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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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Omondi G, Alkhamis MA, Obanda V, Gakuya F, Sangula A, Pauszek S, Perez A, Ngulu S, van Aardt R, Arzt J, VanderWaal K. Phylogeographical and cross-species transmission dynamics of SAT1 and SAT2 foot-and-mouth disease virus in Eastern Africa. Mol Ecol 2019; 28:2903-2916. [PMID: 31074125 DOI: 10.1111/mec.15125] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2019] [Revised: 04/28/2019] [Accepted: 04/29/2019] [Indexed: 12/15/2022]
Abstract
Understanding the dynamics of foot-and-mouth disease virus (FMDV), an endemic and economically constraining disease, is critical in designing control programmes in Africa. This study investigates the evolutionary epidemiology of SAT1 and SAT2 FMDV in Eastern Africa, as well as between cattle and wild African buffalo. Bayesian phylodynamic models were used to analyse SAT1 and SAT2 VP1 gene segments collected between 1975 and 2016, focusing on the SAT1 and SAT2 viruses currently circulating in Eastern Africa. The root state posterior probabilities inferred from our analyses suggest Zimbabwe as the ancestral location for SAT1 currently circulating in Eastern Africa (p = 0.67). For the SAT2 clade, Kenya is inferred to be the ancestral location for introduction of the virus into other countries in Eastern Africa (p = 0.72). Salient (Bayes factor >10) viral dispersal routes were inferred from Tanzania to Kenya, and from Kenya to Uganda for SAT1 and SAT2, respectively. Results suggest that cattle are the source of the SAT1 and SAT2 clades currently circulating in Eastern Africa. In addition, our results suggest that the majority of SAT1 and SAT2 in livestock come from other livestock rather than wildlife, with limited evidence that buffalo serve as reservoirs for cattle. Insights from the present study highlight the role of cattle movements and anthropogenic activities in shaping the evolutionary history of SAT1 and SAT2 in Eastern Africa. While the results may be affected by inherent limitations of imperfect surveillance, our analysis elucidates the dynamics between host species in this region, which is key to guiding disease intervention activities.
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Affiliation(s)
- George Omondi
- Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, St. Paul, Minnesota
| | - Moh A Alkhamis
- Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, St. Paul, Minnesota.,Department of Epidemiology and Biostatistics, Faculty of Public Health, Health Sciences Center, Kuwait University, Kuwait, Kuwait
| | - Vincent Obanda
- Veterinary Services Department, Kenya Wildlife Service, Nairobi, Kenya
| | - Francis Gakuya
- Veterinary Services Department, Kenya Wildlife Service, Nairobi, Kenya
| | | | - Steven Pauszek
- Plum Island Animal Disease Center, Foreign Animal Disease Research Unit, USDA, Orient Point, New York
| | - Andres Perez
- Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, St. Paul, Minnesota
| | | | | | - Jonathan Arzt
- Plum Island Animal Disease Center, Foreign Animal Disease Research Unit, USDA, Orient Point, New York
| | - Kim VanderWaal
- Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, St. Paul, Minnesota
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Alkhamis MA, Gallardo C, Jurado C, Soler A, Arias M, Sánchez-Vizcaíno JM. Phylodynamics and evolutionary epidemiology of African swine fever p72-CVR genes in Eurasia and Africa. PLoS One 2018; 13:e0192565. [PMID: 29489860 PMCID: PMC5831051 DOI: 10.1371/journal.pone.0192565] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2017] [Accepted: 01/25/2018] [Indexed: 12/11/2022] Open
Abstract
African swine fever (ASF) is a complex infectious disease of swine that constitutes devastating impacts on animal health and the world economy. Here, we investigated the evolutionary epidemiology of ASF virus (ASFV) in Eurasia and Africa using the concatenated gene sequences of the viral protein 72 and the central variable region of isolates collected between 1960 and 2015. We used Bayesian phylodynamic models to reconstruct the evolutionary history of the virus, to identify virus population demographics and to quantify dispersal patterns between host species. Results suggest that ASFV exhibited a significantly high evolutionary rate and population growth through time since its divergence in the 18th century from East Africa, with no signs of decline till recent years. This increase corresponds to the growing pig trade activities between continents during the 19th century, and may be attributed to an evolutionary drift that resulted from either continuous circulation or maintenance of the virus within Africa and Eurasia. Furthermore, results implicate wild suids as the ancestral host species (root state posterior probability = 0.87) for ASFV in the early 1700s in Africa. Moreover, results indicate the transmission cycle between wild suids and pigs is an important cycle for ASFV spread and maintenance in pig populations, while ticks are an important natural reservoir that can facilitate ASFV spread and maintenance in wild swine populations. We illustrated the prospects of phylodynamic methods in improving risk-based surveillance, support of effective animal health policies, and epidemic preparedness in countries at high risk of ASFV incursion.
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Affiliation(s)
- Moh A Alkhamis
- Faculty of Public Heath, Health Sciences Centre, Kuwait University, Kuwait City, Kuwait
- Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, St. Paul, Minnesota, United States of America
| | - Carmina Gallardo
- European Union Reference Laboratory for African swine fever. Centro de Investigación en Sanidad Animal (INIA-CISA), Madrid, Spain
| | - Cristina Jurado
- VISAVET Health Surveillance Centre and Animal Health Department, Veterinary School, Complutense University of Madrid, Madrid, Spain
| | - Alejandro Soler
- European Union Reference Laboratory for African swine fever. Centro de Investigación en Sanidad Animal (INIA-CISA), Madrid, Spain
| | - Marisa Arias
- European Union Reference Laboratory for African swine fever. Centro de Investigación en Sanidad Animal (INIA-CISA), Madrid, Spain
| | - José M Sánchez-Vizcaíno
- VISAVET Health Surveillance Centre and Animal Health Department, Veterinary School, Complutense University of Madrid, Madrid, Spain
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Dibia IN, Sumiarto B, Susetya H, Putra AAG, Scott-Orr H, Mahardika GN. Phylogeography of the current rabies viruses in Indonesia. J Vet Sci 2016; 16:459-66. [PMID: 25643792 PMCID: PMC4701738 DOI: 10.4142/jvs.2015.16.4.459] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2014] [Revised: 11/23/2014] [Accepted: 12/30/2014] [Indexed: 12/25/2022] Open
Abstract
Rabies is a major fatal zoonotic disease in Indonesia. This study was conducted to determine the recent dynamics of rabies virus (RABV) in various areas and animal species throughout Indonesia. A total of 27 brain samples collected from rabid animals of various species in Bali, Sumatra, Kalimantan, Sulawesi, Java, and Flores in 2008 to 2010 were investigated. The cDNA of the nucleoprotein gene from each sample was generated and amplified by one-step reverse transcription-PCR, after which the products were sequenced and analyzed. The symmetric substitution model of a Bayesian stochastic search variable selection extension of the discrete phylogeographic model of the social network was applied in BEAST ver. 1.7.5 software. The spatial dispersal was visualized in Cartographica using Spatial Phylogenetic Reconstruction of Evolutionary Dynamics. We demonstrated inter-island introduction and reintroduction, and dog was found to be the only source of infection of other animals. Ancestors of Indonesian RABVs originated in Java and its descendants were transmitted to Kalimantan, then further to Sumatra, Flores, and Bali. The Flores descendent was subsequently transmitted to Sulawesi and back to Kalimantan. The viruses found in various animal species were transmitted by the dog.
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Affiliation(s)
- I Nyoman Dibia
- Animal Disease Investigation Centre, Denpasar 80226, Indonesia.,Veterinary Science Post Graduate Program, Faculty of Veterinary Medicine, Gajah Mada University, Yogyakarta 55281, Indonesia
| | - Bambang Sumiarto
- Veterinary Public Health Department, Faculty of Veterinary Medicine, Gajah Mada University, Yogyakarta 55281, Indonesia
| | - Heru Susetya
- Veterinary Public Health Department, Faculty of Veterinary Medicine, Gajah Mada University, Yogyakarta 55281, Indonesia
| | | | - Helen Scott-Orr
- Faculty of Veterinary Science, University of Sydney, Camden 2570, Australia
| | - Gusti Ngurah Mahardika
- The Animal Biomedical and Molecular Biology Laboratory, Faculty of Veterinary Medicine, Udayana University, Denpasar 80226, Indonesia
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What has molecular epidemiology ever done for wildlife disease research? Past contributions and future directions. EUR J WILDLIFE RES 2014. [DOI: 10.1007/s10344-014-0882-4] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Strickland SL, Rife BD, Lamers SL, Nolan DJ, Veras NMC, Prosperi MCF, Burdo TH, Autissier P, Nowlin B, Goodenow MM, Suchard MA, Williams KC, Salemi M. Spatiotemporal dynamics of simian immunodeficiency virus brain infection in CD8+ lymphocyte-depleted rhesus macaques with neuroAIDS. J Gen Virol 2014; 95:2784-2795. [PMID: 25205684 DOI: 10.1099/vir.0.070318-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Despite the success of combined antiretroviral therapy in controlling viral replication in human immunodeficiency virus (HIV)-infected individuals, HIV-associated neurocognitive disorders, commonly referred to as neuroAIDS, remain a frequent and poorly understood complication. Infection of CD8(+) lymphocyte-depleted rhesus macaques with the SIVmac251 viral swarm is a well-established rapid disease model of neuroAIDS that has provided critical insight into HIV-1-associated neurocognitive disorder onset and progression. However, no studies so far have characterized in depth the relationship between intra-host viral evolution and pathogenesis in this model. Simian immunodeficiency virus (SIV) env gp120 sequences were obtained from six infected animals. Sequences were sampled longitudinally from several lymphoid and non-lymphoid tissues, including individual lobes within the brain at necropsy, for four macaques; two animals were sacrificed at 21 days post-infection (p.i.) to evaluate early viral seeding of the brain. Bayesian phylodynamic and phylogeographic analyses of the sequence data were used to ascertain viral population dynamics and gene flow between peripheral and brain tissues, respectively. A steady increase in viral effective population size, with a peak occurring at ~50-80 days p.i., was observed across all longitudinally monitored macaques. Phylogeographic analysis indicated continual viral seeding of the brain from several peripheral tissues throughout infection, with the last migration event before terminal illness occurring in all macaques from cells within the bone marrow. The results strongly supported the role of infected bone marrow cells in HIV/SIV neuropathogenesis. In addition, our work demonstrated the applicability of Bayesian phylogeography to intra-host studies in order to assess the interplay between viral evolution and pathogenesis.
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Affiliation(s)
- Samantha L Strickland
- Emerging Pathogens Institute, University of Florida, Gainesville, FL, USA.,Department of Pathology, Immunology, and Laboratory Medicine, University of Florida, Gainesville, FL, USA
| | - Brittany D Rife
- Emerging Pathogens Institute, University of Florida, Gainesville, FL, USA.,Department of Pathology, Immunology, and Laboratory Medicine, University of Florida, Gainesville, FL, USA
| | | | - David J Nolan
- Department of Pathology, Immunology, and Laboratory Medicine, University of Florida, Gainesville, FL, USA
| | - Nazle M C Veras
- Emerging Pathogens Institute, University of Florida, Gainesville, FL, USA.,Department of Pathology, Immunology, and Laboratory Medicine, University of Florida, Gainesville, FL, USA
| | - Mattia C F Prosperi
- Emerging Pathogens Institute, University of Florida, Gainesville, FL, USA.,Department of Pathology, Immunology, and Laboratory Medicine, University of Florida, Gainesville, FL, USA
| | - Tricia H Burdo
- Department of Biology, Boston College, Chestnut Hill, MA, USA
| | | | - Brian Nowlin
- Department of Biology, Boston College, Chestnut Hill, MA, USA
| | - Maureen M Goodenow
- Department of Pathology, Immunology, and Laboratory Medicine, University of Florida, Gainesville, FL, USA
| | - Marc A Suchard
- Departments of Biomathematics, Biostatistics and Human Genetics, University of California (UCLA), Los Angeles, CA, USA
| | | | - Marco Salemi
- Emerging Pathogens Institute, University of Florida, Gainesville, FL, USA.,Department of Pathology, Immunology, and Laboratory Medicine, University of Florida, Gainesville, FL, USA
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Alfonso-Morales A, Martínez-Pérez O, Dolz R, Valle R, Perera CL, Bertran K, Frías MT, Majó N, Ganges L, Pérez LJ. Spatiotemporal Phylogenetic Analysis and Molecular Characterisation of Infectious Bursal Disease Viruses Based on the VP2 Hyper-Variable Region. PLoS One 2013; 8:e65999. [PMID: 23805195 PMCID: PMC3689766 DOI: 10.1371/journal.pone.0065999] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2013] [Accepted: 04/29/2013] [Indexed: 12/13/2022] Open
Abstract
Background Infectious bursal disease is a highly contagious and acute viral disease caused by the infectious bursal disease virus (IBDV); it affects all major poultry producing areas of the world. The current study was designed to rigorously measure the global phylogeographic dynamics of IBDV strains to gain insight into viral population expansion as well as the emergence, spread and pattern of the geographical structure of very virulent IBDV (vvIBDV) strains. Methodology/Principal Findings Sequences of the hyper-variable region of the VP2 (HVR-VP2) gene from IBDV strains isolated from diverse geographic locations were obtained from the GenBank database; Cuban sequences were obtained in the current work. All sequences were analysed by Bayesian phylogeographic analysis, implemented in the Bayesian Evolutionary Analysis Sampling Trees (BEAST), Bayesian Tip-association Significance testing (BaTS) and Spatial Phylogenetic Reconstruction of Evolutionary Dynamics (SPREAD) software packages. Selection pressure on the HVR-VP2 was also assessed. The phylogeographic association-trait analysis showed that viruses sampled from individual countries tend to cluster together, suggesting a geographic pattern for IBDV strains. Spatial analysis from this study revealed that strains carrying sequences that were linked to increased virulence of IBDV appeared in Iran in 1981 and spread to Western Europe (Belgium) in 1987, Africa (Egypt) around 1990, East Asia (China and Japan) in 1993, the Caribbean Region (Cuba) by 1995 and South America (Brazil) around 2000. Selection pressure analysis showed that several codons in the HVR-VP2 region were under purifying selection. Conclusions/Significance To our knowledge, this work is the first study applying the Bayesian phylogeographic reconstruction approach to analyse the emergence and spread of vvIBDV strains worldwide.
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Affiliation(s)
| | | | - Roser Dolz
- Centre de Recerca en Sanitat Animal (CReSA), Barcelona, Spain
| | - Rosa Valle
- Centre de Recerca en Sanitat Animal (CReSA), Barcelona, Spain
| | - Carmen L. Perera
- Centro Nacional de Sanidad Agropecuaria (CENSA), La Habana, Cuba
| | - Kateri Bertran
- Centre de Recerca en Sanitat Animal (CReSA), Barcelona, Spain
| | - Maria T. Frías
- Centro Nacional de Sanidad Agropecuaria (CENSA), La Habana, Cuba
| | - Natàlia Majó
- Centre de Recerca en Sanitat Animal (CReSA), Barcelona, Spain
- Departament de Sanitat i Anatomia Animals, Universitat Autònoma de Barcelona, Barcelona, Spain
| | | | - Lester J. Pérez
- Centro Nacional de Sanidad Agropecuaria (CENSA), La Habana, Cuba
- * E-mail:
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