Typing tool
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Typing tool
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Complete norovirus genomes
| MF140658 | GII.4 Hunter | |
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| GII.P4 Yerseke |
ORF1: 1..5083
ORF2: 5064..6686
ORF3: 6686..7487
LOCUS MF140658 7487 bp RNA linear VRL 24-OCT-2017
DEFINITION Norovirus GII strain
Norovirus/GII/Hu/NL/2009/GII.P4-GII.4/Rotterdam/E1300265_p15_d102
ORF1 gene, partial cds; ORF2 gene, complete cds; and ORF3 gene,
partial cds.
ACCESSION MF140658
VERSION MF140658.1
KEYWORDS .
SOURCE Norovirus GII
ORGANISM Norovirus GII
Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes;
Picornavirales; Caliciviridae; Norovirus; Norovirus norwalkense.
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/2009/GII.P4-
GII.4/Rotterdam/E1300265_p15_d102"
/host="Homo sapiens"
/db_xref="taxon:122929"
/geo_loc_name="Netherlands"
/collection_date="14-Sep-2009"
/note="genotype: GII.P4-GII.4"
CDS <1..5083
/codon_start=2
/product="ORF1"
/protein_id="ATN23670.1"
/translation="DASAAAVANSNNDTAKSSSDGVLSSMAVTFKRALGARPKQPPPR
EIPQRPPRPPTPELVKNIPPPPPNGEDEIVVSYSVKDGISGLPDLSTVRQPEESNTAF
SVPPLNQRENRDAKEPLPGTILEMWDGEIYHYGIYVERGLVLGVHKPPAAISLARIEL
TPLSLYWRPVYTPQYLISPDALKKLHEETFPYTAFDNNCYAFCCWVLDLNDSWLSRRM
IQRTTGFFRPYQEWNRKPLPTMDDSKLKKVANIFLCALSSLFTRPIKDIIGKLRPLNI
LNILASCDWTFAGIVESLILLAELFGVFWTPPDVSAMIAPLLGDFQLQGPEDLAVELV
PVVMGGIGLVLGFTKEKIGKMLSSAASTLRACKDLGAYGLEILKLVMKWFFPKKEEAN
ELAIVRSIEDAVLDLEAIENNHLTILLKDKDSLATYMRTLDLEEEKARKLSTKSASPD
IVGTINALLARIAAARSLVHRAKEELSSRLRPVVLMISGRPGIGKTHLAREVAKKIAA
SLTGDQRVGLIPRNGVDHWDAYKGERVVLWDDYGMSNPIHDALRLQELADTCPLTLNC
DRIENKGKVFDSDVIIITTNLANPAPLDYVNFEACSRRIDFLVYAEAPEVEKAKRDFP
GQPDMWKNAFSSDFSHIKLALAPQGGFDKNGNTPHGKGVMKTLTTGSLIARASGLLHE
RLDDFEMQGPTITTFNFDRNKLLAFRQLAAENKYGLMDTMKVGRQLKDVRTMPELKQA
LKNISIKKCQIVYGGCTYTLESDGKGNVKVDKVQSASVQTNNELTGALHHLRCARIRY
YVKCVQEALYSIIQIAGAAFVTTRIVKRMNIQDLWSKPQVENTEETTSKDGCPKPRDD
EEFVISSDDIKTEGKKGKNKTGRGKKHTAFSSKGLSDEEYDEYKRIREERNGRYSIEE
YLQDRDKYYEEVAIARATEEDFCEEEEAKIRQRIFRPSRKQRKEERASLGLVTGSEIR
KRNPDDFKPKGKLWADDDRSVDYNEKLSFEAPPSIWSRIVNFGSGWGFWVSPSLFITS
THVIPQGAKEFFGVPIKQIQVHKSGEFCRLRFPKPIRTDVTGMILEEGAPEGTVVTLL
IKRPTGELMPLAVRMGTHATMRIQGRAVGGQMGMLLTGSNAKSMDLGTTPGDCGCPYI
YKRGNDYVVIGVHTAAARGGNTVICATQGSEGEAVLEGGDNKGTYCGAPILGPGNAPK
LSTKTKFWRSSTAPLPPGTYEPAYLGGKDPRVKGGPSLQQVMRDQLKPFTEPRGKPPK
PSVLEAAKKTIINVLEQTIDPPEKWSFAQACASLDKTTSSGHPHHMRKNDCWNGESFT
GKLADQASKANLMFEEGKNMTPVYTAALKDELVKTDKIYNKIKKRLLWGSDLATMIRC
ARAFGGLMDELKAHCVSLPIRVGMNMNEDGPIIFERHSRYAYHYDADYSRWDSTQQRD
VLAAALEIMVKFSPEPHLAQVVAEDLLSPSVVDVGDFTISINEGLPSGVPCTSQWNSI
AHWLLTLCALSEVTNLSPDTIQANSLFSFYGDDEIVSTDIKLDPEKLTAKLREYGLKP
TRPDKTEGPLVISDDLNGLTFLRRTVTRDPAGWFGKLEQSSILRQMYWTRGPNHGDPA
ETMIPHSQRPIQLMSLLGEAALHGPAFYSKISKLVIAELKEGGMDFYVPRQEPMFRWM
RFSDLSTWEGDRNLAPSFVNEDGVE"
CDS 5064..6686
/codon_start=1
/product="ORF2"
/protein_id="ATN23671.1"
/translation="MKMASSDAAPSDGPTANLVPAVNNEVMALEPVAGAAIAAPVAGQ
QNVIDPWIRNNFVQAPGGEFTVSPRNAPGEILWSAPLGPDLNPYLSHLARMYNGYAGG
FEVQVILAGNAFTAGKIIFAAVPPNFPTEGISPCQVTMFPHIITDVRQLEPVLIPLPD
VRNNFYHYNQSNEPTIKLIAMLYTPLRANNAGDDVFTVSCRVLTRPSPDFDFIFLVPP
TVESRTKPFSVPVLTVEEMTNSRFPIPLEKLFTGPSSAFVVQPQNGRCTTDGVLLGTT
QLSPVNICTFRGDVTQIGSTQTYTMNLASQNWNNYDPTEEIPAPLGTPDFVGRIRGML
TQTTKSDGSTRGHVATVSTGSAHFTPKLGRVQFSTDTSNDLEARQNTRFTPVGVIQDG
STTHRNEPQQWVLPDYSGRDSHNVHLAPAVAPTFPGEQLLFFRSTIPGCSGYPNMELD
CLLPQEWVQHFYQESAPAQSDVALLRFVNPDTSRVLFECKLHKQGFLTVAHTGQHDLI
IPPNGYFRFDSWVNQFYTLAPMGNGTGRRRAL"
CDS 6686..>7487
/codon_start=1
/product="ORF3"
/protein_id="ATN23672.1"
/translation="MAGAFFAGLASDVLGSGLSSLINAGAGTINQKVDFDNNRKLQQA
SFQYSSNLQQASFQHDKEMLQAQIEATKKLQQEMMKIKQTMLLEGGFSETDAARGAVN
APMTKVLDWSGTRYWAPDARITTYNAGHFSTPQPSGAPPGRTNLRATTPARGSSSTLS
NASTVTSVHSNQTASTRLGSTAGSGTSVSSLPSTARTRSWVEDQNRNLSPFMRGVHNI
SFVTPPSSRSSSQGTVSTVPKEVLDSWTGAFNTRRQPLFAHIHKRGESR"
ORIGIN
1 cgacgcttcc gctgccgctg ttgctaacag caacaacgac accgcaaaat cttcaagtga
61 cggagtgctt tctagcatgg ctgtcacttt taaacgagcc ctcggggcgc ggcctaagca
121 gcctcccccg agggaaatac cacaaagacc cccacgacca cctaccccag aactggtcaa
181 aaatatcccc cctcccccgc ccaatggaga ggatgaaata gtggtttctt atagtgtcaa
241 agatggtatt tccggtttgc ctgatctttc caccgtcagg caaccggaag aatctaacac
301 ggccttcagt gtccctccac tcaatcagag ggagaataga gatgctaagg agccattacc
361 tggaacaatt ctggaaatgt gggatggaga aatctaccat tatggcatat atgtggagcg
421 aggtcttgta ctaggcgtgc acaaaccacc agccgccatc agcctcgcta ggatagagtt
481 aacaccactc tccttgtact ggaggcctgt gtatacccct caatacctca tctctccaga
541 cgctctcaag aaattacatg aagagacgtt cccctacaca gccttcgaca acaactgcta
601 tgccttttgt tgctgggtcc tggacctaaa cgactcgtgg ctgagtagga ggatgatcca
661 gagaacaact ggctttttca ggccctacca agaatggaac aggaaacccc tccccactat
721 ggatgactcc aagttaaaga aggtggctaa catattcctg tgtgctctgt cttcgctatt
781 caccagaccc ataaaagata taatagggaa actaaggcct cttaacatcc ttaacatctt
841 ggcctcatgt gattggactt ttgcaggcat agtggagtct ttgatactct tggcagaact
901 ctttggagtt ttctggacac ccccagatgt gtctgcgatg attgccccct tgctcggtga
961 ttttcagttg caaggaccgg aggaccttgc agtggaactc gtccctgtag tgatgggggg
1021 aattggtttg gtgctaggat tcaccaaaga gaagattggt aaaatgttgt catctgctgc
1081 gtccaccttg agagcttgta aagatcttgg tgcatatggg ttagagatcc taaagttggt
1141 tatgaagtgg ttcttcccga agaaagagga agcaaatgaa ctggctatag tgagatccat
1201 cgaggatgca gtcctggatc tcgaggcaat tgaaaacaat catttaacca tcttgctcaa
1261 agacaaagac agtctggcaa cctacatgag aacccttgat cttgaggagg agaaagccag
1321 aaaactctca accaagtctg cttcacctga cattgtgggc acaatcaacg cccttttggc
1381 gaggatcgct gctgcacgtt ctctggtgca tcgagcgaag gaggaacttt ccagcagact
1441 aagacctgta gtattgatga tatcaggcag accaggaata gggaagaccc accttgctag
1501 ggaagtggcc aagaaaatcg cagcctccct tacaggggac caacgtgtgg gcctcatccc
1561 acgcaatggt gttgaccatt gggatgcgta caagggtgag agggtcgtcc tatgggatga
1621 ctatggaatg agcaatccca tccacgatgc cctcaggttg caagaactcg ctgacacttg
1681 ccctcttacc ctaaactgtg acaggattga gaataaagga aaggtttttg acagcgatgt
1741 catcatcatc accactaatc tggctaatcc agcaccactg gactatgtca actttgaagc
1801 atgctcaagg cgcatcgact tcctcgtgta tgcagaagct cctgaagtcg agaaggcgaa
1861 gcgtgatttc ccaggccagc ccgacatgtg gaagaacgcc ttcagctctg atttctcaca
1921 cataaaacta gcattggctc cacagggtgg cttcgacaag aacgggaaca ccccacacgg
1981 gaagggcgtc atgaagactc tcaccactgg ctcccttatt gctcgggcat cagggctact
2041 ccatgagagg ttagatgatt ttgaaatgca gggcccaact atcaccacct tcaactttga
2101 tcgcaacaaa ttgcttgcct ttagacaact tgctgctgaa aacaaatatg ggttgatgga
2161 cacaatgaaa gttgggaggc agctcaagga tgtcagaaca atgccagaac ttaagcaagc
2221 actcaagaat atctcaatta agaagtgcca gatagtgtat ggtggttgca cctatacact
2281 tgagtctgat ggcaagggca atgtgaaagt tgacaaagtt caaagcgcct ccgtgcagac
2341 caataatgag ctgactggcg cactgcacca tctaaggtgc gccagaatca gatactacgt
2401 caagtgtgtc caggaggccc tgtattccat catccagatt gctggggctg catttgtcac
2461 cacgcgcatc gtcaagcgca tgaacataca agacctatgg tccaaaccac aagtggaaaa
2521 cacagaggag actaccagca aggacgggtg tccaaaaccc agagatgatg aggagttcgt
2581 catttcatcc gacgacatca aaactgaggg taagaaagga aagaacaaga ctggccgcgg
2641 caagaaacac acagccttct caagcaaagg tctcagtgat gaagagtacg atgagtacaa
2701 gaggattaga gaggaaagga atggcaggta ctccatagaa gagtaccttc aggacaggga
2761 caaatactac gaggaggtgg ccattgccag ggcaaccgag gaggacttct gtgaagagga
2821 agaggccaag atccggcaaa ggatcttcag gccatcaagg aaacaacgca aggaggaaag
2881 agcttctctc ggtttagtca caggttctga aattaggaaa agaaatccag atgatttcaa
2941 acccaaagga aaactgtggg ctgatgatga cagaagtgtg gactacaacg agaaactcag
3001 ttttgaagcc ccaccaagca tctggtcaag gatagtcaac tttggttcag gttggggatt
3061 ctgggtctcc cctagtttgt tcataacatc aacccacgtc ataccccagg gcgcaaagga
3121 gttctttgga gtccctatca aacaaattca ggtacacaaa tcaggcgagt tctgtcgctt
3181 gagattccca aagccaatca ggactgatgt gacaggcatg atcttagaag aaggtgcacc
3241 cgagggcact gtggtcacac tgctcatcaa aaggcccact ggagaactca tgcccctggc
3301 agttaggatg gggacccatg caaccatgag aattcaaggg cgcgctgttg gaggccaaat
3361 gggcatgctt ctgacagggt ccaacgccaa aagcatggat ctaggtacca caccaggtga
3421 ttgtggctgt ccctacatct acaagagagg aaatgactat gtggtcattg gagtccacac
3481 ggctgccgct cgtgggggaa acactgttat atgtgccacc caggggagtg agggagaggc
3541 tgtacttgaa ggtggtgaca ataaagggac atactgtggt gcaccaatcc taggaccagg
3601 aaatgctcca aaactcagca ccaaaaccaa gttctggaga tcgtccacag caccactccc
3661 acctggtacc tatgaaccag cctatcttgg tggcaaggac cccagagtca agggtggccc
3721 ttcactgcag caagtcatga gggatcaatt gaagccattc acagagccta ggggcaagcc
3781 accaaagcca agtgtgctag aagctgccaa gaaaaccatc atcaatgtcc ttgagcaaac
3841 aattgatcca cctgagaaat ggtcattcgc acaagcttgc gcgtcccttg acaagaccac
3901 atccagtggc catccgcacc acatgcggaa aaatgactgt tggaacgggg aatccttcac
3961 aggcaagctg gcagatcagg cttctaaggc caacctaatg tttgaagaag gaaagaacat
4021 gaccccagtc tacacagctg cacttaagga tgaattagtt aaaactgaca aaatttataa
4081 taagatcaag aagaggctcc tctggggttc ggatttggcg accatgatcc ggtgtgctcg
4141 agcattcgga ggcctgatgg atgaactcaa agcgcactgc gtctcacttc ccattagagt
4201 tggtatgaat atgaacgagg atggccccat catcttcgag aggcattcca ggtacgcata
4261 ccactatgat gctgattact cacgatggga ttcaacacaa cagagagacg tattggcagc
4321 agctctagaa attatggtta aattctcccc agaaccacat ttggctcagg tagtcgcaga
4381 agaccttctc tctcctagcg tggtggacgt gggtgacttc acaatatcaa tcaacgaggg
4441 tctcccctct ggggtgccct gcacctccca atggaattcc atcgcccact ggcttctcac
4501 tctctgtgcg ctctctgaag ttacaaactt gtcccctgac accatacagg ctaattccct
4561 cttctctttt tatggtgatg atgaaattgt tagcacagac ataaaattgg acccagaaaa
4621 gttaacagca aaactcaggg aatatgggtt aaaaccaacc cgccctgata aaactgaagg
4681 accccttgtc atctctgacg acttaaatgg cctgactttc ctgcggagaa ctgtgacccg
4741 cgacccagct ggttggtttg gaaaactgga acagagttca atactcaggc aaatgtactg
4801 gactaggggt cccaaccatg gagatccagc tgaaacaatg attccacact cccaaagacc
4861 catacaattg atgtccctac tgggggaggc cgcacttcac ggcccagcat tctacagcaa
4921 aatcagcaag ttggtcatcg cagagctaaa agagggtggc atggattttt acgtgcccag
4981 acaagagcca atgttcaggt ggatgagatt ctcagatctg agcacgtggg agggcgatcg
5041 caatctggct cccagttttg tgaatgaaga tggcgtcgag tgacgccgcc ccatctgatg
5101 ggcccacagc taacctcgtc ccagcggtca acaatgaggt tatggctttg gagcccgttg
5161 ccggtgccgc tattgcggca cctgtagcgg gccaacaaaa tgtaattgac ccctggatta
5221 gaaataattt tgtacaagcc cctggtggag aatttacagt atcccctaga aacgctccag
5281 gtgaaatatt atggagcgcg cccttgggtc ctgacttgaa tccctacctt tcccatttgg
5341 ccagaatgta taatggttat gcaggtggtt ttgaggtgca ggtaatcctc gcggggaacg
5401 cgttcaccgc tgggaaaatc atatttgcag cagttccacc aaattttcca accgaaggga
5461 taagcccctg ccaagtcact atgttccccc atataataac agatgttaga caactggaac
5521 ctgtgttaat ccccttgcct gatgttagga acaacttcta tcattataat caatcaaatg
5581 aacccaccat caaattgata gcaatgctgt acacaccact tagggctaat aatgctgggg
5641 acgatgtctt cacagtctct tgtcgagttc tcacgagacc atcccccgat tttgatttca
5701 tatttctggt gccacccaca gttgagtcaa gaaccaaacc attctctgtc ccagtcttaa
5761 ctgttgagga gatgaccaac tcaagattcc ccattccttt agaaaagttg ttcacgggtc
5821 ccagcagtgc ctttgttgtt caaccacaaa atggcagatg cacgactgat ggcgtgctct
5881 taggtactac tcaactgtct cctgtcaaca tctgcacctt cagaggggat gtcactcaaa
5941 ttggaagtac tcaaacttac acaatgaacc tggcctccca aaattggaat aattatgatc
6001 caacagaaga aatcccagcc cccctgggaa ccccagattt tgtaggaagg atccgaggca
6061 tgctcaccca aaccacaaag agtgatggct cgacccgtgg tcacgtagcc acagtgagca
6121 ctggaagtgc tcattttact ccaaagttgg gcagagttca attctccact gacacaagca
6181 atgaccttga agctcgccaa aacacgagat tcaccccagt cggcgtcatc caggatggta
6241 gtaccaccca ccgaaatgaa ccccaacaat gggtgctccc agattattca ggtagagata
6301 gtcacaatgt acacctagca cctgctgtgg cccccacttt tccgggcgag caacttcttt
6361 tctttaggtc cactataccc ggatgcagcg ggtaccccaa catggaattg gattgcctac
6421 tcccccagga gtgggtgcag cacttctacc aagaatcagc cccagcacaa tctgatgtgg
6481 cactgctgag atttgtgaat ccagacacaa gtagggtttt gtttgagtgc aagcttcaca
6541 agcaaggctt tttaacagtg gctcatactg gccaacatga tttgattatc cctcccaatg
6601 gctattttag atttgattcc tgggttaacc aattctacac acttgccccc atgggaaatg
6661 gaacggggcg aagacgtgca ttataatggc tggagctttc tttgctggat tagcatctga
6721 tgtccttggc tctgggctta gctctctaat caatgctggg gctgggacca ttaatcaaaa
6781 agttgatttt gacaataata gaaaattgca acaagcttcc ttccaatata gtagcaatct
6841 acaacaggct tcctttcaac atgataaaga gatgctccaa gcacaaattg aggccaccaa
6901 aaagttgcaa caagaaatga tgaaaattaa acagacaatg ctcctagagg gtgggttctc
6961 tgagacagat gcagcccgtg gggcagtcaa cgcccccatg acaaaggttt tggactggag
7021 cggaacaagg tactgggctc ccgatgctag gattacaaca tacaatgcag gccacttttc
7081 cacccctcaa ccctcgggag caccaccagg gagaaccaat ctcagggcta ccacccccgc
7141 tcgaggctcc tccagtacac tttcaaatgc ttctactgtc acttctgtgc actcaaatca
7201 aactgcttca acgagacttg gttctacagc tggttctggc accagtgtct cgagcctccc
7261 gtcaactgca aggactagga gctgggttga ggatcaaaac aggaacttgt cacctttcat
7321 gaggggggtc cacaacatat catttgtcac cccaccatct agcagatcct ctagccaagg
7381 cacagtctca accgtgccta aagaagtttt ggactcctgg actggcgctt tcaacacgcg
7441 caggcagcct ctcttcgccc acattcataa gcgaggggag tcacggg
//