Typing tool
|
Complete norovirus genomes
MH260496 | GII.4 Sydney | ||
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GII.P16 |
ORF1: 1..5077 ORF2: 5058..6680 ORF3: 6680..7449LOCUS MH260496 7449 bp RNA linear VRL 16-JUN-2018 DEFINITION Norovirus GII isolate ST165 nonstructural polyprotein (ORF1) gene, partial cds; VP1 (ORF2) gene, complete cds; and VP2 (ORF3) gene, partial cds. ACCESSION MH260496 VERSION MH260496.1 DBLINK BioProject: PRJNA338014 KEYWORDS . SOURCE Norovirus GII ORGANISM Norovirus GII Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes; Picornavirales; Caliciviridae; Norovirus; Norwalk virus. REFERENCE 1 (bases 1 to 7449) AUTHORS Casto,A.M., Adler,A., Huang,M.-L., Makhsous,N., Xie,H., Zerr,D. and Greninger,A. TITLE The limits of epidemiology: Real-time metagenomic sequencing during norovirus outbreak reveals discrete transmission clusters and elucidates long-term sequelae of hospital acquired infections JOURNAL Unpublished REFERENCE 2 (bases 1 to 7449) AUTHORS Casto,A.M., Adler,A., Huang,M.-L., Makhsous,N., Xie,H., Zerr,D. and Greninger,A. TITLE Direct Submission JOURNAL Submitted (25-APR-2018) Department of Laboratory Medicine, University of Washington, 1100 Fairview Ave. N, E5-110, PO Box 19024, Seattle, WA 98109, USA FEATURES Location/Qualifiers source 1..7449 /organism="Norovirus GII" /mol_type="genomic RNA" /isolate="ST165" /host="Homo sapiens" /db_xref="taxon:122929" /country="USA" /collection_date="2017" /note="genotype: GII" gene <1..5077 /gene="ORF1" CDS <1..5077 /gene="ORF1" /codon_start=2 /product="nonstructural polyprotein" /protein_id="AWT08342.1" /translation="TVAVACNNNNDKEKSSGEGLFTNMSSTLKKALGARPKQPAPRDE PQKPPRPPTPELVKRIPPPPPNGEEEEEPVIRYEVKSGISGLPELTTVPQPDVANTAF SVPPLSLRENREAKEPLTGAILEMWDGEIYHYGLYVEKGLVLGVHKPPAAISMARVEL APLSLYWRVVYTPQYLISPETLRRLNGEAFPYTAFDNNCYAFCCWVLDLNDSWLSRRM VQRTTGFFRPYQEWNRKPLPTMDDSKIKKVANIFLCSLSTLFTRPIKDLIGKIKPLNI LNILATCDWTFAGIVESLILLAELFGVFWTPPDVSAMIAPLLGDYELQGPEDLAVELV PVVMGGIGLVLGFTKERIGKMLSSAASTLRACKDLGAYGLEILKLVMKWFFPKKEEAN ELAMVRAIEDAVLDLEAIENNHMTTLLKDKDSLATYMKALDMEEEKARRLSTKSASPD IVGTINALLARIAAARSLVHRAKEELSSRIRPVVVMISGKPGIGKTHLAREVARKVAS TLTGDQRVGLIPRNGVDHWDAYKGERVVLWDDYGMSNPIHDALRIQELADTCPLTLNC DRIENKGKVFDSEVIIITTNLANPAPLDYVNFEACSRRIDFLVYAEAPEVEKAKRDFP GQPDMWKDAFKPDFSHIKLQLAPQGGFDKNGNTPHGKGVMKTLTTGSLIARASGLLHE RMDEFELQGPTITTFNFDRNRITAFRQLAAENKYGLVDTMKVGNQLKGVKTMEELKQA IRNVTIKRCRIIYGGSTYDLESDGKGKVLVEKVKNTSVQTNNELAGALHHLKHARIRY YVKCVQEAVYSIIQIAGAAFVTTRIARRMNIQELWSKPQLDQNESETKEEVPKSEDDE FIISSKDIKEEGKKGKNKTGRGKKHTAFSSKGLSDEEYDEYKRIREERNGKYSIEEYL QDRDRYYEELAIAKATEEDFCEEEEIKIRQRIFRPTRKQRKEERATLGLVTGSEIRKR NPDDFKPKGKLWADDNRSVDYNEKLDFEAPPSIWSRIVSFGSGWGFWVSPSLFITSTH VIPAGVTEAFGVPIKQIQIHKSGEFCRFRFPKPIRPDVTGMILEEGAPEGTVATVLIK RPTGELMPLAARMGTHATMKIQGRMVGGQMGMLLTGSNAKGMDLGTTPGDCGCPYIYK RGNDYVVIGVHTAAARGGNTVICATQGSEGEATLEGGDDKGTYCGAPILGPGGAPKLS TKTKFWRSSNTPLPPGTYEPAYLGGRDPRVKGGPSLQQVMRDQLKPFTEPRGKPPRPN VLEAAKQTIINVLEQTLDPPQKWTYAQACASLDKTTSSGHPHHVRKNEFWNGETFTGK LADQASKANLMFEEGKHMTPVYTAALKDELVKTEKIYGKIKKRLLWGSDLSTMIRCAR SFGGLMDEMKTHCISLPVRVGMNMNEDGPIIFEKHSRYKYHYDADYSRWDSTQQRAVL AAALEIMVRFSAEPQLAQIVAEDLLAPSVVDVGDFKITINEGLPSGVPCTSQWNSIAH WLLTLCALSEVTKLSPDIIQANSMFSFYGDDEIVSTDIKLDPEQLTAKLKEYGLKPTR PDKTEGPLIISEDLNGLTFLRRTVTRDPAGWFGKLDQSSILRQMYWTRGPNHEDPNET MIPHSQRPIQLMALLGEASLHGPSFYSKISKLVITELKEGGMDFYVPRQEPMFRWMRF SDLSTWEGDRNLAPNFVNEDGVE" mat_peptide <1..973 /gene="ORF1" /product="p48" mat_peptide 974..2071 /gene="ORF1" /product="NTPase" mat_peptide 2072..2602 /gene="ORF1" /product="p22" mat_peptide 2603..3001 /gene="ORF1" /product="VPg" mat_peptide 3002..3544 /gene="ORF1" /product="Pro" mat_peptide 3545..5074 /gene="ORF1" /product="RdRp" gene 5058..6680 /gene="ORF2" CDS 5058..6680 /gene="ORF2" /note="major capsid protein" /codon_start=1 /product="VP1" /protein_id="AWT08343.1" /translation="MKMASSDANPSDGSAANLVPEVNNEVMALEPVVGAAIAAPVAGQ QNVIDPWIRNNFVQAPGGEFTVSPRNAPGEILWSAPLGPDLNPYLSHLARMYNGYAGG FEVQVILAGNAFTAGKIIFAAVPPNFPTEGLSPSQVTMFPHIIVDVRQLEPVLIPLPD VRNNFYHYSQSNDSTIKLIAMLYTPLRANNAGDDVFTVSCRVLTRPSPDFDFIFLVPP TVESRTKPFSIPVLTVEEMTNSRFPIPLEKLFTGPSSAFVVQPQNGRCTTDGVLLGTT QLSPVNICTFRGDVTHITGSRNYTMNLASQNWNNYDPTEEIPAPLGTPDFVGKIQGML TQTTRTDGSTRGHKATVYTGSADFAPKLGRVQFETDTDHDFEANQNTKFTPVGVIQDG STTHRNEPQQWVLPSYSGRNTHNVHLAPAVAPTFPGEQLLFFRSTMPGCSGYPNMDLD CLLPQEWVQYFYQEAAPAQSDVALLRFVNPDTGRVLFECKLHKSGYVTVAHTGQHDLV IPPNGYFRFDSWVNQFYTLAPMGNGTGRRRVV" gene 6680..>7449 /gene="ORF3" CDS 6680..>7449 /gene="ORF3" /note="minor structural protein; small basic protein" /codon_start=1 /product="VP2" /protein_id="AWT08344.1" /translation="MAGAFFAGLASDVLGSGLGSLINAGAGAINQKVEFENNRKLQQA SFQFSSNLQQASFQHDKEMLQAQIEATKKLQQEMMKVKQAVLLEGGFSETDAARGAIN APMTKALDWSGTRYWAPDARTTTYNAGRFSTPQPSGALPGRANLRDTVPARGPSNKSS NSSTATSVYSNQTISTRLGSTAGSGTSVSSLPSTARTRSWVEDQSRNLSPFMRGAHNI SFVTPPSSRSSSQGTVSTVPKEILDSWTGAFNTRRQPL" ORIGIN 1 taccgttgcc gttgcttgca acaacaacaa cgacaaggaa aaatcttcag gtgaaggctt 61 attcacaaat atgtcttcca ccttaaagaa agccctcggg gctaggccca aacagcctgc 121 cccgagagac gaaccacaaa agcccccaag accaccaact cccgagttgg tcaagaggat 181 accccctcct ccacctaatg gcgaagaaga agaggaacca gtcattaggt atgaggttaa 241 gagtgggatc tctggcctgc ccgagctcac aacagtcccc caaccggacg tggccaacac 301 agcattcagt gttccaccac tgagcttgag agaaaacagg gaggccaagg aaccgctaac 361 aggggcgata ttagagatgt gggatggaga gatataccac tatggcctgt acgtggagaa 421 aggcttagtg ttgggtgtgc acaaaccacc tgcagccata agcatggcaa gagtggagct 481 ggcgccgctt tcattgtact ggcgtgtggt gtacactccc caatacctca tctcccctga 541 aactctcagg aggctcaacg gagaggcgtt cccttacacc gccttcgaca acaactgcta 601 tgccttttgc tgctgggtgt tagacctcaa tgactcatgg cttagcagga ggatggtgca 661 aagaacgacg ggcttcttca gaccttacca agagtggaac agaaaacccc tgcctaccat 721 ggatgactcc aaaattaaga aggtggcaaa tatattccta tgttcattgt ccacattgtt 781 caccagaccc ataaaagacc tcatagggaa aattaaacca ttaaacatac tgaacatcct 841 ggcaacgtgt gactggacgt ttgccggaat agtggagtct ctgatattac ttgctgagct 901 cttcggagtt ttctggacac ccccagatgt gtctgctatg atcgctccct tactcgggga 961 ctacgagttg caagggccag aagaccttgc cgttgaactc gtacctgtgg taatgggagg 1021 gattggtttg gtgttgggat tcaccaaaga gagaattggc aaaatgttgt cctcagcagc 1081 atcaacactc agggcttgca aagatcttgg tgcctatggc ttagagatac tcaaattagt 1141 catgaagtgg ttcttcccaa agaaagagga ggccaatgag ctagccatgg tgagggccat 1201 agaggatgcc gtactagatc ttgaggcaat agaaaataac cacatgacaa ccctgttgaa 1261 agacaaagac agcttagcaa catacatgaa agcactggac atggaggagg agaaagccag 1321 aaggttgtcc acaaaatctg catcccctga catagttggg acaatcaacg ccctactggc 1381 tcggatagca gcggccaggt cattagtcca cagggccaag gaagagctat ctagcaggat 1441 aagaccagta gttgttatga tatctggcaa accaggaata ggcaaaactc atctggccag 1501 ggaggtggca agaaaggtgg catctactct cacaggggat caaagagtcg gactcatacc 1561 aagaaacggt gtggaccatt gggatgcata caaaggtgag agagtcgtgc tgtgggacga 1621 ctatggcatg agtaacccca ttcatgatgc tcttcgcata caagaattgg ctgatacgtg 1681 tcccctcacc ttaaactgtg acagaattga aaataaggga aaagtttttg acagtgaagt 1741 cataataatt acaacaaacc ttgccaatcc agccccactt gattatgtca actttgaggc 1801 ctgttccagg agaattgatt tcctggtgta cgctgaggca ccagaagtag aaaaggcaaa 1861 acgggatttt cctggtcagc cagatatgtg gaaggatgcc tttaaaccgg acttttcaca 1921 catcaagcta cagcttgcac ctcagggcgg ctttgacaag aatggcaaca ccccacatgg 1981 gaaaggagtg atgaagaccc tcactaccgg ttctctgatt gcccgtgcat caggcctact 2041 gcatgagagg atggatgaat ttgaactcca aggtcccaca atcaccacct tcaatttcga 2101 ccggaacaga atcacagcat tcagacaact ggctgcagaa aacaagtatg gattggtgga 2161 caccatgaaa gttggcaatc aactaaaagg agtgaaaacc atggaagaac tcaaacaagc 2221 aatcaggaat gtgaccatca agaggtgccg gatcatctac ggtggctcca cgtatgacct 2281 tgaatctgat ggcaagggta aagttttggt ggaaaaggtc aagaacacct ctgtacagac 2341 caacaacgag ttggccgggg ccctgcacca tctcaaacac gcccgaatca ggtactatgt 2401 caaatgtgtg caagaagcag tctattccat catacaaatt gccggcgctg cgttcgtcac 2461 cacgcgcatt gcacgccgca tgaacataca agaactctgg tcgaaaccac aattagatca 2521 aaatgaatca gagactaagg aagaggtccc caagtcagaa gatgacgagt tcatcatatc 2581 ttctaaggac atcaaggagg aaggaaagaa gggcaaaaac aaaactggcc gtggtaagaa 2641 acacactgca ttctccagca agggtttgag cgatgaggag tatgacgagt acaagaggat 2701 aagagaagag agaaatggga agtactctat agaggagtat cttcaagaca gagacaggta 2761 ctatgaggag ctcgccattg ccaaggccac ggaagaagac ttctgtgaag aggaggagat 2821 caaaatccgt cagagaattt tccgtcccac caggaaacaa agaaaggaag agagggccac 2881 attagggcta gtaacaggtt cagaaatcag aaaaagaaac cctgatgact tcaaacccaa 2941 agggaagctg tgggccgacg acaacagaag tgttgactac aatgagaaac tggactttga 3001 ggccccccca agcatatggt ctaggattgt gagctttggt tctggctggg gcttctgggt 3061 atcaccaagc ctgttcataa catcaactca cgtgatcccc gcaggcgtaa cagaagcgtt 3121 tggagtcccc atcaaacaaa ttcagatcca caaatcaggt gaattttgtc gattcagatt 3181 cccaaaacca attagaccag atgtgacagg aatgatcttg gaagaaggtg cgcctgaagg 3241 caccgtggca actgtgctca tcaaacgccc caccggagag ctcatgcctc ttgcagccag 3301 aatgggaaca cacgcaacca tgaaaattca aggccgcatg gttggtggac agatgggtat 3361 gttgctcact gggtcaaatg ctaaagggat ggatttgggg acaactcctg gtgactgtgg 3421 ctgtccctac atctataaaa ggggcaatga ctatgtagtc attggggtgc acactgcagc 3481 agcccgtggt ggaaacaccg tcatctgtgc cacacaggga agtgagggtg aggcaactct 3541 tgagggtgga gatgacaaag gaacatactg tggggcaccc attctaggcc ctgggggtgc 3601 accaaaattg agcaccaaaa ccaaattttg gaggtcatcg aacacgcccc ttccaccagg 3661 gacatatgag cctgcctacc tcggtggccg tgatccgcgt gttaagggtg ggccctcctt 3721 gcagcaggta atgagagacc agttgaagcc attcactgaa cccaggggca aacctccaag 3781 accaaatgta ttggaagcag ccaaacaaac cattatcaat gtcctcgaac aaactctgga 3841 ccctccacaa aaatggacat acgcacaggc gtgtgcctca cttgacaaaa ccacctccag 3901 cgggcatccc catcacgtcc gaaagaatga attctggaat ggtgagacct tcactggtaa 3961 attggcagac caagcatcaa aagcaaacct aatgtttgag gaagggaaac acatgacacc 4021 agtgtataca gcagcactca aggacgagct agtcaagacc gagaaaatct atggaaagat 4081 caagaagaga ctgctctggg gctctgactt gtccaccatg atccggtgcg ctaggtcatt 4141 tggtgggctc atggatgaga tgaagacaca ctgcatatca ctcccagtac gagttggcat 4201 gaatatgaat gaagatggcc caataatatt tgagaaacat tccagataca aataccacta 4261 tgatgcagac tactctcgtt gggattcaac acaacagagg gcagtactag cagcagcctt 4321 ggaaatcatg gtcagattct ctgcagaacc acaattggca caaatagtcg ctgaggatct 4381 gctggcccct agtgtggtag atgtaggaga ctttaagatc acaataaatg aagggctccc 4441 atctggtgtg ccatgcactt ctcaatggaa ctccatcgca cactggctgc taactctctg 4501 tgccttgtct gaagtcacca aactgtcccc tgacattata caagcaaatt ccatgttctc 4561 attttacggt gatgacgaga ttgtcagcac cgacataaaa ttggaccctg aacagttaac 4621 cgccaagttg aaggagtacg gcctgaaacc aacccgccca gacaagaccg agggaccctt 4681 gatcatcagt gaagatttga acggactcac tttcctccga agaacggtga ctcgtgaccc 4741 agctggctgg tttggaaaac tggaccaaag ctcaattttg aggcagatgt actggactag 4801 aggaccaaat catgaagacc ccaatgagac aatgataccc cattctcaaa gacccataca 4861 gctcatggca ctgcttggtg aagcctctct ccacggaccc tctttctaca gcaaaatcag 4921 taaattggtc ataactgaac tcaaagaagg tgggatggac ttttacgtgc caaggcagga 4981 acccatgttc aggtggatga ggttttctga cttgagcacg tgggagggcg atcgcaatct 5041 ggctcccaat tttgtgaatg aagatggcgt cgagtgacgc caacccatct gatgggtccg 5101 cagccaacct cgtaccagag gtcaacaatg aggttatggc tttggaaccc gttgttggtg 5161 ccgctattgc ggcacctgta gcgggccaac aaaatgtaat tgacccctgg attagaaata 5221 attttgtaca agcccctggt ggggagttta cagtatcccc tagaaacgct ccaggtgaaa 5281 tactatggag cgcgccccta ggccctgacc taaatcccta cctatcccat ttggccagaa 5341 tgtataatgg ttatgcaggt ggttttgaag tgcaggtaat tctcgcgggg aacgcgttca 5401 ccgccgggaa gatcatattt gcagcagtcc caccaaattt tccaactgaa ggcttaagtc 5461 ctagccaggt cactatgttc ccccatataa tagtagatgt tagacaatta gaacctgtgc 5521 tgattccctt acccgatgtt aggaataatt tctatcatta tagtcagtca aatgattcca 5581 ctattaagtt gatagcaatg ttgtatacac cacttagggc taataatgct ggggatgatg 5641 ttttcacagt ttcgtgccga gttctcacga gaccatcccc cgattttgat ttcatatttt 5701 tagtgccacc cacagttgag tcaagaacta aaccattctc tatcccagtc ttaactgttg 5761 aggagatgac caattcaaga ttccccattc ctttggaaaa gttgttcacg ggccccagca 5821 gtgcctttgt tgttcaacca caaaacggca ggtgcacaac tgatggcgtg ctcctaggca 5881 ccacccaact gtctcctgtc aacatctgca ccttcagagg ggatgtcact cacatcacag 5941 gtagtcgcaa ctacacaatg aatttggctt ctcaaaattg gaacaactat gacccaacag 6001 aagaaatccc agcccctcta ggaactccag attttgtggg gaagattcaa ggcatgctca 6061 cccaaaccac aaggacagat ggttcaacac gcggccacaa agctacagtg tacactggga 6121 gcgccgactt tgctccaaaa ctgggtagag ttcaatttga aactgacaca gaccatgatt 6181 ttgaggctaa tcaaaacaca aagttcaccc cagtcggtgt catccaagat ggtagcacca 6241 cccaccgaaa cgaaccccaa cagtgggtgc tcccaagtta ctcaggcaga aacactcaca 6301 atgtacatct ggcccccgct gtagccccca cctttccggg tgagcaactt ctcttcttca 6361 gatccaccat gcccggatgc agcgggtacc ccaacatgga tttggactgt ctgctccccc 6421 aggaatgggt gcagtacttt taccaagagg cagccccagc acaatctgat gtggccctgc 6481 taagatttgt gaatccagac acaggtaggg ttttgtttga gtgcaagctt cacaaatcag 6541 gctatgttac agtggctcac actggccaac atgatctggt tatccccccc aatggttact 6601 ttaggtttga ctcctgggtc aaccagttct acacacttgc ccccatggga aatggaacgg 6661 ggcgtaggcg tgtagtataa tggctggagc tttctttgct ggattggcat ctgatgtcct 6721 tggctctgga cttggttccc ttatcaatgc tggggctggg gccatcaacc aaaaagttga 6781 gtttgaaaat aacagaaaat tgcaacaagc atccttccaa tttagcagca atctgcaaca 6841 ggcttccttt caacatgata aagagatgct ccaagcacaa attgaggcca ccaaaaagct 6901 acaacaggaa atgatgaaag tcaagcaggc agtgctccta gagggtgggt tctctgagac 6961 agatgcagcc cgcggggcaa ttaacgcccc catgacaaaa gctttggact ggagcgggac 7021 aaggtactgg gctcccgatg ctaggactac aacatacaat gcaggccgct tttccacccc 7081 tcaaccatcg ggggcactgc cagggagagc taaccttagg gatactgtcc ctgctcgggg 7141 accctccaac aaatcttcta actcttccac tgccacctct gtgtattcaa atcaaactat 7201 ttcaacgaga cttggttcta cagctggttc tggaaccagt gtctcgagcc tcccgtcaac 7261 tgcaaggact aggagctggg ttgaggatca aagtaggaat ttgtcacctt tcatgagggg 7321 ggcccacaat atatcatttg tcaccccacc atctagcaga tcctctagcc aaggcacagt 7381 ctcaaccgtg cctaaagaga ttttggactc ctggactggc gccttcaaca cgcgcaggca 7441 gcctctctt //