Inferring within-flock transmission dynamics of highly pathogenic avian influenza H5N8 virus in France, 2020.

Timothée Vergne,Hugo Gruson,Mathilde Paul,Mathieu Andraud,Debapriyo Chakraborty,Simon Gubbins,Jean‐Luc Guérin,Mattias Delpont,Claire Guinat,Benjamin Roche,Billy Bauzile

doi:10.1111/tbed.14202

Abstract

Following the emergence of highly pathogenic avian influenza (H5N8) in France in early December 2020, we used duck mortality data from the index farm to investigate within‐flock transmission dynamics. A stochastic epidemic model was fitted to the daily mortality data and model parameters were estimated using an approximate Bayesian computation sequential Monte Carlo (ABC‐SMC) algorithm. The model predicted that the first bird in the flock was infected 5 days (95% credible interval, CI: 3–6) prior to the day of suspicion and that the transmission rate was 4.1 new infections per day (95% CI: 2.8–5.8). On average, ducks became infectious 4.1 h (95% CI: 0.7–9.1) after infection and remained infectious for 4.3 days (95% CI: 2.8–5.7). The model also predicted that 34% (50% prediction interval: 8%–76%) of birds would already be infectious by the day of suspicion, emphasizing the substantial latent threat this virus could pose to other poultry farms and to neighbouring wild birds. This study illustrates how mechanistic models can help provide rapid relevant insights that contribute to the management of infectious disease outbreaks of farmed animals. These methods can be applied to future outbreaks and the resulting parameter estimates made available to veterinary services within a few hours.

Highlights

On 21 October 2020, the detection of highly pathogenic avian influenza (HPAI) H5N8 virus in two mute swans in the Netherlands raised concerns about the re-emergence and further spread of this subtype, which has caused regular epidemics in the past few years
We considered a single homogeneously mixing population of ducks since the mortality data were only available for the whole farm, corresponding to the deaths from the two adjacent fields together
Because the flock was culled on 6 December, the number of dead ducks observed on the morning of that day (300) did not represent a full day’s mortality and, was not used for fitting the model

Summary

Introduction

On 21 October 2020, the detection of highly pathogenic avian influenza (HPAI) H5N8 virus in two mute swans in the Netherlands raised concerns about the re-emergence and further spread of this subtype, which has caused regular epidemics in the past few years. The transmission rate, the parameters for the latent and infectious period distributions and the date of virus introduction were estimated by fitting the model to the mortality data using an approximate Bayesian computation sequential Monte Carlo algorithm (Guinat et al, 2018; Toni et al, 2009 ).

Results

Conclusion