Typing tool
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Typing tool
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Complete norovirus genomes
| MF140648 | GII.7 | |
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| GII.P7 |
ORF1: 1..5084
ORF2: 5065..6687
ORF3: 6687..7460
LOCUS MF140648 7525 bp RNA linear VRL 24-OCT-2017
DEFINITION Norovirus GII strain
Norovirus/GII/Hu/NL/2013/GII.P7-GII.7/Rotterdam/E1300276_p12_d76
ORF1 gene, partial cds; and ORF2 and ORF3 genes, complete cds.
ACCESSION MF140648
VERSION MF140648.1
KEYWORDS .
SOURCE Norovirus GII
ORGANISM Norovirus GII
Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes;
Picornavirales; Caliciviridae; Norovirus; Norovirus norwalkense.
REFERENCE 1 (bases 1 to 7525)
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 7525)
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..7525
/organism="Norovirus GII"
/mol_type="genomic RNA"
/strain="Norovirus/GII/Hu/NL/2013/GII.P7-
GII.7/Rotterdam/E1300276_p12_d76"
/host="Homo sapiens"
/db_xref="taxon:122929"
/geo_loc_name="Netherlands"
/collection_date="09-Oct-2013"
/note="genotype: GII.P7-GII.7"
CDS <1..5084
/codon_start=3
/product="ORF1"
/protein_id="ATN23640.1"
/translation="SNDATAAFGSQNSVNDSDNATPSNKEEVGAFSNIKVGFKKMLGA
VPKGTKAPSSGQHCPTVKVGPKTLTIPPEPPNGEDTVQFNAKSETIVGLPDLTTVQNE
HENTPYTVPPLSEREHRPATEPLPGTILEMWDGEFYHYSVYVSDGRALGVHKPPAAIS
LATIELTPISLYWRPVYTPNYLVSPDTLKGLAGEKFPYTAFSNNCYNFCCWVLELNDT
WLNRRCISRTTGFFKPYQSWNRKPLPTVDDGKIKKVANAILCALGSLFSKPIKDLLGK
LKPLNLLHLLASCDWTFAGIVETVILMAELFNVFWTPPDVSNFIASLIGDFELQGPED
LAMELVPVVMGGIGMVLGFTAEKIGRMLSSAASTLRACKDLGNYALDILKLVMKWFFP
KKEEKAEMETLRAIEDAVLDMEAIGNNHLTTLLKDKDSLTAFMKTLDLEEEKARKLST
KSSSPDIVGTINAILARIAAARSLLHKAKEEMFNRIRPVVVMISGRPGIGKTHMARHL
AKSIANTMSGDQRVGLVPRNGVDHWDAYRGERIVLWDDYGMGSPVKDALTLQELADTC
PVTLNCDRIENKGKMFDSDVIIITTNLVNPAPLDYVNFEACSRRVDFLVYAEAPEIEK
VKRDFPGQPDMWKDHFKPDFSHIKLTLAPQGGFDKNGNTPHGKGTMRSLTQGSLTARV
AGLVHERRDEFQLQGNDLQTYNFDTNRVSAFRKLAADNKYGIMETMRVGATLKNVKTL
EDLKIALRDVKFNECEIIYKNSKYRVSSNGKGSVSVDKVKDNASQTVNEVQSAILRLR
QARARYYISCFQDLVYTLMQVAGASFVVNRISRRFCWERWVKPAETQEVNESEKEVAQ
GRWEIEPKDTEPEGKKGKNKKGRGKKHTAFSSKGLSDEEYDEFKRIREERNGKYSIEE
YLQDRDRYYEEVAVARATEEDFCEEEEAKIRQRIFRPTKKQRKEERGVLGLVTGSDIR
KRRPDDFQPKGNLWADDTRSVDYNERLDFEAPPSVWSRIVPLGTGWGFWVSSNLLITT
THVLPKGVKELFGVEIKQIQVHKSGEFCRFRFPRPIRPDVTGLVLEEGAPEGTVCSIL
IKRPTGEMIPLAVRMGTHASMKIQGRTVGGQMGMLLTGANAKNMDLGTGPGDCGCPYI
YKRGNDIVVAGVHTAAARGGNTVICATQGQDGEAVLEGNEDLGTYCGAPILGPGKAPK
LSTKTKFWRSSPDALPPGTYEPAYLGGKDPRVEKGPSLQQVMRDQLRPFTEPRGKPPR
PAVLEEAKKTVMNVLEQTIDPAKPWSYSQACASLDKTTSSGSPHHVKKNDHWNGETFT
GPLADQASKANLMYEQAKHVQPVYTAALKDELVKTDKIYKKIKKRLLWGSDLGTMIRC
ARAFGGLMDSMKASCIALPCRVGMNMNEDGPIIFDKHSKYRYHYDADYSRWDSTQQRN
ILSAAMEVMVRFSAEPELAQVVAEDLVAPSQLDVGDFVISVQEGLPSGVPCTSQWNSI
AHWILTLSAMAEVSGLSPDVVQAHSCFSFYGDDEIVSTDINLDPMKLTQKLREYGLVP
TRPDKTEGPLVITEDLTGLTFLRRSIARDPAGWFGKLDQDSILRQLYWTRGPNHENPY
ESMVPHSQRATQLMALLGEASLHGPQFYKKVSKMVINEIKSGGLEFYVPRQEAMFRWM
RFSDLSTWEGDRNLAPEGVNEDGVE"
CDS 5065..6687
/codon_start=1
/product="ORF2"
/protein_id="ATN23641.1"
/translation="MKMASNDAAPSNDGAAGLVPEINNEVMPLEPVAGASLATPVAGQ
HNIIDPWIRNNFVQAPAGEFTVSPRNSPGEILLDLELGPELNPYLAHLARMYNGHAGG
MEVQIVLAGNAFTAGKIIFAAIPPGFPYENLSPSQITMCPHVIIDVRQLEPVLLPMPD
IRNNFFHYNQSNDPKLRLLAMLYTPLRANNSGDDVFTVSCRVLTKPSPDFEFTFLVPP
TVESKTKQFTLPILKISEMTNSRFPVPVEMMYTARNENQVVQPQNGRVTLDGELLGTT
PLLAVNICKFKGEVIAKNGDVRSYRMDMEITNTDGTPIDPTEDTPGPIGSPDFQGILF
GVASQRNKNEQNPATRAHEANINTGGDQYAPKLAQVKFFSESQDFEVHQPTVFTPVGV
VGDSSHPFRQWVLPRYGGHLTNNTHLAPAVAPLFPGEQILFFRSQIPSSGGHESGYVD
CLVPQEWVQHFYQEAATAQSEVALIRFINPDTGRVLFEAKLHKQGFITVAHTGDNPIV
MPPNGYFRFEAWVNQFYSLAPVGTGNGRRRIQ"
CDS 6687..7460
/codon_start=1
/product="ORF3"
/protein_id="ATN23642.1"
/translation="MASAFFANLAGGVASNGISSLINAGANAINQKVEFDYNKQLQNA
SFSHDKEMLQAQIEATKRLQQEMIDIKQGVLTAAGFSPTDAARGSVGTPMTKLVDWSG
TRYWAPGAMRTTGYSGTFTHLPPVQSASYVNNQNRQPPKVDPSPPSSSGSSVSSVKTQ
STTLSGTSRVGSSSHLTLSTRPSTRTSDWVRSQNERLSPFMNGALQTTYVTPPSSRAS
SVSTVSTVPKEVLDSWTPMFNTHRQPLFAHLRRRGESQI"
ORIGIN
1 cgtctaacga cgctactgct gcctttggca gtcaaaactc tgtcaatgac agtgacaacg
61 ccaccccttc taataaagaa gaggttggtg cattctccaa catcaaagtt ggattcaaga
121 aaatgctggg tgccgttccc aagggcacca aagcacccag cagtggtcaa cattgcccca
181 cagttaaggt tgggcctaaa acattaacaa tcccccctga gcccccaaat ggtgaagaca
241 ccgtacagtt caatgcaaag tcagaaacta tagttgggtt gccggacttg acaacggtgc
301 aaaatgaaca tgaaaacacc ccatacactg tccctccatt aagtgagagg gagcacaggc
361 cggccaccga accacttcct ggcacaatat tagagatgtg ggatggtgag ttttaccatt
421 attccgtgta cgtcagcgac ggcagagctc tgggagtcca caaaccaccg gcggctataa
481 gcctcgcgac gatagagctc acccccatat cactttactg gaggcccgtt tataccccca
541 attacttggt ctccccggac acattaaaag gtctcgctgg tgagaagttc ccctatacgg
601 ccttcagtaa caactgttat aacttctgtt gctgggtgct tgagctcaac gacacgtggc
661 ttaacagaag atgcatttcc agaaccaccg gcttcttcaa gccataccag tcttggaaca
721 gaaaacctct cccaaccgtt gatgatggaa agattaagaa agtggccaat gcaatcctct
781 gtgcactcgg ctcactgttc tcaaaaccaa tcaaagacct gttaggcaaa ctcaagccat
841 tgaatctact gcacttgctt gcgtcttgtg attggacgtt tgcgggtata gtggagacag
901 tcatcttgat ggcggagctt ttcaatgtct tctggacccc cccagatgtc tctaatttta
961 tagcctccct aataggtgat tttgaattgc aagggcctga ggacctggcc atggagctcg
1021 tccccgtggt catgggcggc atagggatgg ttctcggttt taccgccgag aagataggcc
1081 gcatgctgtc gtccgctgca tcaacactgc gggcgtgcaa agacctaggg aactatgccc
1141 ttgacatact caaattggtc atgaagtggt tcttcccgaa gaaggaagag aaagctgaga
1201 tggaaacctt gagggcgatt gaggatgccg tcctggatat ggaagccata gggaacaacc
1261 acctcacaac ccttcttaag gacaaagata gcctcacggc tttcatgaag accctggatc
1321 tggaagagga gaaggcaagg aaactgtcca ctaaatcatc ttcaccggac atagtcggca
1381 ccatcaatgc catactagct aggatagctg ctgctagatc ccttctacat aaggccaaag
1441 aggagatgtt caacaggatc aggccagtgg ttgttatgat atcaggcagg cctggcattg
1501 gaaaaaccca catggcaaga catttggcta agagcatcgc caacaccatg agtggcgacc
1561 aaagagtcgg gctcgttccg cgcaacggcg tcgatcactg ggatgcctac aggggagaga
1621 ggatagtctt gtgggatgac tacggcatgg ggagccctgt taaggacgct ctaacactgc
1681 aagagctggc cgacacatgc ccagtcactt taaattgtga caggattgag aataagggga
1741 agatgtttga cagtgatgtc atcataatca cgaccaacct agtcaacccc gcgcccctcg
1801 actatgtgaa cttcgaggcg tgttctagga gagttgactt cctggtctat gcagaggcac
1861 cagaaattga aaaggtcaag agagacttcc ctggccagcc tgacatgtgg aaagaccatt
1921 ttaaaccaga cttctcccac atcaagctga ctctagcccc ccagggtggg tttgacaaaa
1981 atggcaacac cccacacggt aagggaacca tgcggtccct aacccagggg tccctgactg
2041 cgagagttgc aggccttgtc catgagagga gagatgaatt ccagctccaa ggaaatgacc
2101 tccaaacata caactttgac accaacagag tctccgcatt caggaaattg gctgcagata
2161 acaagtatgg gatcatggag acgatgagag tgggtgcgac actcaagaat gtgaagaccc
2221 tggaagatct taaaattgca ttgagggatg taaaattcaa tgagtgtgaa ataatctaca
2281 agaactctaa gtatcgagtc tcttccaacg gtaaaggctc agtttctgtt gacaaagtta
2341 aagacaatgc atcccagact gtaaacgagg tacaatccgc aattctcagg ctcaggcaag
2401 cgagggccag atattacatc agctgcttcc aagacctcgt ctatactctc atgcaggttg
2461 ccggagcatc attcgtagtc aacaggatct ccagaaggtt ctgctgggaa aggtgggtca
2521 aaccggccga gacccaggag gtgaatgagt ccgaaaagga agtggcacaa ggcagatggg
2581 aaattgagcc caaggataca gaaccagaag gcaagaaagg taagaacaag aaaggaagag
2641 gtaagaaaca cacagctttc tctagcaaag gcctgagtga tgaagagtat gacgagttca
2701 agagaattag ggaagaaagg aacggaaagt actccattga ggaatacctg caagaccggg
2761 accgctacta tgaagaagtg gcagttgccc gggcgacaga ggaggacttc tgtgaagagg
2821 aagaggccaa gataagacaa aggattttcc gcccgacaaa gaaacagagg aaggaggaga
2881 ggggtgtgct tggcttagtc accggctcag acatcaggaa gaggagacca gatgacttcc
2941 aaccaaaagg caacctgtgg gcagatgaca ccagaagtgt ggactacaat gagaggcttg
3001 attttgaagc gcccccgagt gtttggtcaa gaatagttcc attaggcact ggttggggat
3061 tctgggtttc atccaacctt ctgatcacaa caacacacgt cctgcctaaa ggggttaagg
3121 agctctttgg agttgaaatc aaacaaatcc aagttcacaa gtctggagag ttttgcaggt
3181 tcagattccc aagacctatc aggccagatg tcacaggact cgtgttggag gaaggcgccc
3241 cagaaggcac tgtctgttct atactcataa aaaggcccac aggtgagatg atccccttag
3301 cagtgaggat gggcacacat gcatccatga aaatacaggg cagaaccgtt ggtggccaga
3361 tgggaatgct tctcacagga gcgaacgcga agaacatgga cctcggcact ggtcctggtg
3421 actgcggttg cccttacatc tacaaacgtg gcaacgacat tgttgtcgcg ggtgttcaca
3481 ccgcagcagc ccgaggaggc aacactgtta tatgtgccac ccaagggcaa gatggggaag
3541 cagtccttga gggaaatgag gaccttggca cctattgtgg cgccccaatt ctgggccctg
3601 gcaaggcgcc taaactcagc acgaagacta agttctggcg ttcatcacca gatgccttgc
3661 cacctggcac atatgagcct gcttacctag gaggcaaaga ccctagagtg gaaaaaggtc
3721 cttcccttca acaagtcatg agggaccagt tgagaccctt cacagaaccc aggggcaaac
3781 cacctagacc tgcagtcttg gaggaagcca aaaagacagt gatgaatgtt ctagaacaaa
3841 ccattgaccc cgccaagcca tggtcctatt cgcaggcgtg tgcctcattg gacaaaacca
3901 cctccagtgg tagtccccat catgttaaga aaaatgacca ctggaatggg gagaccttca
3961 ctggtccact tgcagatcag gcatctaaag ccaatctcat gtatgagcag gctaaacatg
4021 tgcagcccgt gtatacggcc gcgctcaaag atgagcttgt taagactgac aagatctaca
4081 agaaaataaa gaagaggctc ctatgggggt cggaccttgg cacaatgatc aggtgcgcca
4141 gggcctttgg tggtctcatg gacagcatga aggcaagttg tatagctctt ccttgcaggg
4201 tagggatgaa catgaatgaa gatggcccta ttatatttga caaacattct aagtacaggt
4261 accactatga tgctgactat tctaggtggg actcaaccca acaaaggaac attctttctg
4321 ccgctatgga agtgatggtg cggttctctg ctgaaccaga attggcacaa gtggttgcag
4381 aggaccttgt agcacctagc cagcttgatg ttggcgattt tgtcatctca gtccaggagg
4441 gtctgccatc aggagtccca tgcacatcac aatggaattc aatagcacac tggatcctaa
4501 ctttgagtgc aatggcagaa gtgtcaggtc tctcaccaga tgttgtccaa gcccactctt
4561 gtttttcctt ttatggggac gatgagatcg tcagtactga catcaatctt gaccccatga
4621 agttgacaca gaaactcagg gagtatggtc tggttcccac ccggcctgat aaaactgaag
4681 gtcccctcgt cataactgaa gacctcaccg gcctgacgtt cctccgtagg tcgattgctc
4741 gggacccagc tggttggttt ggaaagctgg accaagactc aatccttagg cagctgtact
4801 ggacaagggg gcctaaccat gagaacccgt acgagagcat ggttcctcat tctcagcggg
4861 ccacacaact catggccctt cttggtgagg cctcactaca tggcccccag ttttataaga
4921 aagttagcaa gatggtcatc aatgagatta agagtggtgg tctggagttt tatgtgccca
4981 gacaagaggc catgttcagg tggatgagat tctctgacct cagcacatgg gagggcgatc
5041 gcaatcttgc tcccgaaggt gtgaatgaag atggcgtcga atgacgcagc tccatctaat
5101 gatggtgcag caggcctcgt accagagatc aacaatgagg tcatgcccct tgagcccgta
5161 gctggtgcat cgctggcgac accagttgcc gggcaacaca atataattga tccctggata
5221 agaaataatt ttgtacaagc ccctgcaggt gagtttacag tttcccctag aaattcccct
5281 ggtgaaattt tgctcgattt ggagttggga ccagaactaa acccctatct cgctcatctg
5341 gcccgtatgt ataatgggca cgctggtggc atggaagtgc aaattgtgtt ggctgggaat
5401 gcgttcacag ctggcaagat catatttgct gccatccctc cagggttccc atatgaaaac
5461 ttgtcacctt cacaaatcac aatgtgccct catgttataa ttgatgttag acaactagaa
5521 ccagttctat tacctatgcc agatattaga aacaacttct tccattacaa tcagagcaat
5581 gacccaaaat tgagattgtt agctatgctc tacacccctt taagggctaa taattctggt
5641 gatgatgtgt ttacagtttc ttgtagggtc ctcactaaac cgtcacctga ttttgaattc
5701 acattcttgg tcccccctac ggttgaatct aaaaccaaac agttcacact gcccatcctc
5761 aaaatatcag agatgaccaa ctcaagattc ccagtgccag tggaaatgat gtacacagcc
5821 aggaatgaga accaagttgt ccagccacag aatggtaggg tcacacttga tggcgagcta
5881 ttaggcacca cacccttgtt ggctgtcaac atctgcaaat tcaaggggga ggttatagct
5941 aagaatggag atgtgaggtc ctataggatg gacatggaaa ttaccaacac tgatggcacc
6001 ccaattgacc ccacagaaga tacacctggt cccattggtt cacctgactt tcaaggtata
6061 ctctttggcg ttgccagcca acgcaacaag aatgagcaaa acccagccac gagagcccat
6121 gaagccaaca ttaacactgg tggagaccaa tacgccccca aattggccca agtgaaattc
6181 ttctcagagt cccaggattt cgaggtgcac cagcccacag ttttcacccc agttggtgtg
6241 gtaggcgact cctcccatcc tttcagacag tgggtcctgc cccgatacgg tggacatctc
6301 accaacaaca cccacctggc tccagcagtg gcccccctat tcccaggtga gcagattcta
6361 ttctttagat cacaaatacc cagctcaggc ggccatgaat cgggttacgt ggactgcctt
6421 gtcccccaag aatgggtcca acacttctat caagaagctg ccacagctca gtctgaggtg
6481 gcactcataa ggttcatcaa cccagacact ggcagagtcc tctttgaggc caagctgcac
6541 aagcaaggct ttataactgt ggctcacact ggtgataacc caattgtcat gccaccaaat
6601 gggtacttta gatttgaagc ttgggttaat cagttttact cactcgcccc cgtgggaact
6661 gggaatgggc gcaggaggat ccaataatgg ccagtgcttt ctttgcaaat ttggcaggag
6721 gcgttgcctc caatggaatt agttcactca taaatgctgg ggctaatgct attaaccaaa
6781 aagttgagtt tgattataat aaacaactcc aaaatgcatc cttctcccat gataaggaaa
6841 tgctccaagc ccaaattgaa gccaccaaac gtctgcaaca agagatgatt gacataaaac
6901 aaggggtgct gacagctgcg ggattctctc ctacggatgc cgcgaggggt tctgtcggca
6961 caccaatgac aaaattagtt gattggagtg gcactagata ttgggcgcct ggtgccatga
7021 ggacaacagg ctattcaggg acttttactc acttgccccc tgtgcagtct gcttcatatg
7081 ttaataatca gaatagacaa cctcctaaag tagatccctc tcctccttct tcgagtggtt
7141 cttctgtttc ttctgtcaaa acacaatcga ctaccctctc aggcacttca agggtgggct
7201 cctcatccca tttaaccctg tcgaccaggc cgagcacaag gacatctgat tgggtgcgca
7261 gccagaatga aaggttgagt cccttcatga atggagcgtt gcaaacaaca tatgtaacgc
7321 caccatccag tagggcgtca agtgtcagca cagtctcgac cgtgccgaaa gaggttttgg
7381 actcctggac gcctatgttt aacactcaca ggcagccact cttcgcccat ctgcgtaggc
7441 gaggggagtc acagatttag tgaaaagatt ggttaggaaa gttgattagt ttgctcttct
7501 tttccactat tcctttaatt ctttc
//