Typing tool
|
Complete norovirus genomes
KY887599 | GII.4 Sydney | ||
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GII.P16 |
ORF1: 1..5083 ORF2: 5064..6686 ORF3: 6686..7492LOCUS KY887599 7538 bp RNA linear VRL 15-JUL-2017 DEFINITION Norovirus GII isolate Hu/UK/2016/GII.P16_GII.4_Sydney2012/NOR-2559, partial genome. ACCESSION KY887599 VERSION KY887599.1 KEYWORDS . SOURCE Norovirus GII ORGANISM Norovirus GII Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes; Picornavirales; Caliciviridae; Norovirus; Norwalk virus. REFERENCE 1 (bases 1 to 7538) AUTHORS Ruis,C., Roy,S., Brown,J.R., Allen,D.J., Goldstein,R.A. and Breuer,J. TITLE The emerging GII.P16-GII.4 Sydney 2012 norovirus lineage is circulating worldwide, arose by late-2014 and contains polymerase changes that may increase virus transmission JOURNAL PLoS ONE 12 (6), E0179572 (2017) PUBMED 28662035 REMARK Publication Status: Online-Only REFERENCE 2 (bases 1 to 7538) AUTHORS Ruis,C., Roy,S., Brown,J.R., Allen,D.J., Goldstein,R.A. and Breuer,J. TITLE Direct Submission JOURNAL Submitted (03-APR-2017) Infection and Immunity, University College London, Gower Street, London WC1E6BT, United Kingdom COMMENT ##Assembly-Data-START## Assembly Method :: CLC Genomics Workbench v. 8.5 Sequencing Technology :: Illumina ##Assembly-Data-END## FEATURES Location/Qualifiers source 1..7538 /organism="Norovirus GII" /mol_type="genomic RNA" /isolate="Hu/UK/2016/GII.P16_GII.4_Sydney2012/NOR-2559" /host="Homo sapiens" /db_xref="taxon:122929" /country="United Kingdom: London" /collection_date="07-Jan-2016" /note="genotype: GII.P16_GII.4_Sydney2012" CDS <1..5083 /codon_start=2 /product="non-structural polyprotein" /protein_id="ASK12137.1" /translation="DATVAVACNNNNDKEKSSGEGLFTNMSSTLKKALGARPKQPAPR DEPQKPPRPPTPELVKRIPPPPPNGEGEEEPVIRYEVKSGISGLPELTTVPQPDVANT AFSVPPLSLRENREAKEPLTGAILEMWDGEIYHYGLYVEKGLVLGVHKPPAAISMARV ELTPLSLYWRVVYTPQYLISPETLRRLNGEAFPYTAFDNNCYAFCCWVLDLNDSWLSR RMVQRTTGFFRPYQEWNRKPLPTMDDSKIKKVANIFLCSLSTLFTRPIKDLIGKIKPL NILNILATCDWTFAGIVESLILLAELFGVFWTPPDVSAMIAPLLGDYELQGPEDLAVE LVPVVMGGIGLVLGFTKEKIGKMLSSAASTLRACKDLGAYGLEILKLVMKWFFPKKEE ANELAMVRAIEDAVLDLEAIENNHMTTLLKDKDSLATYMKTLDMEEEKARRLSTKSAS PDIVGTINALLARIAAARSLVHRAKEELSSRIRPVVVMISGKPGIGKTHLAREVARKV ASTLTGDQRVGLIPRNGVDHWDAYKGERVVLWDDYGMSNPIHDALRIQELADTCPLTL NCDRIENKGKVFDSEVIIITTNLANPAPLDYVNFEACSRRIDFLVYAEAPEVEKAKRD FPGQPDMWKDAFKSDFSHIKLQLAPQGGFDKNGNTPHGKGVMKTLTTGSLIARASGLL HERMDEFELQGPTITTFNFDRNRITAFRQLAAENKYGLVDTMKVGNQLKGVKTMEELK QAIRNVTIKRCRIIYGGSTYDLESDGKGKVLVEKVKNTSVQTNNELAGALHHLKHARI RYYVKCVQEAVYSIIQIAGAAFVTTRIARRMNIQELWSKPQLDQNESETKEEAPKSED DEFIISSKDIKEEGKKGKNKTGRGKKHTAFSSKGLSDEEYDEYKRIREERNGKYSIEE YLQDRDRYYEELAIAKATEEDFCEEEEIKIRQRIFRPTRKQRKEERATLGLVTGSEIR KRNPDDFKPKGKLWADDNRSVDYNEKLDFEAPPSIWSRIVSFGSGWGFWVSPSLFITS THVIPAGITEAFGVPIKQIQIHKSGEFCRFRFPKPIRPDVTGMILEEGAPEGTVATVL IKRPTGELMPLAARMGTHATMKIQGRMVGGQMGMLLTGSNAKGMDLGTTPGDCGCPYI YKRGNDYIVIGVHTAAARGGNTVICATQGSEGEATLEGGDDKGTYCGAPILGPGGAPK LSTKTKFWRSSNTPLPPGTYEPAYLGGRDPRVKGGPSLQQVMRDQLKPFTEPRGKPPR PSVLEAAKQTIINVLEQTLDPPQKWTYAQACASLDKTTSSGHPHHVRKNEFWNGETFT GKLADQASKANLMFEEGKHMTPVYTAALKDELVKTEKIYGKIKKRLLWGSDLSTMIRC ARSFGGLMDEMKAHCISLPVRVGMNMNEDGPIIFEKHSRYKYHYDADYSRWDSTQQRA VLAAALEIMVRFSAEPQLAQIVAEDLLAPSVVDVGDFKITINEGLPSGVPCTSQWNSI AHWLLTLCALSEVTKLSPDIVQANSMFSFYGDDEIVSTDIKLDPEQLTAKLKEYGLKP TRPDKTEGPLIISEDLNGLTFLRRTVTRDPAGWFGKLDQSSILRQMYWTRGPNHEDPN ETMIPHSQRPIQLMALLGEASLHGPSFYSKISKLVITELKEGGMDFYVPRQEPMFRWM RFSDLSTWEGDRNLAPNFVNEDGVE" CDS 5064..6686 /codon_start=1 /product="VP1" /protein_id="ASK12138.1" /translation="MKMASSDANPSDGSAANLVPEVNNEVMALEPVVGAAIAAPVAGQ QNVIDPWIRNNFVQAPGGEFTVSPRNAPGEILWSAPLGPDLNPYLSHLARMYNGYAGG FEVQVILAGNAFTAGKIIFAAVPPNFPTEGLSPSQVTMFPHVIVDVRQLEPVLIPLPD VRNNFYHYNQSNDPTIKLIAMLYTPLRANNAGDDVFTVSCRVLTRPSPDFDFIFLVPP TVESRTKPFSVPVLTVEEMTNSRFPIPLEKLFTGPSSAFVVQPQNGRCTTDGVLLGTT QLSPVNICTFRGDVTHITGSRNYTMNLASQNWNNYDPTEEIPAPLGTPDFVGKIQGML TQTTRTDGSTRGHKAIVYTGSADFAPKLGRVQFETDTDHDFEANQNTKFTPVGVIQDG STTHRNEPQQWVLPSYSGRNTHNVHLAPAVAPTFPGEQLLFFRSTMPGCSGYPNMDLD CLLPQEWVQYFYQEAAPAQSDVALLRFVNPDTGRVLFECKLHKSGYVTVAHTGQHDLV IPPNGYFRFDSWVNQFYTLAPMGNGTGRRRAV" CDS 6686..7492 /codon_start=1 /product="VP2" /protein_id="ASK12139.1" /translation="MAGAFFAGLASDVLGSGLGSLINAGAGAINQKVEFENNRKLQQA SFQFSSNLQQASFQHDKEMLQAQIEATKKLQQEMMKVKQAMLLEGGFSETDAARGAIN APMTKALDWSGTRYWAPDARTTTYNAGRFSTPQPSGALPGRANLRDAVPARGPSNKSS NSSTATSVYSNQTISTRLGSTAGSGTSVSSLPSTARTKSWVEDQSRNLSPFMRGAHNI SFVTPPSSRSSSQGTVSTVPKEILDSWTGAFNTRRQPLFAHIRKRGESRV" ORIGIN 1 cgacgctacc gttgccgttg cttgcaacaa caacaacgac aaggaaaaat cttcaggtga 61 aggcttattc acaaatatgt cttccacctt aaagaaagcc ctcggggcta ggcccaaaca 121 gcctgccccg agagacgaac cacaaaagcc cccaagacca ccaactcccg agttggtcaa 181 gaggataccc cctcctccac ctaatggcga aggagaagaa gaaccagtca ttaggtatga 241 ggttaagagt gggatctctg gcctgcccga gctcacaaca gtcccccaac cggacgtggc 301 caacacagca ttcagtgttc caccactgag cttgagagaa aacagggagg ccaaggaacc 361 gctaacaggg gcaatattag agatgtggga tggagagata taccactatg gcctgtacgt 421 ggagaaaggc ttagtgttgg gtgtgcacaa accacctgca gccataagca tggcaagagt 481 ggagttgacg ccgctgtcat tgtactggcg tgtggtgtac actccccaat acctcatctc 541 ccctgaaact ctcaggaggc tcaacggaga ggcgttccct tacaccgcct ttgacaacaa 601 ctgctatgcc ttttgctgct gggtgttaga cctcaatgac tcatggctta gcaggaggat 661 ggtgcaaaga acaacgggct tcttcagacc ttaccaagag tggaacagaa aacccctgcc 721 taccatggat gactccaaaa ttaagaaggt agcaaatata ttcctatgtt cattgtccac 781 actattcacc agacccataa aagacctcat aggaaaaatt aaaccattaa acatattgaa 841 catcctggca acgtgtgact ggacgtttgc cggaatagtg gagtctctga tattacttgc 901 cgaactcttc ggagttttct ggacaccccc agatgtgtct gctatgatcg ctcccttact 961 cggggactac gagttgcaag ggccagaaga cctcgccgtt gaactcgtac ctgtggtaat 1021 gggagggatt ggtttggtgt tgggattcac caaagagaaa attggcaaaa tgttgtcctc 1081 agcagcatca acactcaggg cttgcaaaga tcttggtgcc tatggcttag agatactcaa 1141 attggtcatg aagtggttct tcccaaagaa agaggaggcc aatgagctag ccatggtgag 1201 ggccatagag gatgccgtac tagatcttga ggcaatagaa aataaccaca tgacaaccct 1261 gttgaaagac aaagacagct tagcaacata catgaaaaca ctggacatgg aggaggagaa 1321 agccagaagg ttgtccacaa aatctgcatc ccctgacata gttgggacaa tcaacgccct 1381 gctggctcga atagcagcgg ccaggtcatt agtccacagg gccaaggaag agctgtctag 1441 caggataaga ccagtagttg ttatgatatc tggcaaacca ggaataggca aaactcatct 1501 ggccagggag gtggcaagaa aggtggcatc cactctcaca ggggatcaaa gagtcggact 1561 cataccaaga aacggtgtgg accattggga tgcatacaaa ggtgagagag tcgtgctgtg 1621 ggacgactat ggcatgagta accccattca tgatgctctt cgcatacaag aattggctga 1681 tacgtgtccc cttaccttaa attgtgacag aattgaaaat aagggaaaag tttttgacag 1741 tgaagtcata ataattacaa caaaccttgc caatccagcc ccacttgatt atgtcaactt 1801 tgaggcctgt tccaggagaa ttgatttcct ggtgtacgct gaggcaccag aagtagaaaa 1861 ggcaaaacgg gactttcctg gtcagccaga tatgtggaag gacgccttca agtcggactt 1921 ctcacacatc aagctacagc ttgcacctca gggcggcttt gacaagaatg gcaacacccc 1981 acatgggaaa ggagtgatga agaccctcac taccggttct ctgattgccc gtgcgtcagg 2041 cctactgcat gagaggatgg atgaatttga actccaaggt cccacaatca ccaccttcaa 2101 tttcgaccgg aacagaatca cagcattcag acaattggct gcagaaaaca agtatggatt 2161 ggtggatacc atgaaagttg gcaatcaact aaaaggagtg aaaaccatgg aagaactcaa 2221 acaagcaatc aggaatgtga ccatcaagag gtgccggatc atctacggtg gctccacgta 2281 tgaccttgaa tctgatggca agggcaaagt tttggtggaa aaggtcaaga acacctctgt 2341 acagaccaac aacgagttgg ccggggccct gcaccatctc aaacacgccc gaatcaggta 2401 ctatgtcaaa tgtgtgcaag aagcagtcta ttccatcata caaattgccg gcgctgcgtt 2461 tgtcaccacg cgcattgcac gccgcatgaa catacaagaa ctctggtcga agccacaatt 2521 agatcaaaat gaatcagaaa ctaaggaaga ggcccccaag tcagaagatg acgagttcat 2581 catatcttct aaggacatca aggaggaagg aaagaagggc aaaaacaaaa ctggccgtgg 2641 caagaaacac actgcattct ccagtaaggg cttgagcgat gaggagtatg acgagtacaa 2701 gaggataaga gaagagagaa atgggaagta ctctatagag gagtatcttc aagatagaga 2761 caggtactat gaggagctcg ccattgccaa ggccacggaa gaagacttct gtgaagagga 2821 ggagatcaaa atccgtcaga gaattttccg tcccaccagg aaacaaagaa aggaagagag 2881 ggccacatta gggctagtaa caggttcaga aatcagaaaa agaaaccctg atgacttcaa 2941 acccaaaggg aagctgtggg ccgatgacaa cagaagtgtt gattacaatg agaaactgga 3001 ctttgaggcc cccccaagca tatggtctag gattgtgagc tttggttctg gctggggctt 3061 ctgggtatca ccaagcctgt tcataacatc aactcatgta atccccgcag gcataacaga 3121 agcatttgga gtccccatca aacaaattca gatccacaaa tcaggtgaat tttgccgatt 3181 cagattccca aaaccaatta gaccagatgt gacaggaatg atcttggaag aaggtgcgcc 3241 tgaaggcacc gtggcaactg tgctcatcaa acgccccacc ggagagctca tgcctcttgc 3301 agccagaatg ggaacacacg caaccatgaa aattcaaggc cgcatggttg gcggacagat 3361 gggtatgttg ctcactggat caaatgctaa aggaatggat ttgggaacaa ctcctggtga 3421 ctgtggctgt ccttacatct ataaaagggg caatgactat atagtcattg gggtgcacac 3481 tgcagcagcc cgtggtggaa acaccgtcat ctgtgccaca cagggaagtg agggtgaggc 3541 aactcttgag ggtggagatg acaaaggaac atactgtggg gcacccattc taggccctgg 3601 gggtgcacca aaattgagca ccaaaaccaa attttggagg tcatcgaaca cgccccttcc 3661 accagggaca tatgagcctg cctacctcgg tggccgtgat ccgcgtgtta agggtgggcc 3721 ctccttgcag caggtaatga gagaccagtt gaagccattc actgaaccca ggggcaaacc 3781 tccaagacca agtgtattgg aagcagccaa acaaaccatt atcaacgtcc tcgaacaaac 3841 cctggatcct ccacaaaaat ggacatacgc acaggcgtgt gcctcacttg acaaaaccac 3901 ctccagcggg catccccatc acgtccgaaa gaatgaattc tggaatggtg agaccttcac 3961 tggtaaattg gcagaccaag catcaaaagc aaacctaatg tttgaggaag ggaaacacat 4021 gacaccagtg tatacagcag cactcaagga cgagctagtc aagactgaga aaatctatgg 4081 aaagatcaag aagagactac tctggggctc tgacttgtcc accatgatcc ggtgcgctag 4141 gtcatttggt gggctcatgg acgagatgaa ggcacactgc atatcactcc cagtacgagt 4201 tggcatgaat atgaatgaag atggcccaat aatatttgag aaacattcca gatacaaata 4261 ccactatgat gcagactact ctcgttggga ttcaacacaa cagagggcag tgctagcagc 4321 agccttggaa atcatggtca gattctctgc agaaccacaa ttggcacaaa tagtcgctga 4381 ggatctgctg gcccctagtg tagtagatgt aggagacttt aaaatcacaa taaatgaagg 4441 gctcccatct ggtgtgccat gcacttctca atggaactcc atcgcacact ggctgctaac 4501 tctctgtgct ttgtctgaag tcaccaaact gtcccctgac attgtacaag caaattccat 4561 gttctcattt tacggtgatg acgagattgt cagcaccgac ataaaattgg accctgaaca 4621 gttaaccgcc aaattgaagg agtacggcct gaaaccaacc cgcccagaca agaccgaggg 4681 acccctgatc atcagtgaag atttgaacgg actcactttc ctccgaagga cggtgactcg 4741 tgacccagct ggctggtttg gaaaactgga ccaaagctca attttgagac agatgtactg 4801 gactagagga ccaaatcatg aagaccccaa tgagacaatg ataccccatt ctcaaagacc 4861 catacagctc atggcactgc ttggtgaagc ctctcttcac ggaccctctt tctacagtaa 4921 aatcagtaaa ttggtcataa ctgaactcaa agaaggtggg atggactttt acgtgccaag 4981 gcaggaaccc atgttcaggt ggatgaggtt ttctgacttg agcacgtggg agggcgatcg 5041 caatctggct cccaattttg tgaatgaaga tggcgtcgag tgacgccaac ccatctgatg 5101 ggtccgcagc caacctcgta ccagaggtca acaatgaggt tatggctttg gagcccgttg 5161 ttggtgccgc tattgcggca cctgtagcgg gccaacaaaa tgtaattgac ccctggatta 5221 gaaataattt tgtacaagcc cctggtgggg agtttacagt atcccctaga aacgctccag 5281 gtgaaatact atggagcgcg cccctaggcc ctgacctaaa tccctaccta tcccatttgg 5341 ccagaatgta caatggttat gcaggtggtt ttgaagtgca ggtaattctc gcggggaacg 5401 cgttcaccgc cgggaagatc atatttgcag cagtcccacc aaattttcca actgaaggct 5461 taagtcctag ccaggtcact atgttccccc atgtaatagt ggatgttaga caattagaac 5521 ctgtgctgat tcccttaccc gatgtcagga ataatttcta tcattacaat cagtcaaatg 5581 atcccactat taagttgata gcaatgttgt atacaccact tagggctaat aatgctgggg 5641 atgatgtttt cacagtttcg tgccgagttc tcacgagacc atcccccgat tttgatttca 5701 tatttttagt gccacccaca gttgagtcaa gaactaaacc attctctgtc ccagttttga 5761 ctgttgagga gatgaccaat tcaagattcc ccattccttt ggaaaagttg ttcacgggcc 5821 ccagcagtgc ctttgttgtt caaccacaaa acggcaggtg cacaactgat ggcgtgcttc 5881 taggcaccac ccaactgtct cctgtcaaca tctgcacctt cagaggggat gtcacccaca 5941 tcacaggtag tcgcaactac acaatgaatt tggcttctca aaattggaac aactatgacc 6001 caacagaaga aatcccagcc cctctaggaa ctccagattt tgtggggaag atccaaggca 6061 tgctcaccca aaccacaagg acagatggtt caacacgcgg ccacaaagct atagtgtaca 6121 ctgggagcgc cgactttgct ccaaaactgg gtagagttca atttgaaact gacacagacc 6181 atgattttga agctaaccaa aacacaaagt tcaccccagt cggtgtcatc caagatggta 6241 gcaccaccca ccgaaacgaa ccccaacagt gggtgctccc aagttactca ggcagaaata 6301 cccacaatgt acatctggcc cctgctgtag cccccacctt tccgggtgag caacttctct 6361 tcttcagatc caccatgccc ggatgcagcg ggtaccccaa catggatttg gactgtctgc 6421 tcccccagga atgggtgcag tacttctacc aagaggcagc cccagcacaa tctgatgtgg 6481 ctctgctaag atttgtgaat ccagacacag gtagggtttt gtttgagtgc aagcttcaca 6541 aatcaggcta tgttacagtg gctcacactg gccaacatga tttggttatc ccccccaatg 6601 gttactttag gtttgattcc tgggtcaacc agttctacac gcttgccccc atgggaaatg 6661 gaacggggcg tagacgtgca gtataatggc tggagctttc tttgctggat tggcatctga 6721 tgtccttggc tctggacttg gttcccttat caatgctggg gctggggcca tcaaccaaaa 6781 agttgagttt gaaaataaca gaaaattgca acaagcatcc ttccaattta gcagcaatct 6841 gcaacaggct tcctttcaac atgataaaga gatgctccaa gcacaaattg aggccaccaa 6901 aaagctacaa caggaaatga tgaaagttaa gcaggcaatg ctcctagagg gagggttctc 6961 tgagacagat gcagcccgcg gggcaatcaa cgcccccatg acaaaagctt tggactggag 7021 cgggacaagg tactgggctc ccgatgctag gactacaaca tacaatgcag gccgcttttc 7081 cacccctcaa ccatcggggg cactgccagg aagagctaat cttagggatg ctgtccctgc 7141 tcggggaccc tccaacaaat cttctaactc ttctactgcc acctctgtgt attcaaatca 7201 aactatctca acgagacttg gttctacagc tggttctgga accagtgtct cgagcctccc 7261 gtcaactgca aggactaaga gctgggttga ggatcaaagt aggaatttgt cacctttcat 7321 gaggggggcc cacaacatat catttgtcac cccaccatct agcagatcct ctagccaagg 7381 cacagtctca accgtgccta aagagatttt ggactcctgg actggcgctt tcaacacgcg 7441 caggcagcct ctcttcgctc acattcgtaa gcgaggggag tcacgggtgt aatgtgaaaa 7501 gacaaaactg attatctttc tttttcttta gtgtcttt //