1. The construction and analysis of epidemic trees with reference to the 2001 UK FMDV outbreak
Dan Haydon,
Dept Zoology,
University of Guelph, On. Ca.

2. Provide case reproduction ratios from outbreak data as it arises
Explore the consequences of
applying stricter control measures
Woolhouse, MEJ., Topping, M.C., Haydon, D.T. and 8 others Foot-and-mouth disease under control in the UK.
Nature 411,
Haydon, D.T., Topping, M.C., Shaw, D.J., Matthews, L., Friar, J.K., Wilesmith, J., and Woolhouse, M.E.J.
2003. The construction and analysis of epidemic trees with reference to the 2001 UK foot-and-mouth outbreak.
Proceedings: Biological Sciences (The Royal Society, UK) 270,

3. Number of infected premises∞
skiing
Move to Guelph

5. time Always pick the closest Pick candidates with equal probability
Pick candidates with probabiltiy weighted by distance
Reporting
date
Culling
Infection
date
5 km
3 km
13 km
0.5 km
1.5 km
time

6. 1 7 4
time

9. b)

10. time Parent Infected – daughter reporting interval Estimated parent
date
Estimated
parent
infection
Daughter
Parent Infected – daughter reporting interval
time

11. 60%
93%

13. 20th Feb.
Time

14. NMB
20th Feb.
23rd Feb.
Time

15. NMB X X
20th Feb.
23rd Feb.
Time

16. NMB
20th Feb.
23rd Feb.
Time

18. Between 20th – evening of 23rd of February:
17 IPs infected at distance greater than 20km
16 of these IPs have positive contact tracing
13 were infected by animal movements from markets

19. time

20. time

21. time

23. 20th Feb.
23rd Feb.
Time
NMB

24. NMB X X
20th Feb.
23rd Feb.
Time

25. NMB
20th Feb.
23rd Feb.
Time

26. 20th Feb.
Time

28. Number of new infections
Week

29. The government, however, dismisses Woolhouse's figures as an overestimate. It also argues that it could not have acted any faster than it did. "A national ban was imposed as soon as it became clear that there was a national problem," a spokesman for the Department for Environment Food and Rural Affairs told New Scientist. But he did add that such a ban would be imposed immediately if any future outbreak occurred.
New Scientist vol. 176 issue 2372 (07 December 2002)

30. What the foot and
mouth virus looks
like (not actual size)

31. 1.5% yr-1
1.0% yr-1
1.4% yr-1
1.1% yr-1
1.0% yr-1
0.4% yr-1

32. Wildtype virus Mutant virus
WITHIN HOST POPULATION DYNAMICS
Assume:
Simple exponential population growth
Simple Poisson mutation process (no back mutation)
Mutants are either tolerated and equally fit as wildtype
or not tolerated at all
Wildtype
virus
Mutant
virus
Haydon, D.T., Samuel, A.R., and Knowles, N.J. (2001).
The generation and persistence of genetic variation in foot-and-mouth disease virus.
Preventative Veterinary Medicine 51,

34. The fraction of mutant capsid genes in an infected animal?
10-3
10-4
Error Rate
(per base
per replication
cycle)
10-5
10-6
Viral Generations (t)

35. observed rates of change in the field are 0.5 - 1.5 % yr-1
corresponding to nucleotide changes in
capsids genes yr-1
plausible that the bulk of virus excreted by infected
animals differs by at least one point mutation to capsid
genes from that which ‘went in’
therefore sequential chains of infection of
animals yr-1 could give rise to observed rates of change

36. Uncertainty surrounds many of the critical parameters
governing the generation of genetic variation during
a single infection
In particular:
• the mutation rate
• the number of viral generations
• the viability of variants
However, if variation is generated at the rate anticipated,
then transmission networks may be traced at a much finer
resolution than practiced to date

37. Introduce infection Group 1 Group 2 Group 3 Group 4
Hughes, G.J., Mioulet, V., Haydon, D.T., Kitching, P.R., Donaldson, A.I., and Woolhouse, M.E.J. (2002).
Serial passage of foot-and-mouth disease virus in sheep reveals declining levels of viraemia through time.
Journal of General Virology 83,

38. Inoculum Group 1 Group 2 Group 3 Group 407 99 23
487 91 23
487
577 83 23
487
577
NOT DONE 06 98 90 82 23
487
577 23
NOT DONE
NOT DONE 05 97 89 81 23
487
NOT DONE
NOT DONE
NOT DONE
Inoculum a 04 96 23
487
577 88 80 Ø
NOT INFECTED
NOT INFECTED
NOT DONE
Inoculum b 03
487 95 87 79
231,2
487
5771,2
231,2
487
NOT INFECTED
487 02 94 23
487 86
231,2
487 23
487
577 78
NOT INFECTED 01
487 93 85 77
NOT INFECTED
NOT INFECTED
NOT INFECTED 00 92 84 76 23
487
577
NOT DONE
NOT INFECTED
NOT INFECTED