Anticipating the Prevalence of Avian Influenza Subtypes H9 and H5 in Live-Bird Markets

Kim M Pepin,Steven Riley,Jennifer A Hoeting,Yi Guan,Peter J Hudson,Huachen Zhu,Mary Poss,Wenshan Hong,Jia Wang,Colleen T Webb,Maciej F Boni

doi:10.1371/journal.pone.0056157

Abstract

An ability to forecast the prevalence of specific subtypes of avian influenza viruses (AIV) in live-bird markets would facilitate greatly the implementation of preventative measures designed to minimize poultry losses and human exposure. The minimum requirement for developing predictive quantitative tools is surveillance data of AIV prevalence sampled frequently over several years. Recently, a 4-year time series of monthly sampling of hemagglutinin subtypes 1–13 in ducks, chickens and quail in live-bird markets in southern China has become available. We used these data to investigate whether a simple statistical model, based solely on historical data (variables such as the number of positive samples in host X of subtype Y time t months ago), could accurately predict prevalence of H5 and H9 subtypes in chickens. We also examined the role of ducks and quail in predicting prevalence in chickens within the market setting because between-species transmission is thought to occur within markets but has not been measured. Our best statistical models performed remarkably well at predicting future prevalence (pseudo-R2 = 0.57 for H9 and 0.49 for H5), especially considering the multi-host, multi-subtype nature of AIVs. We did not find prevalence of H5/H9 in ducks or quail to be predictors of prevalence in chickens within the Chinese markets. Our results suggest surveillance protocols that could enable more accurate and timely predictive statistical models. We also discuss which data should be collected to allow the development of mechanistic models.

Highlights

H5 and H9 subtypes of avian influenza viruses (AIV) are two of the three avian subtypes (H7 is the third) known to cause infection in humans [1,2]
We focused on prevalence in chickens because this poultry species is a major staple with relatively high AIV prevalence
It has not been possible to forecast the prevalence of any AIV subtype in poultry because the appropriate data have not been available and the ecology and population dynamics of AIV are complex

Summary

Introduction

H5 and H9 subtypes of avian influenza viruses (AIV) are two of the three avian subtypes (H7 is the third) known to cause infection in humans [1,2]. Forecasting the future is challenging in any complex biological system, but is difficult for AIVs in live-bird markets because of: the intricate host population ecology, the rarity of some subtypes that can cause infection in humans (i.e., H5 and H7), and the lack of comprehensive longitudinal prevalence data for multiple subtypes. We reported 6 years of monthly prevalence data for Hemagglutinin (H) subtypes 1–13 [4] in multiple host species in live-bird markets in Shantou, China. To our knowledge, this is the most comprehensive longitudinal time series of AIV prevalence in a domestic poultry setting. The study found striking patterns of host specificity and co-infection bias between subtypes, highlighting that host species composition and the prevalence of multiple subtypes are key in determining subtype-specific prevalence patterns in southern Chinese markets

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Results

Conclusion