Typing tool
|
Complete norovirus genomes
MT537634 | GII.4 Sydney | ||
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GII.P16 |
ORF1: 1..5097 ORF2: 5078..6700 ORF3: 6700..7506LOCUS MT537634 7515 bp RNA linear VRL 31-JUL-2020 DEFINITION Norovirus GII isolate 259-3 nonstructural polyprotein (ORF1) gene, partial cds; and VP1 (ORF2) and VP2 (ORF3) genes, complete cds. ACCESSION MT537634 VERSION MT537634.1 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of whole-genome sequencing for Norovirus outbreak tracking and surveillance efforts in Orange County, CA JOURNAL Unpublished REFERENCE 2 (bases 1 to 7515) AUTHORS Silva,A., Wolfe,J., Ruelle,S., Hirneisen,K. and Yang,Z. TITLE Direct Submission JOURNAL Submitted (29-MAY-2020) Schmid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="259-3" /isolation_source="stool" /host="Homo sapiens" /db_xref="taxon:122929" /country="USA" /collection_date="17-Dec-2018" /note="genotype: GII.4[P16]" gene <1..5097 /gene="ORF1" CDS <1..5097 /gene="ORF1" /codon_start=1 /product="nonstructural polyprotein" /protein_id="QKE61145.1" /translation="KMASNDATVAVACNNNNDKEKSSGEGLFTNMSFTLKKALGARPK QPAPRDEPQKPPRPPTPELVKRIPPPPPNGEGEEEPVIRYEVKSGISGLPELTTVPQP DVANTAFSVPPLSLRENREAKEPLTGAILEMWDGEIYHYGLYVEKGLVLGVHKPPAAI SMARVELTPLSLYWRVVYTPQYLISPETLRRLNGEAFPYTAFDNNCYAFCCWVLDLND SWLSRRMVQRTTGFFRPYQEWNRKPLPTMDDSKIKKVANIFLCSLSTLFTRPIKDLIG KIKPLNILNILATCDWTFAGIVESLILLAELFGVFWTPPDVSAMIAPLLGDYELQGPE DLAVELVPVVMGGIGLVLGFTKEKIGKMLSSAASTLRACKDLGAYGLEILKLVMKWFF PKKEEANELAMVRAIEDAVLDLEAIENNHMTTLLKDKDSLATYMKTLDMEEEKARRLS TKSASPDIVGTINALLARIAAARSLVHRAKEELSSRIRPVVVMISGKPGIGKTHLARE VARKVASTLTGDQRVGLIPRNGVDHWDAYKGERVVLWDDYGMSNPIHDALRIQELADT CPLTLNCDRIENKGKVFDSEVIIITTNLANPAPLDYVNFEACSRRIDFLVYAEAPEVE KAKRDFPGQPDMWKDAFKPDFSHIKLQLAPQGGFDKNGNTPHGKGVMKTLTTGSLIAR ASGLLHERMDEFELQGPTITTFNFDRNRITAFRQLAAENKYGLVDTMKVGNQLKGVKT MEELKQAIRNVTIKRCRIIYGGSTYDLESDGKGKVLVEKVKNTSVQTNNELAGALHHL KHARIRYYVKCVQEAVYSIIQIAGAAFVTTRIARRMNIQELWSKPQLDQNESETKEEA PKSEDDEFIISSKDIKEEGKKGKNKTGRGKKHTAFSSKGLSDEEYDEYKRIREERNGK YSIEEYLQDRDRYYEELAIAKATEEDFCEEEEIKIRQRIFRPTRKQRKEERATLGLVT GSEIRKRNPDDFKPKGKLWADDNRSVDYNEKLDFEAPPSIWSRIVSFGSGWGFWVSPS LFITSTHVIPAGITEAFGVPIKQIQIHKSGEFCRFRFPRPIRPDVTGMILEEGAPEGT VATVLIKRPTGELMPLAARMGTHATMKIQGRMVGGQMGMLLTGSNAKGMDLGTTPGDC GCPYIYKRGNDYIVIGVHTAAARGGNTVICATQGSEGEATLEGGYDKGTYCGAPILGP GGAPKLSTKTKFWRSSNTPLPPGTYEPAYLGGRDPRVKGGPSLQQVMRDQLKPFTEPR GKPPRPSVLEAAKQTVINVLEQTLDPPQKWTYAQACASLDKTTSSGHPHHVRKNEFWN GETFTGKLADQASKANLMFEEGKHMTPVYTAALKDELVKTEKIYRKIKKRLLWGSDLS TMIRCARSFGGLMDEMKAHCISLPVRVGMNVNEDGPIIFEKHSRYKYHYDADYSRWDS TQQRAVLAAALEIMVRFSAEPQLAQIVAEDLLAPSVVDVGDFKITINEGLPSGVPCTS QWNSIAHWLLTLCALSEVTKLSPDIIQANSMFSFYGDDEIVSTDIKLDPEQLTAKLKE YGLKPTRPDKTEGPLIISEDLNGLTFLRRTVTRDPAGWFGKLDQSSILRQMYWTRGPN HEDPNETMIPHSQRPIQLMALLGEASLHGPSFYSRISKLVITELKEGGMDFYVPRQEP MFRWMRFSDLSTWEGDRNLAPNFVNEDGVE" mat_peptide <1..993 /gene="ORF1" /product="p48" mat_peptide 994..2091 /gene="ORF1" /product="NTPase" mat_peptide 2092..2622 /gene="ORF1" /product="p22" mat_peptide 2623..3021 /gene="ORF1" /product="VPg" mat_peptide 3022..3564 /gene="ORF1" /product="Pro" mat_peptide 3565..5094 /gene="ORF1" /product="RdRp" gene 5078..6700 /gene="ORF2" CDS 5078..6700 /gene="ORF2" /note="major capsid protein" /codon_start=1 /product="VP1" /protein_id="QKE61146.1" /translation="MKMASSDANPSDGSAANLVPEVNNEVMALEPVVGAAIAAPVAGQ QNVIDPWIRNNFVQAPGGEFTVSPRNAPGEILWSAPLGPDLNPYLSHLARMYNGYAGG FEVQVILAGNAFTAGKIIFAAVPPNFPTEGLSPSQVTMFPHIIVDVRQLEPVLIPLPD VRNNFYHYNQSNDSTIKLIAMLYTPLRANNAGDDVFTVSCRVLTRPSPDFDFIFLVPP TVESRTKPFSVPVLTVEEMTNSRFPIPLEKLFTGPSSAFVVQPQNGRCTTDGVLLGTT QLSPVNICTFRGDVTHITGSRNYTMNLASQNWNNYDPTEEIPAPLGTPDFVGKIQGML TQTTRTDGSTRGHKATVYTGSADFAPKLGRVQFETDTDHDFEANQNTKFTPVGVIQDG STTHRNEPQQWVLPSYSGRNTHNVHLAPAVAPTFPGEQLLFFRSTMPGCSGYPNMDLD CLLPQEWVQYFYQEAAPAQSDVALLRFVNPDTGRVLFECKLHKSGYVTVAHTGQHDLV IPPNGYFRFDSWVNQFYTLAPMGNGTGRRRVV" gene 6700..7506 /gene="ORF3" CDS 6700..7506 /gene="ORF3" /note="minor structural protein; small basic protein" /codon_start=1 /product="VP2" /protein_id="QKE61147.1" /translation="MAGAFFAGLASDVLGSGLGSLINAGAGAINQKVEFENNRKLQQA SFQFSSNLQQASFQHDKEMLQAQIEATKKLQQEMMKVKQAMLLEGGFSETDAARGAIN APMTKALDWSGTRYWAPDARTTTYNAGRFSTPQPSGALPGRANLRDAVPARGPSNKSS NSSTATSVYSNQTISTRLGSTAGSGTSVSSLPSTARTRSWVEDQNRNLSPFMRGAHNI SFVTPPSSRSSSQGTVSTVPKEILDSWTGAFNTRRQPLFAHIRKRGESRV" ORIGIN 1 aagatggcgt ctaacgacgc taccgttgcc gttgcttgca acaacaacaa cgacaaggaa 61 aaatcttcag gtgaaggctt attcacaaat atgtctttca ccttaaagaa agccctcggg 121 gctaggccca aacagcctgc cccgagagac gaaccacaaa agcccccaag accaccaacc 181 cccgagttgg tcaagaggat accccctcct ccacctaatg gcgaaggaga agaagaacca 241 gtcattaggt atgaggttaa gagtgggatc tctggcctgc ccgagctcac aacagtcccc 301 caaccggacg tggccaacac agcattcagt gttccaccac tgagcttgag agaaaacagg 361 gaggccaagg aaccgctaac aggggcaata ttagagatgt gggatggaga gatataccac 421 tatggcctgt acgtggagaa aggcttagtg ttgggtgtgc acaaaccacc tgcagccata 481 agcatggcaa gagtggagct gacgccgctg tcattgtact ggcgtgtggt gtacactccc 541 caatacctca tctcccctga aactctcagg aggctcaacg gagaggcgtt cccttacacc 601 gccttcgaca acaactgcta cgccttttgc tgctgggtgt tagacctcaa tgactcatgg 661 cttagcagga ggatggtgca aagaacaacg ggcttcttca gaccttacca agagtggaac 721 agaaagcccc tgcctaccat ggatgactcc aaaattaaga aggtagcaaa tatattccta 781 tgttcattgt ccacattatt caccagaccc ataaaagacc tcatagggaa aattaaacca 841 ttaaacatat tgaacatcct ggcaacgtgt gactggacgt ttgccggaat agtggagtct 901 ctgatattac ttgctgaact cttcggagtt ttctggacgc ccccagatgt gtctgctatg 961 atcgctccct tactcgggga ctacgagttg caagggccag aagacctcgc cgttgaactc 1021 gtacctgtgg taatgggagg gattggtttg gtgttgggat tcaccaaaga gaaaattggc 1081 aaaatgttgt cctcagcagc atcaacactc agggcttgca aagatcttgg tgcctatggc 1141 ttagagatac tcaagttggt catgaagtgg ttcttcccaa agaaagagga ggccaatgag 1201 ctagccatgg tgagggccat agaggatgcc gtgctagatc ttgaggcaat agaaaataac 1261 cacatgacaa ccctgttgaa agacaaagac agcttagcaa catacatgaa aacactggac 1321 atggaggagg agaaagccag aaggttgtcc acaaaatctg catcccctga catagttggg 1381 acaatcaacg ccctgctggc tcgaatagca gcggccaggt cattagtcca cagggccaag 1441 gaagagctat ctagcaggat aaggccagta gttgttatga tatctggcaa accaggaata 1501 ggcaaaactc atctggccag ggaggtggca agaaaggtgg catccactct cacaggggac 1561 caaagagtcg gactcatacc aagaaacggt gtggaccatt gggatgcata caaaggtgag 1621 agagtcgtgc tgtgggacga ctatggcatg agtaacccca tccatgatgc tcttcgcata 1681 caagaattgg ctgatacgtg tccccttacc ttaaattgtg acagaattga aaataaggga 1741 aaagtttttg acagtgaagt cataataatt acaacaaacc ttgccaatcc agccccactt 1801 gattatgtca actttgaggc ctgttccagg agaattgatt tcctggtgta cgctgaggca 1861 ccagaagtag aaaaggcaaa acgggacttt cctggtcagc cagatatgtg gaaggacgcc 1921 ttcaagccgg acttttcaca catcaagcta cagcttgcac ctcagggcgg ctttgacaag 1981 aatggcaaca ccccacatgg gaaaggagtg atgaagaccc tcactaccgg ttctctgatt 2041 gcccgtgcat caggcctact acatgagagg atggatgaat ttgaactcca aggtcccaca 2101 atcaccacct tcaatttcga ccgaaacaga atcacagcat tcagacaatt ggctgcagaa 2161 aacaagtatg gattggtgga taccatgaaa gttggcaatc aattaaaagg agtgaaaacc 2221 atggaagaac tcaaacaagc aatcagaaat gtgaccatca agaggtgccg gatcatctac 2281 ggtggctcca cgtatgacct tgaatctgat ggcaagggca aagttttggt ggaaaaggtc 2341 aagaacacct ctgtacagac caacaacgag ttggccgggg ccctgcacca tctcaaacac 2401 gcccgaatca ggtactatgt caaatgtgtg caagaagcag tctattccat catacaaatt 2461 gccggcgctg cgtttgtcac cacgcgcatt gcacgccgca tgaacataca agaactctgg 2521 tcgaagccac aattagatca aaatgaatca gagactaagg aagaggcccc caaatcagaa 2581 gatgacgagt tcatcatatc ttctaaggac atcaaggagg aaggaaagaa gggcaaaaac 2641 aaaactggcc gtggcaagaa acacactgca ttctccagca agggcttgag cgatgaggag 2701 tatgacgagt acaagaggat aagagaagag agaaatggga agtactctat agaggagtat 2761 cttcaagaca gagacaggta ctatgaggag ctcgccattg ccaaggccac ggaagaagac 2821 ttctgtgaag aggaggagat aaaaatccgt cagagaattt tccgtcccac caggaaacaa 2881 agaaaggaag agagggccac attaggactg gtaacaggtt cagaaatcag aaaaagaaac 2941 cctgatgact tcaaacccaa agggaagctg tgggccgatg acaacagaag tgttgactat 3001 aatgagaaac tggactttga ggccccccca agcatatggt ctaggattgt gagctttggt 3061 tctggctggg gcttctgggt atcaccaagc ctgttcataa catcaactca tgtaatcccc 3121 gcaggcataa cagaagcatt tggagtcccc atcaaacaaa ttcagatcca caaatcaggt 3181 gaattttgcc gattcagatt cccaagacca attagaccag acgtgacagg aatgatcttg 3241 gaagaaggtg cgcctgaagg caccgtggca actgtgctca tcaaacgccc caccggagag 3301 ctcatgcctc ttgcagccag aatgggaaca cacgcaacca tgaaaattca aggccgcatg 3361 gttggcggac agatgggtat gttgctcact ggatcaaatg ctaaaggaat ggatttggga 3421 acaactcctg gtgactgtgg ctgtccttac atctacaaaa ggggcaatga ctatatagtc 3481 attggggtgc acactgcagc agcccgtggt ggaaacaccg tcatctgtgc cacacaggga 3541 agtgagggtg aggcaactct tgagggtgga tatgacaaag gaacatactg tggggcaccc 3601 attctaggcc ctgggggtgc accaaagttg agcaccaaaa ccaaattttg gaggtcatcg 3661 aacacgcccc tcccaccagg gacatatgag cctgcctacc tcggtggccg tgatccgcgt 3721 gttaagggtg ggccctcctt gcagcaggta atgagagacc agttgaagcc attcactgaa 3781 cccaggggca aacctccaag accaagtgta ttggaagcag ccaaacaaac cgttatcaat 3841 gtcctcgaac aaaccctgga tcctccacaa aaatggacat acgcacaggc gtgtgcctca 3901 cttgacaaaa ccacttccag cgggcatcct catcacgtcc gaaagaatga attctggaat 3961 ggtgagacct tcaccggcaa attggcagac caagcatcaa aagcaaacct aatgtttgag 4021 gaagggaaac acatgacacc agtgtataca gcagcactca aggacgagct agtcaagact 4081 gagaaaatct atagaaagat caagaagaga ctgctctggg gctctgactt gtccaccatg 4141 atccggtgcg ctaggtcatt tggtgggctc atggacgaga tgaaggcaca ctgcatatca 4201 ctcccagtac gagttggcat gaatgtgaat gaagatggcc caataatatt tgagaaacat 4261 tccagataca aataccacta tgacgcagac tactctcgtt gggattcaac acaacagagg 4321 gcagtactag cagcagcctt ggaaatcatg gtcagattct ctgcagaacc acaattggca 4381 caaatagtcg ctgaggatct tctggcccct agcgtagtag atgtaggaga ctttaaaatc 4441 actataaatg aagggctccc atctggtgtg ccatgcacct cccaatggaa ctccatcgca 4501 cactggctgc taactctctg tgccttgtct gaagtcacca aactgtcccc tgacattata 4561 caagcaaatt ccatgttctc attttacggt gatgacgaga ttgtcagcac cgacataaaa 4621 ttggaccctg aacagttaac cgccaagttg aaggagtatg gcctgaaacc aacccgccca 4681 gacaagaccg agggacccct gatcatcagt gaagatttga acggactcac tttcctccga 4741 aggacggtga ctcgtgaccc agctggctgg tttggaaaac tggaccaaag ttcaattttg 4801 aggcagatgt actggactag aggaccaaat cacgaagatc ccaatgagac aatgataccc 4861 cattctcaaa gacccataca gctcatggca ctgcttggtg aagcctctct tcacggaccc 4921 tctttctaca gtagaatcag taaattggtc ataactgaac tcaaagaagg tgggatggac 4981 ttttacgtgc caaggcagga acccatgttc aggtggatga ggttttctga cttgagcacg 5041 tgggagggcg atcgcaatct ggctcccaat tttgtgaatg aagatggcgt cgagtgacgc 5101 caacccatct gatgggtccg cagccaacct cgtaccagag gtcaacaatg aggttatggc 5161 tttggagccc gttgtcggtg ccgctattgc ggcacctgta gcgggccaac aaaatgtaat 5221 tgacccctgg attagaaata attttgtaca agcccctggt ggggagttta cagtatcccc 5281 cagaaacgct ccaggtgaaa tactatggag cgcgccccta ggccctgacc taaatcccta 5341 cctatcccat ttggccagaa tgtacaatgg ttatgcaggt ggttttgaag tgcaggtaat 5401 tctcgcgggg aacgcgttca ccgccgggaa gatcatattt gcagcagtcc caccaaattt 5461 tccaactgaa ggcttaagtc ctagccaggt cactatgttc ccccatataa tagtagatgt 5521 tagacagtta gaacctgtgc tgattccttt acccgatgtt aggaataatt tctatcatta 5581 caatcagtca aatgactcca ctattaagtt gatagcaatg ttgtacacac cacttagggc 5641 taataatgct ggggatgatg ttttcacagt ttcgtgccga gttctcacga gaccatcccc 5701 cgattttgat ttcatatttt tagtgccacc cacagttgag tcaagaacta aaccattctc 5761 tgtcccagtt ttaactgttg aggagatgac caattcaaga ttccccatcc ctttggaaaa 5821 gctgttcaca ggccccagca gtgcctttgt tgttcaacca caaaacggca ggtgcacaac 5881 tgatggcgtg ctcctaggca ccacccaact ttctcctgtc aacatctgca ccttcagagg 5941 ggatgtcacc cacatcacag gtagtcgcaa ctacacaatg aatttggctt ctcaaaattg 6001 gaacaactat gacccaacag aagaaatccc agcccctcta ggaactccag attttgtggg 6061 gaagattcaa ggcatgctca cccaaaccac aaggacagat ggttcaacac gcggccacaa 6121 agctacagtg tacactggga gcgccgactt tgctccaaaa ctgggtagag ttcaatttga 6181 aactgacaca gaccatgatt ttgaagctaa tcaaaacaca aagttcaccc cagtcggtgt 6241 catccaagat ggtagcacca cccatcgaaa cgaaccccaa cagtgggtgc tcccaagtta 6301 ctcaggcaga aatactcaca atgtacatct ggcccccgct gtagccccca cctttccggg 6361 tgagcaactt ctcttcttca gatccaccat gcccggatgc agcgggtacc ccaacatgga 6421 tttggactgt ctgctccccc aggaatgggt gcagtacttc tatcaagagg cagccccagc 6481 acaatctgat gtggctctgc taagatttgt gaatccagac acaggtaggg ttttgtttga 6541 gtgcaagctt cacaaatcag gctatgttac agtggctcac actggccaac atgatttggt 6601 tatccccccc aatggctact ttagatttga ttcctgggtc aaccagttct atacgcttgc 6661 ccccatggga aatggaacgg ggcgtagacg tgtagtataa tggctggagc tttctttgct 6721 ggattggcat ctgatgtcct tggctctgga cttggttccc tcatcaatgc tggggctggg 6781 gccatcaacc aaaaagttga gtttgaaaat aacagaaaat tgcaacaagc atccttccaa 6841 tttagcagca atctgcaaca ggcttccttt caacatgata aagagatgct ccaagcacaa 6901 attgaggcca ctaaaaagct acaacaggaa atgatgaaag ttaagcaggc aatgctccta 6961 gagggtgggt tctctgagac agatgcagcc cgcggggcaa ttaacgcccc catgacaaaa 7021 gctttggact ggagtgggac aaggtactgg gctcccgatg ctaggactac aacatacaat 7081 gcaggccgct tttccacccc tcaaccatcg ggggcactgc caggaagagc taatcttagg 7141 gatgctgtcc ctgctcgggg accctccaac aaatcttcta actcttctac tgccacctct 7201 gtgtattcaa atcaaactat ttcaacgaga cttggttcta cagctggttc tggaaccagt 7261 gtctcgagcc tcccgtcaac tgcaaggact aggagctggg ttgaggatca aaataggaat 7321 ttgtcacctt tcatgagggg ggcccacaac atatcatttg tcaccccacc atctagcaga 7381 tcctctagcc aaggcacagt ctcaaccgtg cctaaagaga ttttggactc ctggactggc 7441 gctttcaaca cgcgcaggca gcctctcttc gctcacattc gtaagcgagg ggagtcacgg 7501 gtgtaatgtg aaaag //