Elsevier

Virus Research

Volume 150, Issues 1–2, June 2010, Pages 111-118
Virus Research

Temporal and spatial dynamics of rabies viruses in China and Southeast Asia

https://doi.org/10.1016/j.virusres.2010.02.019Get rights and content

Abstract

Phylogenetic studies have revealed a profound understanding about the biodiversity of rabies viruses in China, but little is known about their evolutionary dynamics in the country. In the present study, the complete G gene sequences of 33 rabies virus isolates (RABVs) isolated from distinct Chinese provinces were determined and phylogenetic analysis was conducted using these G sequences and 93 others retrieved from GenBank representing China and Southeast Asia. Further evolutionary history of RABV was estimated using a Bayesian Markov chain Monte Carlo method to understand the temporal and spatial dynamics of this virus. Results showed that rabies viruses in China and Southeast Asia share a common ancestor and form 2 clades with each being further divided into 3 lineages. The time of the most recent common ancestor of current RABV strains was estimated to be year 1654 (1514–1812) and the viruses circulating in Southeast Asia likely derived from China.

Introduction

Rabies is a fatal zoonotic disease caused by classical rabies virus (RABV) and rabies-like viruses, all belonging to the genus Lyssavirus of the family Rhabdoviridae. RABV infects a wide range of mammalian species and causes fatal encephalitis. In Asia rabies presents a severe public health problem, with the highest global incidence of disease and with human rabies cases accounting for 56% of the world total (WHO, 2005). Rabies may have been described before year 2300 BC (Steele and Fernandez, 1991) and has more than a 2000 year history in China (Yu, 2001). In recent years, China has reported the second highest number of human rabies cases in the world (Tang et al., 2005). Since 1950 more than 117,500 persons have died of rabies throughout the country, with three major epidemic peaks (1956–1957, 1980–1990 and 1997–2008) (Tang et al., 2005, Zhang et al., 2005, Zhang et al., 2009b; http://www.moh.gov.cn). In China, the domestic dog (Canis familiaris) plays a pivotal role in rabies transmission, with 85–95% of human rabies cases being ascribed to dog bites (Tang et al., 2005).

RABV contains a single-stranded, nonsegmented, negative-sense RNA genome of approximately 12 kb. Five genes encode a nucleoprotein (N), phosphoprotein (P), matrix protein (M), glycoprotein (G) and polymerase (L). The glycoprotein is a surface protein responsible for receptor recognition and viral antigenicity. There are currently 11 species in the genus Lyssavirus identified by their genetic similarity, as compiled in the official ICTV Master Species List 2009-version 3 (Tordo et al., 2005; http://talk.ictvonline.org/files/ictv_documents/m/msl/1231.aspx). RABV (genotype 1) is the only lyssavirus with a worldwide distribution, with canids, raccoons, skunks, bats and mongooses being the principal reservoir animals and virus transmitters. Dog RABVs are responsible for more than 99% of the human rabies in the world (Knobel et al., 2005) and, based on the most recent phylogenetic study, comprise six clades: Africa 2, Africa 3, Cosmopolitan, Arctic-related, Asian and India subcontinent (Bourhy et al., 2008). The first three clades have been extensively investigated (Davis et al., 2007, Kissi et al., 1995, Nel and Rupprecht, 2007). The remainder circulate mainly in Asia, with the Arctic-related clade circulating in a large region extending from Russia and central Asia to eastern Asia (Nepal, India, Iran, Pakistan and Korea) (Hyun et al., 2005, Nagarajan et al., 2006). The Indian subcontinent clade has been found only in southern India and Sri Lanka. The Asian clade is found mainly in Southeast Asia, including Myanmar, Thailand, Laos, Cambodia, Vietnam, Malaysia, Indonesia, the Philippines and China (Bourhy et al., 2008). The study of Yamagata et al. (2007) has indicated that RABV isolates from Southeast Asia form two groups, Southeast Asia 1 (Malaysia, Vietnam and Thailand) and Southeast Asia 2 (Philippines). Recent studies have also showed that RABVs isolated from China have a close relationship with those from Southeast Asian countries (Bourhy et al., 2008, Liu et al., 2007, Susetya et al., 2008, Zhang et al., 2009b). However, no comprehensive phylogenetic reconstruction of RABV isolates in Asia has been performed to investigate the evolutionary rates and divergence times of the viruses in the most severely rabies-affected continent.

Recently, using Bayesian analysis, Tee et al. (2008) estimated the origin and expansion of HIV CRF08_BC and CRF07_BC in Asia by their divergence time. Here, we describe an extensive phylogenetic analysis of 126 RABV isolates collected from China and Southeast Asia. The spatial and temporal dynamics of these isolates were estimated using Bayesian analysis methods, and the resulting data has indicated that RABVs of China and Southeast Asia may have derived from a common ancestor that diverged around 1654.

Section snippets

Viruses and sequencing

Thirty-three brain samples of rabid animals (dogs, cows and a pig) were collected from different areas in China between 2003 and 2008. All samples were confirmed as rabies positive by the standard fluorescent antibody test (FAT) as described elsewhere (Jiang et al., 2008). Total RNA from these brain samples was extracted using Trizol reagent (Invitrogen, Carlsbad, CA, USA) according to the manufacturer's instructions. The complete G genes were amplified by RT-PCR (Jiang et al., 2008) with

Phylogeography of Asian RABVs

Table 1 chronicles the years of each of the 126 isolates, which spanned 39 years from 1969 to 2008. Of these isolates, 113 were collected from 18 provinces and municipalities, covering the majority of regions in China with particularly high incidences of rabies, and the remaining 13 from 8 Southeast Asian countries. Complete G gene sequences of the 126 isolates were analyzed by using maximum-likelihood and Bayesian approaches to determine their evolutionary relationships and the time of origin.

Discussion

Phylogenetic reconstruction of carnivore RABVs on a global basis has been well described (Kissi et al., 1995, Smith et al., 1992, Bourhy et al., 2008). In Africa, 4 clades of genotype 1 virus have been reported (Africa 1, Africa 2, Africa 3 and Africa 4) and their distribution and host species have been extensively investigated (Bourhy et al., 1999, David et al., 2007, Kissi et al., 1995, Nadin-Davis et al., 2002, Talbi et al., 2009). Although Asian clades of RABVs were known to exist, their

Acknowledgments

This work was supported by the following grants: Chinese National Commonweal Funding Project on Agriculture to CT (No. 200803014); National Key Technology R&D Program to CT (No. 2010BAD04B01); National Nature Science Foundation of China to YJ (No. 30600445). YS was funded by an animal rabies control project (2007–2009) by Guangdong Provincial Department of Agricultural Administration.

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