Typing tool
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Typing tool
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Complete norovirus genomes
| MF140655 | GII.4 Farmington Hills | |
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| GII.P4 Yerseke |
ORF1: 1..5091
ORF2: 5072..6694
ORF3: 6694..7500
LOCUS MF140655 7546 bp RNA linear VRL 24-OCT-2017
DEFINITION Norovirus GII strain
Norovirus/GII/Hu/NL/2009/GII.P4-GII.4/Rotterdam/E7800013_p15_d0
ORF1 gene, partial cds; and ORF2 and ORF3 genes, complete cds.
ACCESSION MF140655
VERSION MF140655.1
KEYWORDS .
SOURCE Norovirus GII
ORGANISM Norovirus GII
Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes;
Picornavirales; Caliciviridae; Norovirus; Norwalk virus.
REFERENCE 1 (bases 1 to 7546)
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 7546)
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..7546
/organism="Norovirus GII"
/mol_type="genomic RNA"
/strain="Norovirus/GII/Hu/NL/2009/GII.P4-
GII.4/Rotterdam/E7800013_p15_d0"
/host="Homo sapiens"
/db_xref="taxon:122929"
/country="Netherlands"
/collection_date="04-Jun-2009"
/note="genotype: GII.P4-GII.4"
CDS <1..5091
/codon_start=1
/product="ORF1"
/protein_id="ATN23661.1"
/translation="ASNDASAAAVANSNNDTAKSSSDGVLSSMAVTFKRALGARPKQP
PPREIPQRPPRPPTPELVKNIPPPPPNGEDEIVVSYSVKDGISGLPDLSTVRQPEESN
TAFSVPPLNQRENRDAVEPLPGTILEMWDGEIYHYGIYVERGLVLGVHKPPAAISLAR
IELTPLSLYWRPVYTPQYLISPDSLKKLHEETFPYTAFDNNCYAFCCWVLDLNDSWLS
RRMIQRTTGFFRPYQEWNRKPLPTMDDSKLKKVANIFLCALSSLFTRPIKDIIGKLRP
LNILNILASCDWTFAGIVESLILLAELFGVFWTPPDVSAMIAPLLGDFQLQGPEDLAV
ELVPVVMGGIGLVLGFTKEKIGKMLSSAASTLRACKDLGAYGLEILKLIMKWFFPKKE
EANELAIVRSIEDAVLDLEAIENNHLTILLKDKDSLATYMRTLDLEEEKARKLSTKSA
SPDIVGTINALLARIAAARSLVHRAKEELSSRPRPVVLMISGRPGIGKTHLAREVAKR
IAASLTGDQRVGLIPRNGVDHWDAYKGERVVLWDDYGMSNPIHDALRLQELADTCPLT
LNCDRIENKGKVFDSDVIIITTNLANPAPLDYVNFEACSRRIDFLVYAEAPEVEKAKR
DFPGQPDMWKNAFSSDFSHIKLALAPQGGFDKNGNTPHGKGVMKTLTTGSLIARASGL
LHERLDEFEMQGPALTTFNFDRNKVLAFRQLAAENKYGLIDTMKVGRQLKDVRTMPEL
KQALKNISIKKCQIVYGGCTYTLESDGKGNVKVDKVQSASVQTNNELTGALHHLRCAR
IRYYVKCVQEALYSIIQIAGAAFVTTRIVKRMNIQDLWSRPQVENTEETTSKDGCPKP
RDDEEFVISSDDIKTEGKKGKNKTGRGKKHTAFSSKGLSDEEYDEYKRIREERNGRYS
IEEYLQDRDKYYEEVAIARATEEDFCEEEEAKIRQRIFRPSRKQRKEERASLGLVTGS
EIRKRNPDDFKPKGKLWADDDRSVDYNEKLSFEAPPSIWSRIVNFGSGWGFWVSPSLF
ITSTHVIPQGTKEFFGVPIKQIQVHKSGEFCRLRFPKPIRTDVTGMILEEGAPEGTVV
TLLIKRPTGELMPLAVRMGTHATMRIQGRAVGGQMGMLLTGSNAKSMDLGTTPGDCGC
PYIYKRGNDYVVIGVHTAAARGGNTVICATQGSEGEAILEGGDNKGTYCGAPILGPGN
APKLSTKTKFWRSSTAPLPPGTYEPAYLGGKDPRVKGGPSLQQVMRDQLKPFTEPRGK
PPKPSVLEAAKKTIINVLEQTIDPPEKWSFAQACASLDKTTSSGHPHHMRKNDCWNGE
SFTGKLADQASKANLMFEEGKNMTPVYTAALKDELVKTDKIYKKIKKRLLWGSDLATM
IRCARAFGGLMDELKAHCVSLPIRVGMNMNEDGPIIFERHSRYTYHYDADYSRWDSTQ
QRDVLAAALEIMVKFSPEPHLAQVVAEDLLSPSVVDVGDFTISINEGLPSGVPCTSQW
NSIAHWLLTLCALSEVTNLSPDTIQANSLFSFYGDDEIVSTDIKLDPEKLTAKLREYG
LKPTRPDKTEGPLVISDDLNGLTFLRRTVTRDPAGWFGKLEQSSILRQMYWTRGPNHG
DPAETMIPHSQRPIQLMSLLGEAALHGPAFYSKVSKLVIAELKEGGMDFYVPRQEPMF
RWMRFSDLSTWEGDRNLAPSFVNEDGVE"
CDS 5072..6694
/codon_start=1
/product="ORF2"
/protein_id="ATN23662.1"
/translation="MKMASNDATPSDGPAASLVPAVNNEVMALDPVVGAAIAAPVAGQ
QNVIDPWIRNNFVQAPGGEFTVSPRNAPGEILWSAPLGPDLNPYLSHLARMYNGYAGG
VEVQVILAGNAFTAGKIIFAAVPPNFPTEGLSPCQVTMFPHLIIDVRQLEPVLIPLPD
VRNNFYHYNQSNDPTIKLIAMLYTPLRANNAGDDVFTVSCRVLTRPSPDFDFIFLVPP
TVESRTKPFSVPVLTVEEMTNSRFPIPLEKLFTGPSSAFVVQPQNGRCTTDGVLLGTT
QLSPVNICTFRGDVTQIGSTQSYTMNLASQNWNNYDPTEEIPAPLGTPDFVGRIRGML
TQTTKSDGSTRGHVATVSTGSAYFTPKLGRVQFSTDTSNDLEARQNTRFTPVGVIQDG
STTHRNEPQQWVLPEYSGRDSHNVHLAPAVAPTFPGEQLLFFRSTIPGCSGYPNMELD
CLLPQEWVQHFYQESAPAQSDVALLRFVNPDTSRVLFECKLHKQGFVTVAHTGQHDLI
IPPNGYFRFDSWVNQFYTLAPMGNGAGRRRAL"
CDS 6694..7500
/codon_start=1
/product="ORF3"
/protein_id="ATN23663.1"
/translation="MAGAFFAGLASDVLGSGLSSLINAGAGTINQKVDFDNNRKLQQA
SFQYSSNLQQASFQHDKEMLQAQIEATKKLQQEMMKIKQTMLLEGGFSETDAARGAVN
APMTKVLDWSGTRYWAPDARITTYNAGHFSTPQPSGAPPGRTNLRATTPARGSSSTLS
NASTVTSVHSNQTASTRLGSTAGSGTSVSSLPSTARTRSWVEDQNRNLSPFMRGVHNI
SFVTPPSSRSSSQGTVSTVPKEVLDSWTGAFNTRRQPLFAHIRKRGESRV"
ORIGIN
1 gcgtctaacg acgcttccgc tgccgctgtt gctaacagca acaacgacac cgcaaaatct
61 tcaagtgacg gagtgctttc tagcatggct gtcactttta aacgagccct cggggcgcgg
121 cctaagcagc ctcccccgag ggaaatacca caaagacccc cacgaccacc tactccagaa
181 ctggtcaaaa atatcccccc tcccccgccc aatggagagg atgaaatagt ggtttcttat
241 agtgtcaaag atggtatttc cggtttgcct gatctttcca ccgtcaggca accggaagaa
301 tctaacacgg ccttcagtgt ccctccactc aatcagaggg agaatagaga tgctgtggag
361 ccattacctg gaacaattct ggaaatgtgg gatggagaaa tctaccatta tggcatatat
421 gtggagcgag gtcttgtact aggcgtgcac aaaccaccag ccgccattag cctcgctagg
481 atcgagctaa caccactctc cttgtactgg agacctgtgt atacccctca atacctcatc
541 tctccagact ctctcaagaa attacatgaa gagacgttcc cctacacagc cttcgacaac
601 aactgctatg ccttttgttg ttgggtcctg gacctaaacg actcgtggct gagtaggagg
661 atgatccaga gaacaactgg cttcttcagg ccctaccaag aatggaacag gaaacctctc
721 cccactatgg atgattccaa gctaaagaag gtggctaaca tattcctgtg tgctctgtct
781 tcgctattca ccaggcccat aaaagatata atagggaagc taaggcctct taacatcctt
841 aacatcttgg cctcatgtga ttggactttt gcaggcatag tggagtcttt gatactcttg
901 gcagaactct ttggagtttt ctggacaccc ccagatgtgt ctgcgatgat tgcccccttg
961 ctcggtgatt tccagttgca aggaccggag gaccttgcgg tggaactcgt ccctgtagtg
1021 atggggggaa ttggtttggt gttagggttc accaaagaga agattggtaa gatgttgtca
1081 tctgctgcgt ccaccttgag agcttgtaaa gatcttggtg catatgggct agagatccta
1141 aagttgatta tgaagtggtt cttcccgaag aaagaggaag caaatgaact ggctatagta
1201 agatccatcg aggatgcagt cctggatctc gaggcaattg aaaacaatca cttaaccatc
1261 ttgctcaaag acaaagacag tctggcaacc tacatgagaa cccttgatct tgaggaggag
1321 aaagccagga aactctcaac caagtctgct tcacctgaca ttgtgggcac aatcaacgcc
1381 cttctggcaa ggatcgctgc tgcacgttct ctggtgcatc gagcgaagga ggaactttcc
1441 agcagaccaa gacctgtagt attgatgata tcaggcagac caggaatagg gaagacccac
1501 cttgctaggg aagtggccaa gagaatcgca gcctccctta caggagacca gcgcgtgggc
1561 ctcatcccac gcaatggtgt cgaccattgg gatgcgtaca agggtgagag ggtcgtccta
1621 tgggatgact atggaatgag caatcccatc cacgatgccc tcaggttgca agaactcgct
1681 gacacttgcc ctctcaccct aaactgtgac aggattgaga ataaaggaaa ggtttttgac
1741 agcgatgtca tcatcatcac cactaatctg gccaacccag caccactgga ctacgtcaac
1801 tttgaagcat gctcgaggcg catcgacttc ctcgtgtatg cagaagctcc tgaagtcgag
1861 aaggcgaagc gtgacttccc aggccagccc gacatgtgga agaacgcctt cagctctgat
1921 ttctcacaca taaaactagc attggctcca cagggtggct tcgacaagaa cgggaacacc
1981 ccacacggga agggcgtcat gaagactctc accactggct cccttattgc tcgggcatca
2041 gggctactcc atgagaggtt agatgagttt gaaatgcagg gtccagctct caccaccttc
2101 aactttgatc gcaacaaagt gcttgccttt agacaacttg ctgctgaaaa caaatatggg
2161 ttgatagaca caatgaaagt tgggaggcag ctcaaggatg tcagaacaat gccagaactt
2221 aagcaagcac tcaagaatat ctcaatcaag aagtgccaga tagtgtatgg tggttgcacc
2281 tacacacttg agtctgatgg caagggtaat gtgaaagttg ataaagttca aagcgcctcc
2341 gtgcagacca acaatgagct gactggcgcc ctgcaccacc tacggtgcgc cagaatcaga
2401 tactacgtca agtgtgtcca ggaggccctg tattccatca tccagattgc tggggctgca
2461 tttgtcacca cgcgcatcgt caagcgcatg aacatacaag acctatggtc cagaccacaa
2521 gtggagaaca cagaggagac taccagcaag gacgggtgtc caaaacccag agatgatgag
2581 gagttcgtca tttcatccga cgacatcaaa actgagggta agaaaggaaa gaacaagact
2641 ggtcgcggca agaaacacac agccttctca agcaaaggtc tcagtgatga agagtacgat
2701 gagtacaaaa ggattagaga ggaaaggaat ggcaggtact ccatagaaga ataccttcag
2761 gacagggaca aatactacga ggaggtggcc attgccaggg caaccgagga ggacttctgt
2821 gaggaggaag aggccaagat ccggcaaagg atcttcaggc catcaaggaa acaacgcaag
2881 gaggaaaggg cttctctcgg tttggtcaca ggctctgaaa ttagaaaaag aaatccagat
2941 gatttcaaac ccaaggggaa actatgggct gatgatgaca gaagtgtgga ctacaacgag
3001 aaactcagtt ttgaagcccc accaagcatc tggtcgagga tagtcaactt tggttcaggt
3061 tggggattct gggtctcccc cagtttgttc ataacatcaa cccatgtcat accccagggc
3121 acaaaggagt tctttggagt ccctatcaaa caaattcagg tacacaaatc aggcgagttc
3181 tgtcgcttga gattcccaaa gccaatcagg actgatgtga caggcatgat cttagaagaa
3241 ggtgcacccg agggcaccgt ggttacactg ctcatcaaaa ggcccactgg agaactcatg
3301 cccctggcag ttaggatggg gacccatgca accatgagaa ttcaagggcg cgctgttgga
3361 ggccaaatgg gcatgcttct gacaggatcc aacgccaaaa gcatggatct gggtaccaca
3421 ccaggtgatt gtggctgtcc ttacatctac aagagaggaa atgactatgt ggtcattggg
3481 gtccacacgg ctgccgctcg tggggggaac actgttatat gtgccaccca gggaagtgag
3541 ggagaggcca tacttgaagg tggtgacaat aaagggacat actgtggtgc accaatccta
3601 ggaccaggga atgccccaaa acttagcacc aagaccaagt tctggagatc gtccacagca
3661 ccactcccac ctggtaccta cgagccagcc tatcttggtg gcaaggaccc cagagtcaag
3721 ggtggccctt cactgcagca agtcatgagg gatcaattga agccgttcac agagcctagg
3781 ggcaagccac caaagccaag tgtgctagaa gctgccaaga aaaccatcat caatgttctt
3841 gagcaaacaa ttgatccgcc tgagaaatgg tcattcgcac aagcttgcgc gtcccttgac
3901 aagaccactt ccagtggcca cccgcaccac atgcggaaaa acgactgctg gaacggggaa
3961 tccttcacag gcaagctggc agaccaggct tccaaggcca acctaatgtt tgaagaagga
4021 aagaacatga ccccagtcta cacagctgcg cttaaggatg aattagttaa aactgacaaa
4081 atctataaaa agatcaagaa gagactcctc tggggctcgg atttggcgac catgatccgg
4141 tgtgctcgag cattcggagg cctaatggat gaactcaaag cgcactgtgt ctcacttccc
4201 attagagttg gtatgaatat gaatgaggat ggccccatca tcttcgagag gcattccagg
4261 tacacatacc actatgatgc tgattactca cgatgggatt caacacaaca gagagacgta
4321 ttggcagcag ctctagaaat catggttaaa ttctccccag aaccacattt ggctcaggta
4381 gtcgcagaag accttctctc tcctagcgtg gtggacgtgg gtgacttcac aatatcaatc
4441 aacgagggtc ttccctctgg ggtgccctgc acctcccaat ggaattccat cgcccactgg
4501 cttctcactc tctgtgcgct ctctgaagtt acaaatttgt ctcctgacac catacaggct
4561 aattccctct tctcttttta tggtgatgat gaaattgtta gcacagacat aaaattggac
4621 ccagaaaagt tgacagcaaa actcagggaa tatgggttaa agccaacccg ccctgataaa
4681 actgaaggac cccttgtcat ctctgacgac ttgaatggcc tgactttcct gcggagaact
4741 gtgacccgcg acccagctgg ttggtttgga aaactggagc agagttcaat actcaggcaa
4801 atgtactgga ctaggggtcc caaccacggg gatccagctg aaacaatgat tccacactct
4861 caaagaccca tacaattgat gtccctactg ggggaggctg cacttcacgg cccagcattc
4921 tacagcaaag tcagcaagtt ggtcatcgca gagctaaaag agggtggcat ggatttttac
4981 gtgcccagac aagagccaat gttcagatgg atgaggttct cagatctgag cacgtgggag
5041 ggcgatcgca atctggctcc cagttttgtg aatgaagatg gcgtcgaatg acgccacccc
5101 atctgatggg cccgcagcca gcctcgtccc agcggtcaac aatgaggtta tggctttgga
5161 tcccgttgtt ggtgccgcta ttgcagcacc tgtagcgggc caacaaaatg taattgaccc
5221 ctggattaga aataattttg tacaagcccc tggtggagaa ttcacagtat cccctagaaa
5281 cgctccaggt gaaatactat ggagcgcgcc cttgggccct gatttgaatc cttacctttc
5341 ccatttggcc agaatgtata atggttatgc aggtggtgtt gaagtgcagg taattctcgc
5401 ggggaacgcg ttcaccgccg ggaaaatcat atttgcagca gtcccaccaa atttcccaac
5461 cgaaggactg agcccctgcc aagtcactat gttcccccat ttgataatag atgttagaca
5521 actggaacct gtgttgatcc ccttgcctga tgttaggaac aatttctacc attacaatca
5581 atcaaatgac cccaccatca aattgatagc aatgctgtac acaccactta gggctaataa
5641 tgctggggac gatgtcttca cagtctcttg tcgagttctc acgagaccat cccccgattt
5701 tgatttcata tttctggtgc cacccacagt tgagtcaaga accaaaccat tctctgtccc
5761 agtcttaact gttgaggaga tgaccaactc aagattcccc attcctttag aaaagttgtt
5821 cacgggtccc agcagtgcct ttgttgttca accacaaaat ggcagatgca cgactgatgg
5881 cgtgctctta ggtactaccc aactgtctcc tgtcaacatc tgcaccttca gaggggatgt
5941 cactcaaatt ggaagtactc aaagttacac aatgaacctg gcctcccaaa attggaataa
6001 ttatgatcca acagaagaaa tcccagcccc cctgggaacc ccagattttg taggaaggat
6061 ccgaggcatg ctcacccaaa ccacaaagag tgatggctcg acccgtggtc acgtagccac
6121 agtgagcact ggaagtgctt attttactcc aaagttgggc agagttcaat tctccactga
6181 cacaagcaat gaccttgaag ctcgccaaaa cacgagattc accccagtcg gcgtcatcca
6241 ggatggtagt accacccacc gaaatgaacc ccaacaatgg gtgctcccag agtattcagg
6301 tagagatagt cacaatgtac acctagcacc tgctgtggcc cccacttttc cgggcgagca
6361 acttcttttc tttaggtcca ctatacccgg atgcagcggg taccccaaca tggaattgga
6421 ttgcctactc ccccaggagt gggtgcagca cttctaccaa gaatcagccc cagcacaatc
6481 tgatgtggca ctgctgagat ttgtgaatcc agacacaagt agggttttgt ttgagtgcaa
6541 gcttcacaag caaggctttg taacagtggc tcatactggc caacatgatt tgattatccc
6601 tcccaatggc tattttagat ttgattcctg ggttaaccaa ttctacacac ttgcccccat
6661 gggaaatgga gcggggcgaa gacgtgcatt ataatggctg gagctttctt tgctggatta
6721 gcatctgatg tccttggctc tggacttagc tctctaatca atgctggggc tgggaccatt
6781 aatcaaaaag ttgattttga caataataga aaattgcaac aagcttcctt ccaatatagt
6841 agcaatctac aacaggcttc ctttcaacat gataaagaga tgctccaagc acaaattgag
6901 gccaccaaaa agttacaaca ggaaatgatg aaaattaaac agacaatgct cctagagggt
6961 gggttctctg agacagatgc agcccgtggg gcagtcaacg cccccatgac aaaggttttg
7021 gactggagcg gaacaaggta ctgggctccc gatgctagga ttacaacata caatgcaggc
7081 cacttttcca cccctcaacc ctcgggagca ccaccaggga gaaccaatct cagggctact
7141 acccccgctc gaggctcctc cagtacactt tcaaatgctt ctactgttac ttctgtgcac
7201 tcaaatcaaa ctgcttcaac gagacttggt tctacagctg gttctggcac cagtgtctcg
7261 agcctcccgt caactgcaag gactaggagc tgggttgagg atcaaaacag gaacttgtca
7321 cctttcatga ggggggtcca caacatatca tttgtcaccc caccatctag cagatcctct
7381 agccaaggca cagtctcaac cgtgcctaaa gaagttttgg actcctggac tggcgctttc
7441 aacacgcgca ggcagcctct cttcgcccac attcgtaagc gaggggagtc acgggtgtaa
7501 tgtgaaaaga caaaattgat tatccttctt ttctttagtg tctttt
//