Typing tool
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Typing tool
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Complete norovirus genomes
| MF140643 | GII.4 Sydney | |
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| GII.P4 New Orleans |
ORF1: 1..5033
ORF2: 5014..6636
ORF3: 6636..7442
LOCUS MF140643 7442 bp RNA linear VRL 24-OCT-2017
DEFINITION Norovirus GII strain
Norovirus/GII/Hu/NL/2013/GII.P4-GII.4/Rotterdam/E1300307_p11_d195
ORF1 gene, partial cds; and ORF2 and ORF3 genes, complete cds.
ACCESSION MF140643
VERSION MF140643.1
KEYWORDS .
SOURCE Norovirus GII
ORGANISM Norovirus GII
Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes;
Picornavirales; Caliciviridae; Norovirus; Norovirus norwalkense.
REFERENCE 1 (bases 1 to 7442)
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 7442)
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..7442
/organism="Norovirus GII"
/mol_type="genomic RNA"
/strain="Norovirus/GII/Hu/NL/2013/GII.P4-
GII.4/Rotterdam/E1300307_p11_d195"
/host="Homo sapiens"
/db_xref="taxon:122929"
/geo_loc_name="Netherlands"
/collection_date="04-Aug-2013"
/note="genotype: GII.P4-GII.4"
CDS <1..5033
/codon_start=3
/product="ORF1"
/protein_id="ATN23625.1"
/translation="SSDGVLSSMAVTFKRALGARPKQPPPREKPQRPPRPPTPELVKN
IPPPPPNGEDEIVVSYSVKDGVSGLPDLSTVRQPEESNTAFSVPPLNQRENRDAKEPL
TGTILEMWDGEIYHYGLYVDRGLVLGVHKPPAAISLAKVELAPLSLYWRPVYTPQYLI
SPDTLKKLSGETFPYTAFDNNCYAFCCWVLDLNDSWLSRRMIQRTTGFFRPYQDWNRK
PLPTMDDSKIKKVANIFLCALSSLFTRPIKDIIGKIRPLNILNILASCDWTFAGIVES
LILLAELFGVFWTPPDVSAMIAPLLGDYELQGTEDLAVELVPVVMGGIGLVLGFTKEK
IGKMLSSAASTLRACKDLGAYGLEILKLVMKWFFPKKEEENELAIVRSIEDAVLDLEA
VESNHLTALLKDKDSLATYMRTLDLEEEKARKLSTKSASPDIVGTINALLARIAAARS
LVHRAKEELSSRPRPVVLMISGRPGIGKTHLAREVAKRIAASLTGDQRVGLIPRNGVD
HWDAYKGERVVLWDDYGMSNPIHDALRLQELADTCPLTLNCDRIENKGKVFDSDVIII
TTNLANPAPLDYVNFEACSRRIDFLVYAEAPDVEKAKRDFPGQPDMWKNAFSSDFSHI
KLALAPQGGFDKNGNTPHGKGVMKTLTTGSLIARASGLLHERLDEFELQGPALTTFNF
DRNKVLAFRQLAAENKYGLMDTMRVGKQLKDVKTMPELKQALKNVSIKKCQIVYSGCT
YMLESDGKGNVKVDRIQSAAVQTNNELAGALHHLRCARIRYYVKCVQEALYSIIQIAG
AAFVTTRIAKRMNIQDLWSKPQVENTEETTSKDGCPKPKDDEEFVISSDDIKTEGKKG
KNKTGRGKKHTAFSSKGLSDEEYDEYKRIREERNGKYSIEEYLQDRDKYYEEVAIARA
TEEDFCEEEEAKIRQRIFRPTRKQRKEERVSLGLVTGSEIRKRNPDDFRPKGKLWADD
DRSVDYNEKLSFEAPPSIWSRIVNFGSGWGFWVSPSLFITSTHVIPQGAKEFFGVPIK
QIQVYKSGEFCRLRFPKPIRTDVTGMILEEGAPEGTVVTLLIKRSTGELMPLAARMGT
HATMKIQGRTVGGQMGMLLTGSNAKGMDLGTTPGDCGCPYIYKRGNDYVVIGVHTAAA
RGGNTIICATQGSEGEATLEGGDNKGTYCGAPILGPGSAPTLSTKTKFWRSSTVPLPP
GTYEPAYLGGKDPRVKGGPSLQQVMREQLKPFTEPRGKPPKPSVLEAAKKTIINVLEQ
TIDPPEKWSFAQACASLDKTTSSGHPHHMRKNDCWNGDSFTGKLADQASKANLMFEEG
KNMTPVYTAALKDELVKTDKIYGKIKKRLLWGSDLATMIRCARAFGGLMDELKAHCVT
LPIRVGMNMNEDGPIIFEKHSRYTYHYDADYSRWDSTQQRAVLAAALEIMVKFSPEPH
LAQVVAEDLLSPSVVDVGDFTISINEGLPSGVPCTSQWNSIAHWLLTLCALSEVTNLS
PDTIQANSLFSFYGDDEIVSTDIKLDPEKLTAKLREYGLKPTRPDKTEGPLVISENLN
GLTFLRRTVTRDPAGWFGKLEQSSILRQMYWTRGPNHGDPSETMIPHSQRPIQLMSLL
GEAALHGPAFYSKISKLVIAELKEGGMDFYVPRQEPMFRWMRFSDLSTWEGDRNLAPS
FVNEDGVE"
CDS 5014..6636
/codon_start=1
/product="ORF2"
/protein_id="ATN23626.1"
/translation="MKMASSDANPSDGSAANLVPEVNNEVMALEPVVGAAIAAPVAGQ
QNVIDPWIRNNFVQAPGGEFTVSPRNAPGEILWSAPLGPDLNPYLSHLARMYNGYAGG
FEVQVILAGNAFTAGKVIFAAVPPNFPTEGLSPSQVTMFPHIVVDVRQLEPVLIPLPD
VRNNFYHYNQSNDPTIKLIAMLYTPLRANNAGDDVFTVSCRVLTRPSPDFDFIFLVPP
TVESRTKPFSVPVLTVEEMTNSRFPIPLEKLFTGPSSAFLVQPQNGRCTTDGVLLGTT
QLSPVNICTFKGGVVHITGSRNYTMNLASQNWNNYDPTEEIPAPLGAPDFVGKIQGML
TQTTRADGSTRGHKATVYTGSADFTPKLGRVQFETDTDHDFEANQNTKFTPVGVIQDG
STTHRNEPQQWVLPSYSGRNTHNVHLAPAVAPTFPGEQLLFFRSTMPGCSGYPNMDLD
CLLPQEWVQYFYQEAAPAQSDVALLRFVNPDTGRVLFECKLHKSGYVTVAHTGQHDLV
IPPNGYFRFDSWVNQFYTLAPMGNGAGRRRVV"
CDS 6636..7442
/codon_start=1
/product="ORF3"
/protein_id="ATN23627.1"
/translation="MAGAFFAGLASDVLGSGLGSLINAGAGAINQKVEFENNRKLQQA
SFQFSSNLQQASFQHDKEMLQAQIEATKKLQQEMMKVKQAMLLEGGFSETDAARGAIN
APMTRALDWSGTRYWAPDARTTTYNAGRFSTPQPSGALSGRANLRDAVPARGSSSKSS
NSSTAISVYSNQTTSTRLGSTAGSGTSVSSLPSTARTRSWVEDQSRNLSPFMRGAHNI
SFVTPPSSRSSSQGTVSTVPKEVLDSWTGAFNTHRQPLFAHIRSRGESRV"
ORIGIN
1 cttcaagtga cggagtgctt tctagcatgg ctgtcacttt taaacgagcc ctcggggcgc
61 ggcctaaaca gcctcccccg agggaaaaac cacaaagacc cccacgacca cctactccag
121 aactggttaa aaatattccc cctcccccac ccaacggaga ggatgaaata gtggtttctt
181 atagtgttaa agatggtgtt tccggtttgc ctgacctttc caccgtcagg caaccggaag
241 aatccaacac ggccttcagt gtccctccac tcaatcagag ggagaataga gatgctaagg
301 aaccactcac tggaacaatt ctggaaatgt gggacgggga aatctaccat tatggcctgt
361 atgtggatcg aggtcttgta ctaggcgtgc acaaaccgcc agctgccatc agcctcgcta
421 aggttgagct agcaccactc tccttgtact ggagacctgt gtacactcct cagtacctca
481 tctctccaga cactctcaag aaattgtccg gagaaacgtt cccctacaca gcctttgata
541 acaactgcta tgccttttgt tgctgggtcc tggacctaaa tgactcgtgg ctgagcagga
601 gaatgatcca gagaacgact ggtttcttca ggccctacca agactggaat aggaaacccc
661 ttcccactat ggatgactcc aaaataaaaa aggtagctaa catatttctg tgtgctctgt
721 cctcgctatt caccagaccc ataaaagata taatagggaa gataaggcct cttaacatcc
781 tcaacatctt agcctcatgt gattggacct ttgcgggcat agtggagtcc ctgatactct
841 tggcagaact ctttggagtt ttctggacac ccccagatgt gtctgcgatg attgccccct
901 tacttggtga ctacgagcta caaggaactg aggaccttgc agtggagctc gtccccgtgg
961 tgatgggggg aattggtttg gtgctaggat tcaccaaaga gaagattggg aagatgttgt
1021 catctgctgc gtccacctta agagcttgca aagaccttgg tgcatatggg ctagagatcc
1081 taaagttagt catgaagtgg ttcttcccga agaaggagga ggaaaatgag ctggctatag
1141 tgaggtccat cgaggatgca gtcctggatc tcgaggcagt tgaaagcaat catttgaccg
1201 ccttgcttaa agataaagac agtctggcaa cctacatgag aacacttgac cttgaagagg
1261 agaaagccag gaaactctca accaagtctg cctcacccga catcgtgggc acaatcaacg
1321 ccctcctggc gagaatcgct gccgcacgtt ctctggtgca tcgagcgaag gaggagcttt
1381 ccagcagacc aagacctgtg gtgttgatga tatcaggcag gccaggaata gggaagaccc
1441 acctcgctag ggaagtggct aagagaatcg cagcctccct tacaggagac cagcgtgttg
1501 gccttatccc acgcaatggc gtcgaccatt gggacgcgta caagggggag agggtcgtcc
1561 tatgggacga ttatggaatg agcaacccta ttcacgatgc cctcagactg caagaactcg
1621 ctgacacttg ccccctcact ctgaactgtg acaggattga aaataaagga aaggtctttg
1681 acagcgatgt catcattatc accaccaatc tggccaaccc agcaccactg gactatgtca
1741 actttgaagc atgctcgagg cgcattgact tcctcgtgta tgcagaagct cctgatgtcg
1801 aaaaggcgaa gcgtgacttc ccaggccagc ctgacatgtg gaagaacgct ttcagttctg
1861 atttctcaca cataaaacta gcactggccc cacagggtgg tttcgacaag aacgggaaca
1921 ccccacacgg aaagggcgtc atgaagactc tcaccactgg ctcccttatt gcccgggcat
1981 cagggctgct ccatgagagg ttagatgaat ttgaactgca gggtccagct ctcaccacct
2041 tcaatttcga tcgcaataaa gtgcttgcct ttagacagct tgctgctgaa aataaatatg
2101 gattgatgga cacaatgagg gttgggaaac agctcaagga tgtcaaaacc atgccagaac
2161 tcaaacaagc actcaagaat gtctcaatca agaagtgtca aatagtgtat agtggttgca
2221 cctacatgct tgagtctgat ggcaagggca atgtgaaagt tgacaggatc cagagcgccg
2281 ccgtgcagac caacaatgag ctggctggtg ccctgcacca tttgaggtgc gccagaatca
2341 gatactatgt caagtgtgtc caggaagccc tgtattccat catccaaatt gctggggctg
2401 catttgtcac cacgcgcatt gccaagcgca tgaacataca agacctatgg tccaagccac
2461 aagtggaaaa cacagaggag actaccagca aggacgggtg cccaaaacct aaggatgatg
2521 aggagtttgt catttcatcc gacgacatca aaactgaggg caagaaaggg aagaacaaga
2581 ctggccgtgg caagaagcac acagcatttt caagcaaagg cctcagtgat gaagagtacg
2641 atgaatacaa gaggattaga gaagaaagga atggcaagta ctctatagaa gagtaccttc
2701 aggacaggga caaatattat gaggaggtgg ccattgccag agcgactgag gaagacttct
2761 gtgaagagga ggaagccaag atccggcaaa ggatctttag gccgacaagg aaacaacgca
2821 aggaggaaag agtctctctc ggcttggtca caggctctga aattaggaaa aggaacccag
2881 atgacttcag acccaaaggg aaattatggg ctgacgatga caggagtgtg gactacaatg
2941 agaaactcag ttttgaggcc ccaccaagca tttggtcgag aatagtcaac tttggttcag
3001 gctggggatt ctgggtctcc cccagcttgt tcataacatc aacccatgtt ataccccagg
3061 gcgcaaagga gttctttgga gtccccatca aacaaataca ggtatacaag tcaggcgagt
3121 tctgtcgctt gagattcccc aaaccaatca ggactgatgt gacgggcatg atcttagaag
3181 aaggcgcacc tgagggcacc gtggtcacac tactcatcaa aaggtccact ggggaactta
3241 tgcccctagc agctaggatg gggacccatg cgaccatgaa gatccaaggg cgcactgttg
3301 ggggccagat gggcatgctt ctgacaggat ccaacgccaa gggtatggac ctgggtacta
3361 caccaggtga ttgtggctgc ccctatatct acaagagagg taatgactat gtggtcattg
3421 gagtccacac ggctgccgca cgtgggggga acactatcat atgtgccacc caggggagtg
3481 aaggagaggc tacacttgag ggtggtgaca acaaggggac atactgtggt gcaccaatcc
3541 taggcccagg gagtgcccca acacttagca ccaagaccaa attctggaga tcgtccacag
3601 taccactccc acctggcacc tatgaaccag cctatcttgg tggtaaggac cctagagtca
3661 agggtggccc ttcactgcag caagtcatga gggaacagtt gaagccattc acagagccca
3721 ggggcaagcc accaaaacca agtgtgttag aagctgccaa gaagaccatc atcaatgtcc
3781 ttgagcaaac aattgatcca cctgagaaat ggtcgttcgc acaagcttgc gcgtcccttg
3841 acaagaccac ttccagtggt catccgcacc acatgcggaa aaacgactgc tggaacgggg
3901 attccttcac aggcaagctg gcagaccagg cttccaaggc taacctgatg tttgaagaag
3961 ggaagaacat gaccccagtc tacacagctg cgctcaagga tgagttagtt aaaactgaca
4021 aaatttatgg caagatcaag aagaggcttc tttggggctc ggacttggcg accatgatcc
4081 ggtgtgctcg agcattcgga ggcttaatgg atgaactcaa agcgcactgt gtcacacttc
4141 ccattagagt tggcatgaat atgaatgagg atggccccat catcttcgag aagcattcca
4201 ggtatacgta ccactatgat gctgattact ctcgatggga ttcaacacaa cagagagccg
4261 tgttggcagc agctctagaa atcatggtta aattctcccc agaaccacat ttggctcagg
4321 tagtcgcgga agatcttctt tctcctagcg tggtggacgt gggcgacttc acaatatcaa
4381 tcaacgaggg tctcccctct ggggtgccct gcacctccca atggaactcc atcgcccact
4441 ggcttctcac tctctgtgcg ctctccgaag tcacaaatct gtcccctgat accatacagg
4501 ccaattctct cttctctttt tatggtgatg atgaaattgt tagcacagac ataaaattgg
4561 acccagagaa attgacagca aagctcagag aatatgggtt aaaaccaacc cgccctgaca
4621 aaactgaagg accccttgtc atctctgaaa acctgaatgg cctaactttc ctgcggagaa
4681 ctgtgacccg cgacccagct ggttggtttg gaaaactgga gcagagttca atactcaggc
4741 aaatgtactg gactaggggt cccaaccatg gagacccatc tgaaacaatg attccacact
4801 cccaaagacc catacaattg atgtccctac tgggggaggc cgctctccac ggtccagcat
4861 tttacagtaa aatcagcaaa ttggtcattg cagagctaaa agaaggtggt atggattttt
4921 acgtgcccag acaagagcca atgttcagat ggatgagatt ctcagatctg agcacgtggg
4981 agggcgatcg caatctggct cccagttttg tgaatgaaga tggcgtcgag tgacgccaac
5041 ccatctgatg ggtccgcagc caacctcgtc ccagaggtca acaatgaggt tatggctctg
5101 gagcccgttg ttggtgccgc cattgcggca cctgtagcgg gccaacaaaa tgtaattgac
5161 ccctggatta gaaacaattt tgtacaagcc cctggtggag agtttacagt gtcccctaga
5221 aacgctccag gtgaaatact atggagcgcg cccttaggcc ctgatctaaa tccctaccta
5281 tcccatttgg ccagaatgta taatggttat gcaggtggtt ttgaagtgca ggtaattctc
5341 gcggggaacg cgttcaccgc cgggaaggtc atatttgcag cagtcccacc aaattttcca
5401 actgaaggct tgagccccag ccaggtcact atgttccccc atatagtagt agatgttagg
5461 caattagaac ctgtgttgat tcccttaccc gatgttagga ataatttcta tcattacaat
5521 caatcaaatg accccaccat caagttgata gcaatgctgt atacaccact tagggctaat
5581 aatgctgggg acgatgtctt cacagtttct tgccgagttc tcacgagacc atcccccgat
5641 tttgatttta tatttctagt gccacccaca gttgagtcta gaactaaacc attctctgtc
5701 ccagttttaa ctgttgagga gatgaccaat tcaagattcc ccattccttt ggaaaagttg
5761 ttcacgggtc ccagcagtgc ctttcttgtt caaccacaaa acggtaggtg cacgactgat
5821 ggcgtgctcc taggcaccac ccaattgtct cctgtcaaca tctgcacctt caaagggggt
5881 gtcgtccaca tcacaggtag tcgtaactac acaatgaatt tggcttctca aaattggaac
5941 aattatgacc caacagaaga aatcccagcc cctctaggag ctccagattt tgtggggaag
6001 attcaaggca tgctcaccca aaccacaagg gcagatggct caacacgcgg ccacaaagct
6061 acagtgtaca ctgggagcgc cgactttact ccaaaactgg gcagagttca atttgaaact
6121 gacacagacc atgattttga agctaaccaa aacacaaagt tcaccccagt cggtgtcatc
6181 caagatggta gcaccaccca ccgaaatgaa ccccaacagt gggtgctccc aagttactca
6241 ggcagaaata ctcataatgt tcatctggcc cccgctgtag cccccacttt tccgggtgaa
6301 caacttctct tctttagatc caccatgccc ggatgtagcg ggtaccccaa catggatttg
6361 gactgtctgc tcccccagga atgggtgcag tacttctacc aagaggcagc cccagcacaa
6421 tctgatgtgg ctctgctaag atttgtgaat ccagacacag gtagggtttt gtttgagtgt
6481 aagctccata aatcaggcta tgttacagtg gctcacactg gccaacatga tttggttatc
6541 ccccccaatg gttattttag gtttgattcc tgggtcaacc agttctacac gcttgccccc
6601 atgggaaatg gagcggggcg tagacgtgta gtataatggc tggagctttc tttgctggat
6661 tagcatctga tgtccttggc tctggacttg gttcccttat caatgctggg gctggggcca
6721 tcaaccaaaa agttgagttt gaaaataaca gaaaattgca acaagcatcc ttccaattta
6781 gcagcaatct acaacaggct tcctttcaac atgacaaaga aatgctccaa gcacaaattg
6841 aggccaccaa aaagctacaa caggaaatga tgaaagttaa gcaggcaatg ctcctagagg
6901 gtgggttctc tgagacagat gcagcccgcg gggcaatcaa cgcccccatg acaagagctt
6961 tggactggag cgggacgagg tactgggctc ccgatgctag gactacaaca tacaatgcag
7021 gccgcttttc cacccctcaa ccatcggggg cactgtcagg aagagccaat cttagggatg
7081 ctgtccctgc tcggggttcc tccagtaaat cttctaactc ttctactgct atttctgtgt
7141 actcaaatca aaccacttca acgagacttg gttctacagc tggttctggt accagtgtct
7201 cgagcctccc gtcaactgca aggactagga gctgggttga ggatcaaagt aggaatttgt
7261 ctcctttcat gaggggggct cacaacatat cgtttgtcac cccaccatct agcagatcct
7321 ctagccaagg cacagtctca accgtgccta aagaggtttt ggactcctgg actggcgctt
7381 tcaacacgca caggcagcct ctcttcgctc acattcgtag tcgaggggag tcacgggtgt
7441 aa
//