Rabies virus emergence in novel hosts: from molecules to landscapes

The invasion of novel host species by pathogens is one of the primary causes of pandemics and emerging diseases. Such host shifts are difficult to anticipate, in part because we lack an understanding of the barriers that prevent maintenance of pathogens by multiple species. Rabies virus provides an ideal model system in which to study these barriers, as well as the mechanisms used by host-shifting pathogens to overcome them. This virus appears to able to infect all mammals, but paradoxically is maintained in species-specific transmission cycles. These maintenance hosts are almost exclusively found within the Carnivora (carnivores) and Chiroptera (bats), and were established by numerous host shifts within and between these taxonomic orders. However, it remains unclear which – if any – adaptations are required when switching to a new host species, nor is it known why the virus is incapable of utilising multiple host species despite evidence of relatively frequent spill-overs between maintenance host species. This thesis describes investigations of the determinants of rabies virus host shifts across multiple scales of organisation, which aim to understand the host-specialisation of this virus. A meta-analysis of within- and cross-species infection studies shows evidence for a reduction in effective dose as the body temperature difference between the original and inoculated species increases. This affects the duration of the incubation period, suggesting adaptation of infectivity may be involved. Crucially, previous studies have linked temperature differences to infectivity differences in cell culture, and to the process of cell entry in particular. These data further show evidence for phylogenetic clustering of incubation period durations, which may be linked to clustering of sensitivity among inoculated host species. This in turn may help explain why only some carnivore and bat species are maintenance hosts of rabies virus. At the molecular level, whole genome sequencing of samples from a system in which rabies virus has made an unusual host shift to bovids suggests involvement of a single amino acid change in the acetylcholine receptor-binding site of the glycoprotein. Phylogenetic analyses involving these and other sequences shows evidence for distinct maintenance cycles in three host species in the same region, despite numerous spill-over infections between species. The involvement of the glycoprotein in this host shift further points to a role for infectivity changes in host adaptation. At the cellular level, the bovid-associated viruses show increased infectivity to a bovid cell line compared to canid-associated viruses. The bovid-associated viruses also show decreased infectivity to a canid cell line representing the original host species. Combined, these results point to a new model for the host adaptation of rabies virus. In this model, the infectivity of viruses is decreased at temperatures to which they are not adapted. This allows the emergence of genotypes with increased infectivity in the novel host species, which can be achieved through relatively minor genomic alterations. Because these adaptations are detrimental in the original host, they may combine with ecological differences between hosts to create the single-species maintenance cycles observed. Identifying the mechanisms constraining maintenance host range will allow better predictions of which host shifts are likely to be successful. In particular, the effect of body temperature difference found here is shown to explain a large part of the previously observed effect of phylogenetic distance between host species in reducing the frequency of rabies virus host shifts. The phylogenetic clustering of host sensitivity meanwhile, may explain how host shifts between very divergent hosts are possible