Phylogeographic analysis and identification of factors impacting the diffusion of Foot-and-Mouth disease virus in Africa

Duchatel, Florian; Bronsvoort, Mark; Lycett, Samantha

doi:10.1101/358044

Cited by 5 publications

(10 citation statements)

References 40 publications

(1 reference statement)

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“…The fact that the SAT serotypes are mainly maintained within wild buffalo populations does not go against the observation that most of the recent spread of the viruses in Africa seems to be driven by livestock movement [36][37][38] . Moreover, this observation is in concordance with the theory that currently circulating lineage of SAT serotypes re-emerged from a small number of wild buffaloes that survived the African rinderpest epidemic of 1975 10 .…”

Section: Discussionmentioning

confidence: 97%

Importance of wildlife in the circulation and maintenance of SAT1 and SAT2 foot-and-mouth disease viruses in Africa

Duchatel

Maree

Schalkwyk

et al. 2023

Preprint

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Foot and mouth disease (FMD) viruses are endemic in sub-Saharan Africa. Due to the complexity of the disease epidemiology and the lack of available data, there is a need to use phylogenetic approaches to understand the role of potential hosts involved in the circulation and maintenance of the viruses. The uneven host sampling of the available sequences requires us to take advantage of the recent advances in phylogenetic reconstruction. Therefore, using two structural coalescent model approximations we estimated the circulation of FMD virus serotypes SAT1 and SAT2 between cattle, buffalo and impala populations. Our results suggest that in Africa, the impala population seems to act as an intermediate host between the cattle and buffalo populations and play a more important role in the circulation of the viruses than was previously suspected. Until now, the role of the impala population in the circulation of FMDV has been suggested, but never explicitly shown.

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Section: Discussionmentioning

confidence: 97%

Importance of wildlife in the circulation and maintenance of SAT1 and SAT2 foot-and-mouth disease viruses in Africa

Duchatel

Maree

Schalkwyk

et al. 2023

Preprint

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“…It is considered that serotype O originated in the Horn of Africa, with a higher probability of origination in Kenya and Sudan, which act as a link between East and North Africa. Four clades (VP1 nucleotide sequence differences among topotypes disseminated to different parts of Africa) of serotype O FMDV (EA1,2,3,4) were identified using phylogeographic analysis [66]. For their geographic origin, the first clade was composed of viral sequences from Kenya, Tanzania, and Uganda; the second was in Ethiopia; the third was in Sudan; and the fourth was in West and Central African countries.…”

Section: Serotype O Topotypes In the Horn Of Africamentioning

confidence: 99%

“…For their geographic origin, the first clade was composed of viral sequences from Kenya, Tanzania, and Uganda; the second was in Ethiopia; the third was in Sudan; and the fourth was in West and Central African countries. Using evolutionary parameter estimation, it was found that a mean evolutionary rate of 3.41 × 10 −3 nucleotide substitutions per site per year over 58 years was recorded (1958-2016) [55,66]. On the other hand, Munsey from Uganda also estimated the VP1 evolutionary rate to be 4.99 × 10 −3 nucleotide substitutions per site per year [67].…”

Section: Serotype O Topotypes In the Horn Of Africamentioning

confidence: 99%

Epidemiological Dynamics of Foot-and-Mouth Disease in the Horn of Africa: The Role of Virus Diversity and Animal Movement

Woldemariyam

Kariuki

Kamau

et al. 2023

Viruses

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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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“…Consequently, there are growing collections of animal virus sequences from around the globe. In this talk, the use of viral sequence data together with phylodynamic methodologies for understanding the transmission patterns in animal populations was discussed, using Avian Influenza (AI), Foot-and-Mouth Disease (FMD) and Porcine Reproductive and Respiratory Syndrome (PRRS) as examples [58,59,60].…”

Section: Sessions and Oral Presentationsmentioning

confidence: 99%

“…Since RNA viruses have fast mutation rates and variable sequences, transmission routes between places and host species can be inferred [59,60]. One approach is to group sequences from individual hosts into discrete locations and/or host species and consider these as discrete traits or subpopulations on time-resolved phylogenetic trees, with the goal to infer which group infected which.…”

Section: Sessions and Oral Presentationsmentioning

confidence: 99%

The Third Annual Meeting of the European Virus Bioinformatics Center

Hufsky

Ibrahim

Modha

et al. 2019

Viruses

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The Third Annual Meeting of the European Virus Bioinformatics Center (EVBC) took place in Glasgow, United Kingdom, 28–29 March 2019. Virus bioinformatics has become central to virology research, and advances in bioinformatics have led to improved approaches to investigate viral infections and outbreaks, being successfully used to detect, control, and treat infections of humans and animals. This active field of research has attracted approximately 110 experts in virology and bioinformatics/computational biology from Europe and other parts of the world to attend the two-day meeting in Glasgow to increase scientific exchange between laboratory- and computer-based researchers. The meeting was held at the McIntyre Building of the University of Glasgow; a perfect location, as it was originally built to be a place for “rubbing your brains with those of other people”, as Rector Stanley Baldwin described it. The goal of the meeting was to provide a meaningful and interactive scientific environment to promote discussion and collaboration and to inspire and suggest new research directions and questions. The meeting featured eight invited and twelve contributed talks, on the four main topics: (1) systems virology, (2) virus-host interactions and the virome, (3) virus classification and evolution and (4) epidemiology, surveillance and evolution. Further, the meeting featured 34 oral poster presentations, all of which focused on specific areas of virus bioinformatics. This report summarizes the main research findings and highlights presented at the meeting.

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Phylogeographic analysis and identification of factors impacting the diffusion of Foot-and-Mouth disease virus in Africa

Cited by 5 publications

References 40 publications

Importance of wildlife in the circulation and maintenance of SAT1 and SAT2 foot-and-mouth disease viruses in Africa

Importance of wildlife in the circulation and maintenance of SAT1 and SAT2 foot-and-mouth disease viruses in Africa

Epidemiological Dynamics of Foot-and-Mouth Disease in the Horn of Africa: The Role of Virus Diversity and Animal Movement

The Third Annual Meeting of the European Virus Bioinformatics Center

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