Abstract
This first extensive retrospective study of the molecular epidemiology of dog rabies in Cambodia included 149 rabies virus (RABV) entire nucleoprotein sequences obtained from 1998–2011. The sequences were analyzed in conjunction with RABVs from other Asian countries. Phylogenetic reconstruction confirmed the South-East Asian phylogenetic clade comprising viruses from Cambodia, Vietnam, Thailand, Laos and Myanmar. The present study represents the first attempt to classify the phylogenetic lineages inside this clade, resulting in the confirmation that all the Cambodian viruses belonged to the South-East Asian (SEA) clade. Three distinct phylogenetic lineages in the region were established with the majority of viruses from Cambodia closely related to viruses from Thailand, Laos and Vietnam, forming the geographically widespread phylogenetic lineage SEA1. A South-East Asian lineage SEA2 comprised two viruses from Cambodia was identified, which shared a common ancestor with RABVs originating from Laos. Viruses from Myanmar formed separate phylogenetic lineages within the major SEA clade. Bayesian molecular clock analysis suggested that the time to most recent common ancestor (TMRCA) of all Cambodian RABVs dated to around 1950. The TMRCA of the Cambodian SEA1 lineage was around 1964 and that of the SEA2 lineage was around 1953. The results identified three phylogenetically distinct and geographically separated lineages inside the earlier identified major SEA clade, covering at least five countries in the region. A greater understanding of the molecular epidemiology of rabies in South-East Asia is an important step to monitor progress on the efforts to control canine rabies in the region.
Highlights
The developing world is severely affected by rabies, causing deaths in humans as well as in animals and resulting in significant economic losses
As there was no information on the exact location where the bite occurred, the cases were attached to the local district health center, which in Cambodia is usually located no more than 5 kilometers from the furthest point of the district. 3.2
The complete nucleoprotein gene (N-gene) sequences of 149 Rabies virus (RABV) isolates collected in 20 provinces of Cambodia were generated and submitted to GenBank (Supplementary Table 1)
Summary
The developing world is severely affected by rabies, causing deaths in humans as well as in animals and resulting in significant economic losses. It is estimated that globally canine rabies causes approximately 59,000 human deaths, over 3.7 million disability-adjusted life years (DALYs) and 8.6 billion USD in economic losses annually (Hampson et al, 2015). The Lyssavirus genus includes classical RABVs, found in a wide range of different animal species throughout the world. All 13 other species of Lyssavirus except two have been isolated from bats, originating from different locations in Europe, Asia, Africa and Australia. The nucleoprotein gene (N-gene) is widely used for molecular characterization and phylogenetic analysis of RABVs (Kissi et al, 1995). The N-gene is suitable for estimations of evolutionary rate and subsequent analysis of evolutionary history (Holmes et al, 2002; Bourhy et al, 2008)
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