Typing tool
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Typing tool
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Complete norovirus genomes
| MF140676 | GII.6 | |
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| GII.P7 |
ORF1: 1..5063
ORF2: 5044..6687
ORF3: 6687..7463
LOCUS MF140676 7475 bp RNA linear VRL 24-OCT-2017
DEFINITION Norovirus GII strain
Norovirus/GII/Hu/NL/2013/GII.P7-GII.6/Rotterdam/E1300311_p5_d0 ORF1
gene, partial cds; and ORF2 and ORF3 genes, complete cds.
ACCESSION MF140676
VERSION MF140676.1
KEYWORDS .
SOURCE Norovirus GII
ORGANISM Norovirus GII
Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes;
Picornavirales; Caliciviridae; Norovirus; Norwalk virus.
REFERENCE 1 (bases 1 to 7475)
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 7475)
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..7475
/organism="Norovirus GII"
/mol_type="genomic RNA"
/strain="Norovirus/GII/Hu/NL/2013/GII.P7-
GII.6/Rotterdam/E1300311_p5_d0"
/host="Homo sapiens"
/db_xref="taxon:122929"
/country="Netherlands"
/collection_date="22-May-2013"
/note="genotype: GII.P7-GII.6"
CDS <1..5063
/codon_start=3
/product="ORF1"
/protein_id="ATN23724.1"
/translation="FGSQKSANDSTNTTPSNKEEAGAFSNIKVGFKKMLGAVPKGTKT
PSSAQHCPTVKIGDKTLTVPPEPPNGEDVVQYDAKSETVHGLPDLTTVQNEHENTPYS
VPPLSEREHRPATEPLPGTILEMWDGEFYHYSVYVSGGKALGVHKPPAAISLATIELT
PISLYWRPVYTPSYLVCPDTLKGLAGEKFPYTAFSNNCYNFCCWVLELNDTWLSRRSI
SRTTGFFKPYQSWNRKPLPTVDDGKIKKVANAILCALGSLFSKPIKDLLGKLKPLNLL
HLLASCDWTFAGVVETVILMAELFNVFWTPPDVSNFISSLVGDFELQGPEDLAVELVP
VVMGGVGMVLGFTAEKIGRMLSSAASTLRACKDLGNYALDILKLVMKWFFPKKEEKAE
METLRAIEDAVLDMEAIGNNHLTTLLKDKDSLSAYMKTLDLEEEKARKLSTKSSSPDI
VGTINAILARIAAARSLLHKAKEEMFSRARPVVVMISGKPGIGKTYMARHLAKGVANT
MSGDQRVGLVPRNGVDHWDAYRGERVVLWDDYGMGNPIKDALTLQELADTCPVTLNCD
RIENKGKMFDSDVIVITTNLVNPAPLDYVNFEACSRRIDFLVYAESPEIEKVKRDFPG
QPDMWKDHFKSDFSHIKLTLAPQGGFDKNGNTPHGRGTMRSLTQGSLIARVAGLVHER
KDEFQLQGNDLQTYNFDTNRVSAFRRLAADNKYGIMETMRVGAALKNVKTLEDLKVAL
RDVKFNECQIIYKSSKYRISSNGKGSVSIDKVGDQVSQTASEVGSAILRLRQARARYY
VSCFQDLIYTLIQVAGASFVVSRISKRFCWERWVKPTETQETNESEKEVVQGGWEIEP
KDTEPEGKKGKNKKGRGKKHTAFSSKGLSDEEYDEYKRIREERNGKYSIEEYLQDRDR
YYEEVAVARATEEDFCEEEEAKIRQRIFRPTKKQRKEERGVLGLVTGSDIRKRRPDDF
QPKGKLWADDSRSVDYNERLDFEAPPSVWSRIVPLGTGWGFWVSSNLLITTTHVLPKG
IKELFGVELKQIQIHKSGEFCRFRFPRPIRPDVTGLVLEEGAPEGTVCSILVKRPTGE
MIPLAVRMGTHASMKIQGRTVGGQMGMLLTGANAKNMDLGTGPGDCGCPYIYKRGNDI
VVAGVHTAAARGGNTVICATQGQDGEAVLEGNEDLGTYCGAPILGPGKAPKLSAKTKF
WRSSPDALPPGTYEPAYLGGKDPRVEKGPSLQQVMRDQLKPFTEPRGKPPRPAILEEA
KKTVMNVLEQTIDPAKPWTYSQACASLDKTTSSGSPHHVRKNDHWNGESFTGPLADQA
SKANLMYEQAKHVQPVYTAALKDELVKTDKIYKKIKKRLLWGSDLGTMIRCARAFGGL
MDSMKASCIALPCRVGMNVNEDGPIIFDKHSKYRYHYDADYSRWDSTQQRCILSAAME
VMVRFSAEPELAQVVAEDLLAPSQLDVGDFVISVQEGLPSGVPCTSQWNSIAHWILTL
SAMAEVSGLSPDVVQAHSCFSFYGDDEIVSTDINLDPMKLTQKLREYGLVPTRPDKTE
GPLVITEDLTGLTFLRRSIVRDPAGWFGKLDQDSILRQLYWTRGPNHENPYESMVPHN
QRATQLMALLGEAALHGPQFYKKVSKMVINEIKSGGLEFYVPRHEAMFRWMRFSDLST
WEGDRNLAPEGVNEDGVE"
CDS 5044..6687
/codon_start=1
/product="ORF2"
/protein_id="ATN23725.1"
/translation="MKMASNDAAPSNDGAANLVPEVNNEVMALEPVAGASIAAPVVGQ
QNIIDPWIRENFVQAPQGEFTVSSRNTTGEVLLNLELGPELNPYLRHLSRMYNGYAGG
MQVQVILAGNAFAAGKIIFAAVPPHFPVENISAAQITMFPHVVIDVRQLEPVLLPLPD
IRNRFFHYNQENTSRMRLVAMLYTPLRANSGEDMFTVSCRVLTRPAPDFEFTFLVPPT
VESKTKPFTLPILTLGELSNSRFPAPIDMLYINPSETIVVRSQNGRCLLDGTLQGTTQ
LAPTQICSFRGTLVRQESRSADSVDSARRAMNHPLYVQLRNLDGTSYDPTDEVPAVLG
AIDFKGTVFGIASQRDTKGSVGATRAHEVTINTRDAKYSPKLGSVLMYSESTDFTSDQ
PIRFTPIGMGEENDWDQWDLPDYSGSLTLNMHLAPAVAPAFPGERILFFRSIVPAAGG
YGKGEIDCLIPQEWIQHFYQEAAPIQSAVALIRYVNPDTGRNLFEAKLHREGFITVAS
SGDNPIVVPSNGYFRFEAWVNQFYTLTPMGAGQGRKRAQ"
CDS 6687..7463
/codon_start=1
/product="ORF3"
/protein_id="ATN23726.1"
/translation="MAGAFLAGLAGDAITNGVGSLINAGANAINQKVEYDFNKQLQLA
SFQHDKEMLQSQVLATKQLQQEMMNIRQGVLTAGGFSPTDAARGAVNAPMTKILDWNG
TRYFAPNSMKTTSYSGQLPSSPVHKQSTLPRPSPSKTNVSSDSASVYSSASSALSQST
HSTVLTAGSGSSRTPSSSSTASTLSRTSDWVRGQNERLSPFMNGALQTTFVTPPSSRA
SSYGSVSTVPKAVLDSWTPMFNTHRQPLFTHIRRRGESQI"
ORIGIN
1 ccttcggcag ccaaaaatct 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 gaatgagcac gaaaacacac
301 cgtactctgt ccccccattg agtgaaagag aacacagacc agccactgaa ccacttcctg
361 gcacaatact ggagatgtgg gatggtgaat tttatcacta ctctgtgtat gtcagtggcg
421 gcaaagccct aggagttcac aaaccccctg cagcaataag cctcgcaact atagagctca
481 cgcccatatc tctctactgg aggcccgttt acacccccag ctacttagtc tgcccagaca
541 cgctgaaagg cctcgctggt gagaagtttc cctacacagc tttcagtaac aactgttaca
601 acttttgttg ctgggtgctt gagctcaacg acacgtggct tagcaggaga agcatctcca
661 ggaccaccgg tttcttcaaa ccataccagt cttggaacag gaaacccctt ccaaccgttg
721 atgatggaaa gatcaagaag gtggccaacg caatcctctg tgcgcttgga tcactgtttt
781 caaaaccaat caaagaccta ttgggcaagc tcaaaccact aaacttgctg cacctgctcg
841 catcatgtga ttggacgttt gcgggtgtag tagagacagt catcctaatg gcggaacttt
901 tcaacgtctt 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 aggacgccgt 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 tgttatgatt tcgggtaaac ctggcattgg caaaacttac atggcaagac
1501 acctagctaa gggcgtcgcc aacaccatga gtggcgacca aagagttggg ctcgttccgc
1561 gtaacggggt cgaccattgg gacgcctaca ggggggagag ggtggtcttg tgggatgact
1621 atggcatggg gaaccctatc aaggatgctc taacactaca agaactggcc 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 ggaacgacct ccaaacatac aactttgaca
2101 ccaacagggt ctccgcattt aggagactag ccgcagacaa caagtatggg atcatggaaa
2161 caatgagagt gggtgcggcg cttaagaatg tcaagacctt ggaagatcta aaggttgccc
2221 tgagggatgt gaagttcaac gagtgtcaga taatttacaa gagctccaaa tatcgaatct
2281 cttccaatgg caaaggttct gtctctattg ataaggttgg ggatcaggtg tcccagactg
2341 caagtgaagt gggttcagca atccttagac tcaggcaggc aagggccaga tactatgtca
2401 gctgcttcca agatctcatc tacactttga tacaggttgc cggagcatca ttcgttgtta
2461 gcagaatctc caagaggttc tgttgggaga ggtgggtcaa accaaccgag acccaggaaa
2521 cgaatgaatc cgagaaggaa gtagtccaag gtggatggga gattgaaccc aaggacacag
2581 aaccagaagg caagaagggc aagaacaaga aaggaagagg caagaaacac acggctttct
2641 ccagcaaagg tctgagtgat gaggagtatg acgagtacaa gaggatcagg 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 tccccctggc 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 gcaatcttgg
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 atggaactca atagcacatt ggatcctaac cttgagtgca atggcagaag
4501 tgtcaggtct ctcaccagat gttgtccaag cccactcttg tttttcattt 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 atgtttagat
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 cttccagaat gagacttgtg
5581 gctatgttgt acacacccct tagagcaaat tctggtgagg atatgtttac ggtgtcttgc
5641 agagtcctga cccgtccagc ccctgacttt gagttcacgt ttctggtgcc gccaactgta
5701 gaatcaaaga ctaagccctt cacactccca 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 gtagactcag ctagacgagc aatgaaccat cctctctacg ttcagctgag gaacctcgat
6001 gggacatcat atgatccaac agatgaggtg ccagcggttc tgggtgccat agattttaaa
6061 ggaactgtgt ttgggatcgc tagtcaaagg gacaccaaag gctctgtagg agcgacccgc
6121 gcccatgaag tgacaataaa caccagagat gctaaatact ctccaaaact tggctctgtg
6181 ttgatgtatt ctgaatctac tgattttaca agtgaccagc ccatccgctt cactcctatt
6241 ggtatggggg aggaaaatga ttgggaccaa tgggatttgc ctgattattc tggcagcctc
6301 accctcaaca tgcacctagc ccccgcagtt gcccctgctt tccctggtga gcgcattctc
6361 ttctttagat caatagtgcc agctgctggt ggttatggga aaggtgaaat agattgcctc
6421 atcccacagg aatggattca gcatttctac caggaggccg ccccaataca atccgcggtg
6481 gcccttatta gatatgttaa tcctgacact gggagaaacc tctttgaggc aaagctacat
6541 agagaagggt tcatcactgt ggcaagttct ggagacaacc ccatagttgt gccctcaaat
6601 ggctacttca gatttgaggc ttgggttaat caattctaca cactcacccc catgggagct
6661 ggacaggggc gcaaaagagc ccagtaatgg caggagcttt cttagctgga ttggcaggtg
6721 acgccataac aaatggtgtc gggtccctga tcaacgctgg ggccaatgca atcaaccaaa
6781 aagtagagta tgacttcaat aaacaactcc aattggcatc ctttcaacat gacaaagaga
6841 tgttgcagtc acaagttctg gccactaaac agctccagca ggagatgatg aacataaggc
6901 aaggggtctt gaccgctggc ggcttttccc ctacagatgc cgcgagaggc gctgtgaacg
6961 cgccgatgac aaaaattctg gattggaatg gaacgaggta ttttgcccca aacagtatga
7021 agacaaccag ttattcaggc cagctcccca gtagccctgt gcataagcaa tccacactac
7081 cccgtcccag cccttcaaaa actaatgtta gtagtgattc tgctagtgtg tatagttctg
7141 catcttctgc tctctcacaa tcaactcatt caacggtttt gactgcgggg tccgggtcgt
7201 ctaggacacc ttcctcttcc tcaacagctt ccaccttgtc tagaactagt gattgggtaa
7261 gaggacaaaa tgagaggctc agcccgttta tgaatggtgc tctccaaaca acttttgtca
7321 caccaccatc gagcagggct tcatcatatg ggtcggtctc aaccgtcccc aaagctgttt
7381 tggactcctg gactcctatg ttcaacaccc ataggcagcc tctcttcact cacattcgta
7441 ggcgagggga gtcacagatt tagtgaaaag attga
//