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

Marston, Denise, Horton, Daniel, Nunez, Javier, Ellis, Richard, Orton, Richard, Johnson, Nicholas, Banyard, Ashley, McElhinney, Lorraine, Freuling, Conrad, Firat, Müge , Ünal, Nil, Thomas, Mueller and Fooks, Anthony (2017) Genetic analysis of a rabies virus host shift event reveals within-host viral dynamics in a new host Virus Evolution, 3 (2), vex038.

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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. Utilisation of Bayesian inferences to investigate whole genome sequences from a cohort of fox and dog brain tissues from Turkey demonstrated that the epizootic occurred in 1997 (+/- 1 year). Furthermore, these data indicate 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 detected for virus adaptation to foxes at consensus sequence level; therefore, the deep sequence data was analysed to investigate the influence of sub-consensus populations on host shift events. Viral heterogeneity was measured in all RABV samples; viruses in the early phase after the host shift had increased heterogeneity, in relation to those in the later stage, possibly indicating a role in establishing transmission within a new host. The dynamics of majority and minority variants are consistent with genetic drift, rather than positive selection. The transient expansion of sub-consensus viral populations in the new host species likely represents the virus adapting to a new environment, perhaps due to increased replication within the CNS resulting in a larger population of viruses, or reflecting the lack of host constraints present in the new host reservoir.

Item Type: Article
Divisions : Faculty of Health and Medical Sciences > School of Veterinary Medicine
Authors :
Marston, Denise
Nunez, Javier
Ellis, Richard
Orton, Richard
Johnson, Nicholas
Banyard, Ashley
McElhinney, Lorraine
Freuling, Conrad
Firat, Müge
Ünal, Nil
Thomas, Mueller
Fooks, Anthony
Date : 13 December 2017
DOI : 10.1093/ve/vex038
Copyright Disclaimer : © The Author(s) 2017. Published by Oxford University Press. This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (, which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact
Uncontrolled Keywords : Lyssavirus; Viral heterogeneity; Whole genome sequencing; Next generation sequencing, cross species transmission, rabies virus
Depositing User : Clive Harris
Date Deposited : 13 Dec 2017 11:50
Last Modified : 16 Jan 2019 19:05

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