Fig 1.
Two possible transmission trees and three possible pathogen phylogenies for a household outbreak.
A, B, and C were infected in alphabetical order such that their infectious sets are ,
, and
. We have a single pathogen sequence from each person. The top shows the two possible transmission trees within the household: either A infected B and B infected C (left) or A infected B and C (right). The bottom shows the three rooted, bifurcating phylogenies linking pathogen sequences from A, B, and C. In each phylogeny, the possible hosts are written underneath each interior node and arrows indicate how each assignment of interior node hosts determines a transmission tree via Assumption 5.
Fig 2.
Relative locations of the 12 farms in the Durham cluster.
These were infected in the 2001 FMDV outbreak in the UK.
Fig 3.
Timeline of latent and infectious periods in the Durham cluster.
The gray bars represent the range of days on which each farm might have been infected.
Table 1.
Statistical performance of estimators under exponential contact intervals.
Fig 4.
Relative efficiencies of βinf estimates based on squared widths of confidence intervals.
The dashed and dotted lines are smoothed means.
Fig 5.
Relative efficiencies of ln λ0 estimates based on squared widths of confidence intervals.
The dashed and dotted lines are smoothed means.
Table 2.
Statistical performance of estimators using infecteds only.
Table 3.
Statistical performance of estimators under Weibull contact intervals.
Fig 6.
First hosts in the Durham cluster.
Rooted phylogeny for RNA sequences from the 12 farms in the Durham cluster with tips at the onset of infectiousness. Each interior node x has first(x) written next to it.
Fig 7.
Postorder host sets in the Durham cluster.
The postorder host set Dx is written next to each interior node x. These are calculated in a postorder traversal using the leaf hosts and the infectious sets.
Fig 8.
Host sets in the Durham cluster.
The host set Hx is written next to each interior node x. These are calculated in a preorder traversal using the root host and the postorder host sets.
Fig 9.
Interior node host assignments (left) and transmission trees (right) consistent with the phylogeny and the epidemiologic data.
Dashed lines on the right indicate transmissions fixed by the phylogeny to the left. Dotted lines indicate that the infector of an individual depends on a choice of hosts in the phylogeny. At the top, K infects C, C infects P, and either K or L infects E. At the bottom, O infects C, either O or C infects P, and either K or L infects E. There are six possible transmission trees—two on top and four on the bottom.
Table 4.
Log-logistic rate and shape parameter estimates.
Fig 10.
Predicted farm-to-farm infectiousness with (black) and without (gray) phylogenies.
These are log-logistic hazard functions based on the rate and shape parameters estimates in Table 4.
Fig 11.
Point estimates and approximate 95% confidence bands for the hazard function estimates.
These assume no farms escaped infection. The bands for the estimates using a phylogeny are narrower.