Typing tool
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Typing tool
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Complete norovirus genomes
| MF140680 | GII.6 | |
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| GII.P7 |
ORF1: 1..5063
ORF2: 5044..6696
ORF3: 6696..7472
LOCUS MF140680 7489 bp RNA linear VRL 24-OCT-2017
DEFINITION Norovirus GII strain
Norovirus/GII/Hu/NL/2014/GII.P7-GII.6/Rotterdam/E1300315_p5_d441
ORF1 gene, partial cds; and ORF2 and ORF3 genes, complete cds.
ACCESSION MF140680
VERSION MF140680.1
KEYWORDS .
SOURCE Norovirus GII
ORGANISM Norovirus GII
Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes;
Picornavirales; Caliciviridae; Norovirus; Norwalk virus.
REFERENCE 1 (bases 1 to 7489)
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 7489)
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..7489
/organism="Norovirus GII"
/mol_type="genomic RNA"
/strain="Norovirus/GII/Hu/NL/2014/GII.P7-
GII.6/Rotterdam/E1300315_p5_d441"
/host="Homo sapiens"
/db_xref="taxon:122929"
/country="Netherlands"
/collection_date="06-Aug-2014"
/note="genotype: GII.P7-GII.6"
CDS <1..5063
/codon_start=3
/product="ORF1"
/protein_id="ATN23736.1"
/translation="FGSQKSANDSTNTTPSNKEEAGAFSNIKVGFKKMLGAVPKGTKT
PSSAQHCPTVKIGDKTLTVPPEPPNGEDVVQYDAKSETVHGLPDLTTVQNEHENTPYS
VPPLSEREHRPATEPLPGTILEMWDGEFYHYSVYVSGGKALGVHKPPAAISLATIELT
PISLYWRPVYTPSYLVCPDTLKGLAGEKFPYTAFSNNCYNFCCWVLELNDTWLSRRSI
SRTTGFFKPYQSWNRKPLPTVDDGKIKKVANAILCALGSLFSKPIKDLLGKLKPLNLL
HLLASCDWTFAGVVETVILMAELFNIFWTPPDVSNFISSLVGDFELQGPEDLAVELVP
VVMGGVGMVLGFTAEKIGRMLSSAASTLRACKDLGNYALDILKLVMKWFFPKKEEKAE
METLRAIEDAVLDMEAIGNNHLTTLLKDKDSLSAYMKTLDLEEEKARKLSTKSSSPDI
VGTINAILARIAAARSLLHKAKEEMFSRARPVVVMISGKPGIGKTYMARHLAKGVANT
MSGDQRVGLVPRNGVDHWDAYRGERVVLWDDYGMGNPIKDALTLQELADTCPVTLNCD
RIENKGKMFDSDVIVITTNLVNPAPLDYVNFEACSRRIDFLVYAESPEIEKVKRDFPG
QPDMWKDHFKSDFSHIKLTLAPQGGFDKNGNTPHGRGTMRSLTQGSLIARVAGLVHER
KDEFQLQGGDLQTYNFDTNRVSAFRRLAADNKYGIMETMRVGAALKNVKTLEDLKVAL
RDVKFNECQIIYKSSKYRISSNGKGCVTIDKVGDQVSQTASEVGSAILRLRQARARYY
VSCFQDLIYTLMQVAGASFVVSRISKRFCWERWVKPTETQETNESEKEVVQGGWEIEP
KDTEPEGKKGKNKKGRGKKHTAFSSKGLSDEEYDEYKRIREERNGKYSIEEYLQDRDR
YYEEVAVARATEEDFCEEEEAKIRQRIFRPTKKQRKEERGVLGLVTGSDIRKRRPDDF
QPKGKLWADDSRSVDYNERLDFEAPPSVWSRIVPLGTGWGFWVSSNLLITTTHVLPKG
IKELFGVELKQIQIHKSGEFCRFRFPRPIRPDVTGLVLEEGAPEGTVCSILVKRPTGE
MIPLAVRMGTHASMKIQGRTVGGQMGMLLTGANAKNMDLGTGPGDCGCPYIYKRGNDI
VVAGVHTAAARGGNTVICATQGQDGEAVLEGNEDLGTYCGAPILGPGKAPKLSAKTKF
WRSSPDALPPGTYEPAYLGGKDPRVEKGPSLQQVMRDQLKPFTEPRGKPPRPAILEEA
KKTVMNVLEQTIDPAKPWTYSQACASLDKTTSSGSPHHVRKNDHWNGESFTGPLADQA
SKANLMYEQAKHVQPVYTAALKDELVKTDKIYKKIKKRLLWGSDLGTMIRCARAFGGL
MDSMKASCIALPCRVGMNVNEDGPIIFDKHSKYRYHYDADYSRWDSTQQRCILSAAME
VMVRFSAEPELAQVVAEDLLAPSQLDVGDFVISVQEGLPSGVPCTSQWNSIAHWILTL
SAMAEVSGLSPDVVQAHSCFSFYGDDEIVSTDINLDPMKLTQKLREYGLVPTRPDKTE
GPLVITEDLTGLTFLRRSIVRDPAGWFGKLDQDSILRQLYWTRGPNHENPYESMVPHN
QRATQLMALLGEAALHGPQFYKKVSKMVINEIKSGGLEFYVPRHEAMFRWMRFSDLST
WEGDRNLAPEGVNEDGVE"
CDS 5044..6696
/codon_start=1
/product="ORF2"
/protein_id="ATN23737.1"
/translation="MKMASNDAAPSNDGAANLVPEVNNEVMALEPVAGASIAAPVVGQ
QNIIDPWIRENFVQAPQGEFTVSSRNTTGEVLLNLELGPELNPYLRHLSRMYNGYAGG
MQVQVILAGNAFAAGKIIFAAVPPHFPVENISAAQITMFPHVVIDVRQLEPVLLPLPD
IRNRFFHYNQENTSRMRLVAMLYTPLRANSGEDMFTVSCRVLTRPAPDFEFTFLVPPT
VESKTKPFTLPILTLGELSNSRFPAPIDMLYINPSETIVVRSQNGRCLLDGTLQGTTQ
LAPTQICSFRGTLVRQESRSADSVDSVDSARRTMNHPLYVQLRNLDGTSYDPTDEVPA
VLGAIDFKGTVYGVASQRDTKGSVGATRAHEVTINTRDAKYSPKLGSVLMHSESTDFF
SDQPIRFTPIGMGEENDWSQWDLPDYSGALTLNMHLAPAVAPAFPGERILFFRSVVPA
AGGYGKGEIDCLIPQEWIQHFYQEAAPTQSAVALIRYVNPDTGRSLFEAKLHREGFIT
VASSGDNPIVVPSNGYFRFEAWVNQFYTLTPMGAGQGRKRAQ"
CDS 6696..7472
/codon_start=1
/product="ORF3"
/protein_id="ATN23738.1"
/translation="MAGAFLAGLAGDAITNGVGSLINAGANAINQKVEYDFNKQLQLA
SFQHDKEMLQSQVLATKQLQQEMMNIKQGVLTAGGFSPTDAARGAVNAPMTKILDWNG
TRYFAPNSMKTTSYSGQLSSNPVHKQSTLPRPSPSKTNVSSGSSSVYSSLSSASSQST
HSTVLTAGSGSSRTAPSSSTASTLSRTSDWVRGQNERLSPFMNGALQTTFVTPPSSRA
SSYGSVSTVPKAVLDSWTPMFNTNRQPLFAHIRRRGESQI"
ORIGIN
1 ccttcggcag tcaaaaatct gccaatgaca gtactaacac caccccttct aataaagaag
61 aggctggtgc attctccaac attaaagttg gttttaagaa gatgctgggt gccgttccca
121 aggggaccaa aacacccagt agtgctcagc actgccccac agtcaagatc ggggacaaaa
181 cattaacagt tccacccgag cccccaaatg gtgaggacgt tgtgcagtat gatgcgaagt
241 cagaaactgt gcatggacta ccagacttga cgacggtgca aaatgagcac gaaaacacac
301 cgtactctgt ccccccattg agtgaaagag aacacagacc agccactgaa ccgcttcctg
361 gcacaatact ggagatgtgg gatggtgaat tttatcacta ctccgtgtat gtcagtggcg
421 gcaaagccct aggagttcac aaaccccctg cagcaataag cctcgcaact atagagctca
481 cgcccatatc tctttactgg aggcccgttt acacccccag ctacttagtc tgcccagaca
541 cgctgaaagg cctcgctggt gagaagtttc cctacacagc tttcagtaac aactgttaca
601 acttttgttg ctgggtgctt gagctcaacg acacgtggct tagcaggaga agcatctcca
661 gaaccaccgg tttcttcaaa ccataccaat cttggaacag gaaacccctt ccaaccgttg
721 atgatggaaa gattaagaag gtggccaacg caatcctctg tgcgcttgga tcactgtttt
781 caaaaccaat caaagaccta ttgggaaagc tcaaaccact aaacttgctg cacctgctcg
841 catcatgtga ttggacgttt gcgggtgtag tagagacagt catcctaatg gcggaacttt
901 tcaacatctt ttggacaccg ccagatgttt ccaacttcat atcctccctg gtgggcgact
961 ttgaactgca agggcctgag gacctggctg tggagcttgt ccccgtggtc atgggcggcg
1021 tagggatggt tctcggcttc actgctgaga agataggccg tatgctgtct tccgccgcat
1081 caacgctgcg agcatgcaaa gacctgggga attacgccct tgacatacta aagctggtta
1141 tgaagtggtt cttcccaaag aaagaagaga aggccgagat ggaaacttta agggcaattg
1201 aagacgccgt cctggacatg gaagctatag ggaacaatca tcttacaacc ctcctcaagg
1261 acaaggatag cctctcggcc tacatgaaga ctctggacct ggaagaagaa aaggcaagga
1321 agctgtccac caagtcatcc tcgccagaca ttgtcggcac tatcaatgcc atactggcca
1381 gaatagctgc tgccagatcc ctcctacaca aggctaaaga agaaatgttt agtagggcca
1441 ggcccgtggt tgttatgatc tcgggtaaac ctggcattgg caagacttac atggcaagac
1501 acctagctaa gggcgtcgcc aacaccatga gtggcgacca aagagttggg ctcgttccgc
1561 gcaacggggt cgaccattgg gacgcctaca ggggggagag ggtggtcttg tgggatgact
1621 atggcatggg gaaccccatc aaggatgctc taacactaca agaattggcc gacacttgtc
1681 cagtcactct aaactgtgat aggattgaaa acaaagggaa gatgttcgac agtgatgtca
1741 ttgtaatcac gaccaattta gtcaacccag cgcccctcga ttatgtaaac ttcgaggcgt
1801 gctccaggag gattgacttt ctggtctatg cagagtcacc agagattgag aaagttaaga
1861 gagacttccc tggccaacct gacatgtgga aagaccattt caaatcagac ttctcccaca
1921 taaagctgac tctggctccc cagggcggat tcgacaagaa tggcaacacc ccacatggta
1981 ggggcaccat gcgatccctg acccaggggt ccctgatcgc aagggtcgcg ggtcttgttc
2041 atgagaggaa agatgagttc cagctccaag ggggcgacct ccaaacatac aactttgaca
2101 ccaacagggt ctccgcattt aggagactag ccgcagacaa caaatatggg atcatggaaa
2161 caatgagagt gggtgcggcg cttaagaatg tcaagacctt ggaagatcta aaggttgccc
2221 tgagggatgt gaagttcaac gagtgtcaga taatttacaa gagctccaaa taccgaatct
2281 cttccaatgg caaaggttgt gtcactattg ataaagttgg ggatcaagtg tcccagactg
2341 caagtgaagt gggttcagca atccttagac tcaggcaggc aagggccaga tactatgtca
2401 gctgcttcca agatctcatc tacactttga tgcaggttgc tggagcatca ttcgttgtta
2461 gcagaatctc caagaggttc tgttgggaga ggtgggtcaa accaaccgag acccaggaaa
2521 cgaatgaatc cgagaaggaa gtagtccaag gtggatggga gattgaaccc aaggacacag
2581 aaccagaagg caagaagggc aagaacaaga aaggaagagg caagaaacac acggctttct
2641 ccagcaaagg cctgagtgat gaggagtatg acgagtacaa gagaatcagg gaagagagga
2701 acggaaaata ctccattgag gaatacctgc aagaccggga tcgctactat gaggaagtgg
2761 cagttgcccg ggcgacagag gaggactttt gtgaggaaga ggaggccaag ataagacaaa
2821 gaatcttccg ccccacaaag aaacagagga aggaagaaag gggggtgctt ggtttggtca
2881 ccggctcaga catcaggaag aggagaccag acgatttcca accaaagggc aaactgtggg
2941 cagacgactc cagaagtgtg gactacaacg agagacttga cttcgaggct cccccgagcg
3001 tctggtcgag aatagttcca ttgggcactg gatggggctt ctgggtttca tccaatctcc
3061 tgatcacaac aacacacgtc ctgcctaagg ggatcaagga actttttgga gttgaactca
3121 aacagatcca aattcataag tctggagaat tttgcaggtt caggttccca agaccaatta
3181 ggccagatgt cacagggctc gtgctggagg agggcgctcc agaaggcacc gtctgttcca
3241 tactcgtgaa gagacctaca ggtgaaatga tccccctagc agtgaggatg ggcacacatg
3301 cgtccatgaa gatacagggt aggaccgtcg gtggccagat gggaatgctt ctcacaggag
3361 caaacgcgaa gaacatggat cttggcaccg gtcctggtga ctgcggttgt ccttacatct
3421 acaaacgtgg caacgacata gttgtcgcgg gtgtccatac cgcagcagcc cgggggggca
3481 acactgtcat atgtgccacc cagggacaag atggggaggc agtccttgag ggaaatgagg
3541 accttggcac ttactgcggt gccccaattc tgggcccagg caaagcaccc aaactcagcg
3601 cgaagaccaa gttctggcgc tcatcaccag acgctttgcc accaggcacc tatgagcctg
3661 cctatctggg gggtaaggac cccagagtgg aaaaaggacc atctctacaa caagtcatga
3721 gggatcagct aaaacctttt acagaaccca ggggtaaacc tcctagacct gcaatcttag
3781 aagaagccaa aaagacagtt atgaatgttc tagaacaaac cattgaccct gctaaaccat
3841 ggacctattc ccaagcatgt gcttcactgg acaagaccac ttccagtggt agcccccacc
3901 atgtcaggaa aaatgaccac tggaatggag aatccttcac tggccccctt gcagaccaag
3961 catccaaagc caacctcatg tatgaacagg ccaaacatgt gcagcccgta tacacggccg
4021 cgctcaaaga cgagcttgtt aagactgata agatctacaa aaagataaag aagaggctct
4081 tgtgggggtc ggaccttggc acgatgatca ggtgcgccag ggcttttggt ggtctcatgg
4141 atagcatgaa ggcaagttgc atagccctcc catgtagagt ggggatgaac gtgaatgagg
4201 atggtcctat catatttgac aagcactcta agtacaggta ccactatgat gctgactatt
4261 ctagatggga ttccacccag caaaggtgca ttctctcggc cgctatggaa gtgatggtgc
4321 ggttttctgc cgagccagag ctggcgcaag tggttgcaga ggatctacta gcacccagcc
4381 aactagacgt tggcgatttt gtcatctcag tccaggaggg tctgccatca ggggtcccgt
4441 gcacatcaca gtggaactca atagcacatt ggatcctaac cttgagtgca atggcagaag
4501 tgtcaggtct ctcaccagat gttgtccaag cccactcttg tttttccttt tacggcgatg
4561 atgagatcgt cagcactgac atcaaccttg accccatgaa gttgacacag aaactcagag
4621 aatatggtct ggtccccacc cgacctgaca aaactgaagg tccccttgta atcactgaag
4681 acctcaccgg cctgacgttc ttgcgtaggt caattgtgag agatccagct gggtggtttg
4741 gaaaattgga ccaagactca atcctcaggc agttatactg gacaaggggc cccaatcatg
4801 agaatccata cgagagcatg gtccctcata accagcgggc aacacagctc atggcccttc
4861 taggtgaggc tgcactgcat ggccctcagt tttacaagaa agttagcaaa atggtcatca
4921 atgaaattaa aagtggtggt ctggaatttt atgtgcccag acatgaggcc atgttcagat
4981 ggatgagatt ctctgacctc agcacatggg agggcgatcg caatcttgct cccgaaggtg
5041 tgaatgaaga tggcgtcgaa tgacgctgct ccatcgaatg atggtgctgc caacctcgta
5101 ccagaggtca acaatgaggt tatggcactt gaaccggtgg cgggagcctc aattgcagct
5161 cctgtcgtcg gccaacaaaa tataattgac ccctggatta gagaaaattt tgttcaggca
5221 ccacagggtg agttcactgt ttcatcaagg aacacaaccg gtgaggtact tctgaatctt
5281 gaattaggcc ctgagctcaa cccttatctg agacatttgt cccgcatgta caacggttat
5341 gctggtggta tgcaggttca ggtgatccta gctgggaatg cgttcgcagc tggtaaaatc
5401 atctttgccg ccgtcccacc acatttccct gtagaaaata ttagtgcagc ccaaatcaca
5461 atgttccccc atgtagttat tgatgtaaga cagcttgagc cagtgctttt acccctccct
5521 gacataagga ataggttctt tcattacaat caggaaaaca cttctagaat gagacttgtg
5581 gctatgttgt acacacccct tagggcaaat tctggtgagg atatgtttac ggtgtcttgc
5641 agagtcctga cccgtccagc ccctgacttt gagttcacgt ttctggtgcc gccaactgta
5701 gaatcaaaga ctaagccctt tacactccca attctaactc ttggagaact atctaattct
5761 agattccctg ccccaataga catgctgtac ataaatccca gtgagacaat tgtggtgagg
5821 tcacaaaatg gccggtgtct tctggacgga acacttcaag ggaccaccca gctggcgccc
5881 acccaaattt gctccttcag gggcacgctg gttcgccagg agtcgaggtc tgcagattca
5941 gtagattcag tagactcagc tagacgaaca atgaaccatc ctctctacgt tcagctgagg
6001 aacctcgatg ggacatcata tgatccaaca gatgaggtgc cagcggttct gggtgccata
6061 gattttaaag gaactgtgta tggggtcgct agtcaaaggg acaccaaagg ctctgtagga
6121 gcgacccgcg cccatgaagt gacaataaac accagagatg ctaaatactc tccaaaactt
6181 ggctctgtgt tgatgcattc tgaatccact gatttcttca gtgaccagcc catccgcttt
6241 actcctattg gtatggggga ggaaaatgat tggagccaat gggatttgcc tgattattct
6301 ggtgccctca ccctcaacat gcacctagcc cccgcagttg cccctgcttt ccctggtgag
6361 cgcattctct tctttagatc agtggtgcca gctgctggtg gttatggaaa aggtgaaata
6421 gactgtctca tcccacagga atggattcag catttctacc aggaggccgc cccaacacaa
6481 tccgcggtgg cccttattag atatgttaat cctgacactg ggagaagcct ctttgaggca
6541 aagctacata gagaagggtt catcactgtg gcaagttctg gagacaaccc catagttgtg
6601 ccatcaaatg gctacttcag atttgaggct tgggttaatc aattctatac acttaccccc
6661 atgggagctg gacaggggcg caaaagagcc cagtaatggc aggagctttc ttagctggat
6721 tggcaggtga cgccataaca aatggtgtcg ggtccctgat caacgctggg gccaatgcaa
6781 tcaaccaaaa ggtagagtat gacttcaata aacaactcca attggcatcc tttcaacatg
6841 acaaagagat gttgcagtca caagttctgg ccactaaaca gctccaacag gagatgatga
6901 acataaagca aggggtcttg accgctggcg gcttttcccc tacagatgct gcaagaggcg
6961 ctgtgaacgc gccgatgaca aaaattctgg attggaatgg aacgaggtat tttgccccaa
7021 acagtatgaa gacaaccagt tattcaggcc agctctccag taaccctgta cataagcaat
7081 ccacactacc ccgtcccagc ccttcaaaaa ctaatgttag tagtggttct tctagtgtgt
7141 atagttcttt atcttctgct tcctcacaat caactcattc aacggttttg actgcgggat
7201 ccgggtcgtc taggacagct ccctcctcct caacagcttc caccttgtct agaactagtg
7261 attgggtaag aggacaaaat gagagactca gcccgtttat gaatggtgct ctccaaacaa
7321 cttttgtcac accaccatcg agcagggctt catcatatgg gtcggtctca accgtcccca
7381 aagctgtttt ggactcctgg actcctatgt tcaataccaa taggcagcct ctcttcgctc
7441 acattcgtag gcgaggggag tcacagattt agtgaaaaga ttgattagg
//