Taxonomy of Picornaviridae: Current Situation and Future Proposals Nick J. Knowles1, Tapani Hovi2, Timo Hyypiä3, Andrew M.Q. King4, A. Michael Lindberg5, Philip D. Minor6, Mark A. Pallansch7, Ann C. Palmenberg8, Tim Skern9, Glyn Stanway10, Teruo Yamashita11 and Roland Zell12 (ICTV Picornaviridae Study Group) 1) Institute for Animal Health, Pirbright, UK; 2) Enterovirus Laboratory, KTL, Finland; 3) Dept. of Virology, University of Turku, Finland; 4) ‘Sunfield’, Dawney Hill, Pirbright, Woking, Surrey, UK; 5) Dept. of Chemistry and Biomedical Sciences, Univ. of Kalmar, Sweden; 6) National Institute for Biological Standards and Control, South Mimms, UK; 7) Enterovirus Team, CDC, Atlanta, USA; 8) Dept. of Animal Health and Biomedical Science, University of Wisconsin, USA; 9) Max F. Perutz Laboratories, Medical University of Vienna, Vienna, Austria; 10) Dept. of Biological Sciences, University of Essex, UK; 11) Dept. of Microbiology, Aichi Prefectural Institute of Public Health, Aichi, Japan; 12) Klinikum der Friedrich-Schiller-Universitaet, Institut fuer Virologie und Antivirale Therapie, Jena, Germany. ABSTRACT The family Picornaviridae currently consists of 23 species in 9 genera (Enterovirus, Rhinovirus, Cardiovirus, Aphthovirus, Hepatovirus, Parechovirus, Erbovirus, Kobuvirus and Teschovirus). Three new taxonomic proposals have been approved by the ICTV Executive Committee and await ratification by the ICTV membership. They are: i) to combine the enterovirus and rhinovirus genera, keeping the existing name Enterovirus; ii) to combine the species’ Poliovirus and Human enterovirus C, retaining the latter name; and iii) to assign Human enterovirus C as the type species of the enterovirus genus. Two further proposals are in preparation: i) to create a new genus, Sapelovirus, consisting of three species, Porcine enterovirus A, Simian virus 2 and duck picornavirus TW90A (each to be renamed); and ii) to create a new unassigned species, Seneca Valley virus. Overall this will leave the number of genera unchanged, but result in the addition of two species. A number of issues are also being considered by the Study Group: i) the genus placement of Seneca Valley virus; ii) the position of avian encephalomyelitis virus as a tentative member of the genus Hepatovirus; iii) the proposal to place duck hepatitis virus type 1 (for which a number of genome sequences have recently been reported) in a new genus; iv) the proposal that bovine rhinovirus type 2 is classified as a new species in the genus Aphthovirus; and v) the proposal to divide bovine enteroviruses into two species. The Picornaviridae Study Group has a new website: www.picornastudygroup.com where the latest classification and proposals may be viewed. Polioviruses are to be incorporated into the species Human Enterovirus C (which now becomes the Enterovirus type species) It has been realised for many years that the sequences of members of the Human enterovirus C and Poliovirus species of the genus Enterovirus are very similar, particularly in the region encoding the non-structural proteins (Hughes et al., 1987; Hughes et al., 1989; Supanaranond et al., 1992). Recent complete nucleotide sequence analysis of representatives of all known serotypes contained within Human enterovirus C has definitively demonstrated this relationship (Brown et al., 2003; Newcombe et al., 2003). The species are not monophyletic in either of the regions used for Picornaviridae taxonomy, P1 and 2C+3CD, and in the 2C+3CD region amino acid identity is generally in excess of 90%. It has also been suggested in a number of studies that homologous recombination may take place between polioviruses and members of the Human enterovirus C species (e.g. Liu et al., 2003; Arita et al., 2005), which is one measure taken into account in the definition of picornavirus species. Although polioviruses have a distinct and specific receptor usage from other Human enterovirus C members, differences in receptor usage are also evident within the species Human enterovirus B and so this characteristic is currently not being considered equitably in Enterovirus taxonomy. These factors make the current division into two species untenable and the purpose of this proposal is to rationalize this situation by combining the Human enterovirus C and Poliovirus species, creating a single species. New genus to be proposed: Sapelovirus Porcine enterovirus A to be renamed Porcine Sapelovirus Simian virus 2 and related viruses to be named Simian sapelovirus A Duck picornavirus TW90A to be named Avian sapelovirus Complete genome sequences of PEV-8 (Krumbholz et al., 2002), SV2 (Oberste et al., 2003) and DPV (Tseng & Tsai, unpublished) show these viruses to be related to, but distinguishable from, enteroviruses in the conserved genome regions (P1, 2C, 3C & 3D), however, they have a number of distinct genome features (hepatitis C-like IRES, a leader polypeptide, highly divergent 2A, 2B and 3A regions) which we consider warrants the creation of a new genus. Proposals awaiting ratification by the ICTV membership. Proposals agreed by the Picornaviridae Study Group. Proposals to be considered by the Picornaviridae Study Group. Teschovirus DPV TW90A Porcine enterovirus A (AY563023) (AF406813) SV2 2383 Human enterovirus C (D00538) (AY064708) Poliovirus (J02281) Rhinovirus genus incorporated into the genus Enterovirus Historically, the human pathogens enteroviruses and rhinoviruses have been Human enterovirus B (X67706) classified into separate genera Human rhinovirus B (K02121) (Enterovirus and Rhinovirus respectively), largely on the basis of classical criteria such as pathogenicity and the acid Human rhinovirus A (X02316) stability of enteroviruses/ lability of rhinoviruses. Sequence analysis reveals that there are no significant differences in genome organisation or particle structure Simian enterovirus A (AF201894) (Kitamura et al., 1981; Stanway et al., 1984; Laine et al., 2005). In both the Human enterovirus A (U05876) standard regions used for picornavirus taxonomy (P1 and 2C+3CD) species representing these genera are much more Human enterovirus D (D00820) closely related that those representing other distinct Picornaviridae genera. Also, Porcine enterovirus B (AF363453) in the P1 region, the genera are not BEV-2 (DQ092770) monophyletic. Furthermore, it has recently been found that in sequence terms human BEV-1 (D00214) rhinovirus 87 is in fact an acid labile Bovine enterovirus member of the species Human enterovirus D, suggesting that acid stability/lability is not always a reliable classification criterion (Blomqvist et al., 2002; Savolainen et al., 2002). Thus, it is 0.2 difficult to justify the current enterovirus/rhinovirus division and it is Fig. 1. Neighbor-joining tree based proposed to merge these genera, giving a on comparisons of the P1 capsid single genus, Enterovirus. Your opinions are important to us: If you have any views on the classification/taxonomy of the Picornaviridae please contact one of the Study Group members. Porcine teschovirus (AJ011380) Cardiovirus Encephalomyocarditis virus (M81861) Theilovirus (M20562) Equine rhinitis B virus (X96871) Aphthovirus Foot-and-mouth disease virus (X00871) Bovine rhinovirus 2 New aphthovirus species Bovine rhinovirus 2 Aichi virus (AB040749) Kobuvirus Parechovirus Ljungan virus (AF327920) Erbovirus Equine rhinitis A virus (X96870) Bovine kobuvirus (AB084788) It has recently been shown that the serotypes BEV-1 and BEV-2 are two distinct genetic clusters between which recombination is rare (possibly only occurring within the untranslated regions) and that each group contains a number of (sero)types. It has therefore been decided to submit a proposal to the ICTV Executive Committee to split the species into two. Although SVV is most closely related to the cardioviruses in the P1, 2C, 3C & 3D regions of the genome, it is distinct and differs considerably in the 5’ UTR (e.g. hepatitis C-like IRES), L, 2B, 3A & 3’ UTR. 2A is a short aphthovirus-like peptide (Knowles & Hallenbeck, 2005). Seneca Valley virus (DQ641257) Enterovirus Proposal to split bovine enteroviruses into two species, Bovine enterovirus A and Bovine enterovirus B (Zell et al., 2006). New species to be proposed: Seneca Valley virus But should it also be classified in a new genus? BRV-2 is more closely related to FMDV than is ERAV and is therefore proposed as a candidate new species in the genus Aphthovirus (Knowles, 2005; Hollister et al., 2006). Hepatovirus Hepatitis A virus (M14707) Avian encephalomyelits-like viruses (AJ225173) Human parechovirus (L02971) Duck hepatitis virus 1 (DQ249300) However, its classification as a tentative member genus Hepatovirus will be discussed by the Group. 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