Typing tool
|
Complete norovirus genomes
MF140636 | GII.4 Sydney | ||
---|---|---|---|
GII.P31 |
ORF1: 1..4925 ORF2: 4906..6528 ORF3: 6528..7334LOCUS MF140636 7334 bp RNA linear VRL 24-OCT-2017 DEFINITION Norovirus GII strain Norovirus/GII/Hu/NL/2013/GII.Pe-GII.4/Rotterdam/E7800008_p10_d0 ORF1 gene, partial cds; and ORF2 and ORF3 genes, complete cds. ACCESSION MF140636 VERSION MF140636.1 KEYWORDS . SOURCE Norovirus GII ORGANISM Norovirus GII Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes; Picornavirales; Caliciviridae; Norovirus; Norwalk virus. REFERENCE 1 (bases 1 to 7334) AUTHORS van Beek,J., de Graaf,M., Smits,S.L., Schapendonk,C.M.E., Verjans,G.M.G.M., Vennema,H., van der Eijk,A.A., Phan,M.V.T., Cotten,M.L. and Koopmans,M.P.G. TITLE Whole genome next generation sequencing to study within-host evolution of chronic norovirus infection among immunocompromised patients JOURNAL J. Infect. Dis. (2017) In press PUBMED 29029115 REMARK Publication Status: Available-Online prior to print REFERENCE 2 (bases 1 to 7334) AUTHORS van Beek,J., de Graaf,M., Smits,S.L., Schapendonk,C.M.E., Verjans,G.M., Vennema,H., van der Eijk,A.A., Phan,M.V.T., Cotten,M.L. and Koopmans,M.P.G. TITLE Direct Submission JOURNAL Submitted (19-MAY-2017) Centre for infectious Disease Control (Cib), National Institute for Public Health and the Environment (RIVM), Antonie van Leeuwenhoeklaan 9, Bilthoven, Utrecht 3721 MA, Netherlands COMMENT ##Assembly-Data-START## Assembly Method :: SPAdes v. 3.9.0 Sequencing Technology :: Illumina ##Assembly-Data-END## FEATURES Location/Qualifiers source 1..7334 /organism="Norovirus GII" /mol_type="genomic RNA" /strain="Norovirus/GII/Hu/NL/2013/GII.Pe- GII.4/Rotterdam/E7800008_p10_d0" /host="Homo sapiens" /db_xref="taxon:122929" /country="Netherlands" /collection_date="24-Jan-2013" /note="genotype: GII.Pe-GII.4" CDS <1..4925 /codon_start=3 /product="ORF1" /protein_id="ATN23604.1" /translation="PTPELVKKIPPPPPNGEDELVVSYSAKDGVSGLPELTTVRQPEE TNTAFSVPPLNQRESRDAKEPLTGTIIEMWDGEIYHYGLYVERGLILGVHKPPAAISL AKVELAPLSLFWRPVYTPQYLISPDTLRRLHGESFPYTAFDNNCYAFCCWVLDLNDSW LSRRMIQRTTGFFRPYQDWNRKPLPTMDDSKLKKVANIFLCTLSSLFTRPIKDIIGKL KPLNILNILATCDWTFAGIVESLILLAELFGVFWTPPDVSAMIAPLLGDYELQGPEDL AVELVPIVMGGIGLVLGFTKEKIGKMLSSAASTLRACKDLGAYGLEILKLVMKWFFPK KEEANELAMVRSIEDAVLDLEAIENNHMTTLLKDKDSLATYMRTLDLEEEKARKLSTK SASPDIVGTINSLLARIAAARSLVHRAKEELSSRPRPVVVMISGRPGIGKTHLARELA KKIAASLTGDQRVGLIPRNGVDHWDAYKGERVVLWDDYGMSNPIHDALRLQELADTCP LTLNCDRIENKGKVFDSDAIIITTNLANPAPLDYVNFEACSRRIDFLVYAEAPEVEKA KRDFPGQPDMWKNAFSPDFSHIKLSLAPQGGFDKNGNTPHGKGVMKTLTTGSLIARAS GLLHERLDEYELQGPALTTFNFDRNKILAFRQLAAENKYGLMDTMRVGKQLKDVKTMS DLKQALKNIAIKKCQIVYNGGTYTLEADGKGSVKVDKVQSATVQTNNELAGALHHLRC ARIRYYVKCVQEALYSIIQIAGAAFVTTRIAKRMNIQNLWSKPQVEDTEEMANKDGCL KPKDDEEFVVSSDDIKTEGKKGKNKSGRGKKHTAFSSKGLSDEEYDEYKRIREERNGK YSIEEYLQDRDRYYEEVAIARATEEDFCEEEEAKIRQRIFRPTRKQRKEERASLGLVT GSEIRKRNPEDFKPKGKLWADDDRSVDYNEKLNFEAPPSIWSRIVNFGSGWGFWVSPS LFITSTHVIPQGAKEFFGVPIKQIQIHKSGEFCRLRFPKPIRTDVTGMILEEGAPEGT VATLLIKRPTGELMPLAARMGTHATMKIQGRTVGGQMGMLLTGSNAKSMDLGTTPGDC GCPYIYKRGNDYVVIGVHTAAARGGNTVICATQGSEGEATLEGGDSKGTYCGAPILGP GSAPKLSTKTKFWRSSTTPLPPGTYEPAYLGGKDPRVKGGPSLQQVMRDQLKPFTEPR GKPPRPNVLEAAKKTIINVLEQTIDPPQKWSFAQACASLDKTTSSGHPHHMRKNDCWN GESFTGKLADQASKANLMFEEGKNMTPVYTGALKDELVKTDKVYGKVKKRLLWGSDLA TMIRCARAFGGLMDELKAHCVTLPVRVGMNMNEDGPIIFEKHSRYRYHYDADYSRWDS TQQRDVLAAALEIMVKFSPEPHLAQIVAEDLLSPSVMDVGDFQISISEGLPSGVPCTS QWNSIAHWLLTLCALSEVTDLSPDIIQANSLFSFYGDDEIVSTDIKLDPEKLTAKLKE YGLKPTRPDKTEGPLVISEDLDGLTFLRRTVTRDPAGWFGKLEQSSILRQMYWTRGPN HEDPFETMIPHSQRPIQLMSLLGEAALHGPAFYSKISKLVIAELKEGGMDFYVPRQEP MFRWMRFSDLSTWEGDRNLAPSFVNEDGVE" CDS 4906..6528 /codon_start=1 /product="ORF2" /protein_id="ATN23605.1" /translation="MKMASSDANPSDGSAANLVPEVNNEVMALEPVVGAAIAAPVAGQ QNVIDPWIRNNFVQAPGGEFTVSPRNAPGEILWSAPLGPDLNPYLSHLARMYNGYAGG FEVQVILAGNAFTAGKVIFAAVPPNFPTEGLSPSQVTMFPHIVVDVRQLEPVLIPLPD VRNNFYHYNQSNDPTIKLIAMLYTPLRANNAGDDVFTVSCRVLTRPSPDFDFIFLVPP TVESRTKPFSVPVLTVEEMTNSRFPIPLEKLFTGPSSAFVVQPQNGRCTTDGVLLGTT QLSPVNICTFRGDVTHITGSRNYTMNLASQNWSNYDPTEEIPAPLGTPDFVGKIQGVL TQTTRTDGSTRGHKATVYTGSADFAPKLGRVQFETDTDRDFEANQNTKFTPVGVIQDG GTTHRNEPQQWVLPSYSGRNTPNVHLAPAVAPTFPGEQLLFFRSTMPGCSGYPNMDLD CLLPQEWVQYFYQEAAPAQSDVALLRFVNPDTGRVLFECKLHKSGYVTVAHTGQHDLV IPPNGYFRFDSWVNQFYTLAPMGNGTGRRRAL" CDS 6528..7334 /codon_start=1 /product="ORF3" /protein_id="ATN23606.1" /translation="MAGAFFAGLASDVLGSGLGSLINAGAGAINQKVEFENNRKLQQA SFQFSSNLQQASFQHDKEMLQAQIEATKRLQQEMMKVKQAMLLEGGFSETDAARGAIN APMTKALDWSGTRYWAPDARTTTYNAGRFSTPQPSGALPGRANLRDAVPARGSSSKSS NSSTATSVYSNQTTSTRLGSTAGSGTSVSSFPSTARTRSWVEDQSRNLSPFMSGAHNI SFVTPPSSRSSSQGTVSTVPKEILDSWTGAFNTRRQPLFAHIRKRGESRA" ORIGIN 1 cacccacacc agaattggtc aaaaagatcc ctcctccccc acccaacggg gaggatgaac 61 tagtggtctc ctacagcgcc aaagatggcg tttccggact gcctgagctc accactgtca 121 gacaaccgga agaaaccaac acggcgttca gtgtcccccc acttaaccaa agggagagca 181 gggacgccaa ggagccacta actggaacaa tcattgaaat gtgggatgga gaaatctacc 241 attacggcct gtacgtggaa cgaggtctta tacttggtgt gcacaagcca ccggcagcca 301 ttagccttgc caaggtcgag ctagcaccgc tctctttgtt ctggagacct gtatacaccc 361 cccagtatct catctctcca gacactctta ggagattaca tggagagtca ttcccctaca 421 ctgcatttga caacaattgc tacgcctttt gttgttgggt attagaccta aacgactcat 481 ggctaagcag gagaatgatt cagagaacaa caggcttctt caggccgtac caggattgga 541 acaggaaacc cctccccact atggatgatt ccaaattaaa gaaggtagcc aacatattct 601 tgtgcacttt gtcttcacta ttcaccagac ccattaagga cataataggg aagttgaaac 661 ctcttaacat ccttaacatt ctggctacat gtgattggac cttcgcaggc atagtggaat 721 ccttaatact cttggcagaa ctctttggag ttttctggac acccccagat gtgtctgcga 781 tgatcgcccc cttgctaggt gattatgaac tgcaaggacc tgaggacctt gcagtggaac 841 tggtcccaat agtgatgggg gggataggtt tggtgctagg atttaccaaa gagaaaatcg 901 gaaagatgct atcatccgct gcatccactt taagagcttg taaagacctt ggtgcatacg 961 gactggaaat cttaaaattg gtcatgaagt ggttcttccc aaagaaagag gaagcaaatg 1021 aactggctat ggtgagatcc atcgaggatg cagtactaga cctcgaggca attgaaaaca 1081 accacatgac caccctactc aaagacaaag acagcttggc aacctacatg agaacccttg 1141 accttgagga ggagaaagcc agaaaactct caaccaaatc tgcttcaccc gatattgtgg 1201 gcacaattaa ctctcttctg gcaagaatcg ctgctgcacg ctccctagtg catcgggcga 1261 aagaagagct ctccagcagg ccgagacctg tcgttgtgat gatatcggga agaccaggga 1321 tagggaaaac tcaccttgcc agggagctgg ccaagaagat cgcggcctcc ctcacagggg 1381 accagcgtgt gggtcttatc ccacgcaatg gtgtcgacca ctgggacgca tacaagggcg 1441 aaagagttgt cctatgggac gactatggaa tgagcaaccc catccatgat gccctcaggt 1501 tgcaggagct tgctgacact tgccccctca cgctaaattg tgacagaatt gagaacaaag 1561 ggaaagtctt tgacagtgat gccataatta tcaccaccaa tctggccaac ccagcaccac 1621 tggattatgt caactttgaa gcgtgctcga gacgcattga tttcctcgtg tacgcagaag 1681 cccctgaggt ggagaaggca aagcgcgact tcccaggtca acctgacatg tggaagaacg 1741 ctttcagtcc tgacttctca cacataaaac tgtcattggc tccacagggt ggttttgaca 1801 agaacggcaa caccccgcat ggaaaagggg tcatgaagac cctcaccact ggctccctca 1861 tcgcccgagc atcagggtta ctccatgaga ggctagatga atatgaactg caaggcccag 1921 ccctcaccac tttcaacttt gaccgcaaca agatacttgc ttttagacag cttgctgctg 1981 aaaacaagta tgggctgatg gacacaatga gagttggaaa acagctcaag gatgtcaaga 2041 ccatgtcaga cctcaaacaa gcactcaaga acatcgcgat caagaagtgc cagatagtgt 2101 acaatggtgg cacctacaca cttgaggctg atggcaaggg tagtgtgaaa gttgacaaag 2161 tgcaaagtgc cactgtgcag accaacaatg aactagccgg tgccctacac cacctaaggt 2221 gcgctagaat cagatactat gttaagtgcg tccaggaggc actgtattcc atcatccaaa 2281 tcgctggggc tgcattcgtc accacgcgca tcgctaagcg catgaatata cagaatctct 2341 ggtccaagcc acaggtggaa gacacagaag agatggccaa caaagatggt tgcctaaaac 2401 ccaaagatga tgaagagttt gtcgtctcat ccgacgacat caaaactgag ggcaagaaag 2461 ggaagaacaa gtccggccgt ggcaagaagc acacagcctt ttcaagtaaa gggctcagtg 2521 atgaggagta cgatgagtac aagagaatca gagaagaaag gaatggtaag tactccatag 2581 aagagtacct tcaggacaga gacaggtact acgaggaggt ggccattgcc agggcaaccg 2641 aagaggactt ctgtgaagaa gaagaggcca aaatccggca gagaattttc agaccaacaa 2701 ggaaacaacg caaagaagag agggcctctc tcggcttggt cacaggctct gaaatcagga 2761 agagaaaccc agaagacttc aaacccaagg gaaagttgtg ggctgatgat gacagaagtg 2821 ttgactacaa tgagaaactc aactttgagg ccccaccaag catctggtcg cggatagtca 2881 actttggttc aggctggggc ttctgggtct cccccagtct gtttataaca tcaacccatg 2941 tcatacccca aggtgcaaaa gagttcttcg gagtccctat taagcaaatc cagatacaca 3001 agtcaggtga attctgccgg ttgagattcc caaagccaat cagaactgat gtgacgggca 3061 tgattctaga agaaggtgcg cccgagggga ccgtggccac actgctcatc aagagaccaa 3121 ctggagagct catgcctctg gcagccagaa tggggaccca tgcaaccatg aaaattcagg 3181 ggcgcacagt tggagggcaa atgggtatgc tcctgacagg atccaacgcc aagagtatgg 3241 acctaggcac aacaccaggc gactgcggct gcccctacat ctacaagagg gggaatgact 3301 acgtggtcat aggagtccat acggccgctg cccgtggagg aaacactgtc atatgtgcca 3361 cccaggggag tgagggagaa gccacacttg aaggaggtga cagtaaaggg acatactgtg 3421 gcgcaccaat cttgggccca gggagcgctc cgaagctcag taccaagact aagttttgga 3481 gatcatccac aacaccactc ccacctggca cctacgaacc agcctacctc ggtggcaaag 3541 accctagagt caaaggtggc ccttcattgc aacaagttat gagggaccag ctgaagccat 3601 tcacagaacc cagaggcaaa ccaccaagac caaatgtgtt ggaagctgcc aagaaaacca 3661 tcatcaatgt ccttgagcaa acaattgatc caccccaaaa atggtcattt gcgcaagctt 3721 gcgcatccct tgacaaaacc acctccagcg gccacccgca ccacatgcgg aaaaacgact 3781 gttggaatgg ggagtccttc acaggaaaat tggctgatca agcctccaag gccaacctaa 3841 tgtttgaaga gggaaagaac atgactccag tctacacagg tgcacttaaa gatgagttgg 3901 taaagaccga taaagtttat ggtaaggtca agaagaggct tctgtggggt tcagatctgg 3961 cgaccatgat acggtgcgcc cgagcttttg gaggccttat ggatgaactc aaggcgcact 4021 gtgtcacact tcctgtcaga gttggtatga acatgaatga ggatggcccc atcatctttg 4081 agaagcactc cagatataga tatcactatg atgctgatta ttcccggtgg gactcaacac 4141 aacaaaggga tgtgctagca gcagcactag aaatcatggt taagttctct ccagaaccac 4201 acctggccca gatagttgca gaagacctcc tttcccctag cgtgatggat gtaggtgact 4261 ttcaaatatc aataagtgag ggtctcccct ctggggtacc ttgtacctcc cagtggaatt 4321 ccatcgccca ctggctcctc actctgtgtg cactctctga agtcacggac ctgtcccctg 4381 atatcattca ggccaactcc cttttctcct tctatggtga tgatgagatt gtaagcacag 4441 acataaagtt ggacccagag aagctgacag caaaactcaa ggagtacggg ctgaaaccaa 4501 cccgccccga caaaactgaa ggacccctcg ttatctctga agacctggat ggcctgacat 4561 tcctccggag aactgtgacc cgtgatccag ctggctggtt tggaaagttg gaacaaagtt 4621 caattctcag gcaaatgtac tggaccaggg gtcccaacca tgaagatcca tttgaaacaa 4681 tgataccaca ctcccaaaga cccatacaat tgatgtcctt gctgggcgag gctgcactcc 4741 acggcccggc attctatagc aaaattagca aattagtcat tgcagagttg aaggaaggtg 4801 gcatggattt ttacgtaccc agacaagagc caatgttcag atggatgaga ttctcagatc 4861 tgagcacgtg ggagggcgat cgcaatctgg ctcccagttt tgtgaatgaa gatggcgtcg 4921 agtgacgcca acccatctga tgggtccgca gccaacctcg tcccagaggt caacaatgag 4981 gttatggctc tggagcccgt tgttggtgcc gccattgcgg cacctgtagc gggccaacaa 5041 aatgtaattg acccctggat tagaaataat tttgtacaag cccctggtgg agagtttaca 5101 gtatccccca gaaacgctcc aggtgaaata ctatggagcg cgcccttggg ccctgatcta 5161 aatccctacc tatcccattt ggccagaatg tacaatggtt atgcaggtgg ttttgaagtg 5221 caggtaattc tcgcggggaa cgcgttcacc gccgggaagg tcatatttgc agcagtccca 5281 ccaaattttc caactgaagg cttgagcccc agccaggtca ctatgttccc ccatatagta 5341 gtagatgtta ggcaactaga acctgtgttg attcccttac ccgatgttag gaataatttc 5401 tatcattaca atcaatcaaa tgaccccacc attaagttga tagcaatgtt gtatacacca 5461 cttagggcta ataatgctgg ggatgatgtc ttcacagttt cttgccgagt tctcacgaga 5521 ccatcccccg attttgactt catatttcta gtgccaccca cagttgagtc aagaactaaa 5581 ccattctctg tcccagtttt aactgttgag gagatgacca attcaagatt ccccattcct 5641 ttggaaaagt tgttcacggg tcccagcagt gcctttgttg tccaaccaca aaacggtagg 5701 tgcacgactg atggcgtgct cctaggcacc acccagctgt ctcctgtcaa catctgcacc 5761 ttcagaggag atgtcaccca tatcacaggt agtcgtaact acacaatgaa tttggcttct 5821 caaaattgga gcaattatga cccaacagaa gaaatcccag cccctctagg aactccagat 5881 tttgtgggga agattcaagg cgtgctcacc caaaccacaa ggacagatgg ctcaacacgc 5941 ggccacaaag ccacagtgta cactgggagc gccgactttg ctccaaaact gggtagagtt 6001 caatttgaaa ctgacacaga ccgtgatttt gaagctaacc aaaacacaaa gttcacccca 6061 gttggtgtca tccaagatgg tggcaccacc caccgaaatg aaccccaaca gtgggtgctc 6121 ccaagttact caggcagaaa cactcctaat gtgcatctgg cccccgctgt agcccccact 6181 tttccgggtg agcaacttct cttcttcaga tccaccatgc ccggatgcag cgggtacccc 6241 aacatggatt tggactgtct gctcccccag gaatgggtgc agtacttcta ccaagaggca 6301 gccccagcac aatctgatgt ggctctgcta agatttgtga atccagacac aggtagggtt 6361 ttgtttgagt gtaagcttca taaatcaggc tatgttacag tggctcacac tggccaacat 6421 gatttggtta tcccccccaa tggttatttt aggtttgatt cctgggtcaa ccagttttac 6481 acgcttgccc ccatgggaaa tggaacgggg cgtagacgtg cactataatg gctggagctt 6541 tctttgctgg attggcatct gatgtccttg gctctggact tggttccctt atcaatgctg 6601 gggctggggc catcaaccaa aaagttgagt ttgaaaataa cagaaaattg caacaagcat 6661 ccttccaatt tagcagcaat ctacaacagg cttcctttca acatgacaaa gagatgctcc 6721 aagcacaaat tgaggccacc aaaaggctac aacaggaaat gatgaaagtt aagcaggcaa 6781 tgctcctaga gggtgggttc tctgagacag atgcagcccg cggggcaatc aacgccccca 6841 tgacaaaagc tttggactgg agcgggacaa ggtactgggc tcccgatgct aggactacaa 6901 catacaatgc aggccgcttt tccacccctc aaccatcggg ggcactgcca ggaagagcta 6961 atcttaggga tgctgtccct gctcggggtt cctccagtaa gtcttctaat tcttctactg 7021 ctacttctgt gtactcaaat caaactactt caacgagact tggttctaca gctggttctg 7081 gtaccagtgt ctcgagcttc ccgtcaactg caaggactag gagctgggtt gaggatcaaa 7141 gtaggaattt gtcacctttc atgagtgggg cccacaacat atcgtttgtc accccaccat 7201 ctagcagatc ctctagccaa ggcacagtct caaccgtgcc taaagagatt ttggactcct 7261 ggactggcgc tttcaacacg cgcaggcagc cactcttcgc tcacattcgt aagcgagggg 7321 agtcacgggc gtaa //