title: Duck hepatitis A virus (DHAV) genotype definition: comment on the article by Cha et al.
abstract: Duck hepatitis A virus (DHAV) is genetically divided into three different genotypes: the original type DHAV-1, a type recently isolated in Taiwan (DHAV-2), and a recently described type isolated in South Korea and China (DHAV-3). Recently, Cha et al. (2013) concluded that the existence that both DHAV-1 and DHAV-2 had been classified into one branch, with DHAV genotype 3 (DHAV-3) in another, and that the phylogenetic distance unit showed was 0.5, a tremendous value. However, there might be some concerns on the methodology application to define the genotypes of DHAV. Based on 110 genomic and 100 amino acid sequences of DHAV which included all the sequences from Cha et al. (2013) respectively, phylogenetic analysis in the present study showed a distinct and proposed DHAV genotype definition, that both DHAV-2 and DHAV-3 were clustered in one branch while DHAV-1 in another branch only, and that the phylogenetic distance unit of 0.02 was confirmed, which was much smaller than the value 0.5. Taking into account the genotype definition of DHAV, we also conducted the pairwise sequence comparisons (PASC) analysis of 110 genomic sequences, and proposed that the distance genotype definition threshold was 0.045.
authors.affiliation: Laboratory Animal and Comparative Medicine Unit, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150001, People's Republic of China. Electronic address: wen_huiqiang@163.com.
authors.forename: Huiqiang
authors.initials: H
authors.lastname: Wen
authors.affiliation: Laboratory Animal and Comparative Medicine Unit, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150001, People's Republic of China. Electronic address: hlx1993@126.com.
authors.forename: Lingxia
authors.initials: L
authors.lastname: Han
authors.affiliation: Laboratory Animal and Comparative Medicine Unit, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150001, People's Republic of China. Electronic address: hailanzhixin.hi@163.com.
authors.forename: Xiaona
authors.initials: X
authors.lastname: Zhang
authors.affiliation: Laboratory Animal and Comparative Medicine Unit, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150001, People's Republic of China. Electronic address: cjl121916@163.com.
authors.forename: Chuanjiang
authors.initials: C
authors.lastname: Lian
authors.affiliation: Laboratory Animal and Comparative Medicine Unit, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150001, People's Republic of China. Electronic address: zhaolili213@163.com.
authors.forename: Lili
authors.initials: L
authors.lastname: Zhao
authors.affiliation: Laboratory Animal and Comparative Medicine Unit, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150001, People's Republic of China. Electronic address: sichangde2008@yahoo.com.cn.
authors.forename: Changde
authors.initials: C
authors.lastname: Si
authors.affiliation: Laboratory Animal and Comparative Medicine Unit, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150001, People's Republic of China. Electronic address: chenhongyan@caas.cn.
authors.forename: Hongyan
authors.initials: H
authors.lastname: Chen
mesh_terms: D000818:Animals; D004372:Ducks; D004371:Hepatitis Virus, Duck / Q000145:classification*; D006524:Hepatitis, Viral, Animal / Q000821:virology*; D010850:Picornaviridae Infections / Q000662:veterinary*; D011201:Poultry Diseases / Q000821:virology*
keywords: Duck hepatitis A virus; Genotype definition; Pairwise sequence comparisons (PASC)