Characterization of the biological properties and complete genome sequence analysis of a cattle-derived rabies virus isolate from the Guangxi province of southern China

Different rabies outbreaks on two beef cattle farms in the same province of China: Diagnosis, virus characterization and epidemiological analysis

Eliminating rabies is challenging in many developing countries, especially in rural areas. In contrast to the annual decline of human cases in China in last decade, the incidence of rabies in livestock has been increasingly reported. This paper reports the rabies outbreaks in beef cattle (Angus) in Shaanxi Province, China, which caused 31 and 5 deaths at an attack rate of 19.4% (95% CI: 13.6%-26.4%) and 0.25% (95% CI: 0.1%-0.6%) in a satellite cow farm (farm A) and a core intensive farm (farm B), respectively. The rabies infection was confirmed by several laboratory tests, and rabies virus (RABV) strains SXBJ15 and SXYL15 were isolated and characterized from farm A and B, respectively. The two strains were found to have a high genomic sequence similarity to the dog-associated China clade I strains previously identified in the neighbouring area. SXBJ15 was shown to have a higher mouse pathogenicity (1.07) than SXYL15 (0.45). RABV was also detected in the saliva and salivary glands from the affected cattle. The potential causes were investigated on the farm, and the biosecurity scores were 20 and 64 (a full score of 82) for farms A and B, respectively. The rabies infection is likely to result from rabid free-roaming dogs (FRDs). On farm A with more cow deaths, the rabies transmission between animals can be attributed to the improper disposal of aborted foetuses and placental materials as a food source for rabid FRDs, high stocking density and drinking water sharing. Additionally, vaccinating cattle with a canine vaccine was shown to help stop the spread of rabies in herds. These results indicate that the occurrence of RABV on cattle farms can be prevented by improving biosecurity measures to control the entry of rural FRDs on the farm and immunizing farm cattle against rabies.

Large-Scale Phylogenomic Analysis Reveals the Complex Evolutionary History of Rabies Virus in Multiple Carnivore Hosts

The natural evolution of rabies virus (RABV) provides a potent example of multiple host shifts and an important opportunity to determine the mechanisms that underpin viral emergence. Using 321 genome sequences spanning an unprecedented diversity of RABV, we compared evolutionary rates and selection pressures in viruses sampled from multiple primary host shifts that occurred on various continents. Two major phylogenetic groups, bat-related RABV and dog-related RABV, experiencing markedly different evolutionary dynamics were identified. While no correlation between time and genetic divergence was found in bat-related RABV, the evolution of dog-related RABV followed a generally clock-like structure, although with a relatively low evolutionary rate. Subsequent molecular clock dating indicated that dog-related RABV likely underwent a rapid global spread following the intensification of intercontinental trade starting in the 15^th century. Strikingly, although dog RABV has jumped to various wildlife species from the order Carnivora, we found no clear evidence that these host-jumping events involved adaptive evolution, with RABV instead characterized by strong purifying selection, suggesting that ecological processes also play an important role in shaping patterns of emergence. However, specific amino acid changes were associated with the parallel emergence of RABV in ferret-badgers in Asia, and some host shifts were associated with increases in evolutionary rate, particularly in the ferret-badger and mongoose, implying that changes in host species can have important impacts on evolutionary dynamics.

Zoonoses account for most recently emerged infectious diseases of humans, although little is known about the evolutionary mechanisms involved in cross-species virus transmission. Understanding the evolutionary patterns and processes that underpin such cross-species transmission is of importance for predicting the spread of zoonotic infections, and hence to their ultimate control. We present a large-scale and detailed reconstruction of the evolutionary history of rabies virus (RABV) in domestic and wildlife animal species. RABV is of particular interest as it is capable of infecting many mammals but, paradoxically, is only maintained in distinct epidemiological cycles associated with animal species from the orders Carnivora and Chiroptera. We show that bat-related RABV and dog-related RABV have experienced very different evolutionary dynamics, and that host jumps are sometimes characterized by significant increases in evolutionary rate. Among Carnivora, the association between RABV and particular host species most likely arose from a combination of the historical human-mediated spread of the virus and jumps into new primary host species. In addition, we show that changes in host species are associated with multiple evolutionary pathways including the occurrence of host-specific parallel evolution. Overall, our data indicate that the establishment of dog-related RABV in new carnivore hosts may only require subtle adaptive evolution.