Inferring within-herd transmission parameters for African swine fever virus using mortality data from outbreaks in the Russian Federation

Abstract

Mortality data are routinely collected for many livestock and poultry species, and they are often used for epidemiological purposes, including estimating transmission parameters. In this study, we infer transmission rates for African swine fever virus (ASFV), an important transboundary disease of swine, using mortality data collected from nine pig herds in the Russian Federation with confirmed outbreaks of ASFV. Parameters in a stochastic model for the transmission of ASFV within a herd were estimated using approximate Bayesian computation. Estimates for the basic reproduction number varied amongst herds, ranging from 4.4 to 17.3. This was primarily a consequence of differences in transmission rate (range: 0.7-2.2), but also differences in the mean infectious period (range: 4.5-8.3 days). We also found differences amongst herds in the mean latent period (range: 5.8-9.7 days). Furthermore, our results suggest that ASFV could be circulating in a herd for several weeks before a substantial increase in mortality is observed in a herd, limiting the usefulness of mortality data as a means of early detection of an outbreak. However, our results also show that mortality data are a potential source of data from which to infer transmission parameters, at least for diseases which cause high mortality.

Keywords: approximate Bayesian computation; disease control; epidemiology; modelling; mortality data; pigs.

Figure 1

Dynamics of African swine fever virus (ASFV) in nine pig herds in the Russian Federation. Each column shows the predicted number of susceptible (S, cyan), exposed (E, magenta), infectious (I, red) and dead pigs (D, blue), respectively, as well as the observed number of dead pigs. Predicted dynamics are shown as the median (solid black line), 25th and 75th percentiles (dashed black lines) and five percentile bands (up to the 5th and 95th percentiles; shading). Observed daily mortalities are shown as black circles (last column). The grey shaded area indicates the observation period for the mortality data, and the black dotted line indicates the day on which ASFV was confirmed in the herd. Results are based on 1,000 replicates of the model sampling from the joint posterior distribution assuming informative priors for all parameters

Figure 2

Transmission parameters for African swine fever virus (ASFV) inferred using mortality data for nine pig herds in the Russian Federation with confirmed outbreaks of ASFV. Plots show the marginal posterior distributions for the parameters for each herd: (a) basic reproduction number (R ₀); (b) transmission rate (β); (c) mean latent period (μ_E); (d) shape parameter for latent period (k_E); (e) mean infectious period (μ_I); (f) shape parameter for infectious period (k_I); (g) natural mortality rate (r_M); and (h) time of introduction (t _intro). The violin plots show the posterior density (shape), median (circle) and interquartile range (line) for the parameter (column) for the parameter. The dashed and dotted lines indicate the mean and 2.5th and 97.5th percentiles, respectively, for the informative prior distribution used for the parameter