Combined Phylogeographic Analyses and Epidemiologic Contact Tracing to Characterize Atypically Pathogenic Avian Influenza (H3N1) Epidemic, Belgium, 2019

The high economic impact and zoonotic potential of avian influenza call for detailed investigations of dispersal dy-namics of epidemics. We integrated phylogeographic and epidemiologic analyses to investigate the dynamics of a low pathogenicity avian influenza (H3N1) epidemic that occurred in Belgium during 2019. Virus genomes from 104 clinical samples originating from 85% of affected farms were sequenced. A spatially explicit phylogeographic analysis confirmed a dominating northeast to southwest dispersal direction and a long-distance dispersal event linked to direct live animal transportation between farms. Spatiotemporal clustering, transport, and social contacts strongly correlated with the phylogeographic pattern of the epidemic. We detected only a limited association between wind direction and direction of viral lineage dispersal. Our results highlight the multifactorial nature of avian influenza epidemics and illustrate the use of genomic analyses of virus dispersal to complement epidemiologic and environ-mental data, improve knowledge of avian influenza epide-miologic dynamics, and enhance control strategies.

Automated summary

Phylogeographic and epidemiologic analyses were integrated to investigate the dynamics of a low pathogenicity avian influenza epidemic in Belgium in 2019. The study revealed a dominant northeast to southwest dispersal direction and a long-distance dispersal event associated with live animal transportation between farms. The spatial and temporal patterns of the epidemic were strongly correlated with transport, social contacts, and the phylogeographic analysis.