Molecular epidemiology of the foot-and-mouth disease virus outbreak in the United Kingdom in 2001

Abstract

The objective of this study was to quantify the extent to which the genetic diversity of foot-and-mouth disease virus (FMDV) arising over the course of infection of an individual animal becomes fixed, is transmitted to other animals, and thereby accumulates over the course of an outbreak. Complete consensus sequences of 23 genomes (each of 8,200 nucleotides) of FMDV were recovered directly from epithelium tissue acquired from 21 farms infected over a nearly 7-month period during the 2001 FMDV outbreak in the United Kingdom. An analysis of these consensus sequences revealed very few apparently ambiguous sites but clear evidence of 197 nucleotide substitutions at 191 different sites. We estimated the rate of nucleotide substitution to be 2.26 x 10(-5) per site per day (95% confidence interval [CI], 1.75 x 10(-5) to 2.80 x 10(-5)) and nucleotide substitutions to accrue in the consensus sequence at an average rate of 1.5 substitutions per farm infection. This is a sufficiently high rate showing that detailed histories of the transmission pathways can be reliably reconstructed. Coalescent methods indicated that the date at which FMDV first infected livestock in the United Kingdom was 7 February 2001 (95% CI, 20 January to 19 February 2001), which was identical to estimates obtained on the basis of purely clinical evidence. Nucleotide changes appeared to have occurred evenly across the genome, and within the open reading frame, the ratio of nonsynonymous-to-synonymous change was 0.09. The ability to recover particular transmission pathways of acutely acting RNA pathogens from genetic data will help resolve uncertainties about how virus is spread and could help in the control of future epidemics.

FIG. 1.

Location of FMDV-infected premises investigated. The figure shows a map of Great Britain with total designated FMD-infected premises (•) in 2001; 20 of those from which virus has been sequenced are highlighted (□).

FIG. 2.

TCS analysis of 23 United Kingdom Pan Asia O FMDV sequences. Statistical parsimony analysis of 23 sequences by TCS; each sequence is represented by the IP number from which it was isolated. Each connecting branch line represents a nucleotide substitution, with each dot representing a putative ancestor virus. Nonsynonymous mutations are shown in boldface. The arrow represents the introduction of virus into the United Kingdom via IP4, where replication occurred for ∼2 weeks before clinical samples were collected. IP4 was the source of virus for IP1, where the disease was first detected, and also for IP6, from where virus was disseminated throughout the United Kingdom. IP2027 is the last IP of the outbreak. Gray shading indicates changes located within VP1.

FIG. 3.

Synonymous and nonsynonymous substitutions across the genome. Shown is a graph of cumulative substitutions against nucleotide positions, depicting the rate of substitution for total (black), synonymous (gray), and nonsynonymous (light gray) point mutations. The rate of accumulation of silent changes throughout the genome is constant and faster than the rate of amino acid substitutions which also appears to vary more. The dN/dS ratio for each genomic region is shown in the lower graph, but likelihood analyses provide no support for different dN/dS ratios for different genes.

FIG. 4.

Accumulation of substitutions with respect to time. Shown is the accumulation of mutations (a measure of genetic distance) increasing linearly with time, compatible with a molecular clock. ▪, all substitutions; ⋄, silent substitutions; Δ, nonsilent substitutions.

FIG. 5.

TCS analysis of two clusters of infected premises. Statistical parsimony analysis of known and unknown virus transmission events. Each connecting branch line represents a nucleotide substitution, with each dot representing a putative ancestor virus. Black arrows indicate the transmission route determined by traditional contact tracing, gray arrows indicate the route supported by the genetic data. The data show the close genetic relationship of IP1692 to IP1597 and IP1654, although epidemiological tracing suggested IP1692 was infected from a more distantly related source.