Phylogenetic trees of HA (a), NA (b), PB2 (c), PB1 (d), PA (e), NP (f), M (g), and NS (h) genes of H9N2 subtype AIVs. Neighbor-joining (NJ) trees were generated using MEGA 5.01. Estimates of the phylogenies were calculated by performing 1000 neighbor-joining bootstrap replicates, all rooted to the sequence of Turkey/Wisconsin/1/66 (H9N2). Our 22 isolates are highlighted in red and representative strains are shown in blue. Abbreviations: Agt, American green-winged teal; Aw, American wigeon; Bd, black duck; Bh, bufflehead; Bs, Bewick’s swan; Bt, baikal teal; Ch, chukar; Ck, chicken; Dk, duck; Eg, egret; En, environment; Ew, Eurasian wigeon; Fe, feces; Gw, gadwall; Gf, guinea fowl; Gs, goose; Gt, green-winged teal; Lg, laughing gull; Ltd, longtail duck; Md, mallard; Mud, Muscovy duck; Np, northern pintail; Ns, northern shoveler; Os, Ostrich; Pfg, pink-footed goose; Pi, pintail duck; Qa, quail; Rcp, red crested pochard; Rt, ruddy turnstone; Sb, Shorebird; Sg, snow goose; Sw, swine; Suw, surface water; Tbm, thick-billed murre; Ty, turkey; Wb, wild bird; Wd, wild duck; Wfg, white-fronted goose; AH, Anhui; AL, Alaska; ALB, Alberta; AR, Arkansas; BJ, Beijing; CA, California; DE, Delaware; EG, Egypt; GD, Guangdong; GE, Germany; GX, Guangxi; GZ, Guangzhou; HLJ, Heilongjiang; HK, Hong Kong; HN, Hunan; HO, Hokkaido; IA, Interior Alaska; IL, Illinois; IR, Iran; JX, Jiangxi; Js, Jiangsu; KR, Korea; LO, Louisiana; MG, Mongolia; MI, Minnesota; MIS, Missouri; MT, Montana; ML, Maryland; NanJ, Nanjing; NE, Netherlands; NJ, New Jersey; OH, Ohio; PA, Pakistan; QB, Quebec; RZ, Rizhao; SA, South Africa; SD, Shandong; SH, Shanghai; ST, Shantou; TX, Texas; VN, Vietnam; WA, Washington; Wi, Wisconsin; XH, Xianghai; ZJ, Zhejiang.