Typing tool
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Typing tool
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Complete norovirus genomes
| KM198558 | GII.4 Den Haag | |
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| GII.P4 Den Haag |
ORF1: 1..5100
ORF2: 5081..6703
ORF3: 6703..7443
LOCUS KM198558 7443 bp RNA linear VRL 13-NOV-2014
DEFINITION Norovirus Hu/GII/30257/2009/VNM nonstructural polyprotein and
capsid protein VP1 genes, complete cds; and capsid protein VP2
gene, partial cds.
ACCESSION KM198558
VERSION KM198558.1
KEYWORDS .
SOURCE Norovirus Hu/GII/30257/2009/VNM
ORGANISM Norovirus Hu/GII/30257/2009/VNM
Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes;
Picornavirales; Caliciviridae; Norovirus; Norovirus norwalkense.
REFERENCE 1 (bases 1 to 7443)
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 7443)
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..7443
/organism="Norovirus Hu/GII/30257/2009/VNM"
/mol_type="genomic RNA"
/isolate="Hu/GII/30257/2009/VNM"
/host="Homo sapiens"
/db_xref="taxon:1291808"
/geo_loc_name="Viet Nam"
/collection_date="30-Oct-2009"
/note="genotype: GII"
CDS 1..5100
/note="ORF1"
/codon_start=1
/product="nonstructural polyprotein"
/protein_id="AII02802.1"
/translation="MKMASNDASAAAVANSNNDTAKSSSDKMFSNMAVTFKRALGARP
KQPPPREIPQRPPRPPTPELVKKIPPPPPNGEDEAVVSYSAKDGVSGLPELSTVRQPE
ETNTAFSVPPLNQRENRDAKEPLTGTILEMWDGEIYHYGLYVERGLVLGVHKPPAAIS
LAKVELTPLSLFWRPVYTPQYLISPDTLKKLHGETFPYTAFDNNCYAFCCWVLDLNDS
WLSRRMIQRTTGFFRPYQDWNRKPLPTMDDSKLKKVANIFLCALSSLFTRPIKDIIGK
LRPLNIINILASCDWTFAGIVESLILLAELFGVFWTPPDVSAMIAPLLGDFELQGPED
LVVELVPVVMGGIGLVLGFTKEKIGKMLSSAASTLRACKDLGAYGLEILKLVMKWFFP
KKEEANELAMVRSIEDAVLDLEAIENNHMTTLLKDKDSLATYMRTLDLEEEKARKLST
KSASPDIVGTINALLARIAAARSLVHRAKEELSSRPRPVVLMISGRPGIGKTHLAREV
AKRIAASLTGDQRVGLIPRNGVDHWDAYKGERVVLWDDYGMSNPIHDALRLQELADTC
PLTLNCDRIENKGKVFDSDVIIITTNLANPAPLDYVNFEACSRRIDFLVYAEAPEVEK
AKRDFPGQPDMWKNAFSSDFSHIKLALAPQGGFDKNGNTPHGKGVMKTLTTGSLIARA
SGLLHERLDEFELQGPALTTFNFDRNKVLAFRQLAAENKYGLIDTMKVGRQLKDVKTM
PELKQALKNISIKKCQIVYSGCTYTLESDGKGNVKVDRIQSTSVQTNNELAGALHHLR
CARIRYYVKCVQEALYSIIQIAGAAFVTTRIIKRVNIQDLWSKPQVENTEEATNKDGC
PKPEDDEEFVISSDDIKTEGKKGKNKTGRGKKHTAFSSKGLSDEEYDEYKRIREERNG
RYSIEEYLQDRDKYYEEVAIARATEEDFCEEEEAKIRQRIFRPTRKQRKEERASLGLV
TGSEIRKRNPDDFKPKGKLWADDDRSVDYNEKLSFEAPPSIWSRIVNFGSGWGFWVSP
SLFITSTHVIPQGAKEFFGVPIKQIQVHKSGEFCRLRFPKPIRTDVTGMILEEGAPEG
TVVTLLIKRSTGELMPLAARMGTHATMKIQGRTVGGQMGMLLTGSNAKSMDLGTTPGD
CGCPYIYKRGNDYVVIGVHTAAARGGNTVICATQGGEGEATLEGGDSKGTYCGAPILG
PGSAPKLSTKTKFWRSSTAPLPPGTYEPAYLGGKDPRVKGGPSLQQVMRDQLKPFTEP
RGKPPKPSVLEAAKKTIINVLEQTIDPPERWSFAQACASLDKTTSSGHPHHMRKNDCW
NGESFTGKLADQASKANLMFEEGKNMTPVYTGALKDELVKTDKIYGKIKKRLLWGSDL
ATMIRCARAFGGLMDELKAHCVTLPIRVGMNMNEDGPIIFEKHSRYRYHYDADYSRWD
STQQRAVLAAALEIMVKFSSEPHLAQVVAEDLLSPSVVDVGDFTISINEGLPSGVPCT
SQWNSIAHWLLTLCALSEVTNLSPDIIQANSLFSFYGDDEIVSTDIKLDPEKLTAKLK
EYGLKPTRPDKTEGPLVISEDLDGLTFLRRTVTRDPAGWFGKLEQSSILRQMYWTRGP
NHEDPSESMIPHSQRPIQLMSLLGEAALHGPTFYSKISKLVIAELKEGGMDFYVPRQE
PMFRWMRFSDLSTWEGDRNLAPSFVNEDGVE"
CDS 5081..6703
/note="ORF2"
/codon_start=1
/product="capsid protein VP1"
/protein_id="AII02803.1"
/translation="MKMASNDANPSDGSAANLVPEVSNEVMALEPVVGAAIAAPVAGQ
QNVIDPWIRNNFVQAPGGEFTVSPRNAPGEILWSAPLGPDLNPYLSHLARMYNGYAGG
FEVQVILAGNAFTAGKIIFAAVPPNFPTEGLSPSQVTMFPHIIVDVRQLEPVLIPLPD
VRNNFYHYNQTNDPTIKLIAMLYTPLRANNAGEDVFTVSCRVLTRPSPDFDFIFLVPP
TVESRTKPFTVPILTVEEMTNSRFPIPLEKLFTGPSGAFVVQPQNGRCTTDGVLLGTT
QLSPVNICTFRGDVTHIAGSRDYTMNLASLNWNNYDPTEEIPAPLGTPDFVGKIQGVL
TQTTRGDGSTRGHKATVYTGSAPFAPKLGSVQFSTDTENDFETHQNTKFTPVGVIQDG
GTTHRNEPQQWVLPSYSGRDVHNVHLAPAVAPTFPGEQLLFFRSTMPGCSGYPNMDLD
CLLPQEWVQHFYQEAAPAQSDVALLRFVNPDTGRVLFECKLHKSGYVTVAHTGQHDLV
IPPNGYFRFDSWVNQFYTLAPMGNGTGRRRAL"
CDS 6703..>7443
/note="ORF3"
/codon_start=1
/product="capsid protein VP2"
/protein_id="AII02804.1"
/translation="MAGAFFAGLASDVLGSGLGSLINAGAGAINQKIDFENNRKLQQA
SFQFSSNLQQASFQHDKEMLQAQIEATKKLQQEMMKVKQAMLLEGGFSETDAARGAIS
APMTKVLDWSGTRYWAPDARTTTYNSGRFSTPQPSGTLPGRINPRTPTPARGSSSTSS
NASTATSIHLNQTVSTRLGSTAGSGTNVSSLPSTARTRSWVEDQNRNLSPFMRGAHNI
SFVTPPSSRSSSQGTVSTVPKEILDSWAG"
ORIGIN
1 atgaagatgg cgtctaacga cgcttccgct gccgctgttg ctaacagcaa caacgacacc
61 gcaaaatctt caagtgacaa aatgttttct aacatggctg tcacttttaa acgagccctc
121 ggggcgcggc ctaaacagcc ccccccgagg gaaataccac aaagaccccc acgaccacct
181 actccagaac tggtcaaaaa gatccctcct cccccgccca acggagagga tgaagcagtg
241 gtttcttata gtgccaaaga tggcgtttcc ggtttacctg agctttccac cgtcaggcaa
301 ccggaagaaa ccaatacggc cttcagtgtc cctccactca accagaggga gaatagagat
361 gctaaggaac ctctgactgg aacaattctg gaaatgtggg atggagaaat ctaccattat
421 ggcctgtatg ttgagcgagg tcttgtgctg ggtgtgcaca aaccaccagc tgccataagc
481 ctcgccaagg tcgaactaac accactctcc ttgttctgga gacctgtgta cactccccag
541 tacctcatct ctccagacac tctcaagaaa ttacacggag aaacgtttcc ctacacagcc
601 tttgacaaca attgctatgc cttttgttgt tgggtcctgg atctaaatga ctcgtggctg
661 agtaggagaa tgatccagag aacaactggc ttctttagac cctaccaaga ctggaatagg
721 aaacccctcc ccactatgga tgattccaag ttaaagaagg tagctaacat attcctgtgc
781 gccctgtctt cgctattcac caggcccata aaagacataa taggaaagct aagacctctc
841 aacatcatca acatcctggc ttcatgtgat tggactttcg caggcatagt ggagtctttg
901 atactcttgg cagagctctt tggagtcttc tggacacccc cagatgtgtc tgcgatgatt
961 gcccccttac tcggtgattt cgagttacaa ggacctgagg accttgtagt ggagctcgtc
1021 cctgtagtaa tggggggaat tggtttggtg ttgggattca ccaaagagaa gattgggaaa
1081 atgttgtcat ctgctgcatc caccttgaga gcttgtaaag atcttggtgc atatgggcta
1141 gagatcctaa agttagtcat gaagtggttc ttcccgaaga aagaggaggc aaatgaactg
1201 gctatggtga gatccatcga ggatgcagta ctggaccttg aggcaattga aaacaaccat
1261 atgaccacct tgctcaaaga caaagacagc ctggcaacct acatgagaac ccttgacctc
1321 gaggaagaga aagccagaaa actctcaacc aagtctgctt cacctgacat cgtgggcaca
1381 attaacgccc ttctggcgag aatcgccgct gcacgctccc tggtgcaccg agcgaaggag
1441 gagctttcca gcagaccaag acctgtagtc ttgatgatat caggcagacc agggatagga
1501 aaaacccacc ttgctaggga agtggctaag agaatcgcag cctccctcac aggagaccag
1561 cgtgtaggcc tcatcccacg caatggcgtc gatcactggg atgcgtacaa gggggagagg
1621 gtcgtcctat gggacgacta tggaatgagc aaccccattc acgacgccct taggctgcaa
1681 gaactcgctg acacttgccc ccttactcta aattgtgaca ggattgagaa taaaggaaag
1741 gtctttgaca gcgatgtcat cattatcacc actaatctgg ccaacccagc accactggac
1801 tatgtcaact ttgaagcgtg ctcgaggcgc atcgatttcc tcgtgtatgc agaagccccc
1861 gaggtcgaaa aggcgaagcg tgacttcccg ggccaacctg acatgtggaa aaacgctttt
1921 agttctgatt tctcacacat aaaattggca ctggctccac aaggtggctt tgataagaac
1981 gggaacaccc cacacgggaa gggcgtcatg aagactctca ccactggctc cctcattgcc
2041 cgggcatcag ggctgctcca tgagagattg gatgagtttg aactacaggg cccagctctc
2101 accaccttca actttgatcg caacaaagta cttgccttca gacagcttgc agctgaaaac
2161 aaatatgggt tgatagacac aatgaaagtt gggaggcagc tcaaggatgt caaaaccatg
2221 ccagaactta aacaagcact caaaaacatc tcaatcaaga agtgccagat tgtgtatagt
2281 ggttgcacct acacacttga gtctgatggc aagggcaatg tgaaagttga cagaatccag
2341 agcacctccg tacagaccaa caatgagctt gctggcgccc tgcatcatct gaggtgcgcc
2401 agaatcagat actatgtcaa gtgtgtccag gaggccctat attctatcat ccagattgct
2461 ggggccgcat ttgtcaccac gcgcattatc aagcgtgtga acattcaaga cttatggtcc
2521 aagccacaag tggaaaacac agaggaggcc accaacaagg acgggtgccc aaaacccgaa
2581 gatgatgagg agttcgtcat ttcatctgac gacattaaaa ctgagggtaa gaaagggaag
2641 aacaagactg gccgtggcaa gaagcataca gccttttcaa gtaaaggtct cagtgatgaa
2701 gagtatgatg agtacaagag aattagagag gaaaggaatg gcaggtattc catagaagag
2761 taccttcagg acagggacaa atactatgag gaggtggcca ttgccagggc gaccgaggaa
2821 gacttctgtg aagaggagga ggccaagatc cggcaaagga tctttagacc aacaaggaaa
2881 caacgcaagg aagaaagagc ttctctcggt ttagtcacag gttctgagat taggaaaaga
2941 aacccagatg acttcaagcc taagggaaaa ctgtgggctg acgatgacag aagtgtggac
3001 tacaatgaga aactcagttt tgaggcccca ccaagcatct ggtcaaggat agtcaacttt
3061 ggttcaggtt ggggcttctg ggtctcacct agcctgttca taacatcaac ccacgtcata
3121 ccccagggcg caaaggagtt ctttggagtt cccatcaaac aaattcaggt acacaagtca
3181 ggcgaatttt gtcgcttgag gttcccaaaa ccaatcagga ctgacgtgac tggcatgatc
3241 ttggaagaag gtgcgcccga aggcaccgtg gtcacactac tcatcaaaag gtctactgga
3301 gaactcatgc ccctagcagc tagaatgggg acccatgcaa ccatgaaaat tcaagggcgc
3361 accgttggag gtcagatggg catgcttctg acaggatcca acgccaaaag catggatcta
3421 ggcaccacac caggtgattg cggctgtccc tacatctaca agagaggaaa tgactatgtg
3481 gtcattggag tccatacggc tgccgctcgt gggggaaaca ctgtcatatg tgccacccag
3541 gggggcgagg gggaagctac acttgaaggt ggtgacagta agggaacata ctgtggtgca
3601 ccaatcctag gcccagggag tgccccaaaa cttagcacca aaaccaaatt ctggagatca
3661 tccacagcac cactcccacc tggcacctat gaaccagcat accttggtgg caaggacccc
3721 agagtaaagg gtggcccttc gttgcagcaa gtcatgaggg accagctgaa accattcaca
3781 gagcccaggg gtaagccacc aaagccaagt gtgttagaag ctgccaagaa aaccatcatc
3841 aatgtccttg aacaaacaat tgacccacct gagaggtggt cgttcgcaca agcttgcgcc
3901 tcccttgaca agaccacttc tagcggccat ccgcaccata tgcggaaaaa cgactgctgg
3961 aatggggagt ccttcacagg caagctggca gaccaggctt ctaaggctaa cctgatgttt
4021 gaagaaggga agaacatgac cccagtctac acaggtgcac ttaaggatga attagtcaaa
4081 actgacaaaa tttatggtaa gatcaagaag aggcttctct ggggctcgga tttagcaacc
4141 atgatccggt gtgctcgagc attcggaggc ctaatggatg aactcaaagc acactgtgtc
4201 acacttccca ttagagttgg tatgaatatg aatgaggatg gccccatcat cttcgagaag
4261 cattccaggt acagatacca ctatgatgct gattactctc ggtgggattc aacacaacag
4321 agagccgtgc tggcagctgc tctagaaatc atggttaaat tctcctcaga accacatttg
4381 gctcaggtag tcgcagaaga tcttctttcc cctagcgtgg tggatgtggg tgatttcaca
4441 atatcaatca acgagggcct tccctctggg gtgccctgca cctcccaatg gaactccatc
4501 gcccactggc ttctcactct ttgtgcactc tccgaagtca caaatttatc cccagacatc
4561 atacaggcta attctctctt ctccttctat ggtgatgatg aaattgttag tacagacata
4621 aaattggacc cagagaagtt gacagcaaag cttaaggaat atgggttgaa accaacccgc
4681 cctgacaaaa ctgaaggacc tctcgttatt tctgaagact tagatggttt gactttcctg
4741 cggagaactg tgacccgcga cccagctggt tggtttggaa aactggagca gagctcaata
4801 ctcaggcaaa tgtactggac taggggcccc aaccatgaag atccatctga atcaatgatt
4861 ccacactctc aaagacccat acaattgatg tccttactgg gagaggccgc actccacggc
4921 ccaacattct acagtaaaat cagcaaatta gtcattgcag agctaaaaga aggtggtatg
4981 gatttttacg tgcccaggca agagccaatg ttcagatgga tgagattctc agatctgagc
5041 acgtgggagg gcgatcgcaa tctggctccc agttttgtga atgaagatgg cgtcgaatga
5101 cgccaaccca tctgatgggt ccgcagccaa cctcgtccca gaggtcagca atgaggttat
5161 ggctttggag cccgttgtcg gtgccgctat tgcggcgcct gtagcgggcc aacaaaatgt
5221 aattgacccc tggattagaa acaattttgt acaagcccct ggtggagagt tcacagtatc
5281 ccctagaaac gctccaggtg aaatactatg gagcgcgccc ttaggccctg atctgaatcc
5341 ctacctatct catttggcca gaatgtataa tggttatgca ggtggttttg aagtgcaggt
5401 gatcctcgcg gggaacgcgt tcaccgccgg aaaaattata tttgcagcag tcccaccaaa
5461 ttttccaact gaaggcctga gtcccagcca agtcactatg ttcccccaca taatagtaga
5521 tgttaggcaa ttggaacctg tgttgatccc cttacctgat gttaggaata acttctatca
5581 ttataatcag acaaatgatc ctaccattaa attgatagca atgctgtata caccacttag
5641 ggccaataat gctggggaag atgtcttcac agtctcttgt cgagtcctca ctaggccgtc
5701 ccctgatttt gattttatat ttttggtgcc acccacagtt gagtcaagaa ctaaaccatt
5761 tactgtccca atcttaaccg ttgaagaaat gaccaattca agattcccca tccctttgga
5821 aaagttgttc acgggtccca gcggtgcctt tgttgtccaa ccacaaaatg gcaggtgcac
5881 gactgatggc gtgctcttag gcaccaccca actgtctcct gtcaacatct gcaccttcag
5941 aggggatgtc acccacattg caggttctcg tgattacaca atgaatttgg catctctaaa
6001 ttggaacaat tatgacccaa cagaagaaat tccagcccct ctgggaactc cagatttcgt
6061 gggaaagatc caaggtgtgc tcactcaaac cacaagagga gatggctcga cccgtggcca
6121 taaagctaca gtttacactg ggagtgcccc ctttgctcca aaactgggca gtgttcaatt
6181 cagtactgac acagaaaatg attttgaaac tcaccaaaac acaaaattca ccccagtcgg
6241 tgtcatccag gatggtggca ccacccaccg aaatgaaccc caacaatggg tgctcccaag
6301 ttattcaggt agagatgttc ataatgtaca cctagcccct gctgtagccc ccacttttcc
6361 gggtgaacaa cttcttttct tcaggtccac tatgcccgga tgcagcgggt atcccaacat
6421 ggatttggat tgcctactcc cccaggagtg ggtgcagcac ttctaccaag aggcagctcc
6481 agcacaatct gatgtggctc tattgagatt tgtgaatcca gacacgggta gggtcctgtt
6541 cgagtgcaaa cttcataaat caggctatgt cacagtggct cacaccggtc agcatgattt
6601 ggtcatcccc cctaatggct attttaggtt tgattcttgg gtcaatcagt tctacacgct
6661 tgcccccatg ggaaacggaa cggggcgtag gcgcgcctta taatggctgg agctttcttt
6721 gctggattgg catctgatgt ccttggctct ggacttggtt ccctaatcaa tgctggggct
6781 ggggccatca accaaaagat tgattttgaa aataatagaa aattgcagca agcttccttc
6841 cagtttagca gtaatctaca acaggcttcc tttcaacacg ataaagagat gcttcaagca
6901 caaattgagg ccactaaaaa gttgcaacag gaaatgatga aagtcaaaca ggcaatgctc
6961 ctagaaggtg gattctctga aacagatgca gcccgtgggg caatcagcgc ccccatgaca
7021 aaggttttgg actggagcgg aacaaggtac tgggcccctg atgctaggac cacaacatac
7081 aattcaggcc gcttttccac cccccaacct tcggggacgc tgccaggaag aatcaatccc
7141 aggactccta cccccgctcg gggctcctct agcacatctt ctaatgcttc tactgctact
7201 tctatacatt taaatcaaac tgtttcaacg agacttggtt ctacagctgg ttctggcacc
7261 aatgtctcga gtctcccgtc aactgcaagg actaggagtt gggttgagga tcaaaacaga
7321 aatttgtcac ctttcatgag gggggctcat aacatatcgt ttgtcacccc accatctagc
7381 agatcctcta gccaaggcac agtctcaacc gtgcctaaag aaattttgga ctcctgggct
7441 ggc
//