Improved time estimates of avian influenza introduction on poultry farms

Published on
September 7, 2020

Epidemiologists from Wageningen Bioveterinary Research (WBVR) have developed an improved method for estimating the time window for the introduction of avian influenza virus on poultry farms. The method was developed in collaboration with colleagues from Utrecht University. They published their results in the journal Scientific Reports of the Nature Publishing Group.

The method is part of the EpiTools toolbox. It can be used for controlling notifiable animal diseases, for example by the Ministry of Agriculture, Nature and Food Quality and the Netherlands Food and Consumer Product Safety Authority.

Identifying the source of infection

“Estimating the time window for the introduction of the highly pathogenic avian influenza virus (HPAI) on poultry farms is especially important to help trace the source of infection (back tracing),” says epidemiologist Armin Elbers, project leader of this study. “It also helps officials to compile a list of farms (and to monitor them clinically and diagnostically) that have had contact with the infected farm during the infectious period. This may limit the further spread of the infection (forward tracing)”.

Mortality data for poultry

This method is based partly on the mortality data of the poultry on the farm in the period prior to the notification of a suspicious clinical situation. Finding, securing and quickly obtaining mortality data of the poultry flock is therefore crucial to estimate the time window of introduction as quickly as possible.

EpiTools toolbox

In addition to the module for estimating the time window of introduction of a virus on a livestock farm, the EpiTools toolbox contains four modules that help officials monitor the development of the epidemic, and which enable them to intervene with stronger measures if the epidemic continues unabated:

  1. A risk map showing the locations of higher risk and lower risk farms in different colours;
  2. The most important transmission parameters such as the reproduction number(infection rate) for the current epidemic;
  3. The expected magnitude and duration of the current epidemic; and
  4. The effect of various scenarios, including interventions.

The EpiTools toolbox has been developed for outbreaks of avian influenza, foot and mouth disease and classical swine fever.


Previously developed methods for estimating the time window of virus introduction on farms often overestimate the number of animals that can be infected by one sick animal within a certain period of time. This may result in an incorrect (later) estimation of the time window of introduction. Due to the amount of data required, these previous methods are also less suitable for estimating farm-specific virus introduction time windows because under field conditions data on increased mortality of only a limited number of days is present.


This study aimed to develop an effective approach for estimating farm-specific time windows for virus introduction, and to evaluate this approach by applying it to 11 outbreaks of HPAI subtype H5N8 on commercial poultry farms in the Netherlands between 2014 and 2016. Two approaches were developed and evaluated. Thomas Hagenaars, senior mathematical modeller within the project team, explains: “When using existing field data, we were able to conclude that one of the two models is generally more useful when data on disease-induced mortality is scarce. This approach was successfully applied to 8 out of 11 HPAI H5N8 outbreaks”.