In order to clarify the genetic relationships and dynamics of rabies viruses that are epidemic in Indonesia, we determined and analyzed 1307 nucleotides of nucleoprotein genes of 34 rabies field isolates collected from Sumatra, Java, Kalimantan, Sulawesi and Flores islands. Results of phylogenetic analysis indicated that rabies isolates in Indonesia formed one cluster, were of Asian lineage, and were closely related to a rabies isolate in China rather than to rabies isolates in Thailand, India or Sri Lanka. Rabies isolates in Indonesia were divided into three phylogroups (ID1, ID2 and ID3) that included seven lineages. There was a correlation between phylogroup and geographical distribution of the isolates. Isolates in four lineages (SC1, SC2, SC3 and ST) of the ID1 phylogroup were mainly present in Sumatra. Isolates in the ST lineage were distributed widely in Sumatra, while isolates in the SC1, SC2 and SC3 lineages were limited to central Sumatra. ID2 and ID3 phylogroups included one lineage (JA) and two lineages (KS and SF), respectively. Results of phylogenetic analysis and historical background suggest that rabies viruses in China might have been transferred to Indonesia and spread to each island due to human activities.
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