Typing tool
|
|
|
|
|
|
Typing tool
|
Complete norovirus genomes
| MF140650 | GII.4 New Orleans | |
|
|---|---|---|---|
| GII.P4 New Orleans |
ORF1: 1..5090
ORF2: 5071..6693
ORF3: 6693..7499
LOCUS MF140650 7545 bp RNA linear VRL 24-OCT-2017
DEFINITION Norovirus GII strain
Norovirus/GII/Hu/NL/2011/GII.P4-GII.4/Rotterdam/E1300300_p13_d51
ORF1 gene, partial cds; and ORF2 and ORF3 genes, complete cds.
ACCESSION MF140650
VERSION MF140650.1
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/2011/GII.P4-
GII.4/Rotterdam/E1300300_p13_d51"
/host="Homo sapiens"
/db_xref="taxon:122929"
/country="Netherlands"
/collection_date="11-Feb-2011"
/note="genotype: GII.P4-GII.4"
CDS <1..5090
/codon_start=3
/product="ORF1"
/protein_id="ATN23646.1"
/translation="SHDASAAAVANSNNDIAKSSSDGVLSSMAVTFKRALGARPKQPP
PREKPQRPPRPPTPELVKNIPPPPPNGEDEVVVSYSVKDGVSGLPDLSTVRQPEESNT
AFSVPPLSQRENRDAKEPLTGTILEMWDGEIYHYGLYVERGLVLGVHKPPAAISLAKV
ELAPLSLYWRPVYTPQYLIPPDTLKKLSGETFPYTAFDNNCYAFCCWVLDLNDSWLSR
RMIQRTTGFFRPYQDWNRKPLPTMDDSKIKKVANIFLCALSSLFTRPIKDIIGKIRPL
NILNILASCDWTFAGIVESLILLAELFGVFWTPPDVSAMIAPLLGDYELQGPEDLAVE
LVPVVMGGIGLVLGFTKEKIGKMLSSAASTLRACKDLGAYGLEILKLVMKWFFPKKEE
ANELAIVRSIEDAVLDLEAIENNHMTTLLKDKDSLATYMRTLDLEEEKARKLSTKSAS
PDIVGTINALLARIAAARSLVHRAKEELSSRPRPVVLMISGRPGIGKTHLAREVAKRI
AASLTGDQRVGLIPRNGVDHWDAYKGERVVLWDDYGMSNPIHDALRLQELADTCPLTL
NCDRIENKGKVFDSDVIIITTNLANPAPLDYVNFEACSRRIDFLVYAEAPEVEKAKRD
FPGQPDMWKNAFSSDFSHIKLALAPQGGFDKNGNTPHGKGVMKTLTTGSLIARASGLL
HERLDEFELQGPALTTFNFDRNKVLAFRQLAAENKYGLMDTMRVGKQLKDVRTMPELK
QALKNVSIKKCQIVYSGCTYILESDGKGNVKVDRIQSAAVQTNNELTGALHHLRCARI
RYYVKCVQEALYSIIQIAGAAFVTTRIAKRMNIQDLWSKPQVENTEETTSKDGCPKPK
DDEEFVISSNDIKTEGKKGKNKTGRGKKHTAFSSKGLSDEEYDEYKRIREERNGKYSI
EEYLQDRDKYYEEVAIARATEEDFCEEEEAKIRQRIFRPTRKQRKEERASLGLVTGSE
IRKRNPDDFKPKGKLWADDDRSVDYNEKLSFEAPPSIWSRIVNFGSGWGFWVSPSLFI
TSTHVIPQGAKEFFGVPIKQIQVHKSGEFCRLRFPKPIRTDVTGMILEEGAPEGTVVT
LLIKRSTGELMPLAARMGTHATMKIQGRTVGGQMGMLLTGSNAKSMDLGTTPGDCGCP
YIYKRGNDYVVIGVHTAAARGGNTVICATQGSEGEATLEGGDNKGTYCGAPILGPGSA
PTLSTKTKFWRSSTASLPPGTYEPAYLGGKDPRVKGGPSLQQVMREQLKPFTEPRGKP
PKPSVLEAAKKTIINVLEQTIDPPEKWSFAQACASLDKTTSSGHPHHVRKNDCWNGES
FTGKLADQASKANLMFEEGKNMTPVYTAALKDELVKTDKIYGKIKKRLLWGSDLATMI
RCARAFGGLMDELKAHCVTLPIRVGMNMNEDGPIIFERHSRYTYHYDADYSRWDSTQQ
RAVLAAALEIMVKFSPEPHLAQVVAEDLLSPSVVDVGDFTISINEGLPSGVPCTSQWN
SIAHWLLTLCALSEVTNLSPDTIQANSLFSFYGDDEIVSTDIKLDPEKLTAKLREYGL
KPTRPDKTEGPLVISEDLNGLTFLRRTVTRDPAGWFGKLEQSSILRQMYWTRGPNHGD
PSETMIPHSQRPIQLMSLLGEAALHGPAFYSKISKLVIAELKEGGMDFYVPRQEPMFR
WMRFSDLSTWEGDRNLAPSFVNEDGVE"
CDS 5071..6693
/codon_start=1
/product="ORF2"
/protein_id="ATN23647.1"
/translation="MKMASSDANPSDGSTANLVPEVNNEVMALEPVVGAAIAAPVAGQ
QNVIDPWIRNNFVQAPGGEFTVSPRNAPGEILWSAPLGPDLNPYLSHLARMYNGYAGG
FEVQVILAGNAFTAGKIIFAAVPPNFPTEGLSPSQVTMFPHIIVDVRQLEPVLIPLPD
VRNNFYHYNQSNDPTIKLIAMLYTPLRANNAGDDVFTVSCRVLTRPSPDFDFIFLVPP
TVESRTKPFSVPVLTVEEMTNSRFPIPLEKLFTGPSSAFVVQPQNGRCTTDGVLLGTT
QLSPVNICTFRGDVIHIPGSRNYTMNLASQNWNSYDPTEEIPAPLGTPDFVGKIQGVL
TQTTRTNGSTRGHKATVYTGSADFSPKLGRVQFATDTDNDFETNQNTKFTPVGVIQDG
STTHRNEPQQWVLPSYSGRNIHNVHLAPAVAPTFPGEQLLFFRSTMPGCSGYPNMDLD
CLLPQEWVQYFYQEAAPAQSDVALLRFVNPDTGRVLFECKLHKSGYVTVAHTGQHDLV
IPPNGYFRFDSWVNQFYTLAPMGNGTGRRRAL"
CDS 6693..7499
/codon_start=1
/product="ORF3"
/protein_id="ATN23648.1"
/translation="MAGAIFAGLASDVLSSGLGSLISAGAGVINQKVEFENNRKLQQA
SFQFSSNQQQASFQHDKEMLQAQIEATKKLQQEMMRVKQAMLLEGGFSETDAARGAIN
APMTKTLDWSGTRYWAPDARTTTYNAGRFSTPQPSGAPPGRANLRATVPARGSSSTPS
NSSIATSVYSNQTTSTRLGSTAGSGTSVSSLPSTARTRSWIEDQNRNLSPFMRGAHNI
SFVTPPSSRSSSQGTVSTVPKEVLDSWTGAFNTRRQPLFAHIRKRGESRV"
ORIGIN
1 cctctcacga cgcttccgct gccgctgttg ctaacagcaa caacgacatc gcaaaatctt
61 caagtgacgg tgtgctttct agcatggctg tcacttttaa acgagccctc ggggcgcggc
121 ctaaacagcc tcccccgagg gaaaaaccac aaagaccccc acgaccacct actccagaac
181 tggtcaaaaa tattccccct cccccaccca acggagagga tgaagtagtg gtttcttata
241 gtgtcaaaga tggtgtttcc ggcttgcctg acctttccac cgtcaggcaa ccggaagaat
301 ctaacacggc cttcagtgtc cctccactca gtcagaggga gaatagagat gctaaggagc
361 cacttactgg aacaattctg gaaatgtggg acggggaaat ctaccattat ggcctgtatg
421 tggagcgagg tcttgtacta ggtgtgcaca aaccaccagc tgccatcagc ctcgctaagg
481 ttgagctagc accactctcc ttgtactgga gacctgtgta cactcctcag tacctcatcc
541 ctccagacac tctcaagaaa ttatccggag aaacgttccc ctacacagcc tttgacaaca
601 actgttatgc cttttgttgc tgggtcctgg accttaatga ctcgtggctg agcaggagaa
661 tgatccagag aacaactggt ttcttcaggc cctaccaaga ctggaatagg aaaccccttc
721 ccactatgga tgactccaaa ataaagaagg tagctaacat attcctgtgt gctctgtcct
781 cgctgttcac cagacccata aaagatataa tagggaagat aaggcctctt aacatcctca
841 acatcctagc ctcatgtgat tggacttttg caggcatagt ggaatccctg atactcttgg
901 cagaactctt tggagttttc tggacacccc cagatgtgtc tgcgatgatt gcccccttac
961 tcggtgacta cgaactacaa ggacctgagg atcttgcagt ggagctcgtc cccgtggtga
1021 tggggggaat tggtttggtg ctaggattca ccaaagagaa gattgggaaa atgttgtcat
1081 ctgccgcgtc caccttgagg gcttgtaaag accttggtgc atatgggcta gagatcctga
1141 agttggtcat gaagtggttc ttcccgaaga aggaggaggc aaatgagctg gctatagtga
1201 ggtccatcga ggatgcagtc ctggatctcg aggcaattga aaacaaccat atgaccacct
1261 tgctcaaaga caaagacagt ctggcaacct atatgagaac acttgacctt gaggaggaga
1321 aagccaggaa actctcaacc aagtctgcct cacccgacat cgtgggcaca atcaacgccc
1381 tcctggcgag gatcgctgcc gcacgttctc tggtgcatcg ggcgaaggag gagctttcca
1441 gcagaccaag acctgtggtg ttgatgatat caggcaggcc aggaataggg aagacccacc
1501 tcgctaggga agtggctaag agaatcgcag cctcccttac aggagaccag cgtgtgggcc
1561 tcatcccacg caatggcgtc gaccattggg atgcgtacaa gggggagagg gtcgtcctgt
1621 gggacgatta tggaatgagc aaccctattc acgacgccct caggctgcaa gaactcgctg
1681 atacatgccc cctcactcta aactgtgaca ggattgaaaa taaaggaaag gtctttgaca
1741 gcgatgtcat cattatcacc actaatctgg ccaacccagc accactggac tatgtcaact
1801 ttgaagcatg ctcgaggcgc atcgacttcc tcgtgtatgc agaagcccct gaagtcgaaa
1861 aggcgaagcg tgacttccca ggccagcctg acatgtggaa gaacgctttc agttctgatt
1921 tctcacacat aaaactagca ctggccccac agggtggttt cgacaagaac gggaacaccc
1981 cacacggaaa gggcgtcatg aagactctca ccactggctc ccttattgcc cgggcatcag
2041 ggctactcca tgagaggtta gatgaatttg aattacaggg cccagctctc accaccttca
2101 atttcgatcg caataaagtg cttgccttca ggcagcttgc tgctgaaaat aaatatggat
2161 tgatggacac aatgagagtt gggaaacagc tcaaggatgt cagaaccatg ccagaactca
2221 aacaagcact caagaatgtc tcaatcaaga agtgccaaat agtgtatagt ggttgcacct
2281 acatacttga gtctgatggc aagggcaatg tgaaagttga cagaatccaa agcgccgccg
2341 tgcagaccaa caatgagctg actggtgccc tgcaccattt gaggtgcgcc agaatcagat
2401 actatgtcaa gtgtgtccag gaggccctgt actccatcat acaaattgct ggggctgcat
2461 tcgtcaccac gcgcattgcc aagcgcatga acatacaaga cctatggtcc aagccacaag
2521 tggaaaacac agaggagacc accagcaagg acgggtgccc aaaacctaag gatgatgagg
2581 agtttgtcat ttcatccaac gacatcaaaa ctgagggtaa gaaggggaag aacaagactg
2641 gccgcggcaa gaagcacaca gcattttcaa gcaaaggtct cagtgatgaa gagtacgatg
2701 agtacaagag gattagagaa gaaaggaatg gcaagtactc catagaagag taccttcaag
2761 acagggacaa atactatgag gaggtggcca ttgccagggc gactgaggaa gacttctgtg
2821 aagaggagga ggccaagatc cggcaaagga tctttaggcc aacaaggaaa caacgcaagg
2881 aggaaagagc ttctctcggt ctggtcacag gctctgaaat taggaaaaga aacccagatg
2941 acttcaagcc caaggggaag ttgtgggctg acgatgacag gagtgtggac tacaatgaga
3001 aactcagttt tgaggcccca ccaagcatct ggtcgagaat agtcaacttt ggttcaggct
3061 ggggattctg ggtctccccc agcctgttca taacatcaac ccatgtcata ccccaaggcg
3121 caaaggagtt ctttggagtc cccatcaaac aaatacaggt gcacaagtca ggcgagttct
3181 gtcgcttgag attcccaaaa ccaatcagga ctgatgtgac gggcatgatc ttagaagaag
3241 gcgcacctga gggcaccgtg gtcacactac tcatcaaaag gtccactggg gaactcatgc
3301 ccctagcagc taggatgggg acccatgcga ccatgaagat ccaagggcgc actgttggag
3361 gccagatggg catgcttctg acaggatcca acgccaagag catggacctg ggtactacac
3421 caggtgattg tggctgcccc tatatctaca agagaggtaa tgactatgtg gtcattggag
3481 tccacacggc tgccgcacgt gggggaaaca ctgtcatatg tgccacccag gggagtgaag
3541 gagaggccac acttgaaggt ggtgacaaca aggggacata ctgtggtgca ccaatcctag
3601 gcccagggag tgccccaaca cttagcacca agaccaaatt ctggagatcg tccacagcat
3661 cactcccacc tggcacctat gagccagcct atcttggtgg caaggaccct agagtcaagg
3721 gtggcccttc actgcagcaa gtcatgaggg aacagttgaa gccattcaca gagccaaggg
3781 gtaagccacc aaaaccaagt gtattagaag ctgccaagaa gaccatcatc aatgtccttg
3841 agcaaacaat tgatccacct gagaaatggt cgttcgcaca agcttgcgcg tcccttgaca
3901 agaccacttc cagtggtcat ccgcaccatg tgcggaaaaa cgactgctgg aacggagagt
3961 ccttcacagg caagctggca gaccaggctt ctaaggccaa cctgatgttt gaagaaggga
4021 agaacatgac cccagtctac acagctgcac tcaaggatga gttagtcaaa actgacaaaa
4081 tttatggtaa gatcaagaag aggcttctct ggggctcgga cttggcgacc atgatccggt
4141 gtgctcgagc attcggaggc ctaatggatg aactcaaagc acactgtgtc acacttccca
4201 ttagagttgg catgaatatg aatgaggatg gccccatcat cttcgagagg cattccagat
4261 acacatatca ctatgatgct gattactctc gatgggactc aacacaacag agagccgtgc
4321 tggcagcagc tttagaaatc atggttaaat tctccccaga accacatttg gctcaggtag
4381 tcgcggaaga ccttctttct cctagcgtgg tggacgtggg cgacttcaca atatcaatca
4441 acgagggtct tccctctggg gtgccctgca cctcccaatg gaactccatc gcccactggc
4501 ttctcactct ctgtgcgctc tctgaagtca cgaacctatc ccctgatacc atacaggcta
4561 actccctctt ctctttttat ggtgatgatg aaattgttag cacagacata aaattggacc
4621 cagaaaaatt gacagcgaag ctcagagaat atgggttaaa accaacccgc cctgacaaaa
4681 ctgaagggcc ccttgtcatc tctgaagacc tgaatggcct aactttcctg cggagaactg
4741 tgacccgcga cccggctggt tggtttggaa aactggaaca gagttcaata ctcaggcaaa
4801 tgtactggac taggggtccc aaccatggag acccatctga aacaatgatt ccacactccc
4861 aaaggcccat acaattgatg tccctactgg gggaggccgc tctccacggc ccagcatttt
4921 acagcaaaat cagcaaattg gtcattgcag agctaaaaga aggtggcatg gatttttacg
4981 tgcccaggca agagccaatg ttcagatgga tgagattctc agatctgagc acgtgggagg
5041 gcgatcgcaa tctggctccc agttttgtga atgaagatgg cgtcgagtga cgctaaccca
5101 tctgatgggt ccacagccaa cctcgtccca gaggtcaaca atgaggttat ggctttggag
5161 cccgtagttg gtgccgctat tgcggcacct gtagcgggcc aacaaaatgt aattgacccc
5221 tggattagaa acaattttgt gcaagcccct ggtggagagt tcacagtatc ccctagaaac
5281 gctccaggtg aaatactatg gagcgcgccc ttaggtcctg atttgaatcc ctacctttcc
5341 catttggcca gaatgtacaa tggttatgca ggtggttttg aagtgcaggt aatcctcgcg
5401 gggaacgcgt tcaccgccgg gaaaatcata tttgcagcag tcccaccaaa tttcccaact
5461 gaaggtttga gccccagcca ggtcactatg ttcccccaca taatagtaga tgttaggcaa
5521 ttggaaccag tgttgatccc cttacccgat gttaggaata atttctacca ctacaatcaa
5581 tcaaatgacc ccaccatcaa attgatagca atgttgtaca caccacttag ggctaataat
5641 gccggggatg atgtcttcac agtttcttgt cgagttctca cgagaccatc ccccgatttt
5701 gatttcatat ttttggtgcc acccacagtt gaatcaagaa ctaaaccatt ctctgtccca
5761 gttttaactg ttgaggagat gaccaattca aggttcccca ttcctttgga aaagttgttt
5821 acgggcccca gtagtgcctt tgttgttcaa ccacaaaacg gcaggtgcac gactgatggc
5881 gtgctcctag gtactaccca gctgtcccct gtcaacatct gcaccttcag aggggatgtc
5941 atccatattc caggcagtcg taactacaca atgaatttgg cctcccaaaa ttggaatagt
6001 tacgatccaa cagaagaaat cccagcccct ctaggaactc cagatttcgt ggggaagatt
6061 caaggtgtgc tcacccaaac cacaagaaca aatggctcga ctcgcggcca caaagccaca
6121 gtgtatactg ggagcgccga cttttctcca aaactgggta gagttcaatt tgccactgac
6181 acagacaatg attttgaaac taaccaaaac acaaagttta ccccagtcgg tgttatccag
6241 gatggtagta ctacccaccg aaatgaaccc cagcaatggg tgctcccaag ttactcaggc
6301 agaaacattc ataatgtgca cctggccccc gctgtggccc ccacttttcc gggcgagcag
6361 ctcctcttct tcagatctac tatgcccgga tgcagcgggt accccaacat ggatttggac
6421 tgcctgctcc cccaggaatg ggtgcagtat ttctaccagg aggcagcccc agcacaatct
6481 gacgtggctc tgttaagatt tgtgaatcca gacacaggta gggttttgtt tgagtgtaag
6541 ctccataaat caggctatgt tacagtggct cacactggcc aacatgattt ggtcatcccc
6601 cccaatggtt attttagatt tgattcctgg gtcaaccagt tctacacact tgcccccatg
6661 ggaaatggga cggggcgtag acgtgcatta taatggctgg agctatcttt gctggattgg
6721 catctgacgt ccttagctct ggacttggtt ccctaatcag tgctggggct ggggtcatca
6781 atcaaaaagt tgaatttgaa aacaacagaa aattgcaaca agcttccttc caatttagta
6841 gcaatcaaca acaggcttcc tttcaacatg acaaggagat gctccaagca caaattgagg
6901 ccaccaaaaa gttgcaacag gaaatgatga gagttaaaca agcaatgctc ctagagggtg
6961 gattctctga gacagatgca gcccgtgggg caatcaacgc ccccatgaca aaaactttgg
7021 actggagcgg gacaaggtac tgggctcccg atgctaggac tacaacatat aatgcaggtc
7081 gcttttccac ccctcaaccc tcgggggcac caccaggaag agctaatctt agggctactg
7141 tccccgcccg gggttcctcc agcacgcctt ctaattcttc tattgctact tctgtgtatt
7201 caaatcaaac cacctcaacg agacttggtt ctacagctgg ttctggtacc agtgtctcga
7261 gcctcccgtc aactgcaagg actaggagct ggattgagga tcaaaatagg aatttgtcac
7321 ctttcatgag gggggcccac aacatctcgt ttgtcacccc accatctagc agatcctcta
7381 gccaaggcac agtctcaacc gtgcccaaag aagttttgga ctcctggact ggcgctttca
7441 acacgcgcag gcagcctctc ttcgcccaca ttcgcaagcg aggggagtca cgggtgtaat
7501 gtgaaaagac aaaattgatt atctttcttt tctttagtgt ctttt
//