African swine fever (ASF) is a highly contagious, lethal and economically devastating haemorrhagic
disease of domestic pigs. Insights into the dynamics and scale of virus transmission
can be obtained from estimates of the basic reproduction number (R0). We estimate R0
for ASF virus in small holder, free-range pig production system in Gulu, Uganda. The estimation
was based on data collected from outbreaks that affected 43 villages (out of the 289
villages with an overall pig population of 26,570) between April 2010 and November 2011.
A total of 211 outbreaks met the criteria for inclusion in the study. Three methods were
used, specifically; (i) GIS- based identification of the nearest infectious neighbour based on
the Euclidean distance between outbreaks, (ii) epidemic doubling time, and (iii) a compartmental
susceptible-infectious (SI) model. For implementation of the SI model, three approaches
were used namely; curve fitting (CF), a linear regression model (LRM) and the SI/
N proportion. The R0 estimates from the nearest infectious neighbour and epidemic doubling
time methods were 3.24 and 1.63 respectively. Estimates from the SI-based method
were 1.58 for the CF approach, 1.90 for the LRM, and 1.77 for the SI/N proportion. Since all
these values were above one, they predict the observed persistence of the virus in the population.
We hypothesize that the observed variation in the estimates is a consequence of
the data used. Higher resolution and temporally better defined data would likely reduce this
variation. This is the first estimate of R0 for ASFV in a free range smallholder pig keeping
system in sub-Saharan Africa and highlights the requirement for more efficient application
of available disease control measures.
S1 Data. The data that was used in all the computations and Figures.
S1 Fig. Generation tree following the nearest infectious neighbour route. Nearest infectious
neighbour generation tree also known as a transmission network. Epidemic is suspected to
have been introduced at herd/ node 1 coloured red (bottom extreme left). The critical node at
which the disease could have been stopped from further spread as highlighted in green in the
generation tree. (Designed in network analysis tool ORA)
S2 Fig. The SIR model used to simulate outbreak data of African swine fever, Gulu District,
Uganda, April 2010—November 2011.
S3 Fig. Distribution of bootstrapped monthly transmission rate coefficient β estimates.
S4 Fig. Sensitivity of basic reproduction number R0 to variation in initial number of herds.
S5 Fig. Spatial distribution of ASF infected herds (April 2010—November 2011).