Gene 538 (2014) 207–208
Contents lists available at ScienceDirect
Gene journal homepage: www.elsevier.com/locate/gene
Letter to the Editor
Comments on duck circovirus (DuCV) genotype definition Huiqiang Wen 1, Yongshu Wu 1, Chao Yang 1, Xiaona Zhang 1, Chuanjiang Lian 1, Hongyan Chen 1, Lingxia Han ⁎,1 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
a r t i c l e
i n f o
Article history: Accepted 4 January 2014 Available online 11 January 2014 Keywords: Duck circovirus Genotype Pairwise sequence comparisons (PASC)
a b s t r a c t A standardised methodology has been used to define genotypes based on pairwise sequence comparisons (PASC). PASC is a widely accepted method in virus taxonomy, which is based on the histogram of pairwised differences among sequences. Recently, Zhang et al. (2013) concluded that the average p-distance of duck circovirus (DuCV) between genotypes 1 and 2 was 0.170, and subtype distance thresholds were 0.032 in DuCV-1 and 0.018 in DuCV-2, respectively. However, there might be some concerns on the methodology application to define the genotype of DuCV. Taking into account the concerns mentioned above, our authors conducted the PASC analyses of 54 capsid gene (ORF2) and genomic sequences including all the sequences from Zhang et al. (2013). Our results confirmed the existence of two DuCV genotypes (1 and 2) and, we suggest that DuCV ORF2 and genomic distance genotype thresholds were 0.061 and 0.038, respectively. © 2014 Elsevier B.V. All rights reserved.
Duck circovirus (DuCV), a new species in the genus Circovirus of the Circoviridae family, was originally isolated from two female sixweek-old Mulard ducks in Germany (Hattermann et al., 2003). Besides DuCV, the genus Circovirus also includes porcine circovirus type 1 (PCV1), porcine circovirus type 2 (PCV2), goose circovirus (GoCV) and other circoviruses, according to the rule of the International Committee on Taxonomy of Viruses (ICTV) (http://ictvonline. org/index.asp). According to the standardised methodology application of genotype definition on PCV2 (Segales et al., 2008), evolution analysis and genotyping of DuCV could be made more clearly and more validly. This standardised methodology has been used to define genotypes based on pairwise sequence comparisons (PASC) (GrauRoma et al., 2008). PASC is a widely accepted method in virus taxonomy (Biagini et al., 1999; Huang et al., 2010; Munir et al., 2012), which is based on the histogram of pairwised differences among sequences (Rogers and Harpending, 1992). Recently, Zhang et al. (2013) published an article titled with Identification, genotyping, and molecular evolution analysis of duck circovirus in the journal Gene. Based on a PASC analysis of genomic sequences, the authors
Abbreviations: DuCV, duck circovirus; PASC, pairwise sequence comparisons; PCV1, porcine circovirus type 1; PCV2, porcine circovirus type 2; GoCV, goose circovirus; ICTV, International Committee on Taxonomy of Viruses. ⁎ Corresponding author. E-mail addresses: [email protected] (H. Wen), [email protected] (Y. Wu), [email protected] (C. Yang), [email protected] (X. Zhang), [email protected] (C. Lian), [email protected] (H. Chen), [email protected] (L. Han). 1 Tel.:+86 189 4606 6097; fax: +86 451 51997166. 0378-1119/$ – see front matter © 2014 Elsevier B.V. All rights reserved. http://dx.doi.org/10.1016/j.gene.2014.01.004
concluded that the average p-distance between genotypes 1 and 2 was 0.170, and subtype distance thresholds were 0.032 in DuCV-1 and 0.018 in DuCV-2, respectively (Zhang et al., 2013). However, there might be some concerns on the methodology application to define the genotype of DuCV. In PASC analysis, the cut-off values tested for the definition of genotypes is based on the histogram of pairwise distance among nucleotide sequences, also known as frequency distribution (Rogers and Harpending, 1992). Taking into account the concerns mentioned above, our authors conducted the PASC analyses of 54 capsid gene (ORF2, Fig. 1a) and genomic (Fig. 1b) sequences including all the sequences from Zhang et al. (2013). First, a similar p-distance/frequency histogram is obtained using between ORF2 and genomic DuCV sequences, and our results confirmed the existence of the two DuCV genotypes (1 and 2). Second, as shown in Figs. 1a and b, the cut-off values for DuCV genotyping in ORF2 and genomic sequence analyses, should be in the range from 0.043 to 0.105 and from 0.028 to 0.082, respectively. This implied that the value 0.170 for the average genotype distance of genome sequences mentioned in Zhang et al. (2013), was out of the range from 0.028 to 0.082, meanwhile the value 0.032 mentioned for subtype distance threshold in DuCV-1, was also inappropriate. We suggest that the distance genotype definition thresholds of DuCV ORF2 (Fig. 1c) and genomic (Fig. 1d) were 0.061 and 0.038, respectively. Zhang and co-authors' conclusion may attribute to a misunderstanding to the histogram for frequency distribution of pairwise distance. Further explanation would be clearer in the literature (Rogers and Harpending, 1992). The major interest of this letter wishes to induce constructive discussions for the use of the criteria for DuCV genotyping to allow the comparison of molecular epidemiology data worldwide.
208
Letter to the Editor
Fig. 1. (a) Linearized neighbour-joining tree based on the p-distance using 54 DuCV capsid gene (ORF2) sequences. (b) Linearized neighbour-joining tree based on the p-distance using 54 DuCV genomic sequences. (c) Plot: frequency distribution of pairwise distances between ORF2 DuCV. (d) Plot: frequency distribution of pairwise distances between genomic DuCV. The dashed lines indicate the theoretical thresholds of 0.061 and 0.038 respectively, proposed in the present study for the genotype definition of ORF2 and genomic sequences in DuCV. Two goose circovirus (GoCV) ORF2 sequences (for rooting purposes) (accession numbers AJ304456 and DQ192282) were used to construct a matrix of p-distance values.
Conflict of interest I state that there is no conflict of interest in the present study. 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. Grau-Roma, L., et al., 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.
Hattermann, K., Schmitt, C., Soike, D., Mankertz, A., 2003. Cloning and sequencing of duck circovirus (DuCV). Arch. Virol. 148, 2471–2480. 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. Munir, M., et al., 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., et al., 2008. PCV-2 genotype definition and nomenclature. Vet. Rec. 162, 867–868. Zhang, Z., et al., 2013. Identification, genotyping, and molecular evolution analysis of duck circovirus. Gene 529, 288–295.
Contents lists available at ScienceDirect
Gene journal homepage: www.elsevier.com/locate/gene
Letter to the Editor
Comments on duck circovirus (DuCV) genotype definition Huiqiang Wen 1, Yongshu Wu 1, Chao Yang 1, Xiaona Zhang 1, Chuanjiang Lian 1, Hongyan Chen 1, Lingxia Han ⁎,1 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
a r t i c l e
i n f o
Article history: Accepted 4 January 2014 Available online 11 January 2014 Keywords: Duck circovirus Genotype Pairwise sequence comparisons (PASC)
a b s t r a c t A standardised methodology has been used to define genotypes based on pairwise sequence comparisons (PASC). PASC is a widely accepted method in virus taxonomy, which is based on the histogram of pairwised differences among sequences. Recently, Zhang et al. (2013) concluded that the average p-distance of duck circovirus (DuCV) between genotypes 1 and 2 was 0.170, and subtype distance thresholds were 0.032 in DuCV-1 and 0.018 in DuCV-2, respectively. However, there might be some concerns on the methodology application to define the genotype of DuCV. Taking into account the concerns mentioned above, our authors conducted the PASC analyses of 54 capsid gene (ORF2) and genomic sequences including all the sequences from Zhang et al. (2013). Our results confirmed the existence of two DuCV genotypes (1 and 2) and, we suggest that DuCV ORF2 and genomic distance genotype thresholds were 0.061 and 0.038, respectively. © 2014 Elsevier B.V. All rights reserved.
Duck circovirus (DuCV), a new species in the genus Circovirus of the Circoviridae family, was originally isolated from two female sixweek-old Mulard ducks in Germany (Hattermann et al., 2003). Besides DuCV, the genus Circovirus also includes porcine circovirus type 1 (PCV1), porcine circovirus type 2 (PCV2), goose circovirus (GoCV) and other circoviruses, according to the rule of the International Committee on Taxonomy of Viruses (ICTV) (http://ictvonline. org/index.asp). According to the standardised methodology application of genotype definition on PCV2 (Segales et al., 2008), evolution analysis and genotyping of DuCV could be made more clearly and more validly. This standardised methodology has been used to define genotypes based on pairwise sequence comparisons (PASC) (GrauRoma et al., 2008). PASC is a widely accepted method in virus taxonomy (Biagini et al., 1999; Huang et al., 2010; Munir et al., 2012), which is based on the histogram of pairwised differences among sequences (Rogers and Harpending, 1992). Recently, Zhang et al. (2013) published an article titled with Identification, genotyping, and molecular evolution analysis of duck circovirus in the journal Gene. Based on a PASC analysis of genomic sequences, the authors
Abbreviations: DuCV, duck circovirus; PASC, pairwise sequence comparisons; PCV1, porcine circovirus type 1; PCV2, porcine circovirus type 2; GoCV, goose circovirus; ICTV, International Committee on Taxonomy of Viruses. ⁎ Corresponding author. E-mail addresses: [email protected] (H. Wen), [email protected] (Y. Wu), [email protected] (C. Yang), [email protected] (X. Zhang), [email protected] (C. Lian), [email protected] (H. Chen), [email protected] (L. Han). 1 Tel.:+86 189 4606 6097; fax: +86 451 51997166. 0378-1119/$ – see front matter © 2014 Elsevier B.V. All rights reserved. http://dx.doi.org/10.1016/j.gene.2014.01.004
concluded that the average p-distance between genotypes 1 and 2 was 0.170, and subtype distance thresholds were 0.032 in DuCV-1 and 0.018 in DuCV-2, respectively (Zhang et al., 2013). However, there might be some concerns on the methodology application to define the genotype of DuCV. In PASC analysis, the cut-off values tested for the definition of genotypes is based on the histogram of pairwise distance among nucleotide sequences, also known as frequency distribution (Rogers and Harpending, 1992). Taking into account the concerns mentioned above, our authors conducted the PASC analyses of 54 capsid gene (ORF2, Fig. 1a) and genomic (Fig. 1b) sequences including all the sequences from Zhang et al. (2013). First, a similar p-distance/frequency histogram is obtained using between ORF2 and genomic DuCV sequences, and our results confirmed the existence of the two DuCV genotypes (1 and 2). Second, as shown in Figs. 1a and b, the cut-off values for DuCV genotyping in ORF2 and genomic sequence analyses, should be in the range from 0.043 to 0.105 and from 0.028 to 0.082, respectively. This implied that the value 0.170 for the average genotype distance of genome sequences mentioned in Zhang et al. (2013), was out of the range from 0.028 to 0.082, meanwhile the value 0.032 mentioned for subtype distance threshold in DuCV-1, was also inappropriate. We suggest that the distance genotype definition thresholds of DuCV ORF2 (Fig. 1c) and genomic (Fig. 1d) were 0.061 and 0.038, respectively. Zhang and co-authors' conclusion may attribute to a misunderstanding to the histogram for frequency distribution of pairwise distance. Further explanation would be clearer in the literature (Rogers and Harpending, 1992). The major interest of this letter wishes to induce constructive discussions for the use of the criteria for DuCV genotyping to allow the comparison of molecular epidemiology data worldwide.
208
Letter to the Editor
Fig. 1. (a) Linearized neighbour-joining tree based on the p-distance using 54 DuCV capsid gene (ORF2) sequences. (b) Linearized neighbour-joining tree based on the p-distance using 54 DuCV genomic sequences. (c) Plot: frequency distribution of pairwise distances between ORF2 DuCV. (d) Plot: frequency distribution of pairwise distances between genomic DuCV. The dashed lines indicate the theoretical thresholds of 0.061 and 0.038 respectively, proposed in the present study for the genotype definition of ORF2 and genomic sequences in DuCV. Two goose circovirus (GoCV) ORF2 sequences (for rooting purposes) (accession numbers AJ304456 and DQ192282) were used to construct a matrix of p-distance values.
Conflict of interest I state that there is no conflict of interest in the present study. 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. Grau-Roma, L., et al., 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.
Hattermann, K., Schmitt, C., Soike, D., Mankertz, A., 2003. Cloning and sequencing of duck circovirus (DuCV). Arch. Virol. 148, 2471–2480. 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. Munir, M., et al., 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., et al., 2008. PCV-2 genotype definition and nomenclature. Vet. Rec. 162, 867–868. Zhang, Z., et al., 2013. Identification, genotyping, and molecular evolution analysis of duck circovirus. Gene 529, 288–295.
