Typing tool
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Complete norovirus genomes
MH279823 | GII.4 Sydney | ||
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GII.P16 |
ORF1: 1..5094 ORF2: 5075..6697 ORF3: 6697..7403LOCUS MH279823 7403 bp RNA linear VRL 01-JUL-2018 DEFINITION Norovirus GII strain ST374 nonstructural polyprotein (ORF1) gene, partial cds; VP1 (ORF2) gene, complete cds; and VP2 (ORF3) gene, partial cds. ACCESSION MH279823 VERSION MH279823.1 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 7403) 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reveals discrete transmission clusters and elucidates long-term sequelae of hospital acquired infections JOURNAL Unpublished REFERENCE 2 (bases 1 to 7403) AUTHORS Casto,A.M., Adler,A., Huang,M.-L., Makhsous,N., Xie,H., Zerr,D. and Greninger,A. TITLE Direct Submission JOURNAL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..7403 /organism="Norovirus GII" /mol_type="genomic RNA" /strain="ST374" /host="Homo sapiens" /db_xref="taxon:122929" /country="USA" /collection_date="2017" gene <1..5095 /gene="ORF1" CDS <1..5094 /gene="ORF1" /codon_start=1 /product="nonstructural polyprotein" /protein_id="AWX06069.1" /translation="MASNDATVAVACNNNNDKEKSSGEGLFTNMSSTLKKALGARPKQ PAPRDEPQKPPRPPTPELVKRIPPPPPNGEEEEEPVIRYEVKSGISGLPELTTVPQPD VANTAFSVPPLSLRENREAKEPLTGAILEMWDGEIYHYGLYVEKGLVLGVHKPPAAIS MARVELTPLSLYWRVVYTPQYLISPETLRRLNGEAFPYTAFDNNCYAFCCWVLDLNDS WLSRRMVQRTTGFFRPYQDWNRKPLPTMDDSKIKKVANIFLCSLSALFTRPIKDLIGK IKPLNILNILATCDWTFAGIVESLILLAELFGVFWTPPDVSAMIAPLLGDYELQGPED LAVELVPVVMGGVGLVLGFTKEKIGKMLSSAASTLRACKDLGAYGLEILKLVMKWFFP KKEEANELAMVRAIEDAVLDLEAIENNHMTALLKDKDSLATYMKTLDMEEEKARKLST KSASPDIVGTVNALLARIAAARSLVHRAKEELTSRIRPVVVMISGKPGIGKTHLAREV ARKVASTLTGDQRVGLIPRNGVDHWDAYKGERVVLWDDYGMSNPIHDALRIQELADTC PLTLNCDRIENKGKVFDSEVIIITTNLANPAPLDYVNFEACSRRIDFLVYAEAPEVEK AKRDFPGQPDMWKDAFKPDFSHIKLQLAPQGGFDKNGNTPHGKGVMKTLTTGSLIARA SGLLHERMDEFELQGPTITTYNFDRNRITTFRQLAAENKYGLVDTMKVGNQLKGVKTM EELKQAIRNVTIKRCRIIYGGSTYDLESDGKGKVLVEKVKNTSVQTNNELVGALHHLK HARIRYYVKCVQEAVYSIIQIAGAAFVTTRIARRMNIQELWSKPQLDQNESETKEEAP KSEDDEFIISSKDIKEEGKKGKNKTGRGKKHTAFSSKGLSDEEYDEYKRIREERNGKY SIEEYLQDRDRYYEELAIAKATEEDFCEEEEIKIRQRIFRPTRKQRKEERATLGLVTG SEIRKRNPDDFKPKGKLWADDNRSVDYNEKLDFEAPPSIWSRIVSFGSGWGFWVSPSL FITSTHVIPAGITEAFGVPVKQIQIHKSGEFCRFRFPKPIRPDVTGMILEEGAPEGTV ATVLIKRPTGELMPLAARMGTHATMKIQGRMVGGQMGMLLTGSNAKGMDLGTTPGDCG CPYIYKRGNDYIVIGVHTAAARGGNTVICATQGSEGEATLEGGDDKGTYCGAPILGPG GAPKLSTKTKFWRSSNTPLPPGTYEPAYLGGRDPRVKGGPSLQQVMRDQLKPFTEPRG KPPRPSVLEAAKQTIINVLEQTLDPPQKWTYAQACASLDKTTSSGHPHHVRKNEFWNG ETFTGKLADQASKANLMYEEGKHMTPVYTAALKDELVKTEKIYGKIKKRLLWGSDLST MIRCARSFGGLMDEMKAHCISLPVRVGMNMNEDGPIVFEKHSRYKYHYDADYSRWDST QQRAVLAAALEIMVRFSAEPQLAQIVAEDLLAPSVVDVGDFKITINEGLPSGVPCTSQ WNSIAHWLLTLCALSEVTKLSPDIIQANSMFSFYGDDEIVSTDIKLDPEQLTAKLKEY GLKPTRPDKTEGPLIISEDLNGLTFLRRTVTRDPAGWFGKLDQSSILRQMYWTRGPNH EDPNETMIPHSQRPIQLMALLGEASLHGPSFYSRISKLVITELKEGGMDFYVPRQEPM FRWMRFSDLSTWEGDRNLAPNFVNEDGVE" mat_peptide <1..990 /gene="ORF1" /product="p48" mat_peptide 991..2088 /gene="ORF1" /product="NTPase" mat_peptide 2089..2619 /gene="ORF1" /product="p22" mat_peptide 2620..3018 /gene="ORF1" /product="VPg" mat_peptide 3019..3561 /gene="ORF1" /product="Pro" mat_peptide 3562..5091 /gene="ORF1" /product="RdRp" gene 5075..6697 /gene="ORF2" CDS 5075..6697 /gene="ORF2" /codon_start=1 /product="VP1" /protein_id="AWX06067.1" /translation="MKMASSDANPSDGSAANLVPEVNNEVMALEPVVGAAIAAPVAGQ QNVIDPWIRNNFVQAPGGEFTVSPRNAPGEILWSAPLGPDLNPYLSHLARMYNGYAGG FEVQVILAGNAFTAGKIIFAAVPPNFPTEGLSPSQVTMFPHIIVDVRQLEPVLIPLPD VRNNFYHYNQSNDSTIKLIAMLYTPLRANNAGDDVFTVSCRVLTRPSPDFDFIFLVPP TVESRTKPFSVPVLTVEEMTNSRFPIPLEKLFTGPSSAFIVQPQNGRCTTDGVLLGTT QLSSVNVCTFRGGVTHITGSRNYTMNLASQNWNNYDPTEEIPAPLGTPDFVGKIQGML TQTTRTDGSTRGHRATVYTGSADFAPKLGRVQFETDTDHDFEANQNTKFTPVGVIQDG STTHRNEPQQWVLPSYSGRNTHNVHLAPAVAPTFPGEQLLFFRSTMPGCSGYPNMDLD CLLPQEWVQYFYQEAAPAQSDVALLRFVNPDTGRVLFECKLHKSGYVTVAHTGQHDLV IPPNGYFRFDSWVNQFYTLAPMGNGTGRRRVV" gene 6697..>7403 /gene="ORF3" CDS 6697..>7403 /gene="ORF3" /codon_start=1 /product="VP2" /protein_id="AWX06068.1" /translation="MAGAFFAGLASDVLGSGLGSLINAGAGAINQKVEFENNRKLQQA SFQFSSNLQQASFQHDKEMLQAQIEATKKLQQEMMKVKQAMLLEGGFSETDAARGAIN APMTKALDWSGTRYWAPDARITTYNAGHFSTPQPSRALPGRANLRDAVPARGPSNKSS NSSIATSVYSNQTISTRLGSTAGSGTSVSSLPSTARTRSWVEDQNRNLSPFMRGAHNI SFVTPPSSRSSSQGTVST" ORIGIN 1 atggcgtcta acgacgctac cgttgccgtt gcttgcaaca acaacaacga caaggaaaaa 61 tcttcaggtg aaggcttatt cacaaatatg tcttccacct taaagaaagc cctcggggct 121 aggcccaaac agcctgcccc gagagacgaa ccacaaaagc ccccaagacc accaactccc 181 gagttggtca agaggatacc ccctcctcca cctaatggcg aagaagaaga agaaccagtc 241 attaggtatg aggttaagag tgggatctct ggcctgcccg agctcacaac agtcccccag 301 ccggacgtgg ccaacacagc attcagtgtt ccaccactga gcttgagaga aaacagggag 361 gccaaggaac cgctaacagg ggcaatatta gagatgtggg acggagagat ataccactat 421 ggcctgtacg tggagaaagg cttagtgttg ggtgtgcaca aaccacctgc agccataagc 481 atggcaagag tggagctgac gccgttgtca ttgtactggc gtgtggtgta cactccccaa 541 tacctcatct cccctgaaac tctcaggagg ctcaacggag aggcgttccc ttacaccgcc 601 ttcgacaaca actgctatgc cttttgctgc tgggtgttag acctcaatga ctcatggctt 661 agcaggagga tggtgcaaag aacaacgggc ttcttcagac cttaccaaga ttggaacaga 721 aaacccctgc ctaccatgga tgactccaaa ataaagaagg tagcaaatat attcctatgt 781 tcattgtccg cattgtttac cagacccata aaagacctca taggaaaaat taaaccatta 841 aacatattga acatcctggc aacgtgtgac tggacgtttg ccggaatagt ggagtctctg 901 atattacttg ctgaactctt cggagttttc tggacacccc cagatgtgtc tgctatgatc 961 gctcccttac tcggggacta cgagttgcaa gggccagaag acctcgccgt tgaactcgta 1021 cctgtggtaa tgggaggggt tggtttggtg ttgggattca ccaaagagaa aattggcaaa 1081 atgttgtcct cagcagcatc aacactcagg gcttgcaaag atcttggtgc ctatggctta 1141 gagatactca aattggtcat gaagtggttc ttcccaaaga aagaggaggc caatgaacta 1201 gccatggtga gggccataga ggatgccgta ctagatcttg aggcgataga aaataaccac 1261 atgacagccc tgttgaaaga caaagacagc ttagcaacat acatgaaaac actggacatg 1321 gaggaggaga aagccagaaa gttgtccaca aaatctgcat cccctgacat agttgggaca 1381 gtcaacgccc tgctggctcg aatagcagcg gccaggtcat tagtccacag ggccaaggaa 1441 gagcttacta gcaggataag accagtagtt gttatgatat ctggcaaacc aggaataggc 1501 aaaactcatc tggccaggga ggtggcaaga aaggtggcat ccactctcac aggggatcaa 1561 agagtcggac tcataccaag aaacggtgtg gaccactggg atgcatacaa aggtgagaga 1621 gtcgtgctgt gggacgacta tggcatgagt aaccccattc atgatgctct tcgcatacag 1681 gaattggctg atacgtgccc ccttacctta aattgtgaca gaattgaaaa taagggaaaa 1741 gtttttgaca gtgaagtcat aataattaca acaaaccttg ccaacccagc cccacttgat 1801 tatgtcaact ttgaggcctg ttccaggaga attgatttcc tggtgtacgc tgaggcacca 1861 gaagtagaaa aggcaaaacg ggactttcct ggtcagccag atatgtggaa ggacgccttc 1921 aagccggact tttcacacat caagttacag cttgcacctc agggcggctt tgacaagaat 1981 ggcaacaccc cacatgggaa aggagtgatg aagaccctca ctactggttc tctgattgcc 2041 cgtgcatcag gcctactgca tgagaggatg gatgaatttg aactccaagg tcccacaatc 2101 accacctaca atttcgaccg gaacagaatc acaacattca gacaattggc cgcagaaaac 2161 aagtatggat tggtggatac catgaaagtt ggcaatcaac taaaaggagt gaaaaccatg 2221 gaagaactca aacaagcaat caggaatgtg accatcaaga ggtgccgaat catctatggt 2281 ggctccacgt atgaccttga atctgatggc aagggcaaag ttttggtgga aaaggtcaag 2341 aacacctctg tacagaccaa caacgagttg gtcggggccc tgcaccacct caaacacgcc 2401 cgaatcaggt actatgtcaa atgtgtgcaa gaagcagtct attccatcat acaaattgcc 2461 ggcgctgcgt ttgtcaccac gcgcattgca cgccgcatga acatacaaga actctggtcg 2521 aagccacaat tagaccaaaa tgaatcagag actaaggaag aggcccccaa gtcagaagat 2581 gacgagttca tcatatcttc taaggacatc aaggaggaag gaaagaaggg caaaaacaaa 2641 actggccgtg gcaagaaaca cactgcattc tccagcaagg gcttgagcga tgaagagtat 2701 gacgagtaca agaggataag agaagagaga aatgggaagt actctataga ggagtatctt 2761 caagacagag acaggtacta tgaggagctc gccattgcca aggccacgga ggaagacttc 2821 tgtgaagagg aggagatcaa aatccgtcag agaattttcc gtcccaccag gaaacaaaga 2881 aaggaagaga gggccacatt agggctggtg acaggttcag aaatcagaaa aagaaacccc 2941 gatgacttca aacccaaagg gaagctgtgg gccgatgaca acagaagtgt tgactacaat 3001 gagaaactgg actttgaggc ccccccaagc atatggtcta ggattgtgag ctttggttct 3061 ggctggggct tctgggtatc accaagcctg ttcataacat caactcatgt aatccccgca 3121 ggcataacag aagcatttgg agtccccgtc aaacaaattc agatccacaa atcaggtgaa 3181 ttctgccgat tcagattccc aaaaccaatt agaccagatg tgacagggat gatcttggaa 3241 gaaggtgcgc ctgaaggcac cgtggcaact gtgctcatca aacgccccac cggagagctc 3301 atgcctcttg cagccagaat gggaacacac gcaaccatga aaattcaagg ccgcatggtt 3361 ggcggacaga tgggtatgtt gctcactgga tcaaatgcta aaggaatgga tttgggaaca 3421 actcctggtg actgtggctg tccttacatc tataaaaggg gcaatgacta tatagtcatt 3481 ggggtgcaca ctgcagcagc ccgtggtgga aacaccgtca tctgtgccac acagggaagt 3541 gagggtgagg caactcttga gggtggagat gacaaaggaa catactgtgg ggcacccatt 3601 ctaggccctg ggggtgcacc aaaattgagc accaaaacca aattttggag gtcatcgaac 3661 acgccccttc caccagggac atatgagcct gcctacctcg gtggccgtga tccgcgcgtt 3721 aagggtgggc cctccttgca gcaggtgatg agagaccagt tgaagccatt cactgaaccc 3781 aggggcaaac ctccaagacc aagtgtattg gaagcagcca aacaaaccat tatcaatgtt 3841 ctcgaacaaa ccctggaccc tccgcaaaag tggacatacg cacaggcgtg tgcctcactt 3901 gacaagacca cctccagcgg gcatccccat cacgtccgaa agaatgaatt ctggaatggt 3961 gagaccttca ctggtaaact ggcagaccaa gcatcaaaag caaacctaat gtatgaggaa 4021 gggaaacaca tgacaccagt gtatacagca gcactcaagg acgagctagt caagactgag 4081 aaaatctatg gaaagatcaa gaagagactg ctctggggct ctgacttgtc cactatgatc 4141 cggtgcgcta ggtcatttgg tgggctcatg gacgagatga aggcacactg catatcactc 4201 ccagtacgag ttggcatgaa tatgaatgaa gatggcccaa tagtatttga gaaacattcc 4261 agatacaaat accactatga tgcagactac tctcgttggg attcaacaca acagagggca 4321 gtgctagcag cagccttgga aatcatggtc agattctctg cagaaccaca attggcacaa 4381 atagtcgctg aggatctact ggcccctagt gtagtagatg taggagactt taaaatcaca 4441 ataaatgaag ggctcccatc tggtgtgcca tgcacttctc aatggaactc catcgcacac 4501 tggctgctaa ctctctgtgc cttgtctgaa gtcaccaaac tgtcccctga cattatacaa 4561 gcaaattcca tgttctcatt ttacggtgat gacgagattg tcagcaccga cataaaattg 4621 gaccctgaac agttaactgc caagctgaag gagtacggcc tgaaaccaac ccgcccagac 4681 aagaccgagg gacccctgat catcagtgaa gatttaaacg gactcacctt cctccgtagg 4741 acggtgactc gtgacccagc tggctggttt ggaaaactgg accaaagttc aatcttgagg 4801 caaatgtact ggactagagg accaaatcat gaagacccca atgaaacaat gataccccac 4861 tctcaaagac ccatacagct catggcactg cttggtgaag cctctcttca cggaccctct 4921 ttctatagta gaatcagtaa attggtcata actgaactca aagaaggtgg gatggacttt 4981 tacgtgccaa ggcaggaacc catgttcagg tggatgaggt tttctgactt gagcacgtgg 5041 gagggcgatc gcaatctggc tcccaatttt gtgaatgaag atggcgtcga gtgacgccaa 5101 cccatctgat gggtccgcag ccaacctcgt accagaggtc aacaatgagg ttatggcttt 5161 ggagcccgtt gttggtgccg ctattgcggc acctgtagcg ggccaacaaa atgtaattga 5221 cccctggatt agaaataatt ttgtacaagc ccctggtggg gagtttacag tatcccctag 5281 aaacgctcca ggtgaaatac tatggagcgc gcccctaggc cctgacctaa atccctacct 5341 atcccatttg gccagaatgt acaatggtta tgcaggtggt tttgaagtgc aggtaattct 5401 cgcggggaac gcgttcaccg ccgggaagat tatatttgca gcagtcccac caaattttcc 5461 aactgaaggc ttaagtccta gccaggttac tatgttcccc catataatag tagatgttag 5521 acaattagaa cctgtgctga ttcccttacc cgatgttagg aataacttct atcattacaa 5581 tcagtcaaat gattccacta ttaagttgat agcaatgttg tatacaccac ttagggctaa 5641 taatgctggg gatgatgttt tcacagtttc gtgtcgagtc ctcacgagac catcccccga 5701 ttttgatttc atatttttgg tgccacccac ggttgagtca agaactaagc cattctctgt 5761 cccagtttta actgttgagg agatgaccaa ttcaagattc cccatccctt tggaaaagtt 5821 gttcacaggc cccagcagtg cctttattgt tcaaccacaa aacggcaggt gcacaactga 5881 tggcgtgctc ctaggcacca cccaactttc ttctgtcaac gtctgcacct tcagaggggg 5941 tgtcacccac atcacaggta gtcgcaacta cacaatgaat ttggcttctc aaaattggaa 6001 caactatgac ccaacagaag aaatcccagc ccctctagga actccagatt ttgtggggaa 6061 gattcaaggc atgctcaccc aaaccacaag gacagatggc tcaacacgcg gccacagagc 6121 tacagtgtac actgggagcg ccgactttgc tccaaaactg ggtagagttc aatttgaaac 6181 tgacacagac catgattttg aagctaatca aaacacaaag ttcaccccag tcggtgtcat 6241 ccaagatggt agcaccaccc accgaaacga accccaacag tgggtgctcc caagttactc 6301 aggcagaaat actcacaatg tacatttggc ccccgctgta gcccccactt ttccgggtga 6361 gcaacttctc ttcttcagat ccaccatgcc cggatgcagc gggtacccca acatggattt 6421 ggactgtctg ctcccccagg aatgggtgca gtatttctac caagaggcag ccccagcaca 6481 atctgatgtg gctctgctaa gatttgtgaa tccagacaca ggtagggttt tgtttgagtg 6541 caagcttcac aaatcaggct atgttacagt ggctcacact ggccaacatg atttggttat 6601 cccccccaat ggttacttta ggtttgattc ctgggtcaac cagttctaca cgcttgcccc 6661 catgggaaat ggaacggggc gtagacgtgt agtataatgg ctggagcttt ctttgctgga 6721 ttggcatctg atgtccttgg ctctggactt ggttccctta tcaatgctgg ggctggggcc 6781 atcaaccaaa aagttgagtt tgaaaataac agaaaattgc aacaagcatc cttccaattt 6841 agcagcaatc tgcaacaggc ttcttttcaa catgataaag agatgctcca agcacaaatt 6901 gaggccacca aaaagctaca acaggaaatg atgaaagtta agcaggcaat gctcctagag 6961 ggtgggttct ctgagacaga tgcagcccgc ggggcaatta acgcccccat gacaaaagct 7021 ttggactgga gcgggacaag gtactgggct ccagatgcta ggattacaac atacaatgca 7081 ggccactttt ccacccctca accatcgagg gcactgccag gaagagctaa tcttagggat 7141 gctgtccctg cacggggacc ctccaataaa tcttctaact cttctattgc cacctctgtg 7201 tactcaaatc aaactatttc aacgagactt ggttctacag ctggttctgg aaccagtgtc 7261 tcgagcctcc cgtcaactgc aaggactagg agctgggttg aggatcaaaa taggaatttg 7321 tcacctttca tgaggggggc ccacaacata tcgtttgtca ccccaccatc tagcagatcc 7381 tctagccaag gcacagtctc aac //