Micro-evolution of foot-and-mouth disease virus

Cottam, Eleanor Myfanwy (2008) Micro-evolution of foot-and-mouth disease virus. PhD thesis, University of Glasgow.

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Foot-and-mouth disease virus (FMDV) causes an acute vesicular disease of domesticated and wild ruminants, and pigs. The virus is highly variable with 7 serotypes and numerous subtypes. A method was developed to sequence the complete genome of the Pan Asia O serotype FMDV that caused the UK 2001 epidemic. The sequence data was used to quantify the genetic diversity of FMDV that arose over the course of this epidemic. 197 nucleotide substitutions were observed at 191 different sites across the genome, with a ratio of non-synonymous to synonymous change of 0.09. It was estimated that the date at which FMDV first infected livestock in the UK was the 7th February 2001 (95% CI Jan 20th – Feb 19th) using coalescent methods, which is in close agreement to that generated on the basis of lesion aging at the first infected premises. The rate of nucleotide substitution during the epidemic was estimated to be 2.26 x 10-5 per site per day (95% CI 1.75-2.80 x 10-5). This was a sufficiently high rate that detailed histories of transmission pathways could be reliably reconstructed and motivated a comprehensive study of genetic changes that arose between infected premises in the Darlington area. This study highlighted the potential of tracing virus transmission between farms using genetic data. A maximum likelihood methodology was proposed to combine epidemiological data (describing the infection profile of individual farms) with the genetic data. Integration of genetic and epidemiological data reduced the number of transmission trees (describing infection transmission within this cluster) that were consistent with the genetic data from 41,472, to 1,728, of which 9 represented 95% of the total likelihood calculated. An average of 4.3 (S.D. 2.1) variant nucleotides within the complete genome, were observed between consecutive farm infections. Difficulties in identifying direct transmission events in this analysis arose mainly as a result of limited data on the extent of genetic variation on a single premises (complicated by variation in animal types, and farm sizes), and the manner in which mutations become fixed within the consensus sequence (i.e. upon replication and selection, and transmission through a ‘bottleneck’). This encouraged an analysis of the minimum mutant frequency of Pan Asia O FMDV from a single lesion sampled from naturally infected hosts which led to an estimate of 3.06 x 10-4 mutations per nucleotide sequenced (this parameter has previously only been measured in cell culture). In addition an experiment was initiated to measure the spontaneous mutation rate of O1BFS FMDV. The relevance of this analysis of the evolution of FMDV during the UK 2001 epidemic was demonstrated during the outbreak of O1BFS FMDV in Surrey in 2007, where complete genome sequencing was used in real time to trace virus spread. Genetic analysis of complete viral genomes generated in real-time revealed a chain of transmission events, predicting undisclosed infected premises, and connecting a second cluster of outbreaks in September to the initial outbreaks in August. Thus, this thesis has pioneered the use of complete genome sequencing for fine scale molecular epidemiology.

Item Type: Thesis (PhD)
Qualification Level: Doctoral
Keywords: Foot-and-mouth disease virus, complete genome sequencing, virus mutation rates, molecular epidemiology, genetic tracing
Subjects: Q Science > QH Natural history > QH301 Biology
Q Science > QR Microbiology > QR355 Virology
Colleges/Schools: College of Medical Veterinary and Life Sciences
Supervisor's Name: Haydon, Professor Daniel T, Paton, Dr David J and King, Dr Donald P
Date of Award: 2008
Depositing User: Miss E M Cottam
Unique ID: glathesis:2008-92
Copyright: Copyright of this thesis is held by the author.
Date Deposited: 20 Feb 2008
Last Modified: 10 Dec 2012 13:15
URI: https://theses.gla.ac.uk/id/eprint/92

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