@article{fdi:010082583,
  title = {{I}nferring within-flock transmission dynamics of highly pathogenic avian influenza {H}5{N}8 virus in {F}rance, 2020},
  author = {{V}ergne, {T}. and {G}ubbins, {S}. and {G}uinat, {C}. and {B}auzile, {B}. and {D}elpont, {M}. and {C}hakraborty, {D}. and {G}ruson, {H}ugo and {R}oche, {B}enjamin and {A}ndraud, {M}. and {P}aul, {M}. and {G}uerin, {J}. {L}.},
  editor = {},
  language = {{ENG}},
  abstract = {{F}ollowing the emergence of highly pathogenic avian influenza ({H}5{N}8) in {F}rance in early {D}ecember 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 {B}ayesian computation sequential {M}onte {C}arlo ({ABC}-{SMC}) algorithm. {T}he 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). {O}n 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). {T}he 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. {T}his study illustrates how mechanistic models can help provide rapid relevant insights that contribute to the management of infectious disease outbreaks of farmed animals. {T}hese methods can be applied to future outbreaks and the resulting parameter estimates made available to veterinary services within a few hours.},
  keywords = {avian flu ; beta ; duck ; inference ; mechanistic model ; mortality ; {R}0 ; spread ; {FRANCE}},
  booktitle = {},
  journal = {{T}ransboundary and {E}merging {D}iseases},
  volume = {68},
  numero = {6},
  pages = {3151--3155},
  ISSN = {1865-1674},
  year = {2021},
  DOI = {10.1111/tbed.14202},
  URL = {https://www.documentation.ird.fr/hor/fdi:010082583},
}