Typing tool
|
Complete norovirus genomes
MF140643 | GII.4 Sydney | ||
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GII.P4 New Orleans |
ORF1: 1..5033 ORF2: 5014..6636 ORF3: 6636..7442LOCUS MF140643 7442 bp RNA linear VRL 24-OCT-2017 DEFINITION Norovirus GII strain Norovirus/GII/Hu/NL/2013/GII.P4-GII.4/Rotterdam/E1300307_p11_d195 ORF1 gene, partial cds; and ORF2 and ORF3 genes, complete cds. ACCESSION MF140643 VERSION MF140643.1 KEYWORDS . SOURCE Norovirus GII ORGANISM Norovirus GII Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes; Picornavirales; Caliciviridae; Norovirus; Norwalk virus. REFERENCE 1 (bases 1 to 7442) 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 7442) 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..7442 /organism="Norovirus GII" /mol_type="genomic RNA" /strain="Norovirus/GII/Hu/NL/2013/GII.P4- GII.4/Rotterdam/E1300307_p11_d195" /host="Homo sapiens" /db_xref="taxon:122929" /country="Netherlands" /collection_date="04-Aug-2013" /note="genotype: GII.P4-GII.4" CDS <1..5033 /codon_start=3 /product="ORF1" /protein_id="ATN23625.1" /translation="SSDGVLSSMAVTFKRALGARPKQPPPREKPQRPPRPPTPELVKN IPPPPPNGEDEIVVSYSVKDGVSGLPDLSTVRQPEESNTAFSVPPLNQRENRDAKEPL TGTILEMWDGEIYHYGLYVDRGLVLGVHKPPAAISLAKVELAPLSLYWRPVYTPQYLI SPDTLKKLSGETFPYTAFDNNCYAFCCWVLDLNDSWLSRRMIQRTTGFFRPYQDWNRK PLPTMDDSKIKKVANIFLCALSSLFTRPIKDIIGKIRPLNILNILASCDWTFAGIVES LILLAELFGVFWTPPDVSAMIAPLLGDYELQGTEDLAVELVPVVMGGIGLVLGFTKEK IGKMLSSAASTLRACKDLGAYGLEILKLVMKWFFPKKEEENELAIVRSIEDAVLDLEA VESNHLTALLKDKDSLATYMRTLDLEEEKARKLSTKSASPDIVGTINALLARIAAARS LVHRAKEELSSRPRPVVLMISGRPGIGKTHLAREVAKRIAASLTGDQRVGLIPRNGVD HWDAYKGERVVLWDDYGMSNPIHDALRLQELADTCPLTLNCDRIENKGKVFDSDVIII TTNLANPAPLDYVNFEACSRRIDFLVYAEAPDVEKAKRDFPGQPDMWKNAFSSDFSHI KLALAPQGGFDKNGNTPHGKGVMKTLTTGSLIARASGLLHERLDEFELQGPALTTFNF DRNKVLAFRQLAAENKYGLMDTMRVGKQLKDVKTMPELKQALKNVSIKKCQIVYSGCT YMLESDGKGNVKVDRIQSAAVQTNNELAGALHHLRCARIRYYVKCVQEALYSIIQIAG AAFVTTRIAKRMNIQDLWSKPQVENTEETTSKDGCPKPKDDEEFVISSDDIKTEGKKG KNKTGRGKKHTAFSSKGLSDEEYDEYKRIREERNGKYSIEEYLQDRDKYYEEVAIARA TEEDFCEEEEAKIRQRIFRPTRKQRKEERVSLGLVTGSEIRKRNPDDFRPKGKLWADD DRSVDYNEKLSFEAPPSIWSRIVNFGSGWGFWVSPSLFITSTHVIPQGAKEFFGVPIK QIQVYKSGEFCRLRFPKPIRTDVTGMILEEGAPEGTVVTLLIKRSTGELMPLAARMGT HATMKIQGRTVGGQMGMLLTGSNAKGMDLGTTPGDCGCPYIYKRGNDYVVIGVHTAAA RGGNTIICATQGSEGEATLEGGDNKGTYCGAPILGPGSAPTLSTKTKFWRSSTVPLPP GTYEPAYLGGKDPRVKGGPSLQQVMREQLKPFTEPRGKPPKPSVLEAAKKTIINVLEQ TIDPPEKWSFAQACASLDKTTSSGHPHHMRKNDCWNGDSFTGKLADQASKANLMFEEG KNMTPVYTAALKDELVKTDKIYGKIKKRLLWGSDLATMIRCARAFGGLMDELKAHCVT LPIRVGMNMNEDGPIIFEKHSRYTYHYDADYSRWDSTQQRAVLAAALEIMVKFSPEPH LAQVVAEDLLSPSVVDVGDFTISINEGLPSGVPCTSQWNSIAHWLLTLCALSEVTNLS PDTIQANSLFSFYGDDEIVSTDIKLDPEKLTAKLREYGLKPTRPDKTEGPLVISENLN GLTFLRRTVTRDPAGWFGKLEQSSILRQMYWTRGPNHGDPSETMIPHSQRPIQLMSLL GEAALHGPAFYSKISKLVIAELKEGGMDFYVPRQEPMFRWMRFSDLSTWEGDRNLAPS FVNEDGVE" CDS 5014..6636 /codon_start=1 /product="ORF2" /protein_id="ATN23626.1" /translation="MKMASSDANPSDGSAANLVPEVNNEVMALEPVVGAAIAAPVAGQ QNVIDPWIRNNFVQAPGGEFTVSPRNAPGEILWSAPLGPDLNPYLSHLARMYNGYAGG FEVQVILAGNAFTAGKVIFAAVPPNFPTEGLSPSQVTMFPHIVVDVRQLEPVLIPLPD VRNNFYHYNQSNDPTIKLIAMLYTPLRANNAGDDVFTVSCRVLTRPSPDFDFIFLVPP TVESRTKPFSVPVLTVEEMTNSRFPIPLEKLFTGPSSAFLVQPQNGRCTTDGVLLGTT QLSPVNICTFKGGVVHITGSRNYTMNLASQNWNNYDPTEEIPAPLGAPDFVGKIQGML TQTTRADGSTRGHKATVYTGSADFTPKLGRVQFETDTDHDFEANQNTKFTPVGVIQDG STTHRNEPQQWVLPSYSGRNTHNVHLAPAVAPTFPGEQLLFFRSTMPGCSGYPNMDLD CLLPQEWVQYFYQEAAPAQSDVALLRFVNPDTGRVLFECKLHKSGYVTVAHTGQHDLV IPPNGYFRFDSWVNQFYTLAPMGNGAGRRRVV" CDS 6636..7442 /codon_start=1 /product="ORF3" /protein_id="ATN23627.1" /translation="MAGAFFAGLASDVLGSGLGSLINAGAGAINQKVEFENNRKLQQA SFQFSSNLQQASFQHDKEMLQAQIEATKKLQQEMMKVKQAMLLEGGFSETDAARGAIN APMTRALDWSGTRYWAPDARTTTYNAGRFSTPQPSGALSGRANLRDAVPARGSSSKSS NSSTAISVYSNQTTSTRLGSTAGSGTSVSSLPSTARTRSWVEDQSRNLSPFMRGAHNI SFVTPPSSRSSSQGTVSTVPKEVLDSWTGAFNTHRQPLFAHIRSRGESRV" ORIGIN 1 cttcaagtga cggagtgctt tctagcatgg ctgtcacttt taaacgagcc ctcggggcgc 61 ggcctaaaca gcctcccccg agggaaaaac cacaaagacc cccacgacca cctactccag 121 aactggttaa aaatattccc cctcccccac ccaacggaga ggatgaaata gtggtttctt 181 atagtgttaa agatggtgtt tccggtttgc ctgacctttc caccgtcagg caaccggaag 241 aatccaacac ggccttcagt gtccctccac tcaatcagag ggagaataga gatgctaagg 301 aaccactcac tggaacaatt ctggaaatgt gggacgggga aatctaccat tatggcctgt 361 atgtggatcg aggtcttgta ctaggcgtgc acaaaccgcc agctgccatc agcctcgcta 421 aggttgagct agcaccactc tccttgtact ggagacctgt gtacactcct cagtacctca 481 tctctccaga cactctcaag aaattgtccg gagaaacgtt cccctacaca gcctttgata 541 acaactgcta tgccttttgt tgctgggtcc tggacctaaa tgactcgtgg ctgagcagga 601 gaatgatcca gagaacgact ggtttcttca ggccctacca agactggaat aggaaacccc 661 ttcccactat ggatgactcc aaaataaaaa aggtagctaa catatttctg tgtgctctgt 721 cctcgctatt caccagaccc ataaaagata taatagggaa gataaggcct cttaacatcc 781 tcaacatctt agcctcatgt gattggacct ttgcgggcat agtggagtcc ctgatactct 841 tggcagaact ctttggagtt ttctggacac ccccagatgt gtctgcgatg attgccccct 901 tacttggtga ctacgagcta caaggaactg aggaccttgc agtggagctc gtccccgtgg 961 tgatgggggg aattggtttg gtgctaggat tcaccaaaga gaagattggg aagatgttgt 1021 catctgctgc gtccacctta agagcttgca aagaccttgg tgcatatggg ctagagatcc 1081 taaagttagt catgaagtgg ttcttcccga agaaggagga ggaaaatgag ctggctatag 1141 tgaggtccat cgaggatgca gtcctggatc tcgaggcagt tgaaagcaat catttgaccg 1201 ccttgcttaa agataaagac agtctggcaa cctacatgag aacacttgac cttgaagagg 1261 agaaagccag gaaactctca accaagtctg cctcacccga catcgtgggc acaatcaacg 1321 ccctcctggc gagaatcgct gccgcacgtt ctctggtgca tcgagcgaag gaggagcttt 1381 ccagcagacc aagacctgtg gtgttgatga tatcaggcag gccaggaata gggaagaccc 1441 acctcgctag ggaagtggct aagagaatcg cagcctccct tacaggagac cagcgtgttg 1501 gccttatccc acgcaatggc gtcgaccatt gggacgcgta caagggggag agggtcgtcc 1561 tatgggacga ttatggaatg agcaacccta ttcacgatgc cctcagactg caagaactcg 1621 ctgacacttg ccccctcact ctgaactgtg acaggattga aaataaagga aaggtctttg 1681 acagcgatgt catcattatc accaccaatc tggccaaccc agcaccactg gactatgtca 1741 actttgaagc atgctcgagg cgcattgact tcctcgtgta tgcagaagct cctgatgtcg 1801 aaaaggcgaa gcgtgacttc ccaggccagc ctgacatgtg gaagaacgct ttcagttctg 1861 atttctcaca cataaaacta gcactggccc cacagggtgg tttcgacaag aacgggaaca 1921 ccccacacgg aaagggcgtc atgaagactc tcaccactgg ctcccttatt gcccgggcat 1981 cagggctgct ccatgagagg ttagatgaat ttgaactgca gggtccagct ctcaccacct 2041 tcaatttcga tcgcaataaa gtgcttgcct ttagacagct tgctgctgaa aataaatatg 2101 gattgatgga cacaatgagg gttgggaaac agctcaagga tgtcaaaacc atgccagaac 2161 tcaaacaagc actcaagaat gtctcaatca agaagtgtca aatagtgtat agtggttgca 2221 cctacatgct tgagtctgat ggcaagggca atgtgaaagt tgacaggatc cagagcgccg 2281 ccgtgcagac caacaatgag ctggctggtg ccctgcacca tttgaggtgc gccagaatca 2341 gatactatgt caagtgtgtc caggaagccc tgtattccat catccaaatt gctggggctg 2401 catttgtcac cacgcgcatt gccaagcgca tgaacataca agacctatgg tccaagccac 2461 aagtggaaaa cacagaggag actaccagca aggacgggtg cccaaaacct aaggatgatg 2521 aggagtttgt catttcatcc gacgacatca aaactgaggg caagaaaggg aagaacaaga 2581 ctggccgtgg caagaagcac acagcatttt caagcaaagg cctcagtgat gaagagtacg 2641 atgaatacaa gaggattaga gaagaaagga atggcaagta ctctatagaa gagtaccttc 2701 aggacaggga caaatattat gaggaggtgg ccattgccag agcgactgag gaagacttct 2761 gtgaagagga ggaagccaag atccggcaaa ggatctttag gccgacaagg aaacaacgca 2821 aggaggaaag agtctctctc ggcttggtca caggctctga aattaggaaa aggaacccag 2881 atgacttcag acccaaaggg aaattatggg ctgacgatga caggagtgtg gactacaatg 2941 agaaactcag ttttgaggcc ccaccaagca tttggtcgag aatagtcaac tttggttcag 3001 gctggggatt ctgggtctcc cccagcttgt tcataacatc aacccatgtt ataccccagg 3061 gcgcaaagga gttctttgga gtccccatca aacaaataca ggtatacaag tcaggcgagt 3121 tctgtcgctt gagattcccc aaaccaatca ggactgatgt gacgggcatg atcttagaag 3181 aaggcgcacc tgagggcacc gtggtcacac tactcatcaa aaggtccact ggggaactta 3241 tgcccctagc agctaggatg gggacccatg cgaccatgaa gatccaaggg cgcactgttg 3301 ggggccagat gggcatgctt ctgacaggat ccaacgccaa gggtatggac ctgggtacta 3361 caccaggtga ttgtggctgc ccctatatct acaagagagg taatgactat gtggtcattg 3421 gagtccacac ggctgccgca cgtgggggga acactatcat atgtgccacc caggggagtg 3481 aaggagaggc tacacttgag ggtggtgaca acaaggggac atactgtggt gcaccaatcc 3541 taggcccagg gagtgcccca acacttagca ccaagaccaa attctggaga tcgtccacag 3601 taccactccc acctggcacc tatgaaccag cctatcttgg tggtaaggac cctagagtca 3661 agggtggccc ttcactgcag caagtcatga gggaacagtt gaagccattc acagagccca 3721 ggggcaagcc accaaaacca agtgtgttag aagctgccaa gaagaccatc atcaatgtcc 3781 ttgagcaaac aattgatcca cctgagaaat ggtcgttcgc acaagcttgc gcgtcccttg 3841 acaagaccac ttccagtggt catccgcacc acatgcggaa aaacgactgc tggaacgggg 3901 attccttcac aggcaagctg gcagaccagg cttccaaggc taacctgatg tttgaagaag 3961 ggaagaacat gaccccagtc tacacagctg cgctcaagga tgagttagtt aaaactgaca 4021 aaatttatgg caagatcaag aagaggcttc tttggggctc ggacttggcg accatgatcc 4081 ggtgtgctcg agcattcgga ggcttaatgg atgaactcaa agcgcactgt gtcacacttc 4141 ccattagagt tggcatgaat atgaatgagg atggccccat catcttcgag aagcattcca 4201 ggtatacgta ccactatgat gctgattact ctcgatggga ttcaacacaa cagagagccg 4261 tgttggcagc agctctagaa atcatggtta aattctcccc agaaccacat ttggctcagg 4321 tagtcgcgga agatcttctt tctcctagcg tggtggacgt gggcgacttc acaatatcaa 4381 tcaacgaggg tctcccctct ggggtgccct gcacctccca atggaactcc atcgcccact 4441 ggcttctcac tctctgtgcg ctctccgaag tcacaaatct gtcccctgat accatacagg 4501 ccaattctct cttctctttt tatggtgatg atgaaattgt tagcacagac ataaaattgg 4561 acccagagaa attgacagca aagctcagag aatatgggtt aaaaccaacc cgccctgaca 4621 aaactgaagg accccttgtc atctctgaaa acctgaatgg cctaactttc ctgcggagaa 4681 ctgtgacccg cgacccagct ggttggtttg gaaaactgga gcagagttca atactcaggc 4741 aaatgtactg gactaggggt cccaaccatg gagacccatc tgaaacaatg attccacact 4801 cccaaagacc catacaattg atgtccctac tgggggaggc cgctctccac ggtccagcat 4861 tttacagtaa aatcagcaaa ttggtcattg cagagctaaa agaaggtggt atggattttt 4921 acgtgcccag acaagagcca atgttcagat ggatgagatt ctcagatctg agcacgtggg 4981 agggcgatcg caatctggct cccagttttg tgaatgaaga tggcgtcgag tgacgccaac 5041 ccatctgatg ggtccgcagc caacctcgtc ccagaggtca acaatgaggt tatggctctg 5101 gagcccgttg ttggtgccgc cattgcggca cctgtagcgg gccaacaaaa tgtaattgac 5161 ccctggatta gaaacaattt tgtacaagcc cctggtggag agtttacagt gtcccctaga 5221 aacgctccag gtgaaatact atggagcgcg cccttaggcc ctgatctaaa tccctaccta 5281 tcccatttgg ccagaatgta taatggttat gcaggtggtt ttgaagtgca ggtaattctc 5341 gcggggaacg cgttcaccgc cgggaaggtc atatttgcag cagtcccacc aaattttcca 5401 actgaaggct tgagccccag ccaggtcact atgttccccc atatagtagt agatgttagg 5461 caattagaac ctgtgttgat tcccttaccc gatgttagga ataatttcta tcattacaat 5521 caatcaaatg accccaccat caagttgata gcaatgctgt atacaccact tagggctaat 5581 aatgctgggg acgatgtctt cacagtttct tgccgagttc tcacgagacc atcccccgat 5641 tttgatttta tatttctagt gccacccaca gttgagtcta gaactaaacc attctctgtc 5701 ccagttttaa ctgttgagga gatgaccaat tcaagattcc ccattccttt ggaaaagttg 5761 ttcacgggtc ccagcagtgc ctttcttgtt caaccacaaa acggtaggtg cacgactgat 5821 ggcgtgctcc taggcaccac ccaattgtct cctgtcaaca tctgcacctt caaagggggt 5881 gtcgtccaca tcacaggtag tcgtaactac acaatgaatt tggcttctca aaattggaac 5941 aattatgacc caacagaaga aatcccagcc cctctaggag ctccagattt tgtggggaag 6001 attcaaggca tgctcaccca aaccacaagg gcagatggct caacacgcgg ccacaaagct 6061 acagtgtaca ctgggagcgc cgactttact ccaaaactgg gcagagttca atttgaaact 6121 gacacagacc atgattttga agctaaccaa aacacaaagt tcaccccagt cggtgtcatc 6181 caagatggta gcaccaccca ccgaaatgaa ccccaacagt gggtgctccc aagttactca 6241 ggcagaaata ctcataatgt tcatctggcc cccgctgtag cccccacttt tccgggtgaa 6301 caacttctct tctttagatc caccatgccc ggatgtagcg ggtaccccaa catggatttg 6361 gactgtctgc tcccccagga atgggtgcag tacttctacc aagaggcagc cccagcacaa 6421 tctgatgtgg ctctgctaag atttgtgaat ccagacacag gtagggtttt gtttgagtgt 6481 aagctccata aatcaggcta tgttacagtg gctcacactg gccaacatga tttggttatc 6541 ccccccaatg gttattttag gtttgattcc tgggtcaacc agttctacac gcttgccccc 6601 atgggaaatg gagcggggcg tagacgtgta gtataatggc tggagctttc tttgctggat 6661 tagcatctga tgtccttggc tctggacttg gttcccttat caatgctggg gctggggcca 6721 tcaaccaaaa agttgagttt gaaaataaca gaaaattgca acaagcatcc ttccaattta 6781 gcagcaatct acaacaggct tcctttcaac atgacaaaga aatgctccaa gcacaaattg 6841 aggccaccaa aaagctacaa caggaaatga tgaaagttaa gcaggcaatg ctcctagagg 6901 gtgggttctc tgagacagat gcagcccgcg gggcaatcaa cgcccccatg acaagagctt 6961 tggactggag cgggacgagg tactgggctc ccgatgctag gactacaaca tacaatgcag 7021 gccgcttttc cacccctcaa ccatcggggg cactgtcagg aagagccaat cttagggatg 7081 ctgtccctgc tcggggttcc tccagtaaat cttctaactc ttctactgct atttctgtgt 7141 actcaaatca aaccacttca acgagacttg gttctacagc tggttctggt accagtgtct 7201 cgagcctccc gtcaactgca aggactagga gctgggttga ggatcaaagt aggaatttgt 7261 ctcctttcat gaggggggct cacaacatat cgtttgtcac cccaccatct agcagatcct 7321 ctagccaagg cacagtctca accgtgccta aagaggtttt ggactcctgg actggcgctt 7381 tcaacacgca caggcagcct ctcttcgctc acattcgtag tcgaggggag tcacgggtgt 7441 aa //