Typing tool
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Typing tool
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Complete norovirus genomes
| MF140636 | GII.4 Sydney | |
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| GII.P31 |
ORF1: 1..4925
ORF2: 4906..6528
ORF3: 6528..7334
LOCUS MF140636 7334 bp RNA linear VRL 24-OCT-2017
DEFINITION Norovirus GII strain
Norovirus/GII/Hu/NL/2013/GII.Pe-GII.4/Rotterdam/E7800008_p10_d0
ORF1 gene, partial cds; and ORF2 and ORF3 genes, complete cds.
ACCESSION MF140636
VERSION MF140636.1
KEYWORDS .
SOURCE Norovirus GII
ORGANISM Norovirus GII
Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes;
Picornavirales; Caliciviridae; Norovirus; Norovirus norwalkense.
REFERENCE 1 (bases 1 to 7334)
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 7334)
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..7334
/organism="Norovirus GII"
/mol_type="genomic RNA"
/strain="Norovirus/GII/Hu/NL/2013/GII.Pe-
GII.4/Rotterdam/E7800008_p10_d0"
/host="Homo sapiens"
/db_xref="taxon:122929"
/geo_loc_name="Netherlands"
/collection_date="24-Jan-2013"
/note="genotype: GII.Pe-GII.4"
CDS <1..4925
/codon_start=3
/product="ORF1"
/protein_id="ATN23604.1"
/translation="PTPELVKKIPPPPPNGEDELVVSYSAKDGVSGLPELTTVRQPEE
TNTAFSVPPLNQRESRDAKEPLTGTIIEMWDGEIYHYGLYVERGLILGVHKPPAAISL
AKVELAPLSLFWRPVYTPQYLISPDTLRRLHGESFPYTAFDNNCYAFCCWVLDLNDSW
LSRRMIQRTTGFFRPYQDWNRKPLPTMDDSKLKKVANIFLCTLSSLFTRPIKDIIGKL
KPLNILNILATCDWTFAGIVESLILLAELFGVFWTPPDVSAMIAPLLGDYELQGPEDL
AVELVPIVMGGIGLVLGFTKEKIGKMLSSAASTLRACKDLGAYGLEILKLVMKWFFPK
KEEANELAMVRSIEDAVLDLEAIENNHMTTLLKDKDSLATYMRTLDLEEEKARKLSTK
SASPDIVGTINSLLARIAAARSLVHRAKEELSSRPRPVVVMISGRPGIGKTHLARELA
KKIAASLTGDQRVGLIPRNGVDHWDAYKGERVVLWDDYGMSNPIHDALRLQELADTCP
LTLNCDRIENKGKVFDSDAIIITTNLANPAPLDYVNFEACSRRIDFLVYAEAPEVEKA
KRDFPGQPDMWKNAFSPDFSHIKLSLAPQGGFDKNGNTPHGKGVMKTLTTGSLIARAS
GLLHERLDEYELQGPALTTFNFDRNKILAFRQLAAENKYGLMDTMRVGKQLKDVKTMS
DLKQALKNIAIKKCQIVYNGGTYTLEADGKGSVKVDKVQSATVQTNNELAGALHHLRC
ARIRYYVKCVQEALYSIIQIAGAAFVTTRIAKRMNIQNLWSKPQVEDTEEMANKDGCL
KPKDDEEFVVSSDDIKTEGKKGKNKSGRGKKHTAFSSKGLSDEEYDEYKRIREERNGK
YSIEEYLQDRDRYYEEVAIARATEEDFCEEEEAKIRQRIFRPTRKQRKEERASLGLVT
GSEIRKRNPEDFKPKGKLWADDDRSVDYNEKLNFEAPPSIWSRIVNFGSGWGFWVSPS
LFITSTHVIPQGAKEFFGVPIKQIQIHKSGEFCRLRFPKPIRTDVTGMILEEGAPEGT
VATLLIKRPTGELMPLAARMGTHATMKIQGRTVGGQMGMLLTGSNAKSMDLGTTPGDC
GCPYIYKRGNDYVVIGVHTAAARGGNTVICATQGSEGEATLEGGDSKGTYCGAPILGP
GSAPKLSTKTKFWRSSTTPLPPGTYEPAYLGGKDPRVKGGPSLQQVMRDQLKPFTEPR
GKPPRPNVLEAAKKTIINVLEQTIDPPQKWSFAQACASLDKTTSSGHPHHMRKNDCWN
GESFTGKLADQASKANLMFEEGKNMTPVYTGALKDELVKTDKVYGKVKKRLLWGSDLA
TMIRCARAFGGLMDELKAHCVTLPVRVGMNMNEDGPIIFEKHSRYRYHYDADYSRWDS
TQQRDVLAAALEIMVKFSPEPHLAQIVAEDLLSPSVMDVGDFQISISEGLPSGVPCTS
QWNSIAHWLLTLCALSEVTDLSPDIIQANSLFSFYGDDEIVSTDIKLDPEKLTAKLKE
YGLKPTRPDKTEGPLVISEDLDGLTFLRRTVTRDPAGWFGKLEQSSILRQMYWTRGPN
HEDPFETMIPHSQRPIQLMSLLGEAALHGPAFYSKISKLVIAELKEGGMDFYVPRQEP
MFRWMRFSDLSTWEGDRNLAPSFVNEDGVE"
CDS 4906..6528
/codon_start=1
/product="ORF2"
/protein_id="ATN23605.1"
/translation="MKMASSDANPSDGSAANLVPEVNNEVMALEPVVGAAIAAPVAGQ
QNVIDPWIRNNFVQAPGGEFTVSPRNAPGEILWSAPLGPDLNPYLSHLARMYNGYAGG
FEVQVILAGNAFTAGKVIFAAVPPNFPTEGLSPSQVTMFPHIVVDVRQLEPVLIPLPD
VRNNFYHYNQSNDPTIKLIAMLYTPLRANNAGDDVFTVSCRVLTRPSPDFDFIFLVPP
TVESRTKPFSVPVLTVEEMTNSRFPIPLEKLFTGPSSAFVVQPQNGRCTTDGVLLGTT
QLSPVNICTFRGDVTHITGSRNYTMNLASQNWSNYDPTEEIPAPLGTPDFVGKIQGVL
TQTTRTDGSTRGHKATVYTGSADFAPKLGRVQFETDTDRDFEANQNTKFTPVGVIQDG
GTTHRNEPQQWVLPSYSGRNTPNVHLAPAVAPTFPGEQLLFFRSTMPGCSGYPNMDLD
CLLPQEWVQYFYQEAAPAQSDVALLRFVNPDTGRVLFECKLHKSGYVTVAHTGQHDLV
IPPNGYFRFDSWVNQFYTLAPMGNGTGRRRAL"
CDS 6528..7334
/codon_start=1
/product="ORF3"
/protein_id="ATN23606.1"
/translation="MAGAFFAGLASDVLGSGLGSLINAGAGAINQKVEFENNRKLQQA
SFQFSSNLQQASFQHDKEMLQAQIEATKRLQQEMMKVKQAMLLEGGFSETDAARGAIN
APMTKALDWSGTRYWAPDARTTTYNAGRFSTPQPSGALPGRANLRDAVPARGSSSKSS
NSSTATSVYSNQTTSTRLGSTAGSGTSVSSFPSTARTRSWVEDQSRNLSPFMSGAHNI
SFVTPPSSRSSSQGTVSTVPKEILDSWTGAFNTRRQPLFAHIRKRGESRA"
ORIGIN
1 cacccacacc agaattggtc aaaaagatcc ctcctccccc acccaacggg gaggatgaac
61 tagtggtctc ctacagcgcc aaagatggcg tttccggact gcctgagctc accactgtca
121 gacaaccgga agaaaccaac acggcgttca gtgtcccccc acttaaccaa agggagagca
181 gggacgccaa ggagccacta actggaacaa tcattgaaat gtgggatgga gaaatctacc
241 attacggcct gtacgtggaa cgaggtctta tacttggtgt gcacaagcca ccggcagcca
301 ttagccttgc caaggtcgag ctagcaccgc tctctttgtt ctggagacct gtatacaccc
361 cccagtatct catctctcca gacactctta ggagattaca tggagagtca ttcccctaca
421 ctgcatttga caacaattgc tacgcctttt gttgttgggt attagaccta aacgactcat
481 ggctaagcag gagaatgatt cagagaacaa caggcttctt caggccgtac caggattgga
541 acaggaaacc cctccccact atggatgatt ccaaattaaa gaaggtagcc aacatattct
601 tgtgcacttt gtcttcacta ttcaccagac ccattaagga cataataggg aagttgaaac
661 ctcttaacat ccttaacatt ctggctacat gtgattggac cttcgcaggc atagtggaat
721 ccttaatact cttggcagaa ctctttggag ttttctggac acccccagat gtgtctgcga
781 tgatcgcccc cttgctaggt gattatgaac tgcaaggacc tgaggacctt gcagtggaac
841 tggtcccaat agtgatgggg gggataggtt tggtgctagg atttaccaaa gagaaaatcg
901 gaaagatgct atcatccgct gcatccactt taagagcttg taaagacctt ggtgcatacg
961 gactggaaat cttaaaattg gtcatgaagt ggttcttccc aaagaaagag gaagcaaatg
1021 aactggctat ggtgagatcc atcgaggatg cagtactaga cctcgaggca attgaaaaca
1081 accacatgac caccctactc aaagacaaag acagcttggc aacctacatg agaacccttg
1141 accttgagga ggagaaagcc agaaaactct caaccaaatc tgcttcaccc gatattgtgg
1201 gcacaattaa ctctcttctg gcaagaatcg ctgctgcacg ctccctagtg catcgggcga
1261 aagaagagct ctccagcagg ccgagacctg tcgttgtgat gatatcggga agaccaggga
1321 tagggaaaac tcaccttgcc agggagctgg ccaagaagat cgcggcctcc ctcacagggg
1381 accagcgtgt gggtcttatc ccacgcaatg gtgtcgacca ctgggacgca tacaagggcg
1441 aaagagttgt cctatgggac gactatggaa tgagcaaccc catccatgat gccctcaggt
1501 tgcaggagct tgctgacact tgccccctca cgctaaattg tgacagaatt gagaacaaag
1561 ggaaagtctt tgacagtgat gccataatta tcaccaccaa tctggccaac ccagcaccac
1621 tggattatgt caactttgaa gcgtgctcga gacgcattga tttcctcgtg tacgcagaag
1681 cccctgaggt ggagaaggca aagcgcgact tcccaggtca acctgacatg tggaagaacg
1741 ctttcagtcc tgacttctca cacataaaac tgtcattggc tccacagggt ggttttgaca
1801 agaacggcaa caccccgcat ggaaaagggg tcatgaagac cctcaccact ggctccctca
1861 tcgcccgagc atcagggtta ctccatgaga ggctagatga atatgaactg caaggcccag
1921 ccctcaccac tttcaacttt gaccgcaaca agatacttgc ttttagacag cttgctgctg
1981 aaaacaagta tgggctgatg gacacaatga gagttggaaa acagctcaag gatgtcaaga
2041 ccatgtcaga cctcaaacaa gcactcaaga acatcgcgat caagaagtgc cagatagtgt
2101 acaatggtgg cacctacaca cttgaggctg atggcaaggg tagtgtgaaa gttgacaaag
2161 tgcaaagtgc cactgtgcag accaacaatg aactagccgg tgccctacac cacctaaggt
2221 gcgctagaat cagatactat gttaagtgcg tccaggaggc actgtattcc atcatccaaa
2281 tcgctggggc tgcattcgtc accacgcgca tcgctaagcg catgaatata cagaatctct
2341 ggtccaagcc acaggtggaa gacacagaag agatggccaa caaagatggt tgcctaaaac
2401 ccaaagatga tgaagagttt gtcgtctcat ccgacgacat caaaactgag ggcaagaaag
2461 ggaagaacaa gtccggccgt ggcaagaagc acacagcctt ttcaagtaaa gggctcagtg
2521 atgaggagta cgatgagtac aagagaatca gagaagaaag gaatggtaag tactccatag
2581 aagagtacct tcaggacaga gacaggtact acgaggaggt ggccattgcc agggcaaccg
2641 aagaggactt ctgtgaagaa gaagaggcca aaatccggca gagaattttc agaccaacaa
2701 ggaaacaacg caaagaagag agggcctctc tcggcttggt cacaggctct gaaatcagga
2761 agagaaaccc agaagacttc aaacccaagg gaaagttgtg ggctgatgat gacagaagtg
2821 ttgactacaa tgagaaactc aactttgagg ccccaccaag catctggtcg cggatagtca
2881 actttggttc aggctggggc ttctgggtct cccccagtct gtttataaca tcaacccatg
2941 tcatacccca aggtgcaaaa gagttcttcg gagtccctat taagcaaatc cagatacaca
3001 agtcaggtga attctgccgg ttgagattcc caaagccaat cagaactgat gtgacgggca
3061 tgattctaga agaaggtgcg cccgagggga ccgtggccac actgctcatc aagagaccaa
3121 ctggagagct catgcctctg gcagccagaa tggggaccca tgcaaccatg aaaattcagg
3181 ggcgcacagt tggagggcaa atgggtatgc tcctgacagg atccaacgcc aagagtatgg
3241 acctaggcac aacaccaggc gactgcggct gcccctacat ctacaagagg gggaatgact
3301 acgtggtcat aggagtccat acggccgctg cccgtggagg aaacactgtc atatgtgcca
3361 cccaggggag tgagggagaa gccacacttg aaggaggtga cagtaaaggg acatactgtg
3421 gcgcaccaat cttgggccca gggagcgctc cgaagctcag taccaagact aagttttgga
3481 gatcatccac aacaccactc ccacctggca cctacgaacc agcctacctc ggtggcaaag
3541 accctagagt caaaggtggc ccttcattgc aacaagttat gagggaccag ctgaagccat
3601 tcacagaacc cagaggcaaa ccaccaagac caaatgtgtt ggaagctgcc aagaaaacca
3661 tcatcaatgt ccttgagcaa acaattgatc caccccaaaa atggtcattt gcgcaagctt
3721 gcgcatccct tgacaaaacc acctccagcg gccacccgca ccacatgcgg aaaaacgact
3781 gttggaatgg ggagtccttc acaggaaaat tggctgatca agcctccaag gccaacctaa
3841 tgtttgaaga gggaaagaac atgactccag tctacacagg tgcacttaaa gatgagttgg
3901 taaagaccga taaagtttat ggtaaggtca agaagaggct tctgtggggt tcagatctgg
3961 cgaccatgat acggtgcgcc cgagcttttg gaggccttat ggatgaactc aaggcgcact
4021 gtgtcacact tcctgtcaga gttggtatga acatgaatga ggatggcccc atcatctttg
4081 agaagcactc cagatataga tatcactatg atgctgatta ttcccggtgg gactcaacac
4141 aacaaaggga tgtgctagca gcagcactag aaatcatggt taagttctct ccagaaccac
4201 acctggccca gatagttgca gaagacctcc tttcccctag cgtgatggat gtaggtgact
4261 ttcaaatatc aataagtgag ggtctcccct ctggggtacc ttgtacctcc cagtggaatt
4321 ccatcgccca ctggctcctc actctgtgtg cactctctga agtcacggac ctgtcccctg
4381 atatcattca ggccaactcc cttttctcct tctatggtga tgatgagatt gtaagcacag
4441 acataaagtt ggacccagag aagctgacag caaaactcaa ggagtacggg ctgaaaccaa
4501 cccgccccga caaaactgaa ggacccctcg ttatctctga agacctggat ggcctgacat
4561 tcctccggag aactgtgacc cgtgatccag ctggctggtt tggaaagttg gaacaaagtt
4621 caattctcag gcaaatgtac tggaccaggg gtcccaacca tgaagatcca tttgaaacaa
4681 tgataccaca ctcccaaaga cccatacaat tgatgtcctt gctgggcgag gctgcactcc
4741 acggcccggc attctatagc aaaattagca aattagtcat tgcagagttg aaggaaggtg
4801 gcatggattt ttacgtaccc agacaagagc caatgttcag atggatgaga ttctcagatc
4861 tgagcacgtg ggagggcgat cgcaatctgg ctcccagttt tgtgaatgaa gatggcgtcg
4921 agtgacgcca acccatctga tgggtccgca gccaacctcg tcccagaggt caacaatgag
4981 gttatggctc tggagcccgt tgttggtgcc gccattgcgg cacctgtagc gggccaacaa
5041 aatgtaattg acccctggat tagaaataat tttgtacaag cccctggtgg agagtttaca
5101 gtatccccca gaaacgctcc aggtgaaata ctatggagcg cgcccttggg ccctgatcta
5161 aatccctacc tatcccattt ggccagaatg tacaatggtt atgcaggtgg ttttgaagtg
5221 caggtaattc tcgcggggaa cgcgttcacc gccgggaagg tcatatttgc agcagtccca
5281 ccaaattttc caactgaagg cttgagcccc agccaggtca ctatgttccc ccatatagta
5341 gtagatgtta ggcaactaga acctgtgttg attcccttac ccgatgttag gaataatttc
5401 tatcattaca atcaatcaaa tgaccccacc attaagttga tagcaatgtt gtatacacca
5461 cttagggcta ataatgctgg ggatgatgtc ttcacagttt cttgccgagt tctcacgaga
5521 ccatcccccg attttgactt catatttcta gtgccaccca cagttgagtc aagaactaaa
5581 ccattctctg tcccagtttt aactgttgag gagatgacca attcaagatt ccccattcct
5641 ttggaaaagt tgttcacggg tcccagcagt gcctttgttg tccaaccaca aaacggtagg
5701 tgcacgactg atggcgtgct cctaggcacc acccagctgt ctcctgtcaa catctgcacc
5761 ttcagaggag atgtcaccca tatcacaggt agtcgtaact acacaatgaa tttggcttct
5821 caaaattgga gcaattatga cccaacagaa gaaatcccag cccctctagg aactccagat
5881 tttgtgggga agattcaagg cgtgctcacc caaaccacaa ggacagatgg ctcaacacgc
5941 ggccacaaag ccacagtgta cactgggagc gccgactttg ctccaaaact gggtagagtt
6001 caatttgaaa ctgacacaga ccgtgatttt gaagctaacc aaaacacaaa gttcacccca
6061 gttggtgtca tccaagatgg tggcaccacc caccgaaatg aaccccaaca gtgggtgctc
6121 ccaagttact caggcagaaa cactcctaat gtgcatctgg cccccgctgt agcccccact
6181 tttccgggtg agcaacttct cttcttcaga tccaccatgc ccggatgcag cgggtacccc
6241 aacatggatt tggactgtct gctcccccag gaatgggtgc agtacttcta ccaagaggca
6301 gccccagcac aatctgatgt ggctctgcta agatttgtga atccagacac aggtagggtt
6361 ttgtttgagt gtaagcttca taaatcaggc tatgttacag tggctcacac tggccaacat
6421 gatttggtta tcccccccaa tggttatttt aggtttgatt cctgggtcaa ccagttttac
6481 acgcttgccc ccatgggaaa tggaacgggg cgtagacgtg cactataatg gctggagctt
6541 tctttgctgg attggcatct gatgtccttg gctctggact tggttccctt atcaatgctg
6601 gggctggggc catcaaccaa aaagttgagt ttgaaaataa cagaaaattg caacaagcat
6661 ccttccaatt tagcagcaat ctacaacagg cttcctttca acatgacaaa gagatgctcc
6721 aagcacaaat tgaggccacc aaaaggctac aacaggaaat gatgaaagtt aagcaggcaa
6781 tgctcctaga gggtgggttc tctgagacag atgcagcccg cggggcaatc aacgccccca
6841 tgacaaaagc tttggactgg agcgggacaa ggtactgggc tcccgatgct aggactacaa
6901 catacaatgc aggccgcttt tccacccctc aaccatcggg ggcactgcca ggaagagcta
6961 atcttaggga tgctgtccct gctcggggtt cctccagtaa gtcttctaat tcttctactg
7021 ctacttctgt gtactcaaat caaactactt caacgagact tggttctaca gctggttctg
7081 gtaccagtgt ctcgagcttc ccgtcaactg caaggactag gagctgggtt gaggatcaaa
7141 gtaggaattt gtcacctttc atgagtgggg cccacaacat atcgtttgtc accccaccat
7201 ctagcagatc ctctagccaa ggcacagtct caaccgtgcc taaagagatt ttggactcct
7261 ggactggcgc tttcaacacg cgcaggcagc cactcttcgc tcacattcgt aagcgagggg
7321 agtcacgggc gtaa
//