Thanks to Greg Folkers for sending the link to this Journal of Virology report: Coexistence of influenza H7N9 and H9N2 in poultry linked to human H7N9 infection and their genome characteristics. The abstract:
Avian influenza virus A of a novel reassortant subtype H7N9 was recently found to cause severe human respiratory infections in China. Live poultry markets were suspected locations of the human H7N9 infection sources, based on the cases' exposure histories and sequence similarities between viral isolates.
To explore the role of live poultry markets in the origin of the novel H7N9 virus, we systematically examined poultry and environmental specimens from local markets and farms in Hangzhou, using real-time RT-PCR as well as high-throughput next generation sequencing (NGS). RT-PCR identified specimens positive for the H7 and N9 genomic segments in all of the twelve poultry markets epidemiologically linked to ten human H7N9 cases.
Chickens, ducks, and environmental specimens from the markets heavily contained mixed subtypes including H7, N9, H9, N2, and sometimes H5 and N1. Coexistence of H7N9 and H9N2 subtypes in chickens were further supported by metagenomic sequencing.
By contrast, human H7N9 infection cases (n=31) were all negative for H9N2 virus according to real-time RT-PCR. The six internal segments were indistinguishable for the H7N9 and H9N2 viruses. The sequences of the H9, N2, and internal segment sequences were very close to the H9N2 virus circulating in chickens in China recently.
Our results provide direct evidence that H9N2 strains coexisted with the novel human pathogenic H7N9 influenza virus in epidemiologically linked live poultry markets. Avian influenza A virus of the H9N2 subtype likely made recent and ongoing contribution to the evolution of the H7N9 virus.