Bayesian phylogeography of Crimean-Congo hemorrhagic fever virus in Europe

Abstract

Crimean-Congo hemorrhagic fever (CCHF) is a zoonosis mainly transmitted by ticks that causes severe hemorrhagic fever and has a mortality rate of 5-60%. The first outbreak of CCHF occurred in the Crimean peninsula in 1944-45 and it has recently emerged in the Balkans and eastern Mediterranean. In order to reconstruct the origin and pathway of the worldwide dispersion of the virus at global and regional (eastern European) level, we investigated the phylogeography of the infection by analysing 121 publicly available CCHFV S gene sequences including two recently characterised Albanian isolates. The spatial and temporal phylogeny was reconstructed using a Bayesian Markov chain Monte Carlo approach, which estimated a mean evolutionary rate of 2.96 x 10(-4) (95%HPD=1.6 and 4.7 x 10(-4)) substitutions/site/year for the analysed fragment. All of the isolates segregated into seven highly significant clades that correspond to the known geographical clades: in particular the two new isolates from northern Albania clustered significantly within the Europe 1 clade. Our phylogeographical reconstruction suggests that the global CCHFV clades originated about one thousand years ago from a common ancestor probably located in Africa. The virus then spread to Asia in the XV century and entered Europe on at least two occasions: the first in the early 1800s, when a still circulating but less or non-pathogenic virus emerged in Greece and Turkey, and the second in the early 1900s, when a pathogenic CCHFV strain began to spread in eastern Europe. The most probable location for the origin of this European clade 1 was Russia, but Turkey played a central role in spreading the virus throughout Europe. Given the close proximity of the infected areas, our data suggest that the movement of wild and domestic ungulates from endemic areas was probably the main cause of the dissemination of the virus in eastern Europe.

Figure 1. The maximum clade credibility (MCC) tree of CCHFV S gene sequences.

The branches are coloured on the basis of the most probable location of the descendent nodes (A=Africa, AL=Albania, ASC=Central Asia, BU=Bulgaria, CH=China, G=Greece, KO=Kosovo, MO=Middle East, PA=Pakistan, T=Turkey). The numbers on the internal nodes indicate significant posterior probabilities (pp>0.8), and the scale at the bottom of the tree represents the number of years before the last sampling time (2010). The main geographical clades (genotypes) have been highlighted.

Figure 2. Significant non-zero CCHFV migration rates worldwide.

Rates supported by a BF of >3 are highlighted: the relative strength of the support is indicated by the colour of the lines (from dark red = weak to light red = strong). Dotted lines indicate non-significant linkages. The map was reconstructed using SPREAD (see Methods). The numbers indicate the mean estimated year in which the virus entered the area.

Figure 3. Phylogeographical mapping of CCHF S gene sequences .

The bubblegrams show the frequency of gene flows (migrations) to/from ten European countries (same code as that used in Figure 1) . The surface of each circle is proportional to the percentage of observed migrations in the ML genealogy. The migrations were inferred using a modified version of the Slatkin and Maddison algorithm.