Veterinary Microbiology 170 (2014) 462–464
Contents lists available at ScienceDirect
Veterinary Microbiology journal homepage: www.elsevier.com/locate/vetmic
Letter to the Editor Duck hepatitis A virus (DHAV) genotype definition: Comment on the article by Cha et al. A B S T R A C T
Keywords: Duck hepatitis A virus Genotype definition Pairwise sequence comparisons (PASC)
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. ß 2014 Elsevier B.V. All rights reserved.
The official name duck hepatitis A virus (DHAV) was used and validated in the ninth Report of the International Committee on Taxonomy of Viruses (ICTV), which was classified as a member of a novel genus Avihepatovirus in the family Picornaviridae (http://ictvonline.org/index. asp). 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) (Tseng and Tsai, 2007). Recently, Cha et al. (2013) published an article titled with Isolation and characterization of a low pathogenic duck hepatitis A virus 3 from South Korea in the journal Veterinary Microbiology, in which 22 amino acid sequences of the entire gene of DHAV isolated in South Korea, China, ATCC and so on, were compared. Cha and coworkers proposed the existence that both DHAV-1 and DHAV-2 had been classified into one branch, with DHAV genotype 3 (DHAV-3) in another using the neighborjoining method based on the MEGA 4.0 program. However, there were several concerns on the methodology application to define DHAV’s genotypes. Based on 110 genomic (Fig. 1a) and 100 amino acid (Fig. 1b) sequences of DHAV retrieved from GenBank which included all the sequences from Cha et al. (2013) respectively, phylogenetic analysis in the present study showed a distinct and 0378-1135/$ – see front matter ß 2014 Elsevier B.V. All rights reserved. http://dx.doi.org/10.1016/j.vetmic.2014.01.037
proposed DHAV genotype definition, that both DHAV-2 and DHAV-3 were clustered in one branch, while DHAV-1 in another branch only, using the same method and the same program. In fact, classification of DHAV into three genotypes was already proposed by Wang et al. (2008), but it was not taken into consideration by Cha et al. (2013). Further, the phylogenetic distance unit was the value 0.02 displayed in Fig. 1a and b, which was much smaller than 0.5 showed in Cha et al. (2013). As we all know, genetic distance unit for virus genotyping is probably not up to 0.5. It is worth to be mentioned, that a standardized methodology has been used to define virus genotypes based on pairwise sequence comparisons (PASC) (Segales et al., 2008). PASC is a widely accepted method in virus taxonomy (Biagini et al., 1999; Grau-Roma et al., 2008; Huang et al., 2010; Munir et al., 2012), which is based on the cut-off values tested for the genotype definition according to the histogram of pairwised differences among sequences (Rogers and Harpending, 1992). Taking into account the genotype definition of DHAV, we also conducted the PASC analysis of 110 DHAV genomic sequences (Fig. 2a and b) including all the sequences from Cha et al. (2013), and proposed that the distance genotype definition threshold was 0.045. Cha and co-workers’
Letter to the Editor / Veterinary Microbiology 170 (2014) 462–464
463
Fig. 1. (a) Phylogenetic analysis of 110 DHAV genomic sequences retrieved from GenBank which included all the sequences (in bold) from Cha et al. (2013). (b) Phylogenetic analysis of 100 amino acid sequences of the entire gene of DHAV retrieved from GenBank which included all the sequences (in bold) from Cha et al. (2013). DHAV is genetically divided into three different genotypes (DHAV-1, -2 and -3). A proposed DHAV genotype definition, that both DHAV-2 and DHAV-3 were clustered in one branch, while DHAV-1 in another branch only, using the neighbor-joining method based on the MEGA 4.0 program.
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Letter to the Editor / Veterinary Microbiology 170 (2014) 462–464
Fig. 2. (a) Linearized neighbor-joining tree based on the p-distance using 110 DHAV genomic sequences. (b) Plot: frequency distribution of pairwise distances among 110 genomic DHAV. The dashed line indicates the theoretical threshold of 0.045, proposed in the present study for the genotype definition of genomic sequences in DHAV. Two avian encephalomyelitis virus (AEV) genomic sequences (for rooting purposes) (accession numbers AJ225173.1 and AY275539.1) were used to construct a matrix of p-distance values.
inappropriate presented results on DHAV genotyping may attribute to a maloperation to phylogenectic analysis using the neighbor-joining method based on the MEGA program. Additional explanation on PASC analysis would be clearer in Rogers and Harpending’s literature (1992). The major interest of this letter wishes to induce constructive discussions for the use of the criteria for phylogenectic analysis of DHAV genotyping to allow the comparison of molecular epidemiology data worldwide. References Biagini, P., Gallian, P., Attoui, H., Cantaloube, J.F., de Micco, P., de Lamballerie, X., 1999. Determination and phylogenetic analysis of partial sequences from TT virus isolates. J. Gen. Virol. 80, 419–424. Cha, S.Y., Roh, J.H., Kang, M., Kim, B., Jang, H.K., 2013. Isolation and characterization of a low pathogenic duck hepatitis A virus 3 from South Korea. Vet. Microbiol. 162, 254–258. Huang, Y.W., Ni, Y.Y., Dryman, B.A., Meng, X.J., 2010. Multiple infection of porcine Torque teno virus in a single pig and characterization of the full-length genomic sequences of four U.S. prototype PTTV strains: implication for genotyping of PTTV. Virology 396, 289–297. Grau-Roma, L., Crisci, E., Sibila, M., Lopez-Soria, S., Nofrarias, M., Cortey, M., Fraile, L., Olvera, A., Segales, J., 2008. A proposal on porcine circovirus type 2 (PCV2) genotype definition and their relation with postweaning multisystemic wasting syndrome (PMWS) occurrence. Vet. Microbiol. 128, 23–35. Munir, M., Cortey, M., Abbas, M., Qureshi, Z.U., Afzal, F., Shabbir, M.Z., Khan, M.T., Ahmed, S., Ahmad, S., Baule, C., Stahl, K., Zohari, S., Berg, M., 2012. Biological characterization and phylogenetic analysis of a novel genetic group of Newcastle disease virus isolated from outbreaks in commercial poultry and from backyard poultry flocks in Pakistan. Infect. Genet. Evol. 12, 1010–1019. Rogers, A.R., Harpending, H., 1992. Population growth makes waves in the distribution of pairwise genetic differences. Mol. Biol. Evol. 9, 552– 569. Segales, J., Olvera, A., Grau-Roma, L., Charreyre, C., Nauwynck, H., Larsen, L., Dupont, K., McCullough, K., Ellis, J., Krakowka, S., Mankertz, A.,
Fredholm, M., Fossum, C., Timmusk, S., Stockhofe-Zurwieden, N., Beattie, V., Armstrong, D., Grassland, B., Baekbo, P., Allan, G., 2008. PCV-2 genotype definition and nomenclature. Vet. Rec. 162, 867–868. Tseng, C.H., Tsai, H.J., 2007. Molecular characterization of a new serotype of duck hepatitis virus. Virus Res. 126, 19–31. Wang, L., Pan, M., Fu, Y., Zhang, D., 2008. Classification of duck hepatitis virus into three genotypes based on molecular evolutionary analysis. Virus Genes 37, 52–59.
Huiqiang Wen Lingxia Han Xiaona Zhang Chuanjiang Lian Lili Zhao Changde Si Hongyan Chen* 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 *Corresponding
author. Tel.: +86 0189 4606 6280; fax: +86 0451 51997166
E-mail addresses: [email protected] (H Wen); [email protected] (L. Han); [email protected] (X. Zhang); [email protected] (C. Lian); [email protected] (L. Zhao); [email protected] (C. Si); [email protected] (H. Chen) 25 January 2014
Contents lists available at ScienceDirect
Veterinary Microbiology journal homepage: www.elsevier.com/locate/vetmic
Letter to the Editor Duck hepatitis A virus (DHAV) genotype definition: Comment on the article by Cha et al. A B S T R A C T
Keywords: Duck hepatitis A virus Genotype definition Pairwise sequence comparisons (PASC)
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. ß 2014 Elsevier B.V. All rights reserved.
The official name duck hepatitis A virus (DHAV) was used and validated in the ninth Report of the International Committee on Taxonomy of Viruses (ICTV), which was classified as a member of a novel genus Avihepatovirus in the family Picornaviridae (http://ictvonline.org/index. asp). 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) (Tseng and Tsai, 2007). Recently, Cha et al. (2013) published an article titled with Isolation and characterization of a low pathogenic duck hepatitis A virus 3 from South Korea in the journal Veterinary Microbiology, in which 22 amino acid sequences of the entire gene of DHAV isolated in South Korea, China, ATCC and so on, were compared. Cha and coworkers proposed the existence that both DHAV-1 and DHAV-2 had been classified into one branch, with DHAV genotype 3 (DHAV-3) in another using the neighborjoining method based on the MEGA 4.0 program. However, there were several concerns on the methodology application to define DHAV’s genotypes. Based on 110 genomic (Fig. 1a) and 100 amino acid (Fig. 1b) sequences of DHAV retrieved from GenBank which included all the sequences from Cha et al. (2013) respectively, phylogenetic analysis in the present study showed a distinct and 0378-1135/$ – see front matter ß 2014 Elsevier B.V. All rights reserved. http://dx.doi.org/10.1016/j.vetmic.2014.01.037
proposed DHAV genotype definition, that both DHAV-2 and DHAV-3 were clustered in one branch, while DHAV-1 in another branch only, using the same method and the same program. In fact, classification of DHAV into three genotypes was already proposed by Wang et al. (2008), but it was not taken into consideration by Cha et al. (2013). Further, the phylogenetic distance unit was the value 0.02 displayed in Fig. 1a and b, which was much smaller than 0.5 showed in Cha et al. (2013). As we all know, genetic distance unit for virus genotyping is probably not up to 0.5. It is worth to be mentioned, that a standardized methodology has been used to define virus genotypes based on pairwise sequence comparisons (PASC) (Segales et al., 2008). PASC is a widely accepted method in virus taxonomy (Biagini et al., 1999; Grau-Roma et al., 2008; Huang et al., 2010; Munir et al., 2012), which is based on the cut-off values tested for the genotype definition according to the histogram of pairwised differences among sequences (Rogers and Harpending, 1992). Taking into account the genotype definition of DHAV, we also conducted the PASC analysis of 110 DHAV genomic sequences (Fig. 2a and b) including all the sequences from Cha et al. (2013), and proposed that the distance genotype definition threshold was 0.045. Cha and co-workers’
Letter to the Editor / Veterinary Microbiology 170 (2014) 462–464
463
Fig. 1. (a) Phylogenetic analysis of 110 DHAV genomic sequences retrieved from GenBank which included all the sequences (in bold) from Cha et al. (2013). (b) Phylogenetic analysis of 100 amino acid sequences of the entire gene of DHAV retrieved from GenBank which included all the sequences (in bold) from Cha et al. (2013). DHAV is genetically divided into three different genotypes (DHAV-1, -2 and -3). A proposed DHAV genotype definition, that both DHAV-2 and DHAV-3 were clustered in one branch, while DHAV-1 in another branch only, using the neighbor-joining method based on the MEGA 4.0 program.
464
Letter to the Editor / Veterinary Microbiology 170 (2014) 462–464
Fig. 2. (a) Linearized neighbor-joining tree based on the p-distance using 110 DHAV genomic sequences. (b) Plot: frequency distribution of pairwise distances among 110 genomic DHAV. The dashed line indicates the theoretical threshold of 0.045, proposed in the present study for the genotype definition of genomic sequences in DHAV. Two avian encephalomyelitis virus (AEV) genomic sequences (for rooting purposes) (accession numbers AJ225173.1 and AY275539.1) were used to construct a matrix of p-distance values.
inappropriate presented results on DHAV genotyping may attribute to a maloperation to phylogenectic analysis using the neighbor-joining method based on the MEGA program. Additional explanation on PASC analysis would be clearer in Rogers and Harpending’s literature (1992). The major interest of this letter wishes to induce constructive discussions for the use of the criteria for phylogenectic analysis of DHAV genotyping to allow the comparison of molecular epidemiology data worldwide. References Biagini, P., Gallian, P., Attoui, H., Cantaloube, J.F., de Micco, P., de Lamballerie, X., 1999. Determination and phylogenetic analysis of partial sequences from TT virus isolates. J. Gen. Virol. 80, 419–424. Cha, S.Y., Roh, J.H., Kang, M., Kim, B., Jang, H.K., 2013. Isolation and characterization of a low pathogenic duck hepatitis A virus 3 from South Korea. Vet. Microbiol. 162, 254–258. Huang, Y.W., Ni, Y.Y., Dryman, B.A., Meng, X.J., 2010. Multiple infection of porcine Torque teno virus in a single pig and characterization of the full-length genomic sequences of four U.S. prototype PTTV strains: implication for genotyping of PTTV. Virology 396, 289–297. Grau-Roma, L., Crisci, E., Sibila, M., Lopez-Soria, S., Nofrarias, M., Cortey, M., Fraile, L., Olvera, A., Segales, J., 2008. A proposal on porcine circovirus type 2 (PCV2) genotype definition and their relation with postweaning multisystemic wasting syndrome (PMWS) occurrence. Vet. Microbiol. 128, 23–35. Munir, M., Cortey, M., Abbas, M., Qureshi, Z.U., Afzal, F., Shabbir, M.Z., Khan, M.T., Ahmed, S., Ahmad, S., Baule, C., Stahl, K., Zohari, S., Berg, M., 2012. Biological characterization and phylogenetic analysis of a novel genetic group of Newcastle disease virus isolated from outbreaks in commercial poultry and from backyard poultry flocks in Pakistan. Infect. Genet. Evol. 12, 1010–1019. Rogers, A.R., Harpending, H., 1992. Population growth makes waves in the distribution of pairwise genetic differences. Mol. Biol. Evol. 9, 552– 569. Segales, J., Olvera, A., Grau-Roma, L., Charreyre, C., Nauwynck, H., Larsen, L., Dupont, K., McCullough, K., Ellis, J., Krakowka, S., Mankertz, A.,
Fredholm, M., Fossum, C., Timmusk, S., Stockhofe-Zurwieden, N., Beattie, V., Armstrong, D., Grassland, B., Baekbo, P., Allan, G., 2008. PCV-2 genotype definition and nomenclature. Vet. Rec. 162, 867–868. Tseng, C.H., Tsai, H.J., 2007. Molecular characterization of a new serotype of duck hepatitis virus. Virus Res. 126, 19–31. Wang, L., Pan, M., Fu, Y., Zhang, D., 2008. Classification of duck hepatitis virus into three genotypes based on molecular evolutionary analysis. Virus Genes 37, 52–59.
Huiqiang Wen Lingxia Han Xiaona Zhang Chuanjiang Lian Lili Zhao Changde Si Hongyan Chen* 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 *Corresponding
author. Tel.: +86 0189 4606 6280; fax: +86 0451 51997166
E-mail addresses: [email protected] (H Wen); [email protected] (L. Han); [email protected] (X. Zhang); [email protected] (C. Lian); [email protected] (L. Zhao); [email protected] (C. Si); [email protected] (H. Chen) 25 January 2014
