Typing tool
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Complete norovirus genomes
MH260509 | GII.2 | ||
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GII.P16 |
ORF1: 1..5028 ORF2: 5009..6637 ORF3: 6637..7416LOCUS MH260509 7457 bp RNA linear VRL 16-JUN-2018 DEFINITION Norovirus GII isolate ST97 nonstructural polyprotein (ORF1) gene, partial cds; and VP1 (ORF2) and VP2 (ORF3) genes, complete cds. ACCESSION MH260509 VERSION MH260509.1 DBLINK BioProject: PRJNA338014 KEYWORDS . SOURCE Norovirus GII ORGANISM Norovirus GII Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes; Picornavirales; Caliciviridae; Norovirus; Norwalk virus. REFERENCE 1 (bases 1 to 7457) AUTHORS Casto,A.M., Adler,A., Huang,M.-L., Makhsous,N., Xie,H., Zerr,D. and Greninger,A. TITLE The limits of epidemiology: Real-time metagenomic sequencing during norovirus outbreak reveals discrete transmission clusters and elucidates long-term sequelae of hospital acquired infections JOURNAL Unpublished REFERENCE 2 (bases 1 to 7457) AUTHORS Casto,A.M., Adler,A., Huang,M.-L., Makhsous,N., Xie,H., Zerr,D. and Greninger,A. TITLE Direct Submission JOURNAL Submitted (25-APR-2018) Department of Laboratory Medicine, University of Washington, 1100 Fairview Ave. N, E5-110, PO Box 19024, Seattle, WA 98109, USA FEATURES Location/Qualifiers source 1..7457 /organism="Norovirus GII" /mol_type="genomic RNA" /isolate="ST97" /host="Homo sapiens" /db_xref="taxon:122929" /country="USA" /collection_date="2017" /note="genotype: GII" gene <1..5028 /gene="ORF1" CDS <1..5028 /gene="ORF1" /codon_start=1 /product="nonstructural polyprotein" /protein_id="AWT08383.1" /translation="GEGLFTNMSSTLKKALGARPKQPAPRDKPQKPPRPPTPELVKRI PPPPPNGEEEEEPVIRYEIKSGVSGLPELTTVPQPDVANTAFSVPPLSLRENREAKEP LTGAILEMWDGEIYHYGLYVEKGLVLGVHKPPAAVSMARVELTPLSLYWRVVYTPQYL ISPETLRRLNGEAFPYTAFDNNCYAFCCWVLDLNDSWLSRRMVQRTTGFFRPYQEWNR KPLPTMDDSKIKKVANIFLCSLSTLFTRPIKDLVGKIKPLNILNILATCDWTFAGIVE SLILLAELFGVFWTPPDVSAMIAPLLGDYELQGPEDLAVELVPVVMGGIGLVLGFTKE KIGKMLSSAASTLRACKDLGAYGLEILKLVMKWFFPKKEEANELAMVRAIEDAVLDLE AIENNHMTTLLKDKDSLATYMKTLDMEEEKARRLSTKSASPDIVGTINALLARIAAAR SLVHRAKEELSSRIKPVVVMISGKPGIGKTHLAREVARKVASTLTGDQRVGLIPRNGV DHWDAYKGERVVLWDDYGMSNPIHDALRIQELADTCPLTLNCDRIENKGKVFDSEVII ITTNLANPAPLDYVNFEACSRRIDFLVYAEAPEVEKAKRDFPGQPDMWKDAFKSDFSH IKLQLAPQGGFDKNGNTPHGKGVMKTLTTGSLIARASGLLHERMDEFELQGPTITTFN FDRNRITAFRQLAAENKYGLVDTMKVGNQLKGVKTMEELKQAIRNVTIKKCRILYGGS TYDLESDGKGKVLVEKVKNTSVQTNNELAGALHHLKHARIRYYVKCVQEAVYSIIQIA GAAFVTTRIARRMNIQELWSKPQLDQNESETKEEAPKSEDDEFIISSKDIKEEGKKGK NKTGRGKKHTAFSSKGLSDEEYDEYKRIREERNGKYSIEEYLQDRDRYYEELAIAKAT EEDFCEEEETKIRQRIFRPTRKQRKEERATLGLVTGSEIRKRNPDDFKPKGKLWADDN RSVDYNEKLDFEAPPSIWSRIVSFGSGWGFWVSPSLFITSTHVIPAGITEAFGVPIKQ IQIHKSGEFCRFRFPKPIRPDVTGMILEEGAPEGTVATVLIKRPTGELMPLAARMGTH ATMRIQGRMVGGQMGMLLTGSNAKGMDLGTTPGDCGCPYIYKRGNDYIVIGVHTAAAR GGNTVICATQGSEGEATLEGGDDKGTYCGAPILGPGGAPKLSTKTKFWRSSNTPLPPG TYEPAYLGGRDPRVKGGPSLQQVMRDQLKPFTEPRGKPPRPSVLEAAKQTIINVLEQT LDPPQKWTYAQACASLDKTTSSGHPYHVRKNEFWNGETFTGKLADQASKANLMFEEGK HMTPVYTAALKDELVKTEKIYGKIKKRLLWGSDLSTMIRCARSFGGLMDEMKAHCISL PVRVGMNMNEDGPIIFEKHSRYKYHYDADYSRWDSTQQRAVLAAALEIMVRFSAEPQL AQIVAEDLLAPSVVDVGDFKITINEGLPSGVPCTSQWNSIAHWLLTLCALSEVTKLSP DIIQANSMFSFYGDDEIVSTDIKLDPEQLTAKLKEYGLKPTRPDKTEGPLIISEDLNG LTFLRRTVTRDPAGWFGKLDQSSILRQMYWTRGPNHEDPNETMIPHSQRPIQLMALLG EASLHGPSFYSKISKLVITELKEGGMDFYVPRQEPMFRWMRFSDLSTWEGDRNLAPNF VNEDGVE" gene 5009..6637 /gene="ORF2" CDS 5009..6637 /gene="ORF2" /note="major capsid protein" /codon_start=1 /product="VP1" /protein_id="AWT08381.1" /translation="MKMASNDAAPSTDGAAGLVPESNNEVMALEPVAGAALAAPVTGQ TNIIDPWIRANFVQAPNGEFTVSPRNAPGEVLLSLELGPELNPYLAHLARMYNGYAGG MEVQVMLAGNAFTAGKLVFAAVPPHFPVENLSPQQITMFPHVIIDVRTLEPVLLPLPD VRNNFFHYNQKDDPKMRIVAMLYTPLRSNGSGDDVFTVSCRVLTRPSPDFDFTYLVPP TVESKTKPFTLPILTLGELSNSRFPVSIDQMYTSPNEVISVQCQNGRCTLDGELQGTT QLQVSGICAFKGEVTAHLHDNDHLYNVTITNLNGSPFDPSEDIPAPLGVPDFQGRVFG IISQRDKHNSPGHNEPANRGHDAVVPTYTAQYTPKLGQIQIGTWQTDDLTVNQPVKFT PVGLNDTEHFNQWVVPRYAGALNLNTNLAPSVAPVFPGERLLFFRSYIPLKGGYGNPA IDCLLPQEWVQHFYQEAAPSMSEVALVRYINPDTGRALFEAKLHRAGFMTVSSNTSAP VVVPANGYFRFDSWVNQFYSLAPMGTGNGRRRVQ" gene 6637..7416 /gene="ORF3" CDS 6637..7416 /gene="ORF3" /note="minor structural protein; small basic protein" /codon_start=1 /product="VP2" /protein_id="AWT08382.1" /translation="MAGAFVAGLAGDVLSNGLSSLINAGANAINQRAEFDFNQKLQQN SFNHDKEMLQAQIQATKQLQADMMAIKQGVLTAGGFSPADAARGAVNAPMTQALDWNG TRYWAPNSMRTTSYSGKFTSTAPVRQADFQHTQSRPSSGSSVSSFATQSSRPTLTTTT GSSHGTVSSNSTRSTSLSQSTVSRATSRTGEWVRDQNRNLEPYMHGALQTAFVTPPSS RASDGTVSTVPKGVLDSWTPAFNTRRQPLFAHLRKRGESQA" ORIGIN 1 ggtgaaggct tattcacaaa tatgtcttcc accttaaaga aagccctcgg ggctaggccc 61 aaacagcctg ccccgagaga caaaccacaa aagcccccaa gaccaccaac tcccgagttg 121 gtcaagagga taccccctcc tccacctaat ggcgaagaag aagaagaacc agtcattagg 181 tatgagatta agagtggggt ctctggcctg cccgagctca caacagtccc ccaaccggac 241 gtggccaaca cagcattcag tgttccacca ctgagcttga gagaaaacag ggaggccaag 301 gaaccgctaa caggggcaat attagagatg tgggatggag agatatacca ttatggcctg 361 tacgtggaga aaggcttagt gttgggtgtg cacaaaccac ctgcagccgt aagcatggca 421 agagtggagc tgacgccgct gtcattgtac tggcgtgtgg tgtacactcc ccaatacctc 481 atctcccctg aaactctcag gagactcaac ggagaggcat tcccttacac cgcctttgac 541 aataactgct atgccttttg ctgctgggtg ttagacctca atgactcatg gcttagcagg 601 aggatggtgc aaagaacaac gggcttcttt agaccttacc aagagtggaa cagaaaaccc 661 ctgcccacca tggatgactc caaaattaag aaggtagcaa atatattcct atgctcattg 721 tccacattat tcaccagacc cataaaagac ctcgtaggaa aaattaaacc attaaacata 781 ttgaatatcc tggcaacgtg tgactggact tttgccggaa tagtggagtc tctgatatta 841 cttgctgaac tcttcggagt tttctggaca cccccagatg tgtctgctat gatcgctccc 901 ttactcgggg actacgagtt gcaggggcca gaagacctcg ccgttgaact cgtacccgtg 961 gtaatggggg ggattggttt ggtgttggga ttcaccaaag agaaaattgg caaaatgttg 1021 tcctcagcag catcaacact cagggcttgc aaagatcttg gtgcctatgg cttagagata 1081 ctcaaattgg tcatgaagtg gttcttccca aagaaagagg aggccaatga gctagccatg 1141 gtgagggcca tagaggatgc tgtactagat cttgaggcaa tagaaaataa ccacatgaca 1201 accctgttaa aagacaaaga cagcttagca acatacatga aaacactgga catggaggag 1261 gagaaagcca ggaggttgtc cacaaaatct gcatcccctg acatagttgg gacaatcaac 1321 gccctgctgg ctcgaatagc agcggccagg tcattagtcc acagggccaa ggaagagcta 1381 tctagcagga taaaaccagt agttgttatg atatctggca aaccaggaat aggcaaaact 1441 catctggcca gggaggtggc aagaaaggtg gcatccactc tcacagggga tcaaagagtc 1501 ggactcatac caagaaacgg tgtggaccat tgggatgcat acaaaggtga gagagtcgtg 1561 ctgtgggacg actatggcat gagtaacccc attcatgatg ctcttcgcat acaagaattg 1621 gctgatacgt gtccccttac cttaaattgt gacagaattg aaaataaggg aaaagttttt 1681 gacagcgagg tcataataat tacaacaaac cttgccaatc cagccccact tgattatgtt 1741 aactttgagg cctgttccag gagaattgat ttcctggtgt acgctgaggc accagaagta 1801 gaaaaggcaa aacgggactt tcctggtcag ccagatatgt ggaaggatgc cttcaagtcc 1861 gacttttcac acatcaagct acagcttgca ccccagggcg gctttgacaa gaatggcaac 1921 accccacatg ggaaaggagt gatgaagacc ctcactaccg gttctctgat tgcccgtgca 1981 tcaggcctac tgcatgagag gatggatgaa tttgaactcc aaggtcccac aatcaccacc 2041 ttcaatttcg accggaacag aatcacagca ttcagacaat tggctgcaga aaacaagtat 2101 ggattggtgg ataccatgaa agtcggcaat caactaaaag gagtgaaaac catggaggaa 2161 cttaaacaag caatcaggaa tgtgaccatc aagaagtgcc ggatcctcta cggtggctcc 2221 acgtatgacc ttgaatctga tggcaagggc aaagttttgg tggaaaaggt caagaacacc 2281 tctgtacaga ccaacaacga gttggctggg gccctgcacc atctcaaaca cgcccgaatc 2341 aggtactacg tcaaatgtgt gcaagaagca gtctattcca tcatacaaat tgccggcgct 2401 gcgtttgtca ccacgcgcat tgcacgccgc atgaacatac aagaactctg gtcgaagcca 2461 caattagatc aaaatgaatc agagactaag gaagaggccc ccaagtcaga agatgacgag 2521 ttcatcatat cttctaagga catcaaggag gaaggaaaga agggcaaaaa caaaactggc 2581 cgtggcaaga aacacactgc attctccagc aagggcttga gcgatgagga gtatgacgag 2641 tacaagagga taagagaaga gaggaatggg aagtactcca tagaggagta tcttcaagac 2701 agagacaggt actatgagga gctcgccatt gccaaggcca cggaagaaga cttctgtgaa 2761 gaagaggaga ccaaaatccg tcagagaatt ttccgtccca ccaggaaaca aagaaaggaa 2821 gagagggcca cattagggct agtaacaggt tcagaaatca gaaaaagaaa ccctgatgac 2881 ttcaaaccca aagggaagct gtgggctgat gacaacagga gtgttgacta caatgagaaa 2941 ctggactttg aggccccccc aagcatatgg tctaggattg tgagctttgg ttctggctgg 3001 ggcttctggg tgtcaccaag ccttttcata acatcaactc atgtaatccc cgcaggcata 3061 acagaagcat ttggagtccc catcaaacaa attcagatcc acaaatcagg tgaattttgc 3121 cgattcagat tcccaaaacc aattagacca gatgtaacag ggatgatctt ggaagaaggt 3181 gcgcctgagg gcaccgtggc aactgtgctc atcaaacgcc ccaccgggga gctcatgccc 3241 cttgcagcca gaatgggaac acacgcaacc atgagaattc aaggccgcat ggttggcgga 3301 cagatgggta tgttgctcac tggatcaaat gctaaaggaa tggatttggg aacaactcct 3361 ggtgattgtg gctgtcctta catctataaa agaggcaatg actatatagt cattggggtg 3421 cacactgcag cagcccgtgg tggaaacacc gtcatctgtg ccacacaggg aagtgagggt 3481 gaggcaactc ttgagggtgg agatgacaaa ggaacatact gtggggcacc cattctaggc 3541 cctgggggtg caccaaaatt gagcaccaaa accaaatttt ggaggtcatc gaacacgccc 3601 cttccaccag ggacatatga gcctgcctac ctcggtggcc gtgatccgcg tgttaagggt 3661 gggccctccc tgcagcaggt aatgagagac cagttgaagc cattcactga acccaggggc 3721 aaacctccaa gaccaagtgt attggaagca gccaaacaaa ccatcatcaa tgtcctcgaa 3781 caaaccctgg accctccaca aaaatggaca tacgcacagg cgtgtgcctc acttgacaaa 3841 accacctcca gcgggcaccc ctatcacgtc cgaaagaatg aattctggaa tggtgagacc 3901 ttcactggaa aattggcaga ccaagcatca aaagcaaacc taatgtttga ggaagggaaa 3961 cacatgacac cagtgtacac agcagcactc aaggacgagc tagtcaagac tgagaaaatc 4021 tatggaaaga tcaagaagag actgctctgg ggctctgact tgtccactat gatccggtgc 4081 gctaggtcat ttggtgggct catggacgag atgaaggcac actgcatatc actcccagtc 4141 cgagttggca tgaatatgaa tgaagatggc ccaataatat ttgagaaaca ttccagatac 4201 aaatatcact atgatgcaga ctactctcgt tgggattcaa cacaacagag ggcagtacta 4261 gcagcagcct tggaaattat ggtcagattc tctgcagaac cacaattggc acaaatagtc 4321 gctgaggatc tgctggcccc tagtgtagta gatgtaggag acttcaaaat tacaataaat 4381 gaagggctcc cctctggtgt gccatgcact tctcaatgga actccatcgc acactggctg 4441 ctaactctct gtgccttgtc tgaagtcacc aaactgtccc ctgacattat acaggcaaat 4501 tccatgttct cattttacgg tgatgacgag attgtcagca ccgacataaa attggaccct 4561 gaacagttaa ccgccaaatt gaaagagtac ggcctgaaac caacccgccc agacaaaacc 4621 gagggacccc tgattatcag tgaagatttg aacggactca ctttcctccg aaggacggtg 4681 actcgtgacc cagctggctg gtttggaaaa ttggaccaaa gctcaatttt gaggcagatg 4741 tactggacta gaggaccaaa tcatgaagac cccaatgaga caatgatacc ccattctcaa 4801 agacccatac agctcatggc actgcttggt gaagcctctc ttcacggacc ctctttctac 4861 agtaaaatca gtaaattggt cataactgaa ctcaaagaag gtgggatgga cttttacgtg 4921 ccaaggcagg aacccatgtt caggtggatg aggttttctg acttgagcac gtgggagggc 4981 gatcgcaatc tggctcccaa ttttgtgaat gaagatggcg tcgaatgacg ccgctccatc 5041 tactgatggt gcagccggcc tcgtgccaga aagtaacaat gaggtcatgg ctcttgaacc 5101 cgtggctggt gccgccttgg cagccccggt cactggtcaa acaaatatta tagatccttg 5161 gattagagca aattttgtcc aggcccccaa tggtgaattt acagtctctc cccgtaatgc 5221 ccctggtgaa gtgctactga gtctagagtt gggtccagaa ttaaatcctt atctggcaca 5281 tttagcaaga atgtacaatg ggtatgccgg tgggatggag gtgcaggtca tgttggctgg 5341 gaacgcgttc acagccggca agttggtctt cgccgccgtg ccacctcact tcccggttga 5401 aaaccttagc ccacagcaaa tcaccatgtt ccctcatgtg atcatagatg tgagaacctt 5461 ggaacctgtt ttattaccac tccctgatgt tagaaataat ttcttccatt ataatcagaa 5521 agatgatccc aagatgagaa ttgtggctat gctttatacc cccctcaggt ctaatggttc 5581 aggtgatgat gtgtttacag tctcctgcag agtgttgact agaccttccc ctgactttga 5641 cttcacatac ctggtgccac caacagtgga gtctaaaaca aaaccattca ccctcccaat 5701 cctcacactt ggggaacttt ccaattccag gttcccagtg tccatagacc agatgtatac 5761 cagccctaat gaagttatat cagtgcagtg tcaaaatggt aggtgcacac tggacgggga 5821 gctccagggg acaacacaac tccaagtcag tggcatttgt gctttcaaag gtgaagtgac 5881 cgcccacttg catgacaatg atcacctata taatgttacc atcacaaact tgaatgggtc 5941 cccttttgat ccctccgagg atatccctgc ccctctgggt gtgcctgact tccagggaag 6001 ggtttttggt atcatctccc aaagagacaa acacaatagt cctgggcata atgaaccagc 6061 aaacagggga cacgacgctg tggttcccac ttacacagca cagtacactc caaaactggg 6121 acaaattcaa attggcacat ggcagactga cgatcttaca gtcaaccaac cagtcaaatt 6181 caccccagtt ggactcaatg acactgaaca tttcaaccaa tgggtggtcc ctaggtatgc 6241 tggtgcccta aacctcaata caaaccttgc cccttctgtt gctccagtat ttccaggaga 6301 gcgtctgctc ttcttcagat catacattcc cctcaagggc ggctatggaa acccagccat 6361 tgattgccta ctaccacaag agtgggtgca acacttctat caggaagcag ccccttcaat 6421 gagtgaggtg gccctcgtca ggtacatcaa cccggacact ggtcgggcac tgtttgaggc 6481 caagctccac agagctggtt tcatgacagt ctcgagcaac accagtgccc cggtggttgt 6541 gcctgccaac ggatacttca gatttgattc ttgggtgaac caattctatt ctctcgcccc 6601 catgggaact gggaatgggc gtagaagggt tcaataatgg ctggagcttt tgtagctggt 6661 cttgcagggg atgtgctcag caatgggctt agttcattaa tcaatgcagg tgctaatgca 6721 ataaatcaga gggcagaatt tgattttaat cagaaattgc agcaaaattc ttttaatcat 6781 gataaggaga tgttgcaggc tcagattcag gcaactaagc agctgcaggc agacatgatg 6841 gctataaaac aaggggtctt gaccgctggc ggcttttccc ctgctgatgc agccagaggt 6901 gctgtgaacg cgcccatgac acaagcgctg gattggaatg gtacaaggta ttgggcacca 6961 aactccatga ggaccacatc ttactctgga aaattcacat caaccgcccc agtgaggcag 7021 gccgacttcc agcacaccca aagccggcct tcgagtggct cctctgtgtc ttcctttgcc 7081 actcagtctt caaggccaac tctgaccaca accactggtt cctcacatgg cacagtctca 7141 tcaaattcaa ctcgcagcac aagcctctcc caatcaacgg tctccagagc cacatctagg 7201 actggtgagt gggttagaga tcaaaataga aatttggaac cctacatgca tggtgcctta 7261 cagacagcct ttgtcacccc accttccagc agggcatctg acgggacagt ctcaaccgtc 7321 ccgaaaggtg ttttggactc ctggacacct gcgtttaaca cccgcaggca gccgcttttt 7381 gcacacctcc gtaagagggg ggagtcacaa gcttagtgaa aaggtgaaga tttatttagg 7441 atgaattgat tttacct //