Typing tool
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Typing tool
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Complete norovirus genomes
| MF140694 | GII.4 New Orleans | |
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| GII.P4 New Orleans |
ORF1: 1..5090
ORF2: 5071..6693
ORF3: 6693..7499
LOCUS MF140694 7545 bp RNA linear VRL 24-OCT-2017
DEFINITION Norovirus GII strain
Norovirus/GII/Hu/NL/2013/GII.P4-GII.4/Rotterdam/E1300280_p9_d0 ORF1
gene, partial cds; and ORF2 and ORF3 genes, complete cds.
ACCESSION MF140694
VERSION MF140694.1
KEYWORDS .
SOURCE Norovirus GII
ORGANISM Norovirus GII
Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes;
Picornavirales; Caliciviridae; Norovirus; Norwalk virus.
REFERENCE 1 (bases 1 to 7545)
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 7545)
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..7545
/organism="Norovirus GII"
/mol_type="genomic RNA"
/strain="Norovirus/GII/Hu/NL/2013/GII.P4-
GII.4/Rotterdam/E1300280_p9_d0"
/host="Homo sapiens"
/db_xref="taxon:122929"
/country="Netherlands"
/collection_date="21-Aug-2013"
/note="genotype: GII.P4-GII.4"
CDS <1..5090
/codon_start=3
/product="ORF1"
/protein_id="ATN23778.1"
/translation="SNDASAAAVANSNNDTAKSSSDGVLSSMAVTFKRALGARPKQPP
PREIPQRPPRPPTPELVKSIPPPPPNGEDEIVVSYSVKDGVSGLPDLSTVRQPEESNT
AFSVPPLNQRESRDAKEPLTGTILEMWDGEIYHYGLYVERGLVLGVHKPPAAISLAKV
ELAPLSLYWRPVYTPQYLISPDTLKKLSGETFPYTAFDNNCYAFCCWVLDLNDSWLNR
RMIQRTTGFFRPYQDWNRKPLPTIDDSKIKKVANIFLCALSSLFTRPIKDIIGKIRPL
NILNILASCDWTFAGIVESLILLAELFGVFWTPPDVSAMIAPLLGDYELQGPEDLAVE
LVPVVMGGIGLVLGFTKEKIGKMLSSAASTLRACKDLGAYGLEILKLVMKWFFPKKEE
ANELAMVRSIEDAVLDLEAIENNHMTTLLKDKDSLATYMRTLDLEEEKARKLSTKSAS
PDIVGTINALLARIAAARSLVHRAKEELSSRPRPVVLMISGRPGIGKTHLAREVAKKI
AASLTGDQRVGLIPRNGVDHWDAYKGERVVLWDDYGMSNPIHDALRLQELADTCPLTL
NCDRIENKGKVFDSDVIIITTNLANPAPLDYVNFEACSRRIDFLVYAEAPEVEKAKRD
FPGQPDMWKNAFSSDFSHIRLALAPQGGFDKNGNTPHGKGVMKTLTTGSLIARASGLL
HERLDEFELQGPALTTFNFDRNKVLAFRQLAAENKYGLMDTMRVGKQLKDVKTMPELK
QALKNVSIKKCQIVYSGCTYILESDGKGNVKVDRIQNTTVQINNELAGALHHLRSARI
RYYVKCVQEALYSIIQIAGAAFVTTRIAKRMNIQNLWSKPQVENTEETTSNDGCPKPK
DDEEFVISSDDIKTEGKKGKNKTGRGKKHTAFSSKGLSDEEYDEYKRIREERNGKYSI
EEYLQDRDKYYEEVAIARATEEDFCEEEEAKIRQRIFRPTRKQRKEERASLGLVTGSE
IRKRNPDDFKPKGKLWADDDRSVDYNEKLSFEAPPSIWSRIVNFGSGWGFWVSPSLFI
TSTHVIPQGAKEFFGVPIKQIQVHKSGEFCRLRFPKPIRTDVTGMILEEGAPEGTVVT
LLIKRSTGELMPLAARMGTHATMKIQGRTVGGQMGMLLTGSNAKSMDMGTTPGDCGCP
YIYKRGNDYVVIGVHTAAARGGNTVICATQGSEGEATLEGGDNKGTYCGAPILGPGSA
PTLSTKTKFWRSSTASLPPGTYEPAYLGGKDPRVKGGPSLQQVMREQLKPFTEPRGKP
PKPSVLEAAKKTIINVLEQTIDPPEKWSFAQACASLDKTTSSGYPHHVRKNDCWNGES
FTGKLADQASKANLMFEEGKNMTPVYTAALKDELVKTDKIYGKIKKRLLWGSDLATMI
RCARAFGGLMDELKAHCVTLPIRVGMNMNEDGPIIFERHSRYTYHYDADYSRWDSTQQ
RAVLAAALEIMVKFSPEPHLAQVVAEDLLSPSVVDVGDFTISINEGLPSGVPCTSQWN
SIAHWLLTLCALSEVTNLSPDTIQANSLFSFYGDDEIVSTDIKLDPEKLTAKLREYGL
KPTRPDKTEGPLVITEDLNGLTFLRRTVTRDPAGWFGKLEQSSILRQMYWTRGPNHGD
PSETMIPHSQRPIQLMSLLGEAALHGPAFYSKISKLVIAELKEGGMDFYVPRQEPMFR
WMRFSDLSTWEGDRNLAPSFVNEDGVE"
CDS 5071..6693
/codon_start=1
/product="ORF2"
/protein_id="ATN23779.1"
/translation="MKMASSDANPSDGSTANLVPEVNNEVMALEPVVGAAIAAPVAGQ
QNVIDPWIRNNFVQAPGGEFTVSPRNAPGEILWSAPLGPDLNPYLSHLARMYNGYAGG
FEVQVILAGNAFTAGKIIFAAVPPNFPTEGLSPSQVTMFPHIIVDVRQLEPVLIPLPD
VRNNFYHYNQSNDSTIKLIAMLYTPLRANNAGDDVFTVSCRVLTRPSPDFDFIFLVPP
TVESRTKPFSVPVLTVEEMTNSRFPIPLEKLFTGPSSDIVVQPQNGRCTTDGVLLGTT
QLSSVNICTFRGDVTQVGKTNRYTMNLASPNWNSYDPTEDTPAPLGTPDFVGKIQGVL
TQTTIPGGSTRAHKATVRTGSADFSPKLGKIQFDTDTSNDLDTNQNTKFTPVGVVQEG
DDTHQKEPIQWELPSYSGRGTHNVHLAPAVAPTFPGEQLLFFRSTMPGCGGYPNMNLD
CLLPQEWVQYFYQEAAPAQSDVALLRFVNPDTGRVLFECKLHKSGYVTVAYTGKHDLV
IPPNGYFRFDSWVNQFYTLAPMGNGTGRRRAL"
CDS 6693..7499
/codon_start=1
/product="ORF3"
/protein_id="ATN23780.1"
/translation="MAGAFFAGLASDVLGSGLGSLINAGAGVINQKVDFENNRKLQQD
SFQFSSNLQQASFQHDKEMLQAQIEATKKLQQEMMRVKQAMLLEGGFSETDAARGAIN
APMTKVLDWNGTRYWAPDARTTTYNAGRFSTPQPSGAPPGRANLRAAAPARGSSSMSS
KSSIASSVYSNQTTSTRLGSTAGSGTSVSSLPSTARTRSWVEDQNRNLSPFMRGAHNI
SFVTPPSSRSSSQGTVSTVPKEILDSWTGAFNTRRQPLFAHIRKRGESRV"
ORIGIN
1 cgtctaacga cgcttccgct gccgctgttg ctaacagcaa caacgacacc gcaaaatctt
61 caagtgacgg agtgctttct agcatggctg tcacttttaa acgagccctc ggggcgcggc
121 ctaaacagcc tcccccgagg gaaataccac aaaggccccc acgaccacct actccagaac
181 tggtcaaaag tattccccct cccccaccca acggagagga tgaaatagtg gtttcttaca
241 gtgttaagga tggtgtttcc ggcttgcctg acctttccac cgttaggcaa ccggaagaat
301 ctaacacggc cttcagtgtc cctccactca atcagaggga gagtagagat gctaaggagc
361 cacttactgg aacaattctg gaaatgtggg acggggaaat ctaccattat ggcctgtatg
421 tggagcgagg tcttgtacta ggcgtgcaca aaccaccagc tgccatcagc ctcgctaagg
481 ttgagctagc accactctcc ttgtactgga gacctgtgta tactcctcag tacctcatct
541 ctccagacac tctcaagaaa ttatccggag aaacgttccc ctacacagcc tttgacaaca
601 actgttatgc cttttgttgc tgggtcctgg acctaaatga ctcatggctg aacaggagaa
661 tgatccagag aacaactggt ttctttaggc cctatcaaga ctggaatagg aaaccccttc
721 ctactataga tgactccaaa ataaagaagg tagctaacat attcctgtgt gctctgtcct
781 cgctgttcac cagacccata aaagatataa tagggaagat aaggcctctt aacatcctca
841 acatcttagc ctcatgtgat tggacttttg caggcatagt ggagtccctg atactcttgg
901 cagaactctt tggagttttc tggacacccc cagatgtgtc tgctatgatt gctcccttac
961 tcggtgacta tgagctacaa ggacctgagg accttgcagt ggagctcgtc cccgtagtga
1021 tggggggaat tggtttggtg ctaggattca ccaaagagaa gattgggaaa atgttgtcat
1081 ctgccgcgtc caccttgaga gcttgtaaag accttggtgc atatgggcta gagatcctga
1141 agttggtcat gaagtggttc tttccgaaga aggaggaggc aaatgagctg gctatggtga
1201 ggtctatcga ggatgcagtt ctagatctcg aggcaattga aaacaaccat atgactacct
1261 tgctcaaaga caaagacagt ctggcaacct atatgagaac acttgacctt gaggaggaga
1321 aagccaggaa actctcaacc aagtctgcct cacccgacat cgtgggcaca atcaacgccc
1381 tcctggcgag aatcgctgcc gcacgttctc tggtgcatcg agcgaaggag gagctttcca
1441 gcagaccaag acctgtggtg ttgatgatat caggcaggcc ggggataggg aagacccacc
1501 tcgctaggga agtggctaag aagatcgcag cctcccttac aggagaccag cgtgtgggcc
1561 tcatcccacg caatggcgtc gaccattggg atgcgtacaa gggagagaga gtcgtcctat
1621 gggacgatta tggaatgagc aaccccattc acgacgccct caggctgcaa gaactcgctg
1681 acacttgccc cctcactcta aactgtgaca ggattgaaaa taaaggaaag gtctttgaca
1741 gcgatgtcat cattatcacc actaatctgg ccaacccagc accactagac tatgtcaact
1801 ttgaagcatg ctcgaggcgc atcgacttcc tcgtgtatgc agaagcccct gaagtcgaga
1861 aggcgaagcg tgacttccca ggccagcctg acatgtggaa gaacgctttc agttctgatt
1921 tctcacacat aagactagca ctggccccac agggtggttt cgacaagaac gggaacaccc
1981 cgcatggaaa gggcgtcatg aagactctca ccactggctc ccttattgcc cgagcgtcag
2041 ggctactcca tgagaggtta gatgaatttg aactacaggg cccagctctc accaccttca
2101 attttgaccg caacaaagtg cttgccttca gacagcttgc tgctgagaat aaatatggat
2161 tgatggacac aatgagggtt gggaaacagc tcaaggatgt caaaaccatg cctgaactca
2221 aacaagcact caagaatgtc tcaatcaaga agtgccaaat agtatatagt ggttgcacct
2281 acatacttga gtctgatggc aagggcaatg tgaaagttga cagaatccaa aacaccaccg
2341 tgcagatcaa caatgagctg gctggtgctc tgcaccattt gaggagcgcc agaatcagat
2401 actatgtcaa gtgtgtccag gaggccctat attccatcat tcaaattgct ggggctgcat
2461 ttgtcaccac gcgcattgcc aagcgcatga acatacaaaa cctatggtcc aaaccacaag
2521 tggaaaacac agaggagact accagcaatg acgggtgccc aaaacctaag gatgatgagg
2581 agtttgtcat ttcatctgac gacatcaaaa ctgagggcaa gaaagggaaa aacaagactg
2641 gtcgcggcaa gaagcacaca gcattttcaa gcaaaggcct cagtgatgaa gagtacgatg
2701 agtacaagag gattagagaa gaaaggaatg gtaagtactc catagaagaa taccttcagg
2761 acagggacaa atactatgag gaggtggcca ttgccagggc gactgaggaa gacttctgtg
2821 aagaggagga ggccaagatc cgtcaaagga tctttaggcc aacaaggaaa caacgcaagg
2881 aggaaagagc ttctctcggt ctggtcacag gttctgaaat taggaaaaga aacccagatg
2941 acttcaaacc caaggggaaa ttgtgggctg acgatgacag gagtgtggac tacaatgaga
3001 aactcagttt tgaggcccca ccaagcatct ggtcaagaat agtcaacttt ggttcaggct
3061 ggggattctg ggtctccccc agtcttttca taacatcaac ccatgtcata ccccagggcg
3121 caaaggagtt ctttggagtc cccatcaaac aaatacaggt acacaaatca ggcgagttct
3181 gtcgcttgag attcccaaaa ccaatcagga ctgatgtgac aggcatgatc ttggaagaag
3241 gcgcacctga gggtaccgtg gtcacactac tcatcaaaag gtccactggg gaactcatgc
3301 ccctagcagc tagaatgggg acccatgcga ccatgaagat ccaagggcgc actgttggag
3361 gccagatggg catgctcctg acagggtcca acgccaagag catggacatg ggtactacac
3421 caggtgattg cggctgtccc tatatttaca agagaggcaa tgactatgtg gtcattggag
3481 tccacacggc tgccgcacgt ggagggaaca ctgtcatatg tgccactcag gggagtgaag
3541 gagaggctac acttgaaggt ggtgacaaca agggaacata ttgtggtgca ccaatcctag
3601 gcccagggag tgccccaact cttagcacca agaccaaatt ctggagatca tctacagcgt
3661 cactcccacc tggcacctat gaaccagcct atcttggtgg caaggacccc agagtcaagg
3721 gtggcccttc actacagcaa gtcatgaggg agcagttgaa accattcaca gagccaaggg
3781 gcaaaccacc aaaaccaagt gtattagaag ctgccaagaa gaccatcatc aatgtccttg
3841 agcaaacaat tgacccacct gagaaatggt cgttcgcaca agcttgcgcg tcccttgaca
3901 agaccacttc cagcggttat ccgcaccatg tgcggaaaaa cgactgctgg aacggggagt
3961 ccttcacagg caagctggca gaccaggctt ccaaggccaa cctgatgttt gaagaaggga
4021 aaaacatgac cccagtctac acagctgcac tcaaggatga gttagttaaa actgacaaaa
4081 tttatggtaa gatcaagaag aggcttctct ggggctcgga cttggcgacc atgatccggt
4141 gtgctcgggc attcggaggc ctaatggatg aactcaaagc acactgtgtc acacttccca
4201 ttagagttgg catgaacatg aatgaggatg gccccatcat cttcgagagg cattctaggt
4261 acacatatca ctatgatgct gattactctc gatgggattc aacacaacag agagccgtgt
4321 tggcagcagc tctcgaaatc atggttaaat tctctccaga accacatttg gcccaggtag
4381 tcgcagaaga ccttctttct cctagcgtgg tggacgtggg cgacttcaca atatcaatca
4441 acgagggtct tccctctggg gtgccttgca cctcccaatg gaactccatc gcccactggc
4501 ttctcactct ctgtgcgctc tctgaagtca caaacctatc ccctgacaca atacaggcta
4561 attccctctt ctctttttat ggtgatgatg aaattgttag cacagacata aaattggacc
4621 cagagaaatt gacagcaaag ctcagagaat atgggttaaa accgacccgc cctgacaaaa
4681 ctgaaggacc ccttgtcatc actgaagacc tgaatggcct aactttcctg cggagaactg
4741 tgacccgcga cccagctggt tggtttggaa aactggagca gagttcaata ctcaggcaaa
4801 tgtactggac taggggtccc aaccatggag acccatctga aacaatgatt ccacactccc
4861 aaagacccat acaattgatg tccctactgg gggaggccgc tctccacggc ccagcctttt
4921 acagcaaaat cagcaagttg gtcattgcag agctaaaaga aggtggcatg gatttttacg
4981 tgcccagaca agagccaatg ttcagatgga tgagattctc agatctgagc acgtgggagg
5041 gcgatcgcaa tctggctccc agttttgtga atgaagatgg cgtcgagtga cgccaaccca
5101 tctgatgggt ccacagccaa cctcgtccca gaggtcaaca atgaggttat ggctttggag
5161 cccgtagttg gtgccgccat tgcggcacct gtagcgggcc aacaaaatgt aattgacccc
5221 tggattagaa ataattttgt acaagcccct ggtggagagt ttacagtatc ccctagaaac
5281 gctccaggtg aaatactatg gagcgcgccc ttaggccctg atctgaaccc ctacctttcc
5341 catttggcca gaatgtacaa tggttatgca ggtggttttg aagtgcaggt aatcctcgcg
5401 gggaacgcgt tcaccgccgg gaaaatcata tttgcagcag tcccaccaaa tttcccaact
5461 gaaggtttga gccccagtca agtcactatg tttccccata taatagtgga tgttaggcaa
5521 ttggaacctg tgttgattcc cttacccgat gttaggaata atttctacca ttataatcaa
5581 tcaaatgact ccaccattaa attgatagca atgttgtata caccacttag ggctaataat
5641 gctggggacg atgtcttcac agtctcttgt cgagtcctca cgagaccatc ccccgatttt
5701 gattttatat ttttggtgcc acctacagtt gaatcaagaa ctaaaccatt ctctgtccca
5761 gttctaactg ttgaagagat gaccaattca aggttcccca tccctttgga aaagttgttc
5821 acaggcccca gtagtgacat cgtagttcaa ccacaaaatg gcaggtgcac gactgatggc
5881 gtgctcctag gtactaccca attgtcctct gtcaacatct gcaccttcag aggggatgtc
5941 acccaagttg gaaaaactaa cagatacaca atgaatttgg cctccccaaa ttggaacagt
6001 tacgatccaa cagaagatac cccagcccct ctaggaactc cagatttcgt ggggaagatt
6061 caaggtgtgc tcacccaaac cacaattcca ggtggctcga cccgcgccca caaggccaca
6121 gtgcgcactg ggagcgccga cttttctccg aaactgggta aaattcaatt tgacactgac
6181 acaagtaatg atcttgacac caaccagaac acaaagttca ccccagtcgg cgttgtccag
6241 gaaggtgatg atacccacca gaaagaaccc atacaatggg agctcccaag ctattcaggc
6301 agaggcactc ataatgtaca cctggccccc gctgtagccc ctactttccc gggcgagcag
6361 ctcctcttct tcagatctac tatgcccgga tgtggcgggt accccaacat gaatttggac
6421 tgtctactcc ctcaggaatg ggtgcagtac ttctaccagg aggcagcccc agcacaatct
6481 gatgtagctc tgttaagatt tgtgaatcca gacacaggta gggttttatt tgaatgtaag
6541 cttcataaat caggctatgt tacagtggct tacactggca aacatgattt ggttatcccc
6601 cctaatggtt attttagatt tgattcctgg gtcaaccagt tctacactct tgcccccatg
6661 ggaaatggaa cggggcgtag acgtgcatta taatggctgg agctttcttt gctggattgg
6721 catctgatgt ccttggctct ggacttggtt ccctaatcaa tgctggggct ggggtcatca
6781 accaaaaagt tgattttgaa aataatagaa aattacaaca agattccttc caatttagta
6841 gcaatctcca acaagcttcc tttcaacatg acaaagagat gctccaagca caaattgagg
6901 ccaccaaaaa gttgcaacag gaaatgatga gagttaaaca agcaatgctc ctagagggtg
6961 gattctctga gacagatgca gcccgtgggg caatcaacgc ccccatgaca aaagttttgg
7021 actggaatgg aacaaggtac tgggctcccg atgctaggac tacaacatac aatgcaggcc
7081 gcttttccac ccctcaaccc tcgggggcac caccaggaag ggctaatctt agggctgctg
7141 cccccgcccg gggctcctct agcatgtctt ctaaatcttc tattgcttct tctgtgtatt
7201 caaatcaaac cacctcaacg agacttggtt ctacagctgg ttctggtacc agtgtctcga
7261 gcctcccgtc aactgcaagg actaggagct gggttgagga tcaaaatagg aatttgtcac
7321 ctttcatgag gggggcccac aacatctcgt ttgtcacccc accatctagc agatcctcta
7381 gccaaggcac agtctcaacc gtgcccaaag aaattttgga ctcctggact ggcgctttca
7441 acacgcgcag gcagcctctc ttcgctcaca ttcgtaagcg aggggagtca cgggtgtaat
7501 gtgaaaagac aaaattgatt atctttcttt tctttagtgt ctttt
//