Geographical distribution of ASF sequences isolated in Eurasia and Africa between 1960 and 2015 (N = 665).

<p>Red circles indicate locations of ASFV isolates, where their CVR and vp72 gene segments were sequenced. The circles’ size is proportional to the number of isolates.</p

Bayesian Skygrid plot for temporal variation in the effective population size of ASF vp72-CVR genes in Eurasia and Africa between 1960 and 2015.

<p>The posterior median estimate is indicated by the red line; the blue lines correspond to the 95% HPD. Vertical dotted line represents the estimated time at which the population growth transitioned from a slow rate to a fast rate.</p

Phylodynamics and evolutionary epidemiology of African swine fever p72-CVR genes in Eurasia and Africa

<div><p>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.</p></div

Time to the most recent common Ancestor (TMRCA) of vp72-CVR genes of ASF in Eurasia and Africa between 1960 and 2015.

<p>Time to the most recent common Ancestor (TMRCA) of vp72-CVR genes of ASF in Eurasia and Africa between 1960 and 2015.</p

Maximum clade credibility (MCC) phylogeny of ASF vp72-CVR genes in Eurasia and Africa between 1960 and 2015 estimated under best fitting demographic model (S4 Table).

<p>The colour of the branches represents the among-branch evolutionary rate and corresponds to the colour gradient legend on the lower left. Well-supported posterior probabilities (P > 0.65) of branching events are indicated by yellow circles. The size of the yellow circles is proportional to the inferred posterior probabilities.</p

Host species Phylodynamics of ASF vp72-CVR genes in Eurasia and Africa between 1960 and 2015.

<p>A) MCC phylogeny with its branches coloured by the most probable host species state of their descendent nodes. B) represents the root location state posterior probability distributions and corresponds to the colour-coding of (A). C) mean forward and reverse transitions estimated by Markov jumps (MJ) approach between hosts (D) represents inferred transmission routes between host species, mean counts MJ of forward and reverse transitions and significant connections (BF > 13) with their directions between hosts.</p