Typing tool
|
Complete norovirus genomes
OR700746 | GII.4 Sydney | ||
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GII.P16 |
ORF1: 1..5100 ORF2: 5081..6703 ORF3: 6703..7509LOCUS OR700746 7509 bp RNA linear VRL 24-OCT-2023 DEFINITION Norovirus GII isolate Hu/US/2022/GII.4 Sydney[P16]/CA-RGDS-1184 nonstructural polyprotein (ORF1), VP1 (ORF2), and VP2 (ORF3) genes, complete cds. ACCESSION OR700746 VERSION OR700746.1 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/2022/GII.4 Sydney[P16]/CA-RGDS-1184" /isolation_source="stool" /host="Homo sapiens" /db_xref="taxon:122929" /country="USA: CA" /collection_date="May-2022" /note="genotype: GII.4 Sydney[P16]" gene 1..5100 /gene="ORF1" CDS 1..5100 /gene="ORF1" /codon_start=1 /product="nonstructural polyprotein" /protein_id="WOE95002.1" /translation="MKMASNDASAAVVCNNNNDKEKSSGEGLFTNMSSTLKKALGARP KRPAPRDEPQKPPRPPTPELVKRIPPPPPNGEEEGEPVIRYEVKSGISGLPELTTVPQ PDVANTAFSVPPLSLRENREAKEPLTGAILEMWDGEIYHYGLYVEKGLVLGVHKPPAA ISMARVELAPLSLYWRVVYTPQYLISPETLRRLNGEAFPYTAFDNNCYAFCCWVLDLN DSWLSRRMVQRTTGFFRPYQEWNRKPLPTMDDSKIKKVANIFLCSLSTLFTRPIKDLI GKIKPLNILNILATCDWTFAGIVESLILLAELFGVFWTPPDVSAMIAPLLGDYELQGP EDLAVELVPVVMGGIGLVLGFTKEKIGKMLSSAASTLRACKDLGAYGLEILKLVMKWF FPKKEEANELAMVRAIEDAVLDLEAIENNHMTTLLKDKDSLATYMKTLDMEEEKARRL STKSASPDIVGTINALLARIAAARSLVHRAKEELSSRIRPVVVMISGKPGIGKTHLAR EVARKVASTLTGDQRVGLIPRNGVDHWDAYKGERVVLWDDYGMSNPIHDALRIQELAD TCPLTLNCDRIENKGKVFDSEVIIITTNLANPAPLDYVNFEACSRRIDFLVYAEAPEV EKAKRDFPGQPDMWKDAFKPDFSHIKLQLAPQGGFDKNGNTPHGKGVMKTLTTGSLIA RASGLLHERMDEFELQGPTTTTFNFDRNRITAFRQLAAENKYGLVDTMKVGNQLKGVK TMEELKQAIRNVTIKRCRIIYGGSTYDLESDGKGKVLVEKVKSASIQTNNELAGALHH LKHARIRYYVKCVQEAVYSIIQIAGAAFVTTRIARRMNIQELWSKPQLDQNESETKEE APKSEDDEFIISSKDIKEEGKKGKNKTGRGKKHTAFSSKGLSDEEYDEYKRIREERNG KYSIEEYLQDRDRYYEELAIAKATEEDFCEEEEIKIRQRIFRPTRKQRKEERATLGLV TGSEIRRRNPDDFKPKGKLWADDNRSVDYNEKLDFEAPPSIWSRIVSFGSGWGFWVSP SLFITSTHVIPAGITEAFGVPIKQVQIHKSGEFCRFRFPKPIRPDVTGMILEEGAPEG TVATVLIKRPTGELMPLAARMGTHATMKIQGRMVGGQMGMLLTGSNAKGMDLGTTPGD CGCPYIYKRGNDYIVIGVHTAAARGGNTVICATQGSEGEATLEGGDDKGTYCGAPILG PGGAPKLSTKTKFWRSSNMPLPPGTYEPAYLGGRDPRVRGGPSLQQVMRDQLKPFTEP RGKPPRPSVLEAAKQTIINVLEQTLDPPQKWTYVQACASLDKTTSSGHPHHVRKNEFW NGETFTGKLADQASKANLMFEEGKHMTPVYTAALKDELVKTEKIYGKIKKRLLWGSDL STMIRCARSFGGLMDEMKAHCISLPVRVGMNMNEDGPIIFEKHSRYKYHYDADYSRWD STQQRAVLAAALEIMVRFSAEPQLAQIVAEDLLAPSVVDVGDFKITINEGLPSGVPCT SQWNSIAHWLLTLCALSEVTKLSPDIIQANSMFSFYGDDEIVSTDIKLDPEQLTAKLK EYGLKPTRPDKTEGPLIIGEDLNGLTFLRRTVTRDPAGWFGKLDQSSILRQMYWTRGP NHEDPNETMIPHSQRPIQLMALLGEASLHGPSFYSRISKLVITELKEGGMDFYVPRQE PMFRWMRFSDLSTWEGDRNLAPSFVNEDGVE" 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="WOE95003.1" /translation="MKMASSDANPSDGSAASLVPEVNNEVMALEPVVGAAIAAPVAGQ QNVIDPWIRNNFVQAPGGEFTVSPRNAPGEILWSAPLGPDLNPYLSHLARMYNGYAGG FEVQVILAGNAFTAGKIIFAAVPPNFPTEGLSPSQVTMFPHIIVDVRQLEPVLIPLPD VRNNFYHYNQSNDSTIKLIAMLYTPLRANNAGDDVFTVSCRVLTRPSPDFDFIFLVPP TVESRTKPFSVPVLTVEEMTNSRFPIPLEKLFTGPSSAFVVQPQNGRCTTDGVLLGTT QLSPVNICTFRGDVTHITGSHNFTMNLASQNWNNYDPTEEIPAPLGTPDFVGKIQGML TQTTRTDGSTRGHKATVYTGSADFAPKLGRVQFETDTNHDFEANQNTKFTPVGVIQDG STTHRNEPQQWVLPSYSGRNTHNVHLAPAVAPTFPGEQLLFFRSTMPGCSGYPNMDLD 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="WOE95004.1" /translation="MAGAFFAGLASDVLGSGLGSLINAGAGAINQKVEFENNRKLQQA SFQFSSNLQQASFQHDKEMLQAQIEATKKLQQEMMRVKQAMLLEGGFSETDAARGAVN APMTKALDWSGTRYWAPDARITTYNAGHFSTPQPSGALPGRANLRDAVPARGSSTKPS NSSTATSVYSNQTISTRLGSTAGSGTSVSSLPPTARTRSWVEDQNRNLSPFMRGAHNI SFVTPPSSRSSSQGTVSTVPKEILDSWTGAFNTRRQPLFAHIRKRGESRV" ORIGIN 1 atgaagatgg cgtctaacga cgcttccgct gccgttgttt gcaacaacaa caacgacaag 61 gaaaaatctt caggtgaagg cttattcaca aatatgtctt ccaccttaaa gaaagccctc 121 ggggctaggc ccaaacgacc tgccccgaga gacgaaccac aaaagccccc aagaccacca 181 actcccgagt tggtcaagag gatacccccc ccgccaccta atggcgaaga agaaggagaa 241 ccagtcatta ggtatgaggt taagagtggg atctctggcc tgcccgagct cacaacagtc 301 ccccaaccgg acgtggccaa cacagcattt agtgttccac cactgagctt gagagaaaac 361 agggaggcca aggaaccgct gacaggggca atactagaga tgtgggacgg agagatatac 421 cactatggcc tgtacgtgga gaaaggctta gtgttgggtg tacacaaacc acctgcagcc 481 ataagcatgg caagagtgga gctggcgccg ctgtcattgt actggcgtgt ggtgtacact 541 ccccaatacc tcatctcccc tgaaactctc aggaggctca atggagaggc gtttccttac 601 accgcttttg acaacaactg ctacgccttt tgctgctggg tgttagacct caatgactca 661 tggcttagca ggaggatggt gcaacgaaca acgggcttct tcaggcctta ccaagagtgg 721 aacagaaaac ccttacccac catggatgac tccaaaataa agaaggtagc aaatatattc 781 ctatgttcac tgtccacatt attcaccaga cccataaagg acctcatagg aaaaattaaa 841 ccattaaaca tattgaacat cctggcaacg tgtgattgga cgttcgccgg aatagtggag 901 tctctgatat tgcttgccga actcttcgga gttttctgga cacccccaga tgtgtctgct 961 atgatcgctc ccttactcgg ggactacgag ttgcaagggc cagaagacct cgccgttgaa 1021 ctcgtacctg tggtaatggg agggattggt ttggtgttgg gattcaccaa agagaaaatt 1081 ggcaaaatgt tgtcctcagc agcatcaaca ctcagggctt gtaaagatct tggtgcctat 1141 ggcttagaga tactcaaatt ggtcatgaag tggtttttcc caaagaaaga agaggccaat 1201 gagctagcca tggtgagggc catagaggat gccgtattag atcttgaggc aatagagaac 1261 aaccacatga caaccctgtt gaaagataaa gacagcttag caacatacat gaaaacactg 1321 gatatggagg aggagaaagc cagaaggttg tccacaaaat ctgcatcccc tgacatagtt 1381 gggacaatca acgccctgct ggctcgaata gcagcagcca ggtcattagt ccacagggcc 1441 aaggaagaac tgtctagcag gataaggcca gtagttgtta tgatatctgg caagccagga 1501 ataggcaaaa ctcatctggc cagagaggtg gcaagaaagg tggcatccac tctcacaggg 1561 gatcaaagag tcggactcat accaagaaac ggtgtggacc attgggatgc atacaaaggt 1621 gagagagtcg tgctgtggga cgactatggc atgagtaacc ccattcatga tgctctccgc 1681 atacaagaat tggctgatac gtgccccctt accctaaatt gtgacagaat 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 cggttttgac 1981 aagaatggca acaccccgca tgggaaagga gtgatgaaga ccctcactac cggttctctg 2041 attgcccgtg catcaggcct attgcatgag aggatggatg aatttgaact ccaaggtccc 2101 acaaccacca ctttcaattt cgaccggaac agaatcacag cattcagaca actggctgca 2161 gaaaacaagt atggactggt ggacaccatg aaagttggta atcaactaaa aggagtgaaa 2221 accatggaag aactcaaaca agcaatcagg aatgtgacca tcaagaggtg ccggatcatc 2281 tacggtggct ccacgtatga ccttgaatct gatggcaagg gcaaagtttt ggtggaaaag 2341 gtcaagagcg cctctataca gaccaacaac gagttggccg gggccctgca tcatcttaaa 2401 catgcccgaa tcaggtacta tgtcaaatgt gtgcaagaag cagtctattc catcatacaa 2461 attgccggcg ctgcgtttgt caccacgcgc attgcacgcc gcatgaacat acaagagctc 2521 tggtcgaagc cacaattaga tcaaaatgaa tcagagacta aggaagaggc ccccaagtca 2581 gaagatgacg agttcatcat atcttctaag gatatcaagg aggaaggaaa gaagggcaaa 2641 aacaaaactg gccgcggcaa gaaacacacc gcattctcca gcaagggctt gagcgatgag 2701 gagtatgacg agtacaagag gataagagaa gagagaaatg ggaagtactc catagaggag 2761 tatcttcaag acagagacag gtattatgag gagctcgcca ttgccaaggc cacggaagaa 2821 gatttctgtg aagaggagga gatcaaaatc cgtcagagga ttttccgtcc caccaggaaa 2881 caaagaaagg aagagagggc cacactagga ctggtaacag gttcagaaat cagaagaaga 2941 aaccctgatg atttcaaacc caaagggaag ctatgggccg atgacaacag aagtgttgac 3001 tacaatgaga aactggattt tgaggccccc ccaagtatat ggtctaggat tgtgagcttt 3061 ggttctggct ggggcttctg ggtgtcacca agcctgttca taacgtcaac tcatgtgatc 3121 cctgcaggca taacagaagc atttggagtc cccatcaaac aagttcagat ccacaaatca 3181 ggcgaatttt gccgattcag attcccaaaa ccaattagac cagatgtgac aggaatgatc 3241 ttggaagaag gtgcgcctga aggcaccgtg gcaactgtgc tcatcaaacg ccccaccgga 3301 gagctcatgc ctcttgcagc cagaatggga acacacgcaa ccatgaagat tcaaggccgc 3361 atggttggtg gacagatggg tatgttactc actgggtcaa atgctaaagg aatggatttg 3421 ggaacaactc ctggtgactg tggctgccct tacatctata aaaggggcaa tgactatata 3481 gtcattgggg tgcacactgc agcagcccgt ggtggaaaca ccgtcatctg tgccacacag 3541 ggaagtgagg gtgaggcaac tcttgagggt ggagatgaca aaggaacata ctgtggggca 3601 cccattctag gccctggggg tgcaccaaaa ttgagcacta aaaccaaatt ttggaggtca 3661 tcgaacatgc cccttccacc agggacgtat gagcctgcct acctcggtgg ccgtgacccg 3721 cgtgttaggg gtgggccctc cttacaacag gtaatgagag accagttgaa gccattcact 3781 gaacccaggg gcaaacctcc aagaccaagt gttttggaag cagccaaaca aaccattatc 3841 aatgtccttg aacaaaccct ggatcctcca caaaaatgga catacgtaca ggcgtgtgcc 3901 tcacttgaca aaaccacctc cagcgggcat ccccaccacg 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 acactgcata 4201 tcactcccag tacgagttgg catgaatatg aatgaagatg gcccaataat attcgagaaa 4261 cattccagat acaaatatca ctatgatgca gactactctc gttgggattc aacacagcag 4321 agggcagtat tagcagcagc cttggaaatt atggtcagat tctctgcaga accacaattg 4381 gcacaaatag tcgctgagga tctactggcc cctagtgtag tagatgtagg agactttaaa 4441 attacaataa atgaagggct cccatctggc gtgccatgca cttctcaatg gaactccatt 4501 gcacactggc tgctaactct ctgtgctctg tctgaagtca ccaaactgtc ccccgacatt 4561 atacaagcaa actccatgtt ctcattttac ggtgatgacg agattgtcag caccgacata 4621 aaattggacc ctgaacagtt gaccgccaag ttgaaggagt acggcctgaa accaacccgc 4681 ccagacaaga ccgagggacc tctgatcatc ggtgaagatt tgaacggact cactttcctc 4741 cgaagaacgg tgactcgtga cccagctggc tggtttggaa aactggacca aagctcaatt 4801 ttgaggcaga tgtactggac tagaggacca aatcatgaag accccaatga gacaatgata 4861 ccccattccc agagacccat acagctcatg gcactgcttg gtgaagcctc tcttcacgga 4921 ccctctttct acagtagaat cagtaaattg gtcataactg aacttaaaga aggtgggatg 4981 gacttttacg tgccaaggca ggaacccatg ttcaggtgga tgaggttctc tgacttgagc 5041 acgtgggagg gcgatcgcaa tctggctccc agctttgtga atgaagatgg cgtcgagtga 5101 cgccaaccca tctgatgggt ccgcagccag ccttgtacca gaggtcaaca atgaggttat 5161 ggctttggag cccgttgttg gtgccgctat tgcggcacct gtagcgggcc aacaaaatgt 5221 aattgacccc tggattagaa ataattttgt acaagcccct ggtggggagt ttacagtgtc 5281 ccctagaaat gctccaggtg aaatactatg gagcgcaccc ctaggccctg acctaaatcc 5341 ctacctatcc cacttggcca gaatgtacaa tggttatgca ggtggttttg aagtgcaggt 5401 aattctcgcg gggaacgcgt tcaccgccgg gaagattata tttgcagcag tcccaccaaa 5461 ttttccaact gaaggcttaa gccctagcca ggtcactatg ttcccccaca taatagtaga 5521 tgttagacaa ttggaacctg tgctgatccc cttacccgat gttaggaata atttctatca 5581 ttataatcag tcaaatgact ccactattaa gttgatagca atgttgtaca caccacttag 5641 ggctaataat gctggggatg atgttttcac agtttcgtgc cgagttctca cgagaccatc 5701 ccccgatttt gatttcatat tcttagtacc acccacagtt gagtcaagaa ctaaaccatt 5761 ctctgtccca gttttaactg ttgaggagat gaccaactca agattcccca tccctttgga 5821 aaagttgttc acaggcccca gtagtgcatt tgttgttcaa ccacaaaacg gcagatgcac 5881 aactgatggc gtgctcctag gcaccaccca actttctcct gtcaacatct gcaccttcag 5941 aggggatgtc acccacatca caggtagtca caacttcact atgaatttgg cttctcaaaa 6001 ttggaacaac tatgacccaa cagaagaaat cccagccccc ctaggaactc cagattttgt 6061 ggggaagatc caaggcatgc tcacccaaac cacaaggaca gatggttcaa cacgcggcca 6121 caaagctaca gtgtacactg ggagcgccga ctttgctcca aaactgggta gggttcaatt 6181 tgaaactgac acaaaccatg actttgaagc taatcaaaac acaaagttca ccccagtcgg 6241 cgtcatccaa gatggtagca ccacccaccg aaacgaaccc caacagtggg tgctcccaag 6301 ttactcaggc agaaatactc acaatgtaca tttggccccc gctgtagccc ccacctttcc 6361 gggtgagcaa ctcctcttct tcaggtccac catgcccgga tgcagcgggt accccaatat 6421 ggatttggac tgtctgctcc cccaggaatg ggtgcagtac ttctaccaag aggcagcccc 6481 agcacaatct gatgtagctc tgctaagatt tgtgaatcca gatacaggta gggttttgtt 6541 tgagtgcaag cttcacaaat caggctatgt cacagtggct cacactggcc aacatgattt 6601 ggttatcccc cccaatggtt actttaggtt tgattcctgg gtcaaccagt tctacacgct 6661 tgcccccatg ggaaatggaa cggggcgtag acgtgcagta taatggctgg agctttcttt 6721 gctggattgg catctgatgt ccttggctct ggacttggtt cccttatcaa tgctggagct 6781 ggggccatca accaaaaagt tgagtttgaa aataatagaa aattgcaaca agcatccttc 6841 caatttagca gcaatttgca acaggcttcc tttcagcatg acaaagagat gctccaagca 6901 caaattgagg ccaccaaaaa gctacagcag gaaatgatga gagttaagca ggcaatgctc 6961 ctagagggtg ggttctctga gacagatgcg gcccgcgggg cagttaacgc ccccatgaca 7021 aaggctttgg actggagcgg gacaaggtac tgggctccag atgctagaat tacaacatac 7081 aatgcaggcc acttttccac ccctcaacca tcgggggcac tgccaggaag agctaatctt 7141 agagatgctg tccctgctcg tggatcatct accaaacctt ctaactcttc tactgccacc 7201 tctgtgtact caaatcaaac tatttcaacg agacttggtt ctacagctgg ttctggaacc 7261 agtgtctcga gcctcccgcc aactgcaagg actaggagct gggttgagga tcagaatagg 7321 aatttgtcac ctttcatgag gggggcccac aacatatcat ttgtcacccc accatctagc 7381 agatcctcta gccaaggcac agtctcaacc gtgcctaaag aaattttgga ctcctggact 7441 ggcgctttca acacgcgcag gcagcctctc ttcgctcaca ttcgtaagcg aggggagtca 7501 cgggtgtaa //