Phylogeography of the current rabies viruses in Indonesia

Abstract

Rabies is a major fatal zoonotic disease in Indonesia. This study was conducted to determine the recent dynamics of rabies virus (RABV) in various areas and animal species throughout Indonesia. A total of 27 brain samples collected from rabid animals of various species in Bali, Sumatra, Kalimantan, Sulawesi, Java, and Flores in 2008 to 2010 were investigated. The cDNA of the nucleoprotein gene from each sample was generated and amplified by one-step reverse transcription-PCR, after which the products were sequenced and analyzed. The symmetric substitution model of a Bayesian stochastic search variable selection extension of the discrete phylogeographic model of the social network was applied in BEAST ver. 1.7.5 software. The spatial dispersal was visualized in Cartographica using Spatial Phylogenetic Reconstruction of Evolutionary Dynamics. We demonstrated inter-island introduction and reintroduction, and dog was found to be the only source of infection of other animals. Ancestors of Indonesian RABVs originated in Java and its descendants were transmitted to Kalimantan, then further to Sumatra, Flores, and Bali. The Flores descendent was subsequently transmitted to Sulawesi and back to Kalimantan. The viruses found in various animal species were transmitted by the dog.

Keywords: Indonesia; phylogeography; rabies virus.

Fig. 1. Location-annotated maximum clade credibility (MCC) phylogeny for the nucleoprotein (N) gene fragment of Indonesia and the recent dynamics of rabies virus (RABV). The highest location probability values are shown next to the nodes. The tree was the result of a Markov chain Monte Carlo (MCMC) analysis in BEAST and visualized with FigTree. The tree was rooted to the China_Guizhou/QX5/2004 sequence.

Fig. 2. Species-annotated MCC phylogeny for N gene fragment of Indonesian RABV. The highest species probability values are shown next to the nodes. The sub-trees are drawn as cartoons for clarity. The tree was the result of MCMC analysis in BEAST and visualized with FigTree. The tree was rooted to the China_Guizhou/QX5/2004 sequence.

Fig. 3. Geographic distribution and proposed dynamics of rabies field viruses in Indonesia determined in this study. A Keyhole Markup Language file of the resulting tree, shown in Fig. 1, was created using the SPREAD software and visualized in Cartographica. The color of the tracks was set to be uniform. Arrows indicate the proposed movements. The cities and islands described in the text are displayed. Numbered circles are The Animal Disease Investigation Centers in Medan (1), Bukittinggi (2), Yogyakarta (3), Denpasar (4), Banjarbaru (5) and Maros (6), where specimens were collected.