Typing tool
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Typing tool
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Complete norovirus genomes
| MF140685 | GII.3 | |
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| GII.P21 |
ORF1: 1..5083
ORF2: 5064..6713
ORF3: 6713..7474
LOCUS MF140685 7478 bp RNA linear VRL 24-OCT-2017
DEFINITION Norovirus GII strain
Norovirus/GII/Hu/NL/2011/GII.P21-GII.3/Rotterdam/E1300323_p7_d287
ORF1 gene, partial cds; and ORF2 and ORF3 genes, complete cds.
ACCESSION MF140685
VERSION MF140685.1
KEYWORDS .
SOURCE Norovirus GII
ORGANISM Norovirus GII
Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes;
Picornavirales; Caliciviridae; Norovirus; Norwalk virus.
REFERENCE 1 (bases 1 to 7478)
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 7478)
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..7478
/organism="Norovirus GII"
/mol_type="genomic RNA"
/strain="Norovirus/GII/Hu/NL/2011/GII.P21-
GII.3/Rotterdam/E1300323_p7_d287"
/host="Homo sapiens"
/db_xref="taxon:122929"
/country="Netherlands"
/collection_date="06-Dec-2011"
/note="genotype: GII.P21-GII.3"
CDS <1..5083
/codon_start=2
/product="ORF1"
/protein_id="ATN23751.1"
/translation="DASAAAAANSNNDNAKSSSDGVLSNMAVTFKRALGARSKQPPPR
DKPPKPPRPPTPELVKAIPPPPPNGEDEPIISYNVKEGVSGLPELSTVTQLEENSTAF
SVPPLSQRENRDAKEPLTGTILEMWDGEIYHYGLYVERGLVLGVHKPPAAVSLAKVEL
TPLSLYWRPVYTPQYLISPDTLKKLHGETFPYTAFDNNCYAFCCWVLDLNDSWLSRRM
IQRTTGFFRPYQDWNRKPLPTMDDSKVKKVANVVLCALSSLFTRPIKDIIGKLKPLNI
LNILATCDWTFAGIVESLILLAELFGVFWTPPDVSAMIAPLLGDYELQGPEDLAVELV
PVVMGGIGLVLGFTKEKIGKMLSSAASTLRACKDLGAYGLEILKLVMKWFFPKKEEKN
ELAMVRSIEDAVLDLEAIENNHMTALLKDKDSLATYMRTLDMEEEKARKLSTKSASPD
IVGTINALLSRIAAARSLVHRAKEELSSRPRPVVVMISGRPGIGKTHLARELAKKIAS
SLTGDQRVGLIPRNGVDHWDAYKGERVVLWDDYGMSNPIHDALRLQELADTCPLTLNC
DRIENKGKVFDSDAIIITTNLANPAPLDYVNFEACSRRIDFLVYADAPEVEKAKRDFP
GQPDMWKDTFKPDFSHIKLTLAPQGGFDKNGNTPHGKGVMKTLTASSLVARASGLLHE
RLDEYELQGPTPTTFNFDRNKVLAFRQLAAENKYGLVDTMRVGSQLKNVKTMTELKQA
LKNISVKKCQLVYGGGTYTLESDGKGNVHVEKVNNTSVQTNNELSGALHHLKCARIRY
YVKCVQEALYSILQIAGAAFITTRITKRMNIQNLWSKPQAEDLEETNNEEGCPKPKND
EEFVISSDDIKTEGKKGKNKTGRGKKHTAFSSKGLSDEEYDEYKRIREERNGKYSIEE
YLQDRDKYYEEVAIARATEEDFCEEEEAKIRQRIFRPTRKQRKEERASLGLVTGSEIR
KRNPDDFKPKGKLWADDDRNVDYNEKLSFEAPPSIWSRIVNFGSGWGFWVSPSLFITS
THVIPQGAQEFFGVSIKQIQIHKSGEFCRLRFPKPIRTDVTGMILEEGAPEGTVATLL
IKRPTGELMPLAARMGTHATMKIQGRTVGGQMGMLLTGSNAKSMDLGTTPGDCGCPYI
YKRGNDYVVIGVHTAAARGGNTVICATQGNEGEAMLEGGDNKGTYCGAPILGPGNAPK
LSTKTKFWRSSTTPLPPGTYEPAYLGGKDPRVKGGPSLQQVMRDQLKPFTEPRGKPPK
PSVLEAAKKTIINVLEQTIDPPQKWTYAQACASLDKTTSSGHPHHMRKNDCWNGETFT
GKLADQASKANLMFEEGKNMTPVYTGALKDELVKTDKIYGTIKKRLLWGSDLSTMIRC
ARAFGGLMDELKAHCVTLPVRVGMNMNEDGPIIFEKHSRYKYHYDADYSRWDSTQQRA
VLAAALEIMVKFSPEPHLAQVVAEDLLSPSVMDVGDFKISINEGLPSGVPCTSQWNSI
AHWLLTLCALSEVTDLSPDIIQANSLFSFYGDDEIVSTDIKLDPEKLTTKLKEYGLKP
TRPDKTEGPLIISEDLDGLTFLRRTVTRDPAGWFGKLDQSSILRQMYWTRGPNHEDPF
ETMIPHSQRPIQLMSLLGEAALHGPSFYSKISKLVISELKEGGMDFYVPRQEPMFRWM
RFSDLSTWEGDRNLAPCFVNEDGVE"
CDS 5064..6713
/codon_start=1
/product="ORF2"
/protein_id="ATN23752.1"
/translation="MKMASNDAAPSNDGAAGLVPEINNEAMALEPVAGAAIAAPLTGQ
QNIIDPWIMNNFVQAPGGEFTVSPRNSPGEVLLNLELGPEINPYLAHLARMYNGYAGG
FEVQVVLAGNAFTAGKIIFAAIPPNFPIDNLSAAQITMCPHVIVDVRQLEPVNLPMPD
VRNNFFHYNQGSDSRLRLIAMLYTPLRANNSGDDVFTVSCRVLTRPSPDFSFNFLVPP
TVESKTKPFSLPILTISEMSNSRFPVPIDSLHTSPTGNIVVQCQNGRVTLDGELMGTT
QLLPSQICAFRGVLTRSTSRASDQADAVAPRLFNYYWHIKLDNLNGTPYDPAEDTPGP
LGTPDFLGKVFGVASQRDPDTTTRAHEAKIDTSSGRFAPKLGSLEISTESADFNPNKP
TRFTPVGIGVDQAEGDFQQWTLPDYAGKITHNMNLAPAVAPNFPGEQLLFFRSHLPSS
GGRSDGILDCLVPQEWVQHFYQESAPSQSQVALVRYINPDTGRVLFEAKLHKLGFITI
AKNGDSPITVPPNGYFRFESWVNPFYTLAPMGTGNGRRRIQ"
CDS 6713..7474
/codon_start=1
/product="ORF3"
/protein_id="ATN23753.1"
/translation="MAGAFIAGLAGDMLTNTVGSLVNAGANAINQTIDFENNKYLQNA
SFNHDKEMLNAQIEATKRLQADMIAIKQGVLTAGGFSPTDAARGAINAPMTKVLDWNG
TRYWAPGATSTTSMSGGFTNQTVHRSTPNFKTNQAPRPTPSSGSSVRSNSTQITSLSS
HSSGSSRSSGSTVVSSISSNRTRDWVNQQNFNLEPHMPGSLRTAFVTPPSSSASSSGT
VSTVPKNVLDSWTSAFNTRRQPLFAHLRRRGESKV"
ORIGIN
1 cgacgcttcc gctgccgctg ctgccaacag caacaacgac aacgcaaaat cttcaagtga
61 cggagtatta tctaatatgg ctgtcacttt taaacgagcc ctcggggcgc ggtctaaaca
121 gccgcccccg agggacaaac caccaaaacc cccaagacca cccacaccag agttggttaa
181 ggcaatcccc cctcccccac ccaacgggga ggacgaacca atcatttctt ataacgtcaa
241 agaaggtgtt tctggtttgc ctgaactctc aactgtcacc caactagagg agaactctac
301 agcgttcagt gttccccctc ttagtcagag ggagaacagg gatgcaaagg aaccattgac
361 tggaaccatc ctggagatgt gggacgggga gatctaccat tatggcttat acgtggaacg
421 agggttagtg ctcggtgtac acaaaccacc ggcagccgtc agtcttgcta aggttgagct
481 gacccccttg tctttgtatt ggagaccagt gtacacccca cagtacctca tttcccctga
541 cactctcaaa aagttgcatg gggagacgtt cccttataca gcctttgata acaactgtta
601 tgccttctgc tgttgggtac ttgacttgaa cgattcatgg ctgagcagaa ggatgataca
661 gaggacaaca ggcttcttcc gaccctacca ggactggaac aggaaacccc tccccacgat
721 ggatgattcc aaagtgaaaa aggtggccaa tgttgtcctt tgtgctctct catcattgtt
781 cacaagacca attaaggaca ttattgggaa gttgaaaccc ctaaacatcc ttaacatcct
841 agccacatgt gattggactt ttgcaggcat agtggaatcc ctgatccttt tggctgaact
901 gtttggagtt ttctggacac ccccagatgt gtctgcaatg atcgctccct tactgggtga
961 ttatgagcta cagggacccg aggacctcgc tgtggaactc gtacccgtag taatgggagg
1021 gataggtttg gtgctgggat tcaccaaaga gaaaattgga aaaatgcttt catctgctgc
1081 ttcaaccctg agggcatgca aagatctcgg tgcatatggg ttggagatcc tcaagttggt
1141 catgaaatgg tttttcccaa agaaagaaga gaaaaacgaa ttggcaatgg tgagatccat
1201 cgaggatgca gtgctagatc ttgaggccat tgagaacaac catatgacag ctctactcaa
1261 ggataaagac agccttgcaa cctacatgag gactcttgac atggaggagg agaaagcgag
1321 gaaactttcc accaagtctg cctcgccgga tattgtgggc acgataaacg ccctactgtc
1381 aaggattgct gctgcccggt ctctagtgca cagggctaag gaggagctgt caagcaggcc
1441 ccgaccggtc gttgtgatga tttcagggag accaggtatt gggaaaaccc acctagctag
1501 agagttggca aagaagatcg cctcctcact cacaggtgac cagagggtgg gtcttatccc
1561 acgcaacggg gtcgaccact gggatgcata caaaggtgaa agagtcgttc tctgggacga
1621 ctacgggatg agcaacccca tccacgacgc cctcagactc caggagctcg ctgacacctg
1681 tcctctcaca ctcaactgtg acaggattga gaataaaggc aaagtctttg acagtgacgc
1741 cataataata accaccaatt tggccaaccc agcgccactg gattacgtta actttgaagc
1801 ttgctcaaga cgcatagatt tcctcgtcta tgctgatgcc cctgaagttg agaaggccaa
1861 acgggacttc ccaggccaac cagacatgtg gaaagacacc tttaaacctg acttctctca
1921 cataaaactg acattagccc cgcaaggagg ttttgacaag aatggtaaca ctcctcatgg
1981 gaagggtgtc atgaagaccc tcacagccag ttctctcgtt gcccgagcat caggtctcct
2041 ccacgagaga ttagacgaat atgaactgca gggcccaacc cccacaacat tcaacttcga
2101 ccgcaacaag gtgcttgctt ttaggcagct tgctgctgaa aacaaatacg gtcttgttga
2161 cacaatgagg gtcggatcac agctcaagaa tgttaaaact atgacagaac tcaagcaggc
2221 tctcaagaac atctcagtca agaaatgtca gcttgtgtat ggtgggggca cgtacacact
2281 tgaatctgat ggcaaaggca atgtgcacgt cgagaaggtg aacaacacta gtgtgcaaac
2341 taacaacgag ctctccgggg ctttgcacca tctcaagtgt gccagaatta ggtactatgt
2401 taagtgtgtc caggaagctc tctactccat cctgcaaatt gccggggctg cattcattac
2461 cacgcgcatc acaaagcgca tgaacataca aaacctctgg tccaaaccac aagcagaaga
2521 tctggaggag accaacaacg aggagggctg tccaaaacct aaaaatgatg aggaatttgt
2581 tatctcctct gatgacatca aaaccgaggg caagaaagga aagaacaaga ctggccgtgg
2641 taagaagcac acagcctttt ccagcaaagg actcagtgat gaggagtacg atgagtacaa
2701 gagaatcagg gaagagagaa atggcaagta ctccatagag gaatacctac aggacagaga
2761 caaatactat gaggaggtgg ccatagccag ggcaactgag gaagacttct gtgaagaaga
2821 ggaggctaaa atccggcaga ggatattcag accaacaagg aaacaacgca aagaggaaag
2881 ggcctctctt ggtttggtta caggttctga gatcaggaag agaaacccag atgacttcaa
2941 gcccaaaggg aaactatggg ccgatgatga caggaatgtt gactacaatg agaaacttag
3001 tttcgaggct ccaccaagca tttggtcacg aatagtcaac tttggctcag ggtggggctt
3061 ttgggtctcg cccagcctct tcataacatc aacccatgtc attccccaag gcgcacagga
3121 gttctttgga gtgtccatca aacaaataca aatccacaag tcaggtgagt tctgccggct
3181 aaggttccca aaaccaatca gaacggatgt cacaggcatg atcttggagg aaggtgctcc
3241 agaaggcact gttgccacac ttctcatcaa gagaccaact ggggaactca tgcccttggc
3301 agccagaatg ggcacccacg cgaccatgaa aattcagggt cgcactgttg gtggacagat
3361 gggcatgcta ctcacagggt ccaacgctaa gagcatggat ttgggcacaa ctcctggcga
3421 ttgtggttgt ccctatatct acaagagagg gaacgactac gtggtcattg gagttcacac
3481 tgccgccgct cgtggaggaa acaccgtcat ctgtgcaacc caaggaaacg agggggaggc
3541 catgctagaa ggtggtgaca acaagggaac ttactgtgga gcaccaatat taggccctgg
3601 aaatgccccc aaactcagca ccaaaaccaa attctggagg tcttccacca cccccttgcc
3661 acctggaacc tatgagccag cctatctggg tggcaaggac cccagagtga aaggtggccc
3721 ctcactgcaa caggttatga gggaccaact aaaaccattc actgagccca gaggcaaacc
3781 acccaaacca agtgtgctag aagccgccaa gaagactata atcaatgtgc ttgaacaaac
3841 aatagaccca cctcaaaaat ggacatacgc gcaggcgtgt gcatcactag acaagaccac
3901 ctccagcggc caccctcacc acatgcggaa gaacgattgt tggaatgggg agactttcac
3961 aggaaaattg gcagaccaag catcaaaggc taacctaatg tttgaggaag ggaagaacat
4021 gaccccagta tacacaggag ctctgaaaga cgagctagtc aagactgata agatctatgg
4081 aacaatcaag aagagactcc tgtggggttc agacctatca actatgatac ggtgtgcacg
4141 agccttcggt gggctaatgg acgagctcaa ggcccactgc gtcacactac cagtcagggt
4201 tggtatgaac atgaatgagg atggacccat aatatttgag aaacattcca gatataaata
4261 tcattatgat gcagattact cccgctggga ctcaacacaa caaagagcag tgctggctgc
4321 agccctggaa ataatggtca aattctcacc agaaccccat ctggcccaag tagttgcaga
4381 agacctcttg tcccccagtg tgatggatgt gggtgatttc aagatatcaa tcaacgaggg
4441 attaccctct ggcgtccctt gcacctcaca atggaactcc attgcccact ggctcctcac
4501 actatgtgca ctgtctgaag tcacagacct atcccctgac atcatccagg caaattccct
4561 gttctccttt tatggtgatg atgaaatagt gagcacagac atcaaattgg acccagagaa
4621 attgacaaca aaattgaagg aatacgggct gaaaccaacc cgtcctgata aaacagaagg
4681 acccttaatc atctctgaag atttggatgg cctgaccttc ttacggagaa cggtaacccg
4741 tgatccggcc gggtggtttg gcaaactgga ccaaagctca atactcaggc agatgtactg
4801 gaccagggga ccaaaccatg aggacccctt tgaaacgatg ataccacact cccaaagacc
4861 catacaactg atgtcattat tgggtgaagc tgcattgcat ggtccatcat tctacagtaa
4921 aatcagcaaa ctagtcatct cagaattgaa agagggtgga atggactttt acgtgcccag
4981 acaagaacca atgttcaggt ggatgagatt ctcagatttg agcacgtggg agggcgatcg
5041 caatctggct ccctgttttg tgaatgaaga tggcgtcgaa tgacgccgct ccatctaatg
5101 atggtgccgc cggcctcgtc ccagagatca acaatgaggc aatggcgcta gagccagtgg
5161 cgggtgcagc gatagcagca cccctcactg gtcagcaaaa tataattgat ccctggatta
5221 tgaacaattt tgtgcaagca cctggtggtg agttcacagt atcccctaga aattcccctg
5281 gtgaagttct tcttaatttg gagttggggc ctgaaataaa tccttatttg gcccatcttg
5341 ctagaatgta taatggttat gcaggtggat ttgaagtgca agtggtccta gctggaaatg
5401 cgtttacagc aggaaagata atctttgcag ctattccccc caattttcca attgacaatc
5461 taagtgcagc acagatcaca atgtgtccac atgtgattgt ggacgtcaga cagttggaac
5521 cagtcaacct cccgatgcct gacgttcgca acaacttctt tcattacaat caagggtctg
5581 attcgagatt gcgcctaatt gcaatgctgt atacacctct tagggcaaat aattctgggg
5641 atgatgtttt cactgtgtcc tgcagagtgc taactagacc tagtcctgac ttctcattta
5701 atttccttgt gccacctact gtggagtcaa agacaaaacc cttttccctc cctattctga
5761 ccatctctga aatgtccaat tctaggttcc cagtgccaat tgattctctg cacactagcc
5821 ctactgggaa tattgttgtc cagtgccaga atgggcgcgt cacccttgac ggtgagttga
5881 tgggcaccac ccaactctta cctagccaaa tttgtgcttt caggggcgtg ctcaccagat
5941 caacaagcag ggccagtgac caggccgatg cagtagcccc taggttgttt aattattatt
6001 ggcatataaa attggataat ctaaatggaa ctccctatga tcctgcagaa gacacaccag
6061 gccccctggg aacaccagat ttcctgggca aagtctttgg cgtggccagc cagagagatc
6121 ctgataccac gactagggca catgaagcaa agatagacac atcatctggc cgtttcgccc
6181 caaaactagg ctcactagag atatccactg agtctgctga tttcaatcca aacaaaccaa
6241 caagattcac cccagttggc attggggttg accaggctga gggagacttt caacaatgga
6301 ctctacccga ctatgctggc aagatcaccc acaacatgaa cttggcccca gctgttgctc
6361 ccaacttccc tggtgagcag ctcctcttct tccgctcaca tttgccatct tctggtgggc
6421 gatccgacgg gattctagac tgcctggtcc cccaagagtg ggtacagcac ttctaccaag
6481 aatcagcccc ctctcaatct caagtggctc tagttaggta catcaaccct gatactggta
6541 gagtattatt tgaggccaag ctgcacaaat taggtttcat aactatagct aagaatggtg
6601 attctccaat aactgtcccc ccaaatggat actttaggtt tgaatcttgg gtgaacccct
6661 tttatacact tgcccccatg ggaactggga atgggcgtag aaggattcaa taatggctgg
6721 agcttttata gcaggattgg ctggtgatat gctcacaaat actgtaggat ctttagttaa
6781 tgcaggggct aatgccatta atcaaacaat tgattttgaa aataataaat atttgcaaaa
6841 tgcttctttt aatcatgata aggagatgtt gaatgcacaa attgaggcaa caaagagatt
6901 acaggctgac atgattgcta tcaaacaagg ggttttgacc gctggcggct tttcccctac
6961 tgatgcagcc cgtggggcaa ttaatgcccc catgacaaaa gtcctagatt ggaatggaac
7021 gagatactgg gcaccaggtg ccacctccac aacctcgatg tcgggtggct tcacaaacca
7081 aactgtgcac agatccacac caaattttaa aacgaaccag gctcccagac ccacacccag
7141 cagtgggtct tcagtaaggt caaattcaac ccaaatcact agcctgagct cacactcgtc
7201 cgggtcgtct cgatccagcg ggtctacagt tgtcagctca atatcctcta acaggactag
7261 ggactgggtc aaccaacaaa attttaattt ggaaccacac atgcctggat ctcttaggac
7321 agcttttgtt actccaccat ctagttcagc ctctagctca ggcacagtct caactgtgcc
7381 caaaaatgtt ttggactcct ggacatctgc gtttaacacg cgcagacagc cgctattcgc
7441 acaccttcgc agaagggggg agtcaaaagt ttagtgaa
//