Unveiling Field Secrets: Using a Double Challenge Model and RNA Transcriptomics for Deeper Insights into Avian Influenza Surveillance

Avian influenza viruses (AIVs) pose significant risks to wildlife, poultry, and global health, with severe economic and ecological consequences. Effective surveillance in wild bird populations is crucial for early detection and risk mitigation. However, current methods provide limited information, missing key details about infection and immune responses. Understanding these processes would enhance effective surveillance and control. This study examines viral dynamics and immune responses in ducks infected with three low-pathogenic avian influenza (LPAI) subtypes (H3N8, H4N6, H6N2) and uses RNA transcriptomics to identify RNA biomarkers to extract more data from field samples. Six-week-old Mallard ducks were infected with one of the subtypes and swabbed daily (oropharyngeal and cloacal) for nine days. Each group was then challenged with a second virus a month later and swabbed again for nine days. Viral titers were analyzed by qPCR and egg infectious dose (EID₅₀), and RNA-seq was performed to identify immune responses. H3N8 produced the most robust infection, followed by H4N6 and H6N2. qPCR was more sensitive for virus detection than EID₅₀, and cloacal swabs showed higher viral loads than oropharyngeal swabs. Heterosubtypic immunity was observed without strong seroconversion, and some evidence of pre-existing immunity was tentatively noted. RNA-seq analysis identified potential RNA markers differentiating between male and female ducks and distinct points in the infection cycle. These findings enhance our understanding of AIV infection patterns and demonstrate the potential for detailed data extraction from field samples for a more comprehensive understanding of AIVs in their natural reservoir.

Walter N. Harrington, Ahmed Kandeil, Jon P. Seiler, Jeri-Carol Crumpton, David Brice, Jonathan Fogo, Eda Ozdemir, Morgan Davis, Lisa Kercher, Richard Webby St. Jude Children’s Research Hospital, Memphis, TN

Notable outbreaks, field and molecular epidemiology, and surveillance in wild birds