Typing tool
|
Complete norovirus genomes
MF140648 | GII.7 | ||
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GII.P7 |
ORF1: 1..5084 ORF2: 5065..6687 ORF3: 6687..7460LOCUS MF140648 7525 bp RNA linear VRL 24-OCT-2017 DEFINITION Norovirus GII strain Norovirus/GII/Hu/NL/2013/GII.P7-GII.7/Rotterdam/E1300276_p12_d76 ORF1 gene, partial cds; and ORF2 and ORF3 genes, complete cds. ACCESSION MF140648 VERSION MF140648.1 KEYWORDS . SOURCE Norovirus GII ORGANISM Norovirus GII Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes; Picornavirales; Caliciviridae; Norovirus; Norwalk virus. REFERENCE 1 (bases 1 to 7525) AUTHORS van Beek,J., de Graaf,M., Smits,S.L., Schapendonk,C.M.E., Verjans,G.M.G.M., Vennema,H., van der Eijk,A.A., Phan,M.V.T., Cotten,M.L. and Koopmans,M.P.G. TITLE Whole genome next generation sequencing to study within-host evolution of chronic norovirus infection among immunocompromised patients JOURNAL J. Infect. Dis. (2017) In press PUBMED 29029115 REMARK Publication Status: Available-Online prior to print REFERENCE 2 (bases 1 to 7525) AUTHORS van Beek,J., de Graaf,M., Smits,S.L., Schapendonk,C.M.E., Verjans,G.M., Vennema,H., van der Eijk,A.A., Phan,M.V.T., Cotten,M.L. and Koopmans,M.P.G. TITLE Direct Submission JOURNAL Submitted (19-MAY-2017) Centre for infectious Disease Control (Cib), National Institute for Public Health and the Environment (RIVM), Antonie van Leeuwenhoeklaan 9, Bilthoven, Utrecht 3721 MA, Netherlands COMMENT ##Assembly-Data-START## Assembly Method :: SPAdes v. 3.9.0 Sequencing Technology :: Illumina ##Assembly-Data-END## FEATURES Location/Qualifiers source 1..7525 /organism="Norovirus GII" /mol_type="genomic RNA" /strain="Norovirus/GII/Hu/NL/2013/GII.P7- GII.7/Rotterdam/E1300276_p12_d76" /host="Homo sapiens" /db_xref="taxon:122929" /country="Netherlands" /collection_date="09-Oct-2013" /note="genotype: GII.P7-GII.7" CDS <1..5084 /codon_start=3 /product="ORF1" /protein_id="ATN23640.1" /translation="SNDATAAFGSQNSVNDSDNATPSNKEEVGAFSNIKVGFKKMLGA VPKGTKAPSSGQHCPTVKVGPKTLTIPPEPPNGEDTVQFNAKSETIVGLPDLTTVQNE HENTPYTVPPLSEREHRPATEPLPGTILEMWDGEFYHYSVYVSDGRALGVHKPPAAIS LATIELTPISLYWRPVYTPNYLVSPDTLKGLAGEKFPYTAFSNNCYNFCCWVLELNDT WLNRRCISRTTGFFKPYQSWNRKPLPTVDDGKIKKVANAILCALGSLFSKPIKDLLGK LKPLNLLHLLASCDWTFAGIVETVILMAELFNVFWTPPDVSNFIASLIGDFELQGPED LAMELVPVVMGGIGMVLGFTAEKIGRMLSSAASTLRACKDLGNYALDILKLVMKWFFP KKEEKAEMETLRAIEDAVLDMEAIGNNHLTTLLKDKDSLTAFMKTLDLEEEKARKLST KSSSPDIVGTINAILARIAAARSLLHKAKEEMFNRIRPVVVMISGRPGIGKTHMARHL AKSIANTMSGDQRVGLVPRNGVDHWDAYRGERIVLWDDYGMGSPVKDALTLQELADTC PVTLNCDRIENKGKMFDSDVIIITTNLVNPAPLDYVNFEACSRRVDFLVYAEAPEIEK VKRDFPGQPDMWKDHFKPDFSHIKLTLAPQGGFDKNGNTPHGKGTMRSLTQGSLTARV AGLVHERRDEFQLQGNDLQTYNFDTNRVSAFRKLAADNKYGIMETMRVGATLKNVKTL EDLKIALRDVKFNECEIIYKNSKYRVSSNGKGSVSVDKVKDNASQTVNEVQSAILRLR QARARYYISCFQDLVYTLMQVAGASFVVNRISRRFCWERWVKPAETQEVNESEKEVAQ GRWEIEPKDTEPEGKKGKNKKGRGKKHTAFSSKGLSDEEYDEFKRIREERNGKYSIEE YLQDRDRYYEEVAVARATEEDFCEEEEAKIRQRIFRPTKKQRKEERGVLGLVTGSDIR KRRPDDFQPKGNLWADDTRSVDYNERLDFEAPPSVWSRIVPLGTGWGFWVSSNLLITT THVLPKGVKELFGVEIKQIQVHKSGEFCRFRFPRPIRPDVTGLVLEEGAPEGTVCSIL IKRPTGEMIPLAVRMGTHASMKIQGRTVGGQMGMLLTGANAKNMDLGTGPGDCGCPYI YKRGNDIVVAGVHTAAARGGNTVICATQGQDGEAVLEGNEDLGTYCGAPILGPGKAPK LSTKTKFWRSSPDALPPGTYEPAYLGGKDPRVEKGPSLQQVMRDQLRPFTEPRGKPPR PAVLEEAKKTVMNVLEQTIDPAKPWSYSQACASLDKTTSSGSPHHVKKNDHWNGETFT GPLADQASKANLMYEQAKHVQPVYTAALKDELVKTDKIYKKIKKRLLWGSDLGTMIRC ARAFGGLMDSMKASCIALPCRVGMNMNEDGPIIFDKHSKYRYHYDADYSRWDSTQQRN ILSAAMEVMVRFSAEPELAQVVAEDLVAPSQLDVGDFVISVQEGLPSGVPCTSQWNSI AHWILTLSAMAEVSGLSPDVVQAHSCFSFYGDDEIVSTDINLDPMKLTQKLREYGLVP TRPDKTEGPLVITEDLTGLTFLRRSIARDPAGWFGKLDQDSILRQLYWTRGPNHENPY ESMVPHSQRATQLMALLGEASLHGPQFYKKVSKMVINEIKSGGLEFYVPRQEAMFRWM RFSDLSTWEGDRNLAPEGVNEDGVE" CDS 5065..6687 /codon_start=1 /product="ORF2" /protein_id="ATN23641.1" /translation="MKMASNDAAPSNDGAAGLVPEINNEVMPLEPVAGASLATPVAGQ HNIIDPWIRNNFVQAPAGEFTVSPRNSPGEILLDLELGPELNPYLAHLARMYNGHAGG MEVQIVLAGNAFTAGKIIFAAIPPGFPYENLSPSQITMCPHVIIDVRQLEPVLLPMPD IRNNFFHYNQSNDPKLRLLAMLYTPLRANNSGDDVFTVSCRVLTKPSPDFEFTFLVPP TVESKTKQFTLPILKISEMTNSRFPVPVEMMYTARNENQVVQPQNGRVTLDGELLGTT PLLAVNICKFKGEVIAKNGDVRSYRMDMEITNTDGTPIDPTEDTPGPIGSPDFQGILF GVASQRNKNEQNPATRAHEANINTGGDQYAPKLAQVKFFSESQDFEVHQPTVFTPVGV VGDSSHPFRQWVLPRYGGHLTNNTHLAPAVAPLFPGEQILFFRSQIPSSGGHESGYVD CLVPQEWVQHFYQEAATAQSEVALIRFINPDTGRVLFEAKLHKQGFITVAHTGDNPIV MPPNGYFRFEAWVNQFYSLAPVGTGNGRRRIQ" CDS 6687..7460 /codon_start=1 /product="ORF3" /protein_id="ATN23642.1" /translation="MASAFFANLAGGVASNGISSLINAGANAINQKVEFDYNKQLQNA SFSHDKEMLQAQIEATKRLQQEMIDIKQGVLTAAGFSPTDAARGSVGTPMTKLVDWSG TRYWAPGAMRTTGYSGTFTHLPPVQSASYVNNQNRQPPKVDPSPPSSSGSSVSSVKTQ STTLSGTSRVGSSSHLTLSTRPSTRTSDWVRSQNERLSPFMNGALQTTYVTPPSSRAS SVSTVSTVPKEVLDSWTPMFNTHRQPLFAHLRRRGESQI" ORIGIN 1 cgtctaacga cgctactgct gcctttggca gtcaaaactc tgtcaatgac agtgacaacg 61 ccaccccttc taataaagaa gaggttggtg cattctccaa catcaaagtt ggattcaaga 121 aaatgctggg tgccgttccc aagggcacca aagcacccag cagtggtcaa cattgcccca 181 cagttaaggt tgggcctaaa acattaacaa tcccccctga gcccccaaat ggtgaagaca 241 ccgtacagtt caatgcaaag tcagaaacta tagttgggtt gccggacttg acaacggtgc 301 aaaatgaaca tgaaaacacc ccatacactg tccctccatt aagtgagagg gagcacaggc 361 cggccaccga accacttcct ggcacaatat tagagatgtg ggatggtgag ttttaccatt 421 attccgtgta cgtcagcgac ggcagagctc tgggagtcca caaaccaccg gcggctataa 481 gcctcgcgac gatagagctc acccccatat cactttactg gaggcccgtt tataccccca 541 attacttggt ctccccggac acattaaaag gtctcgctgg tgagaagttc ccctatacgg 601 ccttcagtaa caactgttat aacttctgtt gctgggtgct tgagctcaac gacacgtggc 661 ttaacagaag atgcatttcc agaaccaccg gcttcttcaa gccataccag tcttggaaca 721 gaaaacctct cccaaccgtt gatgatggaa agattaagaa agtggccaat gcaatcctct 781 gtgcactcgg ctcactgttc tcaaaaccaa tcaaagacct gttaggcaaa ctcaagccat 841 tgaatctact gcacttgctt gcgtcttgtg attggacgtt tgcgggtata gtggagacag 901 tcatcttgat ggcggagctt ttcaatgtct tctggacccc cccagatgtc tctaatttta 961 tagcctccct aataggtgat tttgaattgc aagggcctga ggacctggcc atggagctcg 1021 tccccgtggt catgggcggc atagggatgg ttctcggttt taccgccgag aagataggcc 1081 gcatgctgtc gtccgctgca tcaacactgc gggcgtgcaa agacctaggg aactatgccc 1141 ttgacatact caaattggtc atgaagtggt tcttcccgaa gaaggaagag aaagctgaga 1201 tggaaacctt gagggcgatt gaggatgccg tcctggatat ggaagccata gggaacaacc 1261 acctcacaac ccttcttaag gacaaagata gcctcacggc tttcatgaag accctggatc 1321 tggaagagga gaaggcaagg aaactgtcca ctaaatcatc ttcaccggac atagtcggca 1381 ccatcaatgc catactagct aggatagctg ctgctagatc ccttctacat aaggccaaag 1441 aggagatgtt caacaggatc aggccagtgg ttgttatgat atcaggcagg cctggcattg 1501 gaaaaaccca catggcaaga catttggcta agagcatcgc caacaccatg agtggcgacc 1561 aaagagtcgg gctcgttccg cgcaacggcg tcgatcactg ggatgcctac aggggagaga 1621 ggatagtctt gtgggatgac tacggcatgg ggagccctgt taaggacgct ctaacactgc 1681 aagagctggc cgacacatgc ccagtcactt taaattgtga caggattgag aataagggga 1741 agatgtttga cagtgatgtc atcataatca cgaccaacct agtcaacccc gcgcccctcg 1801 actatgtgaa cttcgaggcg tgttctagga gagttgactt cctggtctat gcagaggcac 1861 cagaaattga aaaggtcaag agagacttcc ctggccagcc tgacatgtgg aaagaccatt 1921 ttaaaccaga cttctcccac atcaagctga ctctagcccc ccagggtggg tttgacaaaa 1981 atggcaacac cccacacggt aagggaacca tgcggtccct aacccagggg tccctgactg 2041 cgagagttgc aggccttgtc catgagagga gagatgaatt ccagctccaa ggaaatgacc 2101 tccaaacata caactttgac accaacagag tctccgcatt caggaaattg gctgcagata 2161 acaagtatgg gatcatggag acgatgagag tgggtgcgac actcaagaat gtgaagaccc 2221 tggaagatct taaaattgca ttgagggatg taaaattcaa tgagtgtgaa ataatctaca 2281 agaactctaa gtatcgagtc tcttccaacg gtaaaggctc agtttctgtt gacaaagtta 2341 aagacaatgc atcccagact gtaaacgagg tacaatccgc aattctcagg ctcaggcaag 2401 cgagggccag atattacatc agctgcttcc aagacctcgt ctatactctc atgcaggttg 2461 ccggagcatc attcgtagtc aacaggatct ccagaaggtt ctgctgggaa aggtgggtca 2521 aaccggccga gacccaggag gtgaatgagt ccgaaaagga agtggcacaa ggcagatggg 2581 aaattgagcc caaggataca gaaccagaag gcaagaaagg taagaacaag aaaggaagag 2641 gtaagaaaca cacagctttc tctagcaaag gcctgagtga tgaagagtat gacgagttca 2701 agagaattag ggaagaaagg aacggaaagt actccattga ggaatacctg caagaccggg 2761 accgctacta tgaagaagtg gcagttgccc gggcgacaga ggaggacttc tgtgaagagg 2821 aagaggccaa gataagacaa aggattttcc gcccgacaaa gaaacagagg aaggaggaga 2881 ggggtgtgct tggcttagtc accggctcag acatcaggaa gaggagacca gatgacttcc 2941 aaccaaaagg caacctgtgg gcagatgaca ccagaagtgt ggactacaat gagaggcttg 3001 attttgaagc gcccccgagt gtttggtcaa gaatagttcc attaggcact ggttggggat 3061 tctgggtttc atccaacctt ctgatcacaa caacacacgt cctgcctaaa ggggttaagg 3121 agctctttgg agttgaaatc aaacaaatcc aagttcacaa gtctggagag ttttgcaggt 3181 tcagattccc aagacctatc aggccagatg tcacaggact cgtgttggag gaaggcgccc 3241 cagaaggcac tgtctgttct atactcataa aaaggcccac aggtgagatg atccccttag 3301 cagtgaggat gggcacacat gcatccatga aaatacaggg cagaaccgtt ggtggccaga 3361 tgggaatgct tctcacagga gcgaacgcga agaacatgga cctcggcact ggtcctggtg 3421 actgcggttg cccttacatc tacaaacgtg gcaacgacat tgttgtcgcg ggtgttcaca 3481 ccgcagcagc ccgaggaggc aacactgtta tatgtgccac ccaagggcaa gatggggaag 3541 cagtccttga gggaaatgag gaccttggca cctattgtgg cgccccaatt ctgggccctg 3601 gcaaggcgcc taaactcagc acgaagacta agttctggcg ttcatcacca gatgccttgc 3661 cacctggcac atatgagcct gcttacctag gaggcaaaga ccctagagtg gaaaaaggtc 3721 cttcccttca acaagtcatg agggaccagt tgagaccctt cacagaaccc aggggcaaac 3781 cacctagacc tgcagtcttg gaggaagcca aaaagacagt gatgaatgtt ctagaacaaa 3841 ccattgaccc cgccaagcca tggtcctatt cgcaggcgtg tgcctcattg gacaaaacca 3901 cctccagtgg tagtccccat catgttaaga aaaatgacca ctggaatggg gagaccttca 3961 ctggtccact tgcagatcag gcatctaaag ccaatctcat gtatgagcag gctaaacatg 4021 tgcagcccgt gtatacggcc gcgctcaaag atgagcttgt taagactgac aagatctaca 4081 agaaaataaa gaagaggctc ctatgggggt cggaccttgg cacaatgatc aggtgcgcca 4141 gggcctttgg tggtctcatg gacagcatga aggcaagttg tatagctctt ccttgcaggg 4201 tagggatgaa catgaatgaa gatggcccta ttatatttga caaacattct aagtacaggt 4261 accactatga tgctgactat tctaggtggg actcaaccca acaaaggaac attctttctg 4321 ccgctatgga agtgatggtg cggttctctg ctgaaccaga attggcacaa gtggttgcag 4381 aggaccttgt agcacctagc cagcttgatg ttggcgattt tgtcatctca gtccaggagg 4441 gtctgccatc aggagtccca tgcacatcac aatggaattc aatagcacac tggatcctaa 4501 ctttgagtgc aatggcagaa gtgtcaggtc tctcaccaga tgttgtccaa gcccactctt 4561 gtttttcctt ttatggggac gatgagatcg tcagtactga catcaatctt gaccccatga 4621 agttgacaca gaaactcagg gagtatggtc tggttcccac ccggcctgat aaaactgaag 4681 gtcccctcgt cataactgaa gacctcaccg gcctgacgtt cctccgtagg tcgattgctc 4741 gggacccagc tggttggttt ggaaagctgg accaagactc aatccttagg cagctgtact 4801 ggacaagggg gcctaaccat gagaacccgt acgagagcat ggttcctcat tctcagcggg 4861 ccacacaact catggccctt cttggtgagg cctcactaca tggcccccag ttttataaga 4921 aagttagcaa gatggtcatc aatgagatta agagtggtgg tctggagttt tatgtgccca 4981 gacaagaggc catgttcagg tggatgagat tctctgacct cagcacatgg gagggcgatc 5041 gcaatcttgc tcccgaaggt gtgaatgaag atggcgtcga atgacgcagc tccatctaat 5101 gatggtgcag caggcctcgt accagagatc aacaatgagg tcatgcccct tgagcccgta 5161 gctggtgcat cgctggcgac accagttgcc gggcaacaca atataattga tccctggata 5221 agaaataatt ttgtacaagc ccctgcaggt gagtttacag tttcccctag aaattcccct 5281 ggtgaaattt tgctcgattt ggagttggga ccagaactaa acccctatct cgctcatctg 5341 gcccgtatgt ataatgggca cgctggtggc atggaagtgc aaattgtgtt ggctgggaat 5401 gcgttcacag ctggcaagat catatttgct gccatccctc cagggttccc atatgaaaac 5461 ttgtcacctt cacaaatcac aatgtgccct catgttataa ttgatgttag acaactagaa 5521 ccagttctat tacctatgcc agatattaga aacaacttct tccattacaa tcagagcaat 5581 gacccaaaat tgagattgtt agctatgctc tacacccctt taagggctaa taattctggt 5641 gatgatgtgt ttacagtttc ttgtagggtc ctcactaaac cgtcacctga ttttgaattc 5701 acattcttgg tcccccctac ggttgaatct aaaaccaaac agttcacact gcccatcctc 5761 aaaatatcag agatgaccaa ctcaagattc ccagtgccag tggaaatgat gtacacagcc 5821 aggaatgaga accaagttgt ccagccacag aatggtaggg tcacacttga tggcgagcta 5881 ttaggcacca cacccttgtt ggctgtcaac atctgcaaat tcaaggggga ggttatagct 5941 aagaatggag atgtgaggtc ctataggatg gacatggaaa ttaccaacac tgatggcacc 6001 ccaattgacc ccacagaaga tacacctggt cccattggtt cacctgactt tcaaggtata 6061 ctctttggcg ttgccagcca acgcaacaag aatgagcaaa acccagccac gagagcccat 6121 gaagccaaca ttaacactgg tggagaccaa tacgccccca aattggccca agtgaaattc 6181 ttctcagagt cccaggattt cgaggtgcac cagcccacag ttttcacccc agttggtgtg 6241 gtaggcgact cctcccatcc tttcagacag tgggtcctgc cccgatacgg tggacatctc 6301 accaacaaca cccacctggc tccagcagtg gcccccctat tcccaggtga gcagattcta 6361 ttctttagat cacaaatacc cagctcaggc ggccatgaat cgggttacgt ggactgcctt 6421 gtcccccaag aatgggtcca acacttctat caagaagctg ccacagctca gtctgaggtg 6481 gcactcataa ggttcatcaa cccagacact ggcagagtcc tctttgaggc caagctgcac 6541 aagcaaggct ttataactgt ggctcacact ggtgataacc caattgtcat gccaccaaat 6601 gggtacttta gatttgaagc ttgggttaat cagttttact cactcgcccc cgtgggaact 6661 gggaatgggc gcaggaggat ccaataatgg ccagtgcttt ctttgcaaat ttggcaggag 6721 gcgttgcctc caatggaatt agttcactca taaatgctgg ggctaatgct attaaccaaa 6781 aagttgagtt tgattataat aaacaactcc aaaatgcatc cttctcccat gataaggaaa 6841 tgctccaagc ccaaattgaa gccaccaaac gtctgcaaca agagatgatt gacataaaac 6901 aaggggtgct gacagctgcg ggattctctc ctacggatgc cgcgaggggt tctgtcggca 6961 caccaatgac aaaattagtt gattggagtg gcactagata ttgggcgcct ggtgccatga 7021 ggacaacagg ctattcaggg acttttactc acttgccccc tgtgcagtct gcttcatatg 7081 ttaataatca gaatagacaa cctcctaaag tagatccctc tcctccttct tcgagtggtt 7141 cttctgtttc ttctgtcaaa acacaatcga ctaccctctc aggcacttca agggtgggct 7201 cctcatccca tttaaccctg tcgaccaggc cgagcacaag gacatctgat tgggtgcgca 7261 gccagaatga aaggttgagt cccttcatga atggagcgtt gcaaacaaca tatgtaacgc 7321 caccatccag tagggcgtca agtgtcagca cagtctcgac cgtgccgaaa gaggttttgg 7381 actcctggac gcctatgttt aacactcaca ggcagccact cttcgcccat ctgcgtaggc 7441 gaggggagtc acagatttag tgaaaagatt ggttaggaaa gttgattagt ttgctcttct 7501 tttccactat tcctttaatt ctttc //