Typing tool
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Typing tool
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Complete norovirus genomes
| MF140640 | GII.4 Sydney | |
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| GII.P31 |
ORF1: 1..5085
ORF2: 5066..6688
ORF3: 6688..7487
LOCUS MF140640 7487 bp RNA linear VRL 24-OCT-2017
DEFINITION Norovirus GII strain
Norovirus/GII/Hu/NL/2014/GII.Pe-GII.4/Rotterdam/E7800017_p10_d508
ORF1 gene, partial cds; ORF2 gene, complete cds; and ORF3 gene,
partial cds.
ACCESSION MF140640
VERSION MF140640.1
KEYWORDS .
SOURCE Norovirus GII
ORGANISM Norovirus GII
Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes;
Picornavirales; Caliciviridae; Norovirus; Norwalk virus.
REFERENCE 1 (bases 1 to 7487)
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 7487)
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..7487
/organism="Norovirus GII"
/mol_type="genomic RNA"
/strain="Norovirus/GII/Hu/NL/2014/GII.Pe-
GII.4/Rotterdam/E7800017_p10_d508"
/host="Homo sapiens"
/db_xref="taxon:122929"
/country="Netherlands"
/collection_date="16-Jun-2014"
/note="genotype: GII.Pe-GII.4"
CDS <1..5085
/codon_start=1
/product="ORF1"
/protein_id="ATN23616.1"
/translation="NDASAAAVANSNNDIAKSSSDGVFSNMAVTFKRALGARPKQPPP
KEIPPRPPRPPTPELVKKIPPPPPNGEDELVVSYSAKDGVSGLPELTTVRQPEETNTA
FSVPPLNQRESRDAKEPLTGTIIEMWDGEIYHYGLYVERGLILGVHKPPAAISLAKVE
LAPLSLFWRPVYTPQYLISPDTLRRLHGESFPYTAFDNNCYAFCCWVLDLNDSWLSRR
MIQRTTGFFRPYQDWNRKPLPTMDDSKLKKVANIFLCTLSSLFTRPIKDIIGKLKPLN
ILNILATCDWTFAGIVESLILLAELFGVFWTPPDVSAMIAPLLGDYELQGPEDLAVEL
VPIVMGGIGLVLGFTKEKIGKMLSSAASTLRACKDLGAYGLEILKLVMKWFFPKKEEA
NELAMVRSIEDAVLDLEAIENNHMTTLLKDKDSLATYMRTLDLEEEKARKLSTKSASP
DIVGTINSLLARIAAARSLVHRAKEELSSRLRPVVVMISGKPGIGKTHFAREVANKVA
ASLTGDQRVGLIPRNGVDHWDAYKGERVVLWDDYGMSNPIHDALRLQELADTCPLTLN
CDRIENKGKVFDSDAIIITTNLANPAPLDYVNFEACSRRIDFLVYAEAPEVEKAKRDF
PGQPDMWKNAFSPDFSHIKLSLAPQGGFDKNGNTPHGKGVMKTLTTGSLIARASGLLH
ERLDEYELQGPALTTFNFDRNKILAFRQLAAENKYGLMDTMRVGKQLKDVKTMSDLKQ
ALKNIAIKKCQIVYNGGTYTLEADGKGSVKVDKVQSATVQTNNELAGALHHLRCARIR
YYVKCVQEALYSIIQIAGAAFVTTRIAKRMNIQNLWSKPQVEDTEEMANKDGCLKPKD
DEEFVVSSDDIKTEGKKGKNKSGRGKKHTAFSSKGLSDEEYDEYKRIREERNGKYSIE
EYLQDRDRYYEEVAIARATEEDFCEEEEAKIRQRIFRPTRKQRKEERASLGLVTGSEI
RKRNPEDFKPKGKLWADDDRSVDYNEKLNFEAPPSIWSRIVNFGSGWGFWVSPSLFIT
STHVIPQGAKEFFGVPIKQIQIHKSGEFCRLRFPKPIRTDVTGMILEEGAPEGTVATL
LIKRPTGELMPLAARMGTHATMKIQGRTVGGQMGMLLTGSNAKSMDLGTTPGDCGCPY
IYKRGNDYVVIGVHTAAARGGNTVICATQGSEGEATLEGGDSKGTYCGAPILGPGSAP
KLSAKTKFWRSSTTPLPPGTYEPAYLGGKDPRVKGGPSLQQVMRDQLKPFTEPRGKPP
RPNVLEAAKKTIINVLEQTIDPPQKWSFAQACASLDKTTSSGHPHHMRKNDCWNGESF
TGKLADQASKANLMFEEGKNMTPVYTGALKDELVKTDKVYGKVKKRLLWGSDLATMIR
CARAFGGLMDELKAHCVTLPVRVGMNMNEDGPIIFEKHSRYRYHYDADYSRWDSTQQR
DVLAAALEIMVKFSPEPHLAQIVAEDLLSPSVMDVGDFQISISEGLPSGVPCTSQWNS
IAHWLLTLCALSEVTDLSPDIIQANSLFSFYGDDEIVSTDIKLDPEKLTAKLKEYGLK
PTRPDKTEGPLVISEDLDGLTFLRRTVTRDPAGWFGKLEQSSILRQMYWTRGPNHEDP
FETMIPHSQRPIQLMSLLGEAALHGPAFYSKISKLVIAELKEGGMDFYVPRQEPMFRW
MRFSDPITWEGDRNLAPSFVNEDGVE"
CDS 5066..6688
/codon_start=1
/product="ORF2"
/protein_id="ATN23617.1"
/translation="MKMASSDANPSDGSTVNLVPEVNNEVMALEPVVGAAIAAPVAGQ
QNVIDPWIRNNFVQAPGGEFTVSPRNAPGEILWSAPLGPDLNPYLSHLARMYNGYAGG
FEVQVILAGNAFTAGKVIFAAVPPNFPTEGLSPSQVTMFPHIVVDVRQLEPVLIPLPD
VRNNFYHYNQSNDPTIKLIAMLYTPLRANNAGDDVFTVSCRVLTRPSPDFDFIFLVPP
TVESRTKPFSVPVLTVEEMTNSRFPIPLEKLFTGPSSAFVVQPQNGRCSTDGVLLGTT
QLSPVNICTFRGDVTQITGSSTYTMNLASQNWSNYDPTEEIPAPLGTPDFVGKIQGVL
TQTTRTVGSTRGHKATVRTGSADFTPKLGRVRFETDTNNDFEVNQNTKFTPVGVIQDG
DTAHRNEPQQWVLPSYSGRNTPNVHLAPAVAPTFPGEQLLFFRSTMPGCSGYPNMDLD
CLLPQEWVQYFYQEAAPAQSDVALLRFVNPDTGRVLFECKLHKSGYVTVAHTGQHDLV
IPPNGYFRFDSWVNQFYTLAPMGNGTGRRRAL"
CDS 6688..>7487
/codon_start=1
/product="ORF3"
/protein_id="ATN23618.1"
/translation="MAGAFFAGLASDVLGSGLGSLINAGAGAINQKVEFENNRKLQQA
SFQFSSNLQQASFQHDKEMLQAQIEATKRLQQEMMKVKQAMLLEGGFSETDAARGAIN
APMTKVLDWSGTRYWAPDARTTTYNAGRFSTPQPSGALPGRANLRDAVPARGSSSKSS
NSSTATSVYSNQTTSTRLGSTAGSGTSVSSFPSTARTRSWVEDQSRNLSPFMSGAHNI
SFVTPPSSRSSSQGTVSTVPKEILDSWTGAFNTRRQPLFAHIRKRGESR"
ORIGIN
1 aacgacgctt ccgctgccgc tgttgccaac agcaacaacg acatcgcaaa atcttcaagt
61 gacggtgtgt tttctaacat ggctgtcact tttaagcggg ccctcggggc gcggcctaaa
121 cagccgcccc cgaaggaaat accacccaga cccccgcgac cacccacacc agaattggtc
181 aaaaagatcc ctcctccccc acccaacggg gaggatgaac tagtggtctc ctacagcgcc
241 aaagatggcg tttccggact gcctgagctc accactgtca gacaaccgga agaaaccaac
301 acggcgttca gtgtcccccc acttaaccaa agggagagca gggacgccaa ggagccacta
361 actggaacaa tcattgaaat gtgggatgga gaaatctacc attacggcct gtacgtggaa
421 cgaggtctta tacttggtgt gcacaagcca ccggcagcca ttagccttgc caaggtcgag
481 ctagcaccgc tctctttgtt ctggagacct gtatacaccc cccagtatct catctctcca
541 gacactctta ggagattaca tggagagtca ttcccctaca ctgcatttga caacaattgc
601 tacgcctttt gttgttgggt attagaccta aacgactcat ggctaagcag gagaatgatt
661 cagagaacaa caggcttctt caggccgtac caggattgga acaggaaacc cctccccact
721 atggatgatt ccaaattaaa gaaggtagcc aacatattct tgtgcacttt gtcttcacta
781 ttcaccagac ccattaagga cataataggg aagttgaaac ctcttaacat ccttaacatt
841 ctggctacat gtgattggac cttcgcaggc atagtggaat ccttaatact cttggcagaa
901 ctctttggag ttttctggac acccccagat gtgtctgcga tgatcgcccc cttgctaggt
961 gattatgaac tgcaaggacc tgaggacctt gcagtggaac tggtcccaat agtgatgggg
1021 gggataggtt tggtgctagg atttaccaaa gagaaaatcg gaaagatgct atcatccgct
1081 gcatccactt taagagcttg taaagacctt ggtgcatacg gactggaaat cttaaaattg
1141 gtcatgaagt ggttcttccc aaagaaagag gaagcaaatg aactggctat ggtgagatcc
1201 atcgaggatg cagtactaga cctcgaggca attgaaaaca accacatgac caccctactc
1261 aaagacaaag acagcttggc aacctacatg agaacccttg accttgagga ggagaaagcc
1321 agaaaactct caaccaaatc tgcttcaccc gatattgtgg gcacaattaa ctctcttctg
1381 gcaagaatcg ctgctgcacg ctccctagtg catcgggcga aagaagagct ctccagcagg
1441 ctgagacctg tcgtagtgat gatatcggga aagccaggga tagggaaaac tcactttgcc
1501 agggaggtgg ccaacaaggt cgcggcctcc ctcacagggg accagcgtgt gggtcttatc
1561 ccacgcaatg gcgtcgacca ctgggacgca tacaagggcg aaagagttgt cctatgggac
1621 gactatggaa tgagcaaccc catccatgat gccctcaggt tgcaggagct tgctgacact
1681 tgccccctca cgctaaattg tgacagaatt gagaacaaag ggaaagtctt tgacagtgat
1741 gccataatta tcaccaccaa tctggccaac ccagcaccac tggattatgt caactttgaa
1801 gcgtgctcga gacgcattga tttcctcgtg tacgcagaag cccctgaggt ggagaaggca
1861 aagcgcgact tcccaggtca acctgacatg tggaagaacg ctttcagtcc tgacttctca
1921 cacataaaac tgtcattggc tccacagggt ggttttgaca agaacggcaa caccccgcat
1981 ggaaaagggg tcatgaagac cctcaccact ggctccctca tcgcccgagc atcagggtta
2041 ctccatgaga ggctagatga atatgaactg caaggcccag ccctcaccac tttcaacttt
2101 gaccgcaaca agatacttgc ttttagacag cttgctgctg aaaacaagta tgggctgatg
2161 gacacaatga gagttggaaa acagctcaag gatgtcaaga ccatgtcaga cctcaaacaa
2221 gcactcaaga acatcgcgat caagaagtgc cagatagtgt acaatggtgg cacctacaca
2281 cttgaggctg atggcaaggg tagtgtgaaa gttgacaaag tgcaaagtgc cactgtgcag
2341 accaacaatg aactagccgg tgccctacac cacctaaggt gcgctagaat cagatactat
2401 gttaagtgcg tccaggaggc actgtattcc atcatccaaa tcgctggggc tgcattcgtc
2461 accacgcgca tcgctaagcg catgaatata cagaatctct ggtccaagcc acaggtggaa
2521 gacacagaag agatggccaa caaagatggt tgcctaaaac ccaaagatga tgaagagttt
2581 gtcgtctcat ccgacgacat caaaactgag ggcaagaaag ggaagaacaa gtccggccgt
2641 ggcaagaagc acacagcctt ttcaagtaaa gggctcagtg atgaggagta cgatgagtac
2701 aagagaatca gagaagaaag gaatggtaag tactccatag aagagtacct tcaggacaga
2761 gacaggtact acgaggaggt ggccattgcc agggcaaccg aagaggactt ctgtgaagaa
2821 gaagaggcca aaatccggca gagaattttc agaccaacaa ggaaacaacg caaagaagag
2881 agggcctctc tcggcttggt cacaggctct gaaatcagga agagaaaccc agaagacttc
2941 aaacccaagg gaaagttgtg ggctgatgat gacagaagtg ttgactacaa tgagaaactc
3001 aactttgagg ccccaccaag catctggtcg cggatagtca actttggttc aggctggggc
3061 ttctgggtct ctcccagtct gtttataaca tcaacccatg tcatacccca aggtgcaaaa
3121 gagttcttcg gagtccctat taagcaaatc cagatacaca agtcaggtga attctgccgg
3181 ttgagattcc caaagccaat cagaactgat gtgacgggca tgattctaga agaaggtgcg
3241 cccgagggga ccgtggccac actgctcatc aagagaccaa ctggagagct catgcctctg
3301 gcagccagaa tggggaccca tgcaaccatg aaaatccagg ggcgcacagt tggggggcaa
3361 atgggtatgc tcctgacagg atccaacgcc aagagtatgg acctaggcac aacaccaggc
3421 gactgcggat gcccctacat ctacaagagg gggaatgact acgtggtcat aggagtccat
3481 acggccgctg cccgtggagg aaacactgtc atatgtgcca cccagggaag tgagggagaa
3541 gccacacttg aaggaggtga cagtaaaggg acatactgtg gcgcaccaat cttgggccca
3601 gggagcgctc cgaagctcag tgccaagact aagttttgga ggtcatccac aacaccactc
3661 ccacctggca cctacgaacc agcctacctc ggtggcaaag accctagagt caaaggtggc
3721 ccttcattgc aacaagttat gagggaccag ctgaagccat tcacagaacc cagaggcaaa
3781 ccaccaagac caaatgtgtt ggaagctgcc aagaaaacca tcatcaatgt ccttgagcaa
3841 acaattgatc caccccaaaa atggtcattt gcgcaagctt gcgcatccct tgacaaaacc
3901 acctccagcg gccacccgca ccacatgcgg aaaaacgact gttggaatgg ggagtccttc
3961 acaggaaaat tggctgacca ggcctccaag gccaacctaa tgtttgaaga gggaaagaac
4021 atgactccag tctacacagg tgcacttaaa gatgagttgg taaagaccga taaagtttat
4081 ggtaaggtca agaagaggct tctgtggggt tcagatctgg cgaccatgat acggtgcgcc
4141 cgagcttttg gaggccttat ggatgaactc aaggcgcact gtgtcacact tcctgtcaga
4201 gttggtatga acatgaatga ggatggcccc atcatctttg agaagcactc cagatataga
4261 tatcactatg atgctgatta ttcccggtgg gactcaacac aacaaaggga tgtgctagca
4321 gcagcactag aaatcatggt taagttctct ccagaaccac acctggccca gatagttgca
4381 gaagacctcc tttcccctag cgtgatggat gtaggtgact ttcaaatatc aataagtgag
4441 ggtctcccct ctggggtacc ttgtacctcc cagtggaatt ccatcgccca ctggctcctc
4501 actctgtgtg cactctctga agtcacggac ctgtcccctg atatcattca ggccaactcc
4561 cttttctcct tctatggtga tgatgagatt gtaagcacag acataaagtt ggacccagag
4621 aagctgacag caaaactcaa ggagtacggg ctgaaaccaa cccgccccga caaaactgaa
4681 ggacccctcg ttatctctga agacctggat ggcctgacat tcctccggag aactgtgacc
4741 cgtgatccag ctggctggtt tggaaagttg gaacaaagtt caattctcag gcaaatgtac
4801 tggaccaggg gtcccaacca tgaagatcca tttgaaacaa tgataccaca ctcccaaaga
4861 cccatacaat tgatgtcctt gctgggcgag gctgcactcc acggcccggc attctatagc
4921 aaaattagca aattagtcat tgcagagttg aaggaaggtg gcatggattt ttacgtaccc
4981 agacaagagc caatgttcag atggatgaga ttctcagatc cgatcacgtg ggagggcgat
5041 cgcaatctgg ctcccagttt tgtgaatgaa gatggcgtcg agtgacgcca acccatctga
5101 tgggtccaca gtcaacctcg tcccagaggt caacaatgag gttatggctc tggagcccgt
5161 tgttggtgcc gccattgcgg cacctgtagc gggccaacaa aatgtaattg acccctggat
5221 tagaaataat tttgtacaag cccctggtgg agagtttaca gtatccccca gaaacgctcc
5281 aggtgaaata ctatggagcg cgcccttggg ccctgatcta aatccctacc tatcccattt
5341 ggccagaatg tacaatggtt atgcaggtgg ttttgaagtg caggtaattc tcgcggggaa
5401 cgcgttcacc gccgggaagg tcatatttgc agcagtccca ccaaattttc caactgaagg
5461 cttgagcccc agccaggtca ctatgttccc ccatatagta gtagatgtta ggcaactaga
5521 acctgtgttg attcccttac ccgatgttag gaataatttc tatcattaca atcaatcaaa
5581 tgaccccacc attaagttga tagcaatgtt gtatacacca cttagggcta ataatgctgg
5641 ggatgatgtc ttcacagttt cttgccgagt tctcacgaga ccatcccccg attttgactt
5701 catatttcta gtgccaccca cagttgagtc aagaactaaa ccattctctg tcccagtttt
5761 aactgttgag gagatgacca attcaagatt ccccattcct ttggaaaagt tgttcacggg
5821 tcccagcagt gcctttgttg tccaaccaca aaacggtagg tgctcgactg atggcgtgct
5881 cctaggcacc acccagctgt ctcctgtcaa catctgcacc ttcagaggag atgtcaccca
5941 gatcacaggt agtagtacct acacaatgaa tttggcttct caaaattgga gcaactatga
6001 cccaacagaa gaaattccag cccctctggg aactccagat tttgtgggga agattcaagg
6061 cgtgctcacc caaaccacaa ggacagttgg ctcaacacgc ggccacaaag ccacagtgcg
6121 cactgggagc gccgacttta ctccaaaact gggtagagtt cgatttgaaa ctgacacaaa
6181 caatgatttt gaagttaacc aaaatacaaa gttcacccca gttggtgtca tccaagatgg
6241 tgacaccgcc caccgaaatg aaccccaaca gtgggtgctc ccaagttact caggcagaaa
6301 cactcctaat gtacacctgg cccccgctgt agcccccact tttccgggtg agcaacttct
6361 cttcttcaga tccaccatgc ccggatgcag cgggtacccc aacatggatt tggactgtct
6421 gctcccccag gaatgggtgc agtacttcta ccaagaggca gccccagcac aatctgatgt
6481 ggctctgctg agatttgtga atccagacac aggtagggtt ttgtttgagt gtaagcttca
6541 taaatcaggc tatgttacag tggctcacac tggccaacat gatttggtta tcccccccaa
6601 tggttatttt aggtttgatt cctgggtcaa ccagttttac acgcttgccc ccatgggaaa
6661 tggaacgggg cgtagacgtg cactataatg gctggagctt tctttgctgg attggcatct
6721 gatgtccttg gctctggact tggttccctt atcaatgctg gggctggggc catcaaccaa
6781 aaagttgagt ttgaaaataa cagaaaattg caacaagcat ccttccaatt tagcagcaat
6841 ctacaacagg cttcctttca acatgacaaa gagatgctcc aagcacaaat tgaggccacc
6901 aaaaggctac aacaggaaat gatgaaagtc aaacaggcaa tgctcctaga gggtgggttt
6961 tctgagacag atgcagcccg tggggcaatc aacgccccca tgacaaaagt tttggactgg
7021 agtgggacaa ggtactgggc tcccgatgct aggaccacaa catacaatgc aggccgcttt
7081 tccacccctc aaccatcggg ggcactgcca ggaagagcta atcttaggga tgctgtccct
7141 gctcggggtt cctccagtaa gtcttctaat tcttctactg ctacttctgt gtactcaaat
7201 caaactactt caacgagact tggttctaca gctggttctg gtaccagtgt ctcgagcttc
7261 ccgtcaactg caaggactag gagctgggtt gaggatcaaa gtaggaattt gtcacctttc
7321 atgagtgggg cccacaacat atcgtttgtc accccaccat ctagcagatc ctctagccaa
7381 ggcacagtct caaccgtgcc taaagagatt ttggactcct ggactggcgc tttcaacacg
7441 cgcaggcagc cactcttcgc tcacattcgt aagcgagggg agtcacg
//