Objective  To investigate the genetic characteristics and phylogeny of Borna disease virus (BDV) in Chongqing

China.   Methods  BDV p24 segment was detected by fluorescence quantitative nested RT-PCR (FQ-nRT-PCR) from peripheral blood mononuclear cells (PBMCs) of 50 healthy cattle

50 healthy goats

50 healthy pigs and 20 patients with viral encephalitis (VE). Phylogenetic analysis of BDV p24 positive samples were performed by alignment with 5 positive gene sequences of healthy goats and patients with neuropsychiatry diseases in preliminary studies in Chongqing and 33 sequences of 7 kinds of animal species in 5 countries from GenBank. The sequence homologous similarity of the nucleotide and the amino acid sequences was analyzed and gene phylogenetic tree was reconstructed.   Results  Among the 10 nucleotide sequences from Chongqing (including 3 strains from cattle

2 from goat

2 from pig and 3 from VE patients)

the sequence of 1 VE patient and those of our preliminary studies formed a Chongqing independent branch

and the other 9 sequences clustered within Germany-Switzerland-Austria-Japan-Chongqing mixed branch. Aligned with standard BDV strain V

H1766 and He/80

the homologous similarity in 9 sequences was 94% to 100% in nucleotide and 82% to 100% in amino acid

and the 1 sequence had a similarity of 95% to 98% in nucleotide and 89% to 93% in amino acid.   Conclusion  There may exist a Chongqing independent BDV strain from geographical origin

and the epidemic strain due to spread of foreign pathogen.