Typing tool
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Typing tool
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Complete norovirus genomes
| MF140675 | GII.4 Sydney | |
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| GII.P31 |
ORF1: 1..5077
ORF2: 5058..6680
ORF3: 6680..7483
LOCUS MF140675 7483 bp RNA linear VRL 24-OCT-2017
DEFINITION Norovirus GII strain
Norovirus/GII/Hu/NL/2014/GII.Pe-GII.4/Rotterdam/E1300309_p4_d355
ORF1 gene, partial cds; ORF2 gene, complete cds; and ORF3 gene,
partial cds.
ACCESSION MF140675
VERSION MF140675.1
KEYWORDS .
SOURCE Norovirus GII
ORGANISM Norovirus GII
Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes;
Picornavirales; Caliciviridae; Norovirus; Norovirus norwalkense.
REFERENCE 1 (bases 1 to 7483)
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 7483)
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..7483
/organism="Norovirus GII"
/mol_type="genomic RNA"
/strain="Norovirus/GII/Hu/NL/2014/GII.Pe-
GII.4/Rotterdam/E1300309_p4_d355"
/host="Homo sapiens"
/db_xref="taxon:122929"
/geo_loc_name="Netherlands"
/collection_date="02-Apr-2014"
/note="genotype: GII.Pe-GII.4"
CDS <1..5077
/codon_start=2
/product="ORF1"
/protein_id="ATN23721.1"
/translation="SAAAVANSNNDIAKSSSDGVFSNMAVTFKRALGARPKQPPPKEI
PPRPPRPPTPELVKKIPPPPPNGEDELVVSYSAKDGVSGLPELTTVRQPEETNTAFSV
PPLNQRESRDAKEPLTGTIIEMWDGEIYHYGLYVERGLILGVHKPPAAISLAKVELAP
LSLFWRPVYTPQYLISPDTLRRLHGESFPYTAFDNNCYAFCCWVLDLNDSWLSRRMIQ
RTTGFFRPYQDWNRKPLPTMDDSKLKKVANIFLCTLSSLFTRPIKDIIGKLKPLNILN
ILATCDWTFAGVVESLILLAELFGVFWTPPDVSAMIAPLLGDYELQGPEDLAVELVPI
VMGGIGLVLGFTKEKIGKMLSSAASTLRACKDLGAYGLEILKLVMKWFFPKKEEANEL
AMVRSIEDAVLDLEAIENNHMTTLLKDKDSLATYMRTLDFEEEKARKLSTKSASPDIV
GTINALLARIAAARSLVHRAKEELSSRPRPVVVMISGRPGIGKTHLARELAKKIAASL
TGDQRVGLIPRNGVDHWDAYKGERVVLWDDYGMSNPIHDALRLQELADTCPLTLNCDR
IENKGKVFDSDAIIITTNLANPAPLDYVNFEACSRRIDFLVYAEAPEVEKAKRDFPGQ
PDMWKNAFSPDFSHIKLSLAPQGGFDKNGNTPHGKGVMKTLTTGSLIARASGLLHERL
DEYELQGPTLTTFNFDRNKILAFRQLAAENKYGLVDTMRVGKQLKDVKTMSDLKQALK
NIAIRKCQIVYNGGTYTLEADGKGSVKVDKVQSATVQTNNELAGALHHLRCARIRYYV
KCVQEALYSIIQIAGAAFVTTRIAKRMNIQDLWSKPQMEDTEEMANKDGCLKPKDDEE
FVVSSDDIKTEGKKGKNKSGRGKKHTAFSSKGLSDEEYDEYKRIREERNGKYSIEEYL
QDRDKYYEEVAIARATEEDFCEEEEAKIRQRIFRPTRKQRKEERASLGLVTGSEIRKR
NPEDFKPKGKLWADDDRSVDYNEKLNFEAPPSIWSRIVNFGSGWGFWVSPSLFITSTH
VIPQGAKEFFGVSIKQIQIHKSGEFCRLRFPKPIRTDVTGMILEEGAPEGTVATLLIK
RPTGELMPLAARMGTHATMKIQGRTVGGQMGMLLTGSNAKSMDLGTTPGDCGCPYIYK
RGNDYVVIGVHTAAARGGNTVICATQGSEGEATLEGGDSKGTYCGAPILGPGSAPKLS
TKTKFWRSSTTPLPPGTYEPAYLGGKDPRVKGGPSLQQVMRDQLKPFTEPRGKPPRPN
VLEAAKKTIINVLEQTIDPPQKWSFAQACASLDKTTSSGHPHHMRKNDCWNGETFTGK
LADQASKANLMFEEGKNMTPVYTGALKDELVKTDKVYGKVKKRLLWGSDLATMIRCAR
AFGGLMDELKAHCVTLPVRVGMNMNEDGPIIFEKHSRYRYHYDADYSRWDSTQQRDVL
AAALEIMVKFSPEPHLAQIVAEDLLSPSVMDVGDFQISISEGLPSGVPCTSQWNSIAH
WLLTLCALSEVTDLSPDIIQANSLFSFYGDDEIVSTDIKLDPEKLTAKLKEYGLKPTR
PDKTEGPLVISEDLDGLTFLRRTVTRDPAGWFGKLEQSSILRQMYWTRGPNHEDPFET
MIPHSQRPIQLMSLLGEAALHGPAFYSKISKLVIAELKEGGMDFYVPRQEPMFRWMRF
SDLSTWEGDRNLAPSFVNEDGVE"
CDS 5058..6680
/codon_start=1
/product="ORF2"
/protein_id="ATN23722.1"
/translation="MKMASSDANPSDGSAANLVPVVNNEVMALEPVVGAAIAAPVAGQ
QNVIDPWIRNNFVQAPGGEFTVSPRNAPGEILWSAPLGPDLNPYLSHLARMYNGYAGG
FEVQVLLAGNAFTAGKVIFAAVPPNFPTEGLSPSQVTMFPNIVVDVRQLEPVLIPLPD
VRNNFYHYNQSNDPTIKLIAMLYTPLRANNAGDDVFTVSCRVLTRPSPDFDFIFLVPP
TVESRTKPFSVPILTVEEMTNSRFPIPLEKLFTGPSSAFVVQPQNGRCTTDGVLLGTT
QLSPVNICTFRGDVTHITGSRNYRMNLASQNWSNYDPTEEIPAPLGIPDFVGKIQGVL
TQTTRTDGSTRGHKATVYTGSADFAPKLGRVQFETDTDHDFETNQNTKFTPAGVIQDG
STTHRNEPQQWVLPSYSGRSTPNVHLAPAVAPTFPGEQLLFFRSTMPGCSGYPNMDLD
CLLPQEWVQYFYQEAAPAQSDVALLRFVNPDTGRVLFECKLHKSGYVTVAHTGQHDLV
IPPNGYFRFDSWVNQFYTLAPMGNGTGRRRAL"
CDS 6680..>7483
/codon_start=1
/product="ORF3"
/protein_id="ATN23723.1"
/translation="MAGAFFAGLASDVLGSGLGSLINAGAGAINQKVEFENNRKLQQA
SFQFSSNLQQASFQHDKEMLQAQIEATKKLQQEMMKVKQAMLLEGGFSETDAARGAIN
APMTKALDWSGTRYWAPDARTTTYNAGRFSTPQPSGALPGRANLRDAVPARGSSSKSS
NSSAATSVYSNQTTSTRLGSTAGSGTSVSSFPPTARTRSWVEDQSRNLSPFMRGAHNI
SFVTPPSSRSSSQGTVSTVPKEILDSWTGAFNTRRQPLFAHIRKRGESRA"
ORIGIN
1 ttccgctgcc gctgttgcca acagcaacaa cgacatcgca aaatcttcaa gtgacggtgt
61 gttttctaac atggctgtca cttttaagcg ggccctcggg gcgcggccta aacagccgcc
121 cccgaaggaa ataccaccca gacccccgcg accacccaca ccagaattgg tcaaaaagat
181 ccctcctccc ccacccaacg gggaggatga actagtggtc tcctacagcg ccaaagatgg
241 cgtttccgga ctgcctgagc tcaccactgt caggcaaccg gaagaaacca acacggcgtt
301 cagtgtcccc ccactcaacc aaagggagag cagggacgcc aaggagccac taactggaac
361 aatcattgaa atgtgggatg gagaaatcta ccattacggc ctgtacgtgg aacgaggtct
421 tatacttggt gtgcacaagc caccggcagc cattagcctt gccaaggtcg agctagcacc
481 gctctctttg ttctggagac ctgtatacac cccccagtac ctcatctctc cagacactct
541 taggagacta catggagagt cattccccta cactgcattt gacaacaatt gctacgcctt
601 ttgttgttgg gtactagacc taaacgactc atggctaagc aggagaatga ttcagagaac
661 aacaggcttc ttcaggccgt accaggattg gaacaggaaa cccctcccca ctatggatga
721 ttccaaatta aagaaggtag ccaacatatt cttgtgcacc ttgtcttcac tattcaccag
781 gcccattaag gacataatag ggaagttgaa acctcttaac atccttaaca ttctggctac
841 atgtgattgg accttcgcag gcgtagtgga atccttaata ctcttggcag aactctttgg
901 agttttctgg acacccccag atgtgtctgc gatgatcgcc cccttgctag gtgattatga
961 actgcaagga cctgaggacc ttgcagtgga actggtccca atagtgatgg gggggatagg
1021 tttggtgcta ggatttacca aagagaaaat cggaaagatg ctgtcatccg ctgcgtccac
1081 tttaagagct tgtaaagacc ttggtgcata cggactggaa atcttaaaat tggtcatgaa
1141 gtggttcttc ccaaagaaag aggaagcgaa tgaactggct atggtgagat ccatcgagga
1201 tgcagtacta gacctcgagg caattgaaaa caaccacatg accaccctac tcaaggacaa
1261 agacagcttg gcaacctaca tgagaaccct tgactttgag gaggagaaag ccagaaaact
1321 ctcaaccaaa tctgcttcac ccgatattgt gggcacaatc aacgctcttc tggcaagaat
1381 cgctgctgca cgctccctag tgcatcgggc gaaagaagag ctctccagca ggccgagacc
1441 tgtcgttgtg atgatatcgg gaagaccagg gatagggaaa actcaccttg ccagggagct
1501 ggccaagaag atcgcggcct ccctcacagg ggaccagcgt gtgggtctta tcccacgcaa
1561 tggtgtcgac cactgggacg catacaaggg cgaaagagtt gtcctatggg acgactatgg
1621 aatgagcaac cccatccatg acgccctcag gttgcaggag cttgctgaca cttgccccct
1681 cacgctaaat tgtgacagaa ttgagaacaa agggaaagtc tttgacagtg atgccataat
1741 tatcaccacc aatctggcca acccagcacc actggattat gtcaactttg aagcgtgctc
1801 gagacgcatt gatttcctcg tgtacgcaga agcccctgag gtggagaagg caaagcgcga
1861 cttcccaggt caacctgaca tgtggaagaa cgctttcagt cctgacttct cacacataaa
1921 actgtcattg gctccacagg gtggttttga caagaacggc aacaccccgc atggaaaagg
1981 ggtcatgaag accctcacca ctggctccct catcgcccga gcatcagggt tactccatga
2041 gaggctagat gaatatgaac tgcaaggccc aaccctcacc actttcaact ttgaccgcaa
2101 caagatactt gcttttagac agcttgctgc tgaaaacaag tatgggctgg tggacacaat
2161 gagagttgga aaacagctca aggatgtcaa gaccatgtca gacctcaaac aagcactcaa
2221 gaacatcgcg atcaggaagt gccagatagt gtacaatggt ggcacctaca cacttgaggc
2281 tgatggcaag ggtagtgtga aagttgacaa agtgcaaagt gccactgtgc agaccaacaa
2341 tgaactagcc ggtgccctac accacctaag gtgcgctaga atcagatact atgttaagtg
2401 cgtccaggag gcactgtatt ccatcatcca aatcgctggg gctgcatttg tcaccacgcg
2461 catcgctaag cgcatgaata tacaggatct ctggtccaag ccacagatgg aagacacaga
2521 agagatggcc aacaaagatg gttgcctaaa acccaaagat gatgaagagt ttgtcgtctc
2581 atccgacgac atcaaaactg agggcaagaa agggaagaac aagtccggcc gtggcaagaa
2641 gcacacagcc ttttcaagta aagggctcag tgatgaggag tacgatgagt acaagagaat
2701 cagagaagaa aggaatggta agtactccat agaagagtac cttcaggaca gagacaagta
2761 ctacgaggag gtggccattg ccagggcaac cgaagaggac ttctgtgaag aagaagaggc
2821 caaaatccgg cagagaattt tcagaccaac aaggaaacaa cgcaaagaag agagggcctc
2881 tctcggcttg gtcacaggct ctgaaatcag gaagagaaac ccagaagact tcaaacccaa
2941 gggaaagctg tgggctgatg atgacagaag tgttgactac aatgagaaac tcaactttga
3001 ggccccacca agcatctggt cgcggatagt caactttggt tcaggctggg gcttctgggt
3061 ctcccccagt ctgtttataa catcaaccca tgtcataccc caaggtgcaa aagagttctt
3121 cggagtctct atcaagcaaa tccagataca caagtcaggt gaattctgcc ggttgagatt
3181 cccaaagcca atcagaactg atgtgacggg catgattcta gaagaaggtg cgcccgaggg
3241 gaccgtggcc acactgctca tcaagagacc aactggagag ctcatgcctc tggcagccag
3301 aatggggacc catgcaacca tgaaaattca ggggcgtaca gttggagggc aaatgggtat
3361 gctcctgaca ggatccaacg ccaagagtat ggacctaggc acaacaccag gcgactgcgg
3421 ctgcccctac atctacaaga gggggaatga ctatgtggtc ataggagtcc atacggccgc
3481 tgcccgtgga ggaaacactg tcatatgtgc cacccagggg agtgagggag aagccacact
3541 tgaaggaggt gacagtaaag ggacatactg tggcgcacca atcttgggcc cagggagcgc
3601 tccgaagctc agtaccaaga ctaagttttg gagatcatcc acaacaccac tcccacctgg
3661 cacctacgaa ccagcctacc tcggtggcaa agaccctaga gtcaaaggtg gcccttcatt
3721 gcaacaagtt atgagggacc agctgaagcc attcacagaa cccagaggca aaccaccaag
3781 accaaatgtg ttggaagctg ccaagaaaac catcatcaat gtccttgagc aaacaattga
3841 tccaccccaa aaatggtcat ttgcgcaagc ttgcgcatcc cttgacaaaa ccacctccag
3901 cggccacccg caccacatgc ggaaaaacga ctgttggaat ggggagacct tcacaggaaa
3961 attggctgat caagcctcca aggccaacct aatgtttgaa gagggaaaga acatgactcc
4021 agtctacaca ggtgcactta aagatgagtt ggtaaagacc gataaagttt atggtaaggt
4081 caagaagagg cttctgtggg gttcagatct ggcgaccatg atacggtgcg cccgagcttt
4141 tggaggcctt atggatgaac tcaaggcaca ctgtgtcaca cttcctgtca gagttggtat
4201 gaacatgaat gaggatggcc ccatcatctt cgagaagcac tccagatata gatatcacta
4261 tgatgctgat tattcccggt gggactcaac acaacaaagg gatgtgctag cagcagcact
4321 agaaatcatg gttaagttct ctccagaacc acacctggcc cagatagttg cagaagacct
4381 cctctcccct agcgtgatgg atgtaggtga ctttcaaata tcaataagtg agggtctccc
4441 ctctggggta ccttgtacct cccagtggaa ttccatcgcc cactggctcc tcactctgtg
4501 tgcactctct gaagtcacgg acctgtcccc tgatatcatt caggccaact cccttttctc
4561 cttctatggt gatgatgaga ttgtgagcac agacataaag ttggacccag agaagctgac
4621 agcaaaactc aaggagtacg ggctgaaacc aacccgcccc gacaaaactg aaggacccct
4681 tgttatctct gaagacctgg atggcctgac attcctccgg agaactgtga cccgtgatcc
4741 agctggctgg tttggaaaat tggaacaaag ttcaattctc aggcaaatgt actggaccag
4801 gggtcccaac catgaagatc catttgaaac aatgatacca cactcccaaa gacccataca
4861 attgatgtcc ttgctgggcg aggctgcact ccacggcccg gcattctata gcaaaattag
4921 caaattagtc attgcagagt tgaaggaagg tggcatggat ttttacgtac ccagacaaga
4981 gccaatgttc agatggatga gattctcaga tctgagcacg tgggagggcg atcgcaatct
5041 ggctcccagt tttgtgaatg aagatggcgt cgagtgacgc caacccatct gatgggtccg
5101 cagccaacct cgtcccagtg gtcaacaatg aggttatggc tctggagccc gttgttggtg
5161 ccgccattgc ggcacctgta gcgggccaac aaaatgtaat tgacccctgg attagaaata
5221 attttgtaca agcccctggt ggagagttta cagtatcccc tagaaacgct ccaggtgaaa
5281 tactatggag cgcgcccttg ggccctgatc taaatcccta cctatcccat ttggccagaa
5341 tgtacaatgg ttatgcaggt ggttttgaag tgcaggtact tctcgcgggg aacgcgttca
5401 ccgccgggaa ggtcatattt gcagcagtcc caccaaattt tccaactgaa ggcttgagcc
5461 ccagccaggt cactatgttc cccaatatag tagtagatgt taggcaatta gaacctgtgt
5521 tgattccctt acccgatgtt aggaataatt tctatcatta caatcaatca aatgacccca
5581 ccattaagtt aatagcaatg ttgtacacac cacttagggc taataatgct ggggatgatg
5641 tcttcacagt ttcttgccga gttctcacga gaccatcccc cgattttgat ttcatatttc
5701 tagtgccacc cacagttgag tcaagaacta aaccattctc tgtcccaatt ttaactgttg
5761 aggagatgac caattcaaga ttccccattc ctttggaaaa gttgttcacg ggtcccagca
5821 gtgcctttgt tgtccaacca caaaacggta ggtgcacgac tgatggcgtg ctcctaggca
5881 ccacccaact gtctcctgtc aacatctgca ccttcagagg agatgtcacc catatcacag
5941 gtagtcgtaa ctacagaatg aatttggctt ctcaaaattg gagcaattat gacccaacag
6001 aagaaatccc agcccctcta ggaattccag attttgtggg gaagattcaa ggcgtgctca
6061 cccaaaccac aaggacagat ggctcaacac gcggccacaa agccacagtg tacactggga
6121 gcgccgactt tgctccaaaa ctgggtagag ttcaatttga aactgacaca gaccatgatt
6181 ttgaaactaa ccaaaacaca aagttcaccc cagctggtgt catccaagat ggtagcacca
6241 cccaccgaaa tgaaccccaa cagtgggtgc tcccaagtta ctcaggcaga agtactccta
6301 atgtgcatct ggcccccgct gtggccccca cttttccggg tgagcaactt ctcttcttca
6361 gatccaccat gcccggatgc agcgggtacc ccaacatgga tttggactgt ctgctccccc
6421 aggaatgggt gcagtacttc taccaagagg cagccccagc acaatctgat gtggctctgc
6481 taagatttgt gaatccagac acaggtaggg ttttgtttga gtgtaagctt cataaatcag
6541 gctatgttac agtggctcac actggccaac atgatttggt tatccccccc aatggttatt
6601 ttaggtttga ttcctgggtc aaccagtttt acacgcttgc ccccatggga aatggaacgg
6661 ggcgtagacg tgcactataa tggctggagc tttctttgct ggattggcat ctgatgtcct
6721 tggctctgga cttggttccc ttatcaatgc tggggctggg gccatcaacc aaaaagttga
6781 gtttgaaaat aacagaaaat tgcaacaagc atccttccaa tttagcagca atctacaaca
6841 ggcttccttt caacatgaca aagagatgct ccaagcacaa attgaggcca ccaaaaagct
6901 acaacaggaa atgatgaaag ttaagcaggc aatgctccta gagggtgggt tctctgagac
6961 agatgcagcc cgcggggcaa tcaacgcccc catgacaaaa gctttggact ggagcgggac
7021 aaggtactgg gctcccgatg ctaggacaac aacatacaat gcaggccgct tttccacccc
7081 tcaaccatcg ggggcactgc caggaagagc taatcttagg gatgctgtcc ctgctcgggg
7141 ttcctccagt aagtcttcta attcttctgc tgctacttct gtgtactcga atcaaactac
7201 ttcaacgaga cttggttcta cagctggttc tggtaccagt gtctcgagct tcccgccaac
7261 tgcaaggact aggagttggg ttgaggatca aagtaggaat ttgtcacctt tcatgagggg
7321 ggcccacaac atatcgtttg tcaccccacc atctagcaga tcctctagcc aaggcacagt
7381 ctcaaccgtg cctaaagaga ttttggactc ctggactggc gctttcaaca cgcgcaggca
7441 gccactcttc gctcacattc gtaagcgagg ggagtcacgg gcg
//