Typing tool
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Typing tool
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Complete norovirus genomes
| KM198568 | GII.4 Den Haag | |
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| GII.P4 Den Haag |
ORF1: 53..5071
ORF2: 5052..6674
ORF3: 6674..7304
LOCUS KM198568 7304 bp RNA linear VRL 13-NOV-2014
DEFINITION Norovirus Hu/GII/C2H-62/2011/VNM nonstructural polyprotein and
capsid protein VP1 genes, complete cds; and capsid protein VP2
gene, partial cds.
ACCESSION KM198568
VERSION KM198568.1
KEYWORDS .
SOURCE Norovirus Hu/GII/C2H-62/2011/VNM
ORGANISM Norovirus Hu/GII/C2H-62/2011/VNM
Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes;
Picornavirales; Caliciviridae; Norovirus; Norovirus norwalkense.
REFERENCE 1 (bases 1 to 7304)
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 7304)
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..7304
/organism="Norovirus Hu/GII/C2H-62/2011/VNM"
/mol_type="genomic RNA"
/isolate="Hu/GII/C2H-62/2011/VNM"
/host="Homo sapiens"
/db_xref="taxon:1527025"
/geo_loc_name="Viet Nam"
/collection_date="14-Dec-2011"
/note="genotype: GII"
CDS 53..5071
/note="ORF1"
/codon_start=1
/product="nonstructural polyprotein"
/protein_id="AII02832.1"
/translation="MFSSMAVTFKRALGARPKQPPPREIPQRPPRPPTPELVKKVPPP
PPNGEDEVVVSYSAKDGISGLPELSTVRQPEETNTAFSVPPLNQRENRDAKEPLTGTI
LEMWDGEIYHYGLYVERGLVLGVHKPPAAISLAKVELTPLSLFWRPVYTPQYLISPDT
LKKLHGETFPYTAFDNNCYAFCCWVLDLNDSWLSRRMIQRTTGFFRPYQDWNRKPLPT
TDDSKLKKVANIFLCTLSSLFTRPIKDIIGKLRPLNIINILASCDWTFAGIVESLILL
AELFGVFWTPPDVSAMIAPLLGDFELQGPEDLVVELVPVVMGGIGLVLGFTKEKIGKM
LSSAASTLRACKDLGAYGLEILKLVMKWFFPKKEEANELAMVRSIEDAVLDLEAIENN
HMTTLLKDKDSLATYMRTLDLEEEKARKLSTKSASPDIVGTINALLARIAAARSLVHR
AKEELSSRPRPVVLMISGRPGIGKTHLAREVAKRIAASLTGDQRVGLIPRNGVDHWDA
YKGERVVLWDDYGMSNPIHDALRLQELADTCPLTLNCDRIENKGKVFDSDVIIITTNL
ANPAPLDYVNFEACSRRIDFLVYAEAPEVEKAKRDFPGQPDMWKNAFSSDFSHIKLAL
APQGGFDKNGNTPHGKGVMKTLTTGSLIARASGLLHERLDEFELQGPALTTFNFDRNK
VLAFRQLAAENKYGLMDTMRVGRQLKDVKTMPELKQALKSISIKKCQIVYSGCTYTLE
SDGKGNVKVDRVQSTSVQTNNELAGALHHLRCARIRYYVKCVQEALYSIIQIAGAAFV
TTRIIKRVNIQNLWSKPQVENIEEATNKDGCPKPKDDEEFVITSDDIKTEGKKGKNKT
GRGKKHTAFSSKGLSDEEYDEYKRIREERNGKYSIEEYLQDRDKYYEEVAIARATEED
FCEEEEAKIRQRIFRPTRKQRKEERASLGLVTGSEIRKRNPDDFKPKGKLWADDDRSV
DYNEKLSFEAPPSIWSRIVNFGSGWGFWVSPSLFITSTHVIPQGAKEFFGVPIKQIQV
HKSGEFCRLRFPKPIRTDVTGMILEEGAPEGTVATLLIKRSTGELMPLAARMGTHATM
KIQGRTVGGQMGMLLTGSNAKSMDLGTTPGDCGCPYIYKRGNDYVVIGVHTAAARGGN
TVICATQGGEGEATLEGGDSKGTYCGAPILGPGSAPKLSTKTKFWRSSTAPLPPGTYE
PAYLGGKDPRVKGGPSLQQVMRDQLKPFTEPRGKPPKPSVLEAAKKTIINVLEQTIDP
PEKWSFAQACASLDKTTSSGHPHHMRKNDCWNGESFTGKLADQASKANLMFEEGKSMT
PVYTGALKDELVKTDKIYGKIKKRLLWGSDLATMIRCARAFGGLMDELKAHCVTLPIR
VGMNMNEDGPVIFEKHSRYRYHYDADYSRWDSTQQRAVLAAALEIMVKFSSEPHLAQV
VAEDLLSPSVVDVGDFTISINEGLPSGVPCTSQWNSIAHWLLTLCALSEVTNLSPDII
QANSLFSFYGDDEIVSTDIKLDPEKLTAKLKEYGLKPTRPDKTEGPLVISEDLDGLTF
LRRTVTRDPAGWFGKLEQSSILRQMYWTRGPNHEDPSESMIPHSQRPIQLMSLLGEAA
LHGPTFYSKISKLVIAELKEGGMDFYVPRQEPMFRWMRFSDLSTWEGDRNLAPSFVNE
DGVE"
CDS 5052..6674
/note="ORF2"
/codon_start=1
/product="capsid protein VP1"
/protein_id="AII02833.1"
/translation="MKMASNDANPSDGSAANLVPEVNNEVMALEPVVGAAIAAPVAGQ
QNVIDPWIRNNFVQAPGGEFTVSPRNAPGEILWSAPLGPDLNPYLSHLARMYNGYAGG
FEVQVILAGNAFTAGKIIFAAVPPNFPTEGLSPSQVTMFPHIIVDVRQLEPVLIPLPD
VRNNFYHYNQSNDSTIKLIAMLYTPLRANNAGEDVFTVSCRVLTRPSPDFDFIFLVPP
TVESRTKPFTVPILTVEEMTNSRFPIPLEKLFTGPSGAFIVQPQNGRCTTDGVLLGTT
QLSPVNICTFRGGVTHIAGSRNYTMNLASLNWNNYDPTEEIPAPLGTPDFVGKIQGVL
TQTTKGDGSTRGHKATVYTGSAPFTPKLGSVQFSTDTENDFEAHQNTKFTPVGVIQDG
GTTHRNEPQQWVLPSYSGRDVHNVHLAPAVAPTFPGEQLLFFRSTMPGCSGYPNMDLD
CLLPQEWVQHFYQEAAPAQSDVALLRFVNPDTGRVLFECKLHKSGYVTVAHTGQHDLV
IPPNGYFRFDSWVNQFYTLAPMGNGTGRRRAL"
CDS 6674..>7304
/note="ORF3"
/codon_start=1
/product="capsid protein VP2"
/protein_id="AII02834.1"
/translation="MAGAFFAGLASDVLGSGLGSLINAGAGAINQKIDFENNRKLQQA
SFQFSSNLQQASFQHDKEMLQAQIEATKKLQQEMMRVKQAMLLEGGFSETDAARGAIN
APMTKVLDWSGTRYWAPDTRTTTYNAGRFSTPQPSGSLPGRTNPRTPTPARASSSTSS
NASTVASIYSNQTVSTRLGSTAGSGTNVSSLPSTARTKSWVEDQNRNLSP"
ORIGIN
1 tgccgctgtt gctaacagca acaacgacac cgcaaaatct tcaagtgaca aaatgttttc
61 tagcatggct gtcactttta aacgagccct cggggcgcgg cctaaacagc ctcccccgag
121 ggaaataccg caaagacccc cacgaccacc tactccagaa ctggtcaaaa aggtccctcc
181 tcccccgccc aacggagagg atgaagtggt ggtttcttat agtgccaaag atggcatttc
241 tggtctacct gagctttcca ccgtcagaca accagaagaa accaatacgg cctttagtgt
301 ccccccactc aatcagaggg agaataggga tgctaaggaa ccactgactg ggacaattct
361 ggaaatgtgg gatggagaaa tctatcatta tggcctgtat gttgaacgag gtcttgtgct
421 gggtgtacac aaaccaccag ctgccattag cctcgccaag gtcgaactaa caccactctc
481 cttgttctgg agacctgtgt acaccccaca gtacctcatc tctccagaca ctctcaagaa
541 attacacgga gaaacatttc cctacacagc ctttgacaac aactgctatg ccttttgttg
601 ctgggtcctg gatctaaacg actcgtggct gagtaggaga atgatccaga gaacaactgg
661 cttcttcaga ccctaccaag attggaatag gaaacccctc cctactacgg atgattccaa
721 attaaagaag gtagctaaca tattcctgtg caccctgtct tcgctattca ccaggcccat
781 aaaagacata ataggaaagt taaggcctct caacatcatc aacatcctag cttcatgtga
841 ctggactttc gcaggcatcg tggaatcctt gatactcttg gcagagctct ttggagtctt
901 ctggacaccc ccagatgtgt ctgcgatgat tgccccctta ctcggtgatt tcgagttaca
961 aggacctgag gaccttgtag tggagctcgt ccctgtggta atggggggaa ttggtttggt
1021 gctgggattc accaaagaga agattggaaa aatgttgtca tctgctgcgt ccaccttgag
1081 agcttgtaaa gatctcggtg catatgggct agagatccta aagctagtca tgaagtggtt
1141 cttcccgaag aaagaggagg caaatgaact ggctatggtg agatccatcg aggatgcagt
1201 actggacctt gaggcaattg aaaacaacca catgaccacc ttgctcaaag ataaagacag
1261 cctggcaacc tacatgagaa cccttgacct cgaggaagag aaagccagaa aactctcaac
1321 caagtccgct tcacccgaca tcgtgggcac aatcaacgcc cttctggcga gaatcgccgc
1381 tgcacgctcc ctggtgcacc gagcgaagga ggagctttcc agcagaccaa gacctgtggt
1441 cttgatgata tcaggtagac cagggatagg gaagacccac cttgctaggg aagtggctaa
1501 gagaatcgca gcctccctca caggagacca gcgcgtaggc ctcatcccac gcaatggcgt
1561 cgatcactgg gatgcgtaca aaggggagag ggtcgtccta tgggacgact atggaatgag
1621 caatcccatc cacgacgccc tcaggctgca agaactcgcc gacacttgcc ccctcactct
1681 aaattgtgac aggattgaga ataaaggaaa ggtctttgac agtgatgtca tcattatcac
1741 tactaatctg gccaacccag caccactgga ctatgtcaac tttgaagcgt gctcgaggcg
1801 catcgatttc ctcgtgtacg cagaagcccc cgaggtcgaa aaggcgaagc gtgacttccc
1861 gggccaacct gacatgtgga aaaacgcttt tagttctgat ttctcacaca taaaactggc
1921 actggctcca caaggtggct tcgataagaa cgggaacacc ccacatggga agggcgtcat
1981 gaagactctc accactggct cccttattgc ccgggcatca gggctgctcc atgagagatt
2041 ggatgagttt gaactacagg gcccagctct caccaccttc aactttgacc gcaacaaagt
2101 gcttgccttc aggcagcttg ctgctgaaaa caaatacggg ttgatggaca caatgagagt
2161 tgggaggcag ctcaaggatg tcaaaaccat gccagaactt aaacaagcac tcaagagcat
2221 ctcaatcaag aagtgtcaga ttgtgtacag tggttgcacc tacacacttg agtctgatgg
2281 caagggcaat gtgaaggttg acagagttca gagcacctcc gtgcagacca acaatgagct
2341 ggctggcgcc ctgcaccatc tgaggtgcgc cagaatcagg tactatgtta agtgtgtcca
2401 ggaggccctg tattctatca ttcagattgc tggagctgca ttcgtcacca cgcgcatcat
2461 caagcgtgtg aacattcaaa acttatggtc caagccacaa gtggaaaaca tagaggaagc
2521 caccaacaag gatgggtgcc caaaacccaa agatgatgag gagttcgtca tcacatctga
2581 cgacattaaa actgagggta agaaaggaaa gaacaagact ggccgtggta agaagcacac
2641 agccttctca agtaaaggtc tcagtgatga agagtatgat gagtacaaga gaattagaga
2701 ggaaaggaat ggcaagtact ccatagaaga gtaccttcag gacagggaca aatactatga
2761 ggaggtggcc attgccaggg cgaccgagga agacttctgt gaagaggagg aggccaagat
2821 ccggcaaagg atcttcagac caacaaggaa acaacgcaag gaagaaagag cttctctcgg
2881 tttagtcaca ggttctgaaa ttaggaaaag aaacccagat gatttcaagc ccaaggggaa
2941 actatgggct gacgatgaca gaagtgttga ctacaatgag aaactcagtt ttgaggctcc
3001 gccaagcatc tggtcaagga tagtcaactt tggctcaggt tggggtttct gggtctcccc
3061 cagcctgttc ataacatcaa cccacgtcat accccagggc gcaaaggagt tctttggagt
3121 ccccatcaaa caaattcagg tgcacaagtc aggcgaattc tgtcgcttga ggttcccaaa
3181 accaatcagg actgatgtga ctggcatgat cttggaagaa ggcgcgcctg aaggcaccgt
3241 ggccacacta ctcatcaaaa ggtctactgg agaactcatg cccctagcag ccagaatggg
3301 gacccatgca accatgaaaa ttcaagggcg cactgttgga ggtcagatgg gcatgcttct
3361 gacaggatcc aacgccaaaa gcatggatct aggcaccaca ccaggtgatt gcggctgtcc
3421 ctacatctac aagagaggga atgactatgt ggtcattgga gtccacacgg ctgccgctcg
3481 tgggggaaac actgttatat gtgccaccca ggggggtgag ggggaagcta cacttgaagg
3541 tggtgacagt aagggaacgt actgcggtgc gccaatccta ggcccaggga gcgccccaaa
3601 acttagtacc aaaaccaaat tctggaggtc atccacagca ccactcccac ctggcaccta
3661 tgagccagcc taccttggtg gcaaggaccc cagagtcaag ggtggcccct cgctgcagca
3721 agtcatgaga gaccagctga aaccattcac agagcccagg ggtaagccac caaagccaag
3781 tgtgttggaa gctgccaaga aaaccatcat caatgttctt gaacaaacaa ttgacccacc
3841 tgagaagtgg tcgttcgcac aggcttgcgc gtcccttgac aagaccactt ctagcggcca
3901 tccgcatcac atgcggaaaa acgactgctg gaacggggag tccttcacag gcaagctggc
3961 agaccaggct tccaaggcca acctgatgtt tgaagaaggg aagagcatga ccccagttta
4021 cacaggtgcg ctcaaggacg agttggtcaa aactgataaa atttatggca agataaagaa
4081 gaggcttctc tggggctcgg atttagcaac catgatccgg tgtgctcgag cattcggagg
4141 cctaatggat gaactcaaag cacactgtgt cacacttcct atcagagttg gtatgaatat
4201 gaatgaggat ggccccgtca tcttcgagaa gcactccagg tacaggtacc actatgatgc
4261 tgattactct cgatgggatt caacacaaca gagagccgtg ctggcagctg ctctagaaat
4321 tatggttaaa ttctcctcag aaccacattt ggctcaggtg gtcgcagaag accttctttc
4381 tcctagcgtg gtggatgtgg gtgacttcac aatatcaatc aatgagggtc ttccctctgg
4441 ggtgccctgc acttctcaat ggaactccat cgcccactgg cttctcactc tatgtgcact
4501 ctccgaagtc acaaatttgt ccccagacat catacaggct aattctctct tctccttcta
4561 tggtgatgat gaaattgtta gtacagacat aaaactagac ccagagaagt tgacagcaaa
4621 gcttaaggaa tatgggttaa aaccaacccg ccctgacaaa actgaaggac ctcttgttat
4681 ttctgaagac ttagatggtt tgactttcct gcggagaact gtgacccgcg acccagctgg
4741 ttggtttgga aaactggagc agagctcaat actcaggcaa atgtactgga ctaggggccc
4801 caaccatgaa gatccatctg aatcaatgat tccacactct caaagaccca tacaactgat
4861 gtccctgctg ggagaggccg cactccacgg cccaacattc tatagtaaaa ttagcaaatt
4921 agtcattgca gagctaaaag aaggtggtat ggatttttac gtgcccaggc aagagccaat
4981 gttcagatgg atgagattct cagatctgag cacgtgggag ggcgatcgca atctggctcc
5041 cagctttgtg aatgaagatg gcgtcgaatg acgccaaccc atctgatggg tccgcagcca
5101 acctcgtccc agaggtcaac aatgaggtta tggctttgga gcccgttgtc ggtgccgcta
5161 ttgcggcgcc tgtagcgggc caacaaaatg taattgaccc ctggattagg aataattttg
5221 tacaagcccc tggtggagaa ttcacagtat cccctagaaa cgctccaggt gaaatactat
5281 ggagcgcgcc cttaggccct gatctgaatc cctacctatc ccatttggcc agaatgtata
5341 atggttatgc aggtggcttt gaagtgcagg tgatcctcgc gggaaacgcg ttcaccgccg
5401 gaaaaattat atttgcagca gttccaccaa attttccaac tgaaggcttg agccccagcc
5461 aggttactat gttcccccac ataatagtag atgttaggca actggaacct gtgttgatcc
5521 ccttacctga tgttaggaat aacttctatc attataatca gtcaaacgat tctaccatta
5581 aattgatagc aatgctgtac acaccactta gggctaataa tgctggggaa gatgtcttca
5641 cagtctcttg tcgagtcctc acgaggccat cccctgattt tgattttata tttttggtgc
5701 cacccacagt tgagtcaaga accaaaccat ttactgtccc aatcttaact gttgaagaaa
5761 tgaccaattc aagattcccc atccctttgg aaaagctgtt cacgggcccc agcggtgcct
5821 ttattgtcca accacaaaat ggtagatgca cgaccgatgg cgtgctctta ggcaccaccc
5881 aactgtctcc tgtcaacatc tgcaccttca gagggggtgt cacccacatt gcaggttctc
5941 gcaattacac gatgaatttg gcttctctaa attggaataa ttatgaccca acagaagaaa
6001 ttccagcccc tctgggaact ccagatttcg tgggaaagat ccaaggtgtg ctcactcaaa
6061 ccacaaaggg agatggctcg acccgtggcc ataaagcaac agtttacact gggagtgccc
6121 cctttactcc aaagctgggc agtgttcaat tcagtactga cacagaaaat gattttgaag
6181 ctcaccaaaa cacaaaattc accccagtcg gtgtcatcca ggatggtggc accacccacc
6241 gaaatgaacc ccaacaatgg gtgctcccaa gttattcagg tagagatgtc cacaatgtac
6301 acctggcccc tgctgtagcc cccacttttc cgggtgaaca acttcttttc ttcaggtcca
6361 ctatgcccgg atgcagtggg tatcccaaca tggatttgga ttgcctactc cctcaggagt
6421 gggtgcagca cttctaccaa gaggcagctc cagcacaatc tgatgtggct ctattgagat
6481 ttgtgaatcc agacacgggt agggtcctgt ttgagtgcaa acttcataaa tcaggctatg
6541 tcacagtggc ccacaccggc cagcatgatt tggtcatccc ccctaatggc tattttaggt
6601 ttgattcctg ggttaaccaa ttctatacac ttgcccccat gggaaatgga acggggcgta
6661 gacgtgcttt ataatggctg gggctttctt tgctggattg gcatctgatg tccttggctc
6721 tggacttggc tccctaatca atgctggggc tggggctatc aaccaaaaga ttgattttga
6781 aaataacaga aaattgcagc aagcttcctt ccagtttagc agtaatctac aacaggcctc
6841 ctttcaacat gacaaagaga tgctccaagc acaaattgag gccactaaaa agttgcaaca
6901 ggaaatgatg agagtcaaac aggcaatgct cttagaaggt gggttctctg aaacagatgc
6961 agctcgtggg gcaatcaacg cccccatgac aaaggttttg gactggagtg gaacaaggta
7021 ctgggcccct gataccagga ctacaacata caatgcaggc cgcttttcca ccccccaacc
7081 ctcggggtca ttgccaggaa gaaccaatcc caggactcct actcccgctc gggcctcctc
7141 cagtacatcc tctaatgctt ctactgttgc ttctatatac tcaaatcaaa ctgtttcaac
7201 gagacttggt tctacagctg gctctggcac caatgtctcg agtctcccgt caactgcaag
7261 gactaagagt tgggttgagg atcaaaacag aaatttgtca cctt
//