Typing tool
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Typing tool
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Complete norovirus genomes
| MF140641 | GII.4 Sydney | |
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| GII.P4 New Orleans |
ORF1: 1..5087
ORF2: 5068..6690
ORF3: 6690..7496
LOCUS MF140641 7527 bp RNA linear VRL 24-OCT-2017
DEFINITION Norovirus GII strain
Norovirus/GII/Hu/NL/2013/GII.P4-GII.4/Rotterdam/E7800009_p11_d0
ORF1 gene, partial cds; and ORF2 and ORF3 genes, complete cds.
ACCESSION MF140641
VERSION MF140641.1
KEYWORDS .
SOURCE Norovirus GII
ORGANISM Norovirus GII
Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes;
Picornavirales; Caliciviridae; Norovirus; Norwalk virus.
REFERENCE 1 (bases 1 to 7527)
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 7527)
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..7527
/organism="Norovirus GII"
/mol_type="genomic RNA"
/strain="Norovirus/GII/Hu/NL/2013/GII.P4-
GII.4/Rotterdam/E7800009_p11_d0"
/host="Homo sapiens"
/db_xref="taxon:122929"
/country="Netherlands"
/collection_date="21-Jan-2013"
/note="genotype: GII.P4-GII.4"
CDS <1..5087
/codon_start=3
/product="ORF1"
/protein_id="ATN23619.1"
/translation="NDASAAAVANSNNDTAKSSSDGVLSSMAVTFKRALGARPKQPPP
REKPQRPPRPPTPELVKNIPPPPPNGEDEIVVSYSVKDGVSGLPDLSTVRQPEESNTA
FSVPPLNQRENRDAKEPLTGTILEMWDGEIYHYGLYVERGLVLGVHKPPAAISLAKVE
LAPLSLYWRPVYTPQYLISPDTLKKLSGETFPYTAFDNNCYAFCCWVLDLNDSWLSRR
MIQRTTGFFRPYQDWNRKPLPTMDDSKIKKVANIFLCALSSLFTRPIKDIIGKIRPLN
ILNILASCDWTFAGIVESLILLAELFGVFWTPPDVSAMIAPLLGDYELQGPEDLAVEL
VPVVMGGIGLVLGFTKEKIGKMLSSAASTLRACKDLGAYGLEILKLVMKWFFPKKEEA
NELAIVRSIEDAVLDLEAIENNHMTTLLKDKDSLATYMRTLDLEEEKARKLSTKSASP
DIVGTINALLARIAAARSLVHRAKEELSSRPRPVVLMISGRPGIGKTHLAREVAKRIA
ASLTGDQRVGLIPRNGVDHWDAYKGERVVLWDDYGMSNPIHDALRLQELADTCPLTLN
CDRIENKGKVFDSDVIIITTNLANPAPLDYVNFEACSRRIDFLVYAEAPDVEKAKRDF
PGQPDMWKNAFSSDFSHIKLALAPQGGFDKNGNTPHGKGVMKTLTTGSLIARASGLLH
ERLDEFELQGPALTTFNFDRNKVLAFRQLAAENKYGLMDTMRVGKQLKDVKTMPELKQ
ALKNVSIKKCQIVYSGCTYMLESDGKGNVKVDRIQSAAVQTNNELAGALHHLRCARIR
YYVKCVQEALYSIIQIAGAAFVTTRIAKRMNIQDLWSKPQVENTEETTSKDGCPKPKD
DEEFVISSDDIKTEGKKGKNKTGRGKKHTAFSSKGLSDEEYDEYKRIREERNGKYSIE
EYLQDRDKYYEEVAIARATEEDFCEEEEAKIRQRIFRPTRKQRKEERVSLGLVTGSEI
RKRNPDDFKPKGKLWADDDRSVDYNEKLSFEAPPSIWSRIVNFGSGWGFWVSPSLFIT
STHVIPQGAKEFFGVPIKQIQVHKSGEFCRLRFPKPIRTDVTGMILEEGAPEGTVVTL
LIKRSTGELMPLAARMGTHATMKIQGRTVGGQMGMLLTGSNAKGMDLGTTPGDCGCPY
IYKRGNDYVVIGVHTAAARGGNTVICATQGSEGEATLEGGDNKGTYCGAPILGPGSAP
TLSTKTKFWRSSTASLPPGTYEPAYLGGKDPRVKGGPSLQQVMREQLKPFTEPRGKPP
KPSVLEAAKKTIINVLEQTIDPPEKWSFAQACASLDKTTSSGHPHHMRKNDCWNGESF
TGKLADQASKANLMFEEGKNMTPVYTAALKDELVKTDKIYGKIKKRLLWGSDLATMIR
CARAFGGLMDELKAHCVTLPIRVGMNMNEDGPIIFERHSRYTYHYDADYSRWDSTQQR
AVLAAALEIMVKFSPEPHLAQVVAEDLLSPSVVDVGDFTISINEGLPSGVPCTSQWNS
IAHWLLTLCALSEVTNLSPDTIQANSLFSFYGDDEIVSTDIKLDPEKLTAKLREYGLK
PTRPDKTEGPLVISEDLNGLTFLRRTVTRDPAGWFGKLEQSSILRQMYWTRGPNHGDP
SETMIPHSQRPIQLMSLLGEAALHGPAFYSKISKLVIAELKEGGMDFYVPRQEPMFRW
MRFSDLSTWEGDRNLAPSFVNEDGVE"
CDS 5068..6690
/codon_start=1
/product="ORF2"
/protein_id="ATN23620.1"
/translation="MKMASSDANPSDGSAANLVPEVNNEVMALEPVVGAAIAAPVAGQ
QNVIDPWIRNNFVQAPGGEFTVSPRNAPGEILWSAPLGPDLNPYLSHLARMYNGYAGG
FEVQVILAGNAFTAGKVIFAAVPPNFPTEGLSPSQVTMFPHIVVDVRQLEPVLIPLPD
VRNNFYHYNQSNDPTIKLIAMLYTPLRANNAGDDVFTVSCRVLTRPSPDFDFIFLVPP
TVESRTKPFSVPVLTVEEMTNSRFPIPLEKLFTGPSSAFVVQPQNGRCTTDGVLLGTT
QLSPVNICTFRGDVTHITGSRNYTMNLASQNWNNYDPTEEIPAPLGAPDFVGKIQGML
TQTTRADGSTRGHKTTVYTGSADFAPKLGRVQFETDTDHDFEANQNTKFTPVGVIQDG
STTHRNEPQQWVLPSYSGRNTHNVHLAPAVAPTFPGEQLLFFRSTMPGCSGYPNMDLD
CLLPQEWVQYFYQEAAPAQSDVALLRFVNPDTGRVLFECKLHKSGYVTVAHTGQHDLV
IPPNGYFRFDSWVNQFYTLAPMGNGAGRRRVV"
CDS 6690..7496
/codon_start=1
/product="ORF3"
/protein_id="ATN23621.1"
/translation="MAGAFFAGLASDVLGSGLGSLINAGAGAINQKVEFENNRKLQQA
SFQFSSNLQQASFQHDKEMLQAQIEATKKLQQEMMKVKQAMLLEGGFSETDAARGAIN
APMTRALDWSGTRYWAPDARTTTYNAGRFSTPQPSGALSGRANLRDAVPARGSSSKSS
NSSTATSVYSNQTTSTRLGSTAGSGTSVSSLPSTARTRSWVEDQSRNLSPFMRGAHNI
SFVTPPSSRSSSQGTVSTVPKEVLDSWTGAFNTRRQPLFAHIRNRGESRV"
ORIGIN
1 ctaacgacgc ttccgctgcc gctgttgcta acagcaacaa cgacaccgca aaatcttcaa
61 gtgacggagt gctttctagc atggctgtca cttttaaacg agccctcggg gcgcggccta
121 aacagcctcc cccgagggaa aaaccacaaa gacccccacg accacctact ccagaactgg
181 ttaaaaatat tccccctccc ccacccaacg gagaggatga aatagtggtt tcttatagtg
241 tcaaagatgg tgtttccggc ttgcctgacc tttccaccgt caggcaaccg gaagaatcca
301 acacggcctt cagtgtccct ccactcaatc agagggagaa tagagatgct aaggaaccac
361 tcactggaac aattctggaa atgtgggacg gggaaatcta ccattatggc ctgtatgtgg
421 agcgaggtct tgtactaggc gtgcacaaac cgccagctgc catcagcctc gctaaggttg
481 agctagcacc actctccttg tactggagac ctgtgtacac tcctcagtac ctcatctctc
541 cagacactct caagaaattg tccggagaaa cgttccccta cacagccttt gataacaact
601 gctatgcctt ttgttgctgg gtcctggacc taaatgactc gtggctgagc aggagaatga
661 tccagagaac gactggtttc ttcaggccct accaagactg gaataggaaa ccccttccca
721 ctatggatga ctccaaaata aaaaaggtag ctaacatatt tctgtgtgct ctgtcctcgc
781 tattcaccag acccataaaa gatataatag ggaagataag gcctcttaac atcctcaaca
841 tcttagcctc atgtgattgg acctttgcgg gcatagtgga gtccctgata ctcttggcag
901 aactctttgg agttttctgg acacccccag atgtgtctgc gatgattgcc cccttacttg
961 gtgactacga gctacaagga cctgaggacc ttgcagtgga gctcgtcccc gtggtgatgg
1021 ggggaattgg tttggtgcta ggattcacca aagagaagat tgggaagatg ttgtcatctg
1081 ctgcgtccac cttaagagct tgcaaagacc ttggtgcata tgggctagag atcctaaagt
1141 tagtcatgaa gtggttcttc ccgaagaagg aggaggcaaa tgagctggct atagtgaggt
1201 ccatcgagga tgcagtcctg gatctcgagg caattgaaaa caatcatatg accaccttgc
1261 ttaaagataa agacagtctg gcaacctaca tgagaacact tgaccttgaa gaggagaaag
1321 ccaggaaact ctcaaccaag tctgcctcac ccgacatcgt gggcacaatc aacgccctcc
1381 tggcgagaat cgctgccgca cgttctctgg tgcatcgagc gaaggaggag ctttccagca
1441 gaccaagacc tgtggtgttg atgatatcag gcaggccagg aatagggaag acccacctcg
1501 ctagggaagt ggctaagaga atcgcagcct cccttacagg agaccagcgt gttggcctta
1561 tcccacgcaa tggcgtcgac cattgggatg cgtacaaggg ggagagggtc gtcctatggg
1621 acgattatgg aatgagcaac cctattcacg atgccctcag actgcaagaa ctcgctgaca
1681 cttgccccct cactctgaac tgtgacagga ttgaaaataa aggaaaggtc tttgacagcg
1741 atgtcatcat tatcaccacc aatctggcca acccagcacc actggactat gtcaactttg
1801 aagcatgctc gaggcgcatt gacttcctcg tgtatgcaga agctcctgat gtcgaaaagg
1861 cgaagcgtga cttcccaggc cagcctgaca tgtggaagaa cgctttcagt tctgatttct
1921 cacacataaa actagcactg gccccacagg gtggtttcga caagaacggg aacaccccac
1981 acggaaaggg cgtcatgaag actctcacca ctggctccct tattgcccgg gcatcagggc
2041 tgctccatga gaggttagat gaatttgaac tgcagggtcc agctctcacc accttcaatt
2101 tcgatcgcaa taaagtgctt gcctttagac agcttgctgc tgaaaataaa tatggattga
2161 tggacacaat gagggttggg aaacagctca aggatgtcaa aaccatgcca gaactcaaac
2221 aagcactcaa gaatgtctca atcaagaagt gtcaaatagt gtatagtggt tgcacctaca
2281 tgcttgagtc tgatggcaag ggcaatgtga aagttgacag gatccagagc gccgccgtgc
2341 agaccaacaa tgagctggct ggtgccctgc accatttgag gtgcgccaga atcagatact
2401 atgtcaagtg tgtccaggaa gccctgtatt ccatcatcca aattgctggg gctgcatttg
2461 tcaccacgcg cattgccaag cgcatgaaca tacaagacct atggtccaag ccacaagtgg
2521 aaaacacaga ggagactacc agcaaggacg ggtgcccaaa acctaaggat gatgaggagt
2581 ttgtcatttc atccgacgac atcaaaactg agggcaagaa agggaagaac aagactggcc
2641 gtggcaagaa gcacacagca ttttcaagca aaggcctcag tgatgaagag tacgatgaat
2701 acaagaggat tagagaagaa aggaatggca agtactctat agaagagtac cttcaggaca
2761 gggacaaata ttatgaggag gtggccattg ccagagcgac tgaggaagac ttctgtgaag
2821 aggaggaagc caagatccgg caaaggatct ttaggccgac aaggaaacaa cgcaaggagg
2881 aaagagtctc tctcggcttg gtcacaggct ctgaaattag gaaaagaaac ccagatgact
2941 tcaaacccaa ggggaaatta tgggctgacg atgacaggag tgtggactac aatgagaaac
3001 tcagttttga ggccccacca agcatttggt cgagaatagt caactttggt tcaggctggg
3061 gattctgggt ctcccccagc ttgttcataa catcaaccca tgttataccc cagggcgcaa
3121 aggagttctt tggagtcccc atcaaacaaa tacaggtaca caagtcaggc gagttctgtc
3181 gcttgagatt ccctaaacca atcaggactg atgtgacggg catgatctta gaagaaggcg
3241 cacctgaggg caccgtggtc acactactca tcaaaaggtc cactggggaa cttatgcccc
3301 tagcagctag gatggggacc catgcgacca tgaagatcca agggcgcact gttgggggcc
3361 agatgggcat gcttctgaca ggatccaacg ccaagggtat ggacctgggt actacaccag
3421 gtgattgtgg ctgcccctat atctacaaga gaggtaatga ctatgtggtc attggagtcc
3481 acacggctgc cgcacgtggg gggaacactg tcatatgtgc cacccagggg agtgaaggag
3541 aggctacact tgagggtggt gacaacaagg ggacatactg tggtgcacca atcctaggcc
3601 cagggagtgc cccaacactt agcaccaaga ccaaattctg gagatcgtcc acagcatcac
3661 tcccacctgg cacctatgaa ccagcctatc ttggtggtaa ggaccctaga gtcaagggtg
3721 gcccttcact gcagcaagtc atgagggaac agttgaagcc attcacagag cccaggggca
3781 agccaccaaa accaagtgtg ttagaagctg ccaagaagac catcatcaat gtccttgagc
3841 aaacaattga tccacctgag aaatggtcgt tcgcacaagc ttgcgcgtcc cttgacaaga
3901 ccacttccag tggtcatccg caccacatgc ggaaaaacga ctgctggaac ggggagtcct
3961 tcacaggcaa gctggcagac caggcttcca aggccaacct gatgtttgaa gaagggaaga
4021 acatgacccc agtctacaca gctgcgctca aggatgagtt agttaaaact gacaaaattt
4081 atggcaagat caagaagagg cttctttggg gctcggactt ggcgaccatg atccggtgtg
4141 ctcgagcatt cggaggccta atggatgaac tcaaagcgca ctgtgtcaca cttcccatta
4201 gagttggcat gaatatgaat gaggatggcc ccatcatctt cgagaggcat tccaggtata
4261 cgtaccacta tgatgctgat tactctcgat gggattcaac acaacagaga gccgtgttgg
4321 cagcagctct agaaatcatg gttaaattct ccccagaacc acatttggct caggtagtcg
4381 cggaagacct tctttctcct agcgtggtgg acgtgggcga cttcacaata tcaatcaacg
4441 agggtctccc ctctggggtg ccctgcacct cccaatggaa ctccatcgcc cactggcttc
4501 tcactctctg tgcgctctcc gaagtcacaa acctgtcccc tgataccata caggccaatt
4561 ctctcttctc tttttatggt gatgatgaaa ttgttagcac agacataaaa ttggacccag
4621 agaaattgac agcaaagctc agagaatatg ggttaaaacc aacccgccct gacaaaactg
4681 aaggacccct tgtcatctct gaagacctga atggcctaac tttcctgcgg agaactgtga
4741 cccgcgaccc agctggttgg tttggaaaac tggagcagag ttcaatactc aggcaaatgt
4801 actggactag gggtcccaac catggagacc catctgaaac aatgattcca cactcccaaa
4861 gacccataca attgatgtcc ctactggggg aggccgctct ccacggccca gcattttaca
4921 gtaaaatcag caaattggtc attgcagagc taaaagaagg tggtatggat ttttacgtgc
4981 ccagacaaga gccaatgttc agatggatga gattctcaga tctgagcacg tgggagggcg
5041 atcgcaatct ggctcccagt tttgtgaatg aagatggcgt cgagtgacgc caacccatct
5101 gatgggtccg cagccaacct cgtcccagag gtcaacaatg aggttatggc tctggagccc
5161 gttgttggtg ccgccattgc ggcacctgta gcgggccaac aaaatgtaat tgacccctgg
5221 attagaaaca attttgtaca agcccctggt ggagagttta cagtgtcccc tagaaacgct
5281 ccaggtgaaa tactatggag cgcgccctta ggccctgacc taaatcccta cctatcccat
5341 ttggccagaa tgtataatgg ttatgcaggt ggttttgaag tgcaggtaat tctcgcgggg
5401 aacgcgttca ccgccgggaa ggtcatattt gcagcagtcc caccaaattt tccaactgaa
5461 ggcttgagcc ccagccaggt cactatgttc ccccatatag tagtagatgt taggcaacta
5521 gaacctgtgt tgattccctt acccgatgtt aggaataatt tctatcatta caatcaatca
5581 aatgacccca ccattaagtt gatagcaatg ctgtatacac cacttagggc taataatgct
5641 ggggacgatg tcttcacagt ttcttgccga gttctcacga gaccatcccc cgattttgat
5701 tttatatttc tagtgccacc cacagttgag tctagaacta aaccattctc tgtcccagtt
5761 ttaactgttg aggagatgac caattcaaga ttccccattc ctttggaaaa gttgttcacg
5821 ggtcccagca gtgcctttgt tgttcaacca caaaacggta ggtgcacgac tgatggcgtg
5881 ctcctaggca ccacccaatt gtctcctgtc aacatctgca ccttcagagg ggatgtcacc
5941 cacatcacag gtagtcgtaa ctacacaatg aatttggctt ctcaaaattg gaacaattat
6001 gacccaacag aagaaatccc agcccctcta ggagctccag attttgtggg gaagattcaa
6061 ggcatgctca cccaaaccac aagggcagat ggctcaacac gcggccacaa aactacagtg
6121 tacactggga gcgccgactt tgctccaaaa ctgggcagag ttcaatttga aactgacaca
6181 gaccatgatt ttgaagctaa ccaaaacaca aagttcaccc cagtcggtgt catccaagat
6241 ggtagcacca cccaccgaaa tgaaccccaa cagtgggtgc tcccaagtta ctcaggcaga
6301 aatactcata atgttcatct ggcccccgct gtagccccca cttttccggg tgaacaactt
6361 ctcttcttta gatccaccat gcccggatgt agcgggtacc ccaacatgga tttggactgt
6421 ctgctccccc aggaatgggt gcagtacttc taccaagagg cagccccagc acaatctgat
6481 gtggctctgc taagatttgt gaatccagac acaggtaggg ttttgtttga gtgtaagctc
6541 cataaatcag gctatgttac agtggctcac actggccaac atgatttggt tatccccccc
6601 aatggttatt ttaggtttga ttcctgggtc aaccagttct acacgcttgc ccccatggga
6661 aatggagcgg ggcgtagacg tgtagtataa tggctggagc tttctttgct ggattagcat
6721 ctgatgtcct tggctctgga cttggttccc ttatcaatgc tggggctggg gccatcaacc
6781 aaaaagttga gtttgaaaat aacagaaaat tgcaacaagc atccttccaa tttagcagca
6841 atctacaaca ggcttccttt caacatgaca aagaaatgct ccaagcacaa attgaggcca
6901 ccaaaaagct acaacaggaa atgatgaaag ttaagcaggc aatgctccta gagggtgggt
6961 tctctgagac agatgcagcc cgcggggcaa tcaacgcccc catgacaaga gctttggact
7021 ggagcgggac aaggtactgg gctcccgatg ctaggactac aacatacaat gcaggccgct
7081 tttccacccc tcaaccatcg ggggcactgt caggaagagc caatcttagg gatgctgtcc
7141 ctgctcgggg ttcctccagt aaatcttcta actcttctac tgctacttct gtgtactcaa
7201 atcaaaccac ttcaacgaga cttggttcta cagctggttc tggtaccagt gtctcgagcc
7261 tcccgtcaac tgcaaggact aggagctggg ttgaggatca aagtaggaat ttgtctcctt
7321 tcatgagggg ggcccacaac atatcgtttg tcaccccacc atctagcaga tcctctagcc
7381 aaggcacagt ctcaaccgtg cctaaagagg ttttggactc ctggactggc gctttcaaca
7441 cgcgcaggca gcctctcttc gctcacattc gtaatcgagg ggagtcacgg gtgtaatgtg
7501 aaaagacaaa attgattatc tttcttt
//