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Virus Evol. 2017 Dec 13;3(2):vex038. doi: 10.1093/ve/vex038. eCollection 2017 Jul.

Genetic analysis of a rabies virus host shift event reveals within-host viral dynamics in a new host.

Author information

Wildlife Zoonoses & Vector-Borne Diseases Research Group, Animal and Plant Health Agency, New Haw, Addlestone, Surrey, KT15 3NB, UK.
UMR "Émergence des Pathologies Virales" (EPV: Aix-Marseille Univ-IRD 190-Inserm 1207 - EHESP - IHU Méditerranée Infection), Faculté de Médecine de Marseille, 27, Bd Jean Moulin,13005 Marseille, cedex 05 France.
School of Veterinary Medicine, University of Surrey, Guildford, GU2 7AL UK.
Surveillance and Laboratory Services Department, Animal and Plant Health Agency, New Haw, Addlestone, Surrey, KT15 3NB UK.
Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, G12 8QQ, UK.
Centre for Virus Research, MRC-University of Glasgow, University of Glasgow, Glasgow, G61 1QH UK.
Faculty of Health and Medical Science, University of Surrey, Guildford, GU2 7XH, UK.
Institute of Infection and Global Health, University of Liverpool, UK.
Friedrich-Loeffler-Institute, (FLI), Institute of Molecular Virology and Cell Biology, Greifswald-Insel Riems, D-17493, Germany.
Etlik Veterinary Control Central Research Institute A.S.Kolayli Street. No.21-21/A, 06020, Etlik, Ankara, Turkey.


Host shift events play an important role in epizootics as adaptation to new hosts can profoundly affect the spread of the disease and the measures needed to control it. During the late 1990s, an epizootic in Turkey resulted in a sustained maintenance of rabies virus (RABV) within the fox population. We used Bayesian inferences to investigate whole genome sequences from fox and dog brain tissues from Turkey to demonstrate that the epizootic occurred in 1997 (±1 year). Furthermore, these data indicated that the epizootic was most likely due to a host shift from locally infected domestic dogs, rather than an incursion of a novel fox or dog RABV. No evidence was observed for genetic adaptation to foxes at consensus sequence level and dN/dS analysis suggested purifying selection. Therefore, the deep sequence data were analysed to investigate the sub-viral population during a host shift event. Viral heterogeneity was measured in all RABV samples; viruses from the early period after the host shift exhibited greater sequence variation in comparison to those from the later stage, and to those not involved in the host shift event, possibly indicating a role in establishing transmission within a new host. The transient increase in variation observed in the new host species may represent virus replication within a new environment, perhaps due to increased replication within the CNS, resulting in a larger population of viruses, or due to the lack of host constraints present in the new host reservoir.


cross-species transmission; lyssavirus; next generation sequencing; rabies virus; viral heterogeneity; whole genome sequencing

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