Estimating within-flock transmission rate parameter for H5N2 highly pathogenic avian influenza virus in Minnesota turkey flocks during the 2015 epizootic

A. Ssematimba, S. Malladi, T.J. Hagenaars, P.J. Bonney, J.T. Weaver, K.A. Patyk, E. Spackman, D.A. Halvorson, C.J. Cardona

Research output: Contribution to journalArticleAcademicpeer-review

Abstract

Better control of highly pathogenic avian influenza (HPAI) outbreaks requires deeper understanding of within-flock virus transmission dynamics. For such fatal diseases, daily mortality provides a proxy for disease incidence. We used the daily mortality data collected during the 2015 H5N2 HPAI outbreak in Minnesota turkey flocks to estimate the within-flock transmission rate parameter (β). The number of birds in Susceptible, Exposed, Infectious and Recovered compartments was inferred from the data and used in a generalised linear mixed model (GLMM) to estimate the parameters. Novel here was the correction of these data for normal mortality before use in the fitting process. We also used mortality threshold to determine HPAI-like mortality to improve the accuracy of estimates from the back-calculation approach. The estimated β was 3.2 (95% confidence interval (CI) 2.3-4.3) per day with a basic reproduction number of 12.8 (95% CI 9.2-17.2). Although flock-level estimates varied, the overall estimate was comparable to those from other studies. Sensitivity analyses demonstrated that the estimated β was highly sensitive to the bird-level latent period, emphasizing the need for its precise estimation. In all, for fatal poultry diseases, the back-calculation approach provides a computationally efficient means to obtain reasonable transmission parameter estimates from mortality data.

LanguageEnglish
Article numbere179
JournalEpidemiology and Infection
Volume147
DOIs
Publication statusPublished - 22 Apr 2019

Fingerprint

Influenza in Birds
Orthomyxoviridae
Mortality
Birds
Disease Outbreaks
Poultry Diseases
Basic Reproduction Number
Confidence Intervals
Proxy
Linear Models
Viruses
Incidence

Keywords

  • Analysis of data
  • avian flu
  • mathematical modelling
  • veterinary epidemiology

Cite this

Ssematimba, A. ; Malladi, S. ; Hagenaars, T.J. ; Bonney, P.J. ; Weaver, J.T. ; Patyk, K.A. ; Spackman, E. ; Halvorson, D.A. ; Cardona, C.J. / Estimating within-flock transmission rate parameter for H5N2 highly pathogenic avian influenza virus in Minnesota turkey flocks during the 2015 epizootic. In: Epidemiology and Infection. 2019 ; Vol. 147.
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abstract = "Better control of highly pathogenic avian influenza (HPAI) outbreaks requires deeper understanding of within-flock virus transmission dynamics. For such fatal diseases, daily mortality provides a proxy for disease incidence. We used the daily mortality data collected during the 2015 H5N2 HPAI outbreak in Minnesota turkey flocks to estimate the within-flock transmission rate parameter (β). The number of birds in Susceptible, Exposed, Infectious and Recovered compartments was inferred from the data and used in a generalised linear mixed model (GLMM) to estimate the parameters. Novel here was the correction of these data for normal mortality before use in the fitting process. We also used mortality threshold to determine HPAI-like mortality to improve the accuracy of estimates from the back-calculation approach. The estimated β was 3.2 (95{\%} confidence interval (CI) 2.3-4.3) per day with a basic reproduction number of 12.8 (95{\%} CI 9.2-17.2). Although flock-level estimates varied, the overall estimate was comparable to those from other studies. Sensitivity analyses demonstrated that the estimated β was highly sensitive to the bird-level latent period, emphasizing the need for its precise estimation. In all, for fatal poultry diseases, the back-calculation approach provides a computationally efficient means to obtain reasonable transmission parameter estimates from mortality data.",
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Estimating within-flock transmission rate parameter for H5N2 highly pathogenic avian influenza virus in Minnesota turkey flocks during the 2015 epizootic. / Ssematimba, A.; Malladi, S.; Hagenaars, T.J.; Bonney, P.J.; Weaver, J.T.; Patyk, K.A.; Spackman, E.; Halvorson, D.A.; Cardona, C.J.

In: Epidemiology and Infection, Vol. 147, e179, 22.04.2019.

Research output: Contribution to journalArticleAcademicpeer-review

TY - JOUR

T1 - Estimating within-flock transmission rate parameter for H5N2 highly pathogenic avian influenza virus in Minnesota turkey flocks during the 2015 epizootic

AU - Ssematimba, A.

AU - Malladi, S.

AU - Hagenaars, T.J.

AU - Bonney, P.J.

AU - Weaver, J.T.

AU - Patyk, K.A.

AU - Spackman, E.

AU - Halvorson, D.A.

AU - Cardona, C.J.

PY - 2019/4/22

Y1 - 2019/4/22

N2 - Better control of highly pathogenic avian influenza (HPAI) outbreaks requires deeper understanding of within-flock virus transmission dynamics. For such fatal diseases, daily mortality provides a proxy for disease incidence. We used the daily mortality data collected during the 2015 H5N2 HPAI outbreak in Minnesota turkey flocks to estimate the within-flock transmission rate parameter (β). The number of birds in Susceptible, Exposed, Infectious and Recovered compartments was inferred from the data and used in a generalised linear mixed model (GLMM) to estimate the parameters. Novel here was the correction of these data for normal mortality before use in the fitting process. We also used mortality threshold to determine HPAI-like mortality to improve the accuracy of estimates from the back-calculation approach. The estimated β was 3.2 (95% confidence interval (CI) 2.3-4.3) per day with a basic reproduction number of 12.8 (95% CI 9.2-17.2). Although flock-level estimates varied, the overall estimate was comparable to those from other studies. Sensitivity analyses demonstrated that the estimated β was highly sensitive to the bird-level latent period, emphasizing the need for its precise estimation. In all, for fatal poultry diseases, the back-calculation approach provides a computationally efficient means to obtain reasonable transmission parameter estimates from mortality data.

AB - Better control of highly pathogenic avian influenza (HPAI) outbreaks requires deeper understanding of within-flock virus transmission dynamics. For such fatal diseases, daily mortality provides a proxy for disease incidence. We used the daily mortality data collected during the 2015 H5N2 HPAI outbreak in Minnesota turkey flocks to estimate the within-flock transmission rate parameter (β). The number of birds in Susceptible, Exposed, Infectious and Recovered compartments was inferred from the data and used in a generalised linear mixed model (GLMM) to estimate the parameters. Novel here was the correction of these data for normal mortality before use in the fitting process. We also used mortality threshold to determine HPAI-like mortality to improve the accuracy of estimates from the back-calculation approach. The estimated β was 3.2 (95% confidence interval (CI) 2.3-4.3) per day with a basic reproduction number of 12.8 (95% CI 9.2-17.2). Although flock-level estimates varied, the overall estimate was comparable to those from other studies. Sensitivity analyses demonstrated that the estimated β was highly sensitive to the bird-level latent period, emphasizing the need for its precise estimation. In all, for fatal poultry diseases, the back-calculation approach provides a computationally efficient means to obtain reasonable transmission parameter estimates from mortality data.

KW - Analysis of data

KW - avian flu

KW - mathematical modelling

KW - veterinary epidemiology

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DO - 10.1017/S0950268819000633

M3 - Article

VL - 147

JO - Epidemiology and Infection

T2 - Epidemiology and Infection

JF - Epidemiology and Infection

SN - 0950-2688

M1 - e179

ER -