Typing tool
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Complete norovirus genomes
MH279825 | GII.4 Sydney | ||
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GII.P16 |
ORF1: 1..5093 ORF2: 5074..6696 ORF3: 6696..7502LOCUS MH279825 7525 bp RNA linear VRL 01-JUL-2018 DEFINITION Norovirus GII strain ST90 nonstructural polyprotein (ORF1) gene, partial cds; and VP1 (ORF2) and VP2 (ORF3) genes, complete cds. ACCESSION MH279825 VERSION MH279825.1 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 7525) 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reveals discrete transmission clusters and elucidates long-term sequelae of hospital acquired infections JOURNAL Unpublished REFERENCE 2 (bases 1 to 7525) AUTHORS Casto,A.M., Adler,A., Huang,M.-L., Makhsous,N., Xie,H., Zerr,D. and Greninger,A. TITLE Direct Submission JOURNAL Submitted (30-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..7525 /organism="Norovirus GII" /mol_type="genomic RNA" /strain="ST90" /host="Homo sapiens" /db_xref="taxon:122929" /country="USA" /collection_date="2017" gene <1..5093 /gene="ORF1" CDS <1..5093 /gene="ORF1" /codon_start=3 /product="nonstructural polyprotein" /protein_id="AWX06075.1" /translation="ASNDATVAVACNNNNDKEKSSGEGLFTNMSSTLKKALGARPKQP APRDEPQKPPRPPTPELVKRIPPPPPNGEGEEEPVIRYEVKSGISGLPELTTVPQPDV ANTAFSVPPLSLRENREAKEPLTGAILEMWDGEIYHYGLYVEKGLVLGVHKPPAAISM ARVELTPLSLYWRVVYTPQYLISPETLRRLNGEAFPYTAFDNNCYAFCCWVLDLNDSW LSRRMVQRTTGFFRPYQDWNRKPLPTMDDSKIKKVANIFLCSLSTLFTRPIKDLIGKI KPLNILNILATCDWTFAGIVESLILLAELFGVFWTPPDVSAMIAPLLGDYELQGPEDL AVELVPVVMGGVGLVLGFTKEKIGKMLSSAASTLRACKDLGAYGLEILKLVMKWFFPK KEEANELAMVRAIEDAVLDLEAIENNHMTALLKDKDSLATYMKTLDMEEEKARRLSTK SASPDIVGTINALLARIAAARSLVHRAKEELSSRIRPVVVMISGKPGIGKTHLAREVA RKVASTLTGDQRVGLIPRNGVDHWDAYKGERVVLWDDYGMSNPIHDALRIQELADTCP LTLNCDRIENKGKVFDSEVIIITTNLANPAPLDYVNFEACSRRIDFLVYAEAPEVEKA KRDFPGQPDMWKDAFKPDFSHIKLQLAPQGGFDKNGNTPHGKGVMKTLTTGSLIARAS GLLHERMDEFELQGPTITTFNFDRNRITAFRQLAAENKYGLVDTMKVGNQLKGVKTME ELKQAIRNVTIKRCRIIYGGSTYDLESDGKGKVLVEKVKNTSVQTNNELVGALHHLKH ARIRYYVKCVQEAVYSIIQIAGAAFVTTRIARRMNIQELWSKPQLDQNESETKEEAPK SEDDEFIISSKDIKEEGKKGKNKTGRGKKHTAFSSKGLSDEEYDEYKRIREERNGKYS IEEYLQDRDRYYEELAIAKATEEDFCEEEEIKIRQRIFRPTRKQRKEERATLGLVTGS EIRKRNPDDFKPKGKLWADDNRSVDYNEKLDFEAPPSIWSRIVSFGSGWGFWVSPSLF ITSTHVIPAGITEAFGVPVKQIQIHKSGEFCRFRFPKPIRPDVTGMILEEGAPEGTVA TVLIKRPTGELMPLAARMGTHATMKIQGRMVGGQMGMLLTGSNAKGMDLGTTPGDCGC PYIYKRGNDYIVIGVHTAAARGGNTVICATQGSEGEATLEGGDDKGTYCGAPILGPGG APKLSTKTKFWRSSNTPLPPGTYEPAYLGGRDPRVKGGPSLQQVMRDQLKPFTEPRGK PPRPSVLEAAKQTIINVLEQTLDPPQKWTYAQACASLDKTTSSGHPHHVRKNEFWNGE TFTGKLADQASKANLMYEEGKHMTPVYTAALKDELVKTEKIYGKIKKRLLWGSDLSTM IRCARSFGGLMDEMKAHCISLPVRVGMNMNEDGPIVFEKHSRYKYHYDADYSRWDSTQ QRAVLAAALEIMVRFSAEPQLAQIVAEDLLAPSVVDVGDFKITINEGLPSGVPCTSQW NSIAHWLLTLCALSEVTKLSPDIIQANSMFSFYGDDEIVSTDIKLDPEQLTAKLKEYG LKPTRPDKTEGPLIISEDLNGLTFLRRTVTRDPAGWFGKLDQSSILRQMYWTRGPNHE DPNETMIPHSQRPIQLMALLGEASLHGPSFYSRISKLVITELKEGGMDFYVPRQEPMF RWMRFSDLSTWEGDRNLAPNFVNEDGVE" mat_peptide <1..989 /gene="ORF1" /product="p48" mat_peptide 990..2087 /gene="ORF1" /product="NTPase" mat_peptide 2088..2618 /gene="ORF1" /product="p22" mat_peptide 2619..3017 /gene="ORF1" /product="VPg" mat_peptide 3018..3560 /gene="ORF1" /product="Pro" mat_peptide 3561..5090 /gene="ORF1" /product="RdRp" gene 5074..6696 /gene="ORF2" CDS 5074..6696 /gene="ORF2" /codon_start=1 /product="VP1" /protein_id="AWX06073.1" /translation="MKMASSDANPSDGSAANLVPEVNNEVMALEPVVGAAIAAPVAGQ QNVIDPWIRNNFVQAPGGEFTVSPRNAPGEILWSAPLGPDLNPYLSHLARMYNGYAGG FEVQVILAGNAFTAGKIIFAAVPPNFPTEGLSPSQVTMFPHIIVDVRQLEPVLIPLPD VRNNFYHYNQSNDSTIKLIAMLYTPLRANNAGDDVFTVSCRVLTRPSPDFDFIFLVPP TVESRTKPFSVPVLTVEEMTNSRFPIPLEKLFTGPSSAFVVQPQNGRCTTDGVLLGTT QLSSVNVCTFRGGVTHITGSRNYTMNLASQNWNNYDPTEEIPAPLGTPDFVGKIQGML TQTTRTDGSTRGHKATVYTGSADFAPKLGRVQFETDTDHDFEANQNTKFTPVGVIQDG STTHRNEPQQWVLPSYSGRNTHNVHLAPAVAPTFPGEQLLFFRSTMPGCSGYPNMDLD CLLPQEWVQYFYQEAAPAQSDVALLRFVNPDTGRVLFECKLHKSGYVTVAHTGQHDLV IPPNGYFRFDSWVNQFYTLAPMGNGTGRRRVV" gene 6696..7502 /gene="ORF3" CDS 6696..7502 /gene="ORF3" /codon_start=1 /product="VP2" /protein_id="AWX06074.1" /translation="MAGAFFAGLASDVLGSGLGSLINAGAGAINQKVEFENNRKLQQA SFQFSSNLQQASFQHDKEMLQAQIEATKKLQQEMMKVKQAMLLEGGFSETDAARGAIN APMTKALDWSGTRYWAPDARITTYNAGHFSTPQPSRALPGRANLRDAVPARGPSNKSS NSSIATSVYSNQTISTRLGSTAGSGTSVSSLPSTARTRSWVEDQNRNLSPFMRGAHNI SFVTPPSSRSSSQGTVSTVPKEILDSWTGAFNTRRQPLFAHIRKRGESRV" ORIGIN 1 tggcgtctaa cgacgctacc gttgccgttg cttgcaacaa caacaacgac aaggaaaaat 61 cttcaggtga aggcttattc acaaatatgt cttccacctt aaagaaagcc ctcggggcta 121 ggcccaaaca gcctgccccg agagacgaac cacaaaagcc cccaagacca ccaactcccg 181 agttggtcaa gaggataccc cctcctccac ctaatggcga aggagaagaa gaaccagtca 241 ttaggtatga ggttaagagt gggatctctg gcctgcccga gctcacaaca gtcccccagc 301 cggacgtggc caacacagca ttcagtgttc caccactgag cttgagagaa aacagggagg 361 ccaaggaacc gctaacaggg gcaatattag agatgtggga cggagagata taccactatg 421 gcctgtacgt ggagaaaggc ttagtgttgg gtgtgcacaa accacctgca gccataagca 481 tggcaagagt ggagctgacg ccgttgtcat tgtactggcg tgtggtgtac actccccaat 541 acctcatctc ccctgaaact ctcaggaggc tcaacggaga ggcgttccct tacaccgcct 601 tcgacaacaa ctgctatgcc ttttgctgct gggtgttaga cctcaatgac tcatggctta 661 gcaggaggat ggtgcaaaga acaacgggct tcttcagacc ttaccaagat tggaacagaa 721 aacccctgcc taccatggat gactccaaaa taaagaaggt agcaaatata ttcctatgtt 781 cattgtccac attgtttacc agacccataa aagacctcat aggaaaaatt aaaccattaa 841 acatattgaa catcctggca acgtgtgact ggacgtttgc cggaatagtg gagtctctga 901 tattacttgc tgaactcttc ggagttttct ggacaccccc agatgtgtct gctatgatcg 961 ctcccttact cggggactac gagttgcaag ggccagaaga cctcgccgtt gaactcgtac 1021 ctgtggtaat gggaggggtt ggtttggtgt tgggattcac caaagagaaa attggcaaaa 1081 tgttgtcctc agcagcatca acactcaggg cttgcaaaga tcttggtgcc tatggcttag 1141 agatactcaa attggtcatg aagtggttct tcccaaagaa agaggaggcc aatgaactag 1201 ccatggtgag ggccatagag gatgccgtac tagatcttga ggcgatagaa aataaccaca 1261 tgacagccct gttgaaagac aaagacagct tagcaacata catgaaaaca ctggacatgg 1321 aggaggagaa agccagaagg ttgtccacaa aatctgcatc ccctgacata gttgggacaa 1381 tcaacgccct gctggctcga atagcagcgg ccaggtcatt agtccacagg gccaaggaag 1441 agctatctag caggataaga ccagtagttg ttatgatatc tggcaaacca ggaataggca 1501 aaactcatct ggccagggag gtggcaagaa aggtggcatc cactctcaca ggggatcaaa 1561 gagtcggact cataccaaga aacggtgtgg accactggga tgcatacaaa ggtgagagag 1621 tcgtgctgtg ggacgactat ggcatgagta accccattca tgatgctctt cgcatacagg 1681 aattggctga tacgtgcccc cttaccttaa attgtgacag aattgaaaat aagggaaaag 1741 tttttgacag tgaagtcata ataattacaa caaaccttgc caacccagcc ccacttgatt 1801 atgtcaactt tgaggcctgt tccaggagaa ttgatttcct ggtgtacgct gaggcaccag 1861 aagtagaaaa ggcaaaacgg gactttcctg gtcagccaga tatgtggaag gacgccttca 1921 agccggactt ttcacacatc aagttacagc ttgcacctca gggcggcttt gacaagaatg 1981 gcaacacccc acatgggaaa ggagtgatga agaccctcac tactggttct ctgattgccc 2041 gtgcatcagg cctactgcat gagaggatgg atgaatttga actccaaggt cccacaatca 2101 ccaccttcaa tttcgaccgg aacagaatca cagcattcag acaattggct gcagaaaaca 2161 agtatggatt ggtggatacc atgaaagttg gcaatcaact aaaaggagtg aaaaccatgg 2221 aagaactcaa acaagcaatc aggaatgtga ccatcaagag gtgccgaatc atctatggtg 2281 gctccacgta tgaccttgaa tctgatggca agggcaaagt tttggtggaa aaggtcaaga 2341 acacctctgt acagaccaac aacgagttgg tcggggccct gcaccacctc aaacacgccc 2401 gaatcaggta ctatgtcaaa tgtgtgcaag aagcagtcta ttccatcata caaattgccg 2461 gcgctgcgtt tgtcaccacg cgcattgcac gccgcatgaa catacaagaa ctctggtcga 2521 agccacaatt agaccaaaat gaatcagaga ctaaggaaga ggcccccaag tcagaagatg 2581 acgagttcat catatcttct aaggacatca aggaggaagg aaagaagggc aaaaacaaaa 2641 ctggccgtgg caagaaacac actgcattct ccagcaaggg cttgagcgat gaagagtatg 2701 acgagtacaa gaggataaga gaagagagaa atgggaagta ctctatagag gagtatcttc 2761 aagacagaga caggtactat gaggagctcg ccattgccaa ggccacggag gaagacttct 2821 gtgaagagga ggagatcaaa atccgtcaga gaattttccg tcccaccagg aaacaaagaa 2881 aggaagagag ggccacatta gggctggtga caggttcaga aatcagaaaa agaaaccccg 2941 atgacttcaa acccaaaggg aagctgtggg ccgatgacaa cagaagtgtt gactacaatg 3001 agaaactgga ctttgaggcc cccccaagca tatggtctag gattgtgagc tttggttctg 3061 gctggggctt ctgggtatca ccaagcctgt tcataacatc aactcatgta atccccgcag 3121 gcataacaga agcatttgga gtccccgtca aacaaattca gatccacaaa tcaggtgaat 3181 tctgccgatt cagattccca aaaccaatta gaccagatgt gacagggatg atcttggaag 3241 aaggtgcgcc tgaaggcacc gtggcaactg tgctcatcaa acgccccacc ggagagctca 3301 tgcctcttgc agccagaatg ggaacacacg caaccatgaa aattcaaggc cgcatggttg 3361 gcggacagat gggtatgttg ctcactggat caaatgctaa aggaatggat ttgggaacaa 3421 ctcctggtga ctgtggctgt ccttacatct ataaaagggg caatgactat atagtcattg 3481 gggtgcacac tgcagcagcc cgtggtggaa acaccgtcat ctgtgccaca cagggaagtg 3541 agggtgaggc aactcttgag ggtggagatg acaaaggaac atactgtggg gcacccattc 3601 taggccctgg gggtgcacca aaattgagca ccaaaaccaa attttggagg tcatcgaaca 3661 cgccccttcc accagggaca tatgagcctg cctacctcgg tggccgtgat ccgcgtgtta 3721 agggtgggcc ctccttgcag caggtgatga gagaccagtt gaagccattc actgaaccca 3781 ggggcaaacc tccaagacca agtgtattgg aagcagccaa acaaaccatt atcaatgttc 3841 tcgaacaaac cctggaccct ccgcaaaagt ggacatacgc acaggcgtgt gcctcacttg 3901 acaaaaccac ctccagcggg catccccatc acgtccgaaa gaatgaattc tggaatggtg 3961 agaccttcac tggtaaactg gcagaccaag catcaaaagc aaacctaatg tatgaggaag 4021 ggaaacacat gacaccagtg tatacagcag cactcaagga cgagctagtc aagactgaga 4081 aaatctatgg aaagatcaag aagagactgc tctggggctc tgacttgtcc actatgatcc 4141 ggtgcgctag gtcatttggt gggctcatgg acgagatgaa ggcacactgc atatcactcc 4201 cagtacgagt tggcatgaat atgaatgaag atggcccaat agtatttgag aaacattcca 4261 gatacaaata ccactatgat gcagactact ctcgttggga ttcaacacaa cagagggcag 4321 tgctagcagc agccttggaa atcatggtca gattctctgc agaaccacaa ttggcacaaa 4381 tagtcgctga ggatctactg gcccctagtg tagtagatgt aggagacttt aaaatcacaa 4441 taaatgaagg gctcccatct ggtgtgccat gcacttctca atggaactcc atcgcacact 4501 ggctgctaac tctctgtgcc ttgtctgaag tcaccaaact gtcccctgac attatacaag 4561 caaattccat gttctcattt tacggtgatg acgagattgt cagcaccgac ataaaattgg 4621 accctgaaca gttaactgcc aagctgaagg agtacggcct gaaaccaacc cgcccagaca 4681 agaccgaggg acccctgatc atcagtgaag atttaaacgg actcaccttc ctccgtagga 4741 cggtgactcg tgacccagct ggctggtttg gaaaactgga ccaaagttca atcttgaggc 4801 aaatgtactg gactagagga ccaaatcatg aagaccccaa tgaaacaatg ataccccact 4861 ctcaaagacc catacagctc atggcactgc ttggtgaagc ctctcttcac ggaccctctt 4921 tctatagtag aatcagtaaa ttggtcataa ctgaactcaa agaaggtggg atggactttt 4981 acgtgccaag gcaggaaccc atgttcaggt ggatgaggtt ttctgacttg agcacgtggg 5041 agggcgatcg caatctggct cccaattttg tgaatgaaga tggcgtcgag tgacgccaac 5101 ccatctgatg ggtccgcagc caacctcgta ccagaggtca acaatgaggt tatggctttg 5161 gagcccgttg ttggtgccgc tattgcggca cctgtagcgg gccaacaaaa tgtaattgac 5221 ccctggatta gaaataattt tgtacaagcc cctggtgggg agtttacagt atcccctaga 5281 aacgctccag gtgaaatact atggagcgcg cccctaggcc ctgacctaaa tccctaccta 5341 tcccatttgg ccagaatgta caatggttat gcaggtggtt ttgaagtgca ggtaattctc 5401 gcggggaacg cgttcaccgc cgggaagatt atatttgcag cagtcccacc aaattttcca 5461 actgaaggct taagtcctag ccaggttact atgttccccc atataatagt agatgttaga 5521 caattagaac ctgtgctgat tcccttaccc gatgttagga ataacttcta tcattacaat 5581 cagtcaaatg attccactat taagttgata gcaatgttgt atacaccact tagggctaat 5641 aatgctgggg atgatgtttt cacagtttcg tgtcgagtcc tcacgagacc atcccccgat 5701 tttgatttca tatttttggt gccacccacg gttgagtcaa gaactaagcc attctctgtc 5761 ccagttttaa ctgttgagga gatgaccaat tcaagattcc ccatcccttt ggaaaagttg 5821 ttcacaggcc ccagcagtgc ctttgttgtt caaccacaaa acggcaggtg cacaactgat 5881 ggcgtgctcc taggcaccac ccaactttct tctgtcaacg tctgcacctt cagagggggt 5941 gtcacccaca tcacaggtag tcgcaactac acaatgaatt tggcttctca aaattggaac 6001 aactatgacc caacagaaga aatcccagcc cctctaggaa ctccagattt tgtggggaag 6061 attcaaggca tgctcaccca aaccacaagg acagatggct caacacgcgg ccacaaagct 6121 acagtgtaca ctgggagcgc cgactttgct ccaaaactgg gtagagttca atttgaaact 6181 gacacagacc atgattttga agctaatcaa aacacaaagt tcaccccagt cggtgtcatc 6241 caagatggta gcaccaccca ccgaaacgaa ccccaacagt gggtgctccc aagttactca 6301 ggcagaaata ctcacaatgt acatttggcc cccgctgtag cccccacttt tccgggtgag 6361 caacttctct tcttcagatc caccatgccc ggatgcagcg ggtaccccaa catggatttg 6421 gactgtctgc tcccccagga atgggtgcag tatttctacc aagaggcagc cccagcacaa 6481 tctgatgtgg ctctgctaag atttgtgaat ccagacacag gtagggtttt gtttgagtgc 6541 aagcttcaca aatcaggcta tgttacagtg gctcacactg gccaacatga tttggttatc 6601 ccccccaatg gttactttag gtttgattcc tgggtcaacc agttctacac gcttgccccc 6661 atgggaaatg gaacggggcg tagacgtgta gtataatggc tggagctttc tttgctggat 6721 tggcatctga tgtccttggc tctggacttg gttcccttat caatgctggg gctggggcca 6781 tcaaccaaaa agttgagttt gaaaataaca gaaaattgca acaagcatcc ttccaattta 6841 gcagcaatct gcaacaggct tcttttcaac atgataaaga gatgctccaa gcacaaattg 6901 aggccaccaa aaagctacaa caggaaatga tgaaagttaa gcaggcaatg ctcctagagg 6961 gtgggttctc tgagacagat gcagcccgcg gggcaattaa cgcccccatg acaaaagctt 7021 tggactggag cgggacaagg tactgggctc cagatgctag gattacaaca tacaatgcag 7081 gccacttttc cacccctcaa ccatcgaggg cactgccagg aagagctaat cttagggatg 7141 ctgtccctgc acggggaccc tccaataaat cttctaactc ttctattgcc acctctgtgt 7201 actcaaatca aactatttca acgagacttg gttctacagc tggttctgga accagtgtct 7261 cgagcctccc gtcaactgca aggactagga gctgggttga ggatcaaaat aggaatttgt 7321 cacctttcat gaggggggcc cacaacatat cgtttgtcac cccaccatct agcagatcct 7381 ctagccaagg cacagtctca accgtgccta aagagatttt ggactcctgg actggcgctt 7441 tcaacacgcg caggcagcct ctcttcgctc acattcgtaa gcgaggggag tcacgggtgt 7501 aatgtgaaaa gacaaaactg attat //