Typing tool
|
Complete norovirus genomes
OR700742 | GII.4 Sydney | ||
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GII.P16 |
ORF1: 1..5100 ORF2: 5081..6703 ORF3: 6703..7509LOCUS OR700742 7509 bp RNA linear VRL 24-OCT-2023 DEFINITION Norovirus GII isolate Hu/US/2023/GII.4[P16]/CA-RGDS-1183 nonstructural polyprotein (ORF1), VP1 (ORF2), and VP2 (ORF3) genes, complete cds. ACCESSION OR700742 VERSION OR700742.1 KEYWORDS . SOURCE Norovirus GII ORGANISM Norovirus GII Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes; Picornavirales; Caliciviridae; Norovirus; Norwalk virus. REFERENCE 1 (bases 1 to 7509) AUTHORS Pan,C.-Y., Hatada,A., Padilla,T., Wright,C. and Morales,C. TITLE Direct Submission JOURNAL Submitted (19-OCT-2023) Viral and Rickettsial Disease Laboratory, California Department of Public Health, 850 Marina Bay Parkway, Richmond, CA 94804, USA COMMENT ##Assembly-Data-START## Assembly Method :: Geneious Prime v. 2022.0.2; SPAdes v. 3.6 Sequencing Technology :: Illumina ##Assembly-Data-END## FEATURES Location/Qualifiers source 1..7509 /organism="Norovirus GII" /mol_type="genomic RNA" /isolate="Hu/US/2023/GII.4[P16]/CA-RGDS-1183" /isolation_source="stool" /host="Homo sapiens" /db_xref="taxon:122929" /country="USA: CA" /collection_date="Mar-2023" /note="genotype: GII.4[P16]" gene 1..5100 /gene="ORF1" CDS 1..5100 /gene="ORF1" /codon_start=1 /product="nonstructural polyprotein" /protein_id="WOE94999.1" /translation="MKMASNDASAAVACNNNNDKEKSSGEGLFTNMSSTLKKALGARP KQPAPRGEPQKPPRPPTPELVKRIPPPPPNGEEEDEPVIRYEVKSGISGLPELTTVPQ PDVANTAFSVPPLSMRENREAKEPLTGAILEMWDGEIYHYGLYVEKGLVLGVHKPPAA ISMARVELAPLSLYWRVVYTPQYLISPETLRRLNGEAFPYTAFDNNCYAFCCWVLDLN DSWLSRRMVQRTTGFFRPYQEWNRKPLPTMDDSKIKKVANIFLCSLSTLFTRPIKDLI GKIKPLNILNILATCDWTFAGIVESLILLAELFGVFWTPPDVSAMIAPLLGDYELQGP EDLAVELVPVVMGGIGLVLGFTKEKIGKMLSSAASTLRACKDLGAYGLEILKLVMKWF FPKKEEANELAMVRAIEDAVLDLEAIENNHMTTLLKDKDSLATYMKTLDMEEEKARRL STKSASPDIVGTINALLARIAAARSLVHRAKEELSSRIRPVVVMISGKPGIGKTHLAR EVARKVASTLTGDQRVGLIPRNGVDHWDAYKGERVVLWDDYGMSNPIHDALRIQELAD TCPLTLNCDRIENKGKVFDSEVIIITTNLANPAPLDYVNFEACSRRIDFLVYAEAPEV EKAKRDFPGQPDMWKDAFKPDFSHIKLQLAPQGGFDKNGNTPHGKGVMKTLTTGSLIA RASGLLHERMDEFELQGPTITTFNFDRNRITAFRQLAAENKYGLVDTMKVGNQLKGVK TMEELKQAIRNVTIKRCRIIYGGSTYDLESDGKGKVLVEKVKNTSIQTNNELTGALHH LKHARIRYYVKCVQEAVYSIIQIAGAAFVTTRIARRMNIQELWSKPQLDQNESETKEE APKSEDDEFIISSKDIKEEGKKGKNKTGRGKKHTAFSSKGLSDEEYDEYKRIREERNG KYSIEEYLQDRDRYYEELAIAKATEEDFCEEEEIKIRQRIFRPTRKQRKEERATLGLV TGSEIRRRNPDDFKPKGKLWADDNRSVDYNEKLDFEAPPSIWSRIVSFGSGWGFWVSP SLFITSTHVIPAGITEAFGVPIKQIQIHKSGEFCRFRFPKPIRPDVTGMILEEGAPEG TVATVLIKRPTGELMPLAARMGTHATMKIQGRMVGGQMGMLLTGSNAKGMDLGTTPGD CGCPYIYKRGNDYIVIGVHTAAARGGNTVICATQGSEGEATLEGGDDKGTYCGAPILG PGGAPKLSTKTKFWRSSNTPLPPGTYEPAYLGGRDPRVKGGPSLQQVMRDQLKPFTEP RGKPPRPSVLEAAKQTIINVLEQTLDPPQKWTYAQACASLDKTTSSGHPHHVRKNEFW NGETFTGKLADQASKANLMFEEGKHMTPVYTAALKDELVKTEKIYGKIKKRLLWGSDL STMIRCARSFGGLMDEMKAHCISLPVRVGMNMNEDGPIIFEKHSRYKYHYDADYSRWD STQQRAVLASALEIMVRFSAEPQLAQIVAEDLLAPSVVDVGDFKIAINEGLPSGVPCT SQWNSIAHWLLTLCALSEVTKLSPDIIQANSMFSFYGDDEIVSTDIKLDPEQLTAKLK EHGLKPTRPDKTEGPLIISEDLDGLTFLRRTVTRDPAGWFGKLDQSSILRQMYWTRGP NHEDPNETMIPHSQRPIQLMALLGEASLHGPSFYSRISKLVITELKEGGMDFYVPRQE PMFRWMRFSDLSTWEGDRNLAPNFVNEDGVE" mat_peptide 1..996 /gene="ORF1" /product="p48" mat_peptide 997..2094 /gene="ORF1" /product="NTPase" mat_peptide 2095..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="WOE95000.1" /translation="MKMASNDANPSDGSAASLVPEVNNEVMALEPVVGAAIAAPVAGQ QNVIDPWIRNNFVQAPGGEFTVSPRNAPGEILWSAPLGPDLNPYLSHLARMYNGYAGG FEVQVILAGNAFTAGKIIFAAVPPNFPTEGLSPSQVTMFPHIIVDVRQLEPVLIPLPD VRNNFYHYNQSNDSTIKLIAMLYTPLRANNAGDDVFTVSCRVLTRPSPDFDFIFLVPP TVESRTKPFSVPILTVEEMTNSRFPIPLEKLFTGPSSAFVVQPQNGRCTTDGVLLGTT QLSPVNICTFRGDVTHVTGSHNFTMNLASQNWNNYDPTEEIPAPLGTPDFVGKIQGML TQTTRTDGSTRGHKATVYTGSADFAPKLGRVQFQTDTDHDFEANQNTKFTPVGVIQDG STTHRNEPQQWVLPSYSGRNAHNVHLAPAVAPTFPGEQLLFFRSTMPGCSGYPNMDLD CLLPQEWVQYFYQEAAPAQSDVALLRFVNPDTGRVLFECKLHKSGYVTVAHTGQHDLV IPPNGYFRFDSWVNQFYTLAPMGNGTGRRRAV" gene 6703..7509 /gene="ORF3" CDS 6703..7509 /gene="ORF3" /note="minor structural protein; small basic protein" /codon_start=1 /product="VP2" /protein_id="WOE95001.1" /translation="MAGAFFAGLASDVLGSGLGSLINAGAGAINQKVEFENNRKLQQA SFQFSSNLQQASFQHDKEMLQAQIEATKKLQQEMMRVKQAMLLEGGFSETDAARGAIN APMTKALDWSGTRYWAPDARITTYNAGHFSTPQPSGALPGRANLRDAVPARGPSTKPS NSPTATSVHSNQTVSTGLGSTAGSGTSVSSLPSTARTRSWVEDQNRNLSPFMKGAYNI SFVTPPSSRSSNQGTVSTVPKEILDSWTGAFNTRRQPLFAHIRKRGESRV" ORIGIN 1 atgaagatgg cgtctaacga cgcttccgct gccgttgctt gcaacaacaa caacgacaag 61 gaaaaatctt caggtgaagg cttattcaca aatatgtctt ccaccttaaa gaaagccctc 121 ggggctaggc ccaaacagcc tgccccgaga ggtgaaccac aaaagccccc aagaccacca 181 actcccgagt tggtcaagag gataccccct cctccaccta atggcgaaga agaagacgaa 241 ccagtcatta ggtatgaggt taagagtggg atctctggcc tgcccgagct cacaacagtc 301 ccccaaccgg acgtggccaa cacagcattt agtgttccac cactgagcat gagagaaaac 361 agggaggcca aagaaccgct gacaggggca atactagaga tgtgggatgg agagatatac 421 cactatggcc tgtacgtgga gaaaggctta gtgttgggtg tgcacaaacc acctgcagcc 481 ataagcatgg caagagtgga gctggcgccg ctgtcattgt actggcgtgt ggtgtacact 541 ccccaatacc tcatctcccc tgagactctc aggaggctca acggtgaggc gtttccttac 601 accgcttttg acaacaactg ctacgctttt tgttgctggg tgttagacct caatgactca 661 tggcttagca ggaggatggt gcaacgaacc acgggcttct tcaggcctta ccaagagtgg 721 aacagaaaac ccttacccac catggatgac tccaaaataa agaaggtagc aaatatattc 781 ctgtgctcat tgtccacatt attcaccagg cccataaaag acctcatagg aaaaattaaa 841 ccattaaaca tattgaacat cctggcaacg tgtgactgga cgtttgccgg aatagtggag 901 tctctgatat tgcttgccga actcttcgga gttttctgga cacccccaga tgtgtctgct 961 atgattgctc ccttacttgg ggactacgag ttgcaggggc cagaagacct cgccgttgaa 1021 ctcgtacctg tggtaatggg agggattggt ttggtgttgg gattcaccaa ggagaaaatt 1081 ggcaaaatgt tgtcctcagc agcatcaaca ctcagagctt gtaaagatct tggtgcctat 1141 ggcttagaga tactcaaatt ggtcatgaag tggtttttcc caaagaaaga agaggccaat 1201 gagctagcta tggtgagggc catagaggat gccgtactag atcttgaggc aatagaaaac 1261 aaccacatga caaccctgtt gaaagacaaa gacagcttag caacatacat gaaaacactg 1321 gacatggagg aggagaaagc cagaaggttg tccacaaaat ctgcatcccc tgacatagtt 1381 gggacaatca acgccctgct ggctcgaata gcagcagcca ggtcattagt ccacagggcc 1441 aaggaagaac tgtctagcag gataaggcca gtagttgtta tgatatctgg caaaccagga 1501 ataggcaaaa ctcatctagc cagagaggtg gcaagaaagg tggcatccac tctcacaggg 1561 gaccaaagag tcggactcat accaagaaac ggtgtggacc actgggatgc atacaaaggt 1621 gagagagtcg tgctgtggga cgactatggc atgagtaacc ccattcatga tgctctccgc 1681 atacaagaat tggctgatac gtgtcccctt accctaaatt gcgacagaat tgaaaataag 1741 gggaaagttt ttgacagtga agtcataata attacaacaa acctcgccaa cccagcccca 1801 cttgattatg tcaactttga ggcctgctcc aggagaattg atttcctggt gtacgctgag 1861 gcaccagaag tagaaaaggc aaaacgggat tttcctggtc agccagatat gtggaaggac 1921 gccttcaagc cggacttttc gcacatcaag ctacagcttg cacctcaggg cggctttgac 1981 aagaatggca acacccctca tgggaaagga gtgatgaaga ccctcactac cggttctctg 2041 attgcccgtg catcaggcct actgcatgag aggatggatg aatttgaact ccaaggtccc 2101 acaatcacca ctttcaattt cgaccggaac agaatcacag cattcagaca attggctgca 2161 gaaaacaagt atggactggt ggacaccatg aaagttggca atcaactaaa aggagtgaaa 2221 accatggaag aactcaaaca agcaatcagg aatgtgacca tcaagaggtg ccggataatc 2281 tacggtggct ccacgtatga ccttgagtct gatggcaagg gcaaagtttt ggtggaaaag 2341 gtcaagaaca cctctataca gaccaacaac gagttgaccg gggccctgca tcatctcaag 2401 catgcccgaa tcaggtacta tgtcaaatgt gtgcaagagg cagtctattc catcatacaa 2461 attgccggcg ctgcgtttgt caccacgcgc attgcacgcc gcatgaacat acaagagctc 2521 tggtcgaagc cacaattaga ccaaaatgaa tcagagacta aggaagaggc ccccaagtca 2581 gaagatgacg agttcatcat atcttctaag gatatcaagg aggaaggaaa gaagggcaaa 2641 aacaaaactg gccgtggcaa gaaacacacc gcattctcca gcaagggctt aagcgatgag 2701 gagtatgacg agtacaagag gataagagaa gagagaaatg ggaagtactc tatagaagag 2761 tatcttcaag acagagacag gtattatgag gagctcgcca ttgccaaggc cacggaagaa 2821 gacttctgtg aagaggagga gatcaaaatc cgtcagagga tttttcgtcc caccaggaaa 2881 caaagaaagg aagagagggc cacactaggg ctggtaactg gctcagaaat cagaagaaga 2941 aaccctgatg atttcaaacc caaagggaag ctgtgggccg atgacaacag aagtgttgac 3001 tacaatgaga aactggattt tgaggctccc ccaagcatat ggtctaggat tgtgagcttt 3061 ggttctggct ggggcttctg ggtatcacca agcctgttca taacgtcaac tcatgtgatc 3121 cctgcaggca taacagaagc atttggagtc cccatcaaac aaatccagat ccacaaatca 3181 ggtgaatttt gccgattcag attcccaaaa ccaatcagac cagacgtgac aggaatgatc 3241 ttggaagaag gtgcgcctga aggcaccgtg gcaactgtgc tcatcaaacg ccccaccgga 3301 gagctcatgc ctcttgcagc cagaatggga acacacgcaa ccatgaagat tcaaggccgc 3361 atggttggtg gacagatggg tatgctgctc actgggtcaa atgctaaagg gatggatttg 3421 ggaacaactc ctggtgactg tggctgccct tacatctata aaaggggcaa tgactatata 3481 gtcattgggg tgcacaccgc agcagcccgt ggtggaaaca ccgtcatctg tgccacacag 3541 ggaagtgagg gtgaggcaac tcttgagggt ggagatgaca aaggaacata ctgtggggca 3601 cccattctag gccctggagg tgcaccaaaa ttgagcacta aaaccaagtt ttggaggtca 3661 tcgaacacgc cccttccacc ggggacgtac gaacctgcct acctcggtgg ccgtgacccg 3721 cgtgttaagg gtgggccctc cttacaacag gtaatgagag atcagttgaa gccattcact 3781 gaacccaggg gcaaacctcc aagaccaagt gttttggaag cagccaaaca aaccattatc 3841 aatgtccttg aacaaaccct ggatcctcca caaaagtgga catacgcaca ggcgtgtgcc 3901 tcacttgaca aaaccacctc cagcgggcat ccccaccatg tccgaaagaa tgaattctgg 3961 aatggtgaga ccttcactgg taaattggca gaccaagcat caaaagcaaa cctaatgttt 4021 gaggaaggga aacacatgac accagtgtac acagcagcac tcaaggacga gctagtcaag 4081 actgagaaaa tctatggaaa gatcaagaag agactgctct ggggctctga cttgtccacc 4141 atgatccggt gcgctaggtc atttggtggg ctcatggacg agatgaaggc acactgtata 4201 tcactcccag tgcgagttgg catgaatatg aatgaagatg gcccaataat attcgagaaa 4261 cactctaggt acaaatatca ctatgatgca gactactctc gttgggattc aacacagcaa 4321 agggcagtat tagcatcagc cttggaaatt atggtcagat tctctgcaga accacaattg 4381 gcacaaatag tcgctgagga tctactggcc cctagtgtag tagatgtggg agactttaaa 4441 attgcaataa atgaagggct cccatctggc gtgccatgca cttctcaatg gaactccatt 4501 gcacactggc tgctaactct ctgtgccttg tctgaagtca ccaaactgtc ccctgacatt 4561 atacaagcaa attccatgtt ctcattttac ggtgatgacg agattgtcag caccgacata 4621 aaattagacc ctgaacagtt gaccgccaag ttgaaggagc acggcctgaa accaacccgc 4681 ccagacaaga ctgagggacc tctgatcatc agtgaagatt tggacggact cactttcctc 4741 cgaaggacgg tgactcgtga cccagctggc tggtttggaa aactggacca aagttcaatt 4801 ttgaggcaga tgtattggac tagaggacca aatcatgaag accccaatga gacaatgata 4861 ccccattccc agaggcccat acagctcatg gcactgcttg gtgaagcctc tcttcacgga 4921 ccctctttct acagtagaat cagtaaattg gttataactg aactcaaaga aggtgggatg 4981 gacttttacg tgccaaggca ggaacccatg ttcaggtgga tgaggttctc tgacttgagc 5041 acgtgggagg gcgatcgcaa tctggctccc aactttgtga atgaagatgg cgtcgaatga 5101 cgccaaccca tctgatgggt ccgcagccag cctcgtacca gaggtcaaca atgaggttat 5161 ggctttggag cccgttgttg gtgccgctat tgcggcaccc gtagcgggcc aacaaaatgt 5221 aattgacccc tggattagaa ataattttgt acaagcccct ggtggggagt tcacagtatc 5281 ccctagaaat gctccaggtg aaatactgtg gagcgcaccc ttaggccctg acctaaatcc 5341 ctacctatcc catttggcca gaatgtacaa tggttatgca ggtggtttcg aggtgcaggt 5401 aattctcgcg gggaacgcgt tcaccgcagg gaagattata tttgcagcag tcccaccaaa 5461 ttttccaact gaaggcttaa gccctagcca ggttaccatg tttccccata taatagtaga 5521 tgttagacaa ttagaacctg tgctgatccc cttacccgat gttaggaata acttctatca 5581 ttacaatcag tcaaatgact ccactatcaa gttgatagca atgttgtaca caccacttag 5641 ggctaataat gctggggatg atgttttcac agtttcgtgc cgagttctca cgagaccatc 5701 ccccgatttt gattttatat tcttagtacc acccacagtt gagtcaagaa ctaaaccatt 5761 ctctgtccca attttaactg ttgaggagat gaccaattca agattcccca tccctttgga 5821 aaagttgttc acaggcccca gtagtgcatt tgttgttcaa ccacaaaacg gcagatgcac 5881 aactgatggc gtgctcctag gtaccaccca actttctcct gtcaacatct gcaccttcag 5941 aggggacgtc acccatgtca caggtagtca caacttcact atgaatttgg cttctcaaaa 6001 ttggaacaac tatgacccaa cagaagaaat cccagccccc ctagggactc cagattttgt 6061 ggggaagatc caaggcatgc tcacccaaac cacaaggaca gatggttcaa cacgcggcca 6121 caaagctaca gtgtacactg ggagcgccga ctttgctcca aaactgggta gagttcaatt 6181 tcaaactgac acagaccatg actttgaagc caatcagaac acaaagttca ccccagtcgg 6241 tgtcattcaa gatggtagca ccacccaccg aaacgaaccc caacagtggg tgctcccaag 6301 ttactcaggc agaaatgctc acaatgtaca tttggccccc gctgtagccc ccacctttcc 6361 gggtgagcaa ctcctcttct ttagatccac catgcccgga tgcagcgggt accccaacat 6421 ggacttggac tgtctgctcc cccaggaatg ggtgcagtac ttctaccaag aggcagcccc 6481 agcacaatct gatgtggctc tgctaaggtt tgtaaaccca gacacaggta gggttctgtt 6541 tgagtgcaag cttcacaaat caggctatgt tacagtggct cacactggtc aacatgattt 6601 ggttatcccc cccaatggtt actttaggtt tgattcctgg gtcaaccagt tctacacgct 6661 tgcccccatg ggaaatggaa cggggcgtag acgtgcagta taatggctgg agctttcttt 6721 gctggattgg catctgatgt ccttggctcc ggacttggtt ctcttatcaa tgctggggct 6781 ggggccatca accaaaaagt tgagtttgaa aataacagaa aattacaaca agcatccttc 6841 caatttagca gcaatttgca acaggcttcc tttcaacatg ataaagagat gctccaagca 6901 caaattgagg ccaccaaaaa gctacagcag gaaatgatga gagttaagca ggcaatgctc 6961 ttagagggtg ggttctctga gacagatgca gcccgcgggg caattaacgc ccccatgaca 7021 aaggctttgg actggagcgg gacaaggtac tgggctccag atgctagaat tacaacatac 7081 aatgcaggcc acttttccac ccctcaacca tcgggggcac tgccaggaag agctaatctc 7141 agggatgctg tccctgctcg tgggccctcc accaaacctt ctaactctcc tactgccacc 7201 tctgtgcact caaaccaaac tgtttcaacg ggacttggtt ctacagctgg ttctggaacc 7261 agtgtctcga gcctcccgtc aactgcaaga actaggagct gggttgagga tcagaatagg 7321 aatttgtcac ctttcatgaa gggggcctac aacatatcat ttgtcacccc accatccagc 7381 agatcctcta accagggcac agtctcaacc gtgcccaaag aaattttgga ctcctggact 7441 ggcgctttca acacgcgcag gcagcctctc ttcgctcaca ttcgtaagcg aggggagtca 7501 cgggtgtaa //