Prevalence of H9n2 Influenza a Viruses in Poultry in Southern China: Implications for the Emergence of a New Pandemic Influenza

This dissertation, "Prevalence of H9N2 Influenza a Viruses in Poultry in Southern China: Implications for the Emergence of a New Pandemic Influenza" by Kemin, Xu, 徐克敏, was obtained from The University of Hong Kong (Pokfulam, Hong Kong) and is being sold pursuant to Creative Commons: Attribution 3.0 Hong Kong License. The content of this dissertation has not been altered in any way. We have altered the formatting in order to facilitate the ease of printing and reading of the dissertation. All rights not granted by the above license are retained by the author. Abstract: Abstract of thesis entitled Prevalence of H9N2 Influenza A Viruses in Poultry in Southern China: Implications for the Emergence of a New Pandemic Influenza Submitted by Kemin Xu for the degree of Doctor of Philosophy at The University of Hong Kong in August, 2007 Influenza viruses with pandemic potential have emerged and re-emerged in southern China during the past ten years, one of which is H9N2 subtype virus. The H9N2 viruses, represented by Chicken/Beijing/1/94 (Ck/Bei-like) and Quail/Hong Kong/G1/97 (G1-like), have become established and maintained long-term endemicity in terrestrial poultry. To control the next pandemic influenza, it is necessary to gain a better understanding of the evolution and dynamics of all those viruses with pandemic potential in this region. Systematic influenza surveillance in the human-animal interface in southern China provides an almost real-time pre- warning system for a potential pandemic. Among the prevailing viruses, H9N2 subtype is considered to be one of the most likely pandemic candidate viruses. The findings of our surveillance studies reveal that H9N2 influenza viruses have become endemic in different types of terrestrial poultry in southern China. From 2000 to 2005, a total of 2,020 H9 viruses have been isolated from 107,901 samples (overall isolation rate, 1.9%). All of the H9 viruses tested were H9N2 except for four duck viruses (two each of H9N1 and H9N3 subtype). These H9N2 influenza viruses were prevalent year-round but with a seasonal variation. In terrestrial poultry, it was found that H9N2 viruses mainly replicated in the respiratory tract and may be transmitted air-borne within the population of birds. Antigenic and genetic analyses demonstrated that the Ck/Bei-like viruses had been transmitted from chicken into all other different types of poultry tested, including quail, partridge, chukkar, pheasant, Guinea fowl as well as domestic duck, while the G1-like viruses were mainly prevalent in quail. These two H9N2 influenza virus lineages underwent frequent reassortment with one another, or with viruses of other origins. Since 2002, all H9N2 isolates identified were reassortant variants with multiple gene origins. Among those viruses tested in the present study, a total of 37 genotypes of H9N2 viruses have been identified with 32 being Ck/Bei-like and five G1-like. Phylogenetic analysis revealed that the prevailing Ck/Bei-like H9N2 viruses were established by multiple 'two-way' transmissions among different types of poultry, thereby forming a complex ecosystem with great genetic diversity, while G1-like viruses were predominantly maintained in quail and showed limited reassortment. Phylogenetic analysis also revealed that gene exchange between current H9N2 viruses and highly pathogenic H5N1 viruses still occur and that these subtypes share some gene segments with common sources. The present study suggests that current H9N2 viruses from poultry in southern China still maintain pandemic potential, as they may be directly introduced into humans or contribute internal genes through reassortment to generate other subtype virus, i.e. H5N1. The findings of our study suggests that the long-term co- circulation of multiple virus lineages (e.g. H5N1 and H9N2 viruses) in different types of poultry have facilitated thes