Typing tool
|
|
|
|
|
|
Typing tool
|
Complete norovirus genomes
| LN854571 | GII.4 New Orleans | |
|
|---|---|---|---|
| GII.P4 New Orleans |
ORF1: 5..5104
ORF2: 5085..6707
ORF3: 6707..7513
LOCUS LN854571 7559 bp RNA linear VRL 12-JUN-2015
DEFINITION Norovirus GII/Hu/NL/2012/GII.4/Nijmegen01, complete genome.
ACCESSION LN854571
VERSION LN854571.1
KEYWORDS complete genome.
SOURCE Norovirus GII/Hu/NL/2012/GII.4/Nijmegen01
ORGANISM Norovirus GII/Hu/NL/2012/GII.4/Nijmegen01
Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes;
Picornavirales; Caliciviridae; Norovirus; Norwalk virus.
REFERENCE 1
AUTHORS Bavelaar,H., Rahamat-Langendoen,J., Niesters,H.G.M., Zoll,J. and
Melchers,W.J.G.
TITLE Whole genome sequencing of faecal samples as a tool for the
diagnosis and genetic characterization of norovirus
JOURNAL Unpublished
REFERENCE 2 (bases 1 to 7559)
AUTHORS Zoll,J.
TITLE Direct Submission
JOURNAL Submitted (18-MAY-2015) Medical Microbiology, RADBOUDUMC, PO Box
9101, 6500 HB Nijmegen, NETHERLANDS
FEATURES Location/Qualifiers
source 1..7559
/organism="Norovirus GII/Hu/NL/2012/GII.4/Nijmegen01"
/mol_type="genomic RNA"
/strain="GII/Hu/NL/2012/GII.4/Nijmegen01"
/host="Homo sapiens"
/db_xref="taxon:1665652"
/note="genotype:GII.4"
gene 5..5104
/gene="POL"
CDS 5..5104
/gene="POL"
/note="ORF1"
/codon_start=1
/product="nonstructural polyprotein"
/protein_id="CRL46975.1"
/translation="MKMASNDASAAAVANSNNDIAKSSSDGVLSSMAVTFKRALGARP
KQPPPREKPQRPPRPPTPELVKNIPPPPPNGEDEIVVSYSVKDGVSGLPDLSTVRQPE
ESNTAFSVPPLNQRENRDAKEPLTGTILEMWDGEIYHYGLYVERGLVLGVHKPPAAIS
LAKVELAPLSLYWRPVYTPQYLISPDTLKKLSGEAFPYTAFDNNCYAFCCWVLDLNDS
WLSRRMIQRTTGFFRPYQDWNRKPLPTMDDSKIKKVANIFLCALSSLFTRPIKDIIGR
IRPLNILNILASCDWTFAGIVESLILLAELFGVFWTPPDVSAMIAPLLGDYELQGPED
LAVELVPVVMGGIGLVLGFTKEKIGKMLSSAASTLRACKDLGAYGLEILKLVMKWFFP
KKEEANELAIVRSIEDAVLDLEAIENNHMTTLLKDKDSLATYMRTLDLEEEKARKLST
KSASPDIVGTINALLARIAAARSLVHRAKEELSSRPRPVVLMISGRPGIGKTHLAREV
AKRIAASLTGDQRVGLIPRNGVDHWDAYKGERVVLWDDYGMSNPIHDALRLQELADTC
PLTLNCDRIENKGKVFDSDVIIITTNLANPAPLDYVNFEACSRRIDFLVYAEAPEVEK
AKRDFPGQPDMWKNAFSSDFSHIKLALAPQGGFDKNGNTPHGKGVMKTLTTGSLIARA
SGLLHERLDEFELQGPALTTFNFDRNKVLAFRQLAAENKYGLMDTMRVGKQLKDVRTM
PELKQALKNVSIKKCQIVYSGCTYVLESDGKGNVKVDRIQSAAVQINNELAGALRHLR
SARIRYYVKCVQEALYSIIQIAGAAFVTTRIAKRMNIQNLWSKPQVENTEETTSKDGC
PKPKDDEEFVISSDDIKTEGKKGKNKTGRGKKHTAFSSKGLSDEEYDEYKRIREERNG
KYSIEEYLQDRDKYYEEVAIARATEEDFCEEEEAKIRQRIFRPTRKQRKEERASLGLV
TGSEIRRRNPDDFKPKGKLWADDDRSVDYNEKLSFEAPPSIWSRIVNFGSGWGFWVSP
SLFITSTHVIPQGAKEFFGVPIKQIQVHKSGEFCRLRFPKPIRTDVTGMILEEGAPEG
TVVTLLIKRSTGELMPLAARMGTHATMKIQGRTVGGQMGMLLTGSNAKSMDLGTTPGD
CGCPYIYKRGNDYVVIGVHTAAARGGNTVICATQGSEGEATLEGGDNKGTYCGAPILG
PGSAPTLSTKTKFWRSSTASLPPGTYEPAYLGGKDPRVKGGPSLQQVMREQLKPFTEP
RGKPPKPSVLESAKKTIINVLEQTIDPPEKWSFAQACASLDKTTSSGHPHHVRKNDCW
NGESFTGKLADQASKANLMFEEGKNMTPVYTAALKDELVKTDKIYGKIKKRLLWGSDL
ATMIRCARAFGGLMDELKAHCVTLPIRVGMNMNEDGPIIFERHSRYTYHYDADYSRWD
STQQRAVLAAALEIMVKFSPEPHLAQVVAEDLLSPSVVDVGDFTISINEGLPSGVPCT
SQWNSIAHWLLTLCALSEVTNLSPDTIQANSLFSFYGDDEIVSTDIKLDPEKLTAKLR
EYGLKPTRPDKTEGPLVISEDLNGLTFLRRTVTRDPAGWFGKLEQSSILRQMYWTRGP
NHGDPSETMIPHSQRPIQLMSLLGEAALHGPAFYSKISKLVIAELKEGGMDFYVPRQE
PMFRWMRFSDLSTWEGDRNLAPSFVNEDGVE"
gene 5085..6707
/gene="VP1"
CDS 5085..6707
/gene="VP1"
/note="ORF2"
/codon_start=1
/product="capsid protein VP1"
/protein_id="CRL46976.1"
/translation="MKMASNDAAPSDGSTANLVPEVNNEVMALEPVVGAAIAAPVAGQ
QNVIDPWIRNNFVQAPGGEFTVSPRNAPGEILWSAPLGPDLNPYLSHLARMYNGYAGG
FEVQVILAGNAFTAGKIIFAAVPPNFPTEGLSPSQVTMFPHIIVDVRQLEPVLIPLPD
VRNNFYHYNQSNDPTIKLIAMLYTPLRANNAGDDVFTVSCRVLTRPSPDFDFIFLVPP
TVESRTKPFSVPVLTVEEMTNSRFPIPLEKLFTGPSSAFVVQPQNGRCTTDGVLLGTT
QLSPVNICTFRGDVIHIPGSRNYTMNLASQNWNSYDPTEEIPAPLGTPDFVGKIQGVL
TQTTRTNGSTRGHKATVYTGSADFSPKLGRVQFATDTDNDFETNQNTKFTPVGVIQDG
STTPRNEPQQWVLPSYSGRNIHNVHLAPAVAPTFPGEQLLFFRSTMPGCSGYPNMDLD
CLLPQEWVQYFYQEAAPAQSDVALLRFVNPDTGRVLFECKLHKSGYVTVAHTGQHDLV
IPPNGYFRFDSWVNQFYTLAPMGNGTGRRRAL"
gene 6707..7513
/gene="VP2"
CDS 6707..7513
/gene="VP2"
/note="ORF3"
/codon_start=1
/product="capsid protein VP2"
/protein_id="CRL46977.1"
/translation="MAGAFFAGLASDVLGSGLGSLINAGAGAINQKVEFENNRKLQQA
SFQFSSSLQQASFQHDKEMLQAQIEATKKLQQEMMRVKQAMLLEGGFSETDAARGAIN
APMTKTLDWSGTRYWAPDARTTTYNAGRFSTPQPSGALPGRANLRATAPARGSSSMSS
NSSIATSVYSNQTTSTRLGSTAGSGTSVSSLPSTARTRSWVEDQNRNLSPFMRGAHNI
SFVTPPSSRSSSQGTVSTVPKEVLDSWTGAFNTRRQPLFAHIRKRGESRA"
ORIGIN
1 gtgaatgaag atggcgtcta acgacgcttc cgctgccgct gttgctaaca gcaacaacga
61 catcgcaaaa tcttcaagtg acggagtgct ttctagcatg gctgtcactt ttaaacgagc
121 cctcggggcg cggcctaaac agcctccccc gagggaaaaa ccacaaagac ccccacgacc
181 acctactcca gaactggtca aaaatattcc ccctccccca cccaacggag aggatgaaat
241 agtggtttct tatagtgtca aggatggtgt ttccggcttg cctgaccttt ccaccgtcag
301 gcaaccggaa gaatctaaca cggccttcag tgtccctcca ctcaatcaga gggagaatag
361 agatgctaag gagccactta ctggaacaat tctggaaatg tgggacgggg aaatctatca
421 ttatggtctg tatgtggagc gaggccttgt actaggtgtg cacaaaccac cagctgccat
481 cagcctcgct aaggttgagc tagcaccact ctccttgtac tggagacctg tgtacactcc
541 tcagtacctc atctctccag acactctcaa gaaattatcc ggagaagcgt tcccctacac
601 ggcctttgac aacaactgct atgccttttg ttgctgggtc ctggacctaa atgactcgtg
661 gctgagcagg agaatgatcc agagaacaac tggtttcttc aggccctacc aagactggaa
721 taggaaaccc cttcccacta tggacgactc caaaataaag aaggtagcta acatattcct
781 gtgtgctctg tcctcgctgt tcaccagacc cataaaagat ataataggga ggataaggcc
841 tcttaacatc ctcaacatct tagcctcgtg tgattggact tttgcaggca tagtggagtc
901 cctgatactc ttggcagaac tctttggtgt tttctggaca cccccagatg tgtctgcgat
961 gattgccccc ttacttggtg actacgagct acaaggacct gaggaccttg cagtggagct
1021 cgtccccgta gtgatggggg gaattggctt ggtgctagga ttcaccaaag agaagattgg
1081 gaaaatgttg tcatctgctg cgtccacctt gagagcttgt aaagaccttg gtgcatatgg
1141 gctagagatc ctaaagttgg tcatgaagtg gttcttcccg aagaaggagg aggcaaatga
1201 gctggctata gtgaggtcta tcgaggatgc agtcctagat ctcgaggcaa ttgaaaacaa
1261 ccatatgacc accttgctca aagacaaaga cagtctggca acctatatga gaacactcga
1321 ccttgaggag gagaaagcca ggaaactttc aaccaagtct gcctcacccg acatcgtggg
1381 cacaatcaac gccctcctgg cgagaatcgc tgccgcacgt tctctggtgc atcgagcgaa
1441 ggaggagctt tccagcagac caagacctgt ggtgttgatg atatcaggca ggccaggaat
1501 agggaagacc cacctcgcta gggaagtggc taagagaatc gcagcctccc ttacaggaga
1561 ccagcgtgtg ggtctcatcc cacgcaatgg cgtcgaccat tgggatgcat acaagggaga
1621 gagggtcgtc ctatgggacg attatggaat gagcaaccct atccacgatg ccctcaggct
1681 gcaagaactt gctgacactt gccccctcac tctaaactgt gacaggattg aaaataaagg
1741 aaaggtcttt gacagcgatg tcatcattat caccactaat ctggccaacc cagcaccact
1801 ggactatgtc aattttgaag catgctcgag gcgcatcgac ttcctcgtgt atgcagaagc
1861 ccctgaagtc gaaaaggcga agcgtgactt cccaggccag cctgacatgt ggaagaacgc
1921 tttcagttct gatttctcac acataaaact agcactggcc ccacagggtg gtttcgacaa
1981 gaacgggaac accccgcacg gaaagggcgt catgaagact ctcaccactg gctcccttat
2041 tgcccgggca tcagggctac tccatgagag gttagatgaa tttgaactac agggcccagc
2101 tctcaccacc ttcaatttcg atcgcaataa agtgcttgcc tttagacagc ttgctgctga
2161 aaataaatat ggattgatgg acacaatgag ggttgggaaa cagctcaagg atgtcagaac
2221 catgccagaa ctcaaacaag cactcaagaa tgtctcaatc aagaagtgcc aaatagtgta
2281 tagtggttgc acctacgtac ttgagtctga tggcaagggc aatgtgaaag ttgacagaat
2341 ccaaagcgcc gccgtgcaga tcaacaatga gctggctggt gccctgcgcc acttgaggag
2401 cgccagaatc agatactatg tcaagtgtgt ccaggaggcc ctgtattcca tcattcaaat
2461 tgctggggct gcatttgtca ccacgcgcat tgccaagcgc atgaacatac aaaacctatg
2521 gtccaagcca caagtggaaa acacagagga gactaccagc aaggacgggt gcccaaagcc
2581 taaggatgac gaggagtttg tcatttcatc cgacgacatc aaaactgagg gtaagaaagg
2641 gaagaacaag actggccgcg gcaagaagca cacagcattt tcaagcaaag gcctcagtga
2701 tgaagagtac gatgagtaca agaggattag agaagaaagg aatggcaagt actccataga
2761 agagtacctt caggacagag acaaatacta tgaggaggtg gccattgcca gggcgactga
2821 ggaagatttc tgtgaagagg aggaggccaa gatccggcaa aggatcttta ggccaacaag
2881 gaaacaacgc aaggaggaaa gagcctctct cggtctggtc acaggctctg aaattaggag
2941 aagaaaccca gatgatttca aacccaaggg gaaattgtgg gctgacgatg acaggagtgt
3001 ggactacaat gagaaactca gttttgaggc cccaccaagc atctggtcga gaatagtcaa
3061 ctttggatca ggctggggat tctgggtctc ccccagtctg ttcataacat caacccatgt
3121 cataccccag ggcgcaaagg agttctttgg agtccccatc aaacaaatac aggtacacaa
3181 gtcaggcgag ttctgtcgct tgagattccc aaaaccaatc aggactgatg tgacgggcat
3241 gattttagaa gaaggcgcac ctgagggcac cgtggtcaca ctactcatca aaaggtccac
3301 tggggaactc atgcccctag cagctaggat ggggacccat gcgaccatga agatccaagg
3361 gcgcactgtt ggaggccaga tgggcatgct tctgacagga tccaacgcca agagcatgga
3421 cctgggtact acaccaggtg attgtggctg cccctatatc tacaagagag gtaatgacta
3481 tgtggtcatt ggagtccaca cggctgccgc acgtggggga aacactgtca tatgtgccac
3541 ccaggggagt gaaggagagg ctacacttga aggtggtgac aacaagggga catactgtgg
3601 tgcaccaatc ctaggcccag ggagtgcccc aacccttagc accaagacca aattctggag
3661 atcgtctaca gcatcactcc cacctggcac ctatgaacca gcctatcttg gtggcaagga
3721 ccctagagtc aagggtggcc cttcactaca gcaagtcatg agggaacagt tgaagccatt
3781 cacagagcca aggggcaagc caccaaaacc aagtgtatta gaatctgcca agaagaccat
3841 catcaatgtc cttgagcaaa caattgatcc acctgagaaa tggtcgttcg cacaagcttg
3901 cgcgtccctt gacaagacca cttccagtgg tcatccgcac cacgtgcgga aaaacgactg
3961 ctggaacggg gagtccttca caggcaagct ggcagaccag gcttccaagg ccaacctgat
4021 gtttgaagaa gggaagaaca tgaccccagt ctacacagct gcgctcaagg atgagttagt
4081 taaaactgac aaaatttatg gtaagatcaa gaagaggctt ctctggggct cggacttggc
4141 gaccatgatc cggtgtgccc gagcattcgg aggcctaatg gatgaactca aagcacactg
4201 tgtcacgctt cccattagag ttggcatgaa tatgaatgag gatggcccca tcatcttcga
4261 gaggcattcc aggtacacat atcactatga tgctgactac tctcgatggg attcaacaca
4321 acagagggcc gtgttggcag cagctctcga aatcatggtt aaattctccc cagaaccaca
4381 tttggcccag gtagtcgcgg aagaccttct ttctcctagc gtggtggacg tgggcgactt
4441 cacaatatca atcaatgagg gtcttccctc tggggtgccc tgcacctccc aatggaactc
4501 catcgcccac tggcttctca ctctctgtgc gctctccgaa gtcacaaacc tatcccctga
4561 taccatacag gctaactccc tcttctcttt ttatggtgat gatgaaattg ttagcacaga
4621 cataaaattg gacccagaga aattgacagc aaagctcaga gaatatgggt taaaaccaac
4681 ccgccctgac aaaactgaag gaccccttgt catctctgaa gacctgaatg gcctaacttt
4741 cctgcggaga actgtgaccc gcgacccagc tggttggttt ggaaaactgg agcagagttc
4801 aatactcagg caaatgtact ggactagggg tcccaaccat ggagacccat ctgaaacaat
4861 gattccacac tcccaaagac ccatacaatt gatgtcccta ctgggggagg ccgctctcca
4921 cggcccagcc ttttatagca aaatcagcaa gttggtcatt gcagagctaa aagaaggtgg
4981 catggatttt tacgtgccca gacaagagcc aatgttccga tggatgaggt tctcagactt
5041 gagcacgtgg gagggcgatc gcaatctggc tcccagtttt gtgaatgaag atggcgtcga
5101 atgacgccgc tccatctgat gggtccacag ccaacctcgt cccagaggtc aacaatgagg
5161 ttatggcttt ggagcccgta gttggtgccg ctattgcggc acctgtagcg ggccaacaaa
5221 atgtaattga cccctggatt agaaacaatt ttgtacaagc ccctggtgga gagtttacag
5281 tatcccctag aaacgctcca ggtgaaatat tatggagcgc gcccttaggc cctgatctga
5341 atccctacct ttctcatttg gccagaatgt ataatggtta tgcaggtggt tttgaagtgc
5401 aggtaatcct cgcggggaac gcgttcaccg ccgggaaaat catatttgca gcagtcccac
5461 caaatttccc aactgaaggt ttgagcccca gccaggtcac tatgttcccc catataatag
5521 tagatgttag gcaattggaa cctgtgttga tccccttacc cgatgttagg aataatttct
5581 accattataa tcaatcaaat gaccccacta tcaaattgat agcaatgctg tacacaccac
5641 ttagggctaa taatgctggg gacgatgtct tcacagtttc ttgtcgagtt ctcacgagac
5701 catcccccga ttttgatttc atatttttgg tgccacccac agttgaatca agaactaaac
5761 cattctctgt cccagtttta actgttgagg agatgaccaa ttcaaggttc cccattcctt
5821 tggaaaaatt gttcacgggc cccagtagtg cctttgttgt tcaaccacaa aatggcaggt
5881 gcacgactga tggcgtgctc ctaggtacta cccaactgtc ccctgtcaac atctgcacct
5941 tcagagggga tgtcatccat attccaggca gtcgtaacta cacaatgaat ttggcctccc
6001 aaaattggaa cagttacgat ccaacagaag aaatcccagc ccctctagga actccagatt
6061 tcgtggggaa gattcaaggt gtgctcaccc aaaccacaag gacaaatggc tcgacccgcg
6121 gccacaaagc tacagtgtac actgggagcg ccgacttttc tccaaaactg ggtagagttc
6181 aatttgccac tgacacagac aatgattttg aaactaacca aaacacaaag ttcaccccag
6241 tcggtgttat ccaggatggt agtaccaccc cccgaaatga acctcaacaa tgggtgctcc
6301 caagttactc aggcagaaac attcataatg tgcacctggc ccccgctgta gcccccactt
6361 tcccgggcga gcagctcctc ttctttagat ctactatgcc cggatgcagc gggtacccca
6421 acatggattt ggactgtctg ctcccccagg agtgggtgca gtacttctac caggaggcag
6481 ccccagcaca atctgatgtg gctctgttga gatttgtgaa tccagacaca ggtagggttt
6541 tgtttgagtg taagctccat aaatcaggct atgttacagt ggctcacact ggtcaacatg
6601 atttggttat cccccccaat ggttatttta gatttgattc ctgggtcaac cagttctaca
6661 cacttgcccc catgggaaat gggacggggc gtagacgtgc attataatgg ctggagcttt
6721 ctttgctgga ttggcatctg acgtccttgg ctctggactt ggttccctaa tcaatgctgg
6781 ggctggggcc atcaaccaaa aagttgaatt tgaaaataat agaaaattgc aacaagcttc
6841 cttccaattt agtagcagtc tacaacaagc ttcctttcaa catgacaaag aaatgctcca
6901 agcacaaatt gaggccacca aaaagttgca acaggaaatg atgagagtta aacaagcaat
6961 gctcctagag ggtggattct ctgagacaga tgcagcccgt ggggcaatca acgcccccat
7021 gacaaaaact ttggactgga gcgggacaag gtactgggct cccgatgcta ggactacaac
7081 atataatgca ggccgctttt ccacccctca accctcgggg gcactaccag gaagagctaa
7141 tcttagggct actgcccccg cccggggttc ctccagcatg tcttctaact cttctattgc
7201 tacttctgtg tattcaaatc aaaccacttc aacgagactt ggttctacag ctggttctgg
7261 taccagtgtc tcgagcctcc cgtcaactgc aaggactagg agctgggttg aggatcaaaa
7321 taggaatttg tcacctttca tgaggggggc ccacaacatc tcgtttgtca ccccaccatc
7381 tagcagatcc tctagccaag gcacagtctc aaccgtgccc aaagaagttt tggactcctg
7441 gactggcgct ttcaacacgc gcaggcagcc tctcttcgct cacattcgca agcgagggga
7501 gtcacgggcg taatgtgaaa agacaaaatt gattaccttt cttttcttta gtgtctttt
//