Influenza A Virus in Backyard Pigs and Poultry in Rural Cambodia

Area of Science:

• Veterinary Virology
• Public Health
• Molecular Epidemiology

Background:

• Influenza virus surveillance in humans and livestock is critical for global health and agriculture.
• Smallholder farming in low-income countries, with close human-animal proximity, drives influenza virus evolution.
• Understanding influenza circulation in backyard animals is essential for pandemic preparedness.

Purpose of the Study:

• To determine the prevalence and genetic characteristics of influenza A virus (IAV) in backyard pigs and poultry in Cambodia.
• To investigate the origins and potential for reassortment of detected IAV subtypes.
• To inform surveillance strategies for influenza in the Mekong subregion.

Main Methods:

• Matrix gene-based real-time reverse transcription PCR (rRT-PCR) testing of 751 animals (pigs, chickens, ducks, pigeons).
• Full-length genome sequencing of detected influenza A viruses.
• Phylogenetic analysis to determine viral gene origins and relationships.

Main Results:

• IAV detected in 1.5% of pigs, 1.4% of chickens, and 1.0% of ducks; not detected in pigeons.
• Triple reassortant H3N2 identified in pigs, with HA and NA genes from human H3N2 strains in Southeast Asia.
• Avian influenza subtypes in poultry showed close relation to internal genes of highly pathogenic H5N1 and H9N2 strains, suggesting reassortment and transboundary introduction.

Conclusions:

• Highly pathogenic influenza subtypes appear rare in backyard poultry, but reassortment involving zoonotic subtypes occurs frequently in smallholder pigs and poultry.
• Findings highlight the potential for virus reassortment and cocirculation of diverse IAV subtypes in the region.
• Enhanced surveillance on smallholdings is recommended to improve understanding of influenza transmission and evolution in humans, pigs, and poultry in the Mekong subregion.