Typing tool
|
Complete norovirus genomes
MN782359 | GII.4 Sydney | ||
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GII.P16 |
ORF1: 1..5066 ORF2: 5047..6669 ORF3: 6669..7475LOCUS MN782359 7517 bp RNA linear VRL 31-MAR-2020 DEFINITION Norovirus GII isolate 011617 nonstructural polyprotein (ORF1) gene, partial cds; and VP1 (ORF2) and VP2 (ORF3) genes, complete cds. ACCESSION MN782359 VERSION MN782359.1 KEYWORDS . SOURCE Norovirus GII ORGANISM Norovirus GII Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes; Picornavirales; Caliciviridae; Norovirus; Norwalk virus. REFERENCE 1 (bases 1 to 7517) AUTHORS Ford-Siltz,L.A., Wales,S., Tohma,K., Gao,Y. and Parra,G.I. TITLE Genotype-Specific Neutralization of Norovirus is Mediated by Antibodies Against the Protruding Domain of the Major Capsid Protein JOURNAL J. Infect. Dis. (2020) In press PUBMED 32179892 REMARK Publication Status: Available-Online prior to print REFERENCE 2 (bases 1 to 7517) AUTHORS Ford-Siltz,L.A., Wales,S., Tohma,K., Gao,Y. and Parra,G.I. TITLE Direct Submission JOURNAL Submitted (04-DEC-2019) CBER/OVRR/DVP/LHV, U.S. Food and Drug Administration, 10903 New Hampshire Avenue, Silver Spring, MD 20993, USA COMMENT ##Assembly-Data-START## Assembly Method :: High-performance Integrated Virtual Environment (HIVE) v. 2.3 Sequencing Technology :: Illumina ##Assembly-Data-END## FEATURES Location/Qualifiers source 1..7517 /organism="Norovirus GII" /mol_type="genomic RNA" /isolate="011617" /isolation_source="stool" /host="Homo sapiens" /db_xref="taxon:122929" /country="USA" /collection_date="06-Nov-2017" /note="genotype: GII.4 Sydney[P16]" gene <1..5066 /gene="ORF1" CDS <1..5066 /gene="ORF1" /codon_start=3 /product="nonstructural polyprotein" /protein_id="QGR25083.1" /translation="VACNNNNDKEKSSGEGLFTNMSSTLKKALGARPKQPAPRDEPQK PPRPPTPELVKRIPPPPPNGEEEEPVIRYEVKSGISGLPELTTVPQSDVANTAFSVPP LSLRENREAKEPLTGAILEMWDGEIYHYGLYVEKGLVLGVHKPPAAISMARVELTPLS LYWRVVYTPQYLISPETLRRLNGEAFPYTAFDNNCYAFCCWVLDLNDSWLSRRTVQRT TGFFRPYQEWNRKPLPTMDDSKIKKVANIFLCSLSTLFTRPIKDLIGKIKPLNILNIL ATCDWTFAGIVESLILLAELFGVFWTPPDVSAMIAPLLGDYELQGPEDLAVELVPVVM GGIGLVLGFTKEKIGKMLSSAASTLRACKDLGAYGLEILKLVMKWFFPKKEEANELAM VRAIEDAVLDLEAIENNHMTTLLKDKDSLATYMKTLDMEEEKARRLSTKSASPDIVGT INALLARIAAARSLVHRAKEELSSRIRPVVVMISGKPGIGKTHLAREVARKVASTLTG DQRVGLVPRNGVDHWDAYKGERVVLWDDYGMSNPIHDALRIQELADTCPLTLNCDRIE NKGKVFDSEVIIITTNLANPAPLDYVNFEACSRRIDFLVYAEAPEVEKAKRDFPGQPD MWKDAFKPDFSHIKLQLAPQGGFDKNGNTPHGKGVMKTLTTGSLIARASGLLHERMDE FELQGPAITTFNFDRNRITAFRQLAAENKYGLVDTMKVGNQLKGVKTMEELKQAIRNV TIKRCRIIYGGSTYDLESDGKGKVLVEKVKNTSVQTNNELAGALHHLKHARIRYYVKC VQEAVYSIIQIAGAAFVTTRIARRMNIQELWSRPQLDQNESEAKEEAPKSEDDEFIIS SKDIKEEGKKGKNKTGRGKKHTAFSSKGLSDEEYDEYKRIREERNGKYSIEEYLQDRD RYYEELAIAKATEEDFCEEEEIKIRQRIFRPTRKQRKEERATLGLVTGSEIRKRNPDD FKPKGKLWADDNRSVDYNEKLDFEAPPSIWSRIVSFGSGWGFWVSSSLFITSTHVIPA GITEAFGVPIKQIQIHKSGEFCRFRFPKPIRPDVTGMILEEGAPEGTVATVLIKRPTG ELMPLAARMGTHATMKIQGRMVGGQMGMLLTGSNAKGMDLGTTPGDCGCPYIYKRGND YIVIGVHTAAARGGNTVICATQGSEGEATLEGGDDKGTYCGAPILGPGGAPKLSTKTK FWRSSNTPLPPGTYEPAYLGGRDPRVKGGPSLQQVMRDQLKPFTEPRGKPPRPSVLEA AKQTIINVLEQTLDPPQKWTYAQACASLDKTTSSGHPHHIRKNEFWNGETFTGKLADQ ASKANLMFEEGKHMTPVYTAALKDELVKTEKIYGKIKKRLLWGSDLSTMIRCARSFGG LMDEMKAHCISLPVRVGMNMNEDGPIIFEKHSRYKYHYDADYSRWDSTQQRAVLAAAL EIMVRFSAEPQLAQIVAEDLLAPSVVDVGDFKITINEGLPSGVPCTSQWNSIAHWLLT LCALSEVTKLSPDIIQANSMFSFYGDDEIVSTDIKLDPEQLTAKLKEYGLKPTRPDKT EGPLIISEDLNGLTFLRRTVTRDPAGWFGKLDQSSILRQMYWTRGPNHEDPNETMIPH SQRPIQLMALLGEASLHGPSFYSRISKLVITELKEGGMDFYVPRQEPMFRWMRFSDLS TWEGDRNLAPNFVNEDGVE" mat_peptide <1..962 /gene="ORF1" /product="p48" mat_peptide 963..2060 /gene="ORF1" /product="NTPase" mat_peptide 2061..2591 /gene="ORF1" /product="p22" mat_peptide 2592..2990 /gene="ORF1" /product="VPg" mat_peptide 2991..3533 /gene="ORF1" /product="Pro" mat_peptide 3534..5063 /gene="ORF1" /product="RdRp" gene 5047..6669 /gene="ORF2" CDS 5047..6669 /gene="ORF2" /note="major capsid protein" /codon_start=1 /product="VP1" /protein_id="QGR25084.1" /translation="MKMASNDANPSDGSAANLVPEVNNEVMALEPVVGAAIAAPVAGQ QNVIDPWIRNNFVQAPGGEFTVSPRNAPGEILWSAPLGPDLNPYLSHLARMYNGYAGG FEVQVILAGNAFTAGKIIFAAVPPNFPTEGLSPSQVTMFPHIIVDVRQLEPVLIPLPD VRNNFYHYNQSNDSTIKLIAMLYTPLRANNAGDDVFTVSCRVLTRPSPDFDFIFLVPP TVESRTKPFSVPVLTVEEMTNSRFPIPLEKLFTGPSSAFVVQPQNGRCTTDGVLLGTT QLSPVNICTFRGDVTHITGSRNYTMNLASQNWNNYDPTEEIPAPLGTPDFVGKIQGML TQTTRTDGSTRGHKATVYTGSADFAPKLGRVQFETDTDHDFEANQNTKFTPVGVIQDG STTHRNEPQQWVLPSYSGRNTHNVHLAPAVAPTFPGEQLLFFRSTMPGCSGYPNMDLD CLLPQEWVQYFYQEAAPAQSDVALLRFVNPDTGRVLFECKLHKSGYVTVAHTGQHDLV IPPNGYFRFDSWVNQFYTLAPMGNGTGRRRVV" gene 6669..7475 /gene="ORF3" CDS 6669..7475 /gene="ORF3" /note="minor structural protein; small basic protein" /codon_start=1 /product="VP2" /protein_id="QGR25085.1" /translation="MAGAFFAGLASDVLGSGLGSLINAGAGAINQKVEFENNRKLQQA SFQFSSNLQQASFQHDKEMLQAQIEATKKLQQEMMKVKQAMLLEGGFSETDAARGAIN APMTKALDWSGTRYWAPDARITTYNAGHFSTPQPSRALPGRANLRDAVPARGPSNQSS NSSTATSVYSNQTISTRLGSTAGSGTSVSSLPSTARTRSWVEDQNRNLSPFMRGAHNI SFVTPPSSRSSSQGTVSTVPKEILDSWTGAFNTRRQPLFAHIRKRGESRV" ORIGIN 1 ccgttgcttg caacaacaac aacgacaagg aaaaatcttc aggtgaaggc ttattcacaa 61 atatgtcttc caccttaaag aaagccctcg gggctaggcc caaacagcct gccccgagag 121 acgaaccaca aaagccccca agaccaccaa ctcccgagtt ggtcaagagg ataccccctc 181 ctccacctaa tggcgaagaa gaagaaccag tcattaggta tgaggttaag agtgggatct 241 ctggcctgcc cgagctcaca acagtccccc aatcggacgt ggccaacaca gcattcagcg 301 ttccaccact gagcttgaga gaaaacaggg aggccaagga accgctaaca ggggcaatat 361 tagagatgtg ggacggagag atataccact atggcctgta cgtggagaaa ggcttagtgt 421 tgggtgtgca caaaccacct gcagccataa gcatggcaag agtggagctg acgccgttgt 481 cattgtactg gcgtgtggtg tacactcccc aatacctcat ctcccctgaa actctcagga 541 ggctcaacgg agaggcgttc ccttacactg ccttcgacaa caactgctat gccttttgct 601 gctgggtgtt agacctcaat gactcatggc ttagcaggag gacggtgcaa agaacaacgg 661 gcttcttcag accttaccaa gagtggaaca gaaaacccct gcccaccatg gatgactcca 721 aaataaagaa ggtagcaaat atattcctat gttcattgtc cacattattc accagaccca 781 taaaagacct cataggaaaa attaaaccat taaacatatt gaacatcctg gcaacgtgtg 841 actggacgtt tgccggaata gtggagtctc tgatattact tgctgaactc ttcggagttt 901 tctggacacc cccagatgtg tctgctatga tcgctccctt actcggggac tacgagttgc 961 aagggccaga agacctcgcc gttgaactcg tacctgtggt aatgggaggg attggtttgg 1021 tgttgggatt caccaaagag aaaattggca aaatgttgtc ctcagcagca tcaacactca 1081 gggcttgcaa agatcttggt gcctatggct tagagatact caaattggtc atgaagtggt 1141 tcttcccaaa gaaagaggag gccaatgagc tagccatggt gagggccata gaggatgccg 1201 tactagatct tgaggcaata gaaaataacc acatgacaac cctgttgaaa gacaaagaca 1261 gcttagcaac atacatgaaa acactggaca tggaggagga gaaagccaga aggttgtcca 1321 caaaatctgc atcccctgac atagttggga caatcaacgc cctgctggct cgaatagcag 1381 cagccaggtc attagtccac agggccaagg aagagctatc tagcaggata agaccagtag 1441 ttgttatgat atctggcaaa ccaggaatag gcaaaactca tctggccagg gaggtggcaa 1501 gaaaggtggc atccactctc acaggggatc aaagagtcgg actcgtacca agaaacggtg 1561 tggaccattg ggatgcatac aaaggtgaga gagtcgtgct gtgggacgac tatggcatga 1621 gtaaccccat tcatgatgct cttcgcatac aagaattggc tgatacgtgt ccccttacct 1681 taaattgtga cagaattgaa aataagggaa aagtttttga cagtgaagtc ataataatta 1741 caacaaacct tgccaaccca gccccacttg attatgtcaa ctttgaggcc tgttccagga 1801 gaattgattt cctggtgtac gctgaggcac cagaagtaga aaaggcaaaa cgggattttc 1861 ctggtcagcc agatatgtgg aaggacgcct tcaagccgga cttttcacac atcaagctac 1921 agcttgcacc tcagggcggc tttgacaaga atggcaacac cccacatggg aaaggggtga 1981 tgaagaccct cactaccggt tctctgattg cccgtgcatc aggcctgctg catgagagga 2041 tggatgaatt tgaactccaa ggtcccgcaa tcaccacctt taatttcgac cggaacagaa 2101 tcacagcatt cagacaattg gctgcagaaa acaagtatgg attggtggat accatgaaag 2161 ttggcaatca actaaaagga gtgaaaacca tggaagaact caaacaagca atcaggaatg 2221 tgaccatcaa gaggtgccgg atcatctacg gtggctccac gtacgacctt gaatctgatg 2281 gcaagggcaa agttttggtg gaaaaggtca agaacacctc tgtacagacc aacaacgagt 2341 tggccggggc cctgcaccat ctcaaacacg cccgaatcag gtactatgtc aaatgtgtgc 2401 aagaagcagt ctattccatc atacaaattg ccggcgctgc gtttgtcacc acgcgcattg 2461 cacgccgcat gaacatacaa gaactctggt cgaggccaca attagatcaa aatgaatcag 2521 aggctaagga agaggccccc aagtcagaag atgacgagtt catcatatct tctaaggaca 2581 tcaaggagga aggaaagaag ggcaaaaaca aaactggccg tggcaagaaa cacactgcat 2641 tctccagcaa gggcttgagc gatgaggagt atgacgagta caagaggata agagaagaga 2701 gaaatgggaa gtactctata gaggagtatc ttcaagacag agacaggtac tatgaggagc 2761 tcgccattgc caaggccacg gaagaagact tctgtgaaga ggaggagatc aaaatccgtc 2821 agagaatttt ccgtcccacc aggaaacaaa gaaaggaaga gagggccaca ttagggctgg 2881 taacaggttc agaaatcaga aaaagaaacc ctgatgactt caaacccaaa gggaagctgt 2941 gggccgatga caacagaagt gttgactaca atgagaaact ggattttgag gcccccccaa 3001 gcatatggtc taggattgtg agctttggtt ctggctgggg cttctgggta tcatcaagcc 3061 tgttcataac atcaactcat gtaatccccg caggcataac agaagcattt ggagtcccca 3121 tcaaacaaat tcagatccac aaatcaggtg aattttgccg attcagattc ccaaagccga 3181 ttagaccaga tgtgacagga atgatcttgg aagagggtgc gcctgaaggc accgtggcaa 3241 ctgtgctcat caaacgcccc accggagagc tcatgcctct tgcagccaga atgggaacac 3301 atgcaaccat gaaaattcaa ggccgcatgg ttggcgggca gatgggtatg ttgctcactg 3361 gatcaaatgc taaaggaatg gatttgggaa caactcctgg tgactgtggc tgtccttaca 3421 tctataaaag gggcaatgac tatatagtca ttggggtgca cactgcagcg gcccgtggtg 3481 gaaacaccgt catctgtgcc acacagggaa gtgagggtga ggcaactctt gagggtggag 3541 atgacaaagg aacatactgt ggggcaccca ttttaggccc tgggggtgca ccaaaattga 3601 gtaccaaaac caaattttgg aggtcatcga acacgcccct tccaccaggg acatatgaac 3661 ctgcctacct cggtggccgt gatccgcgtg ttaagggtgg gccctccttg cagcaggtaa 3721 tgagagacca gttgaagcca ttcactgaac ccaggggcaa acctccaaga ccaagtgtat 3781 tggaagcagc caaacaaacc attatcaatg ttctcgaaca aaccctggac cctccacaaa 3841 aatggacata cgcacaggcg tgtgcctcac ttgacaaaac cacctccagc gggcatcccc 3901 atcacatccg aaagaatgaa ttctggaatg gtgagacctt cactggtaaa ttggcagacc 3961 aagcatcaaa agcaaaccta atgtttgagg aagggaaaca catgacgcca gtgtatacag 4021 cagcactcaa ggacgagcta gtcaagactg agaaaatcta tggaaagatc aagaaaagac 4081 tgctctgggg ctctgacttg tccaccatga tccggtgcgc taggtcattt ggtgggctca 4141 tggacgagat gaaggcacat tgcatatcac tcccagtacg agttggcatg aatatgaatg 4201 aagatggccc aataatattt gagaaacatt ccagatacaa ataccactat gatgcagact 4261 actctcgttg ggattcaaca caacagaggg cagtactagc agcagccttg gaaatcatgg 4321 tcagattctc tgcagaacca caattggcac aaatagtcgc tgaggatcta ctggccccta 4381 gtgtagtaga tgtaggagac tttaaaatca caataaatga aggactccca tctggtgtgc 4441 catgcacttc tcaatggaac tccatcgcac actggctgct aactctctgt gccttgtctg 4501 aagtcaccaa actgtcccct gacattatac aagcaaactc catgttctca ttttacggtg 4561 atgacgagat tgtcagcacc gacataaaat tggatcctga acagttaacc gccaagttga 4621 aggagtacgg cctgaaacca acccgcccag acaagaccga gggacctctg atcatcagtg 4681 aagatttgaa cggactcact ttcctccgaa ggacggtgac tcgtgaccca gctggctggt 4741 ttggaaaact ggaccaaagt tcaattttga ggcagatgta ctggactaga ggaccaaatc 4801 atgaagatcc caatgagacg atgatacccc attctcaaag acccatacag ctcatggcac 4861 tgcttggtga agcctctctt cacggaccct ctttctacag tagaatcagc aaattggtca 4921 taactgaact caaagagggt gggatggact tttacgtgcc aaggcaggaa cccatgttca 4981 ggtggatgag gttttctgac ttgagcacgt gggagggcga tcgcaatctg gctcccaatt 5041 ttgtgaatga agatggcgtc gaatgacgcc aacccatctg atgggtccgc agccaacctc 5101 gtaccagagg tcaacaatga ggttatggct ttggagcccg ttgttggtgc cgctattgcg 5161 gcacctgtag cgggccaaca aaatgtaatt gacccctgga ttagaaataa ttttgtacaa 5221 gcccctggtg gggagttcac agtgtcccct agaaacgctc caggtgaaat actatggagc 5281 gcgcccctag gccctgacct aaatccctac ctatcccatt tggccagaat gtacaatggt 5341 tatgcaggtg gttttgaagt gcaggtaatt ctcgcgggga acgcgttcac cgccggaaag 5401 attatatttg cagcagtccc accaaatttt ccaactgaag gcttaagtcc tagccaggtc 5461 actatgttcc cccatataat agtagatgtt agacaattag aacctgtgct gattccctta 5521 cccgatgtta ggaataattt ctatcattat aatcagtcaa atgactccac tattaagttg 5581 atagcaatgt tgtatacacc acttagggct aataatgctg gagatgatgt tttcacggtt 5641 tcgtgccgag ttctcacgag accatccccc gattttgatt tcatattttt agtgccaccc 5701 acagttgagt caagaactaa accattctct gtcccagttt taactgttga ggagatgacc 5761 aattcaagat tccccatccc tttggaaaag ttgttcacag gccccagcag tgcctttgtt 5821 gttcaaccac aaaacggcag gtgcacaact gatggcgtgc tcctaggcac cacccaactt 5881 tctcctgtca acatctgcac cttcagaggg gatgtcaccc acatcacagg cagtcgcaac 5941 tacacaatga atttggcttc tcaaaattgg aataactatg acccaacaga agaaatccca 6001 gcccctctag gaactccaga ttttgtgggg aagattcaag gcatgctcac ccaaaccaca 6061 aggacagatg gttcaacacg cggccacaaa gctacagtgt acactgggag cgccgacttt 6121 gctccaaaac tgggtagagt tcaatttgaa actgacacag accatgattt tgaagctaat 6181 caaaacacaa agttcacccc agtcggtgtc atccaagatg gtagcaccac ccaccgaaac 6241 gaaccccaac agtgggtgct cccaagttac tcaggcagaa atactcacaa tgtacatttg 6301 gcccccgctg tggcccccac ctttccgggt gagcaacttc tcttcttcag atccaccatg 6361 cccggatgca gcgggtaccc caacatggat ttggactgtc tgctccccca ggaatgggtg 6421 cagtacttct accaagaggc agccccagca caatctgatg tggctctgct aagatttgtg 6481 aatccagaca caggtagggt tttgtttgag tgcaagcttc acaaatcagg ctatgttaca 6541 gtggctcaca ctggccaaca tgatttggtt atccccccca atggttactt taggtttgat 6601 tcctgggtca accagttcta cacgcttgcc cccatgggaa atggaacggg gcgtagacgt 6661 gtagtataat ggctggagct ttctttgctg gattggcatc tgatgtcctt ggctctggac 6721 ttggttccct tatcaatgct ggggctgggg ccatcaacca aaaagttgaa tttgaaaata 6781 acagaaaatt gcaacaagca tccttccaat ttagcagcaa tctgcaacag gcttcctttc 6841 aacatgataa agagatgctc caagcacaaa ttgaggccac caaaaagcta caacaggaaa 6901 tgatgaaagt taagcaggca atgctcctag agggtgggtt ctctgagaca gatgcagccc 6961 gcggggcaat taacgccccc atgacaaaag ctttggactg gagcgggaca aggtactggg 7021 ctccagatgc taggattaca acatacaatg caggccactt ttccacccct caaccatcga 7081 gggcactgcc aggaagagct aatcttaggg atgctgtccc tgctcgggga ccctccaacc 7141 aatcttctaa ctcttctact gccacctctg tgtactcaaa tcaaactatt tcaacgagac 7201 ttggttctac agctggttct ggaaccagtg tctcgagcct cccgtcaact gcaaggacta 7261 ggagctgggt tgaggatcaa aataggaatt tgtcaccttt catgaggggg gcccacaaca 7321 tatcatttgt caccccacca tctagcagat cctctagcca aggcacagtc tcaaccgtgc 7381 ctaaagagat tttggactcc tggactggcg ctttcaacac gcgcaggcag cctctcttcg 7441 ctcacattcg taagcgaggg gagtcacggg tgtaatgtga aaagacaaaa ctgattattt 7501 ttctttttct tttcttt //