Typing tool
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Typing tool
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Complete norovirus genomes
| MF140642 | GII.4 Sydney | |
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| GII.P4 New Orleans |
ORF1: 1..4931
ORF2: 4912..6534
ORF3: 6534..7283
LOCUS MF140642 7283 bp RNA linear VRL 24-OCT-2017
DEFINITION Norovirus GII strain
Norovirus/GII/Hu/NL/2013/GII.P4-GII.4/Rotterdam/E1300306_p11_d83
ORF1 gene, partial cds; ORF2 gene, complete cds; and ORF3 gene,
partial cds.
ACCESSION MF140642
VERSION MF140642.1
KEYWORDS .
SOURCE Norovirus GII
ORGANISM Norovirus GII
Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes;
Picornavirales; Caliciviridae; Norovirus; Norwalk virus.
REFERENCE 1 (bases 1 to 7283)
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 7283)
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..7283
/organism="Norovirus GII"
/mol_type="genomic RNA"
/strain="Norovirus/GII/Hu/NL/2013/GII.P4-
GII.4/Rotterdam/E1300306_p11_d83"
/host="Homo sapiens"
/db_xref="taxon:122929"
/country="Netherlands"
/collection_date="14-Apr-2013"
/note="genotype: GII.P4-GII.4"
CDS <1..4931
/codon_start=3
/product="ORF1"
/protein_id="ATN23622.1"
/translation="RPPTPELVKNIPPPPPNGEDEIVVSYSVKDGVSGLPDLSTVRQP
EESNTAFSVPPLNQRENRDAKEPLTGTILEMWDGEIYHYGLYVDRGLVLGVHKPPAAI
SLAKVELAPLSLYWRPVYTPQYLISPDTLKKLSGETFPYTAFDNNCYAFCCWVLDLND
SWLSRRMIQRTTGFFRPYQDWNRKPLPTMDDSKIKKVANIFLCALSSLFTRPIKDIIG
KIRPLNILNILASCDWTFAGIVESLILLAELFGVFWTPPDVSAMIAPLLGDYELQGPE
DLAVELVPVVMGGIGLVLGFTKEKIGKMLSSAASTLRACKDLGAYGLEILKLVMKWFF
PKKEEANELAIVRSIEDAVLDLEAIENNHMTALLKDKDSLATYMRTLDLEEEKARKLS
TKSASPDIVGTINALLARIAAARSLVHRAKEELSSRPRPVVLMISGRPGIGKTHLARE
VAKRIAASLTGDQRVGLIPRNGVDHWDAYKGERVVLWDDYGMSNPIHDALRLQELADT
CPLTLNCDRIENKGKVFDSDVIIITTNLANPAPLDYVNFEACSRRIDFLVYAEAPDVE
KAKRDFPGQPDMWKNAFSSDFSHIKLALAPQGGFDKNGNTPHGKGVMKTLTTGSLIAR
ASGLLHERLDEFELQGPALTTFNFDRNKVLAFRQLAAENKYGLMDTMRVGKQLKDVKT
MPELKQALKNVSIKKCQIVYSGCTYMLESDGKGNVKVDRIQSAAVQTNNELAGALHHL
RCARIRYYVKCVQEALYSIIQIAGAAFVTTRIAKRMNIQDLWSKPQVENTEETTSKDG
CPKPKDDEEFVISSDDIKTEGKKGKNKTGRGKKHTAFSSKGLSDEEYDEYKRIREERN
GKYSIEEYLQDRDKYYEEVAIARATEEDFCEEEEAKIRQRIFRPTRKQRKEERVSLGL
VTGSEIRKRNPDDFKPKGKLWADDDRSVDYNEKLSFEAPPSIWSRIVNFGSGWGFWVS
PSLFITSTHVIPQGAKEFFGVPIKQIQVYKSGEFCRLRFPKPIRTDVTGMILEEGAPE
GTVVTLLIKRSTGELMPLAARMGTHATMKIQGRTVGGQMGMLLTGSNAKGMDLGTTPG
DCGCPYIYKRGNDYVVIGVHTAAARGGNTVICATQGSEGEATLEGGDNKGTYCGAPIL
GPGSAPTLSTKTKFWRSSTASLPPGTYEPAYLGGKDPRVKGGPSLQQVMREQLKPFTE
PRGKPPKPSVLEAAKKTIINVLEQTIDPPEKWSFAQACASLDKTTSSGHPHHMRKNDC
WNGDSFTGKLADQASKANLMFEEGKNMTPVYTAALKDELVKTDKIYGKIKKRLLWGSD
LATMIRCARAFGGLMDELKAHCVTLPIRVGMNMNEDGPIIFERHSRYTYHYDADYSRW
DSTQQRAVLAAALEIMVKFSPEPHLAQVVAEDLLSPSVVDVGDFTISINEGLPSGVPC
TSQWNSIAHWLLTLCALSEVTNLSPDTIQANSLFSFYGDDEIVSTDIKLDPEKLTAKL
REYGLKPTRPDKTEGPLVISEDLNGLTFLRRTVTRDPAGWFGKLEQSSILRQMYWTRG
PNHGDPSETMIPHSQRPIQLMSLLGEAALHGPAFYSKISKLVIAELKEGGMDFYVPRQ
EPMFRWMRFSDLSTWEGDRNLAPSFVNEDGVE"
CDS 4912..6534
/codon_start=1
/product="ORF2"
/protein_id="ATN23623.1"
/translation="MKMASSDANPSDGSAANLVPEVNNEVMALEPVVGAAIAAPVAGQ
QNVIDPWIRNNFVQAPGGEFTVSPRNAPGEILWSAPLGPDLNPYLSHLARMYNGYAGG
FEVQVILAGNAFTAGKVIFAAVPPNFPTEGLSPSQVTMFPHIVVDVRQLEPVLIPLPD
VRNNFYHYNQSNDPTIKLIAMLYTPLRANNAGDDVFTVSCRVLTRPSPDFDFIFLVPP
TVESRTKPFSVPVLTVEEMTNSRFPIPLEKLFTGPSSAFVVQPQNGRCTTDGVLLGTT
QLSPVNICTFRGDVIHITGSRNYTMNLASQNWNNYDPTEEIPAPLGAPDFVGKIQGML
TQTTRANGSTRGHKATVYTGSADFAPKLGRVQFETDTDHDFEANQNTKFTPVGVIQDG
STTHRNEPQQWVLPSYSGRNTHNVHLAPAVAPTFPGEQLLFFRSTMPGCSGYPNMDLD
CLLPQEWVQYFYQEAAPAQSDVALLRFVNPDTGRVLFECKLHKSGYVTVAHTGQHDLV
IPPNGYFRFDSWVNQFYTLAPMGNGAGRRRVV"
CDS 6534..>7283
/codon_start=1
/product="ORF3"
/protein_id="ATN23624.1"
/translation="MAGAFFAGLASDVLGSGLGSLINAGAGAINQKVEFENNRKLQQA
SFQFSSNLQQASFQHDKEMLQAQIEATKKLQQEMMKVKQAMLLEGGFSETDAARGAIN
APMTRALDWSGTRYWAPDARTTTYNAGRFSTPQPSGALSGRANLRDAVPARGSSSKSS
NSSTATSVYSNQTTSTRLGSTAGSGTSVSSLPSTARTRSWVEDQSRNLSPFMRGAHNI
SFVTPPSSRSSSQGTVSTVPKEVLDSWTGAFN"
ORIGIN
1 cacgaccacc tactccagaa ctggttaaaa atattccccc tcccccaccc aacggagagg
61 atgaaatagt ggtttcttat agtgtcaaag atggtgtttc cggtttgcct gacctttcca
121 ccgtcaggca accggaagaa tccaacacgg ccttcagtgt ccctccactc aatcagaggg
181 agaatagaga tgctaaggaa ccactcactg gaacaattct ggaaatgtgg gacggggaaa
241 tctaccatta tggcctgtat gtggatcgag gtcttgtact aggcgtgcac aaaccgccag
301 ctgccatcag cctcgctaag gttgagctag caccactctc cttgtactgg agacctgtgt
361 acactcctca gtacctcatc tctccagaca ctctcaagaa attgtccgga gaaacgttcc
421 cctacacagc ctttgataac aactgctatg ccttttgttg ctgggtcctg gacctaaatg
481 actcgtggct gagcaggaga atgatccaga gaacgactgg tttcttcagg ccctaccaag
541 actggaatag gaaacccctt cccactatgg atgactccaa aataaaaaag gtagctaaca
601 tatttctgtg tgctctgtcc tcgctattca ccagacccat aaaagatata atagggaaga
661 taaggcctct taacatcctc aacatcttag cctcatgtga ttggaccttt gcgggcatag
721 tggagtccct gatactcttg gcagaactct ttggagtttt ctggacaccc ccagatgtgt
781 ctgcgatgat tgccccctta cttggtgact acgagctaca aggacctgag gaccttgcag
841 tggagctcgt ccccgtggtg atggggggaa ttggtttggt gctaggattc accaaagaga
901 agattgggaa gatgttgtca tctgctgcgt ccaccttaag agcttgcaaa gaccttggtg
961 catatgggct agagatccta aagttagtca tgaagtggtt cttcccgaag aaggaggagg
1021 caaatgagct ggctatagtg aggtccatcg aggatgcagt cctggatctc gaggcaattg
1081 aaaacaatca tatgaccgcc ttgcttaaag ataaagacag tctggcaacc tacatgagaa
1141 cacttgacct tgaagaggag aaagccagga aactctcaac caagtctgcc tcacccgaca
1201 tcgtgggcac aatcaacgcc ctcctggcga gaatcgctgc cgcacgttct ctggtgcatc
1261 gagcgaagga ggagctttcc agcagaccaa gacctgtggt gttgatgata tcaggcaggc
1321 caggaatagg gaagacccac ctcgctaggg aagtggctaa gagaatcgca gcctccctta
1381 caggagacca gcgtgttggc cttatcccac gcaatggcgt cgaccattgg gatgcgtaca
1441 agggggagag ggtcgtccta tgggacgatt atggaatgag caaccctatt cacgatgccc
1501 tcagactgca agaactcgct gacacttgcc ccctcactct gaactgtgac aggattgaaa
1561 ataaaggaaa ggtctttgac agcgatgtca tcattatcac caccaatctg gccaacccag
1621 caccactgga ctatgtcaac tttgaagcat gctcgaggcg cattgacttc ctcgtgtatg
1681 cagaagctcc tgatgtcgaa aaggcgaagc gtgacttccc aggccagcct gacatgtgga
1741 agaacgcttt cagttctgat ttctcacaca taaaactagc actggcccca cagggtggtt
1801 tcgacaagaa cgggaacacc ccacacggaa agggcgtcat gaagactctc accactggct
1861 cccttattgc ccgggcatca gggctgctcc atgagaggtt agatgaattt gaactgcagg
1921 gtccagctct caccaccttc aatttcgatc gcaataaagt gcttgccttt agacagcttg
1981 ctgctgaaaa taaatatgga ttgatggaca caatgagggt tgggaaacag ctcaaggatg
2041 tcaaaaccat gccagaactc aaacaagcac tcaagaatgt ctcaatcaag aagtgtcaaa
2101 tagtgtatag tggttgcacc tacatgcttg agtctgatgg caagggcaat gtgaaagttg
2161 acaggatcca gagcgccgcc gtgcagacca acaatgagct ggctggtgcc ctgcaccatt
2221 tgaggtgcgc cagaatcaga tactatgtca agtgtgtcca ggaagccctg tattccatca
2281 tccaaattgc tggggctgca tttgtcacca cgcgcattgc caagcgcatg aacatacaag
2341 acctatggtc caagccacaa gtggaaaaca cagaggagac taccagcaag gacgggtgcc
2401 caaaacctaa ggatgatgag gagtttgtca tttcatccga cgacatcaaa actgagggca
2461 agaaagggaa gaacaagact ggccgtggca agaagcacac agcattttca agcaaaggcc
2521 tcagtgatga agagtacgat gaatacaaga ggattagaga agaaaggaat ggcaagtact
2581 ctatagaaga gtaccttcag gacagggaca aatattatga ggaggtggcc attgccagag
2641 cgactgagga agacttctgt gaagaggagg aagccaagat ccggcaaagg atctttaggc
2701 cgacaaggaa acaacgcaag gaggaaagag tctctctcgg cttggtcaca ggctctgaaa
2761 ttaggaaaag aaacccagat gacttcaaac ccaaggggaa attatgggct gacgatgaca
2821 ggagtgtgga ctacaatgag aaactcagtt ttgaggcccc accaagcatt tggtcgagaa
2881 tagtcaactt tggttcaggc tggggattct gggtctcccc cagcttgttc ataacatcaa
2941 cccatgttat accccagggc gcaaaggagt tctttggagt ccccatcaaa caaatacagg
3001 tatacaagtc aggcgagttc tgtcgcttga gattccctaa accaatcagg actgatgtga
3061 cgggcatgat cttagaagaa ggcgcacctg agggcaccgt ggtcacacta ctcatcaaaa
3121 ggtccactgg ggaacttatg cccctagcag ctaggatggg gacccatgcg accatgaaga
3181 tccaagggcg cactgttggg ggccagatgg gcatgcttct gacaggatcc aacgccaagg
3241 gtatggacct gggtactaca ccaggtgatt gtggctgccc ctatatctac aagagaggta
3301 atgactatgt ggtcattgga gtccacacgg ctgccgcacg tggggggaac actgtcatat
3361 gtgccaccca ggggagtgaa ggagaggcta cacttgaggg tggtgacaac aaggggacat
3421 actgtggtgc accaatccta ggcccaggga gtgccccaac acttagcacc aagaccaaat
3481 tctggagatc gtccacagca tcactcccac ctggcaccta tgaaccagcc tatcttggtg
3541 gtaaggaccc tagagtcaag ggtggccctt cactgcagca agtcatgagg gaacagttga
3601 agccattcac agagcccagg ggcaagccac caaaaccaag tgtgttagaa gctgccaaga
3661 agaccatcat caatgtcctt gagcaaacaa ttgatccacc tgagaaatgg tcgttcgcac
3721 aagcttgcgc gtcccttgac aagaccactt ccagtggtca tccgcaccac atgcggaaaa
3781 acgactgctg gaacggggat tccttcacag gcaagctggc agaccaggct tccaaggcca
3841 acctgatgtt tgaagaaggg aagaacatga ccccagtcta cacagctgcg ctcaaggatg
3901 agttagttaa aactgacaaa atttatggca agatcaagaa gaggcttctt tggggctcgg
3961 acttggcgac catgatccgg tgtgctcgag cattcggagg cttaatggat gaactcaaag
4021 cgcactgtgt cacacttccc attagagttg gcatgaatat gaatgaggat ggccccatca
4081 tcttcgagag gcattccagg tatacgtacc actatgatgc tgattactct cgatgggatt
4141 caacacaaca gagagccgtg ttggcagcag ctctagaaat catggttaaa ttctccccag
4201 aaccacattt ggctcaggta gtcgcggaag accttctttc tcctagcgtg gtggacgtgg
4261 gcgacttcac aatatcaatc aacgagggtc tcccctctgg ggtgccctgc acctcccaat
4321 ggaactccat cgcccactgg cttctcactc tctgtgcgct ctccgaagtc acaaatctgt
4381 cccctgatac catacaggcc aattctctct tctcttttta tggtgatgat gaaattgtta
4441 gcacagacat aaaattggac ccagagaaat tgacagcaaa gctcagagaa tatgggttaa
4501 aaccaacccg ccctgacaaa actgaaggac cccttgtcat ctctgaagac ctgaatggcc
4561 taactttcct gcggagaact gtgacccgcg acccagctgg ttggtttgga aaactggagc
4621 agagttcaat actcaggcaa atgtactgga ctaggggtcc caaccatgga gacccatctg
4681 aaacaatgat tccacactcc caaagaccca tacaattgat gtccctactg ggggaggccg
4741 ctctccacgg cccagcattt tacagtaaaa tcagcaaatt ggtcattgca gagctaaaag
4801 aaggtggtat ggatttttac gtgcccagac aagagccaat gttcagatgg atgagattct
4861 cagatctgag cacgtgggag ggcgatcgca atctggctcc cagttttgtg aatgaagatg
4921 gcgtcgagtg acgccaaccc atctgatggg tccgcagcca acctcgtccc agaggtcaac
4981 aatgaggtta tggctctgga gcccgttgtt ggtgccgcca ttgcggcacc tgtagcgggc
5041 caacaaaatg taattgaccc ctggattaga aacaattttg tacaagcccc tggtggagag
5101 tttacagtgt cccctagaaa cgctccaggt gaaatactat ggagcgcgcc cttaggccct
5161 gacctaaatc cctacctatc ccatttggcc agaatgtata atggttatgc aggtggtttt
5221 gaagtgcagg taattctcgc ggggaacgcg ttcaccgccg ggaaggtcat atttgcagca
5281 gtcccaccaa attttccaac tgaaggcttg agccccagcc aggtcactat gttcccccat
5341 atagtagtag atgttaggca actagaacct gtgttgattc ccttacccga tgttaggaat
5401 aatttctatc attacaatca atcaaatgac cccaccatca agttgatagc aatgctgtat
5461 acaccactta gggctaataa tgctggggac gatgtcttca cagtttcttg ccgagttctc
5521 acgagaccat cccccgattt tgattttata tttctagtgc cacccacagt tgagtctaga
5581 actaaaccat tctctgtccc agttttaact gttgaggaga tgaccaattc aagattcccc
5641 attcctttgg aaaagttgtt cacgggtccc agcagtgcct ttgttgttca accacaaaac
5701 ggtaggtgca cgactgatgg cgtgctccta ggcaccaccc aattgtctcc tgtcaacatc
5761 tgcaccttca gaggggatgt catccacatc acaggtagtc gtaactacac aatgaatttg
5821 gcttctcaaa attggaacaa ttatgaccca acagaagaaa tcccagcccc tctaggagct
5881 ccagattttg tggggaagat tcaaggcatg ctcacccaaa ccacaagggc aaatggctca
5941 acacgcggcc acaaagctac agtgtacact gggagcgccg actttgctcc aaaactgggc
6001 agagttcaat ttgaaactga cacagaccat gattttgaag ctaaccaaaa cacaaagttc
6061 accccagtcg gtgtcatcca agatggtagc accacccacc gaaatgaacc ccaacagtgg
6121 gtgctcccaa gttactcagg cagaaatact cataatgttc atctggcccc cgctgtagcc
6181 cccacttttc cgggtgaaca acttctcttc tttagatcca ccatgcccgg atgtagcggg
6241 taccccaaca tggatttgga ctgtctgctc ccccaggaat gggtgcagta cttctaccaa
6301 gaggcagccc cagcacaatc tgatgtggct ctgctaagat ttgtgaatcc agacacaggt
6361 agggttttgt ttgagtgtaa gctccataaa tcaggctatg ttacagtggc tcacactggc
6421 caacatgatt tggttatccc ccccaatggt tattttaggt ttgattcctg ggtcaaccag
6481 ttctacacgc ttgcccccat gggaaatgga gcggggcgta gacgtgtagt ataatggctg
6541 gagctttctt tgctggatta gcatctgatg tccttggctc tggacttggt tcccttatca
6601 atgctggggc tggggccatc aaccaaaaag ttgagtttga aaataacaga aaattgcaac
6661 aagcatcctt ccaatttagc agcaatctac aacaggcttc ctttcaacat gacaaagaaa
6721 tgctccaagc acaaattgag gccaccaaaa agctacaaca ggaaatgatg aaagttaagc
6781 aggcaatgct cctagagggt gggttctctg agacagatgc agcccgcggg gcaatcaacg
6841 cccccatgac aagagctttg gactggagcg ggacaaggta ctgggctccc gatgctagga
6901 ctacaacata caatgcaggc cgcttttcca cccctcaacc atcgggggca ctgtcaggaa
6961 gagccaatct tagggatgct gtccctgctc ggggttcctc cagtaaatct tctaactctt
7021 ctactgctac ttctgtgtac tcaaatcaaa ccacttcaac gagacttggt tctacagctg
7081 gttctggtac cagtgtctcg agcctcccgt caactgcaag gactaggagc tgggttgagg
7141 atcaaagtag gaatttgtct cctttcatga ggggggccca caacatatcg tttgtcaccc
7201 caccatctag cagatcctct agccaaggca cagtctcaac cgtgcctaaa gaggttttgg
7261 actcctggac tggcgctttc aac
//