Typing tool
|
Complete norovirus genomes
MT362912 | GII.4 Sydney | ||
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GII.P4 New Orleans |
ORF1: 1..5100 ORF2: 5081..6703 ORF3: 6703..7506LOCUS MT362912 7553 bp RNA linear VRL 01-JUN-2020 DEFINITION Norovirus GII isolate 432-1 nonstructural polyprotein (ORF1), VP1 (ORF2), and VP2 (ORF3) genes, complete cds. ACCESSION MT362912 VERSION MT362912.1 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 7553) AUTHORS Silva,A., Wolfe,J., Yang,Z., Hirneisen,K. and Ruelle,S. TITLE Application of whole-genome sequencing for Norovirus outbreak tracking and surveillance efforts in Orange County, CA JOURNAL Unpublished REFERENCE 2 (bases 1 to 7553) AUTHORS Silva,A., Wolfe,J., Yang,Z., Hirneisen,K. and Ruelle,S. TITLE Direct Submission JOURNAL Submitted (21-APR-2020) Schmid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..7553 /organism="Norovirus GII" /mol_type="genomic RNA" /isolate="432-1" /isolation_source="stool" /host="Homo sapiens" /db_xref="taxon:122929" /country="USA" /collection_date="10-Apr-2017" /note="genotype: GII.4 New Orleans[P4 New Orleans]" gene 1..5100 /gene="ORF1" CDS 1..5100 /gene="ORF1" /codon_start=1 /product="nonstructural polyprotein" /protein_id="QJC69080.1" /translation="MKMASNDATAAAVANSNNDTAKSSSDGVLSSMAVTFKRALGARP KQPPPREKPQRPPRPPTPELVKNIPPPPPNGEDEIVVTYSVKDGVSGLPDLSTVRQPE ESNTAFSVPPLNQRENRDAKEPLTGTILEMWDGEIYHYGLYVERGLVLGVHKPPAAIS LAKVELAPLSLYWRPVYTPQYLISPDTLKKLSGETFPYTAFDNNCYAFCCWVLDLNDS WLSRRMIQRTTGFFRPYQDWNRKPLPTMDDSKIKKVANIFLCALSSLFTRPIKDIIGK IRPLNILNILASCDWTFAGIVESLILLAELFGVFWTPPDVSAMIAPLLGDYELQGPED LAVELVPVVMGGIGLVLGFTKEKIGKMLSSAASTLRACKDLGAYGLEILKLVMKWFFP KKEEANELAMVRSIEDAVLDLEAIENNHMTTLLKDKDSLATYMRTLDLEEEKARKLST KSASPDIVGTINALLARIAAARSLVHRAKEELSSRPRPVVLMISGRPGIGKTHLAREV AKRIAASLTGDQRVGLIPRNGVDHWDAYKGERVVLWDDYGMSNPIHDALRLQELADTC PLTLNCDRIENKGKVFDSDVIIITTNLANPAPLDYVNFEACSRRIDFLVYAEAPDVEK AKRDFPGQPDMWKNAFSSDFSHIKLALAPQGGFDKNGNTPHGKGVMKTLTTGSLIARA SGLLHERLDEFELQGPALTTFNFDRNKVLAFRQLAAENKYGLMDTMRVGKQLKDVKTM PELKQALKNVSIKKCQIVYNGCTYMLESDGKGNVKVDRIQSAAVQTNNELAGALHHLR CARIRYYVKCVQEALYSIIQIAGAAFVTTRIAKRMNIQDLWSKPQVENTEETTSKDGC PKPKDDEEFVISSDDIKTEGKKGKNKTGRGKKHTAFSSKGLSDEEYDEYKRIREERNG KYSIEEYLQDRDKYYEEVAIARATEEDFCEEEEAKIRQRIFRPTRKQRKEERVSLGLV TGSEIRKRNPDDFKPKGKLWADDDRSVDYNEKLSFEAPPSIWSRIVNFGSGWGFWVSP SLFITSTHVIPQGAKEFFGVPIKQIQVHKSGEFCRLRFPKPIRTDVTGMILEEGAPEG TVVTLLIKRSTGELMPLAARMGTHATMKIQGRTVGGQMGMLLTGSNAKSMDLGTTPGD CGCPYIYKRGNDYVVIGVHTAAARGGNTVICATQGSEGEATLEGGDNKGTYCGAPILG PGSAPTLSTKTKFWRSSTASLPPGTYEPAYLGGKDPRVKGGPSLQQVMREQLKPFTEP RGKPPKPSVLEAAKKTIINVLEQTIDPPERWSFAQACASLDKTTSSGHPHHMRKNDCW NGESFTGKLADQASKANLMFEEGKNMTPVYTAALKDELVKTDKIYGKIKKRLLWGSDL ATMIRCARAFGGLMDELKAHCVTLPVRVGMNMNEDGPIIFERHSRYTYHYDADYSRWD STQQRAVLAAALEIMVKFSPEPHLAQVVAEDLLSPSVVDVGDFTISINEGLPSGVPCT SQWNSIAHWLLTLCALSEVTNLSPDTIQANSLFSFYGDDEIVSTDIKLDPEKLTAKLK EYGLKPTRPDKTEGPLVISEDLNGLTFLRRTVTRDPAGWFGKLEQSSILRQMYWTRGP NHGDPSETMIPHSQRPIQLMSLLGEAALHGPAFYSKISKLVIAELKEGGMDFYVPRQE PMFRWMRFSDLSTWEGDRNLAPSFVNEDGVE" mat_peptide 1..990 /gene="ORF1" /product="p48" mat_peptide 991..2088 /gene="ORF1" /product="NTPase" mat_peptide 2089..2625 /gene="ORF1" /product="p22" mat_peptide 2626..3024 /gene="ORF1" /product="VPg" mat_peptide 3025..3567 /gene="ORF1" /product="Pro" mat_peptide 3568..5097 /gene="ORF1" /product="RdRp" gene 5081..6703 /gene="ORF2" CDS 5081..6703 /gene="ORF2" /note="major capsid protein" /codon_start=1 /product="VP1" /protein_id="QJC69081.1" /translation="MKMASSDANPSDGSAANLVPEVNNEVMALEPVVGAAIAAPVAGQ QNVIDPWIRNNFVQAPGGEFTVSPRNAPGEILWSAPLGPDLNPYLSHLARMYNGYAGG FEVQVILAGNAFTAGKVIFAAVPPNFPTEGLSPSQVTMFPHIVVDVRQLEPVLIPLPD VRNNFYHYNQSNDPTIKLIAMLYTPLRANNAGDDVFTVSCRVLTRPSPDFDFIFLVPP TVESRTKPFSVPVLTVEEMTNSRFPIPLEKLFTGPSSAFVVQPQNGRCTTDGVLLGTT QLSPVNICTFRGDVTHITGSRNYTMNLASQNWNNYDPTEEIPAPLGAPDFVGKIQGML TQTTRADGSTRGHKATVYTGSADFAPKLGRVQFETDTDHDFEANQNTKFTPVGVIQDG STTHRNEPQQWVLPSYSGRNTHNVHLAPAVAPTFPGEQLLFFRSTMPGCSGYPNMDLD CLLPQEWVQYFYQEAAPAQSDVALLRFVNPDTGRVLFECKLHKSGYVTVAHTGQHDLV IPPNGYFRFDSWVNQFYTLAPMGNGTGRRRVV" gene 6703..7506 /gene="ORF3" CDS 6703..7506 /gene="ORF3" /note="minor structural protein; small basic protein" /codon_start=1 /product="VP2" /protein_id="QJC69082.1" /translation="MAGAFFAGLASDVLGSGLGSLINAGAGAINQKVEFENNRKLQQA SFQFSSNLQQASFQHDKEMLQAQIEATKKLQQEMMKVKQAMLLEGGFSETDAARGAIN APMTKALDWSGTRYWAPDARTTTYNAGRFSTPQPSGVLPGRTNLRDAVPARGSSKSSN SSTATSVYSNQTTSTRLGSTAGSGTSVSSLPSTARTRSWVEDQSRNLSPFMRGAHNIS FVTPPSSRSSSQGTVSTVPKEVLDSWTGAFNTRRQPLFAHIRKRGESRA" ORIGIN 1 atgaagatgg cgtctaacga cgctaccgct gccgctgttg ctaacagcaa caacgacacc 61 gcaaaatctt caagtgacgg agtgctttct agcatggctg tcacttttaa acgagccctc 121 ggggcgcggc ctaaacagcc ccccccgagg gaaaaaccac aaagaccccc acgaccaccc 181 acaccagaac tggttaaaaa tattcccccc cccccaccca acggagagga tgaaatagtg 241 gttacttata gtgtcaaaga tggtgtttcc ggcttgcctg acctttccac cgtcagacag 301 ccggaagaat ccaacacggc cttcagtgtc cctccactca atcagaggga gaacagagat 361 gctaaggaac cactcactgg aacaattctg gaaatgtggg acggggaaat ctaccattat 421 ggcctgtatg tggagcgagg tcttgtacta ggcgtacaca aaccgccagc tgccatcagc 481 ctcgctaagg ttgagttggc accactctcc ttatactgga ggcctgtgta cactcctcag 541 tacctcatct ctccagacac tctcaagaaa ttgtccgggg aaacgttccc ctacacagca 601 tttgacaaca actgctatgc cttttgttgc tgggttctgg acctaaatga ctcgtggctg 661 agcaggagaa tgatccagag gacaactggt ttcttcaggc cctaccaaga ctggaatagg 721 aaaccccttc ccactatgga tgactccaaa ataaagaagg tggccaatat atttctgtgt 781 gccctgtcct cgctattcac caggcccata aaagatataa tagggaaaat aaggcctctt 841 aacatcctca acatcttggc ctcatgtgat tggacctttg cgggcatagt agagtccctg 901 atactcttag cagagctctt tggagttttc tggacacccc cagatgtgtc tgcaatgatt 961 gcccccttac ttggtgacta cgagctacaa ggacctgagg accttgcagt ggagctcgtc 1021 cccgtggtga tggggggaat tggtttggtg ctaggattca ccaaagagaa aattgggaaa 1081 atgttgtcat cagctgcgtc caccttaaga gcttgcaaag accttggtgc atatgggcta 1141 gagatcctaa agctagtcat gaagtggttc ttcccgaaga aggaggaggc aaatgagctg 1201 gctatggtga ggtccatcga ggatgcagtc ctggatctcg aagcaattga aaacaatcat 1261 atgaccacct tgcttaaaga taaagacagt ctggcaacct acatgagaac actcgatctt 1321 gaagaggaga aagccaggaa actctcaacc aagtctgcct cacctgacat cgtgggcaca 1381 atcaacgccc tcctggcgag aatcgctgcc gcacgttctc tggtgcatcg agcgaaggag 1441 gagctttcca gcagaccaag acctgtggtg ttgatgatat caggtaggcc aggaataggg 1501 aagacccacc tcgctaggga agtggctaag agaatcgcag cctcccttac aggagaccag 1561 cgtgttggtc tcatcccacg caatggcgtc gaccactggg atgcgtataa gggggagagg 1621 gtcgtcctat gggacgatta tggaatgagc aaccctattc acgatgccct caggctgcaa 1681 gaactcgctg acacttgccc cctcactctg aactgtgaca ggattgaaaa taagggaaag 1741 gtctttgaca gcgatgtcat cattatcacc actaatctgg ccaacccagc cccactggac 1801 tatgtcaact ttgaagcatg ctcgaggcgc attgacttcc tcgtatatgc agaagcccct 1861 gatgtcgaaa aggcgaagcg tgacttccca ggccagcctg acatgtggaa gaacgctttc 1921 agttccgatt tctcacacat aaaactagca ctggccccac agggtggttt cgacaagaac 1981 gggaacaccc cacacggaaa gggcgtcatg aagactctca ccactggctc ccttattgcc 2041 cgggcatcag ggctactcca tgagaggtta gatgaatttg aactgcaggg cccagctctc 2101 accaccttca atttcgatcg caataaagtg cttgccttta gacagcttgc tgctgaaaac 2161 aaatatggac tgatggacac aatgagggtt gggaaacagc tcaaggatgt caaaaccatg 2221 ccagaactca aacaagcact caagaatgtc tcaatcaaga agtgtcaaat agtgtataat 2281 ggttgcacct acatgcttga gtctgatggc aagggcaatg tgaaagttga caggatccag 2341 agcgccgccg tgcagaccaa caatgagctg gctggtgccc tgcaccactt gaggtgcgcc 2401 agaatcagat actatgtcaa gtgtgtccag gaagccctgt attccatcat tcaaattgct 2461 ggggctgcat ttgtcaccac gcgcattgcc aagcgcatga acatacagga tctatggtcc 2521 aagccacaag tggaaaatac agaggaaact accagcaagg acgggtgccc aaaacccaag 2581 gatgatgagg agtttgtcat ttcatccgac gacatcaaaa ctgagggcaa gaaagggaag 2641 aacaagactg gccgtggcaa gaagcacaca gcattttcaa gcaaaggcct cagtgatgaa 2701 gagtacgatg aatacaagag gatcagagaa gaaaggaatg gcaagtactc tatagaagag 2761 tacctccagg acagggacaa atattatgag gaggtggcca ttgccagagc gactgaggaa 2821 gacttctgtg aagaggagga agccaagatc cgacaaagga tctttaggcc aacaaggaaa 2881 caacgcaagg aggaaagagt ctctctcggt ttagtcacgg gctctgaaat taggaaaaga 2941 aacccagatg atttcaaacc caaagggaaa ttgtgggctg acgatgacag gagtgtggac 3001 tacaatgaga aactcagttt tgaggccccg ccaagcattt ggtcaagaat agtcaacttt 3061 ggttcaggct ggggattctg ggtctccccc agcttgttca taacatcaac ccatgttata 3121 ccccagggcg caaaggagtt ctttggagtc cccatcaaac aaatacaggt acacaagtca 3181 ggcgagttct gtcgcttgag attccctaaa ccaatcagga ctgatgtgac gggcatgatc 3241 ttagaagaag gcgcacctga gggcaccgtg gttacactac tcatcaaaag gtccaccggg 3301 gaacttatgc ccctagcagc taggatgggg acccatgcga ccatgaagat ccaagggcgc 3361 actgttgggg gccagatggg catgcttctg acagggtcca acgccaagag tatggacctg 3421 ggtactacac caggtgattg tggctgcccc tacatctaca agagaggtaa tgactatgtg 3481 gtcattggag tccacacggc tgccgcacgt ggggggaaca ctgtcatatg tgccacccag 3541 gggagtgaag gagaggctac acttgagggt ggtgacaaca aggggactta ctgtggtgca 3601 ccaatcctag gcccagggag tgccccaaca cttagcacca agaccaaatt ctggagatcg 3661 tccacagcat cactcccacc tggcacctat gaaccagcct atcttggtgg caaggaccct 3721 agagtcaagg gtggcccttc actacagcaa gtcatgaggg aacagttgaa gccattcaca 3781 gagcccagag gtaagccacc aaaaccaagt gtgttagaag ctgccaagaa aaccatcatc 3841 aatgttcttg agcaaacaat tgatccacct gagagatggt cgttcgcaca agcttgcgcg 3901 tctcttgaca agaccacttc cagtggtcat ccgcatcaca tgcggaaaaa cgactgctgg 3961 aacggggagt ccttcacagg caagctggca gaccaggctt ctaaggccaa cctgatgttt 4021 gaagaaggaa agaacatgac cccagtctac acagctgcgc tcaaggatga gctagttaaa 4081 actgacaaaa tttatggtaa gatcaagaag aggcttcttt ggggctcgga cttggcgacc 4141 atgatccggt gtgctcgggc attcggaggc ctaatggatg aactcaaagc acactgtgtc 4201 acacttcccg ttagagttgg catgaatatg aatgaggatg gccccatcat cttcgagagg 4261 cattccaggt acacgtacca ctatgatgct gattactctc gatgggattc aacacaacag 4321 agagccgtgt tggcggcagc tctagaaatc atggtaaagt tctccccaga accacatttg 4381 gcccaggtag tcgctgaaga ccttctttct cctagcgtgg tggacgtggg cgacttcaca 4441 atatcaatca acgagggtct tccctctggg gtgccctgca cctcccaatg gaactccatc 4501 gcccactggc ttctcactct ctgcgcgctc tccgaagtca caaacctgtc tcctgacacc 4561 atacaggcta attctctctt ttctttttat ggtgatgatg aaattgttag cacagacata 4621 aaattggacc cagagaaatt gacagcaaaa ctcaaagaat acgggttaaa accaacccgc 4681 cctgacaaaa ctgaaggacc ccttgtcatc tctgaagacc tgaatggcct aactttcctg 4741 cggagaactg tgacccgcga cccagctggt tggtttggaa aactggagca gagttcaata 4801 ctcaggcaaa tgtactggac taggggtccc aaccatggag acccatctga aacaatgatt 4861 ccacattccc aaagacccat acaattgatg tccctactgg gggaggccgc tctccacggc 4921 ccagcatttt acagtaagat tagcaaattg gtcattgcag agctaaaaga aggtggtatg 4981 gatttttacg tgcccagaca agagccaatg ttcagatgga tgagattctc agatctgagc 5041 acgtgggagg gcgatcgcaa tctggctccc agttttgtga atgaagatgg cgtcgagtga 5101 cgccaaccca tctgatgggt ccgcagccaa cctcgtccca gaggtcaaca atgaggttat 5161 ggctctggag cccgttgttg gtgccgctat tgcggcacct gtagcgggcc aacaaaatgt 5221 aattgacccc tggattagaa acaattttgt acaagcccct ggtggagagt ttacagtgtc 5281 ccccagaaac gctccaggtg aaatactatg gagcgcgccc ttaggccctg atttaaatcc 5341 ctacctatcc cacttggcca gaatgtataa tggttatgca ggtggttttg aagtgcaggt 5401 gattctcgcg gggaacgcgt tcaccgccgg gaaggtcata tttgcagcag tcccaccaaa 5461 ttttccaact gaaggcttga gccccagcca ggtcactatg ttcccccata tagtagtgga 5521 tgttaggcaa ctagaacctg tgttgattcc cttacccgat gttaggaata atttctacca 5581 ttacaatcaa tcaaatgacc ccaccattaa gttgatagca atgttatata caccacttag 5641 ggctaataat gctggggatg atgtcttcac agtttcttgc cgagttctca cgaggccatc 5701 ccccgatttt gatttcatat ttctagtgcc acccacagtt gagtctagaa ccaaaccatt 5761 ttccgtccca gttttgactg ttgaggagat gaccaattca agattcccca ttcctttgga 5821 aaagttgttc acgggcccca gtagtgcctt tgttgttcaa ccacaaaacg gtaggtgcac 5881 gactgatggc gtgctcctag gcaccaccca attgtctcct gtcaacatct gcaccttcag 5941 aggggatgtc acccacatta caggtagtcg taactacaca atgaatttgg cttctcaaaa 6001 ttggaacaat tatgacccaa cagaagaaat cccagcccct ctaggagctc cagattttgt 6061 ggggaagatt caaggcatgc tcacccaaac cacaagggca gatggctcaa cacgcggcca 6121 caaggctacg gtgtacactg ggagcgccga cttcgctcca aaactgggca gagttcaatt 6181 tgaaactgac acagaccatg attttgaagc taaccaaaac acaaagttca ctccagtcgg 6241 tgtcatccaa gatggcagca ccacccaccg aaatgaaccc caacagtggg tgctcccaag 6301 ttactcaggc agaaatactc ataatgttca tctggccccc gctgtggccc ccacttttcc 6361 gggtgaacaa cttctcttct ttagatccac catgcccgga tgtagcgggt atcccaacat 6421 ggatttggac tgtttgctcc cccaggaatg ggtgcagtac ttctaccaag aggcagcccc 6481 agcacaatct gatgtggccc tgctaagatt tgtgaatcca gacacaggta gggttttgtt 6541 tgaatgcaaa cttcataaat caggctatgt tacagtggct cacactggcc aacatgattt 6601 ggtcatcccc cccaatggtt attttaggtt tgattcctgg gtcaaccagt tctacacgct 6661 tgcccccatg ggaaatggaa cggggcgtag acgcgtagta taatggctgg agctttcttt 6721 gctgggttag catctgatgt cctcggctct ggacttggtt cccttatcaa tgctggggct 6781 ggggccatca accaaaaagt tgagtttgaa aataacagaa aattgcaaca agcatccttc 6841 caatttagca gcaatttaca acaggcttcc tttcaacatg acaaagaaat gcttcaagca 6901 caaattgagg ccactaaaaa gctacaacag gaaatgatga aagttaagca ggcaatgctc 6961 ctagagggtg ggttctctga aacagatgca gcccgcgggg caatcaacgc ccccatgaca 7021 aaagctttgg actggagcgg gacaaggtac tgggctcctg atgctaggac tacaacttat 7081 aatgcaggcc gcttttccac ccctcaacca tcgggggtac taccaggaag gactaatctt 7141 agggatgctg tccctgctcg gggttcctct aaatcttcta actcttctac tgctacttct 7201 gtgtactcaa atcaaaccac ttcaacgaga cttggttcta cagctggttc tggcaccagt 7261 gtctcgagtc tcccgtcaac tgcaaggacc aggagctggg ttgaggatca aagtaggaat 7321 ttgtctcctt tcatgagggg ggcccacaac atatcgtttg tcaccccacc atctagcaga 7381 tcctctagcc aaggcacagt ctcaaccgtg cctaaagagg ttttggactc ctggactggc 7441 gccttcaaca cgcgcaggca gcctctcttc gctcacattc gtaaacgagg ggagtcacgg 7501 gcgtaatgtg aaaagacaaa attgattatc tttctttttc tttagtgtct ttt //