This form should be used for all taxonomic proposals. Please complete all those modules that are applicable (and then delete the unwanted sections). For guidance, see the notes written in blue and the separate document Help with completing a taxonomic proposal Please try to keep related proposals within a single document; you can copy the modules to create more than one genus within a new family, for example. MODULE 1: TITLE, AUTHORS, etc Code assigned: 2015.003a,bD (to be completed by ICTV officers) Short title: New species in the Kappatorquevirus (e.g. 6 new species in the genus Zetavirus) Modules attached 1 2 3 4 5 (modules 1 and 10 are required) 6 7 8 9 10 Author(s): Tuija Kekarainen Corresponding author with e-mail address: Tuija Kekarainen tuija.kekarainen@irta.cat List the ICTV study group(s) that have seen this proposal: A list of study groups and contacts is provided at http://www.ictvonline.org/subcommittees.asp. If in doubt, contact the appropriate subcommittee chair (fungal, invertebrate, plant, prokaryote or vertebrate viruses) Anelloviridae Study Group ICTV Study Group comments (if any) and response of the proposer: ICTV SG agreed on this proposal Date first submitted to ICTV: June 5, 2015 Date of this revision (if different to above): June 15, 2015 ICTV-EC comments and response of the proposer: Page 1 of 6
MODULE 2: NEW SPECIES creating and naming one or more new species. If more than one, they should be a group of related species belonging to the same genus. All new species must be placed in a higher taxon. This is usually a genus although it is also permissible for species to be unassigned within a subfamily or family. Wherever possible, provide sequence accession number(s) for one isolate of each new species proposed. Code 2015.003aD (assigned by ICTV officers) To create 1 new species within: Genus: Kappatorquevirus Subfamily: Family: Anelloviridae Order: Name of new species: Representative isolate: (only 1 per species please) Torque teno sus virus k2b 38E23 JQ406846 Fill in all that apply. If the higher taxon has yet to be created (in a later module, below) write (new) after its proposed name. If no genus is specified, enter unassigned in the genus box. GenBank sequence accession number(s) Reasons to justify the creation and assignment of the new species: Explain how the proposed species differ(s) from all existing species. o If species demarcation criteria (see module 3) have previously been defined for the genus, explain how the new species meet these criteria. o If criteria for demarcating species need to be defined (because there will now be more than one species in the genus), please state the proposed criteria. Further material in support of this proposal may be presented in the Appendix, Module 9 The current criterion demarcating species in the genus is: ORF1 nucleotide sequence divergence >35%. The isolate listed above meets this criterion. Page 2 of 6
MODULE 8: RENAME Use this module to change the name of one or more existing taxa (but note that stability of nomenclature is encouraged wherever possible). Insert extra lines in the table if needed.. Renaming one or more taxa Code 2015.003bD (assigned by ICTV officers) To rename the following taxon (or taxa): Current name Torque teno sus virus k2 Proposed name Torque teno sus virus Reasons to justify the renaming: Explain why the taxon (or taxa) should be renamed Until now there was only one species in the genus Kappatorquevirus named Torque teno sus virus k2. When a second species was described, the ICTV SG recommended using similar naming as used in the genus Iotatorquevirus, where the species are referred to with alphabets (a, b). To follow this recommendation, we propose a new name (which is already used in the published works): Torque teno sus virus. Also, see phylogenetic tree below. Page 3 of 6
MODULE 10: APPENDIX: supporting material additional material in support of this proposal References: Cornelissen-Keijsers Vivian, Jiménez-Melsió Alexandra, Sonnemans Denny, Cortey Martí, Segalés Joaquim, van den Born Erwin and Kekarainen Tuija Discovery of a novel Torque teno sus virus species: genetic characterization, epidemiological assessment, and disease association J Gen Virol. 2012; 93(Pt 12):2682-91. Annex: Include as much information as necessary to support the proposal, including diagrams comparing the old and new taxonomic orders. The use of Figures and Tables is strongly recommended but direct pasting of content from publications will require permission from the copyright holder together with appropriate acknowledgement as this proposal will be placed on a public web site. For phylogenetic analysis, try to provide a tree where branch length is related to genetic distance. The study describes a novel Torque teno sus virus (TTSuV) species, provisionally named Torque teno sus virus k2b (TTSuVk2b), originally found in commercial pig sera by applying the rolling circle amplification technique. Full-length sequences of TTSuVk2b were obtained, annotated and used in the phylogenetic analyses, which revealed that TTSuVk2b is a novel anellovirus species within the genus Kappatorquevirus of the family Anelloviridae. Quantitative PCR techniques were developed to determine total TTSuV DNA quantities in pig blood as well as the prevalence and viral DNA quantities. The phylogenetic analyses of the proposed TTSuVk2b nucleotide sequences [GenBank accession numbers: JQ406844 (TTSuVk2b-38E05), JQ406845 (TTSuVk2b-38E19) and JQ406846 (TTSuVk2b-38E23)] were performed using MEGA version 5 (Tamura et al., 2011), including TTSuV1 and TTSuV sequences obtained from GenBank (Cortey et al., 2011; Huang et al., 2010b). The alignments were gained using a CLUSTAL W multiple alignment tool with a gap creation penalty of 10 and a gap extension penalty of 5. Phylogenies were inferred from p-distance matrices using the neighbour-joining method (Saitou & Nei, 1987). Statistical significance of the branching was estimated using bootstrap with 0 replications and from this a consensus phylogenetic tree was built. Pairwise sequence comparison (PASC; http://www.ncbi.nlm.nih.gov/ sutils/pasc/) was performed using available anellovirus sequences from GenBank. The isolate listed above meets the species demarcation criteria used in the family Anelloviridae (cutoff values for sequence divergence: species > 35%, genera > 56%). Page 4 of 6
Genus Iotatorquevirus Genus Kappatorquevirus 58 ORF1_HM633239_TTSuV2 ORF1_GU570206_TTSuV2 ORF1_AY823991_TTSuV2 89 ORF1_GU570207_TTSuV2 ORF1_HM633240_TTSuV2 59 ORF1_GU570208_TTSuV2 ORF1_GU570209_TTSuV2 ORF1_GU570197_TTSuV2 ORF1_GU570204_TTSuV2 ORF1_GU570205_TTSuV2 ORF1_GU570203_TTSuV2 TTSuV2 TTSuV 76 ORF1_GU456385_TTSuV2 ORF1_GU188046_TTSuV2 ORF1_GU456386_TTSuV2 ORF1_JF694118_TTSuV2 ORF1_HQ204188_TTSuV2 ORF1_HM633241_TTSUv2 TTSuV ORF1_HM633236_TTSuV2 ORF1_HM633238_TTSuV2 ORF1_HM633237_TTSuV2 ORF1_38E05_TTSuV3 k2b ORF1_38E23_TTSuV3 k2b ORF1_38E19_TTSuV3 k2b TTSuV3 TTSuV k2b 82 ORF1_HM633258_TTSuV1 96 92 69 98 ORF1_GU456384_TTSuV1 ORF1_JF694117_TTSuV1 ORF1_GQ120664_TTSuV1 OEF1_AY823990_TTSuV1 ORF1_HM633257_TTSuV1 ORF1_GU188045_TTSuV1 TTSuV 1b ORF1_HM633252_TTSuV1 ORF1_HM633242_TTSuV1 ORF1_GU456383_TTSuV1 ORF1_AB076001_TTSuV1 ORF1_GU570202_TTSuV1 ORF1_GU570201_TTSuV1 ORF1_HM633256_TTSuV1 TTSuV1 TTSuV 1a 83 ORF1_JF694116_TTSuV1 ORF1_HM633251_TTSuV1 ORF1_GU570198_TTSuV1 ORF1_GU570200_TTSuV1 93 ORF1_GU570199_TTSuV1 40 50 60 70 Percentage identity 80 90 Figure 1.Neighbour-Joining phylogenetic tree based on the percentage identity of TTSuV ORF1 Page 5 of 6
sequences available in GenBank. Confidence bootstrap values higher than 50% are shown in nodes. Page 6 of 6