Typing tool
|
Complete norovirus genomes
MF140681 | GII.4 Den Haag | ||
---|---|---|---|
GII.P4 Den Haag |
ORF1: 1..5082 ORF2: 5063..6685 ORF3: 6685..7491LOCUS MF140681 7543 bp RNA linear VRL 24-OCT-2017 DEFINITION Norovirus GII strain Norovirus/GII/Hu/NL/2011/GII.P4-GII.4/Rotterdam/E1300319_p6_d0 ORF1 gene, partial cds; and ORF2 and ORF3 genes, complete cds. ACCESSION MF140681 VERSION MF140681.1 KEYWORDS . SOURCE Norovirus GII ORGANISM Norovirus GII Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes; Picornavirales; Caliciviridae; Norovirus; Norwalk virus. REFERENCE 1 (bases 1 to 7543) 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 7543) 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..7543 /organism="Norovirus GII" /mol_type="genomic RNA" /strain="Norovirus/GII/Hu/NL/2011/GII.P4- GII.4/Rotterdam/E1300319_p6_d0" /host="Homo sapiens" /db_xref="taxon:122929" /country="Netherlands" /collection_date="21-Nov-2011" /note="genotype: GII.P4-GII.4" CDS <1..5082 /codon_start=1 /product="ORF1" /protein_id="ATN23739.1" /translation="DASAAAVANSNNDTAKSSSDKMFSNMAVTLKRALGARPKQPPPR EISQGPPRPTTPELVKKIPPPPPNGEDEVVVSYSAKDGVSGLPELSTVRQPEETNTAF SVPPLNQRENKDAKEPLTGTILEMWDGEIYHYGLYVERGLVLGVHKPPAAISLAKVEL TPLSLFWRPVYTPQYLISPDTLKKLHGETFPYTAFDNNCYAFCCWVLDLNDSWLSRRM IQRTTGFFRPYQDWNRKPLPTMDDSKLKKVANIFLCTLSSLFTRPIKDIIGRLRPLNI INILASCDWTFAGIVESLILLAELFGVFWTPPDVSALIAPLLGDFELQGPEDLVVELV PVVMGGIGLVLGFTKEKIGKMLSSAASTLRACKDLGAYGLEILKLVMKWFFPKKEEAN ELAMVRSIEDAVLDLEAIENNHMTTLLKDKDSLATYMRTLDLEEEKARKLSTKSASPD IVGTINALLARIAAARSLVHRAKEELSSRPRPVVLMISGRPGIGKTHLAREVAKRIAA SLTGDQRVGLIPRNGVDHWDAYKGERVVLWDDYGMSNPIHDALRLQELADTCPLTLNC DRIENKGKVFDSDVIIITTNLANPAPLDYVNFEACSRRIDFLVYAEAPEVEKAKRDFP GQPDMWKNAFSPDFSHIKLALAPQGGFDKNGNTPHGKGVMKTLTTGSLIARASGLLHE RLDEFELQGPALTTFNFDRNKVLAFRQLAAENKYGLMDTMKVGRQLKDVKTMPELKQA LKNISIKKCQIVYSGCTYTLESDGKGNVKVDRVQSTSVQTNNELAGALHHLRCARIRY YVKCVQEALYSIIQIAGAAFVTTRIIKRVNIQDLWSKPQVENTEESTNKDGCPKPKDN EEFVISSDDIKTEGKKGKNKTGRGKKHTAFSSKGLSDEEYDEYKRIREERNGKYSIEE YLQDRDKYYEEVAIARATEEDFCEEEEAKIRQRIFRPTRKQRKEERASLGLVTGSEIR KRNPDDFKPKGKLWADDDRSVDYNEKLSFEAPPSVWSRIVNFGSGWGFWVSPSLFITS THVIPQGAKVFFGVPVKQIQVHKSGEFCRLRFPRPIRTDVTGMILEEGAPEGTVVTLL IKRSTGELMPLAARMGTHATMKIQGRTVGGQMGMLLTGSNAKSMDLGTTPGDCGCPYI YKRGNDYVVIGVHTAAARGGNTVICATQGGEGEATLEGGDSKGTYCGAPILGPGSAPK LSTKTKFWRSSTAPLPPCTYEPAYLGGKDPRVKGGPSLQQVMRDQLKPFTEPRGKPPK PSVLEAAKKTIINVLEQTIDPPEKWSFAQACASLDKTTSSGHPHHMRKNDCWNGESFT GKLADQASKANLMFEEGKNMTPVYTGALKDELVKTDKIYGKIKKRLLWGSDLATMIRC ARAFGGLMDELKAHCVTLPIRVGMNMNEDGPIIFEKHSRYRYHYDADYSRWDSTQQRA VLATALEIMVKFSSEPHLAQVVAEDLLSPSVVDVGDFTISINEGLPSGVPCTSQWNSI AHWLLTLCALSEVTNLSPDIIQANSLFSFYGDDEIVSTDIKLDPEKLTAKLKEYGLKP TRPDKTEGPLVISEDLDGLTFLRRTVTRDPAGWFGKLEQSSILRQMYWTRGPNHEDPS ESMIPHSQRPIQLMSLLGEAALHGPTFYNKISKLVIAELKEGGMDFYVPRQEPMFRWM RFSDLSTWEGDRNLAPSFVNEDGVE" CDS 5063..6685 /codon_start=1 /product="ORF2" /protein_id="ATN23740.1" /translation="MKMASNDANPSDGSAANLVPEVNNEVMALEPVVGAAIAAPVAGQ QNVIDPWIRNNFVQAPGGEFTVSPRNAPGEILWSAPLGPDLNPYLSHLARMYNGYAGG FEVQVILAGNAFTAGKIIFAAVPPNFPTEGLSPSQVTMFPHIIVDVRQLEPVLIPLPD VRNNFYHYNQSNDSTIKLIAMLYTPLRANNAGEDVFTVSCRVLTRPSPDFDFIFLVPP TVESRTKPFTVPILTVEEMTNSRFPIPLEKLFTGPSSAFVVQPQNGRCTTDGVLLGTT QLSPVNICTFRGDVTHIAGSRNYTMNLASLNWNNYDPTEEIPAPLGTPDFVGKIQGVL TQTTKGDGSTRGHKATVYTGSAPFTPKLGSVQFSTDTENDFETHQNTKFTPVGVIQDG GTTHRNEPQQWVLPSYSGRDVPNVHLAPAVAPTFPGEQLLFFRSTMPGCSGYPNMDLD CLLPQEWVQHFYQEAAPAQSDVALLRFVNPDTGRVLFECKLHKSGYVTVAHTGQHDLV IPPNGYFRFDSWVNQFYTLAPMGNGTGRRRAL" CDS 6685..7491 /codon_start=1 /product="ORF3" /protein_id="ATN23741.1" /translation="MAGAFFAGLASDVLSSGLGSLINAGAGAINQKIDFENNRKLQQA SFQFSSNLQQASFQHDKEMLQAQIEATKKLQQEMMKVKQAVLLEGGFSETDAARGAIN APMTKALDWSGTRYWAPDARTTTYNAGRFSTPQPSGVLPGRANPRTPTPARGSPNTSS NASTATSIYSNQTVSTRLGSTAGSGTSVSSLPSTARTRSWVEDQNRNLSPFMRGAHNI SFVTPPSSRSSSQGTVSTVPKEVLDSWTGAFNTRRQPLFAHIRRRGESRV" ORIGIN 1 gacgcttccg ctgccgctgt tgctaacagc aacaacgaca ccgcaaaatc ttcaagtgac 61 aaaatgtttt ctaacatggc tgtcactctc aaacgagccc tcggggcgcg gcctaagcag 121 ccccccccga gggaaatatc acaaggaccc ccacgaccaa ctactccaga actggtcaaa 181 aagatccctc cccccccgcc caacggagag gacgaagtag tggtttctta tagtgccaaa 241 gatggtgtct ccggtttgcc tgagctttcc accgtcaggc aaccggaaga aaccaatacg 301 gctttcagtg tccctcccct caatcagagg gagaataagg atgctaagga accactgact 361 ggaacaattc tggaaatgtg ggatggagaa atctaccatt atggcctgta tgttgagcga 421 ggtcttgtgc tgggtgtgca caaaccacca gccgccatca gcctcgccaa ggtcgaacta 481 acaccactct ccttgttctg gaggcctgtg tacactcctc agtacctcat ctctccagac 541 actctcaaga aattacacgg agaaacattt ccctacacag ccttcgacaa caattgctat 601 gccttctgtt gctgggtcct ggatctaaac gactcgtggc tgagtaggag aatgatccag 661 agaacaactg gcttcttcag accctaccaa gattggaata ggaaacccct ccccactatg 721 gatgattcca aattaaagaa ggtagctaac atattcctgt gcaccctgtc ttcgctattc 781 accaggccca taaaagacat aatagggagg ctaaggcctc tcaacatcat caacatcctg 841 gcttcatgtg attggacttt cgcaggcata gtggagtcct tgatactctt ggcagagctc 901 tttggagtct tctggacacc cccagatgtg tctgcgttga ttgccccctt actcggtgat 961 ttcgagttac aagggcctga ggaccttgta gtggagctcg ttcctgtagt aatgggggga 1021 attggtttgg tgctaggatt caccaaagag aagattggaa aaatgttatc atctgctgca 1081 tctaccttaa gagcttgtaa agatcttggt gcgtatgggc tagagatcct aaagttagtc 1141 atgaagtggt tcttcccgaa gaaagaggaa gcaaatgaac tggctatggt gagatccatc 1201 gaggatgcag tgctagacct tgaggcaatt gaaaacaacc atatgaccac cttgctcaaa 1261 gacaaagaca gcctggcaac ctatatgaga acccttgacc tcgaggaaga gaaagccaga 1321 aaactctcaa ccaagtctgc ttcacctgac atcgtgggca caatcaacgc ccttctggcg 1381 agaatcgccg ctgcacgctc cctggtgcac cgagcgaagg aggagctttc tagcagaccg 1441 agacctgtag tcttgatgat atcaggcaga ccaggaatag ggaagaccca ccttgctagg 1501 gaagtggcta agagaatcgc agcctccctc acaggagacc agcgcgtagg cctcatccca 1561 cgcaatggcg tcgaccactg ggatgcgtac aagggggaga gggtcgtcct atgggacgac 1621 tatggaatga gcaatcccat ccacgacgct ctcaggctgc aagaactcgc tgacacttgc 1681 cccctcacac taaactgcga caggattgag aataaaggaa aggtctttga cagcgatgtc 1741 atcattatca ctactaacct ggccaaccca gcaccactgg actatgtcaa ctttgaagcg 1801 tgctcgaggc gcattgattt cctcgtgtat gcagaagccc ccgaggttga aaaggcgaag 1861 cgtgacttcc caggccaacc tgacatgtgg aaaaacgctt ttagtcctga tttctcacac 1921 ataaaattgg cactggctcc acaaggtggc tttgataaga acgggaacac cccacatggg 1981 aagggcgtca tgaagactct caccactggc tccctcattg cccgggcatc agggctgctc 2041 catgagagat tggatgagtt tgaactacag ggcccagctc tcaccacctt caactttgac 2101 cgcaacaaag tgcttgcctt caggcagctt gctgctgaaa ataaatacgg gttgatggac 2161 acaatgaaag ttgggaggca gctcaaggat gtcaaaacca tgccagaact taaacaagca 2221 ctcaagaaca tctcaatcaa gaagtgccag attgtgtata gtggttgcac ctacacactt 2281 gagtctgatg gcaagggcaa tgtgaaagtt gacagagttc agagcacctc cgttcagacc 2341 aacaatgagc tggctggcgc cctgcaccac ctgaggtgcg ccagaatcag gtactacgtc 2401 aagtgtgttc aggaggccct gtattctatc atccagattg ctggggctgc gtttgtcacc 2461 acgcgcatca tcaagcgtgt gaacattcaa gacttatggt ccaagccaca agtggaaaac 2521 acagaggagt ccaccaacaa ggacgggtgc ccgaaaccca aagataatga ggagttcgtc 2581 atttcatctg acgacattaa aactgagggt aagaaaggga agaacaagac aggccgtggc 2641 aagaagcaca cagccttctc aagtaaaggt ctcagtgatg aagagtatga tgagtacaag 2701 agaattagag aggaaaggaa tggtaagtac tccatagaag agtaccttca ggacagagac 2761 aaatactatg aggaggtggc tattgccagg gcgaccgagg aagacttctg tgaagaggag 2821 gaggccaaga tccggcaaag gattttcagg ccaacaagga aacaacgcaa ggaagaaaga 2881 gcttctctcg gtttagtcac aggttctgaa attaggaaaa ggaacccgga cgacttcaag 2941 cctaagggga aactatgggc tgacgatgac agaagtgtgg actacaatga aaaactcagt 3001 tttgaggccc caccaagcgt ctggtcaagg atagtcaact ttggctcagg ttggggcttc 3061 tgggtctccc ccagcctgtt tataacatca acccacgtca taccccaggg cgcaaaggtg 3121 ttctttggag tccccgtcaa acaaattcag gtacacaagt caggcgagtt ctgtcgcttg 3181 aggttcccaa ggccaatcag gactgatgtg actggcatga tcctggaaga aggcgcgccc 3241 gaaggcaccg tggtcacact actcatcaaa aggtctactg gagaactcat gcccttagca 3301 gctagaatgg ggacccatgc aaccatgaaa attcaagggc gcactgttgg aggtcagatg 3361 ggcatgcttc tgacaggatc caacgccaaa agcatggatc taggcaccac accaggtgat 3421 tgcggctgtc cctacatcta caagagagga aatgactatg tggtcattgg agtccacacg 3481 gctgccgctc gtgggggaaa cactgtcata tgtgccaccc aggggggtga gggggaagct 3541 acacttgaag gcggtgacag taagggaaca tactgtggcg caccaatcct aggcccaggg 3601 agcgccccaa aacttagcac caaaaccaaa ttctggagat catccacagc accactccca 3661 ccttgcacct atgaaccagc ctaccttggt ggcaaggacc ccagggtcaa gggtggcccc 3721 tcgttgcagc aagttatgag ggaccagctg aaaccattta cagagcctag gggtaagcca 3781 ccaaaaccaa gtgtgttaga ggctgccaag aaaaccatca tcaatgtcct tgaacaaaca 3841 attgacccac ctgagaagtg gtcgttcgca caagcttgcg cgtcccttga caagaccact 3901 tctagcggcc atccacacca catgcggaaa aacgactgct ggaacgggga atctttcaca 3961 ggcaagctgg cggaccaggc ttccaaggcc aacctgatgt ttgaagaagg gaagaacatg 4021 actccagtct acacaggtgc acttaaggat gaattagtca aaactgacaa aatttatggt 4081 aagatcaaga agaggttact ctggggctcg gatttggcaa ccatgatccg gtgtgctcga 4141 gcattcggag gcctaatgga tgaactcaaa gcacactgtg tcacactccc tatcagagtt 4201 ggtatgaata tgaatgagga tggccccatc atcttcgaga agcattccag gtacagatac 4261 cactatgatg ctgattactc tcggtgggat tcaacacaac agagagccgt gctggcaact 4321 gctctagaaa tcatggttaa attctcctca gaaccacatt tggctcaggt agtagcagaa 4381 gaccttcttt ctcccagcgt ggtggacgtg ggggacttca caatatcaat caacgagggt 4441 cttccctctg gggtgccctg cacctcccaa tggaactcca tcgcccactg gcttctcact 4501 ctctgtgcac tctctgaagt tacaaatttg tccccagaca tcatacaggc taattctctc 4561 ttctccttct atggtgatga tgaaattgtt agtacagaca taaaattaga cccagagaag 4621 ttgacagcaa agcttaagga atacgggttg aaaccaaccc gccctgataa aactgaagga 4681 cctcttgtta tttctgaaga cttagatggc ttgaccttcc tgcggagaac tgtgacccgc 4741 gacccagcag gttggtttgg aaaactggag cagagctcaa tactcaggca aatgtactgg 4801 actaggggcc ctaaccatga agatccatct gaatcaatga ttccacactc tcaaagaccc 4861 atacaattga tgtccttact gggagaggcc gcactccacg gcccaacatt ctacaataaa 4921 atcagcaaat tagtcattgc agagttaaaa gaaggtggta tggattttta cgtgcccagg 4981 caagagccaa tgttcagatg gatgagattc tcagatctga gcacgtggga gggcgatcgc 5041 aatctggctc ccagttttgt gaatgaagat ggcgtcgaat gacgccaacc catctgatgg 5101 gtccgcagcc aacctcgtcc cagaggtcaa caatgaggtt atggctttgg agcccgttgt 5161 cggtgccgct attgcggcgc ctgtagcggg ccaacaaaat gtaattgacc cctggattag 5221 aaataatttt gtacaagccc ctggtggaga gttcacagta tcccctagaa acgctccagg 5281 tgaaatacta tggagcgctc ccttaggccc tgatctgaat ccctacctat ctcatttggc 5341 cagaatgtat aatggttatg caggtggttt tgaagtgcag gtaatcctcg cggggaacgc 5401 gttcaccgcc ggaaaaatca tatttgcagc agtcccacca aatttcccga ctgaaggctt 5461 gagtcccagc caggtcacta tgttccccca cataatagtg gatgttaggc aattggaacc 5521 tgtgttgatc cccttacctg atgttaggaa taacttctat cattataatc aatcaaatga 5581 ttctaccatt aaattgatag caatgctgta tacaccactt agggctaata atgctgggga 5641 agatgtcttc acagtctctt gtcgagtcct cacgaggcca tcccctgatt ttgattttat 5701 atttttggtg ccacctacag ttgagtcaag aactaaacca tttactgtcc caatcttgac 5761 tgttgaggaa atgaccaatt caagattccc cattcctttg gaaaagttgt tcacgggtcc 5821 cagcagtgcc tttgttgttc aaccacaaaa tggcagatgc acgactgatg gcgtgctctt 5881 aggcaccacc caactgtctc ctgtcaacat ctgcaccttc agaggggatg tcacccacat 5941 tgcaggttct cgtaattaca caatgaattt ggcttctcta aattggaaca attatgaccc 6001 aacagaagaa attccagccc ctctaggaac tccagatttc gtgggaaaga ttcaaggtgt 6061 gctcactcaa accacaaagg gagatggttc gacccgtggc cataaagcta cagtttacac 6121 tgggagtgcc ccctttactc caaagctggg cagtgttcaa ttcagtactg atacagaaaa 6181 tgattttgaa actcaccaaa acacaaaatt taccccagtc ggtgtcatcc aggatggtgg 6241 caccacccac cgaaatgaac cccaacaatg ggtgctccca agttattcag gtagagatgt 6301 ccctaatgta cacctagccc ctgctgtagc ccccactttc ccgggtgaac aacttctttt 6361 ctttaggtct actatgcccg gatgcagcgg gtatcccaac atggatttgg attgcctact 6421 cccccaggag tgggtgcagc acttctacca agaggcagct ccagcacaat ctgatgtggc 6481 tctactgaga tttgtgaatc cagacacggg tagggttttg tttgagtgca agcttcataa 6541 atcaggctat gtcacagtgg ctcacaccgg ccagcatgat ttggtcatcc cccccaatgg 6601 ttattttagg tttgattcct gggttaatca attctacaca cttgccccca tgggaaatgg 6661 aacggggcgt agacgtgctt tataatggct ggagctttct ttgctgggtt ggcatctgat 6721 gtccttagct ctggacttgg ttccctaatc aatgctgggg ctggggccat caaccaaaag 6781 attgattttg aaaacaacag aaaattgcag caagcttcct tccagttcag cagtaatcta 6841 caacaggctt cctttcaaca tgataaagaa atgctccaag cacaaattga ggccaccaaa 6901 aagttgcaac aggaaatgat gaaagtcaaa caggcagtgc tcttagaagg tgggttctct 6961 gaaacagatg cagcccgtgg ggcaatcaac gcccctatga caaaggctct ggactggagc 7021 ggaacaaggt actgggcccc tgatgctagg actacaacat acaacgcagg ccgtttttcc 7081 acccctcaac cttcgggggt actgccagga agagccaatc ccaggactcc tacccccgct 7141 cggggctccc ccaatacatc ttctaatgct tctactgcta cttctatata ctcaaatcaa 7201 actgtttcaa cgagacttgg ttctacagct ggttctggta ccagtgtctc gagtctcccg 7261 tcaactgcaa ggactaggag ttgggttgag gatcaaaaca gaaacttgtc acctttcatg 7321 aggggggctc acaacatatc gtttgtcacc ccaccatcta gcagatcctc cagccaaggc 7381 acagtctcaa ccgtgcctaa agaagttttg gactcctgga ctggcgcttt caacacgcgc 7441 aggcagcctc tcttcgctca cattcgtagg cgaggggagt cacgggtgta atgtgaaaag 7501 acaaaattga ttatctttcc ctttctttag tgtcttttaa aaa //