Background: Influenza A virus subtype H9 is enzootic in portions of North and Central Africa, the Middle East, and Asia, where it significantly reduces the chicken industry´s profitability. The H9N2 virus was reported in Indonesia in late 2016, causing decreased egg production and increased mortality. Research on the H9N2 virus is important as an early warning system for the reassortment of potentially pandemic viruses such as HPAI virus subtype H5N1.

Aim: This tracking study aimed to isolate and identify the H9N2 virus in laying hens from samples collected from 2011 to 2018 in Indonesia.

Methods: Sequencing was performed on 2,949 samples obtained from tracheal and cloacal swabs after examination for the H9N2 virus using real-time reverse transcriptase-polymerase chain reaction.

Results: One positive sample was from West Java in 2017. The results of the phylogenetic analysis revealed that this virus belongs to the China-Vietnam-Indonesia lineage and is related to the A/chicken/West Java/VSN791/2017(H9N2) and A/chicken/Viet Nam/QN-2576/2015(H9N2) viruses.

Conclusion: As an early warning system for AI outbreaks, active surveillance is required to track the progress of LPAI viruses like H9N2.