Typing tool
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Typing tool
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Complete norovirus genomes
| MF140687 | GII.3 | |
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| GII.P21 |
ORF1: 1..5088
ORF2: 5069..6718
ORF3: 6718..7479
LOCUS MF140687 7495 bp RNA linear VRL 24-OCT-2017
DEFINITION Norovirus GII strain
Norovirus/GII/Hu/NL/2012/GII.P21-GII.3/Rotterdam/E1300325_p7_d434
ORF1 gene, partial cds; and ORF2 and ORF3 genes, complete cds.
ACCESSION MF140687
VERSION MF140687.1
KEYWORDS .
SOURCE Norovirus GII
ORGANISM Norovirus GII
Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes;
Picornavirales; Caliciviridae; Norovirus; Norwalk virus.
REFERENCE 1 (bases 1 to 7495)
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 7495)
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..7495
/organism="Norovirus GII"
/mol_type="genomic RNA"
/strain="Norovirus/GII/Hu/NL/2012/GII.P21-
GII.3/Rotterdam/E1300325_p7_d434"
/host="Homo sapiens"
/db_xref="taxon:122929"
/country="Netherlands"
/collection_date="01-May-2012"
/note="genotype: GII.P21-GII.3"
CDS <1..5088
/codon_start=1
/product="ORF1"
/protein_id="ATN23757.1"
/translation="SNDASAAAAANSNNDNAKSSSDGVLSNMAVTFKRALGARSKQPP
PRDKPPKPPRPPTPELVKAIPPPPPNGEDEPTISYNVKEGVSGLPELSTVTQLEENST
AFSVPPLSQRENRDAKEPLTGTILEMWDGEIYHYGLYVERGLVLGVHKPPAAVSLAKI
ELTPLSLYWRPVYTPQYLISPDTLKKLHGETFPYTAFDNNCYAFCCWVLDLNDSWLSR
RMIQRTTGFFRPYQDWNRKPLPTMDDSKVKKVANVVLCALSSLFTRPIKDIIGKLKPL
NILNILATCDWTFAGIVESLILLAELFGVFWTPPDVSAMIAPLLGDYELQGPEDLAVE
LVPVVMGGIGLVLGFTKEKIGKMLSSAASTLRACKDLGAYGLEILKLVMKWFFPKKEE
KNELAMVRSIEDAVLDLEAIENNHMTALLKDKDSLATYMRTLDMEEEKARKLSTKSAS
PDIVGTINALLSRIAAARSLVHRAKEELSSRPRPVVVMISGRPGIGKTHLARELAKKI
ASSLTGDQRVGLIPRNGVDHWDAYKGERVVLWDDYGMSNPIHDALRLQELADTCPLTL
NCDRIENKGKVFDSDAIIITTNLANPAPLDYVNFEACSRRIDFLVYADAPEVEKAKRD
FPGQPDMWKDTFKPDFSHIKLTLAPQGGFDKNGNTPHGKGVMKTLTASSLVARASGLL
HERLDEYELQGPTPTTFNFDRNKVLAFRQLAAENKYGLVDTMRVGSQLKNVKTMTELK
QALKNISVKKCQLVYGGGTYTLESDGKGNVHVEKVNNTSVQTNNELSGALHHLKCARI
RYYVKCVQEALYSILQIAGAAFITTRITKRMNIQNLWSKPQAEDLEETNNEEGCPKPK
NDEEFVISSDDIKTEGKKGKNKTGRGKKHTAFSSKGLSDEEYDEYKRIREERNGKYSI
EEYLQDRDKYYEEVAIARATEEDFCEEEEAKIRQRIFRPTRKQRKEERASLGLVTGSE
IRKRNPDDFKPKGKLWADDDRNVDYNEKLSFEAPPSIWSRIVNFGSGWGFWVSPSLFI
TSTHVIPQGAQEFFGVPIKQIQIHKSGEFCRLRFPKPIRTDVTGMILEEGAPEGTVAT
LLIKRPTGELMPLAARMGTHATMKIQGRTVGGQMGMLLTGSNAKSMDLGTTPGDCGCP
YIYKRGNDYVVIGVHTAAARGGNTVICATQGNEGEAMLEGGDNKGTYCGAPILGHGNA
PKLSTKTKFWRSSTTPLPPGTYEPAYLGGKDPRVKGGPSLQQVMRDQLKPFTEPRGKP
PKPSVLEAAKKTIINVLEQTIDPPQKWTYAQACASLDKTTSSGHPHHMRKNDCWNGET
FTGKLADQASKANLMFEEGKNMTPVYTGALKDELVKTDKIYGTIKKRLLWGSDLSTMI
RCARAFGGLMDELKAHCVTLPVRVGMNMNEDGPIIFEKHSRYKYHYDADYSRWDSTQQ
RAVLAAALEIMVKFSPEPHLAQVVAEDLLSPSVMDVGDFKISINEGLPSGVPCTSQWN
SIAHWLLTLCALSEVTDLSPDIIQANSLFSFYGDDEIVSTDIKLDPEKLTAKLKEYGL
KPTRPDKTEGPLIISEDLDGLTFLRRTVTRDPAGWFGKLDQSSILRQMYWTRGPNHED
PFETMIPHSQRPIQLMSLLGEAALHGPSFYSKISKLVISELKEGGMDFYVPRQEPMFR
WMRFSDLSTWEGDRNLAPCFVNEDGVE"
CDS 5069..6718
/codon_start=1
/product="ORF2"
/protein_id="ATN23758.1"
/translation="MKMASNDAAPSNDGAAGLVPEINNEAMALEPVAGAAIAAPLTGQ
QNIIDPWIMNNFVQAPGGEFTVSPRNSPGEVLLNLELGPEINPYLAHLARMYNGYAGG
FEVQVVLAGNAFTAGKIIFAAIPPNFPIDNLSAAQITMCPHVIVDVRQLEPVNLPMPD
VRNNFFHYNQGSDSRLRLIAMLYTPLRANNSGDDVFTVSCRVLTRPSPDFSFNFLVPP
TVESKTKPFSLPILTISEMSNSRFPVPIDSLHTSPTDNIVVQCQNGRVTLDGELMGTT
QLLPSQICAFRGVLTRSTSRASDQADTVAPRLFNYYWHIKLDNLNGTPYDPAEDIPGP
LGTPDFLGKVFGVASQRDPDTTTRAHEAKIDTSSGRFAPKLGSLEISTESADFNPNKP
TRFTPVGIGVDQAEGDFQQWTLPDYAGKITHNMNLAPAVAPNFPGEQLLFFRSHLPSS
GGRSDGILDCLVPQEWVQHFYQESAPSQSQVALIRYINPDNGRVLFEAKLHKLGFITI
AKNGNSPITVPPNGYFRFESWVNPFYTLAPMGTGNGRRRIQ"
CDS 6718..7479
/codon_start=1
/product="ORF3"
/protein_id="ATN23759.1"
/translation="MAGAFIAGLAGDMLTNTVGSLVNAGANAINQTIDFENNKHLQNA
SFNHDKEMLNAQIEATKRLQADMIAIKQGVLTAGGFSPTDAARGAINAPMTKVLDWNG
TRYWAPGATSTTSMSGGFTNQTVHRSTPNFKTNQAPRPAPSSGSSARSNSTQITSLSS
HSSGSSRSSGSTVVSSISTNRTRDWVNQQNFNLEPHMPGSLRTAFVTPPSSSASSSGT
VSTVPKNVLDSWTSAFNTRRQPLFAHLRRRGESKV"
ORIGIN
1 tctaacgacg cttccgctgc cgctgctgcc aacagcaaca acgacaacgc aaaatcttca
61 agtgacggag tattatctaa tatggctgtc acttttaaac gagccctcgg ggcgcggtct
121 aaacagccgc ccccgaggga caaaccacca aaacccccaa gaccacccac accagagttg
181 gttaaggcaa tcccccctcc cccacccaac ggggaggacg aaccaaccat ttcttataac
241 gtcaaagaag gtgtttctgg tttgcctgaa ctctcaactg tcacccaact agaggagaac
301 tctacagcgt tcagtgttcc ccctcttagt cagagggaga acagggatgc taaggaacca
361 ttgactggaa ccatcctgga gatgtgggac ggggagatct accattatgg cttatacgtg
421 gaacgagggt tagtgctcgg tgtacacaaa ccaccggcag ccgtcagtct tgctaagatt
481 gagctgaccc ccttgtcttt gtattggaga ccagtgtaca ccccacagta cctcatttcc
541 cctgacactc tcaaaaagtt gcatggggag acgttccctt atacagcctt tgataacaac
601 tgttatgcct tctgctgttg ggtacttgac ttgaacgatt catggctgag cagaaggatg
661 atacagagga caacaggctt cttccgaccc taccaggact ggaacaggaa acccctcccc
721 acgatggatg attccaaagt gaaaaaggtg gccaatgttg tcctttgtgc tctctcatca
781 ttgttcacaa gaccaattaa ggacattatt gggaagttga aacccctaaa catccttaac
841 atcctagcca catgtgattg gacttttgca ggcatagtgg aatccctgat ccttttggct
901 gaactgtttg gagttttctg gacaccccca gatgtgtctg caatgatcgc tcccttactg
961 ggtgattatg agctacaggg acccgaggac ctcgctgtgg aactcgtacc cgtagtaatg
1021 ggagggatag gtttggtgct gggattcacc aaagagaaaa ttggaaaaat gctttcatct
1081 gctgcttcaa ccctgagggc atgcaaagat ctcggtgcat atgggttgga gatcctcaag
1141 ttggtcatga aatggttttt cccaaagaaa gaagagaaaa acgaattggc aatggtgaga
1201 tccatcgagg atgcagtgct agatcttgag gccattgaga acaaccatat gacagctcta
1261 ctcaaggata aagacagcct tgcaacctac atgaggactc ttgacatgga ggaggagaaa
1321 gcgaggaaac tttccaccaa gtctgcctcg ccggatattg tgggcacgat aaacgcccta
1381 ctgtcaagaa ttgctgctgc ccggtctcta gtgcacaggg ctaaggagga gctgtcaagc
1441 aggccccgac cagtcgttgt gatgatttca gggagaccag gtattgggaa aacccaccta
1501 gctagagagt tggcaaagaa gatcgcctcc tcactcacag gtgaccagag ggtgggtctt
1561 atcccacgca acggggtcga ccactgggat gcatacaaag gtgaaagagt cgttctctgg
1621 gacgactacg ggatgagcaa ccccattcac gacgccctca gactccagga gctcgctgac
1681 acctgtcctc tcacactcaa ctgtgacagg attgagaata aaggcaaagt ctttgacagt
1741 gacgccataa taataaccac caatttggcc aacccagcgc cactggatta cgttaacttt
1801 gaagcttgct caagacgcat agatttcctc gtctatgctg atgcccctga agttgagaag
1861 gccaaacggg acttcccagg ccaaccagac atgtggaaag acacctttaa acctgacttc
1921 tctcacataa aactgacatt agccccgcaa ggaggttttg acaagaatgg taacactcct
1981 catgggaagg gtgtcatgaa gaccctcaca gccagttctc tcgttgcccg agcatcaggt
2041 ctccttcacg agagattgga cgaatatgaa ctgcagggcc caacccccac aacattcaac
2101 ttcgaccgca acaaggtgct tgcttttagg cagcttgctg ctgaaaacaa atacggtctt
2161 gttgacacaa tgagggtcgg atcacagctc aagaatgtta aaaccatgac agaactcaag
2221 caggctctca agaacatctc agtcaagaaa tgtcagcttg tgtatggtgg gggcacgtac
2281 acacttgaat ctgatggcaa aggcaatgtg cacgtcgaga aggtgaacaa cactagtgtg
2341 caaactaaca acgagctctc cggggctttg caccatctca agtgtgccag aattaggtac
2401 tatgttaagt gtgtccagga agctctctac tccatcctgc aaattgccgg ggctgcattc
2461 atcaccacgc gcatcacaaa gcgcatgaac atacaaaacc tctggtccaa accacaagca
2521 gaagatctgg aggagaccaa caacgaggag ggctgtccaa aacctaaaaa tgatgaggaa
2581 tttgttatct cctctgatga catcaaaacc gagggcaaga aaggaaagaa caagactggc
2641 cgtggtaaga agcacacagc cttttccagc aaaggactca gtgatgagga gtacgatgag
2701 tacaagagaa tcagggaaga gagaaatggc aagtactcca tagaggaata cctacaggac
2761 agagacaaat actatgagga ggtggccata gccagggcaa ctgaagaaga cttctgtgaa
2821 gaagaggagg ctaaaatccg gcagaggata ttcagaccaa caaggaaaca acgcaaagag
2881 gaaagggcct ctcttggttt ggttacaggt tctgagatca ggaagagaaa cccagatgac
2941 ttcaagccca aagggaaact atgggccgat gatgacagga atgttgacta caatgagaaa
3001 cttagtttcg aggctccacc aagcatttgg tcacgaatag tcaactttgg ctcagggtgg
3061 ggcttttggg tctcgcccag cctcttcata acatcaaccc atgtcattcc ccaaggcgca
3121 caggagttct ttggagtgcc catcaaacaa atacaaatcc acaagtcagg tgagttctgc
3181 cggcttaggt tcccaaaacc aatcagaacg gatgtcacag gcatgatctt ggaggaaggt
3241 gctccagaag gcactgttgc cacacttctc atcaagagac caactggaga actcatgccc
3301 ttggcagcca gaatgggcac ccacgcgacc atgaaaattc agggtcgcac tgttggtgga
3361 cagatgggca tgctactcac agggtccaac gctaagagca tggatttggg cacgactcct
3421 ggcgattgtg gttgtcccta catctacaag agagggaacg actacgtggt cattggagtt
3481 cacactgccg ccgctcgtgg aggaaacacc gtcatctgtg caacccaagg aaacgagggg
3541 gaggccatgc tagaaggtgg tgacaacaag ggaacttact gtggagcacc aatattaggc
3601 catggaaatg cccccaaact cagcaccaaa accaaattct ggaggtcttc caccaccccc
3661 ttgccacctg gaacctatga gccagcctat ctgggtggca aggaccccag agtgaaaggt
3721 ggcccctcac tgcaacaggt tatgagggac caactaaaac cattcactga gcccagaggc
3781 aaaccaccca aaccaagtgt gctagaagcc gccaagaaga ctataatcaa tgtgcttgaa
3841 caaacaatag acccacctca aaaatggaca tacgcgcagg cgtgtgcatc actagacaag
3901 accacctcca gcggccaccc tcaccacatg cggaagaacg attgttggaa tggggagact
3961 ttcacaggaa aattggcaga ccaagcatca aaggctaacc taatgtttga ggaagggaag
4021 aacatgaccc cagtatacac aggagctctg aaagacgagc tagtcaagac tgataagatc
4081 tatggaacaa tcaagaagag actcctgtgg ggttcagacc tatcaactat gatacggtgt
4141 gcacgagcct tcggtgggct aatggacgag ctcaaggccc actgcgtcac actaccagtc
4201 agggttggta tgaacatgaa tgaggatgga cccataatat ttgagaaaca ttccagatat
4261 aaatatcatt atgatgcaga ttactcccgc tgggactcaa cacaacaaag agcagtgctg
4321 gctgcagccc tggaaataat ggtcaaattc tcaccagaac cccatctggc ccaagtagtt
4381 gcagaagacc tcttgtcccc cagtgtgatg gatgtgggtg atttcaagat atcaatcaac
4441 gagggattac cctctggcgt cccttgcacc tcacaatgga actccattgc ccactggctc
4501 ctcacactat gtgcactgtc tgaagtcaca gacctatccc ctgacatcat ccaggcaaat
4561 tccctgttct ccttttatgg tgatgatgaa atagtgagca cagacatcaa attggaccca
4621 gagaaattga cagcaaaatt gaaggaatac gggctgaaac caacccgtcc tgataaaaca
4681 gaaggaccct taatcatctc tgaagatttg gatggcctga ccttcttacg gagaacggta
4741 acccgtgatc cggccgggtg gtttggcaaa ctggaccaaa gctcaatact caggcagatg
4801 tactggacca ggggaccaaa ccatgaggac ccctttgaaa cgatgatacc acactcccaa
4861 agacccatac aactgatgtc attattgggt gaagctgcat tgcatggtcc atcattctac
4921 agtaaaatca gcaaactagt catctcagaa ttgaaagagg gtggaatgga cttttacgtg
4981 cccagacaag aaccaatgtt caggtggatg agattctcag atttgagcac gtgggagggc
5041 gatcgcaatc tggctccctg ttttgtgaat gaagatggcg tcgaatgacg ccgctccatc
5101 taatgatggt gccgccggcc tcgtcccaga gatcaacaat gaggcaatgg cgctagagcc
5161 agtggcgggt gcagcgatag cagcacccct cactggtcag caaaatataa ttgatccctg
5221 gattatgaac aattttgtgc aagcacctgg tggtgagttc acagtgtccc ctagaaattc
5281 ccctggtgaa gttcttctta atttggagtt ggggcctgaa ataaatcctt atttggccca
5341 tcttgctaga atgtataatg gttatgcagg tggatttgaa gtgcaggtgg tcctagctgg
5401 aaatgcgttt acagcaggaa agataatctt tgcagctatt ccccccaatt ttccaattga
5461 caatctaagt gcagcacaga tcacaatgtg tccacatgtg attgtggacg tcagacagtt
5521 ggaaccagtc aacctcccga tgcctgacgt tcgcaacaac ttctttcatt acaatcaagg
5581 gtctgattcg agattgcgcc taattgcaat gctgtataca cctcttaggg caaataattc
5641 tggggatgat gttttcactg tgtcctgcag agtgctaact agacctagtc ctgacttctc
5701 atttaatttc cttgtgccac ctactgtgga gtcaaagaca aaaccctttt ccctccctat
5761 tctgaccatc tctgaaatgt ccaattctag gttcccagta ccaattgatt ctctgcacac
5821 tagccctact gacaatattg ttgtccagtg ccagaatggg cgcgtcaccc ttgacggtga
5881 gttgatgggc accacccaac tcttgcctag ccaaatttgt gctttcaggg gcgtactcac
5941 cagatcaaca agcagggcca gtgaccaggc cgatacagta gcccctaggt tgtttaatta
6001 ttattggcat ataaaattgg acaatctaaa tggaactccc tatgatcctg cagaagacat
6061 accaggcccc ctgggaacac cagatttcct gggcaaagtc tttggcgtgg ccagccagag
6121 agatcctgat accacgacta gggcacatga agcaaagata gacacatcat ctggccgttt
6181 cgccccaaaa ctaggctcac tagagatatc cactgagtct gctgatttca atccaaacaa
6241 accaacaaga ttcaccccag ttggcattgg ggttgaccag gctgagggag actttcaaca
6301 atggactcta cccgactatg ctggcaagat cacccacaac atgaacttgg ccccagctgt
6361 tgctcccaac ttccctggtg agcagctcct cttcttccgc tcacatttgc catcttctgg
6421 tgggcgatcc gacgggattc tagactgcct ggtcccccaa gagtgggtac agcacttcta
6481 ccaagaatca gccccctctc aatctcaagt ggctctgatt aggtacatca accctgataa
6541 tggtagagta ttatttgagg ccaagctgca caaattaggt ttcataacta tagctaagaa
6601 tggtaattct ccaataactg tccccccaaa tggatacttt aggtttgaat cttgggtgaa
6661 ccccttttat acacttgccc ccatgggaac tgggaatggg cgtagaagga ttcaataatg
6721 gctggagctt ttatagcagg attggctggt gacatgctca caaatactgt aggatcttta
6781 gttaatgcag gggctaatgc cattaatcaa acaattgatt ttgaaaataa taaacatttg
6841 caaaatgctt cttttaatca tgataaggag atgttgaatg cacaaattga ggcaacaaag
6901 agattacagg ctgacatgat tgctatcaaa caaggggttt tgaccgctgg cggcttttcc
6961 cctactgatg cagcccgtgg ggcaattaat gcccccatga caaaagtcct agattggaat
7021 ggaacgagat actgggcacc aggtgccacc tccacaacct cgatgtcggg tggcttcaca
7081 aatcaaactg tgcacagatc cacaccaaat tttaaaacga accaggctcc cagacccgca
7141 cccagcagtg ggtcttcagc aaggtcaaat tcaacccaaa tcactagcct gagctcacac
7201 tcgtccgggt cgtctcgatc cagcgggtct acagttgtca gctcaatatc cactaacagg
7261 actagggact gggtcaacca acaaaatttt aatttggaac cacacatgcc tggatctctt
7321 aggacagctt ttgtcactcc accatctagt tcagcctcta gctcaggcac agtctcaact
7381 gtgcccaaga atgttttgga ctcctggaca tctgcgttta acacgcgcag acagccgcta
7441 ttcgcacacc ttcgcagaag gggggagtca aaagtttagt gggtggggga tctct
//