Typing tool
|
|
|
|
|
|
Typing tool
|
Complete norovirus genomes
| MF140697 | GII.4 New Orleans | |
|
|---|---|---|---|
| GII.P4 New Orleans |
ORF1: 1..5090
ORF2: 5071..6693
ORF3: 6693..7499
LOCUS MF140697 7545 bp RNA linear VRL 24-OCT-2017
DEFINITION Norovirus GII strain
Norovirus/GII/Hu/NL/2014/GII.P4-GII.4/Rotterdam/E1300283_p9_d176
ORF1 gene, partial cds; and ORF2 and ORF3 genes, complete cds.
ACCESSION MF140697
VERSION MF140697.1
KEYWORDS .
SOURCE Norovirus GII
ORGANISM Norovirus GII
Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes;
Picornavirales; Caliciviridae; Norovirus; Norwalk virus.
REFERENCE 1 (bases 1 to 7545)
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 7545)
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..7545
/organism="Norovirus GII"
/mol_type="genomic RNA"
/strain="Norovirus/GII/Hu/NL/2014/GII.P4-
GII.4/Rotterdam/E1300283_p9_d176"
/host="Homo sapiens"
/db_xref="taxon:122929"
/country="Netherlands"
/collection_date="13-Feb-2014"
/note="genotype: GII.P4-GII.4"
CDS <1..5090
/codon_start=3
/product="ORF1"
/protein_id="ATN23787.1"
/translation="SNDASAAAVANSTNDTAKSSSDGVLSSMAVTFKRALGARPKQPP
PREIPQRPPRPPTPELVKSIPPPPPNGEDEIVVSYSVKDGVSGLPDLSTVRQPEESNT
AFSVPPLNQRESRDAKEPLTGTILEMWDGEIYHYGLYVERGLVLGVHKPPAAISLAKV
ELAPLSLYWRPVYTPQYLISPDTLKKLSGETFPYTAFDNNCYAFCCWVLDLNDSWLNR
RMIQRTTGFFRPYQDWNRKPLPTIDDSKIKKVANIFLCALSSLFTRPIKDIIGKIRPL
NILNILASCDWTFAGIVESLILLAELFGVFWTPPDVSAMIAPLLGDYELQGPEDLAVE
LVPVVMGGIGLVLGFTKEKIGKMLSSAASTLRACKDLGAYGLEILKLVMKWFFPKKEE
ANELAMVRSIEDAVLDLEAIENNHMTTLLKDKDSLATYMRTLDLEEEKARKLSTKSAS
PDIVGTINALLARIAAARSLVHRAKEELSSRPRPVVLMISGRPGIGKTYLAREVAKKI
AASLTGDQRVGLIPRNGVDHWDAYKGERVVLWDDYGMSNPIHDALRLQELADTCPLTL
NCDRIENKGKVFDSDVIIITTNLANPAPLDYVNFEACSRRIDFLVYAEAPEVEKAKRD
FPGQPDMWKNAFSSDFSHIRLALAPQGGFDKNGNTPHGKGVMKTLTTGSLIARASGLL
HERLDEFELQGPALTTFNFDRNKVLAFRQLAAENKYGLMDTMRVGKQLKDVKTMPELK
QALKNVSIKKCQIVYSGCTYILESDGKGNVKVDRIQNTTVQINNELAGALHHLRSARI
RYYVKCVQEALYSIIQIAGAAFVTTRIAKRMNIQNLWSKPQVENTEETTSNDGCPKPK
DDEEFVISSDDIKTEGKKGKNKTGRGKKHTAFSSKGLSDEEYDEYKRIREERNGKYSI
EEYLQDRDKYYEEVAIARATEEDFCEEEEAKIRQRIFRPTRKQRKEERASLGLVTGSE
IRKRNPDDFKPKGKLWADDDRSVDYNEKLSFEAPPSIWSRIVNFGSGWGFWVSPSLFI
TSTHVIPQGAKEFFGVPIKQIQVHKSGEFCRLRFPKPIRTDVTGMILEEGAPEGTVVT
LLIKRSTGELMPLAARMGTHATMRIQGRTVGGQMGMLLTGSNAKSMDMGTTPGDCGCP
YIYKRGNDYVVIGVHTAAARGGNTVICATQGSEGEATLEGGDNKGTYCGAPILGPGSA
PTLSTKTKFWRSSTASLPPGTYEPAYLGGKDPRVKGGPSLQQVMREQLKPFTEPRGKP
PKPSVLEAAKKTIINVLEQTIDPPEKWSFAQACASLDKTTSSGYPHHVRKNDCWNGES
FTGKLADQASKANLMFEEGKNMTPVYTAALKDELVKTDKIYGKIKKRLLWGSDLATMI
RCARAFGGLMDELKAHCVTLPIRVGMNMNEDGPIIFERHSRYTYHYDADYSRWDSTQQ
RAVLAAALEIMVKFSPEPHLAQVVAEDLLSPSVVDVGDFTISINEGLPSGVPCTSQWN
SIAHWLLTLCALSEVTNLSPDTIQANSLFSFYGDDEIVSTDIKLDPEKLTAKLREYGL
KPTRPDKTEGPLVITEDLNGLTFLRRTVTRDPAGWFGKLEQSSILRQMYWTRGPNHGD
PSETMIPHSQRPIQLMSLLGEAALHGPAFYSKISKLVIAELKEGGMDFYVPRQEPMFR
WMRFSDLSTWEGDRNLAPSFVNEDGVE"
CDS 5071..6693
/codon_start=1
/product="ORF2"
/protein_id="ATN23788.1"
/translation="MKMASSDANPSDGSAANLVPEVNNEVMALEPVVGAAIAAPVAGQ
QNVIDPWIRNNFVQAPGGEFTVSPRNAPGEILWSAPLGPDLNPYLSHLARMYNGYAGG
FEVQVILAGNAFTAGKIIFAAVPPNFPTEGLSPSQVTMFPHIIVDVRQLEPVLIPLPD
VRNNFYHYNQSNDSTIKLIAMLYTPLRANNAGDDVFTVSCRVLTRPSPDFDFIFLVPP
TVESRTKPFSVPVLTVEEMTNSRFPIPLEKLFTGPSSDIVVQPQNGRCTTDGVLLGTT
QLSSVNICTFRGDVTQVGKSDRYTMNLASLNWNSYDPTEDTPAPLGTPDFVGKIQGVL
TQTTTPGGSTRAHKATVRTGIADFSPKLGKVQFDTDTHNDLDTNQHTKFTPVGVVQEG
DDSHQKEPIQWQLPSYSGRGIHNVHLAPAVAPTFPGEQLLFFRSTMPGCGGYPNMNLD
CLLPQEWVQYFYQEAAPAQSDVALLRFVNPDTGRVLFECKLHKSGYVTVAYTGKHDLV
IPPNGYFRFDSWVNQFYTLAPMGNGTGRRRAQ"
CDS 6693..7499
/codon_start=1
/product="ORF3"
/protein_id="ATN23789.1"
/translation="MAGAFFAGLASDVLGSGLGSLINAGAGVINQKVDFENNRKLQQD
SFQFSSNLQQASFQHDKEMLQAQIEATKKLQQEMMRVKQAMLLEGGFSETDAARGAIN
APMTKVLDWNGTRYWAPDARTTTYNAGRFSTPQPSGAPPGRANLRAAAPARGSSSMSS
KSSIASSVYSNQTTSTRLGSTAGSGTSVSSLPSTARTRSWVEDQNRNLSPFMRGAHNI
SFVTPPSSRSSSQGTVSTVPKEILDSWTGAFNTRRQPLFAHVRRRGESRV"
ORIGIN
1 cgtctaacga cgcttccgct gccgctgttg ctaacagcac caacgacacc gcaaaatctt
61 caagtgacgg agtgctttct agcatggctg tcacttttaa acgagccctc ggggcgcggc
121 ctaaacagcc tcccccgagg gaaataccac aaaggccccc acgaccacct actccagaac
181 tggtcaaaag tattccccct cccccaccca acggagagga tgaaatagtg gtttcttaca
241 gtgttaagga tggtgtttcc ggcttgcctg acctttccac cgttaggcaa ccggaagaat
301 ctaacacggc cttcagcgtc cctccactca atcagaggga gagcagagat gctaaggagc
361 cacttactgg aacaattctg gaaatgtggg acggggaaat ctaccattat ggcctgtatg
421 tggagcgagg tcttgtacta ggcgtgcaca aaccaccagc tgccatcagc ctcgctaagg
481 ttgagctagc accactctct ttgtactgga gacctgtgta tactcctcag tacctcatct
541 ctccggatac tctcaagaaa ttgtccggag aaacgttccc ctacacagcc tttgacaaca
601 actgttatgc cttttgttgc tgggtcctgg acctaaatga ctcatggctg aacaggagaa
661 tgatccagag aacaactggt ttctttaggc cctatcaaga ctggaatagg aaaccccttc
721 ctactataga tgactccaaa ataaagaagg tagctaacat attcctgtgt gctctgtcct
781 cgctgttcac cagacccata aaagatataa tagggaagat aaggcctctt aacatcctca
841 acatcttagc ctcatgtgat tggacttttg caggcatagt ggagtccctg atactcttgg
901 cagaactctt tggagttttc tggacacccc cagatgtgtc tgctatgatt gctcccttac
961 tcggtgacta tgagctacaa ggacctgagg accttgcagt ggagctcgtc cccgtagtga
1021 tggggggaat tggtttggtg ctaggattca ccaaagagaa gattgggaaa atgttgtcat
1081 ctgccgcgtc caccttgaga gcttgtaaag accttggtgc atacgggcta gagatcctga
1141 agttggtcat gaagtggttc tttccgaaga aggaggaggc aaatgaactg gctatggtga
1201 ggtctatcga ggatgcagtt ctagatctcg aggcaattga aaacaaccat atgactacct
1261 tgctcaaaga caaagacagt ctggcaacct acatgagaac acttgacctt gaggaggaga
1321 aagccaggaa actctcaacc aagtctgcct cacccgacat cgtgggcaca atcaacgccc
1381 tcctggcgag aatcgctgcc gcacgttctc tggtgcatcg agcgaaggag gagctttcca
1441 gcagaccaag acctgtggtg ttgatgatat caggcaggcc ggggataggg aagacctacc
1501 tcgctaggga agtggctaaa aagatcgcag cctcccttac aggagatcag cgtgtgggcc
1561 tcatcccacg caatggcgtc gaccattggg acgcgtacaa gggagagaga gtcgtcctat
1621 gggacgatta tggaatgagc aaccccattc acgacgccct caggctgcaa gaactcgctg
1681 acacttgccc cctcactctg aactgtgaca ggattgaaaa taaaggaaag gtctttgaca
1741 gcgatgtcat cattatcacc actaatctgg ccaacccagc accactagac tatgtcaact
1801 ttgaggcatg ctcgaggcgc atcgacttcc tcgtgtatgc agaagcccct gaagtcgaga
1861 aggcgaagcg tgacttccca ggccagcctg acatgtggaa gaacgctttc agctctgatt
1921 tctcacacat aagactagca ctggccccac agggtggttt cgacaagaac gggaacaccc
1981 cgcatgggaa gggcgtcatg aagactctca ccactggctc ccttattgcc cgagcatcag
2041 ggctactcca tgagaggtta gatgaatttg aactacaggg cccagctctc accaccttca
2101 attttgaccg caacaaagtg cttgccttca gacagcttgc tgctgagaat aaatatggat
2161 tgatggacac aatgagggtt gggaaacagc tcaaggatgt caaaaccatg cctgaactca
2221 aacaagcact caagaatgtc tcaatcaaga agtgccaaat agtatatagt ggttgtacct
2281 acatacttga gtctgatggc aagggcaatg tgaaagttga cagaatccaa aacaccaccg
2341 tgcagatcaa caatgagctg gcaggtgctc tgcaccattt gaggagcgcc agaatcagat
2401 actatgtcaa gtgtgtccag gaggccctat attccatcat tcaaattgct ggggctgcat
2461 ttgtcaccac gcgcattgcc aagcgcatga acatacaaaa cctatggtcc aaaccacaag
2521 tggaaaacac agaggagact accagcaatg acgggtgccc aaaacctaag gatgatgagg
2581 agtttgtcat ttcatctgac gacatcaaaa ctgagggcaa gaaagggaaa aacaagactg
2641 gccgcggcaa gaagcacaca gcattttcaa gcaaaggcct cagtgatgaa gagtacgatg
2701 agtacaagag gattagagaa gaaaggaatg gcaagtactc catagaagaa taccttcagg
2761 acagggacaa atactatgag gaggtggcca ttgccagggc gactgaggaa gacttctgtg
2821 aagaggagga ggccaagatc cgtcaaagga tctttaggcc aacaaggaaa caacgcaagg
2881 aggaaagagc ttctctcggt ctagtcacag gttctgaaat caggaaaaga aacccagatg
2941 acttcaaacc caaggggaaa ttgtgggctg acgatgacag gagtgtggac tacaatgaga
3001 aactcagttt tgaggcccca ccaagcatct ggtcaagaat agtcaacttt ggttcaggct
3061 ggggattctg ggtctccccc agtcttttca taacatcaac ccatgtcata ccccagggcg
3121 caaaggagtt ctttggagtc cccatcaaac aaatacaggt acacaaatca ggcgagttct
3181 gtcgcttgag attcccaaaa ccaatcagga ctgatgtgac aggcatgatc ttggaagaag
3241 gcgcacctga gggtaccgtg gtcacactac tcatcaaaag gtccactggg gaactcatgc
3301 ccctagcagc tagaatgggg acccatgcga ccatgaggat ccaagggcgc actgttggag
3361 gccagatggg catgcttctg acagggtcca acgccaagag catggacatg ggtactacac
3421 caggtgattg cggctgtccc tatatttaca agagaggcaa tgactatgtg gtcattggag
3481 tccacacggc tgccgcacgt ggagggaaca ctgtcatatg tgccacccag gggagtgaag
3541 gagaggctac acttgaaggt ggtgacaaca agggaacata ttgtggtgca ccaatcctag
3601 gcccagggag tgccccaact cttagcacca agaccaaatt ctggagatca tctacagcgt
3661 cactcccacc tggcacctat gaaccagcct atcttggtgg caaggacccc agagtcaagg
3721 gtggcccttc actacagcaa gtcatgaggg agcagttgaa accattcaca gagccaaggg
3781 gcaaaccacc aaaaccaagt gtattagaag ctgccaagaa gaccatcatc aatgtccttg
3841 agcaaacaat tgatccacct gagaaatggt cgttcgcaca agcttgcgcg tcccttgaca
3901 agaccacttc cagcggttat ccgcaccatg tgcggaaaaa cgactgctgg aacggggagt
3961 ccttcacagg caagctggca gaccaggctt ccaaggccaa cctgatgttt gaagaaggga
4021 aaaacatgac cccagtctac acagctgcac tcaaggatga gttagttaaa actgacaaaa
4081 tttatggtaa gatcaaaaag aggcttctct ggggctcgga cctggcgacc atgattcggt
4141 gtgctcgagc attcggaggc ctaatggatg aactcaaagc acactgtgtc acacttccca
4201 ttagagttgg catgaacatg aatgaggatg gccccatcat cttcgagagg cattctaggt
4261 acacatatca ctatgatgct gattactctc gatgggattc aacacaacag agagccgtgt
4321 tggcagcagc tctcgaaatc atggttaaat tctccccaga accacatttg gctcaggtag
4381 tcgcagaaga ccttctttct cctagcgtgg tggacgtggg cgacttcaca atatcaatca
4441 acgagggtct tccctctggg gtgccctgca cctcccaatg gaactccatc gcccactggc
4501 tcctcactct ctgtgcgctc tctgaagtca caaacctatc ccctgacacc atacaggcta
4561 attccctctt ctctttttat ggtgatgatg aaattgttag cacagacata aaattggacc
4621 cagagaaatt gacagcaaag ctcagagaat acgggttaaa accaacccgc cctgacaaaa
4681 ctgaaggacc ccttgtcatc actgaagacc tgaatggcct aactttcctg cggagaactg
4741 tgacccgcga cccagctggt tggtttggaa aactggagca gagttcaata ctcaggcaaa
4801 tgtactggac taggggtccc aatcatggag acccatctga aacaatgatt ccacactccc
4861 aaagacccat acaattgatg tccctactgg gggaggccgc tctccacggc ccagcctttt
4921 acagcaaaat cagcaagttg gtcattgcag agctaaaaga aggtggcatg gatttttacg
4981 tgcccagaca agagccaatg ttcagatgga tgagattctc agatctgagc acgtgggagg
5041 gcgatcgcaa tctggctccc agttttgtga atgaagatgg cgtcgagtga cgccaaccca
5101 tctgatgggt ccgcagccaa cctcgtccca gaggtcaaca atgaggttat ggctttggag
5161 cccgtagttg gtgccgccat tgcggcacct gtagcgggcc aacaaaatgt aattgacccc
5221 tggattagaa ataattttgt acaagcccct ggtggagagt ttacagtatc ccctagaaac
5281 gctccaggtg aaatactatg gagcgcgccc ttaggccctg atctgaaccc ctacctttcc
5341 catttggcca gaatgtacaa tggttatgca ggtggctttg aagtgcaggt aatcctcgcg
5401 gggaacgcgt tcaccgccgg aaaaatcata tttgcagcag tcccaccaaa tttcccaact
5461 gaaggtttga gccccagcca ggtcactatg tttccccata taatagtaga tgttaggcaa
5521 ttggaacctg tgttgattcc cttacccgat gttaggaata atttctacca ttataatcag
5581 tcaaatgact ccaccattaa attgatagca atgttgtata caccacttag ggctaataat
5641 gctggggacg atgtctttac agtttcttgt cgagtcctca cgagaccatc ccccgatttt
5701 gattttatat ttttggtgcc acccacagtt gaatcaagaa ctaaaccatt ctctgtccca
5761 gttctaactg ttgaagagat gaccaattca aggttcccca tccctttgga aaagttgttc
5821 acaggcccca gtagtgacat cgtagttcaa ccacaaaatg gcaggtgcac gactgatggc
5881 gtgctcctag gtactaccca attgtcctct gtcaacatct gcaccttcag aggggatgtc
5941 acccaagttg gaaaatctga cagatacaca atgaatttgg cctccctaaa ttggaacagt
6001 tacgacccaa cagaagatac cccagcccct ctaggaactc cagatttcgt ggggaagatt
6061 caaggtgtgc tcacccaaac cacaactcca ggtggctcga cccgtgccca caaggccaca
6121 gtgcgcactg ggatcgccga tttttctcca aaactgggta aagttcaatt tgacactgac
6181 acacataatg atcttgacac caaccagcac acaaagttca ccccagtcgg cgttgtccag
6241 gaaggtgatg actcccacca gaaagaaccc atacaatggc agctcccaag ctactcaggc
6301 agaggcattc ataatgtgca cctggccccc gctgtagccc ctacttttcc gggcgagcag
6361 ctcctcttct tcagatctac tatgcccgga tgcggcgggt accccaacat gaatttggac
6421 tgtctactcc ctcaggaatg ggtgcagtac ttctaccagg aggcagcccc agcacaatct
6481 gatgtagctc tgttaagatt tgtgaatcca gacacaggta gggttttatt tgagtgcaag
6541 cttcataaat caggctatgt tacagtggct tacactggca aacatgattt ggttatcccc
6601 cctaatggtt attttagatt tgattcctgg gtcaaccagt tctacactct tgcccccatg
6661 ggaaatggaa cggggcgtag acgtgcacaa taatggctgg agctttcttt gctggattgg
6721 catctgatgt ccttggctct ggacttggtt ccctaatcaa tgctggggct ggggtcatca
6781 accaaaaagt tgattttgaa aataacagaa aattacaaca agattccttc caatttagta
6841 gcaatcttca acaagcttcc tttcaacatg acaaagagat gctccaagca caaattgagg
6901 ccaccaaaaa gttgcaacag gaaatgatga gagtcaaaca agcaatgctc ctagagggtg
6961 gattctctga gacagatgca gcccgtgggg caatcaacgc ccccatgaca aaagttttgg
7021 actggaatgg aacaaggtac tgggctcccg atgctaggac tacaacatac aatgcaggcc
7081 gcttttccac ccctcaaccc tcgggggcac caccaggaag ggctaatctt agggctgctg
7141 cccccgcccg gggctcctct agcatgtctt ctaaatcttc tattgcttct tctgtgtatt
7201 caaatcaaac cacttcaacg agacttggtt ctacagctgg ttctggtacc agtgtctcga
7261 gcctcccgtc aactgcaagg actaggagct gggttgagga tcaaaatagg aatttgtcac
7321 ctttcatgag gggggcccac aacatctcgt ttgtcacccc accatctagc agatcctcta
7381 gccaaggcac agtctcaacc gtgcccaaag aaattttgga ctcctggact ggcgctttca
7441 acacgcgcag gcagcctctc ttcgctcacg ttcgtaggcg aggggagtca cgggtgtaaa
7501 gtgaaaagac aaaattgatt atctttcttt tctttagtgt ctttt
//