Throughout North America, rabies virus (RV) is endemic in bats. Distinct RV variants exist that are closely associated with infection of individual host species, such that there is little or no sustained spillover infection away from the primary host. Using Bayesian methodology, nucleotide substitution rates were estimated from alignments of partial nucleoprotein (N) gene sequences of nine distinct bat RV variants from North America. Substitution rates ranged from 2?32610 "4 to 1?38610 "3 substitutions per site per year. A maximum-likelihood (ML) molecular clock model was rejected for only two of the nine datasets. In addition, using sequences from bat RV variants across the Americas, the evolutionary rate for the complete N gene was estimated to be 2?32610 "4 . This rate was used to scale trees using Bayesian and ML methods, and the time of the most recent common ancestor for current bat RV variant diversity in the Americas was estimated to be 1660 (range 1267-1782) and 1651 (range 1254-1773), respectively. Our reconstructions suggest that RV variants currently associated with infection of bats from Latin America (Desmodus and Tadarida) share the earliest common ancestor with the progenitor RV. In addition, from the ML tree, times were estimated for the emergence of the three major lineages responsible for bat rabies cases in North America. Adaptation to infection of the colonial bat species analysed (Eptesicus fuscus, Myotis spp.) appears to have occurred much quicker than for the solitary species analysed (Lasionycteris noctivagans, Pipistrellus subflavus, Lasiurus borealis, Lasiurus cinereus), suggesting that the process of virus adaptation may be dependent on host biology.
INTRODUCTIONRabies virus (RV) is the type member of the genus Lyssavirus, family Rhabdoviridae. RV has a negative-sense RNA genome of~12 kb and consists of five genes encoding the nucleoprotein (N), phosphoprotein, matrix protein, glycoprotein and polymerase (Tordo et al., 1986). The N encapsidates the viral RNA, forming the template for transcription and replication (Tordo & Kouknetzoff, 1993). RNA viruses are characterized by a high mutation rate during replication due to the lack of proofreading and postreplication error correction by RNA polymerases (Domingo & Holland, 1994). This genetic diversity seems to provide an adaptive potential for RV that can vary according to natural history (Morimoto et al., 1998; Kissi et al., 1999).Indigenous bat rabies was first recognized in the USA in 1953 (Scatterday & Galton, 1954), although the exact age of its emergence remains uncertain. During 2001, bats were responsible for 17 % of reported wildlife rabies cases and all three cases of human rabies in the USA (Krebs et al., 2002). In North America, rabid bats have been found for almost every species that has been thoroughly investigated (Constantine, 1979). The genetic diversity of current bat RV variants suggests that up to 30 different lineages of RV may exist in the USA alone (Smith, 2002). A more conservative assessment of RV diversity in th...