Objective To analyze the genome characteristics of an avian influenza A (H9N2) virus isolated from an 11-month-old infant, and to look for possible sources of infection.

Methods Throat swabs were collected from an infant with influenza-like illness in influenza sentinel surveillance hospitals and isolated for influenza viruses using cells. The isolates were identified for influenza virus types and subtypes by the method of hemagglutination assay, hemagglutination inhibition assay and fluorescence PCR. Whole genome sequencing of the isolated virus was carried out. The genome nucleic acid sequences and the deduced amino acid sequences were analyzed by comparing the phylogenetic trees which were constructed by bioinformatics software.

Results A seasonal un-typed influenza virus was isolated from the infant with influenza like illness. With fluorescent PCR method , it was identified as H9N2 subtype of avian influenza virus and the case was confirmed as a human infected with an avian influenza A(H9N2) virus. Epidemiological studies revealed that the case had no clear history of poultry contact and exposure. Blast analysis shows that eight segments of the viral genome are avian origin, and 97.5%-99.8% homology with that of viruses isolated from the live-poultry markets. The virus belongs to G57 genotype, deduced amino acid sequence analysis shows that the virus has typical low pathogenic avian influenza characteristics.

Conclusions Although the case does not have a clear history of contact or exposure to poultry, molecular traceability suggests that possible sources of infection may be still from poultry.