Typing tool
|
|
|
|
|
|
Typing tool
|
Complete norovirus genomes
| MF140673 | GII.4 Sydney | |
|
|---|---|---|---|
| GII.P31 |
ORF1: 1..5085
ORF2: 5066..6688
ORF3: 6688..7494
LOCUS MF140673 7496 bp RNA linear VRL 24-OCT-2017
DEFINITION Norovirus GII strain
Norovirus/GII/Hu/NL/2013/GII.Pe-GII.4/Rotterdam/E1300303_p3_d122
ORF1 gene, partial cds; and ORF2 and ORF3 genes, complete cds.
ACCESSION MF140673
VERSION MF140673.1
KEYWORDS .
SOURCE Norovirus GII
ORGANISM Norovirus GII
Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes;
Picornavirales; Caliciviridae; Norovirus; Norwalk virus.
REFERENCE 1 (bases 1 to 7496)
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 7496)
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..7496
/organism="Norovirus GII"
/mol_type="genomic RNA"
/strain="Norovirus/GII/Hu/NL/2013/GII.Pe-
GII.4/Rotterdam/E1300303_p3_d122"
/host="Homo sapiens"
/db_xref="taxon:122929"
/country="Netherlands"
/collection_date="29-Aug-2013"
/note="genotype: GII.Pe-GII.4"
CDS <1..5085
/codon_start=1
/product="ORF1"
/protein_id="ATN23715.1"
/translation="NDASAAAVANSNNDIAKSSSDGVFSNMAVTFKRALGARPKQPPP
KEIPPRPPRPPTPELIKKIPPPPPNGEDELVVSYSAKDGVAGLPELTTVRQPEETNTA
FSVPPLNQRESRDAKEPLTGTIIEMWDGEIYHYGLYVERGLILGVHKPPAAISLAKVE
LAPLSLFWRPVYTPQYLISPDTLRRLHGESFPYTAFDNNCYAFCCWVLDLNDSWLSRR
MIQRTTGFFRPYQDWNRKPLPTMDDSKLKKVANIFLCTLSSLFTRPIKDIIGKLKPLN
ILNILATCDWTFAGIVESLILLAELFGVFWTPPDVSAMIAPLLGDYELQGPEDLAVEL
VPVVMGGIGLVLGFTKEKIGKMLSSAASTLRACKDLGAYGLEILKLVMKWFFPKKEEA
NELAMVRSIEDAVLDLEAIENNHMTTLLKDKDSLATYMRTLDLEEEKARKLSTKSASP
DIVGTINALLARIAAARSLVHRAKEELSSRPRPVVVMISGRPGIGKTHLARELAKKIA
ASLTGDQRVGLIPRNGVDHWDAYKGERVVLWDDYGMSNPIHDALRLQELADTCPLTLN
CDRIENKGKVFDSDAIIITTNLANPAPLDYVNFEACSRRIDFLVYAEAPEVEKAKRDF
PGQPDMWKNAFSPDFSHIKLSLAPQGGFDKNGNTPHGKGVMKTLTTGSLIARASGLLH
ERLDEYELQGPTLTTFNFDRNKILAFRQLAAENKYGLVDTMRVGKQLKDVKTMSDLKQ
ALKNIAIRKCQIVYNGGTYTLEADGKGSVKVDKVQSATVQTNNELAGALHHLRCARIR
YYVKCVQEALYSIIQIAGAAFVTTRIAKRMNIQDLWSKPQVEDTEEMANKDGCLKPKD
DEEFVVSSDDIKTEGKKGKNKSGRGKKHTAFSSKGLSDEEYDEYKRIREERNGKYSIE
EYLQDRDKYYEEVAIARATEEDFCEEEEAKIRQRIFRPTRKQRKEERASLGLVTGSEI
RKRNPEDFKPKGKLWADDDRSVDYNEKLNFEAPPSIWSRIVNFGSGWGFWVSPSLFIT
STHVIPQGAKEFFGVSIKQIQIHKSGEFCRLRFPKPIRTDVTGMILEEGAPEGTVATL
LIKRPTGELMPLAARMGTHATMKIQGRTVGGQMGMLLTGSNAKSMDLGTTPGDCGCPY
IYKRGNDYVVIGVHTAAARGGNTVICATQGSEGEATLEGGDSKGTYCGAPILGPGSAP
KLSTKTKFWRSSTTPLPPGTYEPAYLGGKDPRVKGGPSLQQVMRDQLKPFTEPRGKPP
RPNVLEAAKKTIINVLEQTIDPPQKWSFAQACASLDKTTSSGHPHHMRKNDCWNGESF
TGKLADQASKANLMFEEGKNMTPVYTGALKDELVKTDKVYGKVKKRLLWGSDLATMIR
CARAFGGLMDELKAHCVTLPVRVGMNMNEDGPIIFEKHSRYRYHYDADYSRWDSTQQR
DVLAAALEIMVKFSPEPHLAQIVAEDLLSPSVMDVGDFKISISEGLPSGVPCTSQWNS
IAHWLLTLCALSEVTDLSPDIIQANSLFSFYGDDEIVSTDIKLDPEKLTAKLKEYGLK
PTRPDKTEGPLVISEDLDGLTFLRRTVTRDPAGWFGKLEQSSILRQMYWTRGPNHEDP
FETMIPHSQRPIQLMSLLGEAALHGPAFYSKISKLVIAELKEGGMDFYVPRQEPMFRW
MRFSDLSTWEGDRNLAPSFVNEDGVE"
CDS 5066..6688
/codon_start=1
/product="ORF2"
/protein_id="ATN23716.1"
/translation="MKMASSDANPSDGSAANLVPVVNNEVMALEPVVGAAIAAPVAGQ
QNVIDPWIRNNFVQAPGGEFTISPRNAPGEILWSAPLGPDLNPYLSHLARMYNGYAGG
FEVQVLLAGNAFTAGKVIFAAVPPNFPTEGLSPSQVTMFPNIVVDVRQLEPVLIPLPD
VRNNFYHYNQSNDPTIKLIAMLYTPLRANNAGDDVFTVSCRVLTRPSPDFDFIFLVPP
TVESRTKPFSVPILTVEEMTNSRFPIPLEKLFTGPSSAFVVQPQNGRCTTDGVLLGTT
QLSPVNICTFRGDVTHITGSRNYRMNLASQNWSNYDPTEEIPAPLGIPDFVGKIQGVL
TQTTRTDGSTRGHKATVYTGSADFAPKLGRVQFETDTDHDFETNQNTKFTPAGVIQDG
STTHRNEPQQWVLPSYSGRSTPNVHLAPAVAPTFPGEQLLFFRSTMPGCSGYPNMDLD
CLLPQEWVQYFYQEAAPAQSDVALLRFVNPDTGRVLFECKLHKSGYVTVAHTGQHDLV
IPPNGYFRFDSWVNQFYTLAPMGNGTGRRRAL"
CDS 6688..7494
/codon_start=1
/product="ORF3"
/protein_id="ATN23717.1"
/translation="MAGAFFAGLASDVLGSGLGSLINAGAGAINQKVEFENNRKLQQA
SFQFSSNLQQASFQHDKEMLQAQIEATKRLQQEMMKVKQAMLLEGGFSETDAARGAIN
APMTKALDWSGTRYWAPDARTTTYNAGRFSTPQPSGALPGRANLRDAAPARGSSSKSS
NSSTATSVYSNQTTSTRLGSTAGSGTSVSSFPSTARTRSWVEDQSRNLSPFMRGAHNI
SFVTPPSSRSSSQGTVSTVPKEILDSWTGAFNTRRQPLFAHIRKRGESRV"
ORIGIN
1 aacgacgctt ccgctgccgc tgttgccaac agcaacaacg acatcgcaaa atcttcaagt
61 gacggtgtgt tttctaacat ggctgtcact tttaagcggg ccctcggggc gcggcctaaa
121 cagccgcccc cgaaggaaat accacccaga cccccgcgac cacccacacc agaattgatc
181 aaaaagatcc ctcctccccc acccaacggg gaggatgaac tagtggtctc ttacagcgcc
241 aaagatggcg ttgccggact gcctgagctc accactgtca gacaaccgga agaaaccaac
301 acggcgttca gtgtcccccc actcaaccaa agggagagca gggacgccaa ggagccacta
361 actggaacaa tcattgaaat gtgggatgga gaaatctacc attacggcct gtacgtggaa
421 cgaggtctta tacttggtgt gcacaagcca ccggcagcca ttagccttgc caaggtcgag
481 ctagcaccgc tctctttgtt ctggagacct gtatacaccc cccagtatct catctctcca
541 gacactctta ggagattaca tggagagtca ttcccctaca ctgcatttga caacaattgc
601 tacgcctttt gttgttgggt attagaccta aacgattcat ggctaagcag gagaatgatt
661 cagagaacaa caggcttctt caggccgtac caggattgga acaggaaacc cctccccact
721 atggatgatt ccaaattaaa gaaggtagcc aacatattct tgtgcacttt gtcttcacta
781 ttcaccagac ccattaagga cataataggg aagttgaaac ctcttaacat ccttaacatt
841 ctggctacat gtgattggac cttcgcaggc atagtggaat ccttaatact cttggcagaa
901 ctctttggag ttttctggac acccccagat gtgtctgcga tgatcgcccc cttgctaggt
961 gattatgaac tgcaaggacc tgaggacctt gcagtggaac tggtcccagt agtgatgggg
1021 gggataggtt tggtgctagg atttaccaaa gagaaaatcg gaaagatgct gtcatccgct
1081 gcatccactt taagagcttg taaagacctt ggtgcatacg gactggaaat cttaaaattg
1141 gtcatgaagt ggttcttccc aaagaaagag gaagcaaatg aactggctat ggtgagatcc
1201 atcgaggatg cagtactaga cctcgaggca attgaaaaca accacatgac caccctactc
1261 aaagacaaag acagcttggc aacctacatg agaacccttg accttgagga ggagaaagcc
1321 agaaaactct caaccaaatc tgcttcaccc gatattgtgg gcacaatcaa cgctcttctg
1381 gcaagaatcg ctgctgcacg ctccctagtg catcgggcga aagaagagct ctccagcagg
1441 ccgagacctg tcgttgtgat gatatcggga agaccaggga tagggaaaac tcaccttgcc
1501 agggagctgg ccaagaagat cgcggcctcc ctcacagggg accagcgtgt gggtcttatc
1561 ccacgcaatg gtgtcgacca ctgggacgca tacaagggcg aaagagttgt cctatgggac
1621 gactatggaa tgagcaaccc catccatgac gccctcaggt tgcaggagct tgctgacact
1681 tgccccctca cgctaaattg tgacagaatt gagaacaaag ggaaagtctt tgacagtgat
1741 gccataatta tcaccaccaa tctggccaac ccagcaccac tggattatgt caactttgaa
1801 gcgtgctcga gacgcattga tttcctcgtg tacgcagaag cccctgaggt ggagaaggca
1861 aagcgcgact tcccaggtca acctgacatg tggaagaacg ctttcagtcc tgacttctca
1921 cacataaaac tgtcattggc tccacagggt ggttttgaca agaacggcaa caccccgcat
1981 ggaaaagggg tcatgaagac cctcaccact ggctccctca tcgcccgagc atcagggtta
2041 ctccatgaga ggctagatga atatgaactg caaggcccaa ccctcaccac tttcaacttt
2101 gaccgcaaca agatacttgc ttttagacag cttgctgctg aaaacaagta tgggctggtg
2161 gacacaatga gagttggaaa acagctcaag gatgtcaaga ccatgtcaga cctcaaacaa
2221 gcactcaaga acatcgcgat caggaagtgc cagatagtgt acaatggtgg cacctacaca
2281 cttgaggctg atggcaaggg tagtgtgaaa gttgacaaag tgcaaagtgc cactgtgcag
2341 accaacaatg aactagccgg tgccctacac cacctaaggt gcgctagaat cagatactat
2401 gttaagtgcg tccaggaggc actgtattcc atcatccaaa tcgctggggc tgcatttgtc
2461 accacgcgca tcgctaagcg catgaatata caggatctct ggtccaagcc acaggtggaa
2521 gacacagaag agatggccaa caaagatggt tgcctaaaac ccaaagatga tgaagagttt
2581 gtcgtctcat ccgacgacat caaaactgag ggcaagaaag ggaagaacaa gtccggccgt
2641 ggcaagaagc acacagcctt ttcaagtaaa gggctcagtg atgaggagta cgatgagtac
2701 aagagaatca gagaagaaag gaatggtaag tactccatag aagagtacct tcaggacaga
2761 gacaagtact acgaggaggt ggccattgcc agggcaaccg aagaggactt ctgtgaagaa
2821 gaagaggcca aaatccggca gagaattttc agaccaacaa ggaaacaacg caaagaagag
2881 agggcctctc tcggcttggt cacaggctct gaaatcagga agagaaaccc agaagacttc
2941 aaacccaagg gaaagctgtg ggctgatgat gacagaagtg ttgactacaa tgagaaactc
3001 aactttgagg ccccaccaag catctggtcg cggatagtca actttggttc aggctggggc
3061 ttctgggtct cccccagtct gtttataaca tcaacccatg tcatacccca aggtgcaaaa
3121 gagttcttcg gagtctctat caagcaaatc cagatacaca agtcaggtga attctgccgg
3181 ttgagattcc caaagccaat cagaactgat gtgacgggca tgattctaga agaaggtgcg
3241 cccgagggga ccgtggccac actgctcatc aagagaccaa ctggagagct catgcctctg
3301 gcagccagaa tggggaccca tgcaaccatg aaaattcagg ggcgtacagt tggagggcaa
3361 atgggtatgc tcctgacagg atccaacgcc aagagtatgg acctaggcac aacaccaggc
3421 gactgcggct gcccctacat ctacaagagg gggaatgact acgtggtcat aggagtccat
3481 acggccgctg cccgtggagg aaacactgtc atatgtgcca cccaggggag tgagggagaa
3541 gccacacttg aaggaggtga cagtaaaggg acatactgtg gcgcaccaat cttgggccca
3601 gggagcgctc cgaagctcag taccaagact aagttttgga gatcatccac aacaccactc
3661 ccacctggca cctacgaacc agcctacctc ggtggcaaag accctagagt caaaggtggc
3721 ccttcattgc aacaagttat gagggaccag ctgaagccat tcacagaacc cagaggcaaa
3781 ccaccaagac caaatgtgtt ggaagctgcc aagaaaacca tcatcaatgt ccttgagcaa
3841 acaattgatc caccccaaaa atggtcattt gcgcaagctt gcgcatccct tgacaaaacc
3901 acctccagcg gccacccgca ccacatgcgg aaaaacgact gttggaatgg ggagtccttc
3961 acaggaaaat tggctgatca agcctccaag gccaacctaa tgtttgaaga gggaaagaac
4021 atgactccag tctacacagg tgcacttaaa gatgagttgg taaagaccga taaagtttat
4081 ggtaaggtca agaagaggct tctgtggggt tcagatctgg cgaccatgat acggtgcgcc
4141 cgagcttttg gaggccttat ggatgaactc aaggcacact gtgtcacact tcctgtcaga
4201 gttggtatga acatgaatga ggatggcccc atcatctttg agaagcactc cagatataga
4261 tatcactatg atgctgatta ttcccggtgg gactcaacac aacaaaggga tgtgctagca
4321 gcagcactag aaatcatggt taagttctct ccagaaccac acctggccca gatagttgca
4381 gaagacctcc tctcccctag cgtgatggat gtaggtgact ttaaaatatc aataagtgag
4441 ggtctcccct ctggggtacc ttgtacctcc cagtggaatt ccatcgccca ctggctcctc
4501 actctgtgtg cactctctga agtcacggac ctgtcccctg atatcattca ggccaactcc
4561 cttttctcct tctatggtga tgatgagatt gtgagcacag acataaagtt ggacccagag
4621 aagctgacag caaaactcaa ggagtacggg ctgaaaccaa cccgccccga caaaactgaa
4681 ggaccccttg ttatctctga agacctggat ggcctgacat tcctccggag aactgtgacc
4741 cgtgatccag ctggctggtt tggaaaattg gaacaaagtt caattctcag gcaaatgtac
4801 tggaccaggg gtcccaacca tgaagatcca tttgaaacaa tgataccaca ctcccaaaga
4861 cccatacaat tgatgtcctt gctgggcgag gctgcactcc acggcccggc attctatagc
4921 aaaattagca aattagtcat tgcagagttg aaggaaggtg gcatggattt ttacgtaccc
4981 agacaagagc caatgttcag atggatgaga ttctcagatc tgagcacgtg ggagggcgat
5041 cgcaatctgg ctcccagttt tgtgaatgaa gatggcgtcg agtgacgcca acccatctga
5101 tgggtccgca gccaacctcg tcccagtggt caacaatgag gttatggctc tggagcccgt
5161 tgttggtgcc gccattgcgg cacctgtagc gggccaacaa aatgtaattg acccctggat
5221 tagaaataat tttgtacaag cccctggtgg agagtttaca atatccccta gaaacgctcc
5281 aggtgaaata ctatggagcg cgcccttggg ccctgatcta aatccctacc tatcccattt
5341 ggccagaatg tacaatggtt atgcaggtgg ttttgaagtg caggtacttc tcgcggggaa
5401 cgcgttcacc gccgggaagg tcatatttgc agcagtccca ccaaattttc caactgaagg
5461 cttgagcccc agccaggtca ctatgttccc caatatagta gtagatgtta ggcaactaga
5521 acctgtgttg attcccttac ccgatgttag gaataatttc tatcattaca atcaatcaaa
5581 tgaccccacc attaagttaa tagcaatgtt gtatacacca cttagggcta ataatgctgg
5641 ggatgatgtc ttcacagttt cttgccgagt tctcacgaga ccatcccccg attttgattt
5701 catatttcta gtgccaccca cagttgagtc aagaactaaa ccattctctg tcccaatttt
5761 aactgttgag gagatgacca attcaagatt ccccattcct ttggaaaagt tgttcacggg
5821 tcccagcagt gcctttgttg tccaaccaca aaacggtagg tgcacgactg atggcgtgct
5881 cctaggcacc acccaactgt ctcctgtcaa catctgcacc ttcagaggag atgtcaccca
5941 tatcacaggt agtcgtaact acagaatgaa tttggcttct caaaattgga gcaattatga
6001 cccaacagaa gaaatcccag cccctctagg aattccagat tttgtgggga agattcaagg
6061 cgtgctcacc caaaccacaa ggacagatgg ctcaacacgc ggccacaaag ccacagtgta
6121 cactgggagc gccgactttg ctccaaaact gggtagagtt caatttgaaa ctgacacaga
6181 ccatgatttt gaaactaacc aaaacacaaa gttcacccca gctggtgtca tccaagatgg
6241 tagcaccacc caccgaaatg aaccccaaca gtgggtgctc ccaagttact caggcagaag
6301 tactcctaat gtgcatctgg cccccgctgt ggcccccact tttccgggtg agcaacttct
6361 cttcttcaga tccaccatgc ccggatgcag cgggtacccc aacatggatt tggactgtct
6421 gctcccccag gaatgggtgc agtacttcta ccaagaggca gccccagcac aatctgatgt
6481 ggctctgcta agatttgtga atccagacac aggtagggtt ttgtttgagt gtaagcttca
6541 taaatcaggc tatgttacag tggctcacac tggccaacat gatttggtta tcccccccaa
6601 tggttatttt aggtttgatt cctgggtcaa ccagttttac acgcttgccc ccatgggaaa
6661 tggaacgggg cgtagacgtg cactataatg gctggagctt tctttgctgg attggcatct
6721 gatgtccttg gctctggact tggttccctt atcaatgctg gggctggggc catcaaccaa
6781 aaagttgagt ttgaaaataa cagaaaattg caacaagcat ccttccaatt tagcagcaat
6841 ctacaacagg cttcctttca acatgacaaa gagatgctcc aagcacaaat tgaggccacc
6901 aaaaggctac aacaggaaat gatgaaagtt aagcaggcaa tgctcctaga gggtgggttc
6961 tctgagacag atgcagcccg cggggcaatc aacgccccca tgacaaaagc tttggactgg
7021 agcgggacaa ggtactgggc tcccgatgct aggacaacaa catacaatgc aggccgcttt
7081 tccacccctc aaccatcggg ggcattgcca ggaagagcta atcttaggga tgctgcccct
7141 gctcggggtt cctccagtaa gtcttctaat tcttctactg ctacttctgt gtactcaaat
7201 caaactactt caacgagact tggttctaca gctggttctg gtaccagtgt ctcgagcttc
7261 ccgtcaactg caaggactag gagctgggtt gaggatcaaa gtaggaattt gtcacctttc
7321 atgagggggg cccacaacat atcgtttgtc accccaccat ctagcagatc ctctagccaa
7381 ggcacagtct caaccgtgcc taaagagatt ttggactcct ggactggcgc tttcaacacg
7441 cgcaggcagc cactcttcgc tcacattcgt aagcgagggg agtcacgggt ctaaag
//