Typing tool
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Typing tool
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Complete norovirus genomes
| MF140674 | GII.4 Sydney | |
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| GII.P31 |
ORF1: 1..5080
ORF2: 5061..6683
ORF3: 6683..7485
LOCUS MF140674 7485 bp RNA linear VRL 24-OCT-2017
DEFINITION Norovirus GII strain
Norovirus/GII/Hu/NL/2013/GII.Pe-GII.4/Rotterdam/E1300308_p4_d0 ORF1
gene, partial cds; ORF2 gene, complete cds; and ORF3 gene, partial
cds.
ACCESSION MF140674
VERSION MF140674.1
KEYWORDS .
SOURCE Norovirus GII
ORGANISM Norovirus GII
Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes;
Picornavirales; Caliciviridae; Norovirus; Norovirus norwalkense.
REFERENCE 1 (bases 1 to 7485)
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 7485)
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..7485
/organism="Norovirus GII"
/mol_type="genomic RNA"
/strain="Norovirus/GII/Hu/NL/2013/GII.Pe-
GII.4/Rotterdam/E1300308_p4_d0"
/host="Homo sapiens"
/db_xref="taxon:122929"
/geo_loc_name="Netherlands"
/collection_date="12-Apr-2013"
/note="genotype: GII.Pe-GII.4"
CDS <1..5080
/codon_start=2
/product="ORF1"
/protein_id="ATN23718.1"
/translation="ASAAAVANSNNDIAKSSSDGVFSNMAVTFKRALGARPKQPPPKE
IPPRPPRPPTPELVKKIPPPPPNGEDELVVSYSAKDGVSGLPELTTVRQPEETNTAFS
VPPLNQRESRDAKEPLTGTIIEMWDGEIYHYGLYVERGLILGVHKPPAAISLAKVELA
PLSLFWRPVYTPQYLISPDTLRRLHGESFPYTAFDNNCYAFCCWVLDLNDSWLSRRMI
QRTTGFFRPYQDWNRKPLPTMDDSKLKKVANIFLCTLSSLFTRPIKDIIGKLRPLNIL
NILATCDWTFAGIVESLILLAELFGVFWTPPDVSAMIAPLLGDYELQGPEDLAVELVP
IVMGGIGLVLGFTKEKIGKMLSSAASTLRACKDLGAYGLEILKLVMKWFFPKKEEANE
LAMVRSIEDAVLDLEAIENNHMTTLLKDKDSLATYMRTLDFEEEKARKLSTKSASPDI
VGTINSLLARIAAARSLVHRAKEELSSRPRPVVVMISGRPGIGKTHLARELAKKIAAS
LTGDQRVGLIPRNGVDHWDAYKGERVVLWDDYGMSNPIHDALRLQELADTCPLTLNCD
RIENKGKVFDSDAIIITTNLANPAPLDYVNFEACSRRIDFLVYAEAPEVEKAKRDFPG
QPDMWKNAFSPDFSHIKLSLAPQGGFDKNGNTPHGKGVMKTLTTGSLIARASGLLHER
LDEYELQGPALTTFNFDRNKILAFRQLAAENKYGLMDTMRVGKQLKDVKTMSDLKQAL
KNIAIKKCQIVYNGGTYTLEADGKGSVKVDKVQNATVQTNNELAGALHHLRCARIRYY
VKCVQEALYSIIQIAGAAFVTTRIAKRMNIQNLWSKPQVEDTEEMANKDGCLKPKDDE
EFVVSSDDIKTEGKKGKNKSGRGKKHTAFSSKGLSDEEYDEYKRIREERNGKYSIEEY
LQDRDRYYEEVAIARATEEDFCEEEEAKIRQRIFRPTRKQRKEERASLGLVTGSEIRK
RSPEDFKPKGKLWADDDRSVDYNEKLNFEAPPSIWSRIVNFGSGWGFWVSPSLFITST
HVIPQGAKEFFGVPIKQIQIHKSGEFCRLRFPKPIRTDVTGMILEEGAPEGTVVTLLI
KRPTGELMPLAARMGTHATMKIQGRTVGGQMGMLLTGSNAKSMDLGTTPGDCGCPYIY
KRGNDYVVIGVHTAAARGGNTVICATQGSEGEATLEGGDSKGTYCGAPILGPGSAPKL
STKTKFWRSSTTPLPPGTYEPAYLGGKDPRVKGGPSLQQVMRDQLKPFTEPRGKPPRP
NVLEAAKKTIINVLEQTIDPPQKWSFAQACASLDKTTSSGHPHHMRKNDCWNGESFTG
KLADQASKANLMFEEGKNMTPVYTGALKDELVKTDKVYGKVKKRLLWGSDLATMIRCA
RAFGGLMDELKAHCVTLPVRVGMNMNEDGPIIFEKHSRYRYHYDADYSRWDSTQQRDV
LAAALEIMVKFSPEPHLAQIVAEDLLSPSVMDVGDFQISISEGLPSGVPCTSQWNSIA
HWLLTLCALSEVTDLSPDIIQANSLFSFYGDDEIVSTDIKLDPEKLTAKLKEYGLKPT
RPDKTEGPLVISEDLDGLTFLRRTVTRDPAGWFGKLEQSSILRQMYWTRGPNHEDPFE
TMIPHSQRPIQLMSLLGEAALHGPAFYSKISKLVIAELKEGGMDFYVPRQEPMFRWMR
FSDLSTWEGDRNLAPSFVNEDGVE"
CDS 5061..6683
/codon_start=1
/product="ORF2"
/protein_id="ATN23719.1"
/translation="MKMASSDANPSDGSAANLVPEVNNEVMALEPVVGAAIAAPVAGQ
QNVIDPWIRNNFVQAPGGEFTVSPRNAPGEILWSAPLGPDLNPYLSHLARMYNGYAGG
FEVQVILAGNAFTAGKVIFAAVPPNFPTEGLSPSQVTMFPHIVVDVRQLEPVLIPLPD
VRNNFYHYNQSNDPTIKLIAMLYTPLRANNAGDDVFTVSCRVLTRPSPDFDFIFLVPP
TVESRTKPFSVPVLTVEEMTNSRFPIPLEKLFTGPSSAFVVQPQNGRCTTDGVLLGTT
QLSPVNICTFRGDVTHITGSRNYTMNLASQNWSNYDPTEEIPAPLGTPDFVGKIQGVL
TQTTRTDGSTRGHKATVYTGSADFAPKLGRVQFETDTDRDFEANQNTKFTPVGVIQDG
STTHRNEPQQWVLPSYSGRNTPNVHLAPAVAPTFPGEQLLFFRSTMPGCSGYPNMDLD
CLLPQEWVQYFYQEAAPAQSDVALLRFVNPDTGRVLFECKLHKSGYVTVAHTGQHDLV
IPPNGYFRFDSWVNQFYTLAPMGNGTGRRRAL"
CDS 6683..>7485
/codon_start=1
/product="ORF3"
/protein_id="ATN23720.1"
/translation="MAGAFFAGLASDVLGSGLGSLINAGAGAINQKVEFENNRKLQQA
SFQFNSNLQQASFQHDKEMLQAQIEATKRLQQEMMKVKQAMLLEGGFSETDAARGAIN
APMTKALDWSGTRYWAPDARTTTYNAGRFSTPQPSGALPGRANLRDAVPARGSSSKSS
NSSTATSVYSNQTTSTRLGSTAGSGTSVSSFPSTARTRSWVEDQSRNLSPFMRGAHNI
SFVTPPSSRSSSQGTVSTVPKEILDSWTGAFNTRRQPLFAHIRKRGESRA"
ORIGIN
1 cgcttccgct gccgctgttg ccaacagcaa caacgacatc gcaaaatctt caagtgacgg
61 tgtgttttct aacatggctg tcacttttaa gcgggccctc ggggcgcggc ctaaacagcc
121 gcccccgaag gaaataccac ccagaccccc gcgaccaccc acaccagaat tggtcaaaaa
181 gatccctcct cccccaccca acggggagga tgaactagtg gtctcttaca gcgccaaaga
241 tggcgtttcc ggactgcctg agctcaccac tgtcagacaa ccggaagaaa ccaacacggc
301 gttcagtgtc cccccactca accaaaggga gagcagggac gccaaggagc cactaactgg
361 aacaatcatt gaaatgtggg atggagaaat ctaccattac ggcctgtacg tggaacgagg
421 tcttatactt ggtgtgcaca agccaccggc agccattagc cttgccaagg tcgagctagc
481 accgctctct ttgttctgga gacctgtata caccccccag tatctcatct ctccagacac
541 tcttaggaga ttacatggag agtcattccc ctacactgca tttgacaaca attgctacgc
601 cttttgttgt tgggtattag acctaaacga ctcatggcta agcaggagaa tgattcagag
661 aacaacaggc ttcttcaggc cgtaccagga ttggaacagg aaacccctcc ccactatgga
721 tgattccaaa ttaaagaagg tagccaacat attcttgtgc actttgtctt cactattcac
781 cagacccatt aaggacataa tagggaagtt gagacctctt aacatcctta acattctggc
841 tacatgtgat tggaccttcg caggcatagt ggaatcctta atactcttgg cagaactctt
901 tggagttttc tggacacccc cagatgtgtc tgcgatgatc gcccccttgc taggtgatta
961 tgaactgcaa ggacctgagg accttgcagt ggaactggtc ccaatagtga tgggggggat
1021 aggtttggtg ctaggattta ccaaagagaa aatcggaaag atgctatcat ccgctgcatc
1081 cactttaaga gcttgtaaag accttggtgc atacggactg gaaatcttaa aattggtcat
1141 gaagtggttc ttcccaaaga aagaggaagc gaatgaactg gctatggtga gatccatcga
1201 ggatgcagta ctagacctcg aggcaattga aaacaaccac atgaccaccc tactcaaaga
1261 caaagacagc ttggcaacct acatgagaac ccttgacttt gaggaggaga aagccagaaa
1321 actctcaacc aaatctgctt cacccgatat tgtgggcaca atcaactctc ttctggcaag
1381 aatcgctgct gcacgctccc tagtgcatcg ggcgaaagaa gagctctcca gcaggccgag
1441 acctgtcgtt gtgatgatat cgggaagacc agggataggg aaaactcacc ttgccaggga
1501 gctggccaag aagatcgcgg cctccctcac aggggaccag cgtgtgggtc ttatcccacg
1561 caatggtgtc gaccactggg acgcatacaa gggcgaaaga gttgtcctat gggacgacta
1621 tggaatgagc aaccccatcc atgatgccct caggttgcag gagcttgctg acacttgccc
1681 cctcacgcta aattgtgaca gaattgagaa caaagggaaa gtctttgaca gtgatgccat
1741 aattatcacc accaacctgg ccaacccagc accactggat tatgtcaatt ttgaagcgtg
1801 ctcgagacgc attgatttcc tcgtgtacgc agaagcccct gaggtggaga aggcaaagcg
1861 cgacttccca ggtcaacctg acatgtggaa gaacgctttc agtcctgact tctcacacat
1921 aaaactgtca ttggctccac agggtggttt tgacaagaac ggcaacaccc cgcatggaaa
1981 aggggtcatg aagaccctca ccactggctc cctcatcgcc cgagcatcag ggttactcca
2041 tgagaggcta gatgaatatg aactgcaagg cccagccctc accactttca actttgaccg
2101 caacaagata cttgctttta gacagcttgc tgctgaaaac aagtatgggc tgatggacac
2161 aatgagagtt ggaaaacagc tcaaggatgt caagaccatg tcagacctca aacaagcact
2221 caagaacatc gcgatcaaga agtgccagat agtgtacaat ggtggcacct acacacttga
2281 ggctgatggc aagggtagtg tgaaagttga caaagtgcaa aatgccactg tgcagaccaa
2341 caatgaacta gccggtgccc tacaccacct aaggtgcgct agaatcagat actatgttaa
2401 gtgcgtccag gaggcactgt attccatcat tcaaatcgct ggggctgcat tcgtcaccac
2461 gcgcatcgct aagcgcatga atatacagaa tctctggtcc aagccacagg tggaagacac
2521 agaagagatg gccaacaaag atggttgcct aaaacccaaa gatgatgaag agtttgtcgt
2581 ctcatccgac gacatcaaaa ctgagggcaa gaaagggaag aacaagtccg gccgtggcaa
2641 gaagcacaca gccttttcaa gtaaagggct cagtgatgag gagtacgatg agtacaagag
2701 aatcagagaa gaaaggaatg gtaagtactc catagaagag taccttcagg acagagacag
2761 gtactacgag gaggtggcca ttgccagggc aaccgaagag gacttctgtg aagaagaaga
2821 ggccaaaatc cggcagagaa ttttcagacc aacaaggaaa caacgcaaag aagagagggc
2881 ctctctcggc ttggtcacag gctctgaaat caggaagaga agcccagaag acttcaaacc
2941 caagggaaag ctgtgggctg atgatgacag aagtgttgac tacaatgaga aactcaactt
3001 tgaggcccca ccaagcatct ggtcgcggat agtcaacttt ggttcaggct ggggcttctg
3061 ggtctccccc agtctgttta taacatcaac ccatgtcata ccccaaggtg caaaagagtt
3121 cttcggagtc cctatcaagc aaatccagat acacaagtca ggtgaattct gccggttgag
3181 attcccaaag ccaatcagaa ctgatgtgac gggcatgatt ctagaagaag gtgcgcccga
3241 ggggaccgtg gtcacactgc tcatcaagag accaactgga gagctcatgc ctctggcagc
3301 cagaatgggg acccatgcaa ccatgaaaat tcaggggcgc acagttggag ggcaaatggg
3361 tatgctcctg acaggatcca acgccaagag tatggaccta ggcacaacac caggcgactg
3421 cggctgcccc tacatctaca agagggggaa tgactacgtg gtcataggag tccatacggc
3481 cgctgcccgt ggaggaaaca ctgtcatatg tgccacccag gggagtgagg gagaagccac
3541 acttgaagga ggtgacagta aagggacata ctgtggcgca ccaatcttgg gcccagggag
3601 cgctccgaag ctcagtacca agactaagtt ttggagatca tccacaacac cactcccacc
3661 tggcacctac gaaccagcct acctcggtgg caaagaccct agagtcaaag gtggcccttc
3721 attgcaacaa gttatgaggg accagctgaa gccattcaca gaacccagag gcaaaccacc
3781 aagaccaaat gtgttggagg ctgccaagaa aaccatcatc aatgtccttg agcaaacaat
3841 tgatccaccc caaaaatggt catttgcgca agcttgcgca tcccttgaca agaccacctc
3901 cagcggccac ccgcaccaca tgcggaaaaa cgactgttgg aatggggagt ccttcacagg
3961 aaaattggct gatcaagcct ccaaggccaa cctaatgttt gaagagggaa agaacatgac
4021 tccagtctac acgggtgcac ttaaagatga gttggtaaag accgataaag tttatggtaa
4081 ggtcaagaag aggcttctgt ggggttcaga tctggcgacc atgatacggt gcgcccgagc
4141 ttttggaggc cttatggatg aactcaaggc acactgtgtc acacttcctg tcagagttgg
4201 tatgaacatg aatgaggatg gccccatcat ctttgagaag cactccagat atagatatca
4261 ttatgatgct gattattccc ggtgggactc aacacaacaa agggatgtgc tggcagcagc
4321 actagaaatc atggttaagt tctctccaga accacacctg gcccagatag ttgcagaaga
4381 cctcctttcc cctagcgtga tggatgtagg tgacttccaa atatcaataa gtgagggtct
4441 cccctctggg gtaccttgta cctcccagtg gaattccatc gcccactggc tcctcactct
4501 gtgtgcactc tctgaagtca cggacctgtc ccctgatatc attcaggcca actccctttt
4561 ctccttctat ggtgatgatg agattgtaag cacagacata aagttggacc cagagaagct
4621 gacagcaaag ctcaaggagt acgggctgaa accaacccgt cccgacaaaa ctgaaggacc
4681 ccttgttatc tctgaagacc tggatggcct gacattcctc cggagaactg tgacccgtga
4741 tccagctggc tggtttggaa aattggaaca aagttcaatt ctcaggcaaa tgtactggac
4801 caggggtccc aaccatgaag atccatttga aacaatgata ccacactccc aaagacccat
4861 acaattgatg tccttgctgg gcgaggctgc actccacggc ccggcattct atagcaaaat
4921 tagcaaatta gtcattgcag agttgaagga aggtggcatg gatttttacg tacccagaca
4981 agagccaatg ttcagatgga tgagattctc agatctgagc acgtgggagg gcgatcgcaa
5041 tctggctccc agttttgtga atgaagatgg cgtcgagtga cgccaaccca tctgatgggt
5101 ccgcagccaa cctcgtccca gaggtcaaca atgaggttat ggctctggag cccgttgttg
5161 gtgccgccat tgcggcacct gtagcgggcc aacaaaatgt aattgacccc tggattagaa
5221 ataattttgt acaagcccct ggtggagagt ttacagtatc ccctagaaac gctccaggtg
5281 aaatactatg gagcgcgccc ttgggccctg atctaaatcc ctacctatcc catttggcca
5341 gaatgtacaa tggttatgca ggtggttttg aagtgcaggt aattctcgcg gggaacgcgt
5401 tcaccgccgg gaaggtcata tttgcagcag tcccaccaaa ttttccaact gaaggcttga
5461 gccccagcca ggtcactatg ttcccccata tagtagtaga tgttaggcaa ctagaacctg
5521 tgttgattcc cttacccgat gttaggaata atttctacca ttacaatcaa tcaaatgacc
5581 ccaccattaa gttgatagca atgttgtata caccacttag ggctaataat gctggggatg
5641 atgtcttcac agtttcttgc cgagttctca cgagaccatc ccccgatttt gatttcatat
5701 ttctagtgcc acccacagtt gagtcaagaa ctaaaccatt ctctgtccca gttttaactg
5761 ttgaggagat gaccaattca agattcccca ttcctttgga aaagttgttc acgggtccca
5821 gcagtgcctt tgttgtccaa ccacaaaacg gtaggtgcac gactgatggc gtgctcctag
5881 gcaccaccca actgtctcct gtcaacatct gcaccttcag aggagatgtc acccatatca
5941 caggtagtcg taactacaca atgaatttgg cttctcaaaa ttggagcaat tatgacccaa
6001 cagaagaaat cccagcccct ctaggaactc cagattttgt ggggaagatt caaggcgtgc
6061 tcacccaaac cacaaggaca gatggctcaa cacgcggcca caaagccaca gtgtacactg
6121 ggagcgccga ctttgctcca aaactgggta gagttcaatt tgaaactgac acagaccgtg
6181 attttgaagc taaccaaaac acaaagttca ccccagttgg tgtcatccaa gatggtagca
6241 ccacccaccg aaatgaaccc caacagtggg tgctcccaag ttactcaggc agaaatactc
6301 ctaatgtgca tctggccccc gctgtagccc ccacttttcc gggtgagcaa cttctcttct
6361 tcagatccac catgcccgga tgcagcgggt accccaacat ggatttggac tgtctgctcc
6421 cccaggaatg ggtgcagtac ttttaccaag aggcagcccc agcacaatct gatgtggctc
6481 tgctgagatt tgtgaatcca gacacaggta gggttttgtt tgagtgtaag cttcataaat
6541 caggctatgt tacagtggct cacactggcc aacatgattt ggttatcccc cccaatggtt
6601 attttaggtt tgattcctgg gtcaaccagt tttacacgct tgcccccatg ggaaatggaa
6661 cggggcgtag acgtgcacta taatggctgg agctttcttt gctggattgg catctgatgt
6721 ccttggctct ggacttggtt cccttatcaa tgctggggct ggggccatca accaaaaagt
6781 tgagtttgaa aataacagaa aattgcaaca agcatccttc caatttaaca gcaatctaca
6841 acaggcttcc tttcaacatg acaaagagat gctccaagca caaattgagg ccaccaaaag
6901 gctacaacag gaaatgatga aagttaagca ggcaatgctc ctagagggtg ggttctctga
6961 gacagatgca gcccgcgggg caatcaacgc ccccatgaca aaagctttgg actggagcgg
7021 gacaaggtac tgggctcccg atgctaggac cacaacatac aatgcaggcc gcttttccac
7081 ccctcaacca tcgggggcac tgccaggaag agctaatctt agggatgctg tccctgctcg
7141 gggttcctcc agtaagtctt ctaattcttc tactgctact tctgtgtact caaatcaaac
7201 tacttcaacg agacttggtt ctacagctgg ttctggtacc agtgtctcga gcttcccgtc
7261 aactgcaagg actaggagtt gggttgagga tcaaagtagg aatttgtcac ctttcatgag
7321 gggggcccac aacatatcgt ttgtcacccc accatctagc agatcctcta gccaaggcac
7381 agtctcaacc gtgcctaaag agattttgga ctcctggact ggcgctttca acacgcgcag
7441 gcagccactc ttcgctcaca ttcgtaagcg aggggagtca cgggc
//