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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 (to be completed by ICTV Code assigned: 2011.008aP officers) Short title: Create one new species, Cocksfoot mild mosaic virus, in the genus Panicovirus, family Tombusviridae (e.g. 6 new species in the genus Zetavirus) Modules attached 1 2 3 4 5 (modules 1 and 9 are required) 6 7 8 9 Author(s) with e-mail address(es) of the proposer: D’Ann Rochon ([email protected]) on behalf of Tombusviridae Study Group 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 Tombusviridae SG chair (fungal, invertebrate, plant, prokaryote or vertebrate viruses) ICTV-EC or Study Group comments and response of the proposer: Date first submitted to ICTV: 4 August 2011 Date of this revision (if different to above): Page 1 of 6 MODULE 2: NEW SPECIES Code 2011.008aP (assigned by ICTV officers) To create 1 new species within: Genus: Panicovirus Subfamily: Family: Tombusviridae Order: And name the new species: GenBank sequence accession number(s) of reference isolate: Cocksfoot mild mosaic virus EU081018 = NC_011108 Reasons to justify the creation and assignment of the new species: Cocksfoot mild mosaic virus (CMMV) is a virus of grasses known for many years (Huth & Paul, 1972). More recent data, including a complete genome sequence (Ziegler et al., 2009) has shown that it is most closely related to Panicum mosaic virus (PMV; the type – and currently the only- member of the genus Panicovirus, family Tombusviridae). This is demonstrated by its genome structure (Fig. 1), phylogenetic analyses (Figs. 2-4), and sequence identity in the polymerase and coat proteins (Table 1). The two viruses are serologically distinct and share only 54% amino acid sequence identity in the polymerase and 35% identity in the coat protein (Table 1). As a monotypic genus, there are no formal species demarcation criteria but in line with other genera in the family we suggest that less than 70% amino acid sequence identity in the polymerase and less than 40% in the coat protein would justify a new species. MODULE 9: APPENDIX: supporting material References: Huth & Paul (1972). Cocksfoot mild mosaic virus. AAB Descriptions of Plant Viruses, no 107. Ziegler et al., (2009) Comparative sequence analysis and serological and infectivity studies indicate that cocksfoot mild mosaic virus is a member of the genus Panicovirus. Arch. Virol 154:1545-1549 Fig. 1 MP1 CP R/T p8K p26K 5’ 3’ PMV p48K p112K p6.6K p15K Polymerase MP2 R/T p8K p26K 5’ 3’ p41K p106 p6.8K p15K CMMV (see Zeigler et al., 2009) Figure 1. Comparison of the genome structure of CMMV with that of panicum mosaic virus (PMV) Page 2 of 6 0.1 Cytochrome-C 1000 SYMMV-YP_002333476* 687 CPMoV-NP_619521 MNSV-NP_041226 1000 PSNV-NP_862835-2 9811000 JINRV-NP_038453 TCV-NP_620720-2 991 HCRSV-NP_619671 1000 NLVCV-YP_001039884* 792 AFBV-YP_459959 Carmovirus CMoV-ACT36594* 880 568 444 SgCV-NP_044382 976 417 CarMV-P 04518 725 PFBV-NP_945123 PCRPV-YP_052925* 1000 1000 PLPV-YP_238475* MCMV-NP_619718 Machlomovirus 1000 CMMV-YP_002117834* 1000 PMV-NP_068342 Panicovirus GaMV-NP_044732 1000 FNSV-ACW84407* TNV-A-P22958 837 469 1000 OLV-1-AAZ43259 Necrovirus 866 OMMV-YP_224015 1000 SNMV-ABD34316* CLSV-ABV30916 1000 1000 PoLV-NP_051030 MWLMV-YP_001285474Aureusvirus 1000 JCSMV-NP_945128 1000 TNV-D-P27209-2 1000 1000 BBSV-NP_758810-3Necrovirus LWSV-NP_044740 702 740 MNeSV-YP_459920* CBLV-NP_835253 1000 1000 CIRV-NP_612580 984 PNSV-NP_945114 1000 LNV-YP_588430* 909 PeLV-NP_835239 Tombusvirus 729 1000 CyRSV-P174593 CNV-P 15187 523 817 AMCV-NP_039808 1000 GALV-YP_002308429 991 968TBSV-P 15962 OCSV-NP_619751Avenavirus CtMoV-YP_002302259 1000 PEMV-2-NP_620846 960 BYDV-P AV-CAA30498 980 CRSV-AAA20212 1000 RCNMV-P22956-2 Dianthovirus 1000 SCNMV-NP_620674-2 BVDV-1-BAC55962 HCV-ADC54804 . Figure 2. Phylogenetic (distance) analysis of the polymerase of Tombusviridae members showing the position of CMMV (highlighted in yellow) in the same lineage as PMV. Sequences were aligned using ClustalX 2.1 and trees were generated with the Neighbor Joining algorithm using 1000 bootstrap replicates. Page 3 of 6 0.1 RCNMV-NP_620546 CMMV-YP_002117836 971 PMVp8-NP_068345 Panicovirus 1000 PSNV-NP_862837 MNSV-NP_041228 JINRV-NP_038456 907 CCFV-NP_041885 TCV-NP_620722 59 125 656 HCRSV-NP_619674 NLVCV-YP_001039885 Carmovirus 168 P FBV--ABB79926- 225 785 AFBV-YP_459962 133 41 426 SgCV-NP_044386 303 CarMV-P11794 PCRPV-YP_052927 989 PLPV-YP_238478.1 CMoV-ACT36596 341 LWSV-NP_044742 74 1000 TNV-D-P27211.2 Necrovirus 918 BBSV-NP_758813.2 GaMV-NP_044734 1000 FNSV-ACW84409 OLV-1-AAZ43262 855 Necrovirus 1000 138 TNV-A-NP_056826 MCMV-NP_619721 Machlomovirus 200 CPMoV-NP_613269 1000 SYMMV-YP_002333477 Carmovirus 0.1 RCNM V -NP_620546 CM oV -ACT36597 385 * HCRS V-ABD48711 224 CCFV -NP_041886 988 735 TCV-AAP78488 NLV CV-YP_001039886 286 PFBV -ABB79927 Carmovirus 402 485 AFBV -YP_459963 587 SgCV -NP_044387 669 CarM V -CAB38330 615 SYM M V -YP_002333478 1000 CPM oV -NP_613270 * PLPV -ACJ38437 JINRV -NP_038457 542 666 PS NV -NP_862838- 975 530 M NS V -NP_041230.1 * GaM V -NP_044735 899 FNS V -ACW 84410 987 OLV -1-NP_043910 592 1000 TNV-A-NP_056827 BBS V -NP_758814.2 Necrovirus 998 LW S V -NP_044743 785 TNV-D-P27212 CM M V -YP_002117837 Panicovirus 1000 PM V -NP_068344 Figure 3. Phylogenetic (distance) analysis of MP1 (top) and MP2 (bottom) of Tombusviridae members showing the position of CMMV (highlighted in yellow) in the same lineage as PMV. Sequences were aligned using ClustalX 2.1 and trees were generated with the Neighbor Joining algorithm using 1000 bootstrap replicates. Page 4 of 6 0.05 HEV-AAA45727 367 NLV CV -Y P_001039887* 648 CarM V-CAA26728 PFBV -NP_945127 362 820 CM oV-ACT36598 660 S gCV -NP_044388 920 AFM V-CAJ18242 PCRPV -Y P_052929* PLPV -Y P_238481* 912 1000 Carmovirus ElLV -A A K74061* 899 1000 PRSV-AAK74063 HCRS V -NP_619676 986 518 J INRV -NP_038458 980 T CV -NP_620723 1000 CCFV-NP_041887 CPM o V -NP_613271 988 1000 SYM M V -ACK77413* OCSV -NP_619753 Avenavirus PS NV -NP_862839 Carmovirus 671 392 FNSV-ACW 84411* M NSV-NP_041231 Carmovirus 927 CLSV-ABV30917 Aureusvirus 636 221 CRS V -NP_613255 1000 S CNM V -NP_620675 Dianthovirus 1000 RCNM V -NP_620526 1000 HRV-AAR26609 996 948 CNV -NP_040955 S NM V -A BD34313* + 974 JCSM V-NP_945130 + 999 CBLV -NP_835255 M W LM V-YP_001285476 693 + 1000 GaM V -NP_044736 SW BV-AAT00608 644 520 Cy RSV-P17456 857 Tombusvirus 908 Po LV -NP_051032 1000 + + 883 PNS V -NP_945116 GALV-AAT00610.2 Aureusvirus+ 1000 LFDV-A A T 00604 1000 NRV-AAT 00609 CIRV -NP_612582.2 784 M PV-AAN28378 962 1000 LNV -A BF56559 996 EM CV-AAT00612 992PeLV -NP_835241 925 PLCV -A A B26100 AM CV-P14836 988 1000 PAM V-AAT00603 1000 T BS V -NP_062899 SBM V-P03607.2 LW S V -NP_044744 988 M NeS V -Y P_459922* 996 BBSV -NP_758815.2 555 Necrovirus 889 OLV -1-NP_043911 T NV -D-P27210 490 986 T NV -A-NP_056828 M CM V-NP_619722 Machlomovirus 992 CM M V-YP_002117838* 1000 PM V -NP_068346 Panicovirus Figure 4. Phylogenetic (distance) analysis of the coat protein of Tombusviridae members showing the position of CMMV (highlighted in yellow) in the same lineage as PMV. Sequences were aligned using ClustalX 2.1 and trees were generated with the Neighbor Joining algorithm using 1000 bootstrap replicates. Page 5 of 6 Table 1. Percent amino acid sequence identity between proteins encoded by CMMV and those encoded by PMV and other Tombusviridae members. % Amino acid sequence identity* between CMMV and: PMV Other Tombusviridae members Pre-readthrough of 34 5-27 polymerase Full polymerase 54 22-43 Coat protein 35 5-23 p8 30 8-24 p6.8K 52 5-21 p15 30 Not applicable *Percent identity was determined using Clustal W2. Page 6 of 6 .
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  • Preliminary Analysis of Crystals of Panicum Mosaic Virus

    Preliminary Analysis of Crystals of Panicum Mosaic Virus

    research papers Acta Crystallographica Section D Biological Preliminary analysis of crystals of panicum mosaic Crystallography virus (PMV) by X-ray diffraction and atomic force ISSN 0907-4449 microscopy Debora L. Makino, Steven B. Panicum mosaic virus (PMV), a spherical virus of diameter Received 20 September 2004 Larson and Alexander about 300 AÊ , has been crystallized in a form suitable for high- Accepted 24 November 2004 McPherson* resolution structural analysis. The crystals were grown from 15% PEG 400 at room temperature and could be ¯ash-frozen directly from their mother liquor. The crystals diffracted to University of California at Irvine, Department of beyond 2.7 AÊ resolution. A data set was collected at 100 K to Molecular Biology and Biochemistry, Ê J. Appl. Cryst. 560 Steinhaus Hall, Irvine, CA 92697-3900, an effective resolution of 3.2 A [Weiss (2001), USA 34, 130±135]. The crystals belonged to space group P21, with unit-cell parameters a = 411.7, b = 403.9, c = 412.5 AÊ , = 89.7. Self-rotation functions and molecular replacement with Correspondence e-mail: [email protected] tobacco necrosis virus as the probe model yielded tentative positions and orientations for the two entire virus particles comprising the asymmetric unit and implied a pseudo-face- centered cubic packing arrangement. Investigation of lightly glutaraldehyde-®xed crystals in water using atomic force microscopy con®rms the packing arrangement given by the molecular-replacement result. The images also show that contaminating virions of the satellite virus to PMV, known as satellite panicum mosaic virus (SPMV), can be incorporated into the PMV crystals by insertion into the interstices between PMV virions in the lattice.