Typing tool
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Typing tool
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Complete norovirus genomes
| MF140646 | GII.7 | |
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| GII.P7 |
ORF1: 1..5077
ORF2: 5058..6680
ORF3: 6680..7439
LOCUS MF140646 7439 bp RNA linear VRL 24-OCT-2017
DEFINITION Norovirus GII strain
Norovirus/GII/Hu/NL/2013/GII.P7-GII.7/Rotterdam/E1300274_p12_d26
ORF1 gene, partial cds; ORF2 gene, complete cds; and ORF3 gene,
partial cds.
ACCESSION MF140646
VERSION MF140646.1
KEYWORDS .
SOURCE Norovirus GII
ORGANISM Norovirus GII
Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes;
Picornavirales; Caliciviridae; Norovirus; Norwalk virus.
REFERENCE 1 (bases 1 to 7439)
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 7439)
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..7439
/organism="Norovirus GII"
/mol_type="genomic RNA"
/strain="Norovirus/GII/Hu/NL/2013/GII.P7-
GII.7/Rotterdam/E1300274_p12_d26"
/host="Homo sapiens"
/db_xref="taxon:122929"
/country="Netherlands"
/collection_date="20-Aug-2013"
/note="genotype: GII.P7-GII.7"
CDS <1..5077
/codon_start=2
/product="ORF1"
/protein_id="ATN23634.1"
/translation="DATAAFGSQNSVNDSDNATPSNKEEVGAFSNIKVGFKKMLGAVP
KGTKAPSSGQHCPTVKIGPKTLTIPPEPPNGEDTVQFNAKSETIVGLPDLTTVQNEHE
NTPYTVPPLSEREHRPATEPLPGTILEMWDGEFYHYSVYVSDGRALGVHKPPAAISLA
TIELTPISLYWRPVYTPNYLVSPDTLKGLAGEKFPYTAFSNNCYNFCCWVLELNDTWL
NRRCISRTTGFFKPYQSWNRKPLPTVDDGKIKKVANAILCALGSLFSRPIKDLLGKLK
PLNLLHLLASCDWTFAGVVETVILMAELFNVFWTPPDVSNFIASLIGDFELQGPEDLA
MELVPVVMGGVGMVLGFTAEKIGRMLSSAASTLRACKDLGNYALDILKLVMKWFFPKK
EEKAEMETLRAIEDAVLDMEAIGNNHLTTLLKDKDSLTAFMKTLDLEEEKARKLSTKS
SSPDIVGTINAILARIAAARSLLHKAKEEMFSRIRPVVVMISGRPGIGKTHMARHLAK
SIANTMSGDQRVGLVPRNGVDHWDAYRGERVVLWDDYGMGSPVKDALTLQELADTCPV
TLNCDRIENKGKMFDSDVIIITTNLVNPAPLDYVNFEACSRRVDFLVYAESPEIEKVK
RDFPGQPDMWKDHFKPDFSHIKLTLAPQGGFDKNGNTPHGKGTMRSLTQGSLTARVAG
LVHERRDEFQLQGNDLQTYNFDTNRVSAFRKLAADNKYGIMETMRVGATLKNVKTLED
LKIALRDVKFNECEIIYKNSKYRVSSNGKGSVSVDKVEDNASQTVNEVQSAILRLRQA
RARYYISCFQDLVYTLMQVAGASFVVNRISRRFCWERWVKPAETQEVNESEKEVAQGR
WEIEPKDTEPEGKKGKNKKGRGKKHTAFSSKGLSDEEYDEFKRIREERNGKYSIEEYL
QDRDRYYEEVAVARATEEDFCEEEEAKIRQRIFRPTKKQRKEERGVLGLVTGSDIRKR
RPDDFQPKGNPWADDTRSVDYNERLDFEAPPSVWSRIVPLGTGWGFWVSSNLLITTTH
VLPKGVKELFGVEIKQIQVHKSGEFCRFRFPRPIRPDVTGLVLEEGAPEGTVCSILIK
RPTGEMIPLAVRMGTHASMKIQGRTVGGQMGMLLTGANAKNMDLGTGPGDCGCPYIYK
RGNDIVVAGVHTAAARGGNTVICATQGQDGEAVLEGNEDLGTYCGAPILGPGKAPKLS
TKTKFWRSSPDALPPGTYEPAYLGGKDPRVEKGPSLQQVMRDQLRPFTEPRGKPPRPA
VLEEAKKTVMNVLEQTIDPAKPWSYSQACASLDKTTSSGSPHHVKKNDHWNGETFTGP
LADQASKANLMYEQAKHVQPVYTAALKDELVKTDKIYKKIKKRLLWGSDLGTMIRCAR
AFGGLMDSMKASCIALPCRVGMNMNEDGPIIFDKHSKYRYHYDADYSRWDSTQQRNIL
SAAMEVMVRFSAEPELAQVVAEDLLAPSQLDVGDFVISVQEGLPSGVPCTSQWNSIAH
WILTLSAMAEVSGLSPDVVQAHSCFSFYGDDEIVSTDINLDPMKLTQKLREYGLVPTR
PDKTEGPLVITEDLTGLTFLRRSIARDPAGWFGKLDQDSILRQLYWTRGPNHENPYES
MVPHSQRATQLMALLGEASLHGPQFYKKVSKMVINEIKSGGLEFYVPRQEAMFRWMRF
SDLSTWEGDRNLAPEGVNEDGVE"
CDS 5058..6680
/codon_start=1
/product="ORF2"
/protein_id="ATN23635.1"
/translation="MKMASNDAAPSNDGAAGLVPEINNEVMPLEPVAGASLATPVVGQ
QNVIDPWIRNNFVQAPAGEFTVSPRNSPGEILLDLELGPELNPYLSHLARMYNGHAGG
MEVQIVLAGNAFTAGKIIFAAIPPGFPYENLSPSQITMCPHVIIDVRQLEPVLLPMPD
IRNNFFHYNQGNDPKLRLVAMLYTPLRANNSGDDVFTVSCRVLTKPSPDFEFTFLVPP
TVESKTKQFTLPILKISEMTNSRFPVPVEMMYTARNENQVVQPQNGRVTLDGELLGTT
PLLAVNICKFKGEVIAKNGDVRSYRMDMEITNTDGTPIDPTEDTPGPIGSPDFQGILF
GVASQRNKNEQNPATRAHEANINTGGDQYAPKLAQVKLFSESQDFDVHQPTVFTPVGV
AGDPSHPFRQWVLPRYGGHLTNNTHLAPAVAPLFPGEQILFFRSQIPSSGGYESGYMD
CLVPQEWVQHFYQEAATAQSEVALIRFINPDTGRVLFEAKLHKQGFITVAHTGDNPIV
MPPNGYFRFEAWVNQFYSLAPVGTGNGRRRIQ"
CDS 6680..>7439
/codon_start=1
/product="ORF3"
/protein_id="ATN23636.1"
/translation="MASAFFANLAGGVASNGISSLINAGANAINQKVEFDYNKQLQNA
SFSHDKEMLQAQIEATKRLQQEMIDIKQGVLTAAGFSPTDAARGSVGAPMTKLVDWSG
TRYWAPGAMRTTGYSGTFTHLPPVQSASYVNNQNRQPPKVDPPPPSSSGSSVSSVKTQ
STTLSGTSRVGSSSHLTLSTRPSTRTSDWVRSQNERLSPFMDGALQTTYVTPPSSRAS
SVSTVSTVPKEVLDSWTPMFNTHRQPLFAHLRRRG"
ORIGIN
1 cgacgctact gctgcctttg gcagtcaaaa ctctgtcaat gacagtgata acgccacccc
61 ttctaataaa gaagaggttg gtgcattctc caacatcaaa gttggattca agaaaatgct
121 gggtgccgtt cccaagggca ccaaagcacc cagcagtggt caacattgcc ccacagttaa
181 gattgggcct aaaacattaa caatcccccc tgagccccca aatggtgaag acaccgtaca
241 gtttaatgca aagtcagaaa ctatagttgg gttgccggac ttgacaacgg tgcaaaatga
301 acatgaaaac accccataca ctgtccctcc attaagtgag agggagcaca ggccggccac
361 cgaaccactt cctggcacaa tattagagat gtgggatggt gagttttacc attattccgt
421 gtacgtcagc gacggcagag ctctgggagt ccacaaacca ccggcggcta taagcctcgc
481 gacgatagag ctcaccccca tatcacttta ctggaggccc gtttataccc ccaattactt
541 ggtctccccg gacacattaa aaggtctcgc tggtgagaag ttcccctata cggccttcag
601 taacaactgt tataacttct gttgctgggt gcttgagctc aacgacacgt ggcttaacag
661 aagatgcatt tccagaacca ccggcttctt caagccatac cagtcttgga acagaaaacc
721 tctcccaacc gttgatgatg gaaagattaa gaaagtggcc aatgcaatcc tctgtgcact
781 cggctcactg ttctcaagac caatcaaaga cctgttaggc aaactcaagc cattgaatct
841 actgcacttg cttgcgtctt gtgattggac gtttgcgggt gtagtggaga cagtcatctt
901 gatggcggag cttttcaatg tcttctggac ccccccagat gtctctaatt ttatagcctc
961 cctaataggt gattttgaat tgcaagggcc tgaggacctg gctatggagc tcgtccccgt
1021 ggtcatgggc ggcgtaggga tggttctcgg ttttaccgcc gagaagatag gccgcatgct
1081 gtcgtccgct gcatcaacac tgcgggcgtg caaagaccta gggaactatg cccttgacat
1141 actcaaattg gtcatgaagt ggttcttccc gaagaaggaa gagaaagctg agatggaaac
1201 cttgagggcg attgaggatg ccgtcctgga tatggaagcc atagggaaca accacctcac
1261 aacccttctt aaggacaaag atagcctcac ggctttcatg aagaccctgg atctggaaga
1321 ggagaaggca aggaaactgt ccactaaatc atcttcaccg gacatagtcg gcaccatcaa
1381 tgccatacta gctaggatag ctgctgctag atcccttcta cataaggcca aagaggagat
1441 gttcagcagg atcaggccag tggttgttat gatatcaggc aggcctggca ttggaaaaac
1501 ccacatggcg agacatttgg ctaagagcat cgccaacacc atgagtggcg accaaagagt
1561 cgggctcgtt ccgcgcaacg gcgtcgatca ctgggatgcc tacaggggag agagggtggt
1621 cttgtgggat gactacggca tggggagccc tgttaaggac gctctaacac tgcaagagct
1681 ggccgacaca tgcccagtca ctttaaattg tgacaggatt gagaataagg ggaagatgtt
1741 tgacagtgat gtcatcataa tcacgaccaa cctagtcaac cccgcgcccc tcgactatgt
1801 gaacttcgag gcgtgttcta ggagagttga cttcctggtc tatgcagagt caccagaaat
1861 tgaaaaggtc aagagagact tccctggcca gcctgacatg tggaaagacc attttaaacc
1921 agacttctcc cacatcaagc tgactctagc cccccagggt gggtttgaca aaaatggcaa
1981 caccccacac ggtaagggaa ccatgcggtc cctaacccag gggtccctga ctgcgagagt
2041 tgcaggcctt gtccatgaga ggagagatga attccagctc caaggaaatg acctccaaac
2101 atacaacttt gacaccaaca gagtctccgc attcaggaaa ttggctgcag ataacaagta
2161 tgggatcatg gagacgatga gagtgggtgc gacactcaag aatgtgaaga ccctggaaga
2221 tcttaaaatt gcattgaggg atgtaaaatt caatgagtgt gaaataatct acaagaactc
2281 taagtatcga gtctcttcca acggtaaagg ctcagtttct gttgacaaag ttgaagacaa
2341 tgcatcccag actgtaaacg aggtacaatc cgcaattctc aggctcaggc aagcgagggc
2401 cagatattac atcagctgct tccaagacct cgtctatact ctcatgcagg ttgccggagc
2461 atcattcgta gtcaacagga tctccagaag gttctgctgg gaaaggtggg tcaaaccggc
2521 cgagacccag gaggtgaatg agtccgaaaa ggaagtggca caaggcagat gggaaattga
2581 gcccaaggat acagaaccag aaggcaagaa aggtaagaac aagaaaggaa gaggtaagaa
2641 acacacagct ttctctagca aaggcctgag tgatgaagag tatgacgagt tcaagagaat
2701 tagggaagaa aggaacggaa agtactccat tgaggaatac ctgcaagacc gggaccgcta
2761 ctatgaagaa gtggcagttg cccgggcgac agaggaggac ttctgtgaag aggaagaggc
2821 caagataaga caaaggattt tccgcccgac aaagaaacag aggaaggagg agaggggtgt
2881 gcttggctta gtcaccggct cagacatcag gaagaggaga ccagatgact tccaaccaaa
2941 aggcaacccg tgggcagatg acaccagaag tgtggactac aatgagaggc ttgattttga
3001 agcgcccccg agtgtttggt caagaatagt tccattaggc actggttggg gattctgggt
3061 ttcatccaac cttctgatca caacaacaca cgtcctgcct aaaggggtta aggagctctt
3121 tggagttgaa atcaaacaaa tccaagttca caagtctgga gagttttgca ggttcagatt
3181 cccaagacct atcaggccag atgtcacagg actcgtgctg gaggaaggcg ccccagaagg
3241 cactgtctgt tctatactca taaagaggcc cacaggtgag atgatcccct tagcagtgag
3301 gatgggcaca catgcatcca tgaaaataca gggcagaacc gttggtggcc agatgggaat
3361 gcttctcaca ggagcgaacg cgaagaacat ggacctcggc actggtcctg gtgactgcgg
3421 ttgcccttac atctacaaac gtggcaacga cattgttgtc gcgggtgttc acaccgcagc
3481 agcccgagga ggcaacactg ttatatgtgc cacccaaggg caagatgggg aagcagtcct
3541 tgagggaaat gaggaccttg gcacctattg tggcgcccca attctgggcc ctggcaaggc
3601 gcctaaactc agcacgaaga ctaagttctg gcgttcatca ccagatgcct tgccacctgg
3661 cacatatgag cctgcttacc taggaggcaa agaccctaga gtggaaaaag gtccttccct
3721 tcaacaagtc atgagggacc agttgagacc cttcacagaa cccaggggca aaccacctag
3781 acctgcagtc ttggaggaag ccaaaaagac agtgatgaat gttctagaac aaaccattga
3841 ccccgccaag ccatggtcct attcgcaggc gtgtgcctca ttggacaaaa ccacctccag
3901 tggtagtccc catcatgtta agaaaaatga ccactggaat ggggagacct tcactggtcc
3961 acttgcagat caggcatcta aagccaatct catgtatgag caggctaaac atgtgcagcc
4021 cgtgtatacg gccgcgctca aagatgagct tgttaagact gacaagatct acaagaaaat
4081 aaagaagagg ctcctatggg ggtcggacct tggcacaatg atcaggtgcg ccagggcctt
4141 tggtggtctc atggacagca tgaaggcaag ttgtatagct cttccttgca gggtagggat
4201 gaacatgaat gaagatggcc ctattatatt tgacaaacat tctaagtaca ggtaccacta
4261 tgatgctgac tattctaggt gggactcaac ccaacaaagg aacattcttt ctgccgctat
4321 ggaagtgatg gtgcggttct ctgctgaacc agaattggca caagtggttg cagaggacct
4381 tttagcacct agccagcttg atgttggcga ttttgtcatc tcagtccagg agggtctgcc
4441 atcaggagtc ccatgcacat cacaatggaa ttcaatagca cactggatcc taactttgag
4501 tgcaatggca gaagtgtcag gtctctcacc agatgttgtc caagcccact cttgtttttc
4561 cttttatggg gacgatgaga tcgtcagtac tgacatcaat cttgacccca tgaagttgac
4621 acagaaactc agggagtatg gtctggttcc cacccggcct gataaaactg aaggtcccct
4681 cgtcataact gaagacctca ccggcctgac gttcctccgt aggtcgattg ctcgggaccc
4741 agctggttgg tttggaaagc tggaccaaga ctcaatcctt aggcagctgt actggacaag
4801 ggggcctaac catgagaacc cgtacgagag catggttcct cattctcagc gggccacaca
4861 actcatggcc cttcttggtg aggcctcact acatggcccc cagttttata agaaagttag
4921 caagatggtc atcaatgaga ttaagagtgg tggtctggag ttttatgtgc ccagacaaga
4981 ggccatgttc aggtggatga gattctctga cctcagcaca tgggagggcg atcgcaatct
5041 tgctcccgaa ggtgtgaatg aagatggcgt cgaatgacgc agctccatct aatgatggtg
5101 cagcaggcct cgtaccagag atcaacaatg aggtcatgcc ccttgagccc gtagctggtg
5161 catcgctggc gacaccagtt gtcgggcaac aaaatgtaat tgatccctgg ataagaaata
5221 attttgtaca agctcctgca ggtgagttta cagtttcccc tagaaattcc cctggtgaaa
5281 ttttgctcga tttggagttg ggaccagaac taaaccccta tctctctcat ctggcccgta
5341 tgtataatgg gcacgctggt ggcatggaag tgcaaattgt gttagctggg aatgcgttca
5401 cagctggcaa gatcatattt gctgccatcc ctccagggtt cccatatgaa aacttgtcac
5461 cttcacaaat cacaatgtgc cctcatgtta taattgatgt tagacaacta gaaccagttc
5521 tattacctat gccagatatt agaaacaact tcttccatta caatcagggc aatgacccaa
5581 aattgagatt ggtagctatg ctctacaccc ctttaagggc taataattct ggtgatgatg
5641 tgttcacagt ttcttgtagg gtcctcacta aaccgtcacc tgattttgaa ttcacatttt
5701 tggtcccccc tacggttgaa tctaaaacca aacagttcac actgcccatc ctcaaaatat
5761 cagagatgac caactcaaga ttcccagtgc cagtggaaat gatgtacaca gccaggaatg
5821 agaaccaagt tgtccagcca cagaatggta gggtcacact tgatggcgag ctattaggca
5881 ccacaccctt gttggctgtc aacatctgca aattcaaggg ggaggttata gctaagaatg
5941 gagatgtgag gtcctatagg atggacatgg aaattaccaa cactgatggc accccaattg
6001 accccacaga agatacacct ggtcccattg gttcacctga ctttcaaggt atactctttg
6061 gcgttgccag ccaacgcaac aagaatgagc aaaaccctgc cacgagagcc catgaagcca
6121 acattaacac tggtggagac caatacgccc ccaaattggc ccaagtgaaa ctcttctcag
6181 agtcccagga tttcgatgtg caccagccca cagttttcac cccagttggt gtggcaggcg
6241 acccctccca tcctttcaga cagtgggtcc tgcctcgata cggtggacat ctcaccaaca
6301 acacccacct ggctccagca gtggcccccc tattcccagg tgagcagatt ctattcttta
6361 gatcacaaat acccagctca ggcggctatg aatcgggtta catggactgc cttgtccccc
6421 aagaatgggt ccaacacttc tatcaagaag ctgccacagc tcagtctgag gtggcactca
6481 taaggttcat caacccagac actggcagag tcctctttga ggccaagctg cacaagcaag
6541 gctttataac tgtggctcac actggtgata acccaattgt catgccacca aatgggtact
6601 ttagatttga agcttgggtt aatcagtttt actcactcgc ccccgtggga actgggaatg
6661 ggcgcaggag gatccaataa tggccagtgc tttctttgca aatttggcag gaggcgttgc
6721 ctccaatgga attagttcac tcataaatgc tggggctaat gctattaacc aaaaagttga
6781 gtttgattat aataaacaac tccaaaatgc atccttctcc catgataagg aaatgctcca
6841 agcccaaatt gaagccacca aacgtctgca acaagagatg attgacataa aacaaggggt
6901 gctgacagct gcaggattct ctcctacgga tgccgcgagg ggttctgtcg gcgcaccaat
6961 gacaaaatta gttgattgga gtggcactag atattgggcg cctggtgcca tgaggacaac
7021 aggctattca gggactttta ctcacttgcc ccctgtgcag tctgcttcat atgttaataa
7081 tcagaataga caacctccta aagtagatcc ccctcctcct tcttcgagtg gttcttctgt
7141 ttcttctgtc aaaacacaat cgactaccct ctcaggcact tcaagggtgg gctcctcatc
7201 ccatttaacc ctgtcaacca ggccgagcac aaggacatct gattgggtgc gcagccagaa
7261 tgaaaggttg agtcccttca tggatggagc gttgcaaaca acatatgtaa cgccaccatc
7321 cagtagggcg tcaagtgtca gcacagtctc gaccgtgccg aaagaggttt tggactcctg
7381 gacgcctatg tttaacactc acaggcagcc actcttcgcc catctgcgta ggcgagggg
//