Typing tool
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Typing tool
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Complete norovirus genomes
| MF140695 | GII.4 New Orleans | |
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| GII.P4 New Orleans |
ORF1: 1..5088
ORF2: 5069..6691
ORF3: 6691..7497
LOCUS MF140695 7540 bp RNA linear VRL 24-OCT-2017
DEFINITION Norovirus GII strain
Norovirus/GII/Hu/NL/2013/GII.P4-GII.4/Rotterdam/E1300281_p9_d58
ORF1 gene, partial cds; and ORF2 and ORF3 genes, complete cds.
ACCESSION MF140695
VERSION MF140695.1
KEYWORDS .
SOURCE Norovirus GII
ORGANISM Norovirus GII
Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes;
Picornavirales; Caliciviridae; Norovirus; Norwalk virus.
REFERENCE 1 (bases 1 to 7540)
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 7540)
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..7540
/organism="Norovirus GII"
/mol_type="genomic RNA"
/strain="Norovirus/GII/Hu/NL/2013/GII.P4-
GII.4/Rotterdam/E1300281_p9_d58"
/host="Homo sapiens"
/db_xref="taxon:122929"
/country="Netherlands"
/collection_date="18-Oct-2013"
/note="genotype: GII.P4-GII.4"
CDS <1..5088
/codon_start=1
/product="ORF1"
/protein_id="ATN23781.1"
/translation="SNDASAAAVANSNNDTAKSSSDGVLSSMAVTFKRALGARPKQPP
PREIPQRPPRPPTPELVKSIPPPPPNGEDEIVVSYSVKDGVSGLPDLSTVRQPEESNT
AFSVPPLNQRESRDAKEPLTGTILEMWDGEIYHYGLYVERGLVLGVHKPPAAISLAKV
ELAPLSLYWRPVYTPQYLISPDTLKKLSGETFPYTAFDNNCYAFCCWVLDLNDSWLNR
RMIQRTTGFFRPYQDWNRKPLPTIDDSKIKKVANIFLCALSSLFTRPIKDIIGKIRPL
NILNILASCDWTFAGIVESLILLAELFGVFWTPPDVSAMIAPLLGDYELQGPEDLAVE
LVPVVMGGIGLVLGFTKEKIGKMLSSAASTLRACKDLGAYGLEILKLVMKWFFPKKEE
ANELAMVRSIEDAVLDLEAIENNHMTTLLKDKDSLATYMRTLDLEEEKARKLSTKSAS
PDIVGTINALLARIAAARSLVHRAKEELSSRPRPVVLMISGRPGIGKTHLAREVAKKI
AASLTGDQRVGLIPRNGVDHWDAYKGERVVLWDDYGMSNPIHDALRLQELADTCPLTL
NCDRIENKGKVFDSDVIIITTNLANPAPLDYVNFEACSRRIDFLVYAEAPEVEKAKRD
FPGQPDMWKNAFSSDFSHIRLALAPQGGFDKNGNTPHGKGVMKTLTTGSLIARASGLL
HERLDEFELQGPALTTFNFDRNKVLAFRQLAAENKYGLMDTMRVGKQLKDVKTMPELK
QALKNVSIKKCQIVYSGCTYILESDGKGNVKVDRIQNTTVQINNELAGALHHLRSARI
RYYVKCVQEALYSIIQIAGAAFVTTRIAKRMNIQNLWSKPQVENTEETTSNDGCPKPK
DDEEFVISSDDIKTEGKKGKNKTGRGKKHTAFSSKGLSDEEYDEYKRIREERNGKYSI
EEYLQDRDKYYEEVAIARATEEDFCEEEEAKIRQRIFRPTRKQRKEERASLGLVTGSE
IRKRNPDDFKPKGKLWADDDRSVDYNEKLSFEAPPSIWSRIVNFGSGWGFWVSPSLFI
TSTHVIPQGAKEFFGVPIKQIQVHKSGEFCRLRFPKPIRTDVTGMILEEGAPEGTVVT
LLIKRSTGELMPLAARMGTHATMKIQGRTVGGQMGMLLTGSNAKSMDMGTTPGDCGCP
YIYKRGNDYVVIGVHTAAARGGNTVICATQGSEGEATLEGGDNKGTYCGAPILGPGSA
PTLSTKTKFWRSSTASLPPGTYEPAYLGGKDPRVKGGPSLQQVMREQLKPFTEPRGKP
PKPSVLEAAKKTIINVLEQTIDPPEKWSFAQACASLDKTTSSGYPHHVRKNDCWNGES
FTGKLADQASKANLMFEEGKNMTPVYTAALKDELVKTDKIYGKIKKRLLWGSDLATMI
RCARAFGGLMDELKAHCVTLPIRVGMNMNEDGPIIFERHSRYTYHYDADYSRWDSTQQ
RAVLAAALEIMVKFSPEPHLAQVVAEDLLSPSVVDVGDFTISINEGLPSGVPCTSQWN
SIAHWLLTLCALSEVTNLSPDTIQANSLFSFYGDDEIVSTDIKLDPEKLTAKLREYGL
KPTRPDKTEGPLVITEDLNGLTFLRRTVTRDPAGWFGKLEQSSILRQMYWTRGPNHGD
PSETMIPHSQRPIQLMSLLGEAALHGPAFYSKISKLVIAELKEGGMDFYVPRQEPMFR
WMRFSDLSTWEGDRNLAPSFVNEDGVE"
CDS 5069..6691
/codon_start=1
/product="ORF2"
/protein_id="ATN23782.1"
/translation="MKMASSDANPSDGSTANLVPEVNNEVMALEPVVGAAIAAPVAGQ
QNVIDPWIRNNFVQAPGGEFTVSPRNAPGEILWSAPLGPDLNPYLSHLARMYNGYAGG
FEVQVILAGNAFTAGKIIFAAVPPNFPTEGLSPSQVTMFPHIIVDVRQLEPVLIPLPD
VRNNFYHYNQSNDSTIKLIAMLYTPLRANNAGDDVFTVSCRVLTRPSPDFDFIFLVPP
TVESRTKPFSVPVLTVEEMTNSRFPIPLEKLFTGPSSDIVVQPQNGRCTTDGVLLGTT
QLSSVNICTFRGDVTQVGKTNRYTMNLASPNWNSYDPTEDTPAPLGTPDFVGKIQGVL
TQTTIPGGSTRAHKATVRTGSADFSPKLGKIQFDTDTSNDLDTNQNTKFTPVGVVQEG
DDSHQKEPIQWELPSYSGRGTHNVHLAPAVAPTFPGEQLLFFRSTMPGCGGYPNMNLD
CLLPQEWVQYFYQEAAPAQSDVALLRFVNPDTGRVLFECKLHKSGYVTVAYTGKHDLV
IPPNGYFRFDSWVNQFYTLAPMGNGTGRRRAL"
CDS 6691..7497
/codon_start=1
/product="ORF3"
/protein_id="ATN23783.1"
/translation="MAGAFFAGLASDVLGSGLGSLINAGAGVINQKVDFENNRKLQQD
SFQFSSNLQQASFQHDKEMLQAQIEATKKLQQEMMRVKQAMLLEGGFSETDAARGAIN
APMTKVLDWNGTRYWAPDARTTTYNAGRFSTPQPSGAPPGRANLRAAAPARGSSSMSS
KSSIASSVYSNQTTSTRLGSTAGSGTSVSSLPSTARTRSWVEDQNRNLSPFMRGAHNI
SFVTPPSSRSSSQGTVSTVPKEILDSWTGAFNTRRQPLFAHIRKRGESRV"
ORIGIN
1 tctaacgacg cttccgctgc cgctgttgct aacagcaaca acgacaccgc aaaatcttca
61 agtgacggag tgctttctag catggctgtc acttttaaac gagccctcgg ggcgcggcct
121 aaacagcctc ccccgaggga aataccacaa aggcccccac gaccacctac tccagaactg
181 gtcaaaagta ttccccctcc cccacccaac ggagaggatg aaatagtggt ttcttacagt
241 gttaaggatg gtgtttccgg cttgcctgac ctttccaccg ttaggcaacc ggaagaatct
301 aacacggcct tcagtgtccc tccactcaat cagagggaga gtagagatgc taaggagcca
361 cttactggaa caattctgga aatgtgggac ggggaaatct accattatgg cctgtatgtg
421 gagcgaggtc ttgtactagg cgtgcacaaa ccaccagctg ccatcagcct cgctaaggtt
481 gagctagcac cactctcctt gtactggaga cctgtgtata ctcctcagta cctcatctct
541 ccagacactc tcaagaaatt atccggagaa acgttcccct acacagcctt tgacaacaac
601 tgttatgcct tttgttgctg ggtcctggac ctaaatgact catggctgaa caggagaatg
661 atccagagaa caactggttt ctttaggccc tatcaagact ggaataggaa accccttcct
721 actatagatg actccaaaat aaagaaggta gctaacatat tcctgtgtgc tctgtcctcg
781 ctgttcacca gacccataaa agatataata gggaagataa ggcctcttaa catcctcaac
841 atcttagcct catgtgattg gacttttgca ggcatagtgg agtccctgat actcttggca
901 gaactctttg gagttttctg gacaccccca gatgtgtctg ctatgattgc tcccttactc
961 ggtgactatg agctacaagg acctgaggac cttgcagtgg agctcgtccc cgtagtgatg
1021 gggggaattg gtttggtgct aggattcacc aaagagaaga ttgggaaaat gttgtcatct
1081 gccgcgtcca ccttgagagc ttgtaaagac cttggtgcat atgggctaga gatcctgaag
1141 ttggtcatga agtggttctt tccgaagaag gaggaggcaa atgagctggc tatggtgagg
1201 tctatcgagg atgcagttct agatctcgag gcaattgaaa acaaccatat gactaccttg
1261 ctcaaagaca aagacagtct ggcaacctat atgagaacac ttgaccttga ggaggagaaa
1321 gccaggaaac tctcaaccaa gtctgcctca cccgacatcg tgggcacaat caacgccctc
1381 ctggcgagaa tcgctgccgc acgttctctg gtgcatcgag cgaaggagga gctttccagc
1441 agaccaagac ctgtggtgtt gatgatatca ggcaggccgg ggatagggaa gacccacctc
1501 gctagggaag tggctaagaa gatcgcagcc tcccttacag gagaccagcg tgtgggcctc
1561 atcccacgca atggcgtcga ccattgggat gcgtacaagg gagagagagt cgtcctatgg
1621 gacgattatg gaatgagcaa ccccattcac gacgccctca ggctgcaaga actcgctgac
1681 acttgccccc tcactctaaa ctgtgacagg attgaaaata aaggaaaggt ctttgacagc
1741 gatgtcatca ttatcaccac taatctggcc aacccagcac cactagacta tgtcaacttt
1801 gaagcatgct cgaggcgcat cgacttcctc gtgtatgcag aagcccctga agtcgagaag
1861 gcgaagcgtg acttcccagg ccagcctgac atgtggaaga acgctttcag ttctgatttc
1921 tcacacataa gactagcact ggccccacag ggtggtttcg acaagaacgg gaacaccccg
1981 catggaaagg gcgtcatgaa gactctcacc actggctccc ttattgcccg agcgtcaggg
2041 ctactccatg agaggttaga tgaatttgaa ctacagggcc cagctctcac caccttcaat
2101 tttgaccgca acaaagtgct tgccttcaga cagcttgctg ctgagaataa atatggattg
2161 atggacacaa tgagggttgg gaaacagctc aaggatgtca aaaccatgcc tgaactcaaa
2221 caagcactca agaatgtctc aatcaagaag tgccaaatag tatatagtgg ttgcacctac
2281 atacttgagt ctgatggcaa gggcaatgtg aaagttgaca gaatccaaaa caccaccgtg
2341 cagatcaaca atgagctggc tggtgctctg caccatttga ggagcgccag aatcagatac
2401 tatgtcaagt gtgtccagga ggccctatat tccatcattc aaattgctgg ggctgcattt
2461 gtcaccacgc gcattgccaa gcgcatgaac atacaaaacc tatggtccaa accacaagtg
2521 gaaaacacag aggagactac cagcaatgac gggtgcccaa aacctaagga tgatgaggag
2581 tttgtcattt catctgacga catcaaaact gagggcaaga aagggaaaaa caagactggt
2641 cgcggcaaga agcacacagc attttcaagc aaaggcctca gtgatgaaga gtacgatgag
2701 tacaagagga ttagagaaga aaggaatggt aagtactcca tagaagaata ccttcaggac
2761 agggacaaat actatgagga ggtggccatt gccagggcga ctgaggaaga cttctgtgaa
2821 gaggaggagg ccaagatccg tcaaaggatc tttaggccaa caaggaaaca acgcaaggag
2881 gaaagagctt ctctcggtct ggtcacaggt tctgaaatta ggaaaagaaa cccagatgac
2941 ttcaaaccca aggggaaatt gtgggctgac gatgacagga gtgtggacta caatgagaaa
3001 ctcagttttg aggccccacc aagcatctgg tcaagaatag tcaactttgg ttcaggctgg
3061 ggattctggg tctcccccag tcttttcata acatcaaccc atgtcatacc ccagggcgca
3121 aaggagttct ttggagtccc catcaaacaa atacaggtac acaaatcagg cgagttctgt
3181 cgcttgagat tcccaaaacc aatcaggact gatgtgacag gcatgatctt ggaagaaggc
3241 gcacctgagg gtaccgtggt cacactactc atcaaaaggt ccactgggga actcatgccc
3301 ctagcagcta gaatggggac ccatgcgacc atgaagatcc aagggcgcac tgttggaggc
3361 cagatgggca tgctcctgac agggtccaac gccaagagca tggacatggg tactacacca
3421 ggtgattgcg gctgtcccta tatttacaag agaggcaatg actatgtggt cattggagtc
3481 cacacggctg ccgcacgtgg agggaacact gtcatatgtg ccacccaggg gagtgaagga
3541 gaggctacac ttgaaggtgg tgacaacaag ggaacatatt gtggtgcacc aatcctaggc
3601 ccagggagtg ccccaactct tagcaccaag accaaattct ggagatcatc tacagcgtca
3661 ctcccacctg gcacctatga accagcctat cttggtggca aggaccccag agtcaagggt
3721 ggcccttcac tacagcaagt catgagggag cagttgaaac cattcacaga gccaaggggc
3781 aaaccaccaa aaccaagtgt attagaagct gccaagaaga ccatcatcaa tgtccttgag
3841 caaacaattg atccacctga gaaatggtcg ttcgcacaag cttgcgcgtc ccttgacaag
3901 accacttcca gcggttatcc gcaccatgtg cggaaaaacg actgctggaa cggggagtcc
3961 ttcacaggca agctggcaga ccaggcttcc aaggccaacc tgatgtttga agaagggaaa
4021 aacatgaccc cagtctacac agctgcactc aaggatgagt tagttaaaac tgacaaaatt
4081 tatggtaaga tcaagaagag gcttctctgg ggctcggact tggcgaccat gatccggtgt
4141 gctcgggcat tcggaggcct aatggatgaa ctcaaagcac actgtgtcac acttcccatt
4201 agagttggca tgaacatgaa tgaggatggc cccatcatct tcgagaggca ttctaggtac
4261 acatatcact atgatgctga ttactctcga tgggattcaa cacaacagag agccgtgttg
4321 gcagcagctc tcgaaatcat ggttaaattc tccccagaac cacatttggc ccaggtagtc
4381 gcagaagacc ttctttctcc tagcgtggtg gacgtgggcg acttcacaat atcaatcaac
4441 gagggtcttc cctctggggt gccttgcacc tcccaatgga actccatcgc ccactggctt
4501 ctcactctct gtgcgctctc tgaagtcaca aacctatccc ctgacacaat acaggctaat
4561 tccctcttct ctttttatgg tgatgatgaa attgttagca cagacataaa attggaccca
4621 gagaaattga cagcaaagct cagagaatat gggttaaaac cgacccgccc tgacaaaact
4681 gaaggacccc ttgtcatcac tgaagacctg aatggcctaa ctttcctgcg gagaactgtg
4741 acccgcgacc cagctggttg gtttggaaaa ctggagcaga gttcaatact caggcaaatg
4801 tactggacta ggggtcccaa ccatggagac ccatctgaaa caatgattcc acactcccaa
4861 agacccatac aattgatgtc cctactgggg gaggccgctc tccacggccc agccttttac
4921 agcaaaatca gcaagttggt cattgcagag ctaaaagaag gtggcatgga tttttacgtg
4981 cccagacaag agccaatgtt cagatggatg agattctcag atctgagcac gtgggagggc
5041 gatcgcaatc tggctcccag ttttgtgaat gaagatggcg tcgagtgacg ccaacccatc
5101 tgatgggtcc acagccaacc tcgtcccaga ggtcaacaat gaggttatgg ctttggagcc
5161 cgtagttggt gccgccattg cggcacctgt agcgggccaa caaaatgtaa ttgacccctg
5221 gattagaaat aattttgtac aagcccctgg tggagagttt acagtatccc ctagaaacgc
5281 tccaggtgaa atactatgga gcgcgccctt aggccctgat ctgaacccct acctttccca
5341 tttggccaga atgtacaatg gttatgcagg tggttttgaa gtgcaggtaa tcctcgcggg
5401 gaacgcgttc accgccggga aaatcatatt tgcagcagtc ccaccaaatt tcccaactga
5461 aggtttgagc cccagccagg tcactatgtt tccccatata atagtagatg ttaggcaatt
5521 ggaacctgtg ttgattccct tacccgatgt taggaataat ttctaccatt ataatcaatc
5581 aaatgactcc accattaaat tgatagcaat gttgtataca ccacttaggg ctaataatgc
5641 tggggacgat gtcttcacag tctcttgtcg agtcctcacg agaccatccc ccgattttga
5701 ttttatattt ttggtgccac ctacagttga atcaagaact aaaccattct ctgtcccagt
5761 tctaactgtt gaagagatga ccaattcaag gttccccatc cctttggaaa agttgttcac
5821 aggccccagt agtgacatcg tagttcaacc acaaaatggc aggtgcacga ctgatggcgt
5881 gctcctaggt actacccaat tgtcctctgt caacatctgc accttcagag gggatgtcac
5941 ccaagttgga aaaactaaca gatacacaat gaatttggcc tccccaaatt ggaacagtta
6001 cgatccaaca gaagataccc cagcccctct aggaactcca gatttcgtgg ggaagattca
6061 aggtgtgctc acccaaacca caattccagg tggctcgacc cgcgcccaca aggccacagt
6121 gcgcactggg agcgccgatt tttctccaaa actgggtaaa attcaatttg acactgacac
6181 aagtaatgat cttgacacca accagaacac aaagttcacc ccagtcggcg ttgtccagga
6241 aggtgatgat tcccaccaga aagaacccat acaatgggag ctcccaagct attcaggcag
6301 aggcactcat aatgtacacc tggcccccgc tgtagcccct actttcccgg gcgagcagct
6361 cctcttcttc agatctacta tgcccggatg cggcgggtac cccaacatga atttggactg
6421 tctactccct caggaatggg tgcagtactt ctaccaggag gcagccccag cacaatctga
6481 tgtagctctg ttaagatttg tgaatccaga cacaggtagg gttttatttg aatgtaagct
6541 tcataaatca ggctatgtta cagtggctta cactggcaaa catgatttgg ttatcccccc
6601 taatggttat tttagatttg attcctgggt caaccagttc tacactcttg cccccatggg
6661 aaatggaacg gggcgtagac gtgcattata atggctggag ctttctttgc tggattggca
6721 tctgatgtcc ttggctctgg acttggttcc ctaatcaatg ctggggctgg ggtcatcaac
6781 caaaaagttg attttgaaaa taatagaaaa ttacaacaag attccttcca atttagtagc
6841 aatctccaac aagcttcctt tcaacatgac aaagagatgc tccaagcaca aattgaggcc
6901 accaaaaagt tgcaacagga aatgatgaga gttaaacaag caatgctcct agagggtgga
6961 ttctctgaga cagatgcagc ccgtggggca atcaacgccc ccatgacaaa agttttggac
7021 tggaatggaa caaggtactg ggctcccgat gccaggacta caacatacaa tgcaggccgc
7081 ttttccaccc ctcaaccctc gggggcacca ccaggaaggg ctaatcttag ggctgctgcc
7141 cccgcccggg gctcctctag catgtcttct aaatcttcta ttgcttcttc tgtgtattca
7201 aatcaaacca cctcaacgag acttggttct acagctggtt ctggtaccag tgtctcgagc
7261 ctcccgtcaa ctgcaaggac taggagctgg gttgaggatc aaaataggaa tttgtcacct
7321 ttcatgaggg gggcccacaa catctcgttt gtcaccccac catctagcag atcctctagc
7381 caaggcacag tctcaaccgt gcccaaagaa attttggact cctggactgg cgctttcaac
7441 acgcgcaggc agcctctctt cgctcacatt cgtaagcgag gggagtcacg ggtgtaatgt
7501 gaaaagacaa aattgattat ctttcttttc tttagtgtct
//