Typing tool
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Typing tool
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Complete norovirus genomes
| MF140691 | GII.4 New Orleans | |
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| GII.P4 New Orleans |
ORF1: 1..5083
ORF2: 5064..6686
ORF3: 6686..7492
LOCUS MF140691 7505 bp RNA linear VRL 24-OCT-2017
DEFINITION Norovirus GII strain
Norovirus/GII/Hu/NL/2012/GII.P4-GII.4/Rotterdam/E1300329_p8_d173
ORF1 gene, partial cds; and ORF2 and ORF3 genes, complete cds.
ACCESSION MF140691
VERSION MF140691.1
KEYWORDS .
SOURCE Norovirus GII
ORGANISM Norovirus GII
Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes;
Picornavirales; Caliciviridae; Norovirus; Norwalk virus.
REFERENCE 1 (bases 1 to 7505)
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 7505)
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..7505
/organism="Norovirus GII"
/mol_type="genomic RNA"
/strain="Norovirus/GII/Hu/NL/2012/GII.P4-
GII.4/Rotterdam/E1300329_p8_d173"
/host="Homo sapiens"
/db_xref="taxon:122929"
/country="Netherlands"
/collection_date="19-Dec-2012"
/note="genotype: GII.P4-GII.4"
CDS <1..5083
/codon_start=2
/product="ORF1"
/protein_id="ATN23769.1"
/translation="DASAAAVANSNNDIAKSSSDGVLSSMAVTFKRALGARPKQPPPR
EKPQRPPRPPTPELVKNIPPPPPNGEDEIVVSYSVKDGVSGLPELSTVRQPEESNTAF
SVPPLNQRENRDAKEPLTGTILEMWDGEIYHYGLYVERGLVLGVHKPPAAISLAKVEL
APLSLYWRPVYTPQYLISPDTLKKLSGETFPYTAFDNNCYAFCCWVMDLNDSWLSRRM
IQRTTGFFRPYQDWNRKPLPTMDDSKIKKVANVFLCALSSLFTRPIKDIIGRIRPLNI
LNILASCDWTFAGIVESLILLAELFGVFWTPPDVSAMIAPLLGDYELQGPEDLAVELV
PVVMGGIGLVLGFTKEKIGKMLSSAASTLRACKDLGAYGLEILKLVMKWFFPKKEEAN
ELAIVRSIEDAVLDLEAIENNHMTTLLKDKDSLATYMRTLDLEEEKARKLSTKSASPD
IVGTINALLARIAAARSLVHRAKEELSSRPRPVVLMISGRPGIGKTHLAREVAKRIAA
SLTGDQRVGLIPRNGVDHWDAYKGERVVLWDDYGMSNPIHDALRLQELADTCSLTLNC
DRIENKGKVFDSDVIIITTNLANPAPLDYVNFEACSRRIDFLVYAEAPEVEKAKRDFP
GQPDMWKNAFSSDFSHIKLTLAPQGGFDKNGNTPHGKGVMKTLTTGSLIARASGLLHE
RLDEFELQGPALTTFNFDRNKVLAFRQLAAENKYGLMDTMRVGKQLKDVKTMPELKQA
LKNVSIKKCQIVYSGCTYILESDGKGNVKVDRIQSAAVQINNELAGALHHLRSARIRY
YVKCVQEALYSIIQIAGVAFVTTRIAKRMNIQNLWSKPQVENTEETTSKDGCLKPRDD
EEFVISSDDIKTEGKKGKNKTGRGKKHTAFSSKGLSDEEYDEYKRIREERNGKYSIEE
YLQDRDKYYEEVAIARATEEDFCEEEEAKIRQRIFRPTRKQRKEERASLGLVTGSEIR
RRNPDDFKPKGKLWADDDRSVDYNEKLSFEAPPSIWSRIVNFGSGWGFWVSPSLFITS
THVIPQGAKEFFGVPIKQIQVHKSGEFCRLRFPKPIRTDVTGMILEEGAPEGTVVTLL
IKRSTGELMPLAARMGTHATMKIQGRTVGGQMGMLLTGSNAKSMDLGTTPGDCGCPYI
YKRGNDYVVIGVHTAAARGGNTVICATQGSEGEATLEGGDNKGTYCGAPILGPGSAPT
LSTKTKFWRSSTAPLPPGTYEPAYLGGKDPRVKGGPSLQQVMREQLKPFTEPRGKPPK
PSVLEAAKKTIINVLEQTIDPPEKWSFAQACASLDKTTSSGHPHHVRKNDCWNGESFT
GKLADQASKANLMFEEGKNMTPVYTAALKDELVKTDKIYGKIKKRLLWGSDLATMIRC
ARAFGGLMDEFKAHCVTLPIRVGMNMNEDGPIIFERHSRYTYHYDADYSRWDSTQQRA
VLAAALEIMVKFSPEPHLAQVVAEDLLSPSVVDVGDFTISINEGLPSGVPCTSQWNSI
AHWLLTLCALSEVTNLSPDTIQANSLFSFYGDDEIVSTDIKLDPEKLTAKLREYGLKP
TRPDKTEGPLVISEDLNGLTFLRRTVTRDPAGWFGKLEQSSILRQMYWTRGPNHGDPS
ETMIPHSQRPIQLMSLLGEAALHGPAFYSKISKLVIAELKEGGMDFYVPRQEPMFRWM
RFSDLSTWEGDRNLAPSFVNEDGVE"
CDS 5064..6686
/codon_start=1
/product="ORF2"
/protein_id="ATN23770.1"
/translation="MKMASSDANPSDGSTANLVPEVNNEVMALEPVVGAAIAAPVAGQ
QNVIDPWIRNNFVQAPGGEFTVSPRNAPGEILWSAPLGPDLNPYLSHLARMYNGYAGG
FEVQVLLAGNAFTAGKIIFAAVPPNFPTEGLSPSQITMFPHMIVDVRQLEPVLIPLPD
VRNNFYHYNQSNDPTIKLIAMLYTPLRANNAGDDVFTVSCRVLTRPSPDFDFIFLVPP
TVESRTKPFSVPILTVEEMTNSRFPIPLEKLFTGPSSAFVVQPQNGRCTTDGVLLGTT
QLSPVNICTFRGDVIHTPNSHNYTMNLASQNWNSYDPTEEIPAPLGTPDFVGKIQGVL
TQTTRTDGSTRGHKATVYTGGADFSPKLGRVQFATDTNNDFETNQNTKFTPVGVIQDG
DTTHRNEPQQWVLPSYSGRNIHNVHLAPAVAPTFPGEQLLFFRSTMPGCSGYPNMDLD
CLLPQEWVQYFYQEAAPAQSDVALLRFVNPDTGRVLFECKLHKSGYVTVAHTGQHDLV
IPPNGYFRFDSWVNQFYTLAPMGNGTGRRRAL"
CDS 6686..7492
/codon_start=1
/product="ORF3"
/protein_id="ATN23771.1"
/translation="MAGAFFAGLASDVLGSGLGSLINAGAGAINQKVEFENNRKLQQA
SFQFSSNLQQASFQHDKEMLQAQIEATKKLQQEMMRVKQAMLLEGGFSEVDAARGAIN
APMTKTLDWSGTRYWAPDARTTTYNAGRFSTPQPSGALPGRANLRATAPARGSSSMSS
NSSIATSVYSNQTTSTRLGSTAGSGTSVSSLPSTARTRSWVEDQNRNLSPFMRGAHNI
SFVTPPSSRSSSQGTVSTVPKEVLDSWTGAFNTRRQPLFAHIRKRGESRV"
ORIGIN
1 cgacgcttcc gctgccgctg ttgctaacag caacaacgac atcgcaaaat cttcgagtga
61 cggagtgctt tctagcatgg ctgtcacttt taaacgagcc ctcggggcgc ggcctaaaca
121 gcctcccccg agggaaaaac cacaaagacc cccacgacca cctactccag aactggtcaa
181 aaatattccc cctcccccac ccaacggaga ggatgaaata gtggtttctt atagtgtcaa
241 ggatggtgtt tccggcttgc ctgaactttc caccgtcagg caaccggaag aatctaacac
301 ggccttcagt gtccctccac ttaatcagag ggagaataga gatgctaagg agccacttac
361 tggaacaatt ctggaaatgt gggacgggga aatctaccat tatggcctgt atgtggagcg
421 aggccttgta ctaggtgtgc acaaaccacc agctgccatc agcctcgcta aggttgagct
481 agcaccactc tccttgtact ggagacctgt gtacactcct cagtacctca tctctccaga
541 cactctcaag aaattatccg gagaaacgtt cccctacaca gcctttgaca acaactgcta
601 tgccttttgt tgctgggtca tggacctaaa tgactcgtgg ctgagcagga gaatgatcca
661 gagaacaact ggtttcttca ggccctacca agactggaat aggaaacccc ttcccactat
721 ggatgactcc aaaataaaga aggtagctaa cgtattcctg tgtgctctgt cctcgctgtt
781 caccagaccc ataaaagata taatagggag gataaggcct cttaacatcc tcaacatctt
841 agcctcatgt gattggactt ttgcaggcat agtggagtcc ctgatactct tggcagaact
901 ctttggagtt ttctggacac ccccagatgt gtctgcgatg attgccccct tgcttggtga
961 ctacgagcta caaggacctg aggaccttgc agtggagctc gtccccgtag tgatgggggg
1021 aattggtttg gtgctaggat tcaccaaaga gaagattggg aaaatgttgt catctgctgc
1081 gtccaccttg agagcttgta aagaccttgg tgcatatggg ctagagatcc taaagttggt
1141 catgaagtgg ttcttcccga agaaggagga ggcaaatgag ctggctatag tgaggtctat
1201 cgaggacgca gtcctagatc tcgaggcaat tgaaaacaac catatgacca ccttgctcaa
1261 agacaaagac agtctggcaa cctatatgag aacacttgac cttgaggagg agaaagccag
1321 gaaactctca accaagtctg cctcacccga catcgtgggc acaatcaacg ccctcctggc
1381 gagaatcgct gccgcacgtt ctctggtgca tcgagcgaag gaggagcttt ccagcagacc
1441 aagacctgtg gtgttgatga tatcaggcag gccaggaata gggaagaccc acctcgctag
1501 ggaagtggct aagagaatcg cagcctccct tacaggagac cagcgtgtgg gcctcatccc
1561 acgcaatggc gtcgaccatt gggatgcata caagggagag agggtcgtcc tatgggacga
1621 ttatggaatg agcaacccta tccacgatgc cctcaggctg caagaactcg ctgacacttg
1681 ctccctcact ctaaactgtg acaggattga aaataaagga aaggtctttg acagcgatgt
1741 catcattatc accactaatc tggccaaccc agcaccactg gactatgtca actttgaagc
1801 atgctcgagg cgcatcgact tcctcgtgta tgcagaagcc cctgaagtcg aaaaggcgaa
1861 gcgtgacttc ccaggccagc ctgacatgtg gaagaacgct ttcagttctg atttctcaca
1921 cataaaactg acactggccc cacagggtgg tttcgataag aacgggaaca ccccgcacgg
1981 aaagggcgtc atgaagactc tcaccactgg ctcccttatt gcccgggcat cagggctact
2041 ccatgagagg ttagatgaat ttgaactaca gggcccagct ctcaccacct tcaatttcga
2101 tcgcaataaa gtgcttgcct ttagacagct tgctgctgaa aataaatatg gattgatgga
2161 cacaatgagg gttgggaaac agctcaagga tgtcaaaacc atgccagaac tcaaacaagc
2221 actcaagaat gtctcaatca agaagtgcca aatagtgtat agtggttgca cctacatact
2281 tgagtctgat ggcaagggca atgtgaaagt tgacagaatc caaagcgccg ccgtgcagat
2341 caacaatgag ctggctggtg ccctgcacca tttgaggagc gccagaatca gatactatgt
2401 caagtgtgtc caggaggccc tgtattccat cattcaaatt gctggggttg catttgtcac
2461 cacgcgcatt gccaagcgca tgaacataca aaacctatgg tccaagccac aagtggaaaa
2521 cacagaggag actaccagca aggacgggtg cctaaaacct agggatgatg aggagtttgt
2581 catttcatcc gacgacatca aaactgaggg taagaaaggg aagaacaaga ctggccgcgg
2641 caagaagcac acagcatttt caagcaaagg cctcagtgat gaagagtacg atgagtacaa
2701 gagaattaga gaagaaagga atggcaagta ctccatagaa gagtaccttc aggacaggga
2761 caaatactat gaggaggtgg ccattgccag ggcgactgag gaagacttct gtgaagagga
2821 ggaggccaag atccggcaga ggatctttag gccaacaagg aaacaacgca aggaggaaag
2881 agcctctctc ggtctggtca caggctctga aattaggaga agaaacccag atgatttcaa
2941 acccaagggg aaattgtggg ctgacgatga caggagtgtg gactacaatg agaaactcag
3001 ttttgaggcc ccaccaagca tctggtcaag aatagtcaac tttggttcag gctggggatt
3061 ctgggtctcc cccagtctgt tcataacatc aacccatgtc ataccccagg gcgcaaagga
3121 gttctttgga gtccccatca aacaaataca ggtacacaag tcaggcgagt tctgtcgctt
3181 gagattccca aaaccaatca ggactgatgt gacgggcatg atcttagaag aaggcgcacc
3241 tgagggcacc gtggtcacac tactcatcaa aaggtccact ggggaactca tgcccctagc
3301 agctaggatg gggacccatg cgaccatgaa gatccaaggg cgcactgttg gaggccagat
3361 gggcatgctt ctgacaggat ccaacgccaa gagcatggac ctgggtacta caccaggtga
3421 ttgtggctgc ccctatatct acaagagagg taatgactat gtggtcattg gagtccacac
3481 ggctgccgca cgtgggggaa acactgtcat atgtgccacc caggggagtg aaggagaggc
3541 tacacttgaa ggtggtgaca acaaggggac atactgtggt gcaccaatcc taggcccagg
3601 gagtgcccca actcttagca ccaagaccaa attctggaga tcgtctacag caccactccc
3661 acctggcacc tatgaaccag cctatcttgg tggcaaggac cctagagtca agggtggccc
3721 ttcactacag caagtcatga gggaacagtt gaagccattc acagagccaa ggggcaagcc
3781 accaaaacca agtgtattag aagctgccaa gaagaccatc atcaacgtcc ttgagcaaac
3841 aattgatcca cctgagaaat ggtcgttcgc acaagcttgc gcgtcccttg acaagaccac
3901 ttccagtggt catccgcacc acgtgcggaa aaacgactgc tggaacggag agtccttcac
3961 aggcaagctg gcagaccagg cttccaaggc caacctgatg tttgaagaag ggaagaacat
4021 gaccccagtc tacacagctg cgctcaagga tgagttagtt aaaactgaca aaatttatgg
4081 taagatcaag aagaggcttc tctggggctc ggacttggcg accatgatcc ggtgtgctcg
4141 agcattcgga ggcctaatgg atgaattcaa agcacactgt gtcacgcttc ctattagagt
4201 tggcatgaat atgaatgagg atggccccat catcttcgag aggcattcca ggtacacata
4261 tcactatgat gctgattact ctcgatggga ttcaacacaa cagagagccg tgttggcagc
4321 agctctcgaa atcatggtta aattctcccc agaaccacat ttggctcagg tagtcgcgga
4381 agaccttctt tctcctagcg tggtggacgt gggcgacttc acaatatcaa tcaacgaggg
4441 tcttccctct ggggtgccct gcacctccca atggaactcc atcgcccact ggcttctcac
4501 tctctgtgca ctctccgaag tcacaaacct atctcctgat accatacagg ctaactccct
4561 cttctctttt tatggtgatg atgaaattgt tagcacagac ataaaattgg acccagagaa
4621 attgacagca aagctcagag aatatgggtt aaaaccaacc cgccctgaca aaactgaagg
4681 accccttgtc atctctgaag acctgaatgg cctaactttc ctgcggagaa ctgtgacccg
4741 cgacccagct ggttggtttg gaaaactgga gcagagttca atactcaggc aaatgtactg
4801 gactaggggt cccaatcatg gagacccatc tgaaacaatg attccacact cccaaagacc
4861 catacaattg atgtccctac tgggggaggc cgctctccac ggcccagcct tttatagcaa
4921 aatcagcaag ttggtcattg cagagctaaa agagggtggc atggattttt acgtgcccag
4981 acaagagcca atgttcagat ggatgagatt ctcagatctg agcacgtggg agggcgatcg
5041 caatctggct cccagttttg tgaatgaaga tggcgtcgag tgacgccaac ccatctgatg
5101 ggtccacagc caacctcgtc ccagaggtca acaatgaggt tatggctttg gagcccgtag
5161 ttggtgccgc tattgcggca cctgtagcgg gccaacaaaa tgtaattgac ccctggatta
5221 gaaacaattt tgtacaagcc cctggtggag agtttacagt atcccctaga aacgctccag
5281 gtgaaatatt atggagcgcg cccttaggcc ctgatctgaa tccctacctt tctcatttgg
5341 ccagaatgta caatggttat gcaggtggtt ttgaagtgca ggtactcctc gcggggaacg
5401 cgttcaccgc cgggaaaatc atatttgcag cagtcccacc aaatttccca actgaaggtt
5461 tgagccccag ccagatcact atgttccccc atatgatagt agatgttagg caattggaac
5521 ctgtgttgat ccccttaccc gatgttagga ataattttta ccattataat caatcaaatg
5581 accccactat caaattgata gcaatgctgt atacaccact tagggctaat aatgctgggg
5641 acgatgtctt cacagtttct tgtcgagttc tcacgagacc atcccccgat tttgatttca
5701 tatttttggt gccacccaca gttgaatcaa gaactaaacc attctctgtc ccaattttaa
5761 ctgttgagga gatgaccaat tcaaggttcc ccattccttt ggaaaagttg ttcacgggcc
5821 ccagtagtgc ctttgttgtt caaccacaaa atggcaggtg cacgactgat ggcgtgctcc
5881 taggtactac ccaactgtcc cctgtaaaca tctgcacctt cagaggggat gtcatccaca
5941 ctccaaacag tcataactac acaatgaatt tggcctccca aaattggaac agttacgatc
6001 caacagaaga aatcccagcc cctctaggga ctccagactt cgtggggaag attcaaggtg
6061 tgctcaccca aaccacaagg acagatggct cgacccgcgg ccacaaagct acagtgtaca
6121 ctgggggcgc cgacttttct ccaaaactgg gtagagttca atttgccact gacacaaaca
6181 atgattttga aactaaccaa aacacaaagt tcaccccagt cggtgtcatc caggatggtg
6241 ataccaccca ccgaaatgaa cctcaacaat gggtgctccc aagttactca ggcagaaaca
6301 ttcataatgt acacctggcc cccgctgtag cccccacttt cccgggcgag cagctcctct
6361 ttttcagatc tactatgccc ggatgcagcg ggtaccccaa catggatttg gactgtctgc
6421 tcccccagga atgggtgcag tacttctacc aggaggcagc cccagcgcaa tctgatgtgg
6481 ctctgttgag atttgtgaat ccagacacag gtagggtttt gtttgagtgt aagctccata
6541 aatcaggcta tgttacagtg gctcacactg gccaacatga tttggttatc ccccccaatg
6601 gttattttag atttgattcc tgggtcaacc agttctacac acttgccccc atgggaaatg
6661 ggacggggcg tagacgtgca ctataatggc tggagctttc tttgctggat tggcatctga
6721 cgtccttggc tctggacttg gttccctaat caatgctggg gctggggcca tcaaccaaaa
6781 agttgaattt gaaaataata gaaaattgca acaagcttcc ttccaattta gtagcaatct
6841 acaacaagct tcctttcaac atgacaagga gatgctccaa gcacaaattg aggccaccaa
6901 aaagttgcaa caggaaatga tgagagttaa acaagcaatg ctcctagagg gcggattctc
6961 tgaggtagat gcagcccgtg gggcaatcaa cgcccccatg acaaaaactt tggactggag
7021 cgggacaagg tactgggctc ccgatgctag gactacaaca tataatgcag gccgcttttc
7081 cacccctcaa ccctcggggg cactaccagg aagagctaat cttagggcta ctgcccccgc
7141 ccggggttcc tccagcatgt cttctaactc ttctattgct acttctgtgt attcaaatca
7201 aaccacttca acgagacttg gttctacagc tggttctggt accagtgtct cgagcctccc
7261 gtcaactgca aggactagga gctgggttga ggatcaaaat aggaatttgt cacctttcat
7321 gaggggggcc cataacatct cgtttgtcac cccaccatct agcagatcat ctagccaagg
7381 cacagtctca accgtgccca aagaagtttt ggactcctgg actggcgctt tcaacacgcg
7441 caggcagcct ctcttcgctc acattcgcaa gcgaggggag tcacgggtgt aatgtgaaaa
7501 gacaa
//