Typing tool
|
Complete norovirus genomes
MT537633 | GII.4 Sydney | ||
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GII.P16 |
ORF1: 1..5095 ORF2: 5076..6698 ORF3: 6698..7504LOCUS MT537633 7515 bp RNA linear VRL 31-JUL-2020 DEFINITION Norovirus GII isolate 259-2 nonstructural polyprotein (ORF1) gene, partial cds; and VP1 (ORF2) and VP2 (ORF3) genes, complete cds. ACCESSION MT537633 VERSION MT537633.1 DBLINK BioProject: PRJNA604000 KEYWORDS . SOURCE Norovirus GII ORGANISM Norovirus GII Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes; Picornavirales; Caliciviridae; Norovirus; Norwalk virus. REFERENCE 1 (bases 1 to 7515) AUTHORS Silva,A., Wolfe,J., Ruelle,S., Hirneisen,K. and Yang,Z. TITLE Application of whole-genome sequencing for Norovirus outbreak tracking and surveillance efforts in Orange County, CA JOURNAL Unpublished REFERENCE 2 (bases 1 to 7515) AUTHORS Silva,A., Wolfe,J., Ruelle,S., Hirneisen,K. and Yang,Z. TITLE Direct Submission JOURNAL Submitted (29-MAY-2020) Schmid College of Science and Technology, Chapman University, 1 University Drive, Orange, CA 94526, USA COMMENT ##Assembly-Data-START## Assembly Method :: CLC Genomics Workbench v. 11 Sequencing Technology :: Illumina ##Assembly-Data-END## FEATURES Location/Qualifiers source 1..7515 /organism="Norovirus GII" /mol_type="genomic RNA" /isolate="259-2" /isolation_source="stool" /host="Homo sapiens" /db_xref="taxon:122929" /country="USA" /collection_date="17-Dec-2018" /note="genotype: GII.4[P16]" gene <1..5095 /gene="ORF1" CDS <1..5095 /gene="ORF1" /codon_start=2 /product="nonstructural polyprotein" /protein_id="QKE61142.1" /translation="MASNDATVAVACNNNNDKEKSSGEGLFTNMSFTLKKALGARPKQ PAPRDEPQKPPRPPTPELVKRIPPPPPNGEGEEEPVIRYEVKSGISGLPELTTVPQPD VANTAFSVPPLSLRENREAKEPLTGAILEMWDGEIYHYGLYVEKGLVLGVHKPPAAIS MARVELTPLSLYWRVVYTPQYLISPETLRRLNGEAFPYTAFDNNCYAFCCWVLDLNDS WLSRRMVQRTTGFFRPYQEWNRKPLPTMDDSKIKKVANIFLCSLSTLFTRPIKDLIGK IKPLNILNILATCDWTFAGIVESLILLAELFGVFWTPPDVSAMIAPLLGDYELQGPED LAVELVPVVMGGIGLVLGFTKEKIGKMLSSAASTLRACKDLGAYGLEILKLVMKWFFP KKEEANELAMVRAIEDAVLDLEAIENNHMTTLLKDKDSLATYMKTLDMEEEKARRLST KSASPDIVGTINALLARIAAARSLVHRAKEELSSRIRPVVVMISGKPGIGKTHLAREV ARKVASTLTGDQRVGLIPRNGVDHWDAYKGERVVLWDDYGMSNPIHDALRIQELADTC PLTLNCDRIENKGKVFDSEVIIITTNLANPAPLDYVNFEACSRRIDFLVYAEAPEVEK AKRDFPGQPDMWKDAFKPDFSHIKLQLAPQGGFDKNGNTPHGKGVMKTLTTGSLIARA SGLLHERMDEFELQGPTITTFNFDRNRITAFRQLAAENKYGLVDTMKVGNQLKGVKTM EELKQAIRNVTIKRCRIIYGGSTYDLESDGKGKVLVEKVKNTSVQTNNELAGALHHLK HARIRYYVKCVQEAVYSIIQIAGAAFVTTRIARRMNIQELWSKPQLDQNESETKEEAP KSEDDEFIISSKDIKEEGKKGKNKTGRGKKHTAFSSKGLSDEEYDEYKRIREERNGKY SIEEYLQDRDRYYEELAIAKATEEDFCEEEEIKIRQRIFRPTRKQRKEERATLGLVTG SEIRKRNPDDFKPKGKLWADDNRSVDYNEKLDFEAPPSIWSRIVSFGSGWGFWVSPSL FITSTHVIPAGITEAFGVPIKQIQIHKSGEFCRFRFPRPIRPDVTGMILEEGAPEGTV ATVLIKRPTGELMPLAARMGTHATMKIQGRMVGGQMGMLLTGSNAKGMDLGTTPGDCG CPYIYKRGNDYIVIGVHTAAARGGNTVICATQGSEGEATLEGGYDKGTYCGAPILGPG GAPKLSTKTKFWRSSNTPLPPGTYEPAYLGGRDPRVKGGPSLQQVMRDQLKPFTEPRG KPPRPSVLEAAKQTVINVLEQTLDPPQKWTYAQACASLDKTTSSGHPHHVRKNEFWNG ETFTGKLADQASKANLMFEEGKHMTPVYTAALKDELVKTEKIYRKIKKRLLWGSDLST MIRCARSFGGLMDEMKAHCISLPVRVGMNVNEDGPIIFEKHSRYKYHYDADYSRWDST QQRAVLAAALEIMVRFSAEPQLAQIVAEDLLAPSVVDVGDFKITINEGLPSGVPCTSQ WNSIAHWLLTLCALSEVTKLSPDIIQANSMFSFYGDDEIVSTDIKLDPEQLTAKLKEY GLKPTRPDKTEGPLIISEDLNGLTFLRRTVTRDPAGWFGKLDQSSILRQMYWTRGPNH EDPNETMIPHSQRPIQLMALLGEASLHGPSFYSRISKLVITELKEGGMDFYVPRQEPM FRWMRFSDLSTWEGDRNLAPNFVNEDGVE" mat_peptide <1..991 /gene="ORF1" /product="p48" mat_peptide 992..2089 /gene="ORF1" /product="NTPase" mat_peptide 2090..2620 /gene="ORF1" /product="p22" mat_peptide 2621..3019 /gene="ORF1" /product="VPg" mat_peptide 3020..3562 /gene="ORF1" /product="Pro" mat_peptide 3563..5092 /gene="ORF1" /product="RdRp" gene 5076..6698 /gene="ORF2" CDS 5076..6698 /gene="ORF2" /note="major capsid protein" /codon_start=1 /product="VP1" /protein_id="QKE61143.1" /translation="MKMASSDANPSDGSAANLVPEVNNEVMALEPVVGAAIAAPVAGQ QNVIDPWIRNNFVQAPGGEFTVSPRNAPGEILWSAPLGPDLNPYLSHLARMYNGYAGG FEVQVILAGNAFTAGKIIFAAVPPNFPTEGLSPSQVTMFPHIIVDVRQLEPVLIPLPD VRNNFYHYNQSNDSTIKLIAMLYTPLRANNAGDDVFTVSCRVLTRPSPDFDFIFLVPP TVESRTKPFSVPVLTVEEMTNSRFPIPLEKLFTGPSSAFVVQPQNGRCTTDGVLLGTT QLSPVNICTFRGDVTHITGSRNYTMNLASQNWNNYDPTEEIPAPLGTPDFVGKIQGML TQTTRTDGSTRGHKATVYTGSADFAPKLGRVQFETDTDHDFEANQNTKFTPVGVIQDG STTHRNEPQQWVLPSYSGRNTHNVHLAPAVAPTFPGEQLLFFRSTMPGCSGYPNMDLD CLLPQEWVQYFYQEAAPAQSDVALLRFVNPDTGRVLFECKLHKSGYVTVAHTGQHDLV IPPNGYFRFDSWVNQFYTLAPMGNGTGRRRVV" gene 6698..7504 /gene="ORF3" CDS 6698..7504 /gene="ORF3" /note="minor structural protein; small basic protein" /codon_start=1 /product="VP2" /protein_id="QKE61144.1" /translation="MAGAFFAGLASDVLGSGLGSLINAGAGAINQKVEFENNRKLQQA SFQFSSNLQQASFQHDKEMLQAQIEATKKLQQEMMKVKQAMLLEGGFSETDAARGAIN APMTKALDWSGTRYWAPDARTTTYNAGRFSTPQPSGALPGRANLRDAVPARGPSNKSS NSSTATSVYSNQTISTRLGSTAGSGTSVSSLPSTARTRSWVEDQNRNLSPFMRGAHNI SFVTPPSSRSSSQGTVSTVPKEILDSWTGAFNTRRQPLFAHIRKRGESRV" ORIGIN 1 gatggcgtct aacgacgcta ccgttgccgt tgcttgcaac aacaacaacg acaaggaaaa 61 atcttcaggt gaaggcttat tcacaaatat gtctttcacc ttaaagaaag ccctcggggc 121 taggcccaaa cagcctgccc cgagagacga accacaaaag cccccaagac caccaacccc 181 cgagttggtc aagaggatac cccctcctcc acctaatggc gaaggagaag aagaaccagt 241 cattaggtat gaggttaaga gtgggatctc tggcctgccc gagctcacaa cagtccccca 301 accggacgtg gccaacacag cattcagtgt tccaccactg agcttgagag aaaacaggga 361 ggccaaggaa ccgctaacag gggcaatatt agagatgtgg gatggagaga tataccacta 421 tggcctgtac gtggagaaag gcttagtgtt gggtgtgcac aaaccacctg cagccataag 481 catggcaaga gtggagctga cgccgctgtc attgtactgg cgtgtggtgt acactcccca 541 atacctcatc tcccctgaaa ctctcaggag gctcaacgga gaggcgttcc cttacaccgc 601 cttcgacaac aactgctacg ccttttgctg ctgggtgtta gacctcaatg actcatggct 661 tagcaggagg atggtgcaaa gaacaacggg cttcttcaga ccttaccaag agtggaacag 721 aaagcccctg cctaccatgg atgactccaa aattaagaag gtagcaaata tattcctatg 781 ttcattgtcc acattattca ccagacccat aaaagacctc atagggaaaa ttaaaccatt 841 aaacatattg aacatcctgg caacgtgtga ctggacgttt gccggaatag tggagtctct 901 gatattactt gctgaactct tcggagtttt ctggacgccc ccagatgtgt ctgctatgat 961 cgctccctta ctcggggact acgagttgca agggccagaa gacctcgccg ttgaactcgt 1021 acctgtggta atgggaggga ttggtttggt gttgggattc accaaagaga aaattggcaa 1081 aatgttgtcc tcagcagcat caacactcag ggcttgcaaa gatcttggtg cctatggctt 1141 agagatactc aagttggtca tgaagtggtt cttcccaaag aaagaggagg ccaatgagct 1201 agccatggtg agggccatag aggatgccgt gctagatctt gaggcaatag aaaataacca 1261 catgacaacc ctgttgaaag acaaagacag cttagcaaca tacatgaaaa cactggacat 1321 ggaggaggag aaagccagaa ggttgtccac aaaatctgca tcccctgaca tagttgggac 1381 aatcaacgcc ctgctggctc gaatagcagc ggccaggtca ttagtccaca gggccaagga 1441 agagctatct agcaggataa ggccagtagt tgttatgata tctggcaaac caggaatagg 1501 caaaactcat ctggccaggg aggtggcaag aaaggtggca tccactctca caggggacca 1561 aagagtcgga ctcataccaa gaaacggtgt ggaccattgg gatgcataca aaggtgagag 1621 agtcgtgctg tgggacgact atggcatgag taaccccatc catgatgctc ttcgcataca 1681 agaattggct gatacgtgtc cccttacctt aaattgtgac agaattgaaa ataagggaaa 1741 agtttttgac agtgaagtca taataattac aacaaacctt gccaatccag ccccacttga 1801 ttatgtcaac tttgaggcct gttccaggag aattgatttc ctggtgtacg ctgaggcacc 1861 agaagtagaa aaggcaaaac gggactttcc tggtcagcca gatatgtgga aggacgcctt 1921 caagccggac ttttcacaca tcaagctaca gcttgcacct cagggcggct ttgacaagaa 1981 tggcaacacc ccacatggga aaggagtgat gaagaccctc actaccggtt ctctgattgc 2041 ccgtgcatca ggcctactac atgagaggat ggatgaattt gaactccaag gtcccacaat 2101 caccaccttc aatttcgacc gaaacagaat cacagcattc agacaattgg ctgcagaaaa 2161 caagtatgga ttggtggata ccatgaaagt tggcaatcaa ttaaaaggag tgaaaaccat 2221 ggaagaactc aaacaagcaa tcagaaatgt gaccatcaag aggtgccgga tcatctacgg 2281 tggctccacg tatgaccttg aatctgatgg caagggcaaa gttttggtgg aaaaggtcaa 2341 gaacacctct gtacagacca acaacgagtt ggccggggcc ctgcaccatc tcaaacacgc 2401 ccgaatcagg tactatgtca aatgtgtgca agaagcagtc tattccatca tacaaattgc 2461 cggcgctgcg tttgtcacca cgcgcattgc acgccgcatg aacatacaag aactctggtc 2521 gaagccacaa ttagatcaaa atgaatcaga gactaaggaa gaggccccca aatcagaaga 2581 tgacgagttc atcatatctt ctaaggacat caaggaggaa ggaaagaagg gcaaaaacaa 2641 aactggccgt ggcaagaaac acactgcatt ctccagcaag ggcttgagcg atgaggagta 2701 tgacgagtac aagaggataa gagaagagag aaatgggaag tactctatag aggagtatct 2761 tcaagacaga gacaggtact atgaggagct cgccattgcc aaggccacgg aagaagactt 2821 ctgtgaagag gaggagataa aaatccgtca gagaattttc cgtcccacca ggaaacaaag 2881 aaaggaagag agggccacat taggactggt aacaggttca gaaatcagaa aaagaaaccc 2941 tgatgacttc aaacccaaag ggaagctgtg ggccgatgac aacagaagtg ttgactataa 3001 tgagaaactg gactttgagg cccccccaag catatggtct aggattgtga gctttggttc 3061 tggctggggc ttctgggtat caccaagcct gttcataaca tcaactcatg taatccccgc 3121 aggcataaca gaagcatttg gagtccccat caaacaaatt cagatccaca aatcaggtga 3181 attttgccga ttcagattcc caagaccaat tagaccagac gtgacaggaa tgatcttgga 3241 agaaggtgcg cctgaaggca ccgtggcaac tgtgctcatc aaacgcccca ccggagagct 3301 catgcctctt gcagccagaa tgggaacaca cgcaaccatg aaaattcaag gccgcatggt 3361 tggcggacag atgggtatgt tgctcactgg atcaaatgct aaaggaatgg atttgggaac 3421 aactcctggt gactgtggct gtccttacat ctacaaaagg ggcaatgact atatagtcat 3481 tggggtgcac actgcagcag cccgtggtgg aaacaccgtc atctgtgcca cacagggaag 3541 tgagggtgag gcaactcttg agggtggata tgacaaagga acatactgtg gggcacccat 3601 tctaggccct gggggtgcac caaagttgag caccaaaacc aaattttgga ggtcatcgaa 3661 cacgcccctc ccaccaggga catatgagcc tgcctacctc ggtggccgtg atccgcgtgt 3721 taagggtggg ccctccttgc agcaggtaat gagagaccag ttgaagccat tcactgaacc 3781 caggggcaaa cctccaagac caagtgtatt ggaagcagcc aaacaaaccg ttatcaatgt 3841 cctcgaacaa accctggatc ctccacaaaa atggacatac gcacaggcgt gtgcctcact 3901 tgacaaaacc acttccagcg ggcatcctca tcacgtccga aagaatgaat tctggaatgg 3961 tgagaccttc accggcaaat tggcagacca agcatcaaaa gcaaacctaa tgtttgagga 4021 agggaaacac atgacaccag tgtatacagc agcactcaag gacgagctag tcaagactga 4081 gaaaatctat agaaagatca agaagagact gctctggggc tctgacttgt ccaccatgat 4141 ccggtgcgct aggtcatttg gtgggctcat ggacgagatg aaggcacact gcatatcact 4201 cccagtacga gttggcatga atgtgaatga agatggccca ataatatttg agaaacattc 4261 cagatacaaa taccactatg acgcagacta ctctcgttgg gattcaacac aacagagggc 4321 agtactagca gcagccttgg aaatcatggt cagattctct gcagaaccac aattggcaca 4381 aatagtcgct gaggatcttc tggcccctag cgtagtagat gtaggagact ttaaaatcac 4441 tataaatgaa gggctcccat ctggtgtgcc atgcacctcc caatggaact ccatcgcaca 4501 ctggctgcta actctctgtg ccttgtctga agtcaccaaa ctgtcccctg acattataca 4561 agcaaattcc atgttctcat tttacggtga tgacgagatt gtcagcaccg acataaaatt 4621 ggaccctgaa cagttaaccg ccaagttgaa ggagtatggc ctgaaaccaa cccgcccaga 4681 caagaccgag ggacccctga tcatcagtga agatttgaac ggactcactt tcctccgaag 4741 gacggtgact cgtgacccag ctggctggtt tggaaaactg gaccaaagtt caattttgag 4801 gcagatgtac tggactagag gaccaaatca cgaagatccc aatgagacaa tgatacccca 4861 ttctcaaaga cccatacagc tcatggcact gcttggtgaa gcctctcttc acggaccctc 4921 tttctacagt agaatcagta aattggtcat aactgaactc aaagaaggtg ggatggactt 4981 ttacgtgcca aggcaggaac ccatgttcag gtggatgagg ttttctgact tgagcacgtg 5041 ggagggcgat cgcaatctgg ctcccaattt tgtgaatgaa gatggcgtcg agtgacgcca 5101 acccatctga tgggtccgca gccaacctcg taccagaggt caacaatgag gttatggctt 5161 tggagcccgt tgtcggtgcc gctattgcgg cacctgtagc gggccaacaa aatgtaattg 5221 acccctggat tagaaataat tttgtacaag cccctggtgg ggagtttaca gtatccccca 5281 gaaacgctcc aggtgaaata ctatggagcg cgcccctagg ccctgaccta aatccctacc 5341 tatcccattt ggccagaatg tacaatggtt atgcaggtgg ttttgaagtg caggtaattc 5401 tcgcggggaa cgcgttcacc gccgggaaga tcatatttgc agcagtccca ccaaattttc 5461 caactgaagg cttaagtcct agccaggtca ctatgttccc ccatataata gtagatgtta 5521 gacagttaga acctgtgctg attcctttac ccgatgttag gaataatttc tatcattaca 5581 atcagtcaaa tgactccact attaagttga tagcaatgtt gtacacacca cttagggcta 5641 ataatgctgg ggatgatgtt ttcacagttt cgtgccgagt tctcacgaga ccatcccccg 5701 attttgattt catattttta gtgccaccca cagttgagtc aagaactaaa ccattctctg 5761 tcccagtttt aactgttgag gagatgacca attcaagatt ccccatccct ttggaaaagc 5821 tgttcacagg ccccagcagt gcctttgttg ttcaaccaca aaacggcagg tgcacaactg 5881 atggcgtgct cctaggcacc acccaacttt ctcctgtcaa catctgcacc ttcagagggg 5941 atgtcaccca catcacaggt agtcgcaact acacaatgaa tttggcttct caaaattgga 6001 acaactatga cccaacagaa gaaatcccag cccctctagg aactccagat tttgtgggga 6061 agattcaagg catgctcacc caaaccacaa ggacagatgg ttcaacacgc ggccacaaag 6121 ctacagtgta cactgggagc gccgactttg ctccaaaact gggtagagtt caatttgaaa 6181 ctgacacaga ccatgatttt gaagctaatc aaaacacaaa gttcacccca gtcggtgtca 6241 tccaagatgg tagcaccacc catcgaaacg aaccccaaca gtgggtgctc ccaagttact 6301 caggcagaaa tactcacaat gtacatctgg cccccgctgt agcccccacc tttccgggtg 6361 agcaacttct cttcttcaga tccaccatgc ccggatgcag cgggtacccc aacatggatt 6421 tggactgtct gctcccccag gaatgggtgc agtacttcta tcaagaggca gccccagcac 6481 aatctgatgt ggctctgcta agatttgtga atccagacac aggtagggtt ttgtttgagt 6541 gcaagcttca caaatcaggc tatgttacag tggctcacac tggccaacat gatttggtta 6601 tcccccccaa tggctacttt agatttgatt cctgggtcaa ccagttctat acgcttgccc 6661 ccatgggaaa tggaacgggg cgtagacgtg tagtataatg gctggagctt tctttgctgg 6721 attggcatct gatgtccttg gctctggact tggttccctc atcaatgctg gggctggggc 6781 catcaaccaa aaagttgagt ttgaaaataa cagaaaattg caacaagcat ccttccaatt 6841 tagcagcaat ctgcaacagg cttcctttca acatgataaa gagatgctcc aagcacaaat 6901 tgaggccact aaaaagctac aacaggaaat gatgaaagtt aagcaggcaa tgctcctaga 6961 gggtgggttc tctgagacag atgcagcccg cggggcaatt aacgccccca tgacaaaagc 7021 tttggactgg agtgggacaa ggtactgggc tcccgatgct aggactacaa catacaatgc 7081 aggccgcttt tccacccctc aaccatcggg ggcactgcca ggaagagcta atcttaggga 7141 tgctgtccct gctcggggac cctccaacaa atcttctaac tcttctactg ccacctctgt 7201 gtattcaaat caaactattt caacgagact tggttctaca gctggttctg gaaccagtgt 7261 ctcgagcctc ccgtcaactg caaggactag gagctgggtt gaggatcaaa ataggaattt 7321 gtcacctttc atgagggggg cccacaacat atcatttgtc accccaccat ctagcagatc 7381 ctctagccaa ggcacagtct caaccgtgcc taaagagatt ttggactcct ggactggcgc 7441 tttcaacacg cgcaggcagc ctctcttcgc tcacattcgt aagcgagggg agtcacgggt 7501 gtaatgtgaa aagac //