Highly Pathogenic Avian Influenza: risk models and risk management

The highly pathogenic avian influenza (HPAI) panzootic emerged in China in2006, and since then, despite efforts and resources being directed towardscontrol, continues to circulate in several countries. Additionally the virus hasevolved considerably into fourth order clades, is undergoing frequentreassortments, and has spilled over into wild bird populations on severaloccasions resulting in several waves of global spread. Economic losses fromcontrol measures like movement control, stamping out, cleaning and disinfectionhave run into millions. Further, the threat of zoonotic spillover and loss tolivelihoods and food security is omnipresent in endemic countries.The objective of the present work is to study the ecological factors associatedwith disease emergence, spread and persistence across different spatial scales.The aim is to generate evidence for planning and implementing risk managementinterventions for surveillance and control of HPAI.Firstly, an examination of the risk factors contributing to the epidemiology ofHPAI H5N1 outbreaks was undertaken following a wave of outbreaks of HPAIH5N1 in the eastern part of India. Key risk factors were identified and the risk ofoccurrence of HPAI was mapped using bootstrapped logistic regression andboosted regression trees (BRT). Thereafter, following the emergence and globalspread of HPAI H5Nx viruses in 2014-15, a first global suitability model of HPAIH5N1 sustained transmission was developed and compared with that of theHPAI H5Nx viruses. Even though the H5Nx model was of lower extrapolationcapacity, we demonstrated the association of H5Nx presence with intensivelyraised chicken density and anthropogenic variables, in contrast to the H5N1model which was more associated with extensive chicken production systems.The suitability models in this study were also put into immediate use when HPAIH5Nx viruses were introduced into the African subcontinent during 2016-17.The knowledge of risk factors and high-risk areas gained from the models wasconveyed to the veterinary services of countries at risk to help them target theirsurveillance for early detection and control.The link between evolution and epidemiology of HPAI virus was explored in thethird study by studying the historical and geographical patterns of novel HPAIemergences in poultry. We observed that novel HPAI viruses emerge by twomain mechanisms; first by conversion from low pathogenic to highly pathogenicvirus, and secondly, by reassortment between circulating viruses. Theseevolutionary mechanisms occur in two separate ecological niches, which haveimplications in mitigating the risk of emergence of novel HPAI viruses.The cumulative knowledge gained from this thesis has informed riskmanagement efforts at various spatial scales. The modelling studies areillustrative, identifying key risk factors associated with HPAI presence and areasof risk. Linking epidemiology and evolution has illustrated the two ecologicalniches of novel virus emergence, which will inform long term HPAI riskmanagement for the sustainable development of the poultry sector.Doctorat en Sciences agronomiques et ingénierie biologique