Comparative analysis estimates the relative frequencies of co-divergence and cross-species transmission within viral families

Geoghegan, Jemma L.; Duchêne, Sebastián; Holmes, Edward C.

Despite the overall large nPH85 distances observed among all virus families, our data also revealed that the Hepadnaviridae, Polyomaviridae, Poxviridae, Papillomaviridae and Adenoviridae had the shortest nPH85 distances and were thus relatively more host-specific than the other virus families analyzed here. This is supportive of earlier suggestions that some DNA viruses have a long history of co-divergence with their hosts [4] , which in some cases may be a reflection of relatively long durations of infection. Indeed, long-term virus-host associations have been observed in the Herpesviridae [1] , the Poxviridae [17] and the Polyomaviridae [18] . However, it is also important to note that we found these viruses contain more instances of host jumping than previously thought. For example, although the tanglegram shown in Fig 4 suggests co-divergence in the case of some primate hepadnaviruses, cross-species transmission seemingly occurs more frequently among those hepadnaviruses that infect birds. In addition, it was recently observed that a fish (bluegill) hepadnavirus clusters more closely with mammalian hepadnaviruses than to other fish viruses [11] (see Figs 4 and 5B). Similarly, early studies of RNA viruses suggested that virus-host co-divergence was important in the evolution of two members of the Flaviviridae that infect primates-the pegiviruses and hepaciviruses, [19] [20] [21] . However, more recent phylogenetic analyses of expanded data sets have revealed multiple cross-species transmissions events, including the recent emergence of hepaciviruses in domestic dogs, horses and donkeys [22] , and a newly described pegiviruses in rodents, bats and horses [23] .