Typing tool
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Typing tool
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Complete norovirus genomes
| KM198582 | GII.4 Den Haag | |
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| GII.P4 Den Haag |
ORF1: 77..5095
ORF2: 5076..6698
ORF3: 6698..7438
LOCUS KM198582 7438 bp RNA linear VRL 13-NOV-2014
DEFINITION Norovirus Hu/GII/30192/2010/VNM nonstructural polyprotein and
capsid protein VP1 genes, complete cds; and capsid protein VP2
gene, partial cds.
ACCESSION KM198582
VERSION KM198582.1
KEYWORDS .
SOURCE Norovirus Hu/GII/30192/2010/VNM
ORGANISM Norovirus Hu/GII/30192/2010/VNM
Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes;
Picornavirales; Caliciviridae; Norovirus; Norwalk virus.
REFERENCE 1 (bases 1 to 7438)
AUTHORS Cotten,M., Petrova,V., Phan,M.V., Rabaa,M.A., Watson,S.J.,
Ong,S.H., Kellam,P. and Baker,S.
TITLE Deep sequencing of norovirus genomes defines evolutionary patterns
in an urban tropical setting
JOURNAL J. Virol. 88 (19), 11056-11069 (2014)
PUBMED 25056894
REFERENCE 2 (bases 1 to 7438)
AUTHORS Cotten,M.L., Petrova,V., Phan,M.V.T., Rabaa,M.A., Watson,S.J.,
Kellam,P. and Baker,S.
TITLE Direct Submission
JOURNAL Submitted (13-JUL-2014) Virus Genomics, The Wellcome Trust Sanger
Institute, Hinxton CB10 1SA, United Kingdom
COMMENT ##Assembly-Data-START##
Assembly Method :: SPAdes v. 2.4.0
Sequencing Technology :: Illumina
##Assembly-Data-END##
FEATURES Location/Qualifiers
source 1..7438
/organism="Norovirus Hu/GII/30192/2010/VNM"
/mol_type="genomic RNA"
/isolate="Hu/GII/30192/2010/VNM"
/host="Homo sapiens"
/db_xref="taxon:1526993"
/country="Viet Nam"
/collection_date="21-Sep-2009"
/note="genotype: GII"
CDS 77..5095
/note="ORF1"
/codon_start=1
/product="nonstructural polyprotein"
/protein_id="AII02874.1"
/translation="MFSNMAVTFKRALGARPKQPPPREIPQRPPRPPTPELVKKIPPP
PPNGEDEAVVSYSAKDGVSGLPELSTVRQPEETNTAFSVPPLNQRENRDAKEPLTGTI
LEMWDGEIYHYGLYVERGLVLGVHKPPAAISLAKVELTPLSLFWRPVYTPQYLISPDT
LKRLHGETFPYTAFDNNCYAFCCWVLDLNDSWLSRRMIQRTTGFFRPYQDWNRKPLPT
MDDSKLKKVANIFLCALSSLFTRPIKDIIGKLRPLNIINILASCDWTFAGIVESLILL
AELFGVFWTPPDVSAMIAPLLGDFELQGPEDLVVELVPVVMGGIGLVLGFTKEKIGKM
LSSAASTLRACKDLGAYGLEILKLVMKWFFPKKEEANELAMVRSIEDAVLDLEAIENN
HMTTLLKDKDSLATYMRTLDLEEEKARKLSTKSASPDIVGTINALLARIAAARSLVHR
AKEELSSRPRPVVLMISGRPGIGKTHLAREVAKRIAASLTGDQRVGLIPRNGVDHWDA
YKGERVVLWDDYGMSNPIHDALRLQELADTCPLTLNCDRIENKGKVFDSDVIIITTNL
ANPAPLDYVNFEACSRRIDFLVYAEAPEVEKAKRDFPGQPDMWKNAFSSDFSHIKLAL
APQGGFDKNGNTPHGKGVMKTLTTGSLIARASGLLHERLDEFELQGPALTTFNFDRNK
VLAFRQLAAENKYGLIDTMKVGRQLKDVKTMPELKQALKNISIKKCQIVYSGCTYTLE
SDGKGNVKVDRIQSTSVQTNNELAGALHHLRCARIRYYVKCVQEALYSIIQIAGAAFV
TTRIIKRVNIQDLWSKPQVENTEEATNKDGCPKPKDDEEFVISSDDIKTEGKKGKNKT
GRGKKHTAFSSKGLSDEEYDEYKRIREERNGRYSIEEYLQDRDKYYEEVAIARATEED
FCEEEEAKIRQRIFRPTRKQRKEERASLGLVTGSEIRKRNPDDFKPKGKLWADDDRSV
DYNEKLSFEAPPSIWSRIVNFGSGWGFWVSPSLFITSTHVIPQGAKEFFGVPIKQIQV
HKSGEFCRLRFPKPIRTDVTGMILEEGAPEGTVVTLLIKRSTGELMPLAARMGTHATM
KIQGRTVGGQMGMLLTGSNAKSMDLGTTPGDCGCPYIYKRGNDYVVIGVHTAAARGGN
TVICATQGGEGEATLEGGDSKGTYCGAPILGPGSAPKLSTKTKFWRSSTAPLPPGTYE
PAYLGGKDPRVKGGPSLQQVMRDQLKPFTEPRGKPPKPSVLEAAKKTIINVLEQTIDP
PEKWSFAQACASLDKTTSSGHPHHMRKNDCWNGESFTGKLADQASKANLMFEEGKNMT
PVYTGALKDELVKTDKIYGKIKKRLLWGSDLATMIRCARAFGGLMDELKAHCVTLPIR
VGMNMNEDGPIIFEKHSRYRYHYDADYSRWDSTQQRAVLAAALEIMVKFSSEPHLAQV
VAEDLLSPSVVDVGDFTISINEGLPSGVPCTSQWNSIAHWLLTLCALSEVTNLSPDII
QANSLFSFYGDDEIVSTDIKLDPEKLTAKLKEYGLKPTRPDKTEGPLVISEDLDGLTF
LRRTVTRDPAGWFGKLEQSSILRQMYWTRGPNHEDPSESMIPHSQRPIQLMSLLGEAA
LHGPTFYSKISKLVIAELKEGGMDFYVPRQEPMFRWMRFSDLSTWEGDRNLAPSFVNE
DGVE"
CDS 5076..6698
/note="ORF2"
/codon_start=1
/product="capsid protein VP1"
/protein_id="AII02875.1"
/translation="MKMASNDANPSDGSAANLVPEVSNEVMALEPVVGAAIAAPVAGQ
QNVIDPWIRNNFVQAPGGEFTVSPRNAPGEILWSAPLGPDLNPYLSHLARMYNGYAGG
FEVQVILAGNAFTAGKIIFAAVPPNFPTEGLSPSQVTMFPHIIVDVRQLEPVLIPLPD
VRNNFYHYNQTNDSTIKLIAMLYTPLRANNAGEDVFTVSCRVLTRPSPDFDFIFLVPP
TVESRTKPFTVPILTVEEMTNSRFPIPLEKLFTGPSGAFVVQPQNGRCTTDGVLLGTT
QLSPVNICTFRGDVTHIAGSRNYTMNLASLNWNNYDPTEEIPAPLGTPDFVGKIQGVL
TQTTKGDGSTRGHKATVYTGSAPFTPKLGSVQFSTDTENDFETHQNTKFTPVGVIQDG
GTTHRNEPQQWVLPSYSGRDVHNVHLAPAVAPTFPGEQLLFFRSTMPGCSGYPNMDLD
CLLPQEWVQHFYQEAAPAQSDVALLRFVNPDTGRVLFECKLHKSGYVTVAHTGQHDLV
IPPNGYFRFDSWVNQFYTLAPMGNGTGRRRAL"
CDS 6698..>7438
/note="ORF3"
/codon_start=1
/product="capsid protein VP2"
/protein_id="AII02876.1"
/translation="MAGAFFAGLASDVLGSGLGSLINAGAGAINQKIDFENNRKLQQA
SFQFSSNLQQASFQHDKEMLQAQIEATKKLQQEMMKVKQAMLLEGGFSETDAARGAIN
APMTKVLDWSGTRYWAPDARTTTYNAGRFSTPQPSGTLPGRINPRIPTPARGSSSTSS
NASTATSIYSNQTVSTRLGSAAGSGTNVSSLPSTARTRSWVEDQNRNLSPFMRGAHNI
SFVTPPSSRSSSQGTVSTVPKEVLDSWTG"
ORIGIN
1 ccgatcttct aacgacgctt ccgctgccgc tgttgctaac agcaacaacg acaccgcaaa
61 atcttcaagt gacaaaatgt tttctaacat ggctgtcact tttaaacgag ccctcggggc
121 gcggcctaaa cagccccccc cgagggaaat accacaaaga cccccacgac cacctactcc
181 agaactggtc aaaaagatcc ctcctccccc gcccaacgga gaggatgaag cagtggtttc
241 ttatagtgcc aaagatggcg tttccggttt acctgagctt tccaccgtca ggcaaccgga
301 agaaaccaat acggccttca gtgtccctcc actcaaccag agggagaata gagatgctaa
361 ggaaccactg actggaacaa ttctggaaat gtgggatgga gaaatctacc attatggcct
421 gtatgttgag cgaggtcttg tgctgggtgt gcacaaacca ccagctgcca taagcctcgc
481 caaggtcgaa ctaacaccac tctccttgtt ctggagacct gtgtacactc cccagtacct
541 catctctcca gacaccctca agagattaca cggagaaacg tttccctaca cagcctttga
601 caacaattgc tatgcctttt gttgttgggt cctggatcta aatgactcgt ggctgagtag
661 gagaatgatc cagagaacaa ctggcttctt cagaccctac caagactgga ataggaaacc
721 cctccccact atggatgatt ccaaattaaa gaaggtagct aacatattcc tgtgcgccct
781 gtcttcgcta ttcaccaggc ccataaaaga cataatagga aagctaagac ctctcaacat
841 catcaacatc ctggcttcat gtgattggac tttcgcaggc atagtggagt ctttgatact
901 cttggcagag ctctttggag tcttctggac acccccagat gtgtctgcga tgattgcccc
961 cttactcggt gatttcgagt tgcaaggacc tgaggacctt gtagtggaac tcgtccctgt
1021 agtaatgggg ggaattggtt tggtgctggg atttaccaaa gagaagattg ggaaaatgtt
1081 gtcatctgct gcatccacct tgagagcttg taaagatctt ggtgcatatg ggctagagat
1141 cctaaagtta gtcatgaagt ggttcttccc gaagaaagag gaggcaaatg aactggctat
1201 ggtgagatcc atcgaggatg cagtactgga ccttgaggca attgaaaaca accatatgac
1261 caccttgctc aaagacaaag acagcctggc aacctacatg agaacccttg acctcgagga
1321 agagaaagcc agaaaactct caaccaagtc tgcttcacct gacatcgtgg gcacaatcaa
1381 cgcccttctg gcgagaatcg ccgctgcacg ctccctggtg caccgagcaa aggaggagct
1441 ttccagcaga ccaagacctg tagtcttgat gatatcaggc agaccaggga taggaaaaac
1501 ccaccttgct agggaagtgg ctaagaggat cgcagcctcc ctcacaggag accagcgtgt
1561 aggcctcatc ccacgcaatg gcgtcgacca ttgggatgcg tacaaggggg agagggtcgt
1621 cctatgggac gactatggaa tgagcaaccc cattcacgac gcccttaggc tgcaagaact
1681 cgctgacact tgccccctta ctctaaattg tgacaggatt gagaataaag gaaaagtctt
1741 tgacagcgat gtcatcatta tcaccactaa tctggccaac ccagcaccac tggactatgt
1801 caactttgaa gcgtgctcga ggcgcatcga tttcctcgtg tatgcagaag cccccgaggt
1861 cgaaaaggcg aagcgtgact tcccgggcca acctgacatg tggaaaaacg cttttagttc
1921 tgatttctca cacataaaat tggcactggc tccacaaggt ggctttgata agaacgggaa
1981 caccccacac gggaagggcg tcatgaagac tctcaccact ggctccctca ttgcccgggc
2041 atcagggctg ctccatgaga gattggatga gtttgaacta cagggcccag ctcttaccac
2101 cttcaacttt gaccgcaaca aagtgcttgc cttcagacag cttgcagctg aaaacaaata
2161 tgggttgata gacacaatga aagttgggag gcagctcaag gatgtcaaaa ccatgccaga
2221 acttaaacaa gcactcaaaa acatctcaat caagaagtgc cagattgtgt atagtggttg
2281 cacctacaca cttgagtctg atggcaaggg caatgtgaaa gttgacagaa tccagagcac
2341 ctccgtacag accaacaatg agcttgctgg cgccctgcat catctgaggt gcgccagaat
2401 caggtactat gtcaagtgtg tccaggaggc cctgtattct atcatccaga ttgctggggc
2461 cgcatttgtc accacgcgca ttatcaagcg tgtgaacatt caagacttat ggtccaagcc
2521 acaagtggaa aacacagagg aggccaccaa caaggacggg tgcccaaaac ccaaagatga
2581 tgaggagttc gtcatttcat ctgacgacat taaaactgag ggtaagaaag ggaagaacaa
2641 gactggccgt ggcaagaagc atacagcctt ttcaagtaaa ggtctcagtg atgaagagta
2701 tgatgagtac aagagaatta gagaggaaag gaatggcagg tattccatag aagagtacct
2761 tcaggacagg gacaaatact atgaggaggt ggccattgcc agggcgaccg aggaagactt
2821 ctgtgaagag gaggaggcca agatccggca aaggatcttt agaccaacaa ggaaacaacg
2881 caaggaagaa agagcttctc tcggtttagt cacaggttct gagattagga aaagaaaccc
2941 agatgacttc aagcctaagg gaaaactgtg ggctgacgat gacagaagtg tggactacaa
3001 tgagaaactc agttttgagg ccccaccaag catctggtca aggatagtca actttggttc
3061 aggttggggc ttctgggtct cccctagcct gttcataaca tcaacccacg tcatacccca
3121 gggcgcaaag gagttctttg gagttcccat caaacaaatt caggtacaca agtcaggcga
3181 attttgtcgc ttgaggttcc caaaaccaat caggactgac gtgactggca tgatcttgga
3241 agaaggtgcg cccgaaggca ccgtggtcac actactcatc aaaaggtcta ctggagaact
3301 catgccccta gcagctagaa tggggaccca tgcaaccatg aaaattcaag ggcgcaccgt
3361 tggaggtcag atgggcatgc ttctgacagg atccaacgcc aaaagcatgg atctaggcac
3421 cacaccaggt gattgcggct gtccctacat ctacaagaga ggaaatgact atgtggtcat
3481 tggagtccat acggctgccg ctcgtggggg aaacactgtc atttgtgcca cccagggggg
3541 cgagggggaa gctacacttg aaggtggtga cagtaaggga acatactgtg gtgcaccaat
3601 cctaggccca gggagtgccc caaaacttag caccaaaacc aaattctgga gatcatccac
3661 agcaccactc ccacctggca cctatgaacc agcatacctt ggtggcaagg accccagagt
3721 caagggtggc ccttcgttgc agcaagtcat gagggaccag ctgaaaccat ttacagagcc
3781 caggggtaag ccaccaaagc caagtgtgtt agaagctgcc aagaaaacca tcatcaatgt
3841 ccttgaacaa acaattgacc cacctgagaa gtggtcgttc gcacaagctt gcgcctccct
3901 tgacaagacc acttctagcg gccatccgca ccatatgcgg aaaaacgact gctggaatgg
3961 ggagtccttc acaggcaagc tggcagacca ggcttctaag gctaacctga tgtttgaaga
4021 agggaagaac atgaccccag tctacacagg tgcacttaag gatgaattag tcaaaactga
4081 caaaatttat ggtaagatca agaagaggct tctctggggc tcggatttag caaccatgat
4141 ccggtgtgct cgagcattcg gaggcctaat ggatgaactt aaagcacact gtgtcacact
4201 tcctattaga gttggtatga atatgaatga ggatggcccc atcatcttcg agaagcattc
4261 caggtacaga taccactatg atgctgatta ctctcggtgg gattcaacac aacagagagc
4321 cgtgctggca gctgctctag aaatcatggt taaattctcc tcagaaccac atttggctca
4381 ggtagtcgca gaagatcttc tttcccctag cgtggtggat gtgggtgact tcacaatatc
4441 aatcaacgag ggccttccct ctggggtgcc ctgcacctcc caatggaact ccatcgccca
4501 ctggcttctc actctttgtg cactctccga agtcacaaat ttgtccccag acatcataca
4561 ggcaaattct ctcttctcct tctatggtga tgatgaaatt gttagtacag acataaaatt
4621 ggacccagag aagttgacag caaagcttaa ggagtatggg ttgaaaccaa cccgccctga
4681 caaaactgaa ggacctctcg ttatttctga agacttagat ggtttgactt tcctgcggag
4741 aactgtgacc cgcgacccag ctggttggtt tggaaaactg gagcagagct caatactcag
4801 gcaaatgtac tggactaggg gccccaacca tgaagatcca tctgaatcaa tgattccaca
4861 ctctcaaaga cccatacaat tgatgtcctt actgggagag gccgcactcc acggcccaac
4921 attctacagt aaaatcagca aattagtcat tgcagagcta aaagaaggtg gtatggattt
4981 ttacgtgccc aggcaagagc caatgttcag atggatgaga ttctcagatc tgagcacgtg
5041 ggagggcgat cgcaatctgg ctcccagttt tgtgaatgaa gatggcgtcg aatgacgcca
5101 acccatctga tgggtccgca gccaacctcg tcccagaggt cagcaatgag gttatggctt
5161 tggagcccgt tgtcggtgcc gctattgcgg cgcctgtagc gggccaacaa aatgtaattg
5221 acccctggat tagaaacaat tttgtacaag cccctggtgg agagttcaca gtatccccta
5281 gaaacgctcc aggtgaaata ctatggagcg cgcccttagg ccctgatctg aacccctacc
5341 tatcccattt ggccagaatg tataatggtt atgcaggtgg ttttgaagtg caggtgatcc
5401 tcgcggggaa cgcgttcacc gccggaaaaa taatatttgc agcagtccca ccaaattttc
5461 caactgaagg cctgagtccc agccaggtca ctatgttccc ccacataata gtagatgtta
5521 ggcaattgga acctgtgttg atccccttac ctgatgttag gaataacttc tatcattata
5581 atcaaacaaa tgattctacc attaaattga tagcaatgct gtatacacca cttagggcca
5641 ataatgctgg ggaagatgtc ttcacagtct cttgtcgagt cctcactagg ccgtcccctg
5701 attttgattt tatatttttg gtgccaccca cagttgagtc aagaactaaa ccatttactg
5761 tcccaatctt aaccgttgaa gaaatgacca attcaagatt ccccattcct ttggaaaagt
5821 tgttcacggg tcccagcggt gcctttgttg tccaaccaca aaatggcagg tgcacgactg
5881 atggcgtgct cttaggcacc acccaactgt ctcctgtcaa catctgcacc ttcagagggg
5941 atgtcaccca cattgcaggt tctcgtaatt acacaatgaa tctggcatct ctaaattgga
6001 acaattatga cccaacagaa gaaattccag cccctctggg aactccagat ttcgtgggaa
6061 agatccaagg tgtgctcact caaaccacaa aaggagatgg ctcgacccgt ggccataaag
6121 ctacagttta cactgggagt gcccccttta ctccaaagct gggcagtgtt caattcagta
6181 ctgacacaga aaatgatttt gaaactcacc aaaacacaaa attcacccca gtcggtgtca
6241 tccaggatgg tggcaccacc caccgaaatg aaccccaaca atgggtgctc ccaagttatt
6301 caggtagaga tgttcataat gtacacctag cccctgctgt agcccccact tttccgggtg
6361 aacaacttct tttcttcagg tccactatgc ccggatgcag cgggtatccc aacatggatt
6421 tggattgcct actcccccag gagtgggtgc agcacttcta ccaagaggca gctccagcac
6481 aatctgatgt ggctctattg agatttgtga atccagacac gggtagggtc ctgtttgagt
6541 gcaaacttca taaatcaggc tatgtcacag tggctcacac cggtcagcat gatttggtca
6601 tcccccccaa tggctacttt aggtttgatt cctgggttaa tcagttctat acgcttgccc
6661 ccatgggaaa cggaacgggg cgtaggcgcg ccttataatg gctggagctt tctttgctgg
6721 attggcatct gatgtccttg gttctggact tggttcccta atcaatgctg gggctggggc
6781 catcaaccaa aagattgatt ttgaaaataa tagaaaattg cagcaagctt ccttccagtt
6841 tagcagtaat ctacaacagg cttcctttca acacgataaa gagatgctcc aagcacaaat
6901 tgaggccact aaaaagttgc aacaggaaat gatgaaagtc aaacaggcaa tgctcctaga
6961 aggtggattc tctgaaacag atgcagcccg tggggcaatc aacgccccca tgacaaaggt
7021 tttagactgg agcggaacaa ggtactgggc ccctgatgct aggaccacaa catacaatgc
7081 aggccgcttt tccacccctc aaccttcggg gacgctgcca ggaagaatca atcccaggat
7141 ccctaccccc gctcggggct cctccagcac atcttctaat gcttctactg ctacttctat
7201 atattcaaat caaactgttt caacgagact tggttctgca gctggttctg gtaccaatgt
7261 ctcgagtctc ccgtcaactg caaggactag gagctgggtt gaggatcaaa acagaaattt
7321 gtcacctttc atgagggggg ctcataacat atcgtttgtc accccaccat ctagcagatc
7381 ctctagccaa ggcacagtct caaccgtgcc taaagaagtt ttggactcct ggactggc
//