Typing tool
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Typing tool
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Complete norovirus genomes
| MF140639 | GII.4 Sydney | |
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| GII.P31 |
ORF1: 1..5064
ORF2: 5045..6667
ORF3: 6667..7468
LOCUS MF140639 7468 bp RNA linear VRL 24-OCT-2017
DEFINITION Norovirus GII strain
Norovirus/GII/Hu/NL/2014/GII.Pe-GII.4/Rotterdam/E1300287_p10_d462
ORF1 gene, partial cds; ORF2 gene, complete cds; and ORF3 gene,
partial cds.
ACCESSION MF140639
VERSION MF140639.1
KEYWORDS .
SOURCE Norovirus GII
ORGANISM Norovirus GII
Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes;
Picornavirales; Caliciviridae; Norovirus; Norovirus norwalkense.
REFERENCE 1 (bases 1 to 7468)
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 7468)
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..7468
/organism="Norovirus GII"
/mol_type="genomic RNA"
/strain="Norovirus/GII/Hu/NL/2014/GII.Pe-
GII.4/Rotterdam/E1300287_p10_d462"
/host="Homo sapiens"
/db_xref="taxon:122929"
/geo_loc_name="Netherlands"
/collection_date="01-May-2014"
/note="genotype: GII.Pe-GII.4"
CDS <1..5064
/codon_start=1
/product="ORF1"
/protein_id="ATN23613.1"
/translation="VANSNNDIAKSSSDGVFSNMAVTFKRALGARPKQPPPKEIPPRP
PRPPTPELVKKIPPPPPNGGDELVVSYNAKDGVSGLPELTTVRQPEETNTAFSVPPLN
QRESRDAKEPLTGTIIEMWDGEIYHYGLYVERGLILGVHKPPAAISLAKVELAPLSLF
WRPVYTPQYLISPDTLRRLHGESFPYTAFDNNCYAFCCWVLDLNDSWLSRRMIQRTTG
FFRPYQDWNRKPLPTMDDSKLKKVANIFLCTLSSLFTRPIKDIIGKLKPLNILNILAT
CDWTFAGIVESLILLAELFGAFWTPPDVSAMIAPLLGDYELQGPEDLAVELVPVVMGG
IGLVLGFTKEKIGKILSSAASTLRACKDLGAYGLEILKLVMKWFFPKKEEANELAMVR
SIEDAVLDLEAIENNHMTTLLKDKDSLATYMRTLDLEEEKARKLSTKSASPDIVGTIN
ALLARIAAARSLVHRAKEELSSRLRPVVVMISGKPGIGKTHFAREVANKVAASLTGDQ
RVGLIPRNGVDHWDAYKGERVVLWDDYGMSNPIHDALRLQELADTCPLTLNCDRIENK
GKVFDSDAIIITTNLANPAPLDYVNFEACSRRIDFLVYAEAPEVEKAKRDFPGQPDMW
KNAFSSDFSHMKLSLAPQGGFDKNGNTPHGKGVMKTLTTGSLIARASGLLHERLDEYE
LQGPALTTFNFDRNKILAFRQLAAENKYGLMDTMRVGKQLKDVKTMSDLKQALKNITI
KKCQIVYNGGTYTLEADGKGSVKVDKVQSATVQTNNELAGALHHLRCARIRYYVKCAQ
EALYSIIQIAGAAFVTTRIAKRMNIQNLWSKPQVEDTEEIVNKDGCLKPKDDEEFVVS
SDDIKTEGKKGKNKSGRGKKHTAFSSKGLSDEEYDEYKRIREERNGKYSIEEYLQDRD
KYYEEVAIARATEEDFCEEEEAKIRQRIFRPTRKQRKEERASLGLVTGSEIRKRNPED
FKPKGKLWADDDRSVDYNEKLNFEAPPSIWSRIVNFGSGWGFWVSPSLFITSTHVIPQ
GAKEFFGVPIKQIQIHKSGEFCRLRFPRPIRTDVTGMILEEGAPEGTVVTLLIKRPTG
ELMPLAARMGTHATMKIQGRTVGGQMGMLLTGSNAKSMDLGTTPGDCGCPYIYKRGND
YVVIGVHTAAARGGNTVICATQGSEGEATLEGGDSKGTYCGAPILGPGSAPKLSAKTK
FWRSSTTPLPPGTYEPAYLGGKDPRVKGGPSLQQVMRDQLKPFTEPRGKPPRPNVLEA
AKKTIINVLEQTIDPPQKWSFAQACASLDKTTSSGHPHHMRKNDCWNGESFTGKLADQ
ASKANLMFEEGKNMTPVYTGALKDELVKTDKVYGKIKKRLLWGSDLATMIRCARAFGG
LMDELKAHCVTLPVRVGMNMNEDGPIIFEKHSRYRYHYDADYSRWDSTQQRDVLAAAL
EIMVKFSPEPHLAQIVAEDLLSPSVMDVGDFQISISEGLPSGVPCTSQWNSIAHWLLT
LCALSEVTNLSPDIIQANSLFSFYGDDEIVSTDIKLDPEKLTAKLKEYGLKPTHPDKT
EGPLVISEDLDGLTFLRRTVTRDPAGWFGKLEQSSILRQMYWTRGPNHEDPFETMIPH
SQRPIQLMSLLGEAALHGPAFYSKISKLVIAELKEGGMDFYVPRQEPMFRWMRFSDLS
TWEGDRNLAPSFVNEDGVE"
CDS 5045..6667
/codon_start=1
/product="ORF2"
/protein_id="ATN23614.1"
/translation="MKMASSDANPSDGSTVSLVPEVNNEVMALEPVVGAAIAAPVAGQ
QNVIDPWIRNNFVQAPGGEFTVSPRNAPGEILWSAPLGPDLNPYLSHLARMYNGYAGG
FEVQVVLAGNAFTAGKIIFAAVPPNFPTECLSPSQVTMLPHIIVDVRQLEPVLIPLPD
VRNNFYHYNQSNDSTIKLIAMLYTPLRANNAGDDVFTVSCRVLTRPSPDFDFIFLVPP
TVESRTKPFSVPVLTVEEMTNSRFPIPLEKLFTGPSSTFVVQPQNGRCSTDGVLLGTT
QLSPVNICTFRGDVTQITGSSTYTMNLASQNWSNYDPTEEIPAPLGTPDFVGKIQGVL
TQTTRTVGSTRGHKATVRTGSADFAPKLGRVRFETDTNNDFEVNQNTKFTPVGVIQDG
DTAHRNEPQQWVLPSYSGRNTPNVHLAPAVAPTFPGEQLLFFRSTMPGCSGYPNMDLD
CLLPQEWVQYFYQEAAPAQSDVALLRFVNPDTGRVLFECKLHKSGYITVAHTGQHDLV
IPPNGYFRFDSWVNQFYTLAPMGNGTGRRRAP"
CDS 6667..>7468
/codon_start=1
/product="ORF3"
/protein_id="ATN23615.1"
/translation="MAGAFFAGLASDVLGSGLGSLINAGAGAINQKVEFENNRKLQQA
SFQFSSNLQQASFQHDKEMLQAQIEATKRLQQEMMKVKQAMLLEGGFSETDAARGAIN
APMTKVLDWSGTRYWAPDARTTTYNAGRFSTPQPSGALPGRANLRDAVPARGSSRKSS
NSSTATSVYSNQTTSTRLGSTAGSGTSVSSFPTTARTRSWVEDQSRNLSPFMSGAHNI
SFVTPPSSRSSSQGTVSTVPKEILDSWTGAFNTRRQPLFAHIRKRGESR"
ORIGIN
1 gttgccaaca gcaacaacga catcgcaaaa tcttcaagtg acggtgtgtt ctctaacatg
61 gctgtcactt ttaagcgggc cctcggggcg cggcctaaac agccgccccc gaaggaaata
121 ccacccagac ccccgcgacc acccacacca gaattggtca aaaagatccc tcctccccca
181 cccaacgggg gggatgaact agtggtctcc tacaatgcca aagatggcgt ttccggactg
241 cctgagctca ccactgtcag acaaccggaa gaaaccaaca cggcgttcag tgtcccccca
301 cttaaccaaa gggagagcag ggacgccaag gagccactaa ctggaacaat cattgaaatg
361 tgggatggag aaatctacca ttacggcctg tacgtggaac gaggtcttat acttggtgtg
421 cacaagccac cggcagccat tagccttgcc aaggtcgagc tagcaccgct ctctttgttc
481 tggagacctg tatacacccc ccagtatctc atctctccag acactcttag gagattacat
541 ggagagtcat tcccctacac tgcatttgac aacaattgct acgccttttg ctgttgggta
601 ttagacctaa acgactcatg gctaagcagg agaatgattc agagaacaac aggcttcttt
661 aggccgtacc aggattggaa caggaaaccc ctccccacta tggatgattc caaattaaag
721 aaggtagcca acatattctt gtgcactttg tcttcactat tcaccagacc cattaaggac
781 ataataggga agttgaaacc tcttaacatc cttaacattc tggctacatg tgattggacc
841 ttcgcaggca tagtggaatc cttaatactc ttggcagaac tctttggagc tttctggaca
901 cccccagatg tgtctgcgat gatcgccccc ttgctaggtg attatgaact gcaaggacct
961 gaggaccttg cagtggaact ggtcccagta gtgatggggg ggataggttt ggtgctagga
1021 tttaccaaag agaaaatcgg aaagatacta tcatccgctg catccacttt aagagcttgt
1081 aaagaccttg gtgcatacgg actggaaatc ttaaaattgg tcatgaagtg gttctttcca
1141 aagaaagagg aagcaaatga actggctatg gtgagatcca tcgaggatgc agtactagac
1201 ctcgaggcaa ttgaaaacaa ccacatgacc accctactca aagataaaga cagcttggca
1261 acctacatga gaacccttga ccttgaggag gagaaagcca gaaaactctc aaccaaatct
1321 gcttcacccg atattgtggg cacaatcaac gctcttctgg caagaatcgc tgctgcacgc
1381 tccctagtgc atcgggcgaa agaagagctc tccagcaggc tgagacctgt cgtagtgatg
1441 atatcgggaa agccagggat agggaaaact cactttgcca gggaggtggc caacaaggtc
1501 gcggcctccc tcacagggga ccagcgtgtg ggtcttatcc cacgcaatgg cgtcgaccac
1561 tgggacgcat acaagggcga aagagttgtc ctatgggacg actatggaat gagcaacccc
1621 atccatgatg ccctcaggtt gcaggagctt gctgacactt gccccctcac gctaaattgt
1681 gacagaattg agaacaaagg gaaagtcttt gacagtgatg ccataattat caccaccaat
1741 ctggccaacc cagcaccact ggattatgtc aactttgaag cgtgctcgag acgcattgat
1801 ttcctcgtgt acgcagaagc ccctgaggtg gagaaggcaa agcgcgactt cccaggtcaa
1861 cctgacatgt ggaagaacgc tttcagttct gacttctcac acatgaaact gtcattggct
1921 ccacaaggtg gttttgacaa gaacggcaac accccgcatg gaaaaggtgt catgaagacc
1981 ctcaccactg gctccctcat cgcccgagca tcagggttac ttcatgagag gctagatgaa
2041 tatgaactac aaggcccagc cctcaccacc ttcaactttg accgcaacaa gatacttgct
2101 tttagacagc ttgctgctga aaacaagtat gggctgatgg acacaatgag agttggaaaa
2161 cagctcaagg atgtcaagac catgtcagac ctcaaacaag cactcaagaa catcacgatc
2221 aagaagtgcc agatagtgta caatggtggc acctacacac ttgaggctga tggcaagggt
2281 agtgtgaaag ttgacaaagt gcaaagtgcc actgtgcaga ccaacaatga actagccggt
2341 gccctacacc acctaaggtg cgctagaatc agatactatg ttaagtgcgc ccaggaggca
2401 ctgtattcca tcatccaaat cgctggggct gcattcgtca ccacgcgcat cgctaagcgc
2461 atgaatatac agaatctctg gtccaagcca caggtggaag acacagaaga gatagtcaac
2521 aaagatggtt gcctaaaacc caaagatgat gaagagtttg tcgtctcatc cgacgacatc
2581 aaaactgagg gcaagaaagg gaagaacaag tccggccgtg gcaagaagca cacagccttt
2641 tcaagtaaag ggctcagtga tgaggagtac gatgagtaca agaggatcag agaagaaagg
2701 aatggtaagt actccataga agagtacctt caggacagag acaagtacta cgaggaggtg
2761 gccattgcca gggcaaccga agaggacttc tgtgaagaag aagaggccaa aatccggcag
2821 agaattttta gaccaacaag gaaacaacgt aaagaagaga gggcctctct cggcttggtc
2881 acaggctctg aaatcaggaa gagaaaccca gaagacttca aacccaaggg aaagttgtgg
2941 gctgatgatg acagaagtgt tgactacaat gagaaactca attttgaggc cccaccaagc
3001 atctggtcgc ggatagtcaa ctttggttca ggctggggct tctgggtctc tcccagtctg
3061 tttataacat caacccatgt cataccccaa ggtgcaaaag agttcttcgg agtccctatt
3121 aagcaaatcc agatacacaa gtcaggtgaa ttctgccggt tgagattccc aaggccaatc
3181 agaactgatg tgacgggcat gattctagaa gaaggtgcgc ccgagggaac cgtggtcaca
3241 ctgctcatca agagaccaac tggagagctc atgcctctgg cagccagaat ggggacccat
3301 gcaaccatga aaatccaggg gcgcacagtt ggggggcaaa tgggtatgct cctgacagga
3361 tccaacgcca agagtatgga cctaggcaca acaccaggcg actgcggatg cccctacatc
3421 tacaagaggg ggaatgacta cgtggtcata ggagtccata cggccgctgc ccgtggagga
3481 aacactgtca tatgtgccac ccagggaagt gagggagaag ccacacttga aggaggtgac
3541 agtaaaggga catactgtgg cgcaccaatc ttgggcccag ggagcgctcc gaagctcagt
3601 gccaagacta agttttggag gtcatccaca acaccactcc cacctggcac ctacgaacca
3661 gcctacctcg gtggcaaaga ccctagagtc aaaggtggcc cttcattgca acaagttatg
3721 agggaccagc tgaagccatt cacagaaccc agaggcaaac caccaagacc aaatgtgttg
3781 gaagctgcca agaaaaccat catcaatgtc cttgagcaaa caattgatcc accccaaaaa
3841 tggtcatttg cgcaagcttg cgcatccctt gacaaaacca cctccagcgg ccacccgcac
3901 cacatgcgga aaaacgactg ttggaatggg gagtccttca caggaaaatt ggctgaccag
3961 gcctccaagg ccaacctaat gtttgaagag ggaaagaaca tgactccagt ctacacaggt
4021 gcacttaaag atgagttggt aaagaccgac aaagtttatg gtaaaatcaa gaagaggctt
4081 ctgtggggtt cagatctggc gaccatgata cggtgcgccc gagcttttgg aggccttatg
4141 gatgaactca aggcgcactg tgtcacactt cctgtcagag ttggtatgaa catgaatgag
4201 gatggcccca tcatctttga gaagcactcc agatacagat atcactatga tgctgattat
4261 tcccggtggg actcaacaca acaaagggat gtgctagcag cagcactaga aatcatggtt
4321 aagttctctc cagaaccaca cctggcccag atagttgcag aagacctcct ttcccctagc
4381 gtgatggatg taggtgactt tcaaatatca ataagtgagg gtctcccctc tggggtacct
4441 tgtacctccc agtggaattc catcgcccac tggctcctca ctctgtgtgc actctctgaa
4501 gtcacaaacc tgtcccctga tatcattcag gccaactccc ttttctcctt ctatggtgat
4561 gatgagattg taagcacaga cataaagttg gacccagaga agctgacagc aaagctcaag
4621 gagtacgggc tgaaaccaac ccaccccgac aaaactgaag gacccctcgt tatctctgaa
4681 gacctggatg gcctgacatt cctccggaga actgtgaccc gtgatccagc tggctggttt
4741 ggaaagttgg aacaaagttc aattctcagg caaatgtact ggaccagggg tcccaatcat
4801 gaagatccat ttgaaacaat gataccacac tcccaaagac ccatacaatt gatgtccttg
4861 ctgggcgagg ctgcactcca cggcccggca ttctatagca aaattagcaa attagtcatt
4921 gcagagttga aggaaggtgg catggatttt tacgtgccca gacaagagcc aatgttcaga
4981 tggatgagat tctcagatct gagcacgtgg gagggcgatc gcaatctggc tcccagtttt
5041 gtgaatgaag atggcgtcga gtgacgccaa cccatctgat gggtccacag tcagcctcgt
5101 cccagaggtc aacaatgagg ttatggctct ggagcccgtt gttggtgccg ccattgcggc
5161 acctgtagcg ggccaacaaa atgtaattga cccctggatt agaaataatt ttgtacaagc
5221 ccctggtgga gagtttacag tatcccccag aaacgctcca ggtgaaatac tatggagcgc
5281 gcccttgggc cctgatctaa atccctatct gtcccatttg gccagaatgt acaatggtta
5341 tgcaggtggt tttgaagtgc aggtagttct cgcggggaac gcgttcaccg ccgggaagat
5401 catatttgca gcggtcccac caaattttcc aactgaatgt ttgagcccca gccaggtcac
5461 tatgctcccc catataatag tagatgttag gcaattagaa cctgtgttga ttcccttacc
5521 cgatgttagg aataattttt atcattacaa tcaatcaaat gactccacca ttaagttgat
5581 agcaatgttg tatacaccac ttagggctaa taatgctggg gatgatgtct tcacagtctc
5641 ttgccgagtt ctcacgagac catcccccga ttttgatttc atatttttag tgccacccac
5701 agttgagtca agaactaaac cattctctgt cccagtttta actgttgagg agatgaccaa
5761 ttcaagattc cccattcctt tggaaaagtt gttcacgggt cccagcagta cctttgttgt
5821 ccaaccacaa aacggtaggt gctcgactga tggcgtgctc ctaggcacca cccagctgtc
5881 tcctgtcaac atctgcacct tcagaggaga tgtcacccag atcacaggta gtagtaccta
5941 cacaatgaat ttggcttctc aaaattggag caactatgac ccaacagaag aaatcccagc
6001 ccctctggga actccagatt ttgtggggaa gattcaaggc gtgctcaccc aaaccacaag
6061 gacagttggc tcaacacgcg gccacaaagc cacagtgcgc actgggagcg ccgactttgc
6121 tccaaaactg ggtagagttc gatttgaaac tgacacaaac aatgattttg aagttaacca
6181 aaatacaaag ttcaccccag ttggtgtcat ccaagatggt gacaccgccc accgaaatga
6241 accccaacag tgggtgctcc caagttactc aggcagaaac actcctaatg tacatctggc
6301 ccccgctgta gcccccactt ttccgggtga gcaacttctc ttcttcagat ccaccatgcc
6361 cggatgcagc gggtacccca acatggattt ggactgtctg ctcccccagg aatgggtgca
6421 gtacttctac caagaggcag ccccagcaca atctgatgtg gctctgctga gatttgtgaa
6481 tccagacaca ggtagggttt tgtttgagtg taagcttcat aaatcaggct atattacagt
6541 ggctcacact ggccaacatg atttggttat cccccccaat ggttatttta ggtttgattc
6601 ctgggttaat cagttttaca cgcttgcccc catgggaaat ggaacggggc gtagacgtgc
6661 accataatgg ctggagcttt ctttgctgga ttggcatctg atgtccttgg ctctggactt
6721 ggttccctta tcaatgctgg ggctggggcc atcaaccaaa aagttgagtt tgaaaataac
6781 agaaaattgc aacaagcatc cttccaattt agcagcaatc tacaacaggc ttcctttcaa
6841 catgacaaag agatgctcca agcacaaatt gaggccacca aaaggctaca acaggaaatg
6901 atgaaagtca aacaggcaat gctcctagag ggtgggtttt ctgagacaga tgcagcccgc
6961 ggggcaatca acgcccccat gacaaaagtt ttggactgga gtgggacaag gtactgggct
7021 cccgatgcta ggaccacaac atacaatgca ggccgctttt ccacccctca accatcgggg
7081 gcactgccag gaagagctaa tcttagggat gctgtccctg ctcggggttc ctccagaaag
7141 tcttctaatt cttccactgc tacttctgtg tactcaaatc aaactacttc aacgagactt
7201 ggttctacag ctggttctgg taccagtgtc tcgagcttcc cgacaactgc aaggactagg
7261 agctgggttg aggatcaaag taggaatttg tcacctttca tgagtggggc ccacaacata
7321 tcgtttgtca ccccaccatc tagcagatcc tctagccaag gcacagtctc aaccgtgcct
7381 aaagagattt tggactcctg gactggcgct ttcaacacgc gcaggcagcc actcttcgct
7441 cacattcgta agcgagggga gtcacggg
//