Typing tool
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Typing tool
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Complete norovirus genomes
| MF140693 | GII.4 New Orleans | |
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| GII.P4 New Orleans |
ORF1: 1..5088
ORF2: 5069..6691
ORF3: 6691..7497
LOCUS MF140693 7543 bp RNA linear VRL 24-OCT-2017
DEFINITION Norovirus GII strain
Norovirus/GII/Hu/NL/2011/GII.P4-GII.4/Rotterdam/E7800020_p8_d340
ORF1 gene, partial cds; and ORF2 and ORF3 genes, complete cds.
ACCESSION MF140693
VERSION MF140693.1
KEYWORDS .
SOURCE Norovirus GII
ORGANISM Norovirus GII
Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes;
Picornavirales; Caliciviridae; Norovirus; Norwalk virus.
REFERENCE 1 (bases 1 to 7543)
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 7543)
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..7543
/organism="Norovirus GII"
/mol_type="genomic RNA"
/strain="Norovirus/GII/Hu/NL/2011/GII.P4-
GII.4/Rotterdam/E7800020_p8_d340"
/host="Homo sapiens"
/db_xref="taxon:122929"
/country="Netherlands"
/collection_date="14-Aug-2011"
/note="genotype: GII.P4-GII.4"
CDS <1..5088
/codon_start=1
/product="ORF1"
/protein_id="ATN23775.1"
/translation="SNDASAAAVANSNNDIAKSSSDGVLSSMAVTFKRALGARPKQPP
PREKPQRPPRPPTPELVKNIPPPPPNGEDEIVVSYSVKDGVSGLPELSTVRQPEESNT
AFSVPPLNQRENRDAKEPLTGTILEMWDGEIYHYGLYVEQGLVLGVHKPPAAISLAKV
ELAPLSLYWRPVYTPQYLISPDTLKKLSGETFPYTAFDNNCYAFCCWVMDLNDSWLSR
RMIQRTTGFFRPYQDWNRKPLPTMDDSKIKKVANVFLCALSSLFTRPIKDIIGRIRPL
NILNILASCDWTFAGIVESLILLAELFGVFWTPPDVSAMIAPLLGDYELQGPEDLAVE
LVPVVMGGIGLVLGFTKEKIGKMLSSAASTLRACKDLGAYGLEILKLVMKWFFPKKEE
ANELAIVRSIEDAVLDLEAIENNHMTALLKDKDSLATYMRTLDLEEEKARKLSTKSAS
PDIVGTINALLARIAAARSLVHRAKEELSSRPRPVVLMISGRPGIGKTHLAREVAKRI
AASLTGDQRVGLIPRNGVDHWDAYKGERVVLWDDYGMSNPIHDALRLQELADTCSLTL
NCDRIENKGKVFDSDVIIITTNLANPAPLDYVNFEACSRRIDFLVYAEAPEVEKAKRD
FPGQPDMWKNAFSSDFSHIKLTLAPQGGFDKNGNTPHGKGVMKTLTTGSLIARASGLL
HERLDEFELQGPALTTFNFDRNKVLAFRQLAAENKYGLMDTMRVGKQLKDVKTMPELK
QALKNVSIKKCQIVYSGCTYILESDGKGNVKVDRIQSAAVQINNELAGALHHLRSARI
RYYVKCVQEALYSIIQIAGVAFVTTRIAKRMNIQNLWSKPQVENTEETASKDGCPKPR
DDEEFVISSDDIKTEGKKGKNKTGRGKKHTAFSSKGLSDEEYDEYKRIREERNGKYSI
EEYLQDRDKYYEEVAIARATEEDFCEEEEAKIRQRIFRPTRKQRKEERASLGLVTGSE
IRKRNPDDFKPKGKLWADDDRNVDYNEKLSFEAPPSIWSRIVNFGSGWGFWVSPSLFI
TSTHVIPQGAKEFFGVPIKQIQVHKSGEFCRLRFPKPIRTDVTGMILEEGAPEGTVVT
LLIKRSTGELMPLAARMGTHATMKIQGRTVGGQMGMLLTGSNAKSMDLGTTPGDCGCP
YIYKRGNDYVVIGVHTAAARGGNTVICATQGSEGEATLEGGDNKGTYCGAPILGPGSA
PTLSTKTKFWRSSTAPLPPGTYEPAYLGGKDPRVKGGPSLQQVMREQLKPFTEPRGKP
PKPSVLEAAKKTIINVLEQTIDPPEKWSFAQACASLDKTTSSGHPHHVRKNDCWNGES
FTGKLADQASKANLMFEEGKNMTPVYTAALKDELVKTDKIYGKIKKRLLWGSDLATMI
RCARAFGGLMDEFKAHCVTLPIRVGMNMNEDGPIIFERHSRYTYHYDADYSRWDSTQQ
RAVLAAALEIMVKFSPEPHLAQVVAEDLLSPSVVDVGDFTISINEGLPSGVPCTSQWN
SIAHWLLTLCALSEVTNLSPDIIQANSLFSFYGDDEIVSTDIKLDPEKLTAKLREYGL
KPTRPDKTEGPLVISEDLNGLTFLRRTVTRDPAGWFGKLEQSSILRQMYWTRGPNHGD
PSETMIPHSQRPIQLMSLLGEAALHGPAFYSKISKLVIAELKEGGMDFYVPRQEPMFR
WMRFSDLSTWEGDRNLAPSFVNEDGVE"
CDS 5069..6691
/codon_start=1
/product="ORF2"
/protein_id="ATN23776.1"
/translation="MKMASSDANPSDGSTANLVPEVNNEVMALEPVVGAAIAAPVAGQ
QNVIDPWIRNNFVQAPGGEFTVSPRNAPGEILWSAPLGPDLNPYLSHLARMYNGYAGG
FEVQVLLAGNAFTAGKIIFAAVPPNFPTEGLSPSQITMFPHMIVDVRQLEPVLIPLPD
VRNNFYHYNQSNDSTIKLIAMLYTPLRANNAGDDVFTVSCRVLTRPSPDFDFIFLVPP
TVESRTKPFSVPILTVEEMTNSRFPIPLEKLFTGPSSAFVVQPQNGRCTTDGVLLGTT
QLSPVNICTFRGDVTHTSGSHNYTMNLASQNWNSYDPTEEIPAPLGTPDFVGKIQGVL
TQTTRTDGSTRGHKATVYTGAADFSPKLGRVQFATDTNNDFDTNQNTKFTPIGVIQEG
DTPHRNEPQQWVLPSYSGRNIHNVHLAPAVAPTFPGEQLLFFRSTMPGCSGYPNMDLD
CLLPQEWVQYFYQEAAPAQSDVALLRFVNPDTGRVLFECKLHKSGYVTVAHTGQHDLV
IPPNGYFRFDSWVNQFYTLAPMGNGTGRRRAL"
CDS 6691..7497
/codon_start=1
/product="ORF3"
/protein_id="ATN23777.1"
/translation="MAGAFFAGLASDVLGSGLGSLINAGAGAINQKVEFENNRKLQQA
SFQFSSNLQQASFQHDKEMLQAQIEATKKLQQEMMRVKQAMLLEGGFSEVDAARGAIN
APMTKTLDWSGTRYWAPDARTTTYNAGRFSTPQPSGALPGRANLRATAPARGSSSMSS
NSSIATSVYSNQTTSTRLGSTAGSGTSVSSLPSTARTRSWVEDQNRNLSPFMRGAHNI
SFVTPPSSRSSSQGTVSTVPKEVLDSWTGAFNTRRQPLFAHIRKRGESRV"
ORIGIN
1 tctaacgacg cttccgctgc cgctgttgct aacagcaaca acgacatcgc aaaatcttcg
61 agtgacggag tgctttctag catggctgtc acttttaaac gagccctcgg ggcgcggcct
121 aaacagcctc ccccgaggga aaaaccacaa agacccccac gaccacctac tccagaactg
181 gtcaaaaata ttccccctcc cccacccaac ggagaggatg aaatagtggt ttcttatagt
241 gtcaaggatg gtgtttccgg cttgcctgaa ctttccaccg tcaggcaacc ggaagaatct
301 aacacggcct tcagtgtccc tccacttaat cagagggaga atagagatgc taaggagcca
361 ctcactggaa caattctgga aatgtgggac ggggaaatct accattatgg cctgtatgtg
421 gagcaaggcc ttgtactagg tgtgcacaaa ccaccagctg ccatcagtct cgctaaggtt
481 gagctagcac cactctcctt gtactggaga cctgtgtaca ctcctcagta cctcatctct
541 ccagacactc tcaagaaatt atccggagaa acgttcccct acacagcctt tgacaacaac
601 tgctatgcct tttgttgctg ggtcatggac ctaaatgact cgtggctgag caggagaatg
661 atccagagaa caactggttt cttcaggccc taccaagact ggaataggaa accccttccc
721 actatggatg actccaaaat aaagaaggta gctaacgtat tcctgtgtgc tctgtcctcg
781 ctgttcacca gacccataaa agatataata gggaggataa ggcctcttaa catcctcaac
841 atcttagcct catgtgattg gacttttgca ggcatagtgg agtccctgat actcttggca
901 gaactctttg gagttttctg gacaccccca gatgtgtctg cgatgattgc ccccttgctt
961 ggtgactacg agctacaagg acctgaggac cttgcagtgg agctcgtccc cgtagtgatg
1021 gggggaattg gtttggtgct aggattcacc aaagagaaga ttgggaaaat gttgtcatct
1081 gctgcgtcca ccttgagagc ttgtaaagac cttggtgcat atgggctaga gatcctaaag
1141 ttggtcatga agtggttctt cccgaagaag gaggaggcaa atgagctggc tatagtgagg
1201 tctattgagg acgcagtcct agatctcgag gcaattgaaa acaaccatat gaccgccttg
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 ggcaggccag gaatagggaa gacccacctc
1501 gctagggaag tggctaagag aatcgcagcc tcccttacag gagaccagcg tgtgggcctc
1561 atcccacgca atggcgtcga ccattgggat gcatacaagg gagagagggt cgtcctatgg
1621 gacgattatg gaatgagcaa ccctatccac gatgccctca ggctgcaaga actcgctgac
1681 acttgctccc tcactctaaa ctgtgacagg attgaaaata aaggaaaggt ctttgacagc
1741 gatgtcatca ttatcaccac taatctggcc aacccagcac cactggacta tgtcaacttt
1801 gaagcatgct cgaggcgcat cgacttcctc gtgtatgcag aagcccctga agtcgaaaag
1861 gcgaagcgtg acttcccagg ccaacctgac atgtggaaga acgctttcag ttctgatttc
1921 tcacacataa aactgacact ggccccacag ggtggtttcg acaagaacgg gaacaccccg
1981 cacggaaagg gcgtcatgaa gactctcacc actggctccc ttattgcccg ggcatcaggg
2041 ctactccatg agaggttaga tgaatttgaa ctacagggcc cagctctcac caccttcaat
2101 ttcgatcgca ataaagtgct tgcctttaga cagcttgctg ctgaaaataa atatggattg
2161 atggacacaa tgagggttgg gaaacagctc aaggatgtca aaaccatgcc agaactcaaa
2221 caagcactca agaatgtctc aatcaagaag tgccaaatag tgtatagtgg ttgcacctac
2281 atacttgagt ctgatggcaa gggcaatgtg aaagttgaca gaatccaaag cgccgccgtg
2341 cagatcaaca atgagctggc tggtgccctg caccatttga ggagcgccag aatcagatac
2401 tatgtcaagt gtgtccagga ggccctgtat tccatcattc aaattgctgg ggttgcattt
2461 gtcaccacgc gcattgccaa gcgcatgaac atacaaaacc tatggtccaa gccacaagtg
2521 gaaaacacag aggagactgc cagcaaggac gggtgcccaa aacctaggga tgatgaggag
2581 ttcgtcattt catccgacga catcaaaact gagggtaaga aagggaagaa caagactggc
2641 cgcggcaaga agcacacagc attttcaagc aaaggcctca gtgatgaaga gtacgatgag
2701 tacaagagaa ttagagaaga aaggaatggc aagtactcca tagaagagta ccttcaggac
2761 agggacaaat actatgagga ggtggccatt gccagggcga ctgaggaaga cttctgtgaa
2821 gaggaggagg ccaagatccg gcagaggatt tttaggccaa caaggaaaca acgcaaggag
2881 gaaagagcct ctctcggcct ggtcacaggc tctgaaatta ggaaaagaaa cccagatgat
2941 ttcaaaccca aggggaaatt gtgggctgac gatgacagga atgtggatta caatgagaaa
3001 ctcagttttg aggccccacc aagcatctgg tcaagaatag tcaactttgg ttcaggctgg
3061 ggattctggg tctcccccag tctgttcata acatcaaccc atgtcatacc ccagggcgca
3121 aaggagttct ttggagtccc catcaaacaa atacaggtac acaagtcagg cgagttctgt
3181 cgcttgagat tcccaaaacc aatcaggact gatgtgacgg gcatgatctt agaagaaggc
3241 gcacctgagg gcaccgtggt cacactactc atcaaaaggt ccactgggga actcatgccc
3301 ctagcagcta ggatggggac ccatgcgacc atgaagatcc aagggcgcac tgttggaggc
3361 cagatgggca tgcttctgac aggatccaac gccaagagca tggacctggg tactacacca
3421 ggtgattgtg gctgccccta tatctacaag agaggtaatg actatgtggt cattggagtc
3481 cacacggctg ccgcacgtgg gggaaacact gtcatatgtg ccacccaggg gagtgaagga
3541 gaggctacac ttgaaggtgg tgacaacaag gggacatact gtggtgcacc aatcctaggc
3601 ccagggagtg ccccaactct tagcaccaag accaaattct ggagatcgtc tacagcacca
3661 ctcccacctg gcacctatga accagcctat cttggtggca aggaccctag agtcaagggt
3721 ggcccttcac tacagcaagt catgagggaa cagttgaagc cattcacaga gccaaggggc
3781 aagccaccaa aaccaagtgt attagaagct gccaagaaga ccatcatcaa cgtccttgag
3841 caaacaattg atccacctga gaaatggtcg ttcgcacaag cttgcgcgtc ccttgacaag
3901 accacttcca gtggtcatcc gcaccacgtg cggaaaaacg actgctggaa cggagagtcc
3961 ttcacaggca agctggcaga ccaggcttcc aaggccaacc tgatgtttga agaagggaag
4021 aacatgaccc cagtctacac agctgcgctc aaggatgagt tagttaaaac tgacaaaatt
4081 tatggtaaga tcaagaagag gcttctctgg ggctcggact tggcgaccat gatccggtgt
4141 gctcgagcat tcggaggcct aatggatgaa ttcaaagcac actgtgtcac gcttcctatt
4201 agagttggca tgaacatgaa tgaggatggc cccatcatct tcgagaggca ttccaggtac
4261 acatatcact atgatgctga ttactctcga tgggattcaa cacaacagag agccgtgttg
4321 gcagcagctc tcgaaatcat ggttaaattc tccccagaac cacatttggc tcaggtagtc
4381 gcggaagacc ttctttctcc tagcgtggtg gacgtgggcg acttcacaat atcaatcaac
4441 gagggtcttc cctctggggt gccctgcacc tcccaatgga actccatcgc ccactggctt
4501 ctcactctct gtgcactctc cgaagtcaca aacctatctc ctgacatcat acaggctaac
4561 tccctcttct ctttttatgg tgatgatgaa attgttagca cagacataaa attggaccca
4621 gagaaattga cagcaaagct cagagaatat gggttaaaac caacccgccc tgacaaaact
4681 gaaggacccc ttgtcatctc tgaagacctg aatggcctaa ctttcctgcg gagaactgta
4741 acccgcgacc cagctggttg gtttggaaaa ctggagcaga gttcaatact caggcaaatg
4801 tactggacta ggggtcccaa tcatggagac ccatctgaaa caatgattcc acactcccaa
4861 agacccatac aattgatgtc cctactgggg gaggccgctc tccacggccc agccttttat
4921 agcaaaatca gcaagttggt cattgcagag ctaaaagagg 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 gccgctattg cggcacctgt agcgggccaa caaaatgtaa ttgacccctg
5221 gattagaaac aattttgtac aagcccctgg tggagagttt acagtatccc ctagaaacgc
5281 tccaggtgaa atattatgga gcgcgccctt aggccctgat ctgaatccct acctttctca
5341 tttggccaga atgtacaatg gttatgcagg tggttttgaa gtgcaggtac tcctcgcggg
5401 gaacgcgttc accgccggga aaatcatatt tgcagcagtc ccaccaaatt tcccaactga
5461 aggtttgagc cccagccaga tcactatgtt cccccatatg atagtagatg ttaggcaatt
5521 agaacctgtg ttgatcccct tacccgatgt taggaataat ttttaccatt ataatcaatc
5581 aaatgactcc actatcaaat tgatagcaat gctgtataca ccacttaggg ccaataatgc
5641 tggggacgat gtcttcacag tttcttgtcg agttctcacg agaccatccc ccgattttga
5701 tttcatattt ttggtgccac ccacagttga atcaagaact aaaccattct ctgtcccaat
5761 tttaactgtt gaggagatga ccaattcaag gttccccatt cctttggaaa agttgttcac
5821 gggccccagt agtgcctttg ttgttcaacc acaaaatggc aggtgcacga ctgatggcgt
5881 gctcctaggt actacccaac tgtcccctgt aaacatctgc accttcagag gggatgtcac
5941 ccacacttca ggcagtcata actacacaat gaatttggcc tcccaaaatt ggaacagtta
6001 cgatccaaca gaagaaatcc cagcccctct agggactcca gacttcgtgg ggaagattca
6061 aggtgtgctc acccaaacca caaggacaga tggctcgacc cgcggccaca aagctacagt
6121 gtacactggg gccgccgact tctctccaaa actgggtaga gttcaatttg ccactgacac
6181 aaacaatgat tttgatacta accaaaacac aaagttcacc ccaatcggtg tcatccagga
6241 aggtgatacc ccccaccgaa atgaacctca acaatgggtg ctcccaagtt actcaggcag
6301 aaacattcat aatgtacacc tggcccccgc tgtagccccc actttcccgg gcgagcagct
6361 cctctttttc agatctacta tgcccggatg cagcgggtac cccaacatgg atttggactg
6421 tctgctcccc caggaatggg tgcagtactt ctaccaggag gcagccccag cgcaatctga
6481 tgtggctctg ttgagatttg tgaatccaga cacaggtagg gttttgtttg agtgtaagct
6541 ccataaatca ggctatgtta cagtggctca cactggccaa catgatttgg ttatcccccc
6601 caatggttat tttagatttg attcctgggt caaccagttc tacacacttg cccccatggg
6661 aaatgggacg gggcgtagac gtgcactata atggctggag ctttctttgc tggattggca
6721 tctgacgtcc ttggctctgg acttggttcc ctaatcaatg ctggggctgg ggccatcaac
6781 caaaaagttg aatttgaaaa taatagaaaa ttgcaacaag cttccttcca atttagtagc
6841 aatctacaac aagcttcctt tcaacatgac aaggagatgc tccaagcaca aattgaggcc
6901 accaaaaagt tgcaacagga aatgatgaga gttaaacaag caatgctcct agagggcgga
6961 ttctctgagg tagatgcagc ccgtggggca atcaacgccc ccatgacaaa aactttggac
7021 tggagtggga caaggtactg ggctcccgat gctaggacta caacatataa tgcaggccgc
7081 ttttccaccc ctcaaccctc gggggcacta ccaggaagag ctaatcttag ggctactgcc
7141 cccgcccggg gttcctccag catgtcttct aactcttcta ttgctacttc tgtgtattca
7201 aatcaaacca cttcaacgag acttggttct acagctggtt ctggtaccag tgtctcgagc
7261 ctcccgtcaa ctgcaaggac taggagctgg gttgaggatc aaaataggaa tttgtcacct
7321 ttcatgaggg gggcccataa catctcgttt gtcaccccac catctagcag atcatctagc
7381 caaggcacag tctcaaccgt gcccaaagaa gttttggact cctggactgg cgctttcaac
7441 acgcgcaggc agcctctctt cgctcacatt cgcaagcgag gggagtcacg ggtgtaatgt
7501 gaaaagacaa aattgattat ctttcttttc tttagtgtct ttt
//