Typing tool
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Complete norovirus genomes
MF140649 | GII.4 New Orleans | ||
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GII.P4 New Orleans |
ORF1: 1..5083 ORF2: 5064..6686 ORF3: 6686..7492LOCUS MF140649 7538 bp RNA linear VRL 24-OCT-2017 DEFINITION Norovirus GII strain Norovirus/GII/Hu/NL/2010/GII.P4-GII.4/Rotterdam/E7800012_p13_d0 ORF1 gene, partial cds; and ORF2 and ORF3 genes, complete cds. ACCESSION MF140649 VERSION MF140649.1 KEYWORDS . SOURCE Norovirus GII ORGANISM Norovirus GII Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes; Picornavirales; Caliciviridae; Norovirus; Norwalk virus. REFERENCE 1 (bases 1 to 7538) 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 7538) 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..7538 /organism="Norovirus GII" /mol_type="genomic RNA" /strain="Norovirus/GII/Hu/NL/2010/GII.P4- GII.4/Rotterdam/E7800012_p13_d0" /host="Homo sapiens" /db_xref="taxon:122929" /country="Netherlands" /collection_date="22-Dec-2010" /note="genotype: GII.P4-GII.4" CDS <1..5083 /codon_start=2 /product="ORF1" /protein_id="ATN23643.1" /translation="DASAAAVANSNNDIAKSSSDGVLSSMAVTFKRALGARPKQPPPR EKPQRPPRPPTPELVKNIPPPPPNGEDEVVVSYSVKDGVSGLPDLSTVRQPEESNTAF SVPPLSQRENRDAKEPLTGTILEMWDGEIYHYGLYVERGLVLGVHKPPAAISLAKVEL APLSLYWRPVYTPQYLIPPDTLKKLSGETFPYTAFDNNCYAFCCWVLDLNDSWLSRRM IQRTTGFFRPYQDWNRKPLPTMDDSKIKKVANIFLCALSSLFTRPIKDIIGKIRPLNI LNILASCDWTFAGIVESLILLAELFGVFWTPPDVSAMIAPLLGDYELQGPEDLAVELV PVVMGGIGLVLGFTKEKIGKMLSSAASTLRACKDLGAYGLEILKLVMKWFFPKKEEAN ELAIVRSIEDAVLDLEAIENNHMTTLLKDKDSLATYMRTLDLEEEKARKLSTKSASPD IVGTINALLARIAAARSLVHRAKEELSSRPRPVVLMISGRPGIGKTHLAREVAKRIAA SLTGDQRVGLIPRNGVDHWDAYKGERVVLWDDYGMSNPIHDALRLQELADTCPLTLNC DRIENKGKVFDSDVIIITTNLANPAPLDYVNFEACSRRIDFLVYAEAPEVEKAKRDFP GQPDMWKNAFSSDFSHIKLALAPQGGFDKNGNTPHGKGVMKTLTTGSLIARASGLLHE RLDEFELQGPALTTFNFDRNKVLAFRQLAAENKYGLMDTMRVGKQLKDVRTMPELKQA LKNVSIKKCQIVYSGCTYILESDGKGNVKVDRIQSAAVQTNNELAGALHHLRCARIRY YVKCVQEALYSIIQIAGAAFVTTRIAKRMNIQDLWSKPQVENTEETTSKDGCPKPKDD EEFVISSNDIKTEGKKGKNKTGRGKKHTAFSSKGLSDEEYDEYKRIREERNGKYSIEE YLQDRDKYYEEVAIARATEEDFCEEEEAKIRQRIFRPTRKQRKEERASLGLVTGSEIR KRNPDDFKPKGKLWADDDRSVDYNEKLSFEAPPSIWSRIVNFGSGWGFWVSPSLFITS THVIPQGAKEFFGVPIKQIQVHKSGEFCRLRFPKPIRTDVTGMILEEGAPEGTVVTLL IKRSTGELMPLAARMGTHATMKIQGRTVGGQMGMLLTGSNAKSMDLGTTPGDCGCPYI YKRGNDYVVIGVHTAAARGGNTVICATQGSEGEATLEGGDNKGTYCGAPILGPGSAPT LSTKTKFWRSSTASLPPGTYEPAYLGGKDPRVKGGPSLQQVMREQLKPFTEPRGKPPK PSVLEAAKKTIINVLEQTIDPPEKWSFAQACASLDKTTSSGHPHHVRKNDCWNGESFT GKLADQASKANLMFEEGKNMTPVYTAALKDELVKTDKIYGKIKKRLLWGSDLATMIRC ARAFGGLMDELKAHCVTLPIRVGMNMNEDGPIIFERHSRYTYHYDADYSRWDSTQQRA VLAAALEIMVKFSPEPHLAQVVAEDLLSPSVVDVGDFTISINEGLPSGVPCTSQWNSI AHWLLTLCALSEVTNLSPDTIQANSLFSFYGDDEIVSTDIKLDPEKLTAKLREYGLKP TRPDKTEGPLVISEDLNGLTFLRRTVTRDPAGWFGKLEQSSILRQMYWTRGPNHGDPS ETMIPHSQRPIQLMSLLGEAALHGPAFYSKISKLVIAELKEGGMDFYVPRQEPMFRWM RFSDLSTWEGDRNLAPSFVNEDGVE" CDS 5064..6686 /codon_start=1 /product="ORF2" /protein_id="ATN23644.1" /translation="MKMASSDANPSDGSTANLVPEVNNEVMALEPVVGAAIAAPVAGQ QNVIDPWIRNNFVQAPGGEFTVSPRNAPGEILWSAPLGPDLNPYLSHLARMYNGYAGG FEVQVILAGNAFTAGKIIFAAVPPNFPTEGLSPSQVTMFPHIIVDVRQLEPVLIPLPD VRNNFYHYNQSNDPTIKLIAMLYTPLRANNAGDDVFTVSCRVLTRPSPDFDFIFLVPP TVESRTKPFSVPVLTVEEMTNSRFPIPLEKLFTGPSSAFVVQPQNGRCTTDGVLLGTT QLSPVNICTFRGDVIHIPGSRNYTMNLASQNWNSYDPTEEIPAPLGTPDFVGKIQGVL TQTTRTNGSTRGHKATVYTGSADFSPKLGRVQFATDTDNDFETNQNTKFTPVGVIQDG STTPRNEPQQWVLPSYSGRNIHNVHLAPAVAPTFPGEQLLFFRSTMPGCSGYPNMDLD CLLPQEWVQYFYQEAAPAQSDVALLRFVNPDTGRVLFECKLHKSGYVTVAHTGQHDLV IPPNGYFRFDSWVNQFYTLAPMGNGTGRRRAL" CDS 6686..7492 /codon_start=1 /product="ORF3" /protein_id="ATN23645.1" /translation="MAGAFFAGLASDVLGSGLGSLISAGAGAINQKVEFENNRKLQQA SFQFSSNLQQASFQHDKEMLQAQIEATKKLQQEMMRVKQAMLLEGGFSETDAARGAIN APMTKTLDWSGTRYWAPDARTTTYNAGRFSTPQPSGAPPGRANLRATVPARGSSSTSS NSSIATSVYSNQTTSTRLGSTAGSGTSVSSLPSTARTRSWIEDQNRNLSPFMRGAHNI SFVTPPSSRSSSQGTVSTVPKEVLDSWTGAFNTRRQPLFAHIRKRGESRV" ORIGIN 1 cgacgcttcc gctgccgctg ttgctaacag caacaacgac atcgcaaaat cttcaagtga 61 cggtgtgctt tctagcatgg ctgtcacttt taaacgagcc ctcggggcgc ggcctaaaca 121 gcctcccccg agggaaaaac cacaaagacc cccacgacca cctactccag aactggtcaa 181 aaatattccc cctcccccac ccaacggaga ggatgaagta gtggtttctt atagtgtcaa 241 agatggtgtt tccggcttgc ctgacctttc caccgtcagg caaccggaag aatctaacac 301 ggccttcagt gtccctccac tcagtcagag ggagaataga gatgctaagg agccacttac 361 tggaacaatt ctggaaatgt gggacgggga aatctaccat tatggcctgt atgtggagcg 421 aggtcttgta ctaggtgtgc acaaaccacc agctgccatc agcctcgcta aggttgagct 481 agcaccactc tccttgtact ggagacctgt gtacactcct cagtacctca tccctccaga 541 cactctcaag aaattatccg gagaaacgtt cccctacaca gcctttgaca acaactgtta 601 tgccttttgt tgctgggtcc tggaccttaa tgactcgtgg ctgagcagga gaatgatcca 661 gagaacaact ggtttcttca ggccctacca agactggaat aggaaacccc ttcccactat 721 ggatgactcc aaaataaaga aggtagctaa catattcctg tgtgctctgt cctcgctgtt 781 caccagaccc ataaaagata taatagggaa gataaggcct cttaacatcc tcaacatcct 841 agcctcatgt gattggactt ttgcaggcat agtggagtcc ctgatactct tggcagaact 901 ctttggagtt ttctggacac ccccagatgt gtctgcgatg attgccccct tacttggtga 961 ctacgagcta caaggacctg aggatcttgc agtggagctc gtccccgtgg tgatgggggg 1021 aattggtttg gtgctaggat tcaccaaaga gaagattggg aaaatgttgt catctgccgc 1081 gtccaccttg agagcttgta aagaccttgg tgcatatggg ctagagatcc tgaagttggt 1141 catgaagtgg ttcttcccga agaaggagga ggcaaatgag ctggctatag tgaggtccat 1201 cgaggatgca gtcctggatc tcgaggcaat tgaaaacaac catatgacca ccttgctcaa 1261 agacaaagac agtctggcaa cctatatgag aacacttgac cttgaggagg agaaagccag 1321 gaaactctca accaagtctg cctcacccga catcgtgggc acaatcaacg ccctcctggc 1381 gaggatcgct gccgcacgtt ctctggtgca tcgggcgaag gaggagcttt ccagcagacc 1441 aagacctgtg gtgttgatga tatcaggcag gccaggaata gggaagaccc acctcgctag 1501 ggaagtggct aagagaatcg cagcctccct tacaggagac cagcgtgtgg gcctcatccc 1561 acgcaatggc gtcgaccatt gggatgcgta caagggggag agggtcgtcc tgtgggacga 1621 ttatggaatg agcaacccta ttcacgacgc cctcaggctg caagaactcg ctgatacatg 1681 ccccctcact ctaaactgtg acaggattga aaataaagga aaggtctttg acagcgatgt 1741 catcattatc accactaatc tggccaaccc agcaccactg gactatgtca actttgaagc 1801 atgctcgagg cgcatcgact tcctcgtgta tgcagaagcc cctgaagtcg aaaaggcgaa 1861 gcgtgacttc ccaggccagc ctgacatgtg gaagaacgct ttcagttctg atttctcaca 1921 cataaaacta gcactggccc cacagggtgg tttcgacaag aacgggaaca ccccacacgg 1981 aaagggcgtc atgaagactc tcaccactgg ctcccttatt gcccgggcat cagggctact 2041 ccatgagagg ttagatgaat ttgaattaca gggcccagct ctcaccacct tcaatttcga 2101 tcgcaataaa gtgcttgcct tcaggcagct tgctgctgaa aataaatatg gattgatgga 2161 cacaatgaga gttgggaaac agctcaagga tgtcagaacc atgccagaac tcaaacaagc 2221 actcaagaat gtctcaatca agaagtgcca aatagtgtat agtggttgca cctacatact 2281 tgagtctgat ggcaagggca atgtgaaagt tgacagaatc caaagcgccg ccgtgcagac 2341 caacaatgag ctggctggtg ccctgcacca tttgaggtgc gccagaatca gatactatgt 2401 caagtgtgtc caggaggccc tgtactccat catacaaatt gctggggctg cattcgtcac 2461 cacgcgcatt gccaagcgca tgaacataca agacctatgg tccaagccac aagtggaaaa 2521 cacagaggag accaccagca aggacgggtg cccaaaacct aaggatgatg aggagtttgt 2581 catttcatcc aacgacatca aaactgaggg taagaagggg aagaacaaga ctggccgcgg 2641 caagaagcac acagcatttt caagcaaagg tctcagtgat gaagagtacg atgagtacaa 2701 gaggattaga gaagaaagga atggcaagta ctccatagaa gagtaccttc aagacaggga 2761 caaatactat gaggaggtgg ccattgccag ggcgactgag gaagacttct gtgaagagga 2821 ggaggccaag atccggcaaa ggatctttag gccaacaagg aaacaacgca aggaggaaag 2881 agcttctctc ggtctggtca caggctctga aattaggaaa agaaacccag atgacttcaa 2941 gcccaagggg aagttgtggg ctgacgatga caggagtgtg gactacaatg agaaactcag 3001 ttttgaggcc ccaccaagca tctggtcgag aatagtcaac tttggttcag gctggggatt 3061 ctgggtctcc cccagcctgt tcataacatc aacccatgtc ataccccaag gcgcaaagga 3121 gttctttgga gtccccatca aacaaataca ggtgcacaag tcaggcgagt tctgtcgctt 3181 gagattccca aaaccaatca ggactgatgt gacgggcatg atcttagaag aaggcgcacc 3241 tgagggcacc gtggtcacac tactcatcaa aaggtccact ggggaactca tgcccctagc 3301 agctaggatg gggacccatg cgaccatgaa gatccaaggg cgcactgttg gaggccagat 3361 gggcatgctt ctgacaggat ccaacgccaa gagcatggac ctgggtacta caccaggtga 3421 ttgtggctgc ccctatatct acaagagagg taatgactat gtggtcattg gagtccacac 3481 ggctgccgca cgtgggggaa acactgtcat atgtgccacc caggggagtg aaggagaggc 3541 cacacttgaa ggtggtgaca acaaggggac atactgtggt gcaccaatcc taggcccagg 3601 gagtgcccca acacttagca ccaagaccaa attctggaga tcgtccacag catcactccc 3661 acctggcacc tatgagccag cctatcttgg tggcaaggac cctagagtca agggtggccc 3721 ttcactgcag caagtcatga gggaacagtt gaagccattc acagagccaa ggggtaagcc 3781 accaaaacca agtgtattag aagctgccaa gaagaccatc atcaatgtcc ttgagcaaac 3841 aattgatcca cctgagaaat ggtcgttcgc acaagcttgc gcgtcccttg acaagaccac 3901 ttccagtggt catccgcacc atgtgcggaa aaacgactgc tggaacggag agtccttcac 3961 aggcaagctg gcagaccagg cttctaaggc caacctgatg tttgaagaag ggaagaacat 4021 gaccccagtc tacacagctg cactcaagga tgagttagtc aaaactgaca aaatttatgg 4081 taagatcaag aagaggcttc tctggggctc ggacttggcg accatgatcc ggtgtgctcg 4141 agcattcgga ggcctaatgg atgaactcaa agcacactgt gtcacacttc ccattagagt 4201 tggcatgaat atgaatgagg atggccccat catcttcgag aggcattcca gatacacata 4261 tcactatgat gctgattact ctcgatggga ctcaacacaa cagagagccg tgctggcagc 4321 agctttagaa atcatggtta aattctcccc agaaccacat ttggctcagg tagtcgcgga 4381 agaccttctt tctcctagcg tggtggacgt gggcgacttc acaatatcaa tcaacgaggg 4441 tcttccctct ggggtgccct gcacctccca atggaactcc atcgcccact ggcttctcac 4501 tctctgtgcg ctctctgaag tcacgaacct atcccctgat accatacagg ctaactccct 4561 cttctctttt tatggtgatg atgaaattgt tagcacagac ataaaattgg acccagaaaa 4621 attgacagcg aagctcagag aatatgggtt aaaaccaacc cgccctgaca aaactgaagg 4681 gccccttgtc atctctgaag acctgaatgg cctaactttc ctgcggagaa ctgtgacccg 4741 cgacccggct ggttggtttg gaaaactgga acagagttca atactcaggc aaatgtactg 4801 gactaggggt cccaaccatg gagacccatc tgaaacaatg attccacact cccaaaggcc 4861 catacaattg atgtccctac tgggggaggc cgctctccac ggcccagcat tttacagcaa 4921 aatcagcaaa ttggtcattg cagagctaaa agaaggtggc atggattttt acgtgcccag 4981 acaagagcca atgttcagat ggatgagatt ctcagatctg agcacgtggg agggcgatcg 5041 caatctggct cccagttttg tgaatgaaga tggcgtcgag tgacgctaac ccatctgatg 5101 ggtccacagc caacctcgtc ccagaggtca acaatgaggt tatggctttg gagcccgtag 5161 ttggtgccgc tattgcggca cctgtagcgg gccaacaaaa tgtaattgac ccctggatta 5221 gaaacaattt tgtgcaagcc cctggtggag agttcacagt atcccctaga aacgctccag 5281 gtgaaatact atggagcgcg cccttaggtc ctgatttgaa tccctacctt tcccatttgg 5341 ccagaatgta caatggttat gcaggtggtt ttgaagtgca ggtaatcctc gcggggaacg 5401 cgttcaccgc cgggaaaatc atatttgcag cagtcccacc aaatttccca actgaaggtt 5461 tgagccccag ccaggtcact atgttccccc acataatagt agatgttagg caattggaac 5521 ctgtgttgat ccccttaccc gatgttagga ataatttcta ccactataat caatcaaatg 5581 accccaccat caaattgata gcaatgttgt acacaccact tagggctaat aatgccgggg 5641 atgatgtctt cacagtttct tgtcgagttc tcacgagacc atcccccgat tttgatttca 5701 tatttttggt gccacccaca gttgaatcaa gaactaaacc attctctgtc ccagttttaa 5761 ctgttgagga gatgaccaat tcaaggttcc ccattccttt ggaaaagttg tttacgggcc 5821 ccagtagtgc ctttgttgtt caaccacaaa acggcaggtg cacgactgat ggcgtgctcc 5881 taggtactac ccaactgtcc cctgtcaaca tctgcacctt cagaggggat gtcatccata 5941 ttccaggcag tcgtaactac acaatgaatt tggcctccca aaattggaat agttacgatc 6001 caacagaaga aatcccagcc cctctaggaa ctccagattt cgtggggaag attcaaggtg 6061 tgctcaccca aaccacaaga acaaatggct cgactcgcgg ccacaaagcc acagtgtata 6121 ctgggagcgc cgacttttct ccaaaactgg gtagagttca atttgccact gacacagaca 6181 atgattttga aactaaccaa aacacaaagt ttaccccagt cggtgttatc caggatggta 6241 gtactacccc ccgaaatgaa ccccagcaat gggtgctccc aagttactca ggcagaaaca 6301 ttcataatgt gcacctggcc cccgctgtgg cccccacttt cccgggcgag cagctcctct 6361 tcttcagatc tactatgccc ggatgcagcg ggtaccccaa catggatttg gactgcctgc 6421 tcccccagga atgggtgcag tatttctacc aggaggcagc cccagcacaa tctgacgtgg 6481 ctctgttaag atttgtgaat ccagacacag gtagggtttt gtttgagtgt aagctccata 6541 aatcaggcta tgttacagtg gctcacactg gccaacatga tttggtcatc ccccccaatg 6601 gttattttag atttgattcc tgggtcaacc agttctacac acttgccccc atgggaaatg 6661 ggacggggcg tagacgtgca ttataatggc tggagctttc tttgctggat tggcatctga 6721 cgtccttggc tctggacttg gttccctaat cagtgctggg gctggggcca tcaatcaaaa 6781 agttgaattt gaaaacaaca gaaaattgca acaagcttcc ttccaattta gtagcaatct 6841 acaacaggct tcctttcaac atgacaagga gatgctccaa gcacaaattg aggccaccaa 6901 aaagttgcaa caggaaatga tgagagttaa acaagcaatg ctcctagagg gtggattctc 6961 tgagacagat gcagcccgtg gggcaatcaa cgcccccatg acaaaaactt tggactggag 7021 cgggacaagg tactgggctc ccgatgctag gactacaaca tataatgcag gtcgcttttc 7081 cacccctcaa ccctcggggg caccaccagg aagagctaat cttagggcta ctgtccccgc 7141 ccggggttcc tccagcacgt cttctaattc ttctattgct acttctgtgt attcaaatca 7201 aaccacctca acgagacttg gttctacagc tggttctggt accagtgtct cgagcctccc 7261 gtcaactgca aggactagga gctggattga ggatcaaaat aggaatttgt cacctttcat 7321 gaggggggcc cacaacatct cgtttgtcac cccaccatct agcagatcct ctagccaagg 7381 cacagtctca accgtgccca aagaagtttt ggactcctgg actggcgctt tcaacacgcg 7441 caggcagcct ctcttcgccc acattcgcaa gcgaggggag tcacgggtgt aatgtgaaaa 7501 gacaaaattg attatctttc ttttctttag tgtctttt //