Typing tool
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Typing tool
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Complete norovirus genomes
| MF140663 | GII.4 Farmington Hills | |
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| GII.P4 Yerseke |
ORF1: 1..5085
ORF2: 5066..6688
ORF3: 6688..7494
LOCUS MF140663 7544 bp RNA linear VRL 24-OCT-2017
DEFINITION Norovirus GII strain
Norovirus/GII/Hu/NL/2010/GII.P4-GII.4/Rotterdam/E7800021_p15_d495
ORF1 gene, partial cds; and ORF2 and ORF3 genes, complete cds.
ACCESSION MF140663
VERSION MF140663.1
KEYWORDS .
SOURCE Norovirus GII
ORGANISM Norovirus GII
Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes;
Picornavirales; Caliciviridae; Norovirus; Norwalk virus.
REFERENCE 1 (bases 1 to 7544)
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 7544)
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..7544
/organism="Norovirus GII"
/mol_type="genomic RNA"
/strain="Norovirus/GII/Hu/NL/2010/GII.P4-
GII.4/Rotterdam/E7800021_p15_d495"
/host="Homo sapiens"
/db_xref="taxon:122929"
/country="Netherlands"
/collection_date="12-Oct-2010"
/note="genotype: GII.P4-GII.4"
CDS <1..5085
/codon_start=1
/product="ORF1"
/protein_id="ATN23685.1"
/translation="SDASAAAVANSNNDTAKSSSDGVFSNMAVTFKRALGARPKQPPP
REIPQKPPRPPTPELVKNIPPPPPNGEDEIVVSYSVKDGISGLPDLSTVRQPEESNTA
FSVPPLNQRENRDAVEPLPGTILEMWDGEIYHYGIYVERGLVLGVHKPPAAISLARIE
LTPLSLYWRPVYTPQYLISPDSLKKLHEETFPYTAFDNNCYAFCCWVLDLNDSWLSRR
MIQRTTGFFRPYQEWNRKPLPTMDDSKLKKVANIFLCALSSLFTRPIKDIIGKLRPLN
ILNILASCDWTFAGIVESLILLAELFGVFWTPPDVSAMIAPLLGDFQLQGPEDLAVEL
VPVVMGGIGLVLGFTKEKIGKMLSSAASTLRACKDLGAYGLEILKLIMKWFFPKKEEA
NELAMVRSIEDAVLDLEAIENNHLTILLKDKDSLATYMRTLDLEEEKARKLSTKSASP
DIVGTINALLARIAAARSLVHRAKEELSSRPRPVVLMISGRPGIGKTHLAREVAKKIA
ASLTGDQRVGLIPRNGVDHWDAYKGERVVLWDDYGMSNPIHDALRLQELADTCPLTLN
CDRIENKGKVFDSDVIIITTNLANPAPLDYVNFEACSRRIDFLVYAEAPEVEKAKRDF
PGQPDMWKNAFSSDFSHIKLALAPQGGFDKNGNTPHGKGVMKTLTTGSLIARASGLLH
ERLDEFEMQGPALTTFNFDRNKVLAFRQLAAENKYGLIDTMKVGRQLKDVRTMPELKQ
ALKNISIKKCQIVYGGCTYTLESDGKGNVKVDKVQSASVQTNNELTGALHHLRCARIR
YYVKCVQEALYSIIQIAGAAFVTTRIVKRMNIQDLWSRPQVENTEETTSKDGCPKPRD
DEEFVISSDDIKTEGKKGKNKTGRGKKHTAFSSKGLSDEEYDEYKRIREERNGRYSIE
EYLQDRDKYYEEVAIARATEEDFCEEEEAKIRQRIFRPSRKQRKEERASLGLVTGSEI
RKRNPDDFKPKGKLWADDDRNVDYNEKLSFEAPPSIWSRIVNFGSGWGFWVSPSLFIT
STHVIPQGTKEFFGVPIKQIQVHKSGEFCRLRFPKPIRTDVTGMILEEGAPEGTVVTL
LIKRPTGELMPLAVRMGTHATMRIQGRAVGGQMGMLLTGSNAKSMDLGTTPGDCGCPY
IYKRGNDYVVIGVHTAAARGGNTVICATQGSEGEAILEGGDNKGTYCGAPILGPGNAP
KLSTKTKFWRSSTAPLPPGTYEPAYLGGKDPRVKGGPSLQQVMRDQLKPFTEPRGKPP
KPSVLEAAKKTIINVLEQTIDPPEKWSFAQACASLDKTTSSGHPHHMRKNDCWNGESF
TGKLADQASKANLMFEEGKNMTPVYTAALKDELVKTDKIYKKIKKRLLWGSDLATMIR
CARAFGGLMDELKAHCVSLPIRVGMNMNEDGPIIFERHSRYTYHYDADYSRWDSTQQR
DVLAAALEIMVKFSPEPHLAQVVAEDLLSPSVVDVGDFTISINEGLPSGVPCTSQWNS
IAHWLLTLCALSEVTNLSPDIIQANSLFSFYGDDEIVSTDIKLDPEKLTAKLREYGLK
PTRPDKTEGPLVISDDLNGLTFLRRTVTRDPAGWFGKLEQSSILRQMYWTRGPNHGDP
TETMIPHSQRPIQLMSLLGEAALHGPAFYSKVSKLVIAELKEGGMDFYVPRQEPMFRW
MRFSDLSTWEGDRNLAPSFVNEDGVE"
CDS 5066..6688
/codon_start=1
/product="ORF2"
/protein_id="ATN23686.1"
/translation="MKMASNDATPSDGPAANLVPAVNNEVMALDPVAGAAIAAPVAGQ
QNVIDPWIRNNFVQAPGGEFTVSPRNAPGEILWSAPLGPDLNPYLSHLARMYNGYAGG
FEVQVILAGNAFTAGKIIFAAVPPNFPTEGISPCQVTMFPHIITDVRQLEPVLIPLPD
VRNNFYHYNQSNEPTIKLIAMLYTPLRANNAGDDVFTVSCRVLTRPSPDFDFIFLVPP
TVESRTKPFSVPVLTVEEMTNSRFPIPLEKLFTGPSSAFVVQPQNGRCTTDGVLLGTT
QLSPVNICTFRGDVTQIGSTQTYTMNLASQNWNNYDPTEEIPAPLGTPDFVGRIQGML
TQTTKSDGSTRGHVATVSTGSAHFTPKLGRIQFSTDTSNDLEARQNTRFTPVGVIQDG
STTHRNEPQQWVLPEYSGRDNHNVHLAPAVAPTFPGEQLLFFRSTIPGCSGYPNMELD
CLLPQEWVQHFYQESAPAQSDVALLRFVNPDTSRVLFECKLHKQGFVTVAHTGQHDLI
IPPNGYFRFDSWVNQFYTLAPMGNGTGRRRAL"
CDS 6688..7494
/codon_start=1
/product="ORF3"
/protein_id="ATN23687.1"
/translation="MAGAFFAGLASDVLGSGLSSLINAGAGTINQKVDFDNNRKLQQA
SFQYSSNLQQASFQHDKEMLQAQIEATKKLQQEMMKIKQTMLLEGGFSETDAARGAIN
APMTKVLDWSGTRYWAPDARITTYNAGHFSTPQPSGAPPGRTNLRATTPARGSSSTLS
NASTVTSVHSNQTASTRLGSTAGSGTSVSSLPSTARTRSWVEDQNRNLSPFMRGVHNI
SFVTPPSSRSSSQGTVSTVPKEVLNSWTGAFNTRRQPLFAHIRQRGESRV"
ORIGIN
1 tccgacgctt ccgctgccgc tgttgccaac agcaacaacg acaccgcaaa atcttcaagt
61 gacggagtgt tttctaacat ggctgtcact tttaaacgag ccctcggggc gcggcctaaa
121 cagcctcccc cgagggaaat accacaaaaa cccccacgac cacctactcc agaactggtc
181 aaaaatatcc cccctccccc gcccaacgga gaggatgaaa tagtggtttc ttacagtgtc
241 aaagatggta tttccggttt gcctgatctt tccaccgtca ggcaaccgga agaatctaac
301 acggccttca gtgtccctcc actcaatcag agggaaaata gagacgctgt ggaaccatta
361 cctggaacga ttctggaaat gtgggatgga gaaatctacc attatggcat atatgtggag
421 cgaggtcttg tactaggcgt gcacaaacca ccagccgcca ttagcctcgc taggatcgag
481 ctaacaccac tctccttgta ctggagacct gtgtataccc ctcaatacct catctctcca
541 gactctctca agaaattaca tgaagagacg ttcccctaca cagccttcga caacaactgc
601 tatgcctttt gttgttgggt cctggaccta aacgactcat ggctgagtag gaggatgatc
661 cagagaacaa ctggcttctt caggccctac caagaatgga acaggaaacc tctccccact
721 atggatgatt ccaaactaaa gaaggtggct aacatattcc tgtgtgctct gtcttcgcta
781 ttcaccaggc ccataaaaga tataataggg aagctaaggc ctcttaacat ccttaacatc
841 ttggcctcat gtgattggac ttttgcaggc atagtggagt ctttgatact cttggcagaa
901 ctctttggag ttttctggac acccccagat gtgtctgcga tgattgcccc cttgctcggt
961 gatttccagt tgcaaggacc ggaggacctt gcggtggaac tcgtccctgt agtgatgggg
1021 ggaattggtt tggtgttagg gttcaccaaa gagaagattg gcaagatgct gtcatctgct
1081 gcgtccacct tgagagcttg taaagatctt ggtgcatatg ggctagagat cctaaagttg
1141 attatgaagt ggttcttccc gaagaaagag gaagcaaatg aactggctat ggtaagatcc
1201 atcgaggatg cagtcctgga cctcgaggca attgaaaaca atcacttaac catcttgctc
1261 aaagacaaag acagtctggc aacctacatg agaacccttg atcttgagga ggagaaagcc
1321 aggaaactct caaccaaatc tgcttcacct gacattgtgg gcacaatcaa cgcccttctg
1381 gcaaggatcg ctgctgcacg ttctctggtg catcgagcga aggaggaact ttccagcaga
1441 ccaagacctg tagtgttgat gatatcaggc agaccaggaa tagggaagac ccaccttgct
1501 agggaagtgg ccaagaaaat cgcagcctcc cttacaggag accagcgcgt gggcctcatc
1561 ccacgcaatg gtgtcgacca ttgggatgcg tacaagggtg agagggtcgt cctatgggat
1621 gactatggaa tgagcaatcc catccacgat gccctcaggt tgcaagaact cgctgacact
1681 tgccctctca ccctaaactg tgacaggatt gagaacaaag gaaaggtttt tgacagcgat
1741 gtcatcatca tcaccactaa tctggccaac ccagcaccac tggactacgt caactttgaa
1801 gcatgctcga ggcgcatcga cttcctcgtg tatgcagaag ctcctgaagt cgagaaggcg
1861 aagcgtgact tcccaggcca gcccgacatg tggaagaacg ccttcagctc tgatttctca
1921 cacataaaac tagcattggc tccacagggt ggcttcgaca agaacgggaa caccccacac
1981 gggaagggcg tcatgaagac tctcaccact ggctccctta ttgctcgggc atcaggtctg
2041 ctccatgaga ggttagatga gtttgaaatg cagggtccag ctctcaccac cttcaacttt
2101 gatcgcaaca aagtgcttgc ctttagacaa cttgctgctg aaaacaaata tgggttgata
2161 gacacaatga aagttgggag gcagctcaag gatgtcagaa caatgccaga acttaagcaa
2221 gcactcaaga atatctcaat caagaagtgc cagatagtgt atggtggttg cacctacaca
2281 cttgagtctg atggcaaggg taatgtgaaa gttgataaag ttcaaagcgc ctccgtgcag
2341 accaacaatg agctgactgg cgccctgcac cacctacggt gcgccagaat cagatactac
2401 gtcaagtgtg tccaggaggc cctgtactcc atcatccaga ttgctggagc tgcatttgtc
2461 accacgcgca tcgtcaagcg catgaacata caagacctat ggtccagacc acaagtggag
2521 aacacagagg agactaccag caaggacggg tgtccaaaac ccagagatga tgaggagttc
2581 gtcatttcat ccgacgacat caaaactgag ggtaagaaag gaaagaacaa gactggtcgc
2641 ggcaagaaac acacagcctt ctcaagcaaa ggtctcagtg atgaagagta cgatgagtac
2701 aaaaggatta gagaggaaag gaatggcagg tactccatag aagaatacct tcaggacagg
2761 gacaaatact acgaggaggt ggccattgcc agggcaaccg aggaggactt ctgtgaggag
2821 gaagaggcca agatccggca aaggatcttc aggccgtcaa ggaaacaacg caaggaggaa
2881 agggcttctc tcggtttggt cacaggctct gaaattagaa aaagaaatcc agatgatttc
2941 aaacccaagg ggaaactatg ggctgatgat gacaggaatg tggactacaa cgagaaactc
3001 agttttgaag ccccaccaag catctggtcg aggatagtca actttggttc aggttgggga
3061 ttctgggtct cccccagttt gttcataaca tcaacccatg tcatacccca gggcacaaag
3121 gagttctttg gagtccctat caaacaaatc caggtacaca aatcaggcga gttctgtcgc
3181 ttgagattcc caaagccaat caggactgat gtgacaggca tgatcttaga agaaggtgca
3241 cccgagggca ccgtggttac actgctcatc aaaaggccca ctggagaact catgcccctg
3301 gcagttagga tggggaccca tgcaaccatg agaattcaag ggcgcgctgt tggaggccaa
3361 atgggcatgc ttctgacagg gtccaacgcc aaaagcatgg atctgggaac cacaccaggt
3421 gattgtggct gtccttacat ctacaagaga ggaaatgact atgtggtcat tggggtccac
3481 acggctgccg ctcgtggggg gaacactgtt atatgtgcca cccagggaag tgagggggag
3541 gccatacttg aaggtggtga caataaaggg acatactgtg gtgcaccaat cctaggacca
3601 gggaatgccc caaaacttag caccaagacc aagttctgga gatcgtccac agcaccactc
3661 ccacctggta cctacgagcc agcctatctt ggtggcaagg accctagagt caagggtggc
3721 ccttcactgc agcaagtcat gagggatcaa ttgaagccgt tcacagagcc taggggcaag
3781 ccaccaaagc caagtgtgct agaagctgcc aagaaaacca tcatcaatgt tcttgagcaa
3841 acaattgacc cgcctgagaa atggtcattc gcacaagctt gcgcgtccct tgataagacc
3901 acttccagtg gccacccgca ccacatgcgg aaaaacgact gctggaacgg ggaatccttc
3961 acaggcaagc tggcagacca ggcttccaag gccaacctaa tgtttgaaga aggaaagaac
4021 atgaccccag tctacacagc tgcgcttaag gatgaattag ttaaaactga caaaatctat
4081 aaaaagatca agaagagact cctctggggc tcggatttgg caaccatgat ccgatgtgct
4141 cgagcattcg gaggcctaat ggatgaactc aaagcgcact gtgtctcact tcccattaga
4201 gttggtatga atatgaatga ggatggcccc atcatcttcg agaggcattc caggtacaca
4261 taccactatg atgctgatta ctcacgatgg gattcaacac aacagagaga cgtattggca
4321 gcagctctag aaatcatggt taaattctcc ccagaaccac atttggctca ggtagtcgca
4381 gaagaccttc tctctcctag cgtggtggac gtgggtgact tcacaatatc aatcaacgag
4441 ggtcttccct ctggggtgcc ctgcacctcc caatggaatt ccatcgccca ctggcttctc
4501 actctctgtg cgctctctga agttacaaat ttgtctcctg acatcataca ggctaattcc
4561 ctcttctctt tttatggtga tgatgaaatt gttagcacag acataaaatt agacccagaa
4621 aagttgacag caaaactcag ggaatatggg ttaaagccaa cccgccctga caaaactgaa
4681 ggaccccttg tcatctctga cgacttgaat ggcctgactt tcctgcggag aactgtgacc
4741 cgcgacccag ctggttggtt tggaaaactg gagcagagtt caatactcag gcaaatgtac
4801 tggactaggg gtcctaacca cggggatcca actgaaacaa tgattccaca ctctcaaaga
4861 cccatacaat tgatgtccct actgggggag gctgcacttc acggcccagc attctacagc
4921 aaagtcagca agttggtcat tgcagagcta aaagagggtg gcatggattt ttacgtgccc
4981 agacaagagc cgatgttcag atggatgagg ttctcagatc tgagcacgtg ggagggcgat
5041 cgcaatctgg ctcccagttt tgtgaatgaa gatggcgtcg aatgacgcca ccccatctga
5101 tgggcccgca gccaacctcg tcccagcggt caacaatgag gttatggctt tggaccccgt
5161 tgctggtgcc gctattgcag cacctgtagc gggccaacaa aatgtaattg acccctggat
5221 tagaaataat tttgtacaag cccctggtgg agaattcaca gtatccccta gaaacgctcc
5281 aggtgaaata ctatggagcg cgcccttggg ccctgatttg aatccttacc tttcccattt
5341 ggccagaatg tataatggtt atgcaggtgg ttttgaagtg caggtaatcc tcgcggggaa
5401 cgcgttcacc gccgggaaaa tcatatttgc agcagttcca ccaaattttc caaccgaagg
5461 gataagcccc tgccaagtca ctatgttccc ccatataata acagatgtta gacaattgga
5521 acctgtgtta atccccttgc ctgatgttag gaataacttc tatcattata atcaatcaaa
5581 tgaacccacc atcaaattga tagcaatgct gtacacacca cttagggcta ataatgctgg
5641 ggacgatgtc ttcacagtct cttgtcgagt tctcacgaga ccatcccccg attttgattt
5701 catatttctg gtgccaccca cagttgagtc aagaaccaaa ccattctctg tcccagtctt
5761 aactgttgag gagatgacca attcaagatt ccccattcct ttagaaaagt tgttcacggg
5821 tcccagcagt gcctttgttg ttcaaccaca aaatggcaga tgcacgactg atggcgtgct
5881 cttaggtact actcaactgt ctcctgtcaa catctgcacc ttcagagggg atgtcactca
5941 aattggaagt actcaaactt acacaatgaa cctggcctcc caaaattgga ataattatga
6001 tccaacagaa gaaatcccag cccccctggg aaccccagat tttgtaggaa ggatccaagg
6061 catgctcacc caaaccacaa agagtgatgg ctcgacccgt ggtcacgtag ccacagtgag
6121 cactggaagt gctcatttta ctccaaagtt gggcagaatt caattctcca ctgacacaag
6181 caatgacctt gaagctcgcc aaaacacgag attcacccca gtcggcgtca tccaggatgg
6241 tagtaccacc caccgaaatg aaccccaaca atgggtgctc ccagagtatt caggtagaga
6301 taatcacaat gtacacctag cacctgctgt ggcccccact tttccgggcg agcaacttct
6361 tttctttagg tccactatac ccggatgcag cgggtacccc aacatggaat tggattgcct
6421 actcccccag gagtgggtgc agcacttcta ccaagaatca gccccagcac aatctgatgt
6481 ggcactgctg agatttgtga atccagacac aagtagggtt ttgtttgagt gtaagcttca
6541 caagcaaggc tttgtaacag tggctcatac tggccaacat gatttgatta tccctcccaa
6601 tggctatttt agatttgatt cctgggttaa ccaattctac acacttgccc ccatgggaaa
6661 tggaacgggg cgaagacgtg cattataatg gctggagctt tctttgctgg attagcatct
6721 gatgtccttg gctctggact tagctctcta atcaatgctg gggctgggac cattaatcaa
6781 aaagttgatt ttgacaataa tagaaaattg caacaagctt ccttccaata tagtagcaat
6841 ctacaacagg cttcctttca acatgataaa gagatgctcc aagcacaaat tgaggccacc
6901 aaaaagttgc aacaggaaat gatgaaaatt aaacagacaa tgctcctaga gggtgggttc
6961 tctgagacag atgcagcccg tggggcaatc aacgccccca tgacaaaggt tttggactgg
7021 agcggaacaa ggtactgggc tcccgatgct aggattacaa catacaatgc aggccacttt
7081 tccacccctc aaccctcggg agcaccacca gggagaacca atctcagggc tactaccccc
7141 gctcgaggct cctccagtac actttcaaat gcttctactg tcacttctgt gcactcaaat
7201 caaactgctt caacgagact tggttctaca gctggttctg gcaccagtgt ctcgagcctc
7261 ccgtcaactg caaggactag gagctgggtt gaggatcaaa acaggaactt gtcacccttc
7321 atgagggggg tccacaacat atcatttgtc accccaccat ctagcagatc ctctagccaa
7381 ggcacagtct caaccgtgcc taaagaagtt ttgaactcct ggactggcgc tttcaacacg
7441 cgcaggcagc ctctcttcgc ccacattcgt cagcgagggg agtcacgggt ataatgtgaa
7501 aagacaaaat tgattatctt tcttttcttt agtgtctttt aaaa
//