 DOI: 10.1007/s11538-021-00879-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Accepted: 02/27/2021] [Indexed: 10/21/2022]
Abstract
In this paper, we propose a periodic reaction-diffusion model of Zika virus with seasonal and spatial heterogeneous structure in host and vector population. We introduce the basic reproduction ratio [Formula: see text] for this model and show that the disease-free periodic solution is globally asymptotically stable if [Formula: see text], while the system admits a globally asymptotically stable positive periodic solution if [Formula: see text]. Numerically, we study the Zika transmission in Rio de Janeiro Municipality, Brazil, and investigate the effects of some model parameters on [Formula: see text]. We find that the neglect of seasonality underestimates the value of [Formula: see text] and the maximum carrying capacity affects the spread of Zika virus.
Collapse
|
4
|
Ezanno P, Andraud M, Beaunée G, Hoch T, Krebs S, Rault A, Touzeau S, Vergu E, Widgren S. How mechanistic modelling supports decision making for the control of enzootic infectious diseases. Epidemics 2020; 32:100398. [PMID: 32622313 DOI: 10.1016/j.epidem.2020.100398] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Revised: 05/07/2020] [Accepted: 05/29/2020] [Indexed: 12/28/2022] Open
Abstract
Controlling enzootic diseases, which generate a large cumulative burden and are often unregulated, is needed for sustainable farming, competitive agri-food chains, and veterinary public health. We discuss the benefits and challenges of mechanistic epidemiological modelling for livestock enzootics, with particular emphasis on the need for interdisciplinary approaches. We focus on issues arising when modelling pathogen spread at various scales (from farm to the region) to better assess disease control and propose targeted options. We discuss in particular the inclusion of farmers' strategic decision-making, the integration of within-host scale to refine intervention targeting, and the need to ground models on data.
Collapse
Affiliation(s)
- P Ezanno
- INRAE, Oniris, BIOEPAR, Site de la Chantrerie, CS40706, 44307 Nantes, France.
| | - M Andraud
- Unité épidémiologie et bien-être du porc, Anses Laboratoire de Ploufragan-Plouzané, Ploufragan, France.
| | - G Beaunée
- INRAE, Oniris, BIOEPAR, Site de la Chantrerie, CS40706, 44307 Nantes, France.
| | - T Hoch
- INRAE, Oniris, BIOEPAR, Site de la Chantrerie, CS40706, 44307 Nantes, France.
| | - S Krebs
- INRAE, Oniris, BIOEPAR, Site de la Chantrerie, CS40706, 44307 Nantes, France.
| | - A Rault
- INRAE, Oniris, BIOEPAR, Site de la Chantrerie, CS40706, 44307 Nantes, France.
| | - S Touzeau
- INRAE, CNRS, Université Côte d'Azur, ISA, France; Inria, INRAE, CNRS, Université Paris Sorbonne, Université Côte d'Azur, BIOCORE, France.
| | - E Vergu
- INRAE, Université Paris-Saclay, MaIAGE, 78350 Jouy-en-Josas, France.
| | - S Widgren
- Department of Disease Control and Epidemiology, National Veterinary Institute, 751 89 Uppsala, Sweden.
| |
Collapse
|
5
|
Villard P, Muñoz F, Balenghien T, Baldet T, Lancelot R, Hénaux V. Modeling Culicoides abundance in mainland France: implications for surveillance. Parasit Vectors 2019; 12:391. [PMID: 31387649 PMCID: PMC6683357 DOI: 10.1186/s13071-019-3642-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Accepted: 07/25/2019] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Biting midges of the genus Culicoides Latreille (Diptera: Ceratopogonidae) are involved in the transmission of several viruses affecting humans and livestock, particularly bluetongue (BTV). Over the last decade, Culicoides surveillance has been conducted discontinuously and at various temporal and spatial scales in mainland France following the BTV epizootics in 2008-2009 and its reemergence and continuous circulation since 2015. The ability to predict seasonal dynamics and spatial abundance of Culicoides spp. is a key element in identifying periods and areas at high risk of transmission in order to strengthen surveillance for early detection and to establish seasonally disease-free zones. The objective of this study was to model the abundance of Culicoides spp. using surveillance data. METHODS A mixed-effect Poisson model, adjusted for overdispersion and taking into account temperature data at each trap location, was used to model the weekly relative abundance of Culicoides spp. over a year in 24 vector zones, based on surveillance data collected during 2009-2012. Vector zones are the spatial units used for Culicoides surveillance since 2016 in mainland France. RESULTS The curves of the predicted annual abundance of Culicoides spp. in vector zones showed three different shapes: unimodal, bimodal or plateau, reflecting the temporal variability of the observed counts between zones. For each vector zone, the model enabled to identify periods of vector activity ranging from 25 to 51 weeks. CONCLUSIONS Although the data were collected for surveillance purposes, our modeling approach integrating vector data with daily temperatures, which are known to be major drivers of Culicoides spp. activity, provided areas-specific predictions of Culicoides spp. abundance. Our findings provide decisions makers with essential information to identify risk periods in each vector zone and guide the allocation of resources for surveillance and control. Knowledge of Culicoides spp. dynamics is also of primary importance for modeling the risk of establishment and spread of midge-borne diseases in mainland France.
Collapse
Affiliation(s)
- Pierre Villard
- CIRAD, UMR ASTRE, 34398 Montpellier, France
- ASTRE, CIRAD, INRA, Université de Montpellier, Montpellier, France
- Unité Epidémiologie et Appui à la Surveillance, Laboratoire de Lyon, Université de Lyon - ANSES, 31 Avenue Tony Garnier, 69007 Lyon, France
| | - Facundo Muñoz
- CIRAD, UMR ASTRE, 34398 Montpellier, France
- ASTRE, CIRAD, INRA, Université de Montpellier, Montpellier, France
| | - Thomas Balenghien
- ASTRE, CIRAD, INRA, Université de Montpellier, Montpellier, France
- Unité Microbiologie, Immunologie et Maladies Contagieuses, Institut Agronomique et Vétérinaire Hassan II, 10100 Rabat, Morocco
- CIRAD, UMR ASTRE, 10101 Rabat, Morocco
| | - Thierry Baldet
- CIRAD, UMR ASTRE, 34398 Montpellier, France
- ASTRE, CIRAD, INRA, Université de Montpellier, Montpellier, France
| | - Renaud Lancelot
- CIRAD, UMR ASTRE, 34398 Montpellier, France
- ASTRE, CIRAD, INRA, Université de Montpellier, Montpellier, France
| | - Viviane Hénaux
- Unité Epidémiologie et Appui à la Surveillance, Laboratoire de Lyon, Université de Lyon - ANSES, 31 Avenue Tony Garnier, 69007 Lyon, France
| |
Collapse
|
6
|
Fitzgibbon WE, Morgan JJ, Webb GF, Wu Y. Spatial models of vector-host epidemics with directed movement of vectors over long distances. Math Biosci 2019; 312:77-87. [DOI: 10.1016/j.mbs.2019.04.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Revised: 03/26/2019] [Accepted: 04/19/2019] [Indexed: 11/16/2022]
|
7
|
Qi L, Beaunée G, Arnoux S, Dutta BL, Joly A, Vergu E, Ezanno P. Neighbourhood contacts and trade movements drive the regional spread of bovine viral diarrhoea virus (BVDV). Vet Res 2019; 50:30. [PMID: 31036076 PMCID: PMC6489178 DOI: 10.1186/s13567-019-0647-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Accepted: 04/11/2019] [Indexed: 11/10/2022] Open
Abstract
To explore the regional spread of endemic pathogens, investigations are required both at within and between population levels. The bovine viral diarrhoea virus (BVDV) is such a pathogen, spreading among cattle herds mainly due to trade movements and neighbourhood contacts, and causing an endemic disease with economic consequences. To assess the contribution of both transmission routes on BVDV regional and local spread, we developed an original epidemiological model combining data-driven and mechanistic approaches, accounting for heterogeneous within-herd dynamics, animal movements and neighbourhood contacts. Extensive simulations were performed over 9 years in an endemic context in a French region with high cattle density. The most uncertain model parameters were calibrated on summary statistics of epidemiological data, highlighting that neighbourhood contacts and within-herd transmission should be high. We showed that neighbourhood contacts and trade movements complementarily contribute to BVDV spread on a regional scale in endemically infected and densely populated areas, leading to intense fade-out/colonization events: neighbourhood contacts generate the vast majority of outbreaks (72%) but mostly in low immunity herds and correlated to a rather short presence of persistently infected animals (P); trade movements generate fewer infections but could affect herds with higher immunity and generate a prolonged presence of P. Both movements and neighbourhood contacts should be considered when designing control or eradication strategies for densely populated region.
Collapse
Affiliation(s)
- Luyuan Qi
- BIOEPAR, Oniris, INRA, CS40706, 44307, Nantes, France.,MaIAGE, INRA, Université Paris-Saclay, 78350, Jouy-en-Josas, France
| | - Gaël Beaunée
- BIOEPAR, Oniris, INRA, CS40706, 44307, Nantes, France
| | - Sandie Arnoux
- BIOEPAR, Oniris, INRA, CS40706, 44307, Nantes, France
| | - Bhagat Lal Dutta
- BIOEPAR, Oniris, INRA, CS40706, 44307, Nantes, France.,MaIAGE, INRA, Université Paris-Saclay, 78350, Jouy-en-Josas, France
| | - Alain Joly
- Groupement de Défense Sanitaire de Bretagne, 56019, Vannes, France
| | - Elisabeta Vergu
- MaIAGE, INRA, Université Paris-Saclay, 78350, Jouy-en-Josas, France
| | | |
Collapse
|
8
|
|
9
|
Viet AF, Krebs S, Rat-Aspert O, Jeanpierre L, Belloc C, Ezanno P. A modelling framework based on MDP to coordinate farmers' disease control decisions at a regional scale. PLoS One 2018; 13:e0197612. [PMID: 29897988 PMCID: PMC5999088 DOI: 10.1371/journal.pone.0197612] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2017] [Accepted: 05/04/2018] [Indexed: 11/19/2022] Open
Abstract
The effectiveness of infectious disease control depends on the ability of health managers to act in a coordinated way. However, with regards to non-notifiable animal diseases, farmers individually decide whether or not to implement control measures, leading to positive and negative externalities for connected farms and possibly impairing disease control at a regional scale. Our objective was to facilitate the identification of optimal incentive schemes at a collective level, adaptive to the epidemiological situation, and minimizing the economic costs due to a disease and its control. We proposed a modelling framework based on Markov Decision Processes (MDP) to identify effective strategies to control PorcineReproductive andRespiratorySyndrome (PRRS), a worldwide endemicinfectiousdisease thatsignificantly impactspig farmproductivity. Using a stochastic discrete-time compartmental model representing PRRS virus spread and control within a group of pig herds, we defined the associated MDP. Using a decision-tree framework, we translated the optimal policy into a limited number of rules providing actions to be performed per 6-month time-step according to the observed system state. We evaluated the effect of varying costs and transition probabilities on optimal policy and epidemiological results. We finally identifiedan adaptive policy that gave the best net financial benefit. The proposed framework is a tool for decision support as it allows decision-makers to identify the optimal policy and to assess its robustness to variations in the values of parameters representing an impact of incentives on farmers' decisions.
Collapse
Affiliation(s)
- Anne-France Viet
- BIOEPAR, INRA, Oniris, Université Bretagne Loire, Nantes, France
| | - Stéphane Krebs
- BIOEPAR, INRA, Oniris, Université Bretagne Loire, Nantes, France
| | - Olivier Rat-Aspert
- BIOEPAR, INRA, Oniris, Université Bretagne Loire, Nantes, France
- CESAER, AgroSup Dijon, INRA, Univ. Bourgogne Franche-Comté, Dijon, France
| | | | - Catherine Belloc
- BIOEPAR, INRA, Oniris, Université Bretagne Loire, Nantes, France
| | - Pauline Ezanno
- BIOEPAR, INRA, Oniris, Université Bretagne Loire, Nantes, France
| |
Collapse
|
10
|
White SM, Sanders CJ, Shortall CR, Purse BV. Mechanistic model for predicting the seasonal abundance of Culicoides biting midges and the impacts of insecticide control. Parasit Vectors 2017; 10:162. [PMID: 28347327 PMCID: PMC5369195 DOI: 10.1186/s13071-017-2097-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2016] [Accepted: 03/20/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Understanding seasonal patterns of abundance of insect vectors is important for optimisation of control strategies of vector-borne diseases. Environmental drivers such as temperature, humidity and photoperiod influence vector abundance, but it is not generally known how these drivers combine to affect seasonal population dynamics. METHODS In this paper, we derive and analyse a novel mechanistic stage-structured simulation model for Culicoides biting midges-the principle vectors of bluetongue and Schmallenberg viruses which cause mortality and morbidity in livestock and impact trade. We model variable life-history traits as functional forms that are dependent on environmental drivers, including air temperature, soil temperature and photoperiod. The model is fitted to Obsoletus group adult suction-trap data sampled daily at five locations throughout the UK for 2008. RESULTS The model predicts population dynamics that closely resemble UK field observations, including the characteristic biannual peaks of adult abundance. Using the model, we then investigate the effects of insecticide control, showing that control strategies focussing on the autumn peak of adult midge abundance have the highest impact in terms of population reduction in the autumn and averaged over the year. Conversely, control during the spring peak of adult abundance leads to adverse increases in adult abundance in the autumn peak. CONCLUSIONS The mechanisms of the biannual peaks of adult abundance, which are important features of midge seasonality in northern Europe and are key determinants of the risk of establishment and spread of midge-borne diseases, have been hypothesised over for many years. Our model suggests that the peaks correspond to two generations per year (bivoltine) are largely determined by pre-adult development. Furthermore, control strategies should focus on reducing the autumn peak since the immature stages are released from density-dependence regulation. We conclude that more extensive modelling of Culicoides biting midge populations in different geographical contexts will help to optimise control strategies and predictions of disease outbreaks.
Collapse
Affiliation(s)
- Steven M White
- Centre for Ecology & Hydrology, Benson Lane, Wallingford, Oxfordshire, OX10 8BB, UK. .,Wolfson Centre for Mathematical Biology, Mathematical Institute, Radcliffe Observatory Quarter, Woodstock Road, Oxford, Oxfordshire, OX2 6GG, UK.
| | | | | | - Bethan V Purse
- Centre for Ecology & Hydrology, Benson Lane, Wallingford, Oxfordshire, OX10 8BB, UK
| |
Collapse
|
11
|
da Silva JM, Giachetto PF, da Silva LO, Cintra LC, Paiva SR, Yamagishi MEB, Caetano AR. Genome-wide copy number variation (CNV) detection in Nelore cattle reveals highly frequent variants in genome regions harboring QTLs affecting production traits. BMC Genomics 2016; 17:454. [PMID: 27297173 PMCID: PMC4907077 DOI: 10.1186/s12864-016-2752-9] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2016] [Accepted: 05/19/2016] [Indexed: 11/10/2022] Open
Abstract
Background Copy number variations (CNVs) have been shown to account for substantial portions of observed genomic variation and have been associated with qualitative and quantitative traits and the onset of disease in a number of species. Information from high-resolution studies to detect, characterize and estimate population-specific variant frequencies will facilitate the incorporation of CNVs in genomic studies to identify genes affecting traits of importance. Results Genome-wide CNVs were detected in high-density single nucleotide polymorphism (SNP) genotyping data from 1,717 Nelore (Bos indicus) cattle, and in NGS data from eight key ancestral bulls. A total of 68,007 and 12,786 distinct CNVs were observed, respectively. Cross-comparisons of results obtained for the eight resequenced animals revealed that 92 % of the CNVs were observed in both datasets, while 62 % of all detected CNVs were observed to overlap with previously validated cattle copy number variant regions (CNVRs). Observed CNVs were used for obtaining breed-specific CNV frequencies and identification of CNVRs, which were subsequently used for gene annotation. A total of 688 of the detected CNVRs were observed to overlap with 286 non-redundant QTLs associated with important production traits in cattle. All of 34 CNVs previously reported to be associated with milk production traits in Holsteins were also observed in Nelore cattle. Comparisons of estimated frequencies of these CNVs in the two breeds revealed 14, 13, 6 and 14 regions in high (>20 %), low (<20 %) and divergent (NEL > HOL, NEL < HOL) frequencies, respectively. Conclusions Obtained results significantly enriched the bovine CNV map and enabled the identification of variants that are potentially associated with traits under selection in Nelore cattle, particularly in genome regions harboring QTLs affecting production traits. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-2752-9) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Joaquim Manoel da Silva
- Faculdade de Ciências Agrárias, Biológicas e Sociais Aplicadas, Universidade do Estado de Mato Grosso (UNEMAT), Av. Prof Dr. Renato Figueiro Varella, CEP 78.690-000, Nova Xavantina, Mato Grosso, Brazil.,Programa de Pós-Graduação em Genética e Biologia Molecular-Instituto de Biologia, Universidade Estadual de Campinas (UNICAMP), Campinas, São Paulo, Brazil
| | - Poliana Fernanda Giachetto
- Embrapa Informática Agropecuária - Laboratório Multiusuário de Bioinformática (LMB), Campinas, São Paulo, Brazil
| | | | - Leandro Carrijo Cintra
- Embrapa Informática Agropecuária - Laboratório Multiusuário de Bioinformática (LMB), Campinas, São Paulo, Brazil
| | - Samuel Rezende Paiva
- Embrapa - Secretaria de Relações Internacionais, Brasília, Distrito Federal, Brazil.,Embrapa Recursos Genéticos e Biotecnologia, Brasília, Distrito Federal, Brazil.,CNPq Fellow, ᅟ, ᅟ
| | | | | |
Collapse
|
12
|
Beaunée G, Gilot-Fromont E, Garel M, Ezanno P. A novel epidemiological model to better understand and predict the observed seasonal spread of Pestivirus in Pyrenean chamois populations. Vet Res 2015. [PMID: 26208716 PMCID: PMC4513621 DOI: 10.1186/s13567-015-0218-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Seasonal variations in individual contacts give rise to a complex interplay between host demography and pathogen transmission. This is particularly true for wild populations, which highly depend on their natural habitat. These seasonal cycles induce variations in pathogen transmission. The seasonality of these biological processes should therefore be considered to better represent and predict pathogen spread. In this study, we sought to better understand how the seasonality of both the demography and social contacts of a mountain ungulate population impacts the spread of a pestivirus within, and the dynamics of, this population. We propose a mathematical model to represent this complex biological system. The pestivirus can be transmitted both horizontally through direct contact and vertically in utero. Vertical transmission leads to abortion or to the birth of persistently infected animals with a short life expectancy. Horizontal transmission involves a complex dynamics because of seasonal variations in contact among sexes and age classes. We performed a sensitivity analysis that identified transmission rates and disease-related mortality as key parameters. We then used data from a long-term demographic and epidemiological survey of the studied population to estimate these mostly unknown epidemiological parameters. Our model adequately represents the system dynamics, observations and model predictions showing similar seasonal patterns. We show that the virus has a significant impact on population dynamics, and that persistently infected animals play a major role in the epidemic dynamics. Modeling the seasonal dynamics allowed us to obtain realistic prediction and to identify key parameters of transmission.
Collapse
Affiliation(s)
- Gaël Beaunée
- INRA, Oniris, LUNAM Université, UMR1300 BioEpAR, CS40706, F-44307 Nantes, France.
| | - Emmanuelle Gilot-Fromont
- Université de Lyon, VetAgro Sup-Campus Vétérinaire de Lyon, Marcy l'Etoile, France. .,Université de Lyon, Université Lyon 1, UMR CNRS 5558 Laboratoire de Biométrie et Biologie Evolutive, Villeurbanne, France.
| | - Mathieu Garel
- Office National de la Chasse et de la Faune Sauvage, Centre National d'Études et de Recherche Appliquée Faune de Montagne, Gières, France.
| | - Pauline Ezanno
- INRA, Oniris, LUNAM Université, UMR1300 BioEpAR, CS40706, F-44307 Nantes, France.
| |
Collapse
|
13
|
A Stochastic Model to Study Rift Valley Fever Persistence with Different Seasonal Patterns of Vector Abundance: New Insights on the Endemicity in the Tropical Island of Mayotte. PLoS One 2015; 10:e0130838. [PMID: 26147799 PMCID: PMC4493030 DOI: 10.1371/journal.pone.0130838] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2014] [Accepted: 05/25/2015] [Indexed: 12/24/2022] Open
Abstract
Rift Valley fever (RVF) is a zoonotic vector-borne disease causing abortion storms in cattle and human epidemics in Africa. Our aim was to evaluate RVF persistence in a seasonal and isolated population and to apply it to Mayotte Island (Indian Ocean), where the virus was still silently circulating four years after its last known introduction in 2007. We proposed a stochastic model to estimate RVF persistence over several years and under four seasonal patterns of vector abundance. Firstly, the model predicted a wide range of virus spread patterns, from obligate persistence in a constant or tropical environment (without needing vertical transmission or reintroduction) to frequent extinctions in a drier climate. We then identified for each scenario of seasonality the parameters that most influenced prediction variations. Persistence was sensitive to vector lifespan and biting rate in a tropical climate, and to host viraemia duration and vector lifespan in a drier climate. The first epizootic peak was primarily sensitive to viraemia duration and thus likely to be controlled by vaccination, whereas subsequent peaks were sensitive to vector lifespan and biting rate in a tropical climate, and to host birth rate and viraemia duration in arid climates. Finally, we parameterized the model according to Mayotte known environment. Mosquito captures estimated the abundance of eight potential RVF vectors. Review of RVF competence studies on these species allowed adjusting transmission probabilities per bite. Ruminant serological data since 2004 and three new cross-sectional seroprevalence studies are presented. Transmission rates had to be divided by more than five to best fit observed data. Five years after introduction, RVF persisted in more than 10% of the simulations, even under this scenario of low transmission. Hence, active surveillance must be maintained to better understand the risk related to RVF persistence and to prevent new introductions.
Collapse
|
14
|
Kluiters G, Swales H, Baylis M. Local dispersal of palaearctic Culicoides biting midges estimated by mark-release-recapture. Parasit Vectors 2015; 8:86. [PMID: 25886488 PMCID: PMC4327803 DOI: 10.1186/s13071-015-0658-z] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2014] [Accepted: 01/12/2015] [Indexed: 11/24/2022] Open
Abstract
Background Farm to farm movement of Culicoides midges is believed to play a critical role in the spread of bluetongue (BT), Schmallenberg and other midge-borne diseases. To help understand and predict the spread of diseases carried by midges, there is a need to determine their dispersal patterns, and to identify factors contributing to the direction taken and distance travelled. Methods The dispersal of Obsoletus Group members was studied on 19 farms around Bala, north Wales. Field-collected Culicoides were trapped in a black-light (OVI) trap and self-marked in the collecting vessel, using micronized fluorescent dust. Culicoides were released at a central farm and OVI traps set on 18 surrounding farms, at distances of 1 to 4 km. The study was repeated using six colours of fluorescent dust over an 18 day period. Results An estimated 61,062 (95% CI = 56,298-65,830) marked Culicoides were released during the study and 12 (0.02%) Culicoides were recaptured. Of the females recaptured, six were C. obsoletus/scoticus, two C. dewulfi, two C. pulicaris and one C. festivipennis. The male was C. obsoletus. Recaptures occurred 1–2.5 km from the release site, with greatest numbers at 2.5 km. Most recaptures were 2 nights post-release; none were more than 3 nights post-release. Two females were recovered at 1.5 km on the night of release and one male at 1 km two nights post-release. The mean distance travelled (MDT) for males was 1 km, females was 2.21 km, and all recaptured Culicoides was 2.15 km. Recaptures were made both downwind and upwind of the prevailing wind direction during the trapping periods, highlighting possible passive and active dispersal of Culicoides between farms. Conclusions This is the first study to demonstrate farm to farm movement of the main Palaearctic BT vector species, the Obsoletus Group. Such movement has disease control implications in terms of the vectoral movement of disease between farms. The results suggest that Culicoides control measures applied at an infected farm (trapping or killing Culicoides) will reduce risk of spread to neighbouring farms by lessening the number of Culicoides dispersing from that farm, as well as reducing transmission at the source farm itself.
Collapse
Affiliation(s)
- Georgette Kluiters
- Institute of Infection and Global Health, Liverpool University Climate and Infectious Diseases of Animals (LUCINDA) Group, University of Liverpool, Leahurst Campus, Neston, Cheshire, UK.
| | - Harry Swales
- Institute of Infection and Global Health, Liverpool University Climate and Infectious Diseases of Animals (LUCINDA) Group, University of Liverpool, Leahurst Campus, Neston, Cheshire, UK.
| | - Matthew Baylis
- Institute of Infection and Global Health, Liverpool University Climate and Infectious Diseases of Animals (LUCINDA) Group, University of Liverpool, Leahurst Campus, Neston, Cheshire, UK. .,National Institute for Health Research, Health Protection Research Unit in Emerging and Zoonotic Infections, University of Liverpool, Neston, UK.
| |
Collapse
|
15
|
Ezanno P, Aubry-Kientz M, Arnoux S, Cailly P, L'Ambert G, Toty C, Balenghien T, Tran A. A generic weather-driven model to predict mosquito population dynamics applied to species of Anopheles, Culex and Aedes genera of southern France. Prev Vet Med 2015; 120:39-50. [PMID: 25623972 DOI: 10.1016/j.prevetmed.2014.12.018] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2014] [Revised: 12/18/2014] [Accepted: 12/24/2014] [Indexed: 11/27/2022]
Abstract
An accurate understanding and prediction of mosquito population dynamics are needed to identify areas where there is a high risk of mosquito-borne disease spread and persistence. Simulation tools are relevant for supporting decision-makers in the surveillance of vector populations, as models of vector population dynamics provide predictions of the greatest risk periods for vector abundance, which can be particularly helpful in areas with a highly variable environment. We present a generic weather-driven model of mosquito population dynamics, which was applied to one species of each of the genera Anopheles, Culex, and Aedes, located in the same area and thus affected by similar weather conditions. The predicted population dynamics of Anopheles hyrcanus, Culex pipiens, and Aedes caspius were not similar. An. hyrcanus was abundant in late summer. Cx. pipiens was less abundant but throughout the summer. The abundance of both species showed a single large peak with few variations between years. The population dynamics of Ae. caspius showed large intra- and inter-annual variations due to pulsed egg hatching. Predictions of the model were compared to longitudinal data on host-seeking adult females. Data were previously obtained using CDC-light traps baited with carbon dioxide dry ice in 2005 at two sites (Marais du Viguerat and Tour Carbonnière) in a favourable temperate wetland of southern France (Camargue). The observed and predicted periods of maximal abundance for An. hyrcanus and Cx. pipiens tallied very well. Pearson's coefficients for these two species were over 75% for both species. The model also reproduced the major trends in the intra-annual fluctuations of Ae. caspius population dynamics, with peaks occurring in early summer and following the autumn rainfall events. Few individuals of this species were trapped so the comparison of predicted and observed dynamics was not relevant. A global sensitivity analysis of the species-specific models enabled us to identify the parameters most influencing the maximal abundance of mosquitoes. These key parameters were almost similar between species, but not with the same contributions. The emergence of adult mosquitoes was identified as a key process in the population dynamics of all of the three species considered here. Parameters associated with adult emergence therefore need to be precisely known to achieve accurate predictions. Our model is a flexible and efficient tool that predicts mosquito abundance based on local environmental factors. It is useful to and already used by a mosquito surveillance manager in France.
Collapse
Affiliation(s)
- P Ezanno
- INRA, Oniris, LUNAM Université, UMR1300 BioEpAR, CS40706, F-44307 Nantes, France.
| | - M Aubry-Kientz
- INRA, Oniris, LUNAM Université, UMR1300 BioEpAR, CS40706, F-44307 Nantes, France; Cirad, INRA, UMR1309 CMAEE, F-34398 Montpellier, France.
| | - S Arnoux
- INRA, Oniris, LUNAM Université, UMR1300 BioEpAR, CS40706, F-44307 Nantes, France.
| | - P Cailly
- INRA, Oniris, LUNAM Université, UMR1300 BioEpAR, CS40706, F-44307 Nantes, France; Cirad, UPR AGIRs, F-34398 Montpellier, France.
| | - G L'Ambert
- EID-Méditerranée, 165 Av. Paul-Rimbaud, F-34184 Montpellier Cedex 4, France.
| | - C Toty
- IRD, MIVEGEC, F-34394 Montpellier Cedex 5, France.
| | - T Balenghien
- Cirad, INRA, UMR1309 CMAEE, F-34398 Montpellier, France.
| | - A Tran
- Cirad, UPR AGIRs, F-34398 Montpellier, France; Cirad, UMR TETIS, F-34398 Montpellier, France.
| |
Collapse
|
16
|
Gubbins S, Turner J, Baylis M, van der Stede Y, van Schaik G, Abrahantes JC, Wilson AJ. Inferences about the transmission of Schmallenberg virus within and between farms. Prev Vet Med 2014; 116:380-90. [PMID: 24857371 PMCID: PMC4204990 DOI: 10.1016/j.prevetmed.2014.04.011] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2013] [Revised: 02/27/2014] [Accepted: 04/19/2014] [Indexed: 11/18/2022]
Abstract
In the summer of 2011 Schmallenberg virus (SBV), a Culicoides-borne orthobunyavirus, emerged in Germany and The Netherlands and subsequently spread across much of Europe. To draw inferences about the transmission of SBV we have developed two models to describe its spread within and between farms. The within-farm model was fitted to seroprevalence data for cattle and sheep farms in Belgium and The Netherlands, with parameters estimated using approximate Bayesian computation. Despite the short duration of viraemia in cattle and sheep (mean of 3–4 days) the within-farm seroprevalence can reach high levels (mean within-herd seroprevalence >80%), largely because the probability of transmission from host to vector is high (14%) and SBV is able to replicate quickly (0.03 per day-degree) and at relatively low temperatures (threshold for replication: 12.3 °C). Parameter estimates from the within-farm model were then used in a separate between-farm model to simulate the regional spread of SBV. This showed that the rapid spread of SBV at a regional level is primarily a consequence of the high probability of transmission from host to vector and the temperature requirements for virus replication. Our results, obtained for a region of the UK in a typical year with regard to animal movements, indicate that there is no need to invoke additional transmission mechanisms to explain the observed patterns of rapid spread of SBV in Europe. Moreover, the imposition of movement restrictions, even a total movement ban, has little effect on the spread of SBV at this scale.
Collapse
Affiliation(s)
- Simon Gubbins
- The Pirbright Institute, Ash Road, Pirbright, Surrey GU24 0NF, UK.
| | - Joanne Turner
- Department of Epidemiology and Population Health, Institute of Infection and Global Health, University of Liverpool, Leahurst Campus, Chester High Road, Neston, Cheshire CH64 7TE, UK
| | - Matthew Baylis
- Department of Epidemiology and Population Health, Institute of Infection and Global Health, University of Liverpool, Leahurst Campus, Chester High Road, Neston, Cheshire CH64 7TE, UK
| | - Yves van der Stede
- Unit of Co-ordination Veterinary Diagnosis-Epidemiology and Risk Assessment, CODA-CERVA, Groeselenberg 99, 1180 Brussels, Belgium; Department of Virology, Parasitology and Immunology, Faculty of Veterinary Medicine, Ghent University, Salisburylaan 133, 9820 Merelbeke, Belgium
| | | | | | - Anthony J Wilson
- The Pirbright Institute, Ash Road, Pirbright, Surrey GU24 0NF, UK
| |
Collapse
|