Typing tool
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Typing tool
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Complete norovirus genomes
| MF140660 | GII.4 Farmington Hills | |
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| GII.P4 Yerseke |
ORF1: 1..5093
ORF2: 5074..6696
ORF3: 6696..7495
LOCUS MF140660 7495 bp RNA linear VRL 24-OCT-2017
DEFINITION Norovirus GII strain
Norovirus/GII/Hu/NL/2010/GII.P4-GII.4/Rotterdam/E1300267_p15_d215
ORF1 gene, partial cds; ORF2 gene, complete cds; and ORF3 gene,
partial cds.
ACCESSION MF140660
VERSION MF140660.1
KEYWORDS .
SOURCE Norovirus GII
ORGANISM Norovirus GII
Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes;
Picornavirales; Caliciviridae; Norovirus; Norwalk virus.
REFERENCE 1 (bases 1 to 7495)
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 7495)
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..7495
/organism="Norovirus GII"
/mol_type="genomic RNA"
/strain="Norovirus/GII/Hu/NL/2010/GII.P4-
GII.4/Rotterdam/E1300267_p15_d215"
/host="Homo sapiens"
/db_xref="taxon:122929"
/country="Netherlands"
/collection_date="05-Jan-2010"
/note="genotype: GII.P4-GII.4"
CDS <1..5093
/codon_start=3
/product="ORF1"
/protein_id="ATN23676.1"
/translation="ASNDASAAAVANSNNDTAKSSSDGVFSNMAVTFKRALGARPKQP
PPREIPQKPPRPPTPELVKNIPPPPPNGEDEIVVSYSVKDGISGLPDLSTVRQPEESN
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
DPTETMIPHSQRPIQLMSLLGEAALHGPAFYSKVSKLVIAELKEGGMDFYVPRQEPMF
RWMRFSDLSTWEGDRNLAPSFVNEDGVE"
CDS 5074..6696
/codon_start=1
/product="ORF2"
/protein_id="ATN23677.1"
/translation="MKMASNDATPSDGPAASLVPAVNNEVMALDPVAGAAIAAPVAGQ
QNVIDPWIRNNFVQAPGGEFTVSPRNAPGEILWSAPLGPDLNPYLSHLARMYNGYAGG
VEVQVILAGNAFTAGKIIFAAVPPNFPTEGLSPCQVTMFPHLIIDVRQLEPVLIPLPD
VRNNFYHYNQSNDPTIKLIAMLYTPLRANNAGDDVFTVSCRVLTRPSPDFDFIFLVPP
TVESRTKPFSVPVLTVEEMTNSRFPIPLEKLFTGPSSAFVVQPQNGRCTTDGVLLGTT
QLSPVNICTFRGDVTQIGSTQTYTMNLASQNWNNYDPTEEIPAPLGTPDFVGRIQGML
TQTTKSDGSTRGHVATVSTGSAHFTPKLGRVQFSTDTSNDLEARQNTRFTPVGVIQDG
STTHRNEPQQWVLPDYSGRDSHNVHLAPAVAPTFPGEQLLFFRSTIPGCSGYPNMELD
CLLPQEWVQHFYQESAPAQSDVALLRFVNPDTSRVLFECKLHKQGFLTVAHTGQHDLI
IPPNGYFRFDSWVNQFYTLAPMGNGTGRRRAL"
CDS 6696..>7495
/codon_start=1
/product="ORF3"
/protein_id="ATN23678.1"
/translation="MAGAFFAGLASDVLGSGLSSLINAGAGTINQKVDFDNNRKLQQA
SFQYSSNLQQASFQHDKEMLQAQIEATKKLQQEMMKIKQTMLLEGGFSETDAARGAIN
APMTKVLDWSGTRYWAPDARITTYNAGHFSTPQPSGAPPGRTNLRATTPARGSSSTLS
NASTVTSVHSNQTASTRLGSTAGSGTSVSSLPSTARTRSWVEDQNRNLSPFMRGVHNI
SFVTPPSSRSSSQGTVSTVPKEVLDSWTGAFNTRRQPLFAPTEKRREAR"
ORIGIN
1 tggcgtctaa cgacgcttcc gctgccgctg ttgctaacag caacaacgac accgcaaaat
61 cttcaagtga cggagtgttt tctaacatgg ctgtcacttt taaacgagcc ctcggggcgc
121 ggcctaaaca gcctcccccg agggaaatac cacaaaaacc cccacgacca cctactccag
181 aactggtcaa aaatatcccc cctcccccgc ccaatggaga ggatgaaata gtggtttctt
241 acagtgtcaa agatggtatt tccggtttgc ctgatctttc caccgtcagg caaccggaag
301 aatctaacac ggccttcagt gtccctccac tcaatcagag ggagaataga gacgctgtgg
361 aaccattacc tggaacaatt ctggaaatgt gggatggaga aatctaccat tatggcatat
421 atgtggagcg aggtcttgta ctaggcgtgc acaaaccacc agccgccatt agcctcgcta
481 ggatcgagct aacaccactc tccttgtact ggagacctgt gtatacccct caatatctca
541 tctctccaga ctctctcaag aaattacatg aagagacgtt cccctacaca gccttcgaca
601 acaactgcta tgccttttgt tgttgggtcc tggacctaaa cgactcatgg ctgagtagga
661 ggatgatcca gagaacaact ggcttcttca ggccctacca agaatggaac aggaaacctc
721 tccccactat ggatgattcc aaactaaaga aggtggctaa catattcctg tgtgctctgt
781 cttcgctatt caccaggccc ataaaagata taatagggaa gctaaggcct cttaacatcc
841 ttaacatctt ggcctcatgt gattggactt ttgcaggcat agtggagtct ttgatactct
901 tggcagaact ctttggagtt ttctggacac ccccagatgt gtctgcgatg attgccccct
961 tgctcggtga tttccagttg caaggaccgg aggaccttgc ggtggaactc gtccctgtag
1021 tgatgggggg aattggtttg gtgttagggt tcaccaaaga gaagattggt aagatgttgt
1081 catctgctgc gtccaccttg agagcttgta aagatcttgg tgcatatggg ctagagatcc
1141 taaagttgat tatgaagtgg ttcttcccga agaaagagga agcaaatgaa ctggctatag
1201 taagatccat cgaggatgca gtcctggatc tcgaggcaat tgaaaacaat cacttaacca
1261 tcttgctcaa agacaaagac agtctggcaa cctacatgag aacccttgat cttgaggagg
1321 agaaagccag gaaactctca accaagtctg cttcacctga cattgtgggc acaatcaacg
1381 cccttctggc aaggatcgct gctgcacgtt ctctggtgca tcgagcgaag gaggaacttt
1441 ccagcagacc aagacctgta gtattgatga tatcaggcag accaggaata gggaagaccc
1501 accttgctag ggaagtggcc aagagaatcg cagcctccct tacaggagac cagcgcgtgg
1561 gcctcatccc acgcaatggt gtcgaccatt gggatgcgta caagggtgag agggtcgtcc
1621 tatgggatga ctatggaatg agcaatccca tccacgatgc cctcaggttg caagaactcg
1681 ctgacacttg ccctctcacc ctaaactgtg acaggattga gaataaagga aaggtttttg
1741 acagcgatgt catcatcatc accactaatc tggccaaccc agcaccactg gactacgtca
1801 actttgaagc atgctcgagg cgcatcgact tcctcgtgta tgcagaagct cctgaagtcg
1861 agaaggcgaa gcgtgacttc ccaggccagc ccgacatgtg gaagaacgcc ttcagctctg
1921 atttctcaca cataaaacta gcattggctc cacagggtgg cttcgacaag aacgggaaca
1981 ccccacacgg gaagggcgtc atgaagactc tcaccactgg ctcccttatt gctcgggcat
2041 cagggctact ccatgagagg ttagatgagt ttgaaatgca gggtccagct ctcaccacct
2101 tcaactttga tcgcaacaaa gtgcttgcct ttagacaact tgctgctgaa aacaaatatg
2161 ggttgataga cacaatgaaa gttgggaggc agctcaagga tgtcagaaca atgccagaac
2221 ttaagcaagc actcaagaat atctcaatca agaagtgcca gatagtgtat ggtggttgca
2281 cctacacact tgagtctgat ggcaagggta atgtgaaagt tgataaagtt caaagcgcct
2341 ccgtgcagac caacaatgag ctgactggcg ccctgcacca cctacggtgc gccagaatca
2401 gatactacgt caagtgtgtc caggaggccc tgtattccat catccagatt gctggggctg
2461 catttgtcac cacgcgcatc gtcaagcgca tgaacataca agacctatgg tccagaccac
2521 aagtggagaa cacagaggag actaccagca aggacgggtg tccaaaaccc agagatgatg
2581 aggagttcgt catttcatcc gacgacatca aaactgaggg taagaaagga aagaacaaga
2641 ctggtcgcgg caagaaacac acagccttct caagcaaagg tctcagtgat gaagagtacg
2701 atgagtacaa aaggattaga gaggaaagga atggcaggta ctccatagaa gaataccttc
2761 aggacaggga caaatactac gaggaggtgg ccattgccag ggcaaccgag gaggacttct
2821 gtgaggagga agaggccaag atccggcaaa ggatcttcag gccatcaagg aaacaacgca
2881 aggaggaaag ggcttctctc ggtttggtca caggctctga aattagaaaa agaaatccag
2941 atgatttcaa acccaagggg aaactatggg ctgatgatga cagaagtgtg gactacaacg
3001 agaaactcag ttttgaagcc ccaccaagca tctggtcgag gatagtcaac tttggttcag
3061 gttggggatt ctgggtctcc cccagtttgt tcataacatc aacccatgtc ataccccagg
3121 gcacaaagga gttctttgga gtccctatca aacaaattca ggtacacaaa tcaggcgagt
3181 tctgtcgctt gagattccca aagccaatca ggactgatgt gacaggcatg atcttagaag
3241 aaggtgcacc cgagggcacc gtggttacac tgctcatcaa aaggcccact ggagaactca
3301 tgcccctggc agttaggatg gggacccatg caaccatgag aattcaaggg cgcgctgttg
3361 gaggccaaat gggcatgctt ctgacaggat ccaacgccaa aagcatggat ctgggtacca
3421 caccaggtga ttgtggctgt ccttacatct acaagagagg aaatgactat gtggtcattg
3481 gggtccacac ggctgccgct cgtgggggga acactgttat atgtgccacc cagggaagtg
3541 agggagaggc catacttgaa ggtggtgaca ataaagggac atactgtggt gcaccaatcc
3601 taggaccagg gaatgcccca aaacttagca ccaagaccaa gttctggaga tcgtccacag
3661 caccactccc acctggtacc tacgagccag cctatcttgg tggcaaggac cccagagtca
3721 agggtggccc ttcactgcag caagtcatga gggatcaatt gaagccgttc acagagccta
3781 ggggcaagcc accaaagcca agtgtgctag aagctgccaa gaaaaccatc attaatgttc
3841 ttgagcaaac aattgatccg cctgagaaat ggtcattcgc acaagcttgc gcgtcccttg
3901 acaagaccac ttccagtggc cacccgcacc acatgcggaa aaacgactgc tggaacgggg
3961 aatccttcac aggcaagctg gcagatcagg cttccaaggc caacctaatg tttgaagaag
4021 gaaagaacat gaccccagtc tacacagctg cgcttaagga tgaattagtt aaaactgaca
4081 aaatctataa aaagatcaag aagagactcc tctggggctc ggatttggcg accatgatcc
4141 ggtgtgctcg agcattcgga ggcctaatgg atgaactcaa agcgcactgt gtctcacttc
4201 ccattagagt tggtatgaat atgaatgagg atggccctat catcttcgag aggcattcca
4261 ggtacacata ccactatgat gctgattact cacgatggga ttcaacacaa caaagagacg
4321 tattggcagc agctctagaa atcatggtta aattctcccc agaaccacat ttggctcagg
4381 tagtcgcaga agaccttctc tctcctagcg tggtggacgt gggtgacttc acaatatcaa
4441 tcaacgaggg tcttccctct ggggtgccct gcacctccca atggaattcc atcgcccact
4501 ggcttctcac tctctgtgcg ctctctgaag ttacaaattt gtctcctgac accatacagg
4561 ctaattccct cttctctttt tatggtgatg atgaaattgt tagcacagac ataaaattgg
4621 acccagaaaa gttgacagca aaactcaggg aatatgggtt aaagccaacc cgccctgata
4681 aaactgaagg accccttgtc atctctgacg acttgaatgg cctgactttc ctgcggagaa
4741 ctgtgacccg cgacccagct ggttggtttg gaaaactgga gcagagttca atactcaggc
4801 aaatgtactg gactaggggt cccaaccacg gggatccaac tgaaacaatg attccacact
4861 ctcaaagacc catacaattg atgtccctac tgggggaggc tgcacttcac ggcccagcat
4921 tctacagcaa agtcagcaag ttggtcattg cagagctaaa agagggtggc atggattttt
4981 acgtgcccag acaagagcca atgttcagat ggatgaggtt ctcagatctg agcacgtggg
5041 agggcgatcg caatctggct cccagttttg tgaatgaaga tggcgtcgaa tgacgccacc
5101 ccatctgatg ggcccgcagc cagcctcgtc ccagcggtca acaatgaggt tatggctttg
5161 gaccccgttg ctggtgccgc tattgcagca cctgtagcgg gccaacaaaa tgtaattgac
5221 ccctggatta gaaataattt tgtacaagcc cctggtggag aattcacagt atcccctaga
5281 aacgctccag gtgaaatact atggagcgcg cccttgggcc ctgatttgaa tccttacctt
5341 tcccatttgg ccagaatgta taatggttat gcaggtggtg ttgaagtgca ggtaattctc
5401 gcggggaacg cgttcaccgc cgggaaaatc atatttgcag cagtcccacc aaatttccca
5461 accgaaggac tgagcccctg ccaagtcact atgttccccc atttgataat agatgttaga
5521 caactggaac ctgtgttgat ccccttgcct gatgttagga acaatttcta ccattacaat
5581 caatcaaatg accccaccat caaattgata gcaatgctgt acacaccact tagggctaat
5641 aatgctgggg acgatgtctt cacagtctct tgtcgagttc tcacgagacc atcccccgat
5701 tttgatttca tatttctggt gccacccaca gttgagtcaa gaaccaaacc attctctgtc
5761 ccagtcttaa ctgttgagga gatgaccaac tcaagattcc ccattccttt agaaaagttg
5821 ttcacgggtc ccagcagtgc ctttgttgtt caaccacaaa atggcagatg cacgactgat
5881 ggcgtgctct taggtactac tcaactgtct cctgtcaaca tctgcacctt cagaggggat
5941 gtcactcaaa ttggaagtac tcaaacttac acaatgaacc tggcctccca aaattggaat
6001 aattatgatc caacagaaga aatcccagcc cccctgggaa ccccagattt tgtaggaagg
6061 atccaaggca tgctcaccca aaccacaaag agtgatggct cgacccgtgg tcacgtagcc
6121 acagtgagca ctggaagtgc tcattttact ccaaagttgg gcagagttca attctccact
6181 gacacaagca atgaccttga agctcgccaa aacacgagat tcaccccagt cggcgtcatc
6241 caggatggta gtaccaccca ccgaaatgaa ccccaacaat gggtgctccc agattattca
6301 ggtagagata gtcacaatgt acacctagca cctgctgtgg cccccacttt tccgggcgag
6361 caacttcttt tctttaggtc cactataccc ggatgcagcg ggtaccccaa catggaattg
6421 gattgcctac tcccccagga gtgggtgcag cacttctacc aagaatcagc cccagcacaa
6481 tctgatgtgg cactgctgag atttgtgaat ccagacacaa gtagggtttt gtttgagtgc
6541 aagcttcaca agcaaggctt tttaacagtg gctcatactg gccaacatga tttgattatc
6601 cctcccaatg gctattttag atttgattcc tgggttaacc aattctacac acttgccccc
6661 atgggaaatg gaacggggcg aagacgtgca ttataatggc tggagctttc tttgctggat
6721 tagcatctga tgtccttggc tctgggctta gctctctaat caatgctggg gctgggacca
6781 ttaatcaaaa agttgatttt gacaataata gaaaattgca acaagcttcc ttccaatata
6841 gtagcaatct acaacaggct tcctttcaac atgataaaga gatgctccaa gcacaaattg
6901 aggccaccaa aaagttgcaa caagaaatga tgaaaattaa acagacaatg ctcctagagg
6961 gtgggttctc tgagacagat gcagcccgtg gggcaatcaa cgcccccatg acaaaggttt
7021 tggactggag cggaacaagg tactgggctc ccgatgctag gattacaaca tacaatgcag
7081 gccacttttc cacccctcaa ccctcgggag caccaccagg gagaaccaat ctcagggcta
7141 ctacccccgc tcgaggctcc tccagtacac tttcaaatgc ttctactgtc acttctgtgc
7201 actcaaatca aactgcttca acgagacttg gttctacagc tggttctggc accagtgtct
7261 cgagcctccc gtcaactgca aggactagga gctgggttga ggatcaaaac aggaacttgt
7321 cacctttcat gaggggggtc cacaacatat catttgtcac cccaccatct agcagatcct
7381 ctagccaagg cacagtctca accgtgccta aagaagtttt ggactcctgg actggcgctt
7441 tcaacacgcg caggcagcct ctcttcgccc ccacggaaaa gcgccgggag gcacg
//