Integrating genetic and epidemiological data to determine transmission pathways of foot-and-mouth disease virus

Abstract

Estimating detailed transmission trees that reflect the relationships between infected individuals or populations during a disease outbreak often provides valuable insights into both the nature of disease transmission and the overall dynamics of the underlying epidemiological process. These trees may be based on epidemiological data that relate to the timing of infection and infectiousness, or genetic data that show the genetic relatedness of pathogens isolated from infected individuals. Genetic data are becoming increasingly important in the estimation of transmission trees of viral pathogens due to their inherently high mutation rate. Here, we propose a maximum-likelihood approach that allows epidemiological and genetic data to be combined within the same analysis to infer probable transmission trees. We apply this approach to data from 20 farms infected during the 2001 UK foot-and-mouth disease outbreak, using complete viral genome sequences from each infected farm and information on when farms were first estimated to have developed clinical disease and when livestock on these farms were culled. Incorporating known infection links due to animal movement prior to imposition of the national movement ban results in the reduction of the number of trees from 41 472 that are consistent with the genetic data to 1728, of which just 4 represent more than 95% of the total likelihood calculated using a model that accounts for the epidemiological data. These trees differ in several ways from those constructed prior to the availability of genetic data.

Modelling the spread of infectious salmon anaemia among salmon farms based on seaway distances between farms and genetic relationships between infectious salmon anaemia virus isolates

“…One result from this study was that the projected most probable infection pathways were between farms that were located in closer proximity than expected by chance [8]. However, distances between farms were not explicitly a part of the FMDV model.…”

“…Phylogeographic methods have, for example, been used to trace the global spread of avian influenza over the last decade [7], as well as fine-scale local transmission pathways for the foot-and-mouth disease virus (FMDV) in the UK [8].…”

Genetic diversity of serotype A foot-and-mouth disease viruses in Kenya from 1964 to 2013; implications for control strategies in eastern Africa

“…The VP1 coding region sequence has been widely used to yield this information as well as for inferring the epidemiological dynamics of the disease such as tracing the origins of outbreaks (e.g. Bastos et al, 2003;Cottam et al, 2008;Knowles and Samuel, 2003;Sangula et al, 2010a;ValdazoGonzález et al, 2011). Hence, a large number of such sequences are available in databases.…”

Phylogenetic characterization of foot-and-mouth disease virus recovered from mithuns and yaks in India

“…Characterization of FMDV evolution is often accomplished by phylogenetic analysis of the VP1 capsid gene/protein, which allows for the distinction of lineages within serotypes (Knowles and Samuel, 2003). Sequencing of FMDV VP1 region and clustering into lineages can be associated with a specific temporal and geographical distribution, from which the potential sources of infection may be traced out and epidemiological trends can be characterized (Cottam et al, 2008 Severe drooling of saliva and vesicular lesions in the mouth parts was observed in affected mithun (Fig 1) and erosive lesions with blanched appearance in the tongue and lower dental pad was found in affected yak (Fig 2). These typical clinical signs/lesions of acute FMD have earlier been reported by Arzt et al (2011) with variable severity depending on the causative strain and host species involved (Grubman and Baxt, 2004).…”