Typing tool
|
Complete norovirus genomes
MH260491 | GII.4 Sydney | ||
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GII.P16 |
ORF1: 1..5063 ORF2: 5044..6666 ORF3: 6666..7472LOCUS MH260491 7495 bp RNA linear VRL 16-JUN-2018 DEFINITION Norovirus GII isolate ST256 nonstructural polyprotein (ORF1) gene, partial cds; and VP1 (ORF2) and VP2 (ORF3) genes, complete cds. ACCESSION MH260491 VERSION MH260491.1 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 7495) 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reveals discrete transmission clusters and elucidates long-term sequelae of hospital acquired infections JOURNAL Unpublished REFERENCE 2 (bases 1 to 7495) AUTHORS Casto,A.M., Adler,A., Huang,M.-L., Makhsous,N., Xie,H., Zerr,D. and Greninger,A. TITLE Direct Submission JOURNAL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..7495 /organism="Norovirus GII" /mol_type="genomic RNA" /isolate="ST256" /host="Homo sapiens" /db_xref="taxon:122929" /country="USA" /collection_date="2017" /note="genotype: GII" gene <1..5063 /gene="ORF1" CDS <1..5063 /gene="ORF1" /codon_start=3 /product="nonstructural polyprotein" /protein_id="AWT08329.1" /translation="CNNNNDKEKSSGEGLFTNMSSTLKKALGARPKQPAPRDEPQKPP RPPTPELVKRIPPPPPNGEEEEEPVIRYEVKSGISGLPELTTVPQPDVANTAFSVPPL SLRENREAKEPLTGAILEMWDGEIYHYGMYVEKGLVLGVHKPPAAISMARVELTPLSL YWRVVYTPQYLISPETLRRLNGEAFPYTAFDNNCYAFCCWVLDLNDSWLSRRMVQRTT GFFRPYQDWNRKPLPTMDDSKIKKVANIFLCSLSTLFTRPIKDLIGKIKPLNILNILA TCDWTFAGIVESLILLAELFGVFWTPPDVSAMIAPLLGDYELQGPEDLAVELVPVVMG GVGLVLGFTKEKIGKMLSSAASTLRACKDLGAYGLEILKLVMKWFFPKKEEANELAMV RAIEDAVLDLEAIENNHMTALLKDKDSLATYMKTLDMEEEKARRLSTKSASPDIVGTI NALLARIAAARSLVHRAKEELSSRIRPVVVMISGKPGIGKTHLAREVARKVASTLTGD QRVGLIPRNGVDHWDAYKGERVVLWDDYGMSNPIHDALRIQELADTCPLTLNCDRIEN KGKVFDSEVIIITTNLANPAPLDYVNFEACSRRIDFLVYAEAPEVEKAKRDFPGQPDM WKDAFKPDFSHIKLQLAPQGGFDKNGNTPHGKGVMKTLTTGSLIARASGLLHERMDEF ELQGPTITTFNFDRNRITAFRQLAAENKYGLVDTMKVGNQLKGVKTMEELKQAIRNVT IKRCRIIYGGSTYDLESDGKGKVLVEKVKNTSVQTNNELVGALHHLKHARIRYYVKCV QEAVYSIIQIAGAAFVTTRIARRMNIQELWSKPQLDQNESETKEEAPKSEDDEFIISS KDIKEEGKKGKNKTGRGKKHTAFSSKGLSDEEYDEYKRIREERNGKYSIEEYLQDRDR YYEELAIAKATEEDFCEEEEIKIRQRIFRPTRKQRKEERATLGLVTGSEIRKRNPDDF KPKGKLWADDNRSVDYNEKLDFEAPPSIWSRIVSFGSGWGFWVSPSLFITSTHVIPAG ITEAFGVPVKQIQIHKSGEFCRFRFPKPIRPDVTGMILEEGAPEGTVATVLIKRPTGE LMPLAARMGTHATMKIQGRMVGGQMGMLLTGSNAKGMDLGTTPGDCGCPYIYKRGNDY IVIGVHTAAARGGNTVICATQGSEGEATLEGGDDKGTYCGAPILGPGGAPKLSTKTKF WRSSNTPLPPGTYEPAYLGGRDPRVKGGPSLQQVMRDQLKPFTEPRGKPPRPSVLEAA KQTIINVLEQTLDPPQKWTYAQACASLDKTTSSGHPHHVRKNEFWNGETFTGKLADQA SKANLMYEEGKHMTPVYTAALKDELVKTEKIYGKIKKRLLWGSDLSTMIRCARSFGGL MDEMKAHCISLPVRVGMNMNEDGPIVFEKHSRYKYHYDADYSRWDSTQQRAVLAAALE IMVRFSAEPQLAQIVAEDLLAPSVVDVGDFKITINEGLPSGVPCTSQWNSIAHWLLTL CALSEVTKLSPDIIQANSMFSFYGDDEIVSTDIKLDPEQLTAKLKEYGLKPTRPDKTE GPLIISEDLNGLTFLRRTVTRDPAGWFGKLDQSSILRQMYWTRGPNHEDPNETMIPHS QRPIQLMALLGEASLHGPSFYSRISKLVITELKEGGMDFYVPRQEPMFRWMRFSDLST WEGDRNLAPNFVNEDGVE" mat_peptide <1..959 /gene="ORF1" /product="p48" mat_peptide 960..2057 /gene="ORF1" /product="NTPase" mat_peptide 2058..2588 /gene="ORF1" /product="p22" mat_peptide 2589..2987 /gene="ORF1" /product="VPg" mat_peptide 2988..3530 /gene="ORF1" /product="Pro" mat_peptide 3531..5060 /gene="ORF1" /product="RdRp" gene 5044..6666 /gene="ORF2" CDS 5044..6666 /gene="ORF2" /note="major capsid protein" /codon_start=1 /product="VP1" /protein_id="AWT08327.1" /translation="MKMASSDANPSDGSAANLVPEVNNEVMALEPVVGAAIAAPVAGQ QNVIDPWIRNNFVQAPGGEFTVSPRNAPGEILWSAPLGPDLNPYLSHLARMYNGYAGG FEVQVILAGNAFTAGKIIFAAVPPNFPTEGLSPSQVTMFPHIIVDVRQLEPVLIPLPD VRNNFYHYNQSNDSTIKLIAMLYTPLRANNAGDDVFTVSCRVLTRPSPDFDFIFLVPP TVESRTKPFSVPVLTVEEMTNSRFPIPLEKLFTGPSSAFVVQPQNGRCTTDGVLLGTT QLSSVNVCTFRGGVTHITGSRNYTMNLASQNWNNYDPTEEIPAPLGTPDFVGKIQGML TQTTRTDGSTRGHKATVYTGSADFAPKLGRVQFETDTDHDFEANQNTKFTPVGVIQDG STTHRNEPQQWVLPSYSGRNTHNVHLAPAVAPTFPGEQLLFFRSTMPGCSGYPNMDLD CLLPQEWVQYFYQEAAPAQSDVALLRFVNPDTGRVLFECKLHKSGYVTVAHTGQHDLV IPPNGYFRFDSWVNQFYTLAPMGNGTGRRRVV" gene 6666..7472 /gene="ORF3" CDS 6666..7472 /gene="ORF3" /note="minor structural protein; small basic protein" /codon_start=1 /product="VP2" /protein_id="AWT08328.1" /translation="MAGAFFAGLASDVLGSGLGSLINAGAGAINQKVEFENNRKLQQA SFQFSSNLQQASFQHDKEMLQAQIEATKKLQQEMMKVKQAMLLEGGFSETDAARGAIN APMTKALDWSGTRYWAPDARITTYNAGHFSTPQPSRALPGRANLRDAVPARGPSNKSS NSSIATSVYSNQTISTRLGSTAGSGTSVSSLPSTARTRSWVEDQNRNLSPFMRGAHNI SFVTPPSSRSSSQGTVSTVPKEILDSWTGAFNTRRQPLFAHIRKRGESRV" ORIGIN 1 cttgcaacaa caacaacgac aaggaaaaat cttcaggtga aggcttattt acaaatatgt 61 cttccacctt aaagaaagcc ctcggggcta ggcccaaaca gcctgccccg agagacgaac 121 cacaaaagcc cccaagacca ccaactcccg agttggtcaa gaggataccc cctcctccac 181 ctaatggcga agaagaagaa gaaccagtca ttaggtatga ggttaagagt gggatctctg 241 gcctgcccga gctcacaaca gtcccccagc cggacgtggc caacacagca ttcagtgttc 301 caccactgag cttgagagaa aacagggagg ccaaggaacc gctaacaggg gcaatattag 361 agatgtggga cggagagata taccactatg gcatgtacgt ggagaaaggc ttagtgttgg 421 gtgtgcacaa accacctgca gccataagca tggcaagagt ggagctgacg ccgttgtcat 481 tgtactggcg tgtggtgtac actccccaat acctcatctc ccctgaaact ctcaggaggc 541 tcaacggaga ggcgttccct tacaccgcct tcgacaacaa ctgctatgcc ttttgctgct 601 gggtgttaga cctcaatgac tcatggctta gcaggaggat ggtgcaaaga acaacgggct 661 tcttcagacc ttaccaagat tggaacagaa aacccctgcc taccatggat gactccaaaa 721 taaagaaggt agcaaatata ttcctatgtt cattgtccac attgtttacc agacccataa 781 aagacctcat aggaaaaatt aaaccattaa acatattgaa catcctggca acgtgtgact 841 ggacgtttgc cggaatagtg gagtctctga tattacttgc tgaactcttc ggagttttct 901 ggacaccccc agatgtgtct gctatgatcg ctcccttact cggggattac gagttgcaag 961 ggccagaaga tctcgccgtt gaactcgtac ctgtggtaat gggaggggtt ggtttggtgt 1021 tgggattcac caaagagaaa attggcaaaa tgttgtcctc agcagcatca acactcaggg 1081 cttgcaaaga tcttggtgcc tatggcttag agatactcaa attggtcatg aagtggttct 1141 tcccaaagaa agaggaggcc aatgaactag ccatggtgag ggccatagag gatgccgtac 1201 tagatcttga ggcgatagaa aataaccaca tgacagccct gttgaaagac aaagacagct 1261 tagcaacata catgaaaaca ctggacatgg aggaggagaa agccagaagg ttgtccacaa 1321 aatctgcatc ccctgacata gttgggacaa tcaacgccct gctggctcga atagcagcgg 1381 ccaggtcatt agtccacagg gccaaggaag agctatctag caggataaga ccagtagttg 1441 ttatgatatc tggcaaacca ggaataggca aaactcatct ggccagggag gtggcaagaa 1501 aggtggcatc cactctcaca ggggatcaaa gagtcggact cataccaaga aacggtgtgg 1561 accactggga tgcatacaaa ggtgagagag tcgtgctgtg ggacgactat ggcatgagta 1621 accccattca tgatgctctt cgcatacagg aattggctga tacgtgcccc cttaccttaa 1681 attgtgacag aattgaaaat aagggaaaag tttttgacag tgaagtcata ataattacaa 1741 caaaccttgc caacccagcc ccacttgatt atgtcaactt tgaggcctgt tccaggagaa 1801 ttgatttcct ggtgtacgct gaggcaccag aagtagaaaa ggcaaaacgg gactttcctg 1861 gtcagccaga tatgtggaag gacgccttca agccggactt ttcacacatc aagttacagc 1921 ttgcacctca gggcggcttt gacaagaatg gcaacacccc acatgggaaa ggagtgatga 1981 agaccctcac tactggttct ctgattgccc gtgcatcagg cctactgcat gagaggatgg 2041 atgaatttga actccaaggt cccacaatca ccaccttcaa tttcgaccgg aacagaatca 2101 cagcattcag acaattggct gcagaaaaca agtatggatt ggtggatacc atgaaagttg 2161 gcaatcaact aaaaggagtg aaaaccatgg aagaactcaa acaagcaatc aggaatgtga 2221 ccatcaagag gtgccgaatc atctatggtg gctccacgta tgaccttgaa tctgatggca 2281 agggcaaagt tttggtggaa aaggtcaaga acacctctgt acagaccaac aacgagttgg 2341 tcggggccct gcaccacctc aaacacgccc gaatcaggta ctatgtcaaa tgtgtgcaag 2401 aagcagtcta ttccatcata caaattgccg gcgctgcgtt tgtcaccacg cgcattgcac 2461 gccgcatgaa catacaagaa ctctggtcga agccacaatt agaccaaaat gaatcagaga 2521 ctaaggaaga ggcccccaag tcagaagatg acgagttcat catatcttct aaggacatca 2581 aggaggaagg aaagaagggc aaaaacaaaa ctggccgtgg caagaaacac actgcattct 2641 ccagcaaggg cttgagcgat gaagagtatg acgagtacaa gaggataaga gaagagagaa 2701 atgggaagta ctctatagag gagtatcttc aagatagaga caggtactat gaggagctcg 2761 ccattgccaa ggccacggag gaagacttct gtgaagagga ggagatcaaa atccgtcaga 2821 gaattttccg tcccaccagg aaacaaagaa aggaagagag ggccacatta gggctggtga 2881 caggttcaga aatcagaaaa agaaaccccg atgacttcaa acccaaaggg aagctgtggg 2941 ccgatgacaa cagaagtgtt gactacaatg agaaactgga ctttgaggcc cccccaagca 3001 tatggtctag gattgtgagc tttggttctg gctggggctt ctgggtatca ccaagcctgt 3061 tcataacatc aactcatgta atccccgcag gcataacaga agcatttgga gtccccgtca 3121 aacaaattca gatccacaaa tcaggtgaat tctgccgatt cagattccca aaaccaatta 3181 gaccagatgt gacagggatg atcttggaag aaggtgcgcc tgagggcacc gtggcaactg 3241 tgctcatcaa acgccccacc ggagagctca tgcctcttgc agccagaatg ggaacacacg 3301 caaccatgaa aattcaaggc cgcatggttg gcggacagat gggtatgttg ctcactggat 3361 caaatgctaa aggaatggat ttgggaacaa ctcctggtga ctgtggctgt ccttacatct 3421 ataaaagggg caatgactat atagtcattg gggtgcacac tgcagcagcc cgtggtggaa 3481 acaccgtcat ctgtgccaca cagggaagtg agggtgaggc aactcttgag ggtggagatg 3541 acaaaggaac atactgtggg gcacccattc taggccctgg gggtgcacca aaattgagca 3601 ccaaaaccaa attttggagg tcatcgaaca cgccccttcc accagggaca tatgagcctg 3661 cctacctcgg tggccgtgat ccgcgtgtta agggtgggcc ctccttgcag caggtgatga 3721 gagaccagtt gaagccattc actgaaccca ggggcaaacc tccaagacca agtgtattgg 3781 aagcagccaa acaaaccatt atcaatgttc tcgaacaaac cctggaccct ccgcaaaagt 3841 ggacatacgc acaggcgtgt gcctcacttg acaaaaccac ctccagcggg catccccatc 3901 acgtccgaaa gaatgaattc tggaatggtg agaccttcac tggtaaactg gcagaccaag 3961 catcaaaagc aaacctaatg tatgaggaag ggaaacacat gacaccagtg tatacagcag 4021 cactcaagga cgagctagtc aagactgaga aaatctatgg aaagatcaag aagagactgc 4081 tctggggctc tgacttgtcc actatgatcc ggtgcgctag gtcatttggt gggctcatgg 4141 acgagatgaa ggcacactgc atatcactcc cagtacgagt tggcatgaat atgaatgaag 4201 atggcccaat agtatttgag aaacattcca gatacaaata ccactatgat gcagactact 4261 ctcgttggga ttcaacacaa cagagggcag tgctagcagc agccttggaa atcatggtca 4321 gattctctgc agaaccacaa ttggcacaaa tagtcgctga ggatctactg gcccctagtg 4381 tagtagatgt aggagacttt aaaatcacaa taaatgaagg gctcccatct ggtgtgccat 4441 gcacttctca atggaactcc atcgcacact ggctgctaac tctctgtgcc ttgtctgaag 4501 tcaccaaact gtcccctgac attatacaag caaattccat gttctcattt tacggtgatg 4561 acgagattgt cagcaccgac ataaaattgg accctgaaca gttaactgcc aagctgaagg 4621 agtacggcct gaaaccaacc cgcccagaca agaccgaggg acccctgatc atcagtgaag 4681 atttaaacgg actcaccttc ctccgtagga cggtgactcg tgacccagct ggctggtttg 4741 gaaaactgga ccaaagttca atcttgaggc aaatgtactg gactagagga ccaaatcatg 4801 aagaccccaa tgaaacaatg ataccccact ctcaaagacc catacagctc atggcactgc 4861 ttggtgaagc ctctcttcac ggaccctctt tctatagtag aatcagtaaa ttggtcataa 4921 ctgaactcaa agaaggtggg atggactttt acgtgccaag gcaggaaccc atgttcaggt 4981 ggatgaggtt ttctgacttg agcacgtggg agggcgatcg caatctggct cccaattttg 5041 tgaatgaaga tggcgtcgag tgacgccaac ccatctgatg ggtccgcagc caacctcgta 5101 ccagaggtca acaatgaggt tatggctttg gagcccgttg ttggtgccgc tattgcggca 5161 cctgtagcgg gccaacaaaa tgtaattgac ccctggatta gaaataattt tgtacaagcc 5221 cctggtgggg agtttacagt atcccctaga aacgctccag gtgaaatact atggagcgcg 5281 cccctaggcc ctgacctaaa tccctaccta tcccatttgg ccagaatgta caatggttat 5341 gcaggtggtt ttgaagtgca ggtaattctc gcggggaacg cgttcaccgc cgggaagatt 5401 atatttgcag cagtcccacc aaattttcca actgaaggct taagtcctag ccaggttact 5461 atgttccccc atataatagt agatgttaga caattagaac ctgtgctgat tcccttaccc 5521 gatgttagga ataacttcta tcattacaat cagtcaaatg attccactat taagttgata 5581 gcaatgttgt atacaccact tagggctaat aatgctgggg atgatgtttt cacagtttcg 5641 tgtcgagtcc tcacgagacc atcccccgat tttgatttca tatttttggt gccacccacg 5701 gttgagtcaa gaactaagcc attctctgtc ccagttttaa ctgttgagga gatgaccaat 5761 tcaagattcc ccatcccttt ggaaaagttg ttcacaggcc ccagcagtgc ctttgttgtt 5821 caaccacaaa acggcaggtg cacaactgat ggcgtgctcc taggcaccac ccaactttct 5881 tctgtcaacg tctgcacctt cagagggggt gtcacccaca tcacaggtag tcgcaactac 5941 acaatgaatt tggcttctca aaattggaac aactatgacc caacagaaga aatcccagcc 6001 cctctaggaa ctccagattt tgtggggaag attcaaggca tgctcaccca aaccacaagg 6061 acagatggct caacacgcgg ccacaaagct acagtgtaca ctgggagcgc cgactttgct 6121 ccaaaactgg gtagagttca atttgaaact gacacagacc atgattttga agctaatcaa 6181 aacacaaagt tcaccccagt cggtgtcatc caagatggta gcaccaccca ccgaaacgaa 6241 ccccaacagt gggtgctccc aagttactca ggcagaaata ctcacaatgt acatttggcc 6301 cccgctgtag cccccacttt tccgggtgag caacttctct tcttcagatc caccatgccc 6361 ggatgcagcg ggtaccccaa catggatttg gactgtctgc tcccccagga atgggtgcag 6421 tatttctacc aagaggcagc cccagcacaa tctgatgtgg ctctgctaag atttgtgaat 6481 ccagacacag gtagggtttt gtttgagtgc aagcttcaca aatcaggcta tgttacagtg 6541 gctcacactg gccaacatga tttggttatc ccccccaatg gttactttag gtttgattcc 6601 tgggtcaacc agttctacac gcttgccccc atgggaaatg gaacggggcg tagacgtgta 6661 gtataatggc tggagctttc tttgctggat tggcatctga tgtccttggc tctggacttg 6721 gttcccttat caatgctggg gctggggcca tcaaccaaaa agtcgagttt gaaaataaca 6781 gaaaattgca acaagcatcc ttccaattta gcagcaatct gcaacaggct tcttttcaac 6841 atgataaaga gatgctccaa gcacaaattg aggccaccaa aaagctacaa caggaaatga 6901 tgaaagttaa gcaggcaatg ctcctagagg gtgggttctc tgagacagat gcagcccgcg 6961 gggcaattaa cgcccccatg acaaaagctt tggactggag cgggacaagg tactgggctc 7021 cagatgctag gattacaaca tacaatgcag gccacttttc cacccctcaa ccatcgaggg 7081 cactgccagg aagagctaat cttagggatg ctgtccctgc acggggaccc tccaataaat 7141 cttctaactc ttctattgcc acctctgtgt attcaaatca aactatttca acgagacttg 7201 gttctacagc tggttctgga accagtgtct ctagcctccc gtcaactgca aggactagga 7261 gctgggttga ggatcaaaat aggaatttgt cacctttcat gaggggggcc cacaacatat 7321 cgtttgtcac cccaccatct agcagatcct ctagccaagg cacagtctca accgtgccta 7381 aagagatttt ggactcctgg actggcgctt tcaacacgcg caggcagcct ctcttcgctc 7441 acattcgtaa gcgaggggag tcacgggtgt aatgtgaaaa gacaaaactg attat //