Typing tool
|
Complete norovirus genomes
MT537941 | GII.4 Sydney | ||
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GII.P16 |
ORF1: 1..5092 ORF2: 5073..6695 ORF3: 6695..7501LOCUS MT537941 7512 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 MT537941 VERSION MT537941.1 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 7512) 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of whole-genome sequencing for Norovirus outbreak tracking and surveillance efforts in Orange County, CA JOURNAL Unpublished REFERENCE 2 (bases 1 to 7512) AUTHORS Silva,A., Wolfe,J., Ruelle,S., Hirneisen,K. and Yang,Z. TITLE Direct Submission JOURNAL Submitted (29-MAY-2020) Schmid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..7512 /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..5092 /gene="ORF1" CDS <1..5092 /gene="ORF1" /codon_start=2 /product="nonstructural polyprotein" /protein_id="QKE61148.1" /translation="ASNDATVAVACNNNNDKEKSSGEGLFTNMSFTLKKALGARPKQP APRDEPQKPPRPPTPELVKRIPPPPPNGEGEEEPVIRYEVKSGISGLPELTTVPQPDV ANTAFSVPPLSLRENREAKEPLTGAILEMWDGEIYHYGLYVEKGLVLGVHKPPAAISM ARVELTPLSLYWRVVYTPQYLISPETLRRLNGEAFPYTAFDNNCYAFCCWVLDLNDSW LSRRMVQRTTGFFRPYQEWNRKPLPTMDDSKIKKVANIFLCSLSTLFTRPIKDLIGKI KPLNILNILATCDWTFAGIVESLILLAELFGVFWTPPDVSAMIAPLLGDYELQGPEDL AVELVPVVMGGIGLVLGFTKEKIGKMLSSAASTLRACKDLGAYGLEILKLVMKWFFPK KEEANELAMVRAIEDAVLDLEAIENNHMTTLLKDKDSLATYMKTLDMEEEKARRLSTK SASPDIVGTINALLARIAAARSLVHRAKEELSSRIRPVVVMISGKPGIGKTHLAREVA RKVASTLTGDQRVGLIPRNGVDHWDAYKGERVVLWDDYGMSNPIHDALRIQELADTCP LTLNCDRIENKGKVFDSEVIIITTNLANPAPLDYVNFEACSRRIDFLVYAEAPEVEKA KRDFPGQPDMWKDAFKPDFSHIKLQLAPQGGFDKNGNTPHGKGVMKTLTTGSLIARAS GLLHERMDEFELQGPTITTFNFDRNRITAFRQLAAENKYGLVDTMKVGNQLKGVKTME ELKQAIRNVTIKRCRIIYGGSTYDLESDGKGKVLVEKVKNTSVQTNNELAGALHHLKH ARIRYYVKCVQEAVYSIIQIAGAAFVTTRIARRMNIQELWSKPQLDQNESETKEEAPK SEDDEFIISSKDIKEEGKKGKNKTGRGKKHTAFSSKGLSDEEYDEYKRIREERNGKYS IEEYLQDRDRYYEELAIAKATEEDFCEEEEIKIRQRIFRPTRKQRKEERATLGLVTGS EIRKRNPDDFKPKGKLWADDNRSVDYNEKLDFEAPPSIWSRIVSFGSGWGFWVSPSLF ITSTHVIPAGITEAFGVPIKQIQIHKSGEFCRFRFPRPIRPDVTGMILEEGAPEGTVA TVLIKRPTGELMPLAARMGTHATMKIQGRMVGGQMGMLLTGSNAKGMDLGTTPGDCGC PYIYKRGNDYIVIGVHTAAARGGNTVICATQGSEGEATLEGGYDKGTYCGAPILGPGG APKLSTKTKFWRSSNTPLPPGTYEPAYLGGRDPRVKGGPSLQQVMRDQLKPFTEPRGK PPRPSVLEAAKQTVINVLEQTLDPPQKWTYAQACASLDKTTSSGHPHHVRKNEFWNGE TFTGKLADQASKANLMFEEGKHMTPVYTAALKDELVKTEKIYRKIKKRLLWGSDLSTM IRCARSFGGLMDEMKAHCISLPVRVGMNVNEDGPIIFEKHSRYKYHYDADYSRWDSTQ QRAVLAAALEIMVRFSAEPQLAQIVAEDLLAPSVVDVGDFKITINEGLPSGVPCTSQW NSIAHWLLTLCALSEVTKLSPDIIQANSMFSFYGDDEIVSTDIKLDPEQLTAKLKEYG LKPTRPDKTEGPLIISEDLNGLTFLRRTVTRDPAGWFGKLDQSSILRQMYWTRGPNHE DPNETMIPHSQRPIQLMALLGEASLHGPSFYSRISKLVITELKEGGMDFYVPRQEPMF RWMRFSDLSTWEGDRNLAPNFVNEDGVE" mat_peptide <1..988 /gene="ORF1" /product="p48" mat_peptide 989..2086 /gene="ORF1" /product="NTPase" mat_peptide 2087..2617 /gene="ORF1" /product="p22" mat_peptide 2618..3016 /gene="ORF1" /product="VPg" mat_peptide 3017..3559 /gene="ORF1" /product="Pro" mat_peptide 3560..5089 /gene="ORF1" /product="RdRp" gene 5073..6695 /gene="ORF2" CDS 5073..6695 /gene="ORF2" /note="major capsid protein" /codon_start=1 /product="VP1" /protein_id="QKE61149.1" /translation="MKMASSDANPSDGSAANLVPEVNNEVMALEPVVGAAIAAPVAGQ QNVIDPWIRNNFVQAPGGEFTVSPRNAPGEILWSAPLGPDLNPYLSHLARMYNGYAGG FEVQVILAGNAFTAGKIIFAAVPPNFPTEGLSPSQVTMFPHIIVDVRQLEPVLIPLPD VRNNFYHYNQSNDSTIKLIAMLYTPLRANNAGDDVFTVSCRVLTRPSPDFDFIFLVPP TVESRTKPFSVPVLTVEEMTNSRFPIPLEKLFTGPSSAFVVQPQNGRCTTDGVLLGTT QLSPVNICTFRGDVTHITGSRNYTMNLASQNWNNYDPTEEIPAPLGTPDFVGKIQGML TQTTRTDGSTRGHKATVYTGSADFAPKLGRVQFETDTDHDFEANQNTKFTPVGVIQDG STTHRNEPQQWVLPSYSGRNTHNVHLAPAVAPTFPGEQLLFFRSTMPGCSGYPNMDLD CLLPQEWVQYFYQEAAPAQSDVALLRFVNPDTGRVLFECKLHKSGYVTVAHTGQHDLV IPPNGYFRFDSWVNQFYTLAPMGNGTGRRRVV" gene 6695..7501 /gene="ORF3" CDS 6695..7501 /gene="ORF3" /note="minor structural protein; small basic protein" /codon_start=1 /product="VP2" /protein_id="QKE61150.1" /translation="MAGAFFAGLASDVLGSGLGSLINAGAGAINQKVEFENNRKLQQA SFQFSSNLQQASFQHDKEMLQAQIEATKKLQQEMMKVKQAMLLEGGFSETDAARGAIN APMTKALDWSGTRYWAPDARTTTYNAGRFSTPQPSGALPGRANLRDAVPARGPSNKSS NSSTATSVYSNQTISTRLGSTAGSGTSVSSLPSTARTRSWVEDQNRNLSPFMRGAHNI SFVTPPSSRSSSQGTVSTVPKEILDSWTGAFNTRRQPLFAHIRKRGESRV" ORIGIN 1 ggcgtctaac gacgctaccg ttgccgttgc ttgcaacaac aacaacgaca aggaaaaatc 61 ttcaggtgaa ggcttattca caaatatgtc tttcacctta aagaaagccc tcggggctag 121 gcccaaacag cctgccccga gagacgaacc acaaaagccc ccaagaccac caacccccga 181 gttggtcaag aggatacccc ctcctccacc taatggcgaa ggagaagaag aaccagtcat 241 taggtatgag gttaagagtg ggatctctgg cctgcccgag ctcacaacag tcccccaacc 301 ggacgtggcc aacacagcat tcagtgttcc accactgagc ttgagagaaa acagggaggc 361 caaggaaccg ctaacagggg caatattaga gatgtgggat ggagagatat accactatgg 421 cctgtacgtg gagaaaggct tagtgttggg tgtgcacaaa ccacctgcag ccataagcat 481 ggcaagagtg gagctgacgc cgctgtcatt gtactggcgt gtggtgtaca ctccccaata 541 cctcatctcc cctgaaactc tcaggaggct caacggagag gcgttccctt acaccgcctt 601 cgacaacaac tgctacgcct tttgctgctg ggtgttagac ctcaatgact catggcttag 661 caggaggatg gtgcaaagaa caacgggctt cttcagacct taccaagagt ggaacagaaa 721 gcccctgcct accatggatg actccaaaat taagaaggta gcaaatatat tcctatgttc 781 attgtccaca ttattcacca gacccataaa agacctcata gggaaaatta aaccattaaa 841 catattgaac atcctggcaa cgtgtgactg gacgtttgcc ggaatagtgg agtctctgat 901 attacttgct gaactcttcg gagttttctg gacgccccca gatgtgtctg ctatgatcgc 961 tcccttactc ggggactacg agttgcaagg gccagaagac ctcgccgttg aactcgtacc 1021 tgtggtaatg ggagggattg gtttggtgtt gggattcacc aaagagaaaa ttggcaaaat 1081 gttgtcctca gcagcatcaa cactcagggc ttgcaaagat cttggtgcct atggcttaga 1141 gatactcaag ttggtcatga agtggttctt cccaaagaaa gaggaggcca atgagctagc 1201 catggtgagg gccatagagg atgccgtgct agatcttgag gcaatagaaa ataaccacat 1261 gacaaccctg ttgaaagaca aagacagctt agcaacatac atgaaaacac tggacatgga 1321 ggaggagaaa gccagaaggt tgtccacaaa atctgcatcc cctgacatag ttgggacaat 1381 caacgccctg ctggctcgaa tagcagcggc caggtcatta gtccacaggg ccaaggaaga 1441 gctatctagc aggataaggc cagtagttgt tatgatatct ggcaaaccag gaataggcaa 1501 aactcatctg gccagggagg tggcaagaaa ggtggcatcc actctcacag gggaccaaag 1561 agtcggactc ataccaagaa acggtgtgga ccattgggat gcatacaaag gtgagagagt 1621 cgtgctgtgg gacgactatg gcatgagtaa ccccatccat gatgctcttc gcatacaaga 1681 attggctgat acgtgtcccc ttaccttaaa ttgtgacaga attgaaaata agggaaaagt 1741 ttttgacagt gaagtcataa taattacaac aaaccttgcc aatccagccc cacttgatta 1801 tgtcaacttt gaggcctgtt ccaggagaat tgatttcctg gtgtacgctg aggcaccaga 1861 agtagaaaag gcaaaacggg actttcctgg tcagccagat atgtggaagg acgccttcaa 1921 gccggacttt tcacacatca agctacagct tgcacctcag ggcggctttg acaagaatgg 1981 caacacccca catgggaaag gagtgatgaa gaccctcact accggttctc tgattgcccg 2041 tgcatcaggc ctactacatg agaggatgga tgaatttgaa ctccaaggtc ccacaatcac 2101 caccttcaat ttcgaccgaa acagaatcac agcattcaga caattggctg cagaaaacaa 2161 gtatggattg gtggatacca tgaaagttgg caatcaatta aaaggagtga aaaccatgga 2221 agaactcaaa caagcaatca gaaatgtgac catcaagagg tgccggatca tctacggtgg 2281 ctccacgtat gaccttgaat ctgatggcaa gggcaaagtt ttggtggaaa aggtcaagaa 2341 cacctctgta cagaccaaca acgagttggc cggggccctg caccatctca aacacgcccg 2401 aatcaggtac tatgtcaaat gtgtgcaaga agcagtctat tccatcatac aaattgccgg 2461 cgctgcgttt gtcaccacgc gcattgcacg ccgcatgaac atacaagaac tctggtcgaa 2521 gccacaatta gatcaaaatg aatcagagac taaggaagag gcccccaaat cagaagatga 2581 cgagttcatc atatcttcta aggacatcaa ggaggaagga aagaagggca aaaacaaaac 2641 tggccgtggc aagaaacaca ctgcattctc cagcaagggc ttgagcgatg aggagtatga 2701 cgagtacaag aggataagag aagagagaaa tgggaagtac tctatagagg agtatcttca 2761 agacagagac aggtactatg aggagctcgc cattgccaag gccacggaag aagacttctg 2821 tgaagaggag gagataaaaa tccgtcagag aattttccgt cccaccagga aacaaagaaa 2881 ggaagagagg gccacattag gactggtaac aggttcagaa atcagaaaaa gaaaccctga 2941 tgacttcaaa cccaaaggga agctgtgggc cgatgacaac agaagtgttg actataatga 3001 gaaactggac tttgaggccc ccccaagcat atggtctagg attgtgagct ttggttctgg 3061 ctggggcttc tgggtatcac caagcctgtt cataacatca actcatgtaa tccccgcagg 3121 cataacagaa gcatttggag tccccatcaa acaaattcag atccacaaat caggtgaatt 3181 ttgccgattc agattcccaa gaccaattag accagacgtg acaggaatga tcttggaaga 3241 aggtgcgcct gaaggcaccg tggcaactgt gctcatcaaa cgccccaccg gagagctcat 3301 gcctcttgca gccagaatgg gaacacacgc aaccatgaaa attcaaggcc gcatggttgg 3361 cggacagatg ggtatgttgc tcactggatc aaatgctaaa ggaatggatt tgggaacaac 3421 tcctggtgac tgtggctgtc cttacatcta caaaaggggc aatgactata tagtcattgg 3481 ggtgcacact gcagcagccc gtggtggaaa caccgtcatc tgtgccacac agggaagtga 3541 gggtgaggca actcttgagg gtggatatga caaaggaaca tactgtgggg cacccattct 3601 aggccctggg ggtgcaccaa agttgagcac caaaaccaaa ttttggaggt catcgaacac 3661 gcccctccca ccagggacat atgagcctgc ctacctcggt ggccgtgatc cgcgtgttaa 3721 gggtgggccc tccttgcagc aggtaatgag agaccagttg aagccattca ctgaacccag 3781 gggcaaacct ccaagaccaa gtgtattgga agcagccaaa caaaccgtta tcaatgtcct 3841 cgaacaaacc ctggatcctc cacaaaaatg gacatacgca caggcgtgtg cctcacttga 3901 caaaaccact tccagcgggc atcctcatca cgtccgaaag aatgaattct ggaatggtga 3961 gaccttcacc ggcaaattgg cagaccaagc atcaaaagca aacctaatgt ttgaggaagg 4021 gaaacacatg acaccagtgt atacagcagc actcaaggac gagctagtca agactgagaa 4081 aatctataga aagatcaaga agagactgct ctggggctct gacttgtcca ccatgatccg 4141 gtgcgctagg tcatttggtg ggctcatgga cgagatgaag gcacactgca tatcactccc 4201 agtacgagtt ggcatgaatg tgaatgaaga tggcccaata atatttgaga aacattccag 4261 atacaaatac cactatgacg cagactactc tcgttgggat tcaacacaac agagggcagt 4321 actagcagca gccttggaaa tcatggtcag attctctgca gaaccacaat tggcacaaat 4381 agtcgctgag gatcttctgg cccctagcgt agtagatgta ggagacttta aaatcactat 4441 aaatgaaggg ctcccatctg gtgtgccatg cacctcccaa tggaactcca tcgcacactg 4501 gctgctaact ctctgtgcct tgtctgaagt caccaaactg tcccctgaca ttatacaagc 4561 aaattccatg ttctcatttt acggtgatga cgagattgtc agcaccgaca taaaattgga 4621 ccctgaacag ttaaccgcca agttgaagga gtatggcctg aaaccaaccc gcccagacaa 4681 gaccgaggga cccctgatca tcagtgaaga tttgaacgga ctcactttcc tccgaaggac 4741 ggtgactcgt gacccagctg gctggtttgg aaaactggac caaagttcaa ttttgaggca 4801 gatgtactgg actagaggac caaatcacga agatcccaat gagacaatga taccccattc 4861 tcaaagaccc atacagctca tggcactgct tggtgaagcc tctcttcacg gaccctcttt 4921 ctacagtaga atcagtaaat tggtcataac tgaactcaaa gaaggtggga tggactttta 4981 cgtgccaagg caggaaccca tgttcaggtg gatgaggttt tctgacttga gcacgtggga 5041 gggcgatcgc aatctggctc ccaattttgt gaatgaagat ggcgtcgagt gacgccaacc 5101 catctgatgg gtccgcagcc aacctcgtac cagaggtcaa caatgaggtt atggctttgg 5161 agcccgttgt cggtgccgct attgcggcac ctgtagcggg ccaacaaaat gtaattgacc 5221 cctggattag aaataatttt gtacaagccc ctggtgggga gtttacagta tcccccagaa 5281 acgctccagg tgaaatacta tggagcgcgc ccctaggccc tgacctaaat ccctacctat 5341 cccatttggc cagaatgtac aatggttatg caggtggttt tgaagtgcag gtaattctcg 5401 cggggaacgc gttcaccgcc gggaagatca tatttgcagc agtcccacca aattttccaa 5461 ctgaaggctt aagtcctagc caggtcacta tgttccccca tataatagta gatgttagac 5521 agttagaacc tgtgctgatt cctttacccg atgttaggaa taatttctat cattacaatc 5581 agtcaaatga ctccactatt aagttgatag caatgttgta cacaccactt agggctaata 5641 atgctgggga tgatgttttc acagtttcgt gccgagttct cacgagacca tcccccgatt 5701 ttgatttcat atttttagtg ccacccacag ttgagtcaag aactaaacca ttctctgtcc 5761 cagttttaac tgttgaggag atgaccaatt caagattccc catccctttg gaaaagctgt 5821 tcacaggccc cagcagtgcc tttgttgttc aaccacaaaa cggcaggtgc acaactgatg 5881 gcgtgctcct aggcaccacc caactttctc ctgtcaacat ctgcaccttc agaggggatg 5941 tcacccacat cacaggtagt cgcaactaca caatgaattt ggcttctcaa aattggaaca 6001 actatgaccc aacagaagaa atcccagccc ctctaggaac tccagatttt gtggggaaga 6061 ttcaaggcat gctcacccaa accacaagga cagatggttc aacacgcggc cacaaagcta 6121 cagtgtacac tgggagcgcc gactttgctc caaaactggg tagagttcaa tttgaaactg 6181 acacagacca tgattttgaa gctaatcaaa acacaaagtt caccccagtc ggtgtcatcc 6241 aagatggtag caccacccat cgaaacgaac cccaacagtg ggtgctccca agttactcag 6301 gcagaaatac tcacaatgta catctggccc ccgctgtagc ccccaccttt ccgggtgagc 6361 aacttctctt cttcagatcc accatgcccg gatgcagcgg gtaccccaac atggatttgg 6421 actgtctgct cccccaggaa tgggtgcagt acttctatca agaggcagcc ccagcacaat 6481 ctgatgtggc tctgctaaga tttgtgaatc cagacacagg tagggttttg tttgagtgca 6541 agcttcacaa atcaggctat gttacagtgg ctcacactgg ccaacatgat ttggttatcc 6601 cccccaatgg ctactttaga tttgattcct gggtcaacca gttctatacg cttgccccca 6661 tgggaaatgg aacggggcgt agacgtgtag tataatggct ggagctttct ttgctggatt 6721 ggcatctgat gtccttggct ctggacttgg ttccctcatc aatgctgggg ctggggccat 6781 caaccaaaaa gttgagtttg aaaataacag aaaattgcaa caagcatcct tccaatttag 6841 cagcaatctg caacaggctt cctttcaaca tgataaagag atgctccaag cacaaattga 6901 ggccactaaa aagctacaac aggaaatgat gaaagttaag caggcaatgc tcctagaggg 6961 tgggttctct gagacagatg cagcccgcgg ggcaattaac gcccccatga caaaagcttt 7021 ggactggagt gggacaaggt actgggctcc cgatgctagg actacaacat acaatgcagg 7081 ccgcttttcc acccctcaac catcgggggc actgccagga agagctaatc ttagggatgc 7141 tgtccctgct cggggaccct ccaacaaatc ttctaactct tctactgcca cctctgtgta 7201 ttcaaatcaa actatttcaa cgagacttgg ttctacagct ggttctggaa ccagtgtctc 7261 gagcctcccg tcaactgcaa ggactaggag ctgggttgag gatcaaaata ggaatttgtc 7321 acctttcatg aggggggccc acaacatatc atttgtcacc ccaccatcta gcagatcctc 7381 tagccaaggc acagtctcaa ccgtgcctaa agagattttg gactcctgga ctggcgcttt 7441 caacacgcgc aggcagcctc tcttcgctca cattcgtaag cgaggggagt cacgggtgta 7501 atgtgaaaag ac //