Investigating intra-host and intra-herd sequence diversity of foot-and-mouth disease virus

King, D. J., Freimanis, G. L., Orton, R. , Waters, R. A., Haydon, D. T. and King, D. P. (2016) Investigating intra-host and intra-herd sequence diversity of foot-and-mouth disease virus. Infection, Genetics and Evolution, 44, pp. 286-292. (doi:10.1016/j.meegid.2016.07.010) (PMID:27421209)

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Abstract

Due to the poor-fidelity of the enzymes involved in RNA genome replication, foot-and-mouth disease (FMD) virus samples comprise of unique polymorphic populations. In this study, deep sequencing was utilised to characterise the diversity of FMD virus (FMDV) populations in 6 infected cattle present on a single farm during the series of outbreaks in the UK in 2007. A novel RT–PCR method was developed to amplify a 7.6 kb nucleotide fragment encompassing the polyprotein coding region of the FMDV genome. Illumina sequencing of each sample identified the fine polymorphic structures at each nucleotide position, from consensus level changes to variants present at a 0.24% frequency. These data were used to investigate population dynamics of FMDV at both herd and host levels, evaluate the impact of host on the viral swarm structure and to identify transmission links with viruses recovered from other farms in the same series of outbreaks. In 7 samples, from 6 different animals, a total of 5 consensus level variants were identified, in addition to 104 sub-consensus variants of which 22 were shared between 2 or more animals. Further analysis revealed differences in swarm structures from samples derived from the same animal suggesting the presence of distinct viral populations evolving independently at different lesion sites within the same infected animal.

Item Type:Articles
Status:Published
Refereed:Yes
Glasgow Author(s) Enlighten ID:Haydon, Professor Daniel and King, Dr Donald and Orton, Dr Richard
Authors: King, D. J., Freimanis, G. L., Orton, R., Waters, R. A., Haydon, D. T., and King, D. P.
College/School:College of Medical Veterinary and Life Sciences > Institute of Biodiversity Animal Health and Comparative Medicine
College of Medical Veterinary and Life Sciences > Institute of Infection Immunity and Inflammation
Journal Name:Infection, Genetics and Evolution
Publisher:Elsevier
ISSN:1567-1348
ISSN (Online):1567-7257
Published Online:12 July 2016
Copyright Holders:Copyright © 2016 The Authors
First Published:First published in Infection, Genetics and Evolution 44:286-292
Publisher Policy:Reproduced under a Creative Commons License

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