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Van Borm S, Dellicour S, Martin DP, Lemey P, Agianniotaki EI, Chondrokouki ED, Vidanovic D, Vaskovic N, Petroviċ T, Laziċ S, Koleci X, Vodica A, Djadjovski I, Krstevski K, Vandenbussche F, Haegeman A, De Clercq K, Mathijs E. Complete genome reconstruction of the global and European regional dispersal history of the lumpy skin disease virus. J Virol 2023; 97:e0139423. [PMID: 37905838 PMCID: PMC10688313 DOI: 10.1128/jvi.01394-23] [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: 09/22/2023] [Accepted: 10/02/2023] [Indexed: 11/02/2023] Open
Abstract
IMPORTANCE Lumpy skin disease virus (LSDV) has a complex epidemiology involving multiple strains, recombination, and vaccination. Its DNA genome provides limited genetic variation to trace outbreaks in space and time. Sequencing of LSDV whole genomes has also been patchy at global and regional scales. Here, we provide the first fine-grained whole genome sequence sampling of a constrained LSDV outbreak (southeastern Europe, 2015-2017), which we analyze along with global publicly available genomes. We formally evaluate the past occurrence of recombination events as well as the temporal signal that is required for calibrating molecular clock models and subsequently conduct a time-calibrated spatially explicit phylogeographic reconstruction. Our study further illustrates the importance of accounting for recombination events before reconstructing global and regional dynamics of DNA viruses. More LSDV whole genomes from endemic areas are needed to obtain a comprehensive understanding of global LSDV dispersal dynamics.
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Affiliation(s)
- Steven Van Borm
- Scientific Directorate Animal Infectious Diseases, Sciensano, Brussels, Belgium
| | - Simon Dellicour
- Spatial Epidemiology Lab (SpELL), Université Libre de Bruxelles, Brussels, Belgium
- Laboratory for Clinical and Epidemiological Virology, Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium
| | - Darren P. Martin
- Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Philippe Lemey
- Laboratory for Clinical and Epidemiological Virology, Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium
| | - Eirini I. Agianniotaki
- National Reference Laboratory for Capripoxviruses, Department of Molecular Diagnostics, FMD, Virological, Rickettsial and Exotic Diseases, Directorate of Athens Veterinary Center, Ministry of Rural Development and Food, Athens, Greece
| | - Eleni D. Chondrokouki
- National Reference Laboratory for Capripoxviruses, Department of Molecular Diagnostics, FMD, Virological, Rickettsial and Exotic Diseases, Directorate of Athens Veterinary Center, Ministry of Rural Development and Food, Athens, Greece
| | - Dejan Vidanovic
- Department for laboratory diagnostics, Veterinary Specialized Institute, Kraljevo, Serbia
| | - Nikola Vaskovic
- Department for laboratory diagnostics, Veterinary Specialized Institute, Kraljevo, Serbia
| | - Tamaš Petroviċ
- Department for Virology, Scientific Veterinary Institute, Novi Sad, Serbia
| | - Sava Laziċ
- Department for Virology, Scientific Veterinary Institute, Novi Sad, Serbia
| | - Xhelil Koleci
- Faculty of Veterinary Medicine, The Agricultural University of Tirana, Tirana, Albania
| | - Ani Vodica
- Animal Health Department, Food Safety and Veterinary Institute, Tirana, Albania
| | - Igor Djadjovski
- Faculty of Veterinary Medicine, Ss. Cyril and Methodius University in Skopje, Skopje, Macedonia
| | - Kiril Krstevski
- Faculty of Veterinary Medicine, Ss. Cyril and Methodius University in Skopje, Skopje, Macedonia
| | - Frank Vandenbussche
- Scientific Directorate Animal Infectious Diseases, Sciensano, Brussels, Belgium
| | - Andy Haegeman
- Scientific Directorate Animal Infectious Diseases, Sciensano, Brussels, Belgium
| | - Kris De Clercq
- Scientific Directorate Animal Infectious Diseases, Sciensano, Brussels, Belgium
| | - Elisabeth Mathijs
- Scientific Directorate Animal Infectious Diseases, Sciensano, Brussels, Belgium
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González-Gordon L, Porphyre T, Muwonge A, Nantima N, Ademun R, Ochwo S, Mwiine NF, Boden L, Muhanguzi D, Bronsvoort BMDC. Identifying target areas for risk-based surveillance and control of transboundary animal diseases: a seasonal analysis of slaughter and live-trade cattle movements in Uganda. Sci Rep 2023; 13:18619. [PMID: 37903814 PMCID: PMC10616094 DOI: 10.1038/s41598-023-44518-4] [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: 05/31/2023] [Accepted: 10/09/2023] [Indexed: 11/01/2023] Open
Abstract
Animal movements are a major driver for the spread of Transboundary Animal Diseases (TADs). These movements link populations that would otherwise be isolated and hence create opportunities for susceptible and infected individuals to meet. We used social network analysis to describe the seasonal network structure of cattle movements in Uganda and unravel critical network features that identify districts or sub-regions for targeted risk-based surveillance and intervention. We constructed weighted, directed networks based on 2019 between-district cattle movements using official livestock mobility data; the purpose of the movement ('slaughter' vs. 'live trade') was used to subset the network and capture the risks more reliably. Our results show that cattle trade can result in local and long-distance disease spread in Uganda. Seasonal variability appears to impact the structure of the network, with high heterogeneity of node and edge activity identified throughout the seasons. These observations mean that the structure of the live trade network can be exploited to target influential district hubs within the cattle corridor and peripheral areas in the south and west, which would result in rapid network fragmentation, reducing the contact structure-related trade risks. Similar exploitable features were observed for the slaughter network, where cattle traffic serves mainly slaughter hubs close to urban centres along the cattle corridor. Critically, analyses that target the complex livestock supply value chain offer a unique framework for understanding and quantifying risks for TADs such as Foot-and-Mouth disease in a land-locked country like Uganda. These findings can be used to inform the development of risk-based surveillance strategies and decision making on resource allocation. For instance, vaccine deployment, biosecurity enforcement and capacity building for stakeholders at the local community and across animal health services with the potential to limit the socio-economic impact of outbreaks, or indeed reduce their frequency.
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Affiliation(s)
- Lina González-Gordon
- The Epidemiology, Economics and Risk Assessment (EERA) Group, The Roslin Institute at The Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, UK.
- Global Academy of Agriculture and Food Systems, Royal (Dick) School of Veterinary Studies and The Roslin Institute, University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, UK.
| | - Thibaud Porphyre
- Laboratoire de Biométrie et Biologie Évolutive, UMR 5558, Universite Claude Bernard Lyon 1, CNRS, VetAgro Sup, Marcy l'Étoile, France
| | - Adrian Muwonge
- The Epidemiology, Economics and Risk Assessment (EERA) Group, The Roslin Institute at The Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, UK
- The Digital One Health Laboratory, The Roslin Institute at The Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, UK
| | - Noelina Nantima
- Department of Animal Health, Ministry of Agriculture Animal Industry and Fisheries, Entebbe, Uganda
| | - Rose Ademun
- Department of Animal Health, Ministry of Agriculture Animal Industry and Fisheries, Entebbe, Uganda
| | - Sylvester Ochwo
- Center for Animal Health and Food Safety, College of Veterinary Medicine, University of Minnesota, Saint Paul, MN, 55108, USA
| | - Norbert Frank Mwiine
- Department of Biomolecular Resources and Biolaboratory Sciences (BBS), College of Veterinary Medicine, Makerere University, Kampala, Uganda
| | - Lisa Boden
- Global Academy of Agriculture and Food Systems, Royal (Dick) School of Veterinary Studies and The Roslin Institute, University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, UK
| | - Dennis Muhanguzi
- Department of Biomolecular Resources and Biolaboratory Sciences (BBS), College of Veterinary Medicine, Makerere University, Kampala, Uganda
| | - Barend Mark de C Bronsvoort
- The Epidemiology, Economics and Risk Assessment (EERA) Group, The Roslin Institute at The Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, UK
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Woldemariyam FT, Kariuki CK, Kamau J, De Vleeschauwer A, De Clercq K, Lefebvre DJ, Paeshuyse J. Epidemiological Dynamics of Foot-and-Mouth Disease in the Horn of Africa: The Role of Virus Diversity and Animal Movement. Viruses 2023; 15:v15040969. [PMID: 37112947 PMCID: PMC10143177 DOI: 10.3390/v15040969] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Revised: 04/11/2023] [Accepted: 04/13/2023] [Indexed: 04/29/2023] Open
Abstract
The Horn of Africa is a large area of arid and semi-arid land, holding about 10% of the global and 40% of the entire African livestock population. The region's livestock production system is mainly extensive and pastoralist. It faces countless problems, such as a shortage of pastures and watering points, poor access to veterinary services, and multiple endemic diseases like foot-and-mouth disease (FMD). Foot-and-mouth disease is one of the most economically important livestock diseases worldwide and is endemic in most developing countries. Within Africa, five of the seven serotypes of the FMD virus (FMDV) are described, but serotype C is not circulating anymore, a burden unseen anywhere in the world. The enormous genetic diversity of FMDV is favored by an error-prone RNA-dependent RNA polymerase, intra-typic and inter-typic recombination, as well as the quasi-species nature of the virus. This paper describes the epidemiological dynamics of foot-and-mouth disease in the Horn of Africa with regard to the serotypes and topotypes distribution of FMDV, the livestock production systems practiced, animal movement, the role of wildlife, and the epidemiological complexity of FMD. Within this review, outbreak investigation data and serological studies confirm the endemicity of the disease in the Horn of Africa. Multiple topotypes of FMDV are described in the literature as circulating in the region, with further evolution of virus diversity predicted. A large susceptible livestock population and the presence of wild ungulates are described as complicating the epidemiology of the disease. Further, the husbandry practices and legal and illegal trading of livestock and their products, coupled with poor biosecurity practices, are also reported to impact the spread of FMDV within and between countries in the region. The porosity of borders for pastoralist herders fuels the unregulated transboundary livestock trade. There are no systematic control strategies in the region except for sporadic vaccination with locally produced vaccines, while literature indicates that effective control measures should also consider virus diversity, livestock movements/biosecurity, transboundary trade, and the reduction of contact with wild, susceptible ungulates.
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Affiliation(s)
- Fanos Tadesse Woldemariyam
- Laboratory of Host-Pathogen Interaction in Livestock, Division of Animal and Human Health Engineering, Department of Biosystems, KU Leuven, 3001 Leuven, Belgium
- College of Veterinary Medicine, Addis Ababa University, Bishoftu P.O. Box 34, Ethiopia
| | - Christopher Kinyanjui Kariuki
- Laboratory of Host-Pathogen Interaction in Livestock, Division of Animal and Human Health Engineering, Department of Biosystems, KU Leuven, 3001 Leuven, Belgium
- Institute of Primate Research, Karen, Nairobi P.O. Box 24481-00502, Kenya
| | - Joseph Kamau
- Institute of Primate Research, Karen, Nairobi P.O. Box 24481-00502, Kenya
- Department of Biochemistry, University of Nairobi, Nairobi P.O. Box 30197, Kenya
| | | | - Kris De Clercq
- Sciensano, Service for Exotic and Vector-Borne Diseases, 1050 Brussels, Belgium
| | - David J Lefebvre
- Sciensano, Service for Exotic and Vector-Borne Diseases, 1050 Brussels, Belgium
| | - Jan Paeshuyse
- Laboratory of Host-Pathogen Interaction in Livestock, Division of Animal and Human Health Engineering, Department of Biosystems, KU Leuven, 3001 Leuven, Belgium
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González Gordon L, Porphyre T, Muhanguzi D, Muwonge A, Boden L, Bronsvoort BMDC. A scoping review of foot-and-mouth disease risk, based on spatial and spatio-temporal analysis of outbreaks in endemic settings. Transbound Emerg Dis 2022; 69:3198-3215. [PMID: 36383164 PMCID: PMC10107783 DOI: 10.1111/tbed.14769] [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: 08/26/2022] [Accepted: 11/11/2022] [Indexed: 11/17/2022]
Abstract
Foot-and-mouth disease (FMD) is one of the most important transboundary animal diseases affecting livestock and wildlife species worldwide. Sustained viral circulation, as evidenced by serological surveys and the recurrence of outbreaks, suggests endemic transmission cycles in some parts of Africa, Asia and the Middle East. This is the result of a complex process in which multiple serotypes, multi-host interactions and numerous socio-epidemiological factors converge to facilitate disease introduction, survival and spread. Spatial and spatio-temporal analyses have been increasingly used to explore the burden of the disease by identifying high-risk areas, analysing temporal trends and exploring the factors that contribute to the outbreaks. We systematically retrieved spatial and spatial-temporal studies on FMD outbreaks to summarize variations on their methodological approaches and identify the epidemiological factors associated with the outbreaks in endemic contexts. Fifty-one studies were included in the final review. A high proportion of papers described and visualized the outbreaks (72.5%) and 49.0% used one or more approaches to study their spatial, temporal and spatio-temporal aggregation. The epidemiological aspects commonly linked to FMD risk are broadly categorizable into themes such as (a) animal demographics and interactions, (b) spatial accessibility, (c) trade, (d) socio-economic and (e) environmental factors. The consistency of these themes across studies underlines the different pathways in which the virus is sustained in endemic areas, with the potential to exploit them to design tailored evidence based-control programmes for the local needs. There was limited data linking the socio-economics of communities and modelled FMD outbreaks, leaving a gap in the current knowledge. A thorough analysis of FMD outbreaks requires a systemic view as multiple epidemiological factors contribute to viral circulation and may improve the accuracy of disease mapping. Future studies should explore the links between socio-economic and epidemiological factors as a foundation for translating the identified opportunities into interventions to improve the outcomes of FMD surveillance and control initiatives in endemic contexts.
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Affiliation(s)
- Lina González Gordon
- The Epidemiology, Economics and Risk Assessment (EERA) Group, The Roslin Institute at The Royal (Dick) School of Veterinary StudiesUniversity of EdinburghEaster BushMidlothianUK
- Global Academy of Agriculture and Food SystemsUniversity of EdinburghEaster BushMidlothianUK
| | - Thibaud Porphyre
- Laboratoire de Biométrie et Biologie EvolutiveUniversité de Lyon, Université Lyon 1, CNRS, VetAgro SupMarcy‐l’ÉtoileFrance
| | - Dennis Muhanguzi
- Department of Bio‐Molecular Resources and Bio‐Laboratory Sciences, College of Veterinary Medicine, Animal Resources and BiosecurityMakerere UniversityKampalaUganda
| | - Adrian Muwonge
- The Epidemiology, Economics and Risk Assessment (EERA) Group, The Roslin Institute at The Royal (Dick) School of Veterinary StudiesUniversity of EdinburghEaster BushMidlothianUK
| | - Lisa Boden
- Global Academy of Agriculture and Food SystemsUniversity of EdinburghEaster BushMidlothianUK
| | - Barend M. de C Bronsvoort
- The Epidemiology, Economics and Risk Assessment (EERA) Group, The Roslin Institute at The Royal (Dick) School of Veterinary StudiesUniversity of EdinburghEaster BushMidlothianUK
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Ecological and Anthropogenic Spatial Gradients Shape Patterns of Dispersal of Foot-and-Mouth Disease Virus in Uganda. Pathogens 2022; 11:pathogens11050524. [PMID: 35631045 PMCID: PMC9143568 DOI: 10.3390/pathogens11050524] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Revised: 04/26/2022] [Accepted: 04/27/2022] [Indexed: 02/04/2023] Open
Abstract
Using georeferenced phylogenetic trees, phylogeography allows researchers to elucidate interactions between environmental heterogeneities and patterns of infectious disease spread. Concordant with the increasing availability of pathogen genetic sequence data, there is a growing need for tools to test epidemiological hypotheses in this field. In this study, we apply tools traditionally used in ecology to elucidate the epidemiology of foot-and-mouth disease virus (FMDV) in Uganda. We analyze FMDV serotype O genetic sequences and their corresponding spatiotemporal metadata from a cross-sectional study of cattle. We apply step selection function (SSF) models, typically used to study wildlife habitat selection, to viral phylogenies to show that FMDV is more likely to be found in areas of low rainfall. Next, we use a novel approach, a resource gradient function (RGF) model, to elucidate characteristics of viral source and sink areas. An RGF model applied to our data reveals that areas of high cattle density and areas near livestock markets may serve as sources of FMDV dissemination in Uganda, and areas of low rainfall serve as viral sinks that experience frequent reintroductions. Our results may help to inform risk-based FMDV control strategies in Uganda. More broadly, these tools advance the phylogenetic toolkit, as they may help to uncover patterns of spread of other organisms for which genetic sequences and corresponding spatiotemporal metadata exist.
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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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