http://talk.ictvonline.org/default.aspxICTV Taxonomy, taxonomic proposals, proposal templates, and general ICTV business7.x Productionhttp://talk.ictvonline.org/files/proposals/taxonomy_proposals_prokaryote1/m/bact01/4545.aspxWed, 19 Jun 2013 04:52:00 GMT46ba6630-6a75-403c-a746-b2f48ba04f29:0df039c7-6392-4bca-8c38-191229f131afamqking create two genera ( Cp220likevirus and Cp8unalikevirus ) within a new subfamily ( Eucampyvirinae ) in the family Myoviridae http://talk.ictvonline.org/files/proposals/taxonomy_proposals_prokaryote1/m/bact01/4544.aspxWed, 19 Jun 2013 04:33:00 GMT46ba6630-6a75-403c-a746-b2f48ba04f29:b6d2174f-7548-4e68-aeed-3fd0ec7278b8amqking Create the family Spiraviridae, comprising the new genus Spiravirus and one new species. http://talk.ictvonline.org/files/proposals/taxonomy_proposals_fungal1/m/fung01/4543.aspxWed, 19 Jun 2013 02:17:00 GMT46ba6630-6a75-403c-a746-b2f48ba04f29:6dbc8955-111c-4875-aa36-01584b25042camqking Abolish the families Metaviridae and Pseudoviridae and associated genera and species from ICTV data bases http://talk.ictvonline.org/files/proposals/taxonomy_proposals_plant1/m/plant01/4542.aspxTue, 18 Jun 2013 15:42:00 GMT46ba6630-6a75-403c-a746-b2f48ba04f29:d36de553-cef7-4c9c-82b2-2b86fa56a680amqking Move the Umbravirus genus from “unassigned genus” to Tombusviridae http://talk.ictvonline.org/files/proposals/taxonomy_proposals_plant1/m/plant01/4541.aspxTue, 18 Jun 2013 15:27:00 GMT46ba6630-6a75-403c-a746-b2f48ba04f29:a78711a9-5b8f-4a9b-82c7-2aca012f3df1amqking create new species in the genus Anulavirus , family Bromoviridae http://talk.ictvonline.org/files/proposals/taxonomy_proposals_plant1/m/plant01/4540.aspxTue, 18 Jun 2013 15:21:00 GMT46ba6630-6a75-403c-a746-b2f48ba04f29:69ba5bd0-fdc2-4ba5-8561-7b5db2a77fe4amqking in the genus Endornavirus, create new species and change the name of species Phaseolus vulgaris endornavirus to Phaseolus vulgaris endornavirus 1 http://talk.ictvonline.org/files/proposals/taxonomy_proposals_plant1/m/plant01/4539.aspxTue, 18 Jun 2013 15:09:00 GMT46ba6630-6a75-403c-a746-b2f48ba04f29:485c11f3-091c-4491-9d85-d860d080478camqking Create unassigned species in the family Potyviridae http://talk.ictvonline.org/files/proposals/taxonomy_proposals_plant1/m/plant01/4538.aspxTue, 18 Jun 2013 12:16:00 GMT46ba6630-6a75-403c-a746-b2f48ba04f29:3bf2593b-b381-49df-ba22-487b8a03ee1eamqking Change the name of species Pea enation mosaic virus-1 ( g enus Enamovirus , family Luteoviridae ) to Pea enation mosaic virus 1 and of Pea enation mosaic virus-2 (unassigned genus Umbravirus ) to Pea enation mosaic virus 2 http://talk.ictvonline.org/files/proposals/taxonomy_proposals_plant1/m/plant01/4537.aspxTue, 18 Jun 2013 11:12:00 GMT46ba6630-6a75-403c-a746-b2f48ba04f29:72dd4d79-4a4a-4bba-a1b1-69d0818f7de7amqking create the family Amalgamaviridae , comprising one new genus, Amalgamavirus , and four new species http://talk.ictvonline.org/files/proposals/taxonomy_proposals_plant1/m/plant01/4536.aspxTue, 18 Jun 2013 06:36:00 GMT46ba6630-6a75-403c-a746-b2f48ba04f29:01eb1d88-159e-4f46-ba17-474a4e7491d0amqking create one species in the genus Cheravirus , family Secoviridae , order Picornavirales http://talk.ictvonline.org/files/proposals/taxonomy_proposals_prokaryote1/m/bact01/4535.aspxTue, 18 Jun 2013 03:04:00 GMT46ba6630-6a75-403c-a746-b2f48ba04f29:3dee5dbf-f655-4a85-a25f-dd9d8448da0camqking Create the family Turriviridae, comprising the new genus, Turrivirus, and two new species http://talk.ictvonline.org/files/proposals/taxonomy_proposals_prokaryote1/m/bact01/4534.aspxMon, 17 Jun 2013 15:52:00 GMT46ba6630-6a75-403c-a746-b2f48ba04f29:bcbe68f1-0b05-4708-9418-9214a589d290amqking Create the family Halosphaeroviridae, comprising two new genera and 4 new species http://talk.ictvonline.org/files/proposals/taxonomy_proposals_plant1/m/plant01/4531.aspxSun, 16 Jun 2013 04:40:00 GMT46ba6630-6a75-403c-a746-b2f48ba04f29:8f498363-6b9c-4cbf-ae37-5092a362bad4amqking create new species in the genus Mandarivirus , family Alphaflexiviridae , order Tymovirales http://talk.ictvonline.org/files/proposals/taxonomy_proposals_plant1/m/plant01/4530.aspxSun, 16 Jun 2013 04:37:00 GMT46ba6630-6a75-403c-a746-b2f48ba04f29:6ef9d57e-a5fa-42fc-95b9-6af7b6d24526amqking create 4 species in the family Betaflexiviridae, order Tymovirlaes http://talk.ictvonline.org/files/proposals/taxonomy_proposals_vertebrate1/m/vert01/4529.aspxSun, 16 Jun 2013 04:20:00 GMT46ba6630-6a75-403c-a746-b2f48ba04f29:eb603714-50d5-4ec9-b1ef-859f8a808ab0amqking Create a family named Nyamiviridae , with 1 genus and 3 species, in the order Mononegavirales http://talk.ictvonline.org/d3713454fb/w/sg_flavi/default.aspxFri, 14 Jun 2013 13:29:00 GMT46ba6630-6a75-403c-a746-b2f48ba04f29:5295d5c7-c9a9-49be-a2a9-d5c4a42faf7cUnknownFlaviviridae Study Group wikihttp://talk.ictvonline.org/ictv_wikis/w/sg_flavi/17.table-1-confirmed-hcv-genotypessubtypes.aspxFri, 14 Jun 2013 08:18:00 GMT46ba6630-6a75-403c-a746-b2f48ba04f29:8356d836-4e34-4911-91a6-023b34e3f289Peter Simmonds Genotype 1 Locus/Isolate(s) 2 Accession number(s) Reference(s) Genotype 1 1a HPCPLYPRE, HPCCGAA M62321, M67463 (67, 68) 1b HPCJCG, HPCHUMR D90208, M58335 (69, 70) 1c HPCCGS AY051292, D14853, AY051292 (71), Guntaka et al., 2001 1e 3 148636 KC248194 Li et al., 2013 1g 1804 AM910652 Bracho et al., 2008 1h EBW9, EBW443 KC248198,9 Li et al., 2013 1l EBW424, 136142 KC248193,7 Li et al., 2013 Genotype 2 2a HPCPOLP, JFH-1 D00944, AB047639 (72, 73) 2b HPCJ8G, JPUT971017 D10988, AB030907 (9, 74) 2c BEBE1 D50409 (75) 2d QC259 JF735114 Li et al., 2012 2e QC64 JF735120 Li et al., 2012 2i D54 DQ155561 Noppornpanth et al., 2006 2j C1799, QC232 HM777358 JF735113 Sulbaran et al., 2010, Li et al., 2012 2k AB031663 AB031663 (58) 2m QC178, QC104 AY754621, JX227967 Li et al., 2012,Newman et al.,2012 2q 852, 963 FN666428,9 Martro et al., 2011 2r QC283 EF116059 Li et al., 2012 Genotype 3 3a HPCEGS, HPCK3A D17763, D28917 (76, 77) 3b HPCFG D49374 (78) 3g BID-G1243, QC260 JX227954, EF116087 Newman et al.,2012 Lu et al., 2013 3h QC29 AF279120 Lu et al., 2013 3i IND-HCV, BID-G1244 FJ407092, JX227955 Arankalle & Gupte(2008, unpublished), Newman et al.,2012 3k HPCJK049E1, QC105 D63821, EF116069 (59), Lu et al,. 2013 Genotype 4 4a HCV4APOLY Y11604 (79) 4b QC264 FJ462435 Li et al., 2009a 4c QC381 FJ462436 Li et al., 2009a 4d 03-18, QC382 DQ418786, FJ462437 Timm et al., 2008, Li et al., 2009a 4f IFBT88, PS6 EF589161, EU392175 Hmaied et al., 2007, Kuntzen et al., 2008 4g QC193 FJ462432 Li et al., 2009a 4k PS3, QC383 EU392173, FJ462438 Kuntzen et al., 2008, Li et al., 2009a 4l QC274 FJ839870 Li et al., 2009a 4m QC249 FJ462433 Li et al., 2009a 4n QC97 FJ462441 Li et al., 2009a 4o QC93 FJ462440 Li et al., 2009a 4p QC139 FJ462431 Li et al., 2009a 4q QC262 FJ462434 Li et al., 2009a 4r QC384 FJ462439 Li et al., 2009a 4t QC155 FJ839869 Li et al., 2009a 4v CYHCV073, BID-G1248 HQ537009, JX227959 Demetriou & Kostrikis 2011, Newman et al.,2012 4w 4 P212, P245 FJ025855, 6 Koletzki et al., 2009 Genotype 5 5a EUH1480, SA13 5 Y13184, AF064490 (80, 81) Genotype 6 6a HCV12083, 6a33 Y12083, AY859526 (82), Zhou et al., 2010 6b Th580 D84262 (83) 6c Th846 EF424629 Lu et al., 2007b 6d VN235 D84263 (83) 6e GX004 DQ314805 Li et al., 2006 6f C-0044 DQ835760 Lu et al., 2007a 6g HPCJK046E2 D63822 (59) 6h VN004 D84265 (83) 6i Th-602 DQ835770 Lu et al., 2007a 6j Th553 DQ835769 Lu et al., 2007a 6k VN405 D84264 (83) 6l 537796 EF424628 Lu et al., 2007b 6m B4/92 DQ835767 Lu et al., 2007a 6n D86/93, km42 DQ835768, DQ278894 Lu et al., 2007a, Lu et al., 2005 6o QC227 EF424627 Lu et al., 2007b 6p QC216 EF424626 Lu et al., 2007b 6q QC99 EF424625 Lu et al., 2007b 6r QC245 EU408328 Li et al., 2009b 6s QC66 EU408329 Li et al., 2009b 6t VT21, D49 EF632071, EU246939 Lu et al., 2008, Noppornpanth et al., 2008 6u D83 EU246940 Noppornpanth, et al., 2008] 6v NK46, KMN02 EU158186, EU798760 Lu et al., 2008, Wang et al., 2009 6w GZ52557, D140 DQ278892, EU643834 Lu et al., 200 6, Lee et al., 2010 6xa 6 DH012, DH028 EU408330,2 Xia et al., 2008 1 Consensus proposed genotype/subtype names. Where multiple sequences of a HCV genotype are available, two sequences have been listed, prioritised by (a) publication date or (b) submission date when unpublished. 2 Locus (or isolate name if locus is the same as the accession number). 3 Additions and changes from assignments proposed in Simmonds et al.,(2005) shown in red. 4 Previously described as 4b, Koletzki et al., 2009 and in Nakano et al., 2012 5 Sequence obtained from acute phase plasma of a chimpanzee experimentally infected with (human-derived) isolate SA13. 6 Previously described as 6u Xia et al., 2008 http://talk.ictvonline.org/ictv_wikis/w/sg_flavi/default.aspxFri, 14 Jun 2013 08:13:00 GMT46ba6630-6a75-403c-a746-b2f48ba04f29:24a9c0a6-9834-4cad-8269-d7fefc63d875Abe Lincoln A web resource to manage the classification and genotype and subtype assignments of hepatitis C virus Donald B. Smith, Scott Muerhoff, Charles Rice, Jack Stapelton, Jens Bukh,  Brian Foley, Carla Kuiken, Peter Simmonds This webpage maintains a regularly updated list of current HCV genotype and subtype assignments. This maintained resource is designed to assist researchers investigating the diversity of HCV in designating appropriate assignments for new sequences and maintaining consistency in both the names designated and ensuring that guidelines for their assignment (originally proposed in the published consensus paper (3) and updated recently (4)) are appropriately followed. We urge all researchers describing new variants to contact Donald Smith (donald.smith.mail@gmail.com) or Peter Simmonds ( Peter.Simmonds@ed.ac.uk ) before publishing assignments so that naming conflicts can be avoided and appropriate classifications can be made. All sequence data provided will be treated as strictly confidential. Rules for genotype assignments: In order to be considered a new genotype or subtype, the complete genome sequence should: a)     Form a distinct phylogenetic group from previously described sequences b)     Should be represented by at least epidemiologically unlinked three isolates c)     Should not represent a recombinant between other genotypes or subtypes.   This agreement on nomenclature has mirrored by the establishment of curated databases that organised HCV sequences as they became available (Los Alamos HCV Sequence Database, (2) and euHCVdb (1)) although neither now actively maintained. The current web resource is designed to maintain this function for HCV researchers. Tables 1-3 were based on a total of 965 complete genome sequences downloaded from Genbank on 22 nd May 2013 and Los Alamos. These incorporate a number of additional assignments to those presented previously (3) reflecting the increase from 238 complete genome sequences in 2005 to more than 1300 at present. This has increased the number of confirmed genotypes from 18 in 2005 to 66 listed in Table 1. Reference List   1.     Combet, C., F. Penin, C. Geourjon, and G. Deleage . 2004. HCVDB : Hepatitis C Virus Sequences Database. Appl. Bioinformatics. 3 :237-240 2.     Kuiken, C., K. Yusim, L. Boykin, and R. Richardson . 2005. The Los Alamos hepatitis C sequence database. Bioinformatics. 21 :379-384 3.     Simmonds, P., J. Bukh, C. Combet, G. Deleage, N. Enomoto, S. Feinstone, P. Halfon, G. Inchauspe, C. Kuiken, G. Maertens, M. Mizokami, D. G. Murphy, H. Okamoto, J. M. Pawlotsky, F. Penin, E. Sablon, I. Shin, L. J. Stuyver, H. J. Thiel, S. Viazov, A. J. Weiner, and A. Widell . 2005. Consensus proposals for a unified system of nomenclature of hepatitis C virus genotypes. Hepatology 42 :962-973 4.     Smith, D. B., S. Muerhoff, C. L. Rice, J. T. Stapleton, J. Bukh, B. Foley, C. Kuiken, and P. Simmonds . 2013. A web resource to manage the classification and genotype / subtype assignments of hepatitis C virus. (in preparation) http://talk.ictvonline.org/ictv_wikis/w/sg_flavi/19.table-3-recombinant-hcv-genomes.aspxThu, 13 Jun 2013 16:12:00 GMT46ba6630-6a75-403c-a746-b2f48ba04f29:c1d7f04d-9f36-4d2c-80e8-6006a632d742Elliot Lefkowitz Designation Breakpoint Accession Isolates Reference 2k/1b 3175 AY587845 27 Kalinina et al., 2002 6p/2i 3405-3464 DQ155560 1 Noppornpanth et al., 2006 2b/1b 3466 [3399] DQ364460 1 Kageyama et al., 2006 2/5 3420-3440 AM408911 1 Legrand-Abravanel 2007 2a/1a ? (partial sequence) - 1 Lee et al., 2010 3a/1b ? (partial sequence) - 1 Lee et al., 2010 2b/6w 3429 EU643835 1 Lee et al., 2010 1a/1b 8321 (partial sequence) - 1 Colina et al., 2004 2b/1b 3443 AB622121 1 Yokoyama et al., 2010 2b/1a 3400-3411 JF779679 1 Bhattacharya et al., 2011 2b/1b ~3300 (?ref seq) AB677530 2 Hoshino et al., 2012 http://talk.ictvonline.org/members/admin/activities/default.aspx?ActivityMessageID=feea73f3-989b-407c-beb0-8ea16f2586c4Thu, 13 Jun 2013 15:56:00 GMT46ba6630-6a75-403c-a746-b2f48ba04f29:feea73f3-989b-407c-beb0-8ea16f2586c4adminMessage from Elliot in Taxonomy Proposals - General