Typing tool
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Typing tool
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Complete norovirus genomes
| MF140670 | GII.4 New Orleans | |
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| GII.P4 New Orleans |
ORF1: 1..5089
ORF2: 5070..6692
ORF3: 6692..7453
LOCUS MF140670 7453 bp RNA linear VRL 24-OCT-2017
DEFINITION Norovirus GII strain
Norovirus/GII/Hu/NL/2013/GII.P4-GII.4/Rotterdam/E1300297_p2_d402
ORF1 gene, partial cds; ORF2 gene, complete cds; and ORF3 gene,
partial cds.
ACCESSION MF140670
VERSION MF140670.1
KEYWORDS .
SOURCE Norovirus GII
ORGANISM Norovirus GII
Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes;
Picornavirales; Caliciviridae; Norovirus; Norwalk virus.
REFERENCE 1 (bases 1 to 7453)
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 7453)
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..7453
/organism="Norovirus GII"
/mol_type="genomic RNA"
/strain="Norovirus/GII/Hu/NL/2013/GII.P4-
GII.4/Rotterdam/E1300297_p2_d402"
/host="Homo sapiens"
/db_xref="taxon:122929"
/country="Netherlands"
/collection_date="12-Apr-2013"
/note="genotype: GII.P4-GII.4"
CDS <1..5089
/codon_start=2
/product="ORF1"
/protein_id="ATN23706.1"
/translation="SNDASAAAVANSNNDIAKSSSDGVLSSMAITFKRALGARPKQPP
PREKPQRPPRPPTPELVKNIPPPPPNGEDEIVVSYSVKDGVSGLPDLSTVRQPEESNT
AFSVPPLNQRENRDAKEPLTGTILEMWDGEIYHYGLYVERGLVLGVHKPPAAISLAKV
ELAPLSLYWRPVYTPQYLISPDTLKKLSGETFPYTAFDNNCYAFCCWVLDLNDSWLSR
RMIQRTTGFFRPYQDWNRKPLPTMDDSKIKKVANIFLCALSSLFTRPIKDIIGKIRPL
NILNILASCDWTFAGIVESLILLAELFGVFWTPPDVSAMIAPLLGDYELQGPEDLAVE
LVPVVMGGIGLVLGFTKEKIGKMLSSAASTLRACKDLGAYGLEILKLVMKWFFPKKEE
ANELAIVRSIEDAVLDLEAIENNHMTTLLKDKDSLATYMRTLDLEEEKARKLSTKSAS
PDIVGTINALLARIAAARSLVHRAKEELSSRPRPVVLMISGRPGIGKTHLAREVAKKI
AASLTGDQRVGLIPRNGVDHWDAYKGERVVLWDDYGMSNPIHDALRLQELADTCPLTL
NCDRIENKGKVFDSDVIIITTNLANPAPLDYVNFEACSRRIDFLVYAEAPEVEKAKRD
FPGQPDMWKNAFSSDFSHIRLALAPQGGFDKNGNTPHGKGVMKTLTTGSLIARASGLL
HERLDEFELQGPALTTFNFDRNKVLAFRQLAAENKYGLMDTMRVGKQLKDVRTMPELK
QALKNVSIKKCQIVYSGCTYILESDGKGNVKVDRIQSAAVQINNELAGALHHLRSARI
RYYVKCVQEALYSIMQIAGAAFVTTRIAKRMNIQNLWSKPQVENTEETTSNDGCPKPK
DDEEFVISSDDIKTEGKKGKNKTGRGKKHTAFSSKGLSDEEYDEYKRIREERNGKYSI
EEYLQDRDKYYEEVAIARATEEDFCEEEEAKIRQRIFRPTRKQRKEERASLGLVTGSE
IRKRNPDDFKPKGKLWADDDRSVDYNEKLSFEAPPSIWSRIVNFGSGWGFWVSPSLFI
TSTHVIPQGAKEFFGVPIKQIQVHKSGEFCRLRFPKPIRTDVTGMILEEGAPEGTVVT
LLIKRSTGELMPLAARMGTHATMKIQGRTVGGQMGMLLTGSNAKSMDLGTTPGDCGCP
YIYKRGNDYVVIGVHTAAARGGNTVICATQGSEGEATLEGGDNKGTYCGAPILGPGSA
PTLSTKTKFWRSSTASLPPGTYEPAYLGGKDPRVKGGPSLQQVMREQLKPFTEPRGKP
PKPSVLEAAKKTIINVLEQTIDPPEKWSFAQACASLDKTTSSGHPHHVRKNDCWNGES
FTGKLADQASKANLMFEEGKNMTPVYTAALKDELVKTDKIYGKIKKRLLWGSDLATMI
RCARAFGGLMDELKAHCVTLPIRVGMNMNEDGPIIFERHSRYTYHYDADYSRWDSTQQ
RAVLAAALEIMVKFSPEPHLAQVVAEDLLSPSVVDVGDFTISINEGLPSGVPCTSQWN
SIAHWLLTLCALSEVTNLSPDTIQANSLFSFYGDDEIVSTDIKLDPEKLTAKLREYGL
KPTRPDKTEGPLVISEDLNGLTFLRRTVTRDPAGWFGKLEQSSILRQMYWTRGPNHGD
PSETMIPHSQRPIQLMSLLGEAALHGPAFYSKISKLVIAELKEGGMDFYVPRQEPMFR
WMRFSDLSTWEGDRNLAPSFVNEDGVE"
CDS 5070..6692
/codon_start=1
/product="ORF2"
/protein_id="ATN23707.1"
/translation="MKMASSDANPSDGSTANLVPEVNNEVMALEPVVGAAIAAPVAGQ
QNVIDPWIRNNFVQAPGGEFTVSPRNAPGEILWSAPLGPDLNPYLSHLARMYNGYAGG
FEVQVILAGNAFTAGKIIFAAVPPNFPTEGLSPSQVTMFPHIIVDVRQLEPVLIPLPD
VRNNFYHYNQSNDPTIKLIAMLYTPLRANNAGDDVFTVSCRVLTRPSPDFDFIFLVPP
TVESRTKPFSVPVLTVEEMTNSRFPIPLEKLFTGPSSAFVVQPQNGRCTTDGVLLGTT
QLSPVNICTFRGDVTHIPGSRNYTMNLASQNWNSYDPTEEIPAPLGTPDFVGKIQGVL
TQTTRTNGSTRGHKATVYTGSADFSPKLGRVQFATDTDNDFETNQNTKFTPVGVIQDG
STTPRNEPQQWVLPSYSGRNIHNVHLAPAVAPTFPGEQLLFFRSTMPGCSGYPNMDLD
CLLPQEWVQYFYQEAAPAQSDVALLRFVNPDTGRVLFECKLHKSGYVTVAHTGQHDLV
IPPNGYFRFDSWVNQFYTLAPMGNGTGRRRAL"
CDS 6692..>7453
/codon_start=1
/product="ORF3"
/protein_id="ATN23708.1"
/translation="MAGAFFAGLASDVLGSGLGSLINAGAGAINQKVEFENNRKLQQA
SFQFSSNLQQASFQHDKEMLQAQIEATKKLQQEMMRVKQAMLLEGGFSETDAARGAIN
APMTKTLDWSGTRYWAPDARTTTYNAGRFSTPQPSGALPGRASLRATVPARGSSSTSS
NSSIATSVYSNQTTSTRLGSTAGSGTSVSSLPSTARARSWVEDQNRNLSPFMRGAHNI
SFVTPPSSRSSSQGTVSTVPKEVLDSWTGAFNTRRQ"
ORIGIN
1 gtctaacgac gcttccgctg ccgctgttgc taacagcaac aacgacatcg caaaatcttc
61 aagtgacgga gtgctttcta gcatggctat cacttttaaa cgagccctcg gggcgcggcc
121 taaacagcct cccccgaggg aaaaaccaca aagaccccca cgaccaccta ctccagaact
181 ggtcaaaaat attccccctc ccccacccaa cggagaggat gaaatagtgg tttcttatag
241 tgtcaaggat ggtgtttccg gcttgcctga cctttccacc gtcaggcaac cggaagaatc
301 taacacggcc ttcagtgtcc ctccactcaa tcagagggag aatagagatg ctaaggagcc
361 acttactgga acaattctgg aaatgtggga cggggaaatc taccattatg gcctgtatgt
421 ggagcgaggt cttgtactag gtgtgcacaa accaccagct gccatcagcc tcgctaaggt
481 tgagctagca ccactctcct tgtactggag acctgtgtac actcctcagt acctcatctc
541 tccagacact ctcaagaaat tatccggaga aacgttcccc tacacagcct ttgacaacaa
601 ctgttatgcc ttttgttgct gggtcctgga cctaaatgac tcgtggctga gcaggagaat
661 gatccagaga acaactggtt tcttcaggcc ctatcaagac tggaatagga aaccccttcc
721 cactatggat gactccaaaa taaagaaggt agctaacata ttcctgtgtg ctctgtcctc
781 gctgttcacc agacccataa aagatataat agggaagata aggcctctta acatcctcaa
841 catcttagcc tcatgtgatt ggacttttgc aggcatagtg gagtccctga tactcttggc
901 agaactcttt ggagttttct ggacaccccc agatgtgtct gcgatgattg cccccttact
961 tggtgactac gagctacaag gacctgagga ccttgcagtg gagctcgtcc ccgtagtgat
1021 ggggggaatt ggtttggtgc taggattcac caaagagaag attgggaaaa tgttgtcatc
1081 tgctgcgtcc accttgagag cttgtaaaga ccttggtgca tatgggctag agatcctgaa
1141 gttggtcatg aagtggttct tcccgaagaa ggaggaggca aatgagctgg ctatagtgag
1201 gtctatcgag gatgcagtcc tagatctcga ggcaattgaa aacaaccata tgaccacctt
1261 gctcaaagac aaagacagtc tggcaaccta tatgagaaca cttgaccttg aggaggagaa
1321 agccaggaaa ctctcaacca agtctgcctc acccgacatc gtgggcacaa tcaacgccct
1381 cctggcgaga atcgctgccg cacgttctct ggtgcatcga gcgaaggagg agctttccag
1441 cagaccaaga cctgtggtgt tgatgatatc aggcaggcca ggaataggga agacccacct
1501 cgctagggaa gtggctaaga aaatcgcagc ctcccttaca ggagaccagc gtgtgggcct
1561 catcccacgc aatggcgtcg accattggga tgcgtacaag ggggagaggg tcgtcctatg
1621 ggacgattat ggaatgagca accctattca cgatgccctc aggctgcaag aactcgctga
1681 cacttgcccc ctcactctaa actgtgacag gattgaaaat aaaggaaagg tctttgacag
1741 cgatgtcatc attatcacca ctaatctggc caacccagca ccactggact atgtcaactt
1801 tgaagcatgc tcgaggcgca tcgacttcct cgtgtatgca gaggcccctg aagtcgaaaa
1861 ggcgaagcgt gacttcccag gccagcctga catgtggaag aacgctttca gttctgattt
1921 ctcacacata agactagcac tggccccaca gggtggtttc gacaagaacg ggaacacccc
1981 gcacggaaag ggcgtcatga agactctcac cactggctcc cttattgccc gggcatcagg
2041 gctactccat gagaggttag atgaatttga actacagggc ccagctctca ccaccttcaa
2101 tttcgatcgc aataaagtgc ttgcctttag acagcttgct gctgaaaata aatatggatt
2161 gatggacaca atgagggttg ggaaacagct caaggatgtc agaaccatgc cagaactcaa
2221 acaagcactc aagaatgtct caatcaagaa gtgccaaata gtgtatagtg gttgcaccta
2281 catacttgag tctgatggta agggcaatgt gaaagttgac agaatccaaa gcgccgccgt
2341 gcagatcaac aatgagctgg ctggtgccct gcaccatttg aggagcgcca gaatcagata
2401 ctatgtcaag tgtgtccagg aggccctgta ttccatcatg caaattgctg gggctgcatt
2461 tgtcaccacg cgcattgcca agcgcatgaa catacaaaac ctatggtcca agccacaagt
2521 ggaaaacaca gaggagacta ccagcaatga cgggtgccca aaacctaagg atgatgagga
2581 gtttgtcatt tcatccgacg acatcaaaac tgagggtaag aaagggaaga acaagactgg
2641 ccgcggcaag aagcacacag cattttcaag caaaggcctc agtgatgaag agtacgatga
2701 gtacaagagg attagagaag aaaggaatgg caagtactcc atagaagagt accttcagga
2761 cagggacaaa tactatgagg aggtggccat tgccagggcg actgaggaag acttctgtga
2821 agaggaggag gccaagatcc ggcaaaggat ctttaggcca acaaggaaac aacgcaagga
2881 ggaaagagcc tctctcggtc tggtcacagg ctctgaaatt aggaaaagaa acccagatga
2941 cttcaaaccc aaggggaagt tgtgggctga cgatgacagg agtgtggact acaatgagaa
3001 actcagtttt gaggccccac caagcatctg gtcgagaata gtcaactttg gttcaggctg
3061 gggattctgg gtctctccca gtctgttcat aacatcaacc catgtcatac cccagggcgc
3121 aaaggagttc tttggagtcc ccatcaaaca aatacaggta cacaagtcag gcgagttctg
3181 tcgcttgaga ttcccaaaac caatcaggac tgatgtgaca ggcatgatct tagaagaagg
3241 cgcacctgag ggtaccgtgg tcacactact catcaaaagg tccactgggg aactcatgcc
3301 cctagcagct aggatgggga cccatgcgac catgaagatc caaggacgca ctgttggagg
3361 ccagatgggc atgcttctga caggatccaa cgccaagagc atggacctgg gtactacacc
3421 aggtgattgt ggctgcccct atatctacaa gagaggtaat gactacgtgg tcattggagt
3481 ccacacggct gccgcacgtg gggggaacac tgtcatatgt gccacccagg ggagtgaagg
3541 agaggctaca cttgaaggtg gtgacaacaa ggggacatac tgtggtgcac caatcctagg
3601 cccagggagt gccccaactc ttagcaccaa gaccaaattc tggagatcgt ctacagcgtc
3661 actcccacct ggcacctatg aaccagccta tcttggtggc aaggacccta gagtcaaggg
3721 tggcccttca ctacagcaag tcatgaggga acagttgaag ccattcacag agccaagggg
3781 caagccacca aaaccaagtg tattagaagc tgccaagaag accatcatca atgtccttga
3841 gcaaacaatt gatccacctg agaaatggtc gttcgcacaa gcttgcgcgt cccttgacaa
3901 gaccacttcc agtggtcatc cgcaccacgt gcggaaaaac gactgctgga acggggagtc
3961 cttcacaggc aagctggcag accaggcttc caaggccaac ctgatgtttg aagaagggaa
4021 gaacatgacc ccagtctaca cagctgcgct caaggatgag ctagttaaaa ctgacaaaat
4081 ttatggtaag atcaagaaga ggcttctctg gggctcggac ttggcgacca tgatccggtg
4141 tgctcgagca ttcggaggcc taatggatga actcaaagca cactgtgtca cgcttcccat
4201 tagagttggc atgaatatga atgaggatgg ccccatcatc ttcgagaggc attccaggta
4261 cacatatcac tatgatgctg attactctcg atgggattca acacaacaga gagccgtgtt
4321 ggcagcagct ctcgaaatca tggttaaatt ctccccagaa ccacatttgg ctcaggtagt
4381 cgcggaagac cttctttctc ctagcgtggt ggacgtgggc gacttcacaa tatcaatcaa
4441 cgagggtctt ccctctgggg tgccctgcac ctcccaatgg aactccatcg cccactggct
4501 tctcactctc tgtgcgctct ccgaagtcac aaacctatcc cctgacacca tacaggctaa
4561 ctccctcttc tctttttatg gtgatgatga aattgttagc acagacataa aattggatcc
4621 agagaaattg acagcaaagc tcagagaata tgggttaaaa ccaacccgcc ctgacaaaac
4681 tgaaggaccc cttgtcatct ctgaagacct gaatggccta actttcctgc ggagaactgt
4741 gacccgcgac ccagctggtt ggtttggaaa actggagcag agttcaatac tcaggcaaat
4801 gtactggact aggggtccca accatggaga cccatctgaa acaatgattc cacactccca
4861 aagacccata caattgatgt ccctactggg ggaggccgct ctccacggcc cagcctttta
4921 tagcaaaatc agcaagttgg tcattgcaga gctaaaagaa ggtggcatgg atttttacgt
4981 gcccagacaa gagccaatgt tcagatggat gagattctca gatctgagca cgtgggaggg
5041 cgatcgcaat ctggctccca gctttgtgaa tgaagatggc gtcgagtgac gccaacccat
5101 ctgatgggtc cacagccaac ctcgtcccag aggtcaacaa tgaggttatg gctttggagc
5161 ccgtagttgg tgccgccatt gcggcacctg tagcgggcca acaaaatgta attgacccct
5221 ggattaggaa caattttgta caagcccctg gtggagagtt tacagtatcc cctagaaacg
5281 ctccaggtga aatattatgg agcgcgccct taggccctga tctgaatccc tacctttccc
5341 atttggccag aatgtacaat ggttatgcag gtggttttga agtgcaggta atcctcgcgg
5401 ggaacgcgtt caccgccggg aaaatcatat ttgcagcagt cccaccaaat ttcccaactg
5461 aaggtttgag ccccagtcag gtcactatgt ttccccatat aatagtagat gttaggcaat
5521 tggaacctgt gttgatcccc ttacccgatg ttaggaataa tttctaccat tataatcaat
5581 caaatgaccc caccatcaaa ttgatagcaa tgttgtacac accacttagg gctaataatg
5641 ctggggacga tgtcttcaca gtttcttgtc gagttctcac gagaccatcc cccgattttg
5701 atttcatatt tttggtgcca cctacagttg aatcaagaac taaaccattc tctgtcccag
5761 ttttaactgt tgaggagatg accaattcaa ggttccccat tcctttggaa aagttgttca
5821 cgggccccag tagtgccttt gttgttcaac cacaaaatgg caggtgcacg actgatggcg
5881 tgctcctagg tactacccaa ctgtcccctg tcaacatctg caccttcaga ggggatgtca
5941 cccatattcc aggcagtcgt aactacacaa tgaatttggc ctcccaaaat tggaacagtt
6001 acgatccaac agaagaaatc ccagcccctc taggaactcc agatttcgtg gggaagattc
6061 aaggtgtgct cacccaaacc acaaggacaa atggctcgac ccgcggccac aaagctacag
6121 tgtacactgg gagcgccgac ttttctccaa aactgggtag agttcaattt gccactgaca
6181 cagacaatga ttttgaaact aaccagaaca caaagttcac cccagtcggt gttatccagg
6241 atggtagtac caccccccga aatgaacccc aacaatgggt gctcccaagt tactcaggca
6301 gaaacattca taatgtgcac ctggcccccg ctgtagcccc cactttcccg ggcgagcagc
6361 tcctcttctt cagatctact atgcccggat gcagcgggta ccccaacatg gatttggact
6421 gtctgctccc ccaggaatgg gtgcagtact tctaccagga ggcagcccca gcacaatctg
6481 atgtggctct gttaagattt gtgaatccag acacaggcag ggttttgttt gagtgtaagc
6541 ttcataaatc aggctatgtt acagtggctc acactggcca acatgatttg gttatccccc
6601 ccaatggtta ttttagattt gattcctggg tcaaccagtt ctacacactt gcccctatgg
6661 gaaatgggac ggggcgtaga cgtgcattat aatggctgga gctttctttg ctggattggc
6721 atctgacgtc cttggctctg gacttggttc cctaatcaat gctggggctg gggccatcaa
6781 ccaaaaagtt gaatttgaaa ataacagaaa attgcaacaa gcttccttcc aatttagtag
6841 caatctacaa caagcttcct ttcaacatga caaagagatg ctccaagcac aaattgaggc
6901 caccaaaaag ttgcaacagg aaatgatgag agttaaacaa gcaatgctcc tagagggtgg
6961 attctctgag acagatgcag cccgtggggc aatcaacgcc cccatgacaa aaactttgga
7021 ctggagcggg acaaggtact gggctcccga tgctaggact acaacatata atgcaggccg
7081 cttttccacc cctcaaccct cgggggcact accaggaaga gctagtctta gggctactgt
7141 ccccgcccgg ggttcctcca gcacgtcttc taactcttct attgctactt ctgtgtattc
7201 aaatcaaacc acctcgacga gacttggttc tacagctggt tctggtacca gtgtctcgag
7261 cctcccgtca actgcaaggg ctaggagctg ggttgaggat caaaatagga atttgtcacc
7321 tttcatgagg ggggcccaca acatctcgtt tgtcacccca ccatctagca gatcctctag
7381 ccaaggcaca gtctcaaccg tgcccaaaga agttttggac tcctggactg gcgctttcaa
7441 cacgcgcagg cag
//