Temporal And Spatial Population Dynamics Of Rabies Virus Isolates In China

In order to study phylogeography, population dynamics and molecular evolution of rabies viruses (RABVs) isolates from China, especially spatio-temporal dynamics, the timescale of RABVs evolution and its pattern of migration. In total we have determined 6 new complete genome sequences of rabies field isolates from China and analysised the complete nucleotide and deduced amino acid sequence of the five structural genes (N, P, M, G and L) and non-structural genes, then we compared the complete genome and did evolutionary analysis with 40 available genome sequences from GenBank. All genomes of six omplete genome sequences of rabies field isolates from China have the same structural organization athough their lengths varied between 11907 nt (CQ92) and 11924 nt (SH06 and gg4). In phylogenetic analyses using the full genome dataset, N, P, M, G and L genes, similar topologies of the reconstructed trees were demonstrated. Our data also reveals a strict complementarity limited to the 11 terminal nucleotides of 3'and 5'UTR at both ends of the genome. The extent of genetic diversity, reflected in percentage identity, varies among proteins, in the order N>L>M>G>P (81.9%,81.7%,80.7%,78.3% and 76.7% nucleotide identity at a minimum value, respectively). At the same time, we determined the N gene sequence of CTN vacine strain and 60 street isolates of rabies viruses, and were collected from various areas in China. We performed an extensive comparative analysis of RABV N gene sequence data, representing 167 isolates sampled from 20 provinces in a 78-year period (from 1931 through 2009). The available Chinese isolates could be divided into two distinct clades:Phylogroup clades I comprises Chinese 1-4 group; Phylogroup cladesⅡcontains Chinese 5-8 group.Complete N gene sequences determined for these isolates indicated intra-group identities of nucleotide and amino acid sequences of≧ 93.2% and 94.3%, respectively; Intre-group divergence revealed up to 8.0% at the nucleotide level and 1.7% at the amino acid level. We found no evidence for positive selection (dN/dS>1) acting at any codon and found strong selective constraints for N gene. Bayesian Markov chain Monte Carlo (MCMC) analysis suggested that the Chinese rabies viruses arose 250 ago and the mean rates of nucleotide substitution for the N gene were approximatelately 4×10-4 substitutions per site year-1. The analyses of the spatial and spatio-temporal evolution indicated that RABV isolates from China migrated among different provinces. Phylogenetic analysis of the N gene sequence indicated that the isolates belonging to phylogroup cladesⅠwith isolates from Thailand, Vietnam, Indonesia, Philippines, Malaysia etal. were in the same branch in phylogenetic clades and the isolates belonging to phylogroup cladesⅡare found in many parts of the world.