Typing tool
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Typing tool
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Complete norovirus genomes
| MF140637 | GII.4 Sydney | |
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| GII.P31 |
ORF1: 1..5090
ORF2: 5071..6693
ORF3: 6693..7497
LOCUS MF140637 7497 bp RNA linear VRL 24-OCT-2017
DEFINITION Norovirus GII strain
Norovirus/GII/Hu/NL/2013/GII.Pe-GII.4/Rotterdam/E1300285_p10_d316
ORF1 gene, partial cds; ORF2 gene, complete cds; and ORF3 gene,
partial cds.
ACCESSION MF140637
VERSION MF140637.1
KEYWORDS .
SOURCE Norovirus GII
ORGANISM Norovirus GII
Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes;
Picornavirales; Caliciviridae; Norovirus; Norwalk virus.
REFERENCE 1 (bases 1 to 7497)
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 7497)
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..7497
/organism="Norovirus GII"
/mol_type="genomic RNA"
/strain="Norovirus/GII/Hu/NL/2013/GII.Pe-
GII.4/Rotterdam/E1300285_p10_d316"
/host="Homo sapiens"
/db_xref="taxon:122929"
/country="Netherlands"
/collection_date="06-Dec-2013"
/note="genotype: GII.Pe-GII.4"
CDS <1..5090
/codon_start=3
/product="ORF1"
/protein_id="ATN23607.1"
/translation="SNDASAAAVANSNNDIAKSSSDGVFSNMAVTFKRALGARPKQPP
PKEIPPRPPRPPTPELVKKIPPPPPNGEDELVVSYNAKDGVSGLPELTTVRQPEETNT
AFSVPPLNQRESRDAKEPLTGTIIEMWDGEIYHYGLYVERGLILGVHKPPAAISLAKV
ELAPLSLFWRPVYTPQYLISPDTLRRLHGESFPYTAFDNNCYAFCCWVLDLNDSWLSR
RMIQRTTGFFRPYQDWNRKPLPTMDDSKLKKVANIFLCTLSSLFTRPIKDIIGKLKPL
NILNILATCDWTFAGIVESLILLAELFGAFWTPPDVSAMIAPLLGDYELQGPEDLAVE
LVPIVMGGIGLVLGFTKEKIGKMLSSAASTLRACKDLGAYGLEILKLVMKWFFPKKEE
ANELAMVRSIEDAVLDLEAIENNHMTTLLKDKDSLATYMRTLDLEEEKARKLSTKSAS
PDIVGTINALLARIAAARSLVHRAKEELSSRLRPVVVMISGKPGIGKTHFAREVANKV
AASLTGDQRVGLIPRNGVDHWDAYKGERVVLWDDYGMSNPIHDALRLQELADTCPLTL
NCDRIENKGKVFDSDAIIITTNLANPAPLDYVNFEACSRRIDFLVYAEAPEVEKAKRD
FPGQPDMWKNAFSSDFSHMKLSLAPQGGFDKNGNTPHGKGVMKTLTTGSLIARASGLL
HERLDEYELQGPALTTFNFDRNKILAFRQLAAENKYGLMDTMRVGKQLKDVKTMSDLK
QALKNIAIKKCQIVYNGGTYTLEADGKGSVKVDKVQSATVQTNNELAGALHHLRCARI
RYYVKCAQEALYSIIQIAGAAFVTTRIAKRMNIQNLWSKPQVEDTEEIVNKDGCLKPK
DDEEFVVSSDDIKTEGKKGKNKSGRGKKHTAFSSKGLSDEEYDEYKRIREERNGKYSI
EEYLQDRDRYYEEVAIARATEEDFCEEEEAKIRQRIFRPTRKQRKEERASLGLVTGSE
IRKRNPEDFKPKGKLWADDDRSVDYNEKLNFEAPPSIWSRIVNFGSGWGFWVSPSLFI
TSTHVIPQGAKEFFGVPIKQIQIHKSGEFCRLRFPRPIRTDVTGMILEEGAPEGTVVT
LLIKRPTGELMPLAARMGTHATMKIQGRTVGGQMGMLLTGSNAKSMDLGTTPGDCGCP
YIYKRGNDYVVIGVHTAAARGGNTVICATQGSEGEATLEGGDSKGTYCGAPILGPGSA
PKLSAKTKFWRSSTTPLPPGTYEPAYLGGKDPRVKGGPSLQQVMRDQLKPFTEPRGKP
PRPNVLEAAKKTIINVLEQTIDPPQKWSFAQACASLDKTTSSGHPHHMRKNDCWNGES
FTGKLADQASKANLMFEEGKNMTPVYTGALKDELVKTDKVYGKIKKRLLWGSDLATMI
RCARAFGGLMDELKAHCVTLPVRVGMNMNEDGPIIFEKHSRYRYHYDADYSRWDSTQQ
RDVLAAALEIMVKFSPEPHLAQIVAEDLLSPSVMDVGDFQISISEGLPSGVPCTSQWN
SIAHWLLTLCALSEVTDLSPDIIQANSLFSFYGDDEIVSTDIKLDPEKLTAKLKEYGL
KPTRPDKTEGPLVISEDLDGLTFLRRTVTRDPAGWFGKLEQSSILRQMYWTRGPNHED
PFETMIPHSQRPIQLMSLLGEAALHGPAFYSKISKLVIAELKEGGMDFYVPRQEPMFR
WMRFSDLSTWEGDRNLAPSFVNEDGVE"
CDS 5071..6693
/codon_start=1
/product="ORF2"
/protein_id="ATN23608.1"
/translation="MKMASSDANPSDGSTASLVPEVNNEVMALEPVVGAAIAAPVAGQ
QNVIDPWIRNNFVQAPGGEFTVSPRNAPGEVLWSAPLGPDLNPYLSHLARMYNGYAGG
FEVQVILAGNAFTAGKIIFAAVPPNFPTECLSPSQVTMLPHIIVDVRQLEPVLIPLPD
VRNNFYHYNQSNDSTIKLIAMLYTPLRANNAGDDVFTVSCRVLTRPSPDFDFIFLVPP
TVESRTKPFSVPVLTVEEMTNSRFPIPLEKLFTGPSSAFVVQPQNGRCSTDGVLLGTT
QLSPVNICTFRGDVTQITGSSTYTMNLASQNWSNYDPTEEIPAPLGTPDFVGKIQGVL
TQTTRTVGSTRGHKATVRTGSADFAPKLGRVRFETDTNNDFEVNQNTKFTPVGVIQDG
DTAHRNEPQQWVLPSYSGRNTPNVHLAPAVAPTFPGEQLLFFRSTMPGCSGYPNMDLD
CLLPQEWVQYFYQEAAPAQSDVALLRFVNPDTGRVLFECKLHKSGYITVAHTGQHDLV
IPPNGYFRFDSWVNQFYTLAPMGNGTGRRRAP"
CDS 6693..>7497
/codon_start=1
/product="ORF3"
/protein_id="ATN23609.1"
/translation="MAGAFFAGLASDVLGSGLGSLINAGAGAINQKVEFENNRKLQQA
SFQFSSNLQQASFQHDKEMLQAQIEATKRLQQEMMKVKQAMLLEGGFSETDAARGAIN
APMTKVLDWSGTRYWAPDARTTTYNAGRFSTPQPSGALPGRANLRDAVPARGSSRKSS
NSSTATSVYSNQTTSTRLGSTAGSGTSVSSFPTTARTRSWVEDQSRNLSPFMSGAHNI
SFVTPPSSRSSSQGTVSTVPKEILDSWTGAFNTRRQPLFAHIRKRGESRA"
ORIGIN
1 cgtctaacga cgcttccgct gccgctgttg ccaacagcaa caacgacatc gcaaaatctt
61 caagtgacgg tgtgttttct aacatggctg tcacttttaa gcgggccctc ggggcgcggc
121 ctaaacagcc gcccccgaag gaaataccac ccagaccccc gcgaccaccc acaccagaat
181 tggtcaaaaa gatccctcct cccccaccca acggggagga tgaactagtg gtctcctaca
241 atgccaaaga tggcgtttcc ggactgcctg agctcaccac tgtcagacaa ccggaagaaa
301 ccaacacggc gttcagtgtc cccccactta accaaaggga gagcagggac gccaaggagc
361 cactaactgg aacaatcatt gaaatgtggg atggagaaat ctaccattac ggcctgtacg
421 tggaacgagg tcttatactt ggtgtgcaca agccaccggc agccattagc cttgccaagg
481 tcgagctagc accgctctct ttgttctgga gacctgtata caccccccag tatctcatct
541 ctccagacac tcttaggaga ttacatggag agtcattccc ctacactgca tttgacaaca
601 attgctacgc cttttgctgt tgggtattag acctaaacga ctcatggcta agcaggagaa
661 tgattcagag aacaacaggc ttcttcaggc cgtaccagga ttggaacagg aaacccctcc
721 ccactatgga tgattccaaa ttaaagaagg tagccaacat attcttgtgc actttgtctt
781 cactattcac cagacccatt aaggacataa tagggaagtt gaaacctctt aacatcctta
841 acattctggc tacatgtgat tggaccttcg caggcatagt ggaatcctta atactcttgg
901 cagaactctt tggagctttc tggacacccc cagatgtgtc tgcgatgatc gcccccttgc
961 taggtgatta tgaactgcaa ggacctgagg accttgcagt ggaactggtc ccaatagtga
1021 tgggggggat aggtttggtg ctaggattta ccaaagagaa aatcggaaag atgctatcat
1081 ccgctgcatc cactttaaga gcttgtaaag accttggtgc atacggactg gaaatcttaa
1141 aattggtcat gaagtggttc ttcccaaaga aagaggaagc aaatgaactg gctatggtga
1201 gatccatcga ggatgcagta ctagacctcg aggcaattga aaacaaccac atgaccaccc
1261 tactcaaaga taaagacagc ttggcaacct acatgagaac ccttgacctt gaggaggaga
1321 aagccagaaa actctcaacc aaatctgctt cacccgatat tgtgggcaca atcaacgctc
1381 ttctggcaag aatcgctgct gcacgctccc tagtgcatcg ggcgaaagaa gagctctcca
1441 gcaggctgag acctgtcgtt gtgatgatat cgggaaagcc agggataggg aaaactcact
1501 ttgccaggga ggtggccaac aaggtcgcgg cctccctcac aggggaccag cgtgtgggtc
1561 ttatcccacg caatggtgtc gaccactggg acgcatacaa gggcgaaaga gttgtcctat
1621 gggacgacta tggaatgagc aaccccatcc atgatgccct caggttgcag gagcttgctg
1681 acacttgccc cctcacgcta aattgtgaca gaattgagaa caaagggaaa gtctttgaca
1741 gtgatgccat aattatcacc accaatctgg ccaacccagc accactggat tatgtcaact
1801 ttgaagcgtg ctcgagacgc attgatttcc tcgtgtacgc agaagcccct gaggtggaga
1861 aggcaaagcg cgacttccca ggtcaacctg acatgtggaa gaacgctttc agttctgact
1921 tctcacacat gaaactgtca ttggctccac aaggtggttt tgacaagaac ggcaacaccc
1981 cgcatggaaa aggagtcatg aagaccctca ccactggctc cctcatcgcc cgagcatcag
2041 ggttacttca tgagaggcta gatgaatatg aactacaagg cccagccctc accactttca
2101 actttgaccg caacaagata cttgctttta gacagcttgc tgctgaaaac aagtatgggc
2161 tgatggacac aatgagagtt ggaaaacagc tcaaggatgt caagaccatg tcagacctca
2221 aacaagcact caagaacatc gcgatcaaga agtgccagat agtgtacaat ggtggcacct
2281 acacacttga ggctgatggc aagggtagtg tgaaagttga caaagtgcaa agtgccactg
2341 tgcagaccaa caatgaacta gccggtgccc tacaccacct aaggtgcgct agaatcagat
2401 actatgttaa gtgcgcccag gaggcactgt attccatcat ccaaatcgct ggggctgcat
2461 tcgtcaccac gcgcatcgct aagcgcatga atatacagaa tctctggtcc aagccacagg
2521 tggaagacac agaagagata gtcaacaaag atggttgcct aaaacccaaa gatgatgaag
2581 agtttgtcgt ctcatccgac gacatcaaaa ctgagggcaa gaaagggaag aacaagtccg
2641 gccgtggcaa gaagcacaca gccttttcaa gtaaagggct cagtgatgag gagtacgatg
2701 agtacaagag gatcagagaa gaaaggaatg gtaagtactc catagaagag taccttcagg
2761 acagagacag gtactacgag gaggtggcca ttgccagggc aaccgaagag gacttctgtg
2821 aagaagaaga ggccaaaatc cggcagagaa ttttcagacc aacaaggaaa caacgtaaag
2881 aagagagggc ctctctcggc ttggtcacag gctctgaaat caggaagaga aacccagaag
2941 acttcaaacc caagggaaag ttgtgggctg atgatgacag aagtgttgac tacaatgaga
3001 aactcaactt tgaggcccca ccaagcatct ggtcgcggat agtcaacttt ggttcaggct
3061 ggggcttctg ggtctctccc agtctgttta taacatcaac ccatgtcata ccccaaggtg
3121 caaaagagtt cttcggagtc cctattaagc aaatccagat acacaagtca ggtgaattct
3181 gccggttgag attcccaagg ccaatcagaa ctgatgtgac gggcatgatt ctagaagaag
3241 gtgcgcccga gggaaccgtg gtcacactgc tcatcaagag accaactgga gagctcatgc
3301 ctctggcagc cagaatgggg acccatgcaa ccatgaaaat ccaggggcgc acagttggag
3361 ggcaaatggg tatgctcctg acaggatcca acgccaagag tatggaccta ggcacaacac
3421 caggcgactg cggatgcccc tacatctaca agagggggaa tgactacgtg gtcataggag
3481 tccatacggc cgctgcccgt ggaggaaaca ctgtcatatg tgccacccag gggagtgagg
3541 gagaagccac acttgaagga ggtgacagta aagggacata ctgtggcgca ccaatcttgg
3601 gcccagggag cgctccgaag ctcagtgcca agactaagtt ttggagatca tccacaacac
3661 cactcccacc tggcacctac gaaccagcct acctcggtgg caaagaccct agagtcaaag
3721 gtggcccttc attgcaacaa gttatgaggg accagctgaa gccattcaca gaacccagag
3781 gcaaaccacc aagaccaaat gtgttggaag ctgccaagaa aaccatcatc aatgtccttg
3841 agcaaacaat tgatccaccc caaaaatggt catttgcgca agcttgcgca tcccttgaca
3901 aaaccacctc cagcggccac ccgcaccaca tgcggaaaaa cgactgttgg aatggggagt
3961 ccttcacagg aaaattggct gatcaggcct ccaaggccaa cctaatgttt gaagagggaa
4021 agaacatgac tccagtctac acaggtgcac ttaaagatga gttggtaaag accgataaag
4081 tttatggtaa aatcaagaag aggcttctgt ggggttcaga tctggcgacc atgatacggt
4141 gcgcccgagc ttttggaggc cttatggatg aactcaaggc gcactgtgtc acacttcctg
4201 tcagagttgg tatgaacatg aatgaggatg gccccatcat ctttgagaag cactccagat
4261 atagatatca ctatgatgct gattattccc ggtgggactc aacacaacaa agggatgtgc
4321 tagcagcagc actagaaatc atggttaagt tctctccaga accacacctg gcccagatag
4381 ttgcagaaga cctcctttcc cctagcgtga tggatgtagg tgactttcaa atatcaataa
4441 gtgagggtct cccctctggg gtaccttgta cctcccagtg gaattccatc gcccactggc
4501 tcctcactct gtgtgcactc tctgaagtca cagacctgtc ccctgatatc attcaggcca
4561 actccctttt ctccttctat ggtgatgatg agattgtaag cacagacata aagttggacc
4621 cagagaagct gacagcaaaa ctcaaggagt acgggctgaa accaacccgc cccgacaaaa
4681 ctgaaggacc cctcgttatc tctgaagacc tggatggcct gacattcctc cggagaactg
4741 tgacccgtga tccagctggc tggtttggaa agttggaaca aagttcaatt ctcaggcaaa
4801 tgtactggac caggggtccc aatcatgaag atccatttga aacaatgata ccacactccc
4861 aaagacccat acaattgatg tccttgctgg gcgaggctgc actccacggc ccggcattct
4921 atagcaaaat tagcaaatta gtcattgcag agttgaagga aggtggcatg gatttttacg
4981 tgcccagaca agagccaatg ttcagatgga tgagattctc agatctgagc acgtgggagg
5041 gcgatcgcaa tctggctccc agttttgtga atgaagatgg cgtcgagtga cgccaaccca
5101 tctgatgggt ccacagccag cctcgtccca gaggtcaaca atgaggttat ggctctggag
5161 cccgttgttg gtgccgccat tgcggcacct gtagcgggcc aacaaaatgt aattgacccc
5221 tggattagaa ataattttgt acaagcccct ggtggagagt ttacagtatc ccccagaaac
5281 gctccaggtg aagtactatg gagcgcgccc ttgggccctg atctaaatcc ctacctatcc
5341 catttggcca gaatgtacaa tggttatgca ggtggttttg aagtgcaggt aattctcgcg
5401 gggaacgcgt tcaccgccgg gaagatcata tttgcagcgg tcccaccaaa ttttccaact
5461 gaatgtttga gccccagcca ggtcactatg ctcccccata taatagtaga tgttaggcaa
5521 ttagaacctg tgttgattcc cttacccgat gttaggaata atttctatca ttacaatcaa
5581 tcaaatgact ccaccattaa gttgatagca atgttgtata caccacttag ggctaataat
5641 gctggggatg atgtcttcac agtttcttgc cgagttctca cgagaccatc ccccgatttt
5701 gatttcatat ttttagtgcc acccacagtt gagtcaagaa ctaaaccatt ctctgtccca
5761 gttttaactg ttgaggagat gaccaattca agattcccca ttcctttgga aaagttgttc
5821 acgggtccca gcagtgcctt tgttgtccaa ccacaaaacg gtaggtgctc gactgatggc
5881 gtgctcctag gcaccaccca gctgtctcct gtcaacatct gcaccttcag aggagatgtc
5941 acccagatca caggtagtag tacctacaca atgaatttgg cttctcaaaa ttggagcaac
6001 tatgacccaa cagaagaaat cccagcccct ctaggaactc cagattttgt ggggaagatt
6061 caaggcgtgc tcacccaaac cacaaggaca gttggctcaa cacgcggcca caaagccaca
6121 gtgcgcactg ggagcgccga ctttgctcca aaactgggta gagttcgatt tgaaactgac
6181 acaaacaatg attttgaagt taaccaaaat acaaagttca ccccagttgg tgtcatccaa
6241 gatggtgaca ccgcccaccg aaatgaaccc caacagtggg tgctcccaag ttactcaggc
6301 agaaacactc ctaatgtaca tctggccccc gctgtagccc ccacttttcc gggtgagcaa
6361 cttctcttct tcagatccac catgcccgga tgcagcgggt accccaacat ggatttggac
6421 tgtctgctcc cccaggaatg ggtgcagtac ttctaccaag aggcagcccc agcacaatct
6481 gatgtggctc tgctaagatt tgtgaatcca gacacaggta gggttttgtt tgagtgtaag
6541 cttcataaat caggctatat tacagtggct cacactggcc aacatgattt ggttatcccc
6601 cccaatggtt attttaggtt tgattcctgg gtcaatcagt tttacacgct tgcccccatg
6661 ggaaatggaa cggggcgtag acgtgcacca taatggctgg agctttcttt gctggattgg
6721 catctgatgt ccttggctct ggacttggtt cccttatcaa tgctggggct ggggccatca
6781 accaaaaagt tgagtttgaa aataacagaa aattgcaaca agcatccttc caatttagca
6841 gcaatctaca acaggcttcc tttcaacatg acaaagagat gctccaagca caaattgagg
6901 ccaccaaaag gctacaacag gaaatgatga aagtcaaaca ggcaatgctc ctagagggtg
6961 ggttttctga gacagatgca gcccgcgggg caatcaacgc ccccatgaca aaagttttgg
7021 actggagcgg gacaaggtac tgggctcccg atgctaggac tacaacatac aatgcaggcc
7081 gcttttccac ccctcaacca tcgggggcac tgccaggaag agctaatctt agggatgctg
7141 tccctgctcg gggttcctcc agaaagtctt ctaattcttc cactgctact tctgtgtact
7201 caaatcaaac tacttcaacg agacttggtt ctacagctgg ttctggtacc agtgtctcga
7261 gcttcccgac aactgcaagg actaggagct gggttgagga tcaaagtagg aatttgtcac
7321 ctttcatgag tggggcccac aacatatcgt ttgtcacccc accatctagc agatcctcta
7381 gccaaggcac agtctcaacc gtgcctaaag agattttgga ctcctggact ggcgctttca
7441 acacgcgcag gcagccactc ttcgctcaca ttcgtaagcg aggggagtca cgggcgt
//