Typing tool
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Typing tool
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Complete norovirus genomes
| KC962462 | GII.4 Sydney | |
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| GII.P4 New Orleans |
ORF1: 5..5104
ORF2: 5085..6707
ORF3: 6707..7513
LOCUS KC962462 7570 bp RNA linear VRL 21-APR-2015
DEFINITION Norovirus GII strain GII/Hu/ZAF/2011/GII.P4_GII.4/Empangeni/8491,
partial genome.
ACCESSION KC962462
VERSION KC962462.3
KEYWORDS .
SOURCE Norovirus GII
ORGANISM Norovirus GII
Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes;
Picornavirales; Caliciviridae; Norovirus; Norovirus norwalkense.
REFERENCE 1 (bases 1 to 7570)
AUTHORS Mans,J., Murray,T.Y. and Taylor,M.B.
TITLE Novel norovirus recombinants detected in South Africa
JOURNAL Virol. J. 11, 168 (2014)
PUBMED 25228444
REMARK Publication Status: Online-Only
REFERENCE 2 (bases 1 to 7570)
AUTHORS Murray,T.Y.
TITLE Direct Submission
JOURNAL Submitted (24-APR-2013) Department of Medical Virology, University
of Pretoria, Bophelo Road, Pretoria, Gauteng 0001, South Africa
REFERENCE 3 (bases 1 to 7570)
AUTHORS Mans,J.
TITLE Direct Submission
JOURNAL Submitted (25-JUL-2014) Department of Medical Virology, University
of Pretoria, Bophelo Road, Pretoria, Gauteng 0001, South Africa
REMARK Sequence update by submitter
REFERENCE 4 (bases 1 to 7570)
AUTHORS Botha,J.C. and Mrray,T.
TITLE Direct Submission
JOURNAL Submitted (21-APR-2015) Department of Medical Virology, University
of Pretoria, Bophelo Road, Pretoria, Gauteng 0001, South Africa
REMARK Sequence update by submitter
COMMENT On Apr 21, 2015 this sequence version replaced KC962462.2.
FEATURES Location/Qualifiers
source 1..7570
/organism="Norovirus GII"
/mol_type="genomic RNA"
/strain="GII/Hu/ZAF/2011/GII.P4_GII.4/Empangeni/8491"
/isolation_source="stool"
/host="Homo sapiens"
/db_xref="taxon:122929"
/geo_loc_name="South Africa"
/collection_date="Nov-2011"
/collected_by="T.Y. Murray"
/identified_by="T.Y. Murray"
/note="genotype:
GII.P4_New_Orleans_2009/GII.4_Sydney_2012"
5'UTR <1..4
gene 5..5104
/gene="POL"
CDS 5..5104
/gene="POL"
/codon_start=1
/product="polyprotein"
/protein_id="AKE07102.1"
/translation="MKMASNDASAAAVANSNNNTAKSSSDGVLSSMAVTFKRALGARP
KQPPPREIPQRPPRPPTPELVKSIPPPPPNGEDEIVVSYSVKDGVSGLPDLSTVRQPE
ESNTAFSVPPLNQRENRDAKEPLTGTILEMWDGEIYHYGLYVERGLVLGVHKPPAAIS
LARVELAPLSLYWRPVYTPQYLISPDTLKKLHGETFPYTAFDNNCYAFCCWVLDLNDS
WLSRRMIQRTTGFFRPYQDWNRKPLPTMDDSKLKKVANIFLCALSSLFTRPIKDIMGK
LKPLNILNILASCDWTFAGIVESLILLAELFGIFWTPPDVSAMIAPLLGDYELQGPED
LAVELVPVVMGGIGLVLGFTKEKIGKMLSSAASTLRACKDLGAYGLEILKLVMKWFFP
KKEEANELALVRSIEDAVLDLEAIENNHMTTLLKDKDSLATYMRTLDLEEEKARKLST
KSASPDIVGTINALLARIAAARSLVHRAKEELSSRPRPVVMMISGKPGIGKTHLAREV
AKRIAASLTGDQRVGLIPRNGVDHWDAYKGERVVLWDDYGMSNPIHDALRLQELADTC
PLTLNCDRIENKGKVFDSDVIIITTNLANPAPLDYVNFEACSRRIDFLVYADAPDVEK
AKRDFPGQPDMWKNAFSSDFSHMKLALAPQGGFDKNGNTPHGKGVMKALTTGSLIARA
SGLLHERLDEFELQGPTLTTFNFDRNKVLAFRQLAAENKYGLVDTMKVGRQLKDVKTM
PELKQALKSVSIKKCQIVYSGSTYTLESDGKGSVKVDRIQSASVQTNNELTGALHHLR
CARIRYYVKCVQEALYSIIQIAGAAFVTTRIVKRMNIQDLWSKPQVENTEETTNKDGC
PKPKDDEEFVISSDDIKTEGKKGKNKTGRGKKHTAFSSKGLSDEEYDEYKRIREERNG
KYSIEEYLQDRDKYYEEVAIARATEEDFCEEEEAKIRQRIFRPTRKQRKEERASLGLV
TGSEIRKRNPDDFKPKGKLWADDDRSVDYNEKLSFEAPPSIWSRIVNFGSGWGFWVSP
SLFITSTHVIPQGAKEFFGVPIKQIQVHKSGEFCRLRFPKPIRTDVTGMILEEGAPEG
TVVSLLIKRPTGELMPLAARMGTHATMKIQGRTVGGQMGMLLTGSNAKSMDLGTTPGD
CGCPYIYKRGNDYVVIGVHTAAARGGNTVICATQGSEGEATLEGGDNKGTYCGAPILG
PGSAPTLSTKTKFWRSSTASLPPGTYEPAYLGGKDPRVKGGPSLQQVMREQLKPFTEP
RGKPPKPSVLEAAKKTIINVLEQTIDPPEKWSFAQACASLDKTTSSGHPHHIRKNDGW
NGESFTGKLADQASKANLMFEEGKNMTPVYTAALKDELVKTDKIYGKIKKRLLWGSDL
GTMIRCARAFGGLMDELKAHCVTLPIRVGMNMNEDGPIIFERHSRYAYHYDADYSRWD
STQQRAVLAAALEIMVKFSPEPHLAQVVAEDLLSPSVVDVGDFTISINEGLPSGVPCT
SQWNSIAHWLLTLCALSEVTNLSPDTIQTNSLFSFYGDDEIVSTDIKLDPEKLTAKLR
EYGLKPTRPDKTEGPLVISEDLNGLTFLRRTVTRDPAGWFGKLEQSSILRQMYWTRGP
NHGDPSETMIPHSQRPIQLMSLLGEAALHGPAFYSKISKLVIAELKEGGMDFYVPRQE
PMFRWMRFSDLSTWEGDRNLAPSFVNEDGVE"
mat_peptide 5..994
/gene="POL"
/product="protein p48"
mat_peptide 995..2092
/gene="POL"
/product="NTPase"
mat_peptide 2093..2629
/gene="POL"
/product="protein p22"
mat_peptide 2630..3028
/gene="POL"
/product="viral genome like protein"
/note="VPg"
mat_peptide 3029..3571
/gene="POL"
/product="3C-like protein"
mat_peptide 3572..5101
/gene="POL"
/product="RNA dependent RNA polymerase"
gene 5085..6707
/gene="VP1"
CDS 5085..6707
/gene="VP1"
/note="major capsid protein"
/codon_start=1
/product="capsid protein VP1"
/protein_id="AKE07103.1"
/translation="MKMASSDANPSDGSAANLVPEVNNEVMALEPVVGAAIAAPVAGQ
QNVIDPWIRNNFVQAPGGEFTVSPRNAPGEILWSAPLGPDLNPYLSHLARMYNGYAGG
FEVQVILAGNAFTAGKIIFAAVPPNFPTESLSPSQVTMFPHIIVDVRQLEPVLIPLPD
VRNNFYHYNQSNDPTIKLIAMLYTPLRANNAGDDVFTVSCRVLTRPSPDFDFIFLVPP
TVESRTKPFSVPILTVEEMTNSRFPIPLEKLFTGPSSAFVVQPQNGRCTIDGVLLGTT
QLSPVNICTFRGDVTHIAGTHNYTMNLATQNWNSYDPTEEIPAPLGTPDFVGKIQGVL
TQTTKTDGSTRGHKATVCIGSADFAPKLGRVQFETDTNNDLETNQNTKFTPVGVIQNG
ETAHRNEPQQWVLPSYSGRNTPNVHLAPAVAPTFPGEQLLFFRSTMPGCSGYPNMDLD
CLLPQEWVQYFYQEAAPAQSDVALLRFVNPDTGRVLFECKLHKSGYVTVAHTGSHDLV
IPPNGYFRFDSWVNQFYTLAPMGNGTGRRRAT"
gene 6707..7513
/gene="VP2"
CDS 6707..7513
/gene="VP2"
/note="minor capsid protein"
/codon_start=1
/product="capsid protein VP2"
/protein_id="AKE07104.1"
/translation="MAGAFFAGLASDVLGSGLGSLINAGAGAINQKVEFENNRKLQQA
SFQFSSNLQQASFQHDKEMLQAQIEATKKLQQEMMKVKQAVLLEGGFSETDAARGAIN
APMTKALDWSGTRYWAPDARTTTYNAGRFSTPQPSGILPGRANLRDTVPARGSSSTSS
KSSIATSLYSNQTATTRLGSTAGSGTSVSSLPSTARTRSWVEDQNRNLSPFMRGAHNI
SFVTPPSSRSSSQGTVSTVPKEVLDSWTGAFNTRRQPLFAHIRKRGESRV"
3'UTR 7514..7570
ORIGIN
1 gtgaatgaag atggcctcta acgacgcttc cgctgccgct gttgctaaca gcaacaacaa
61 caccgcaaaa tcttcaagtg acggagtgct ttctagcatg gctgtcactt ttaaacgagc
121 cctcggggcg cggcctaaac agcctccccc gagggaaata ccacaaagac ccccacgacc
181 acccactcca gaactggtta aaagtattcc cccccctccg cccaacggag aggatgaaat
241 agtggtttct tatagtgtca aagatggtgt ttccggtttg cctgaccttt ccaccgtcag
301 gcaaccagaa gaatctaaca cggccttcag tgtccctcca ctcaatcaga gggagaatag
361 agatgctaag gagccactta ctggaacaat tctcgaaatg tgggatggag aaatctacca
421 ttatggcctg tatgtggagc gaggtctcgt actaggtgtg cacaaaccac cagctgccat
481 cagcctcgct agggttgagc tggcaccact ctccttgtac tggagacctg tgtacactcc
541 tcagtacctc atctctccag acactctcaa gaaattacac ggagaaacgt tcccctacac
601 agcctttgac aacaattgct atgccttttg ctgctgggtc ctggatctaa atgactcgtg
661 gctgagcagg agaatgatcc agagaacaac tggtttcttc aggccctacc aagactggaa
721 taggaaaccc cttcccacta tggatgactc caaattaaag aaggtagcta acatattcct
781 gtgtgctctg tcctcgctgt tcaccaggcc cataaaagac ataatgggga agctaaagcc
841 tctcaacatc ctcaacatct tagcctcatg tgattggact tttgcaggca tagtggaatc
901 cctgatactc ttggcagagc tctttggaat tttctggacg cccccagatg tgtctgcgat
961 gattgcaccc ttactcggtg actatgagct gcaaggacct gaggaccttg cagtggagct
1021 cgtccccgta gtgatgggtg gaattggttt ggtgctagga tttaccaaag agaagattgg
1081 gaaaatgttg tcatccgctg catccacctt gagagcatgt aaagaccttg gtgcatatgg
1141 gctagagatc ctaaagttgg tcatgaagtg gttcttcccg aaaaaggagg aggcgaatga
1201 actggcttta gtgagatcta tcgaggatgc agtcttggat ctcgaggcaa ttgaaaacaa
1261 ccatatgacc accctgctca aagacaaaga cagtctggca acctatatga gaacccttga
1321 ccttgaggag gagaaagcca ggaaactctc aaccaaatct gcctcacccg acatcgtggg
1381 cacaatcaac gctctcctgg cgagaatcgc tgctgcacgc tctctggtgc atcgagcgaa
1441 ggaggaactt tccagcagac caagacctgt agtaatgatg atatcaggca aaccaggaat
1501 agggaagacc caccttgcta gggaagtggc taagagaatc gcagcctccc ttacaggaga
1561 ccagcgtgta ggcctcatcc cgcgcaatgg cgtcgaccat tgggatgcgt acaaggggga
1621 gagggtcgtc ctttgggacg attatggaat gagcaacccc attcacgatg ccctcaggtt
1681 gcaagagctc gctgacactt gccccctcac tctaaactgt gacaggattg agaacaaagg
1741 aaaggtcttt gacagcgatg tcatcattat caccactaat ctggccaacc cagcaccact
1801 tgactatgtc aactttgaag catgctcgag gcgcatcgac ttcctcgtgt atgcagatgc
1861 ccctgacgtc gaaaaggcga agcgtgactt cccaggccag cctgacatgt ggaagaacgc
1921 cttcagttct gacttctcac acatgaagct ggcattggcc ccacaaggtg gcttcgacaa
1981 gaacgggaac accccacacg gaaagggcgt catgaaggct ctcaccacag gctcccttat
2041 tgcccgggca tctgggttgc tccatgagag attagatgaa tttgaactac aaggcccaac
2101 tctcaccacc ttcaattttg atcgcaacaa agtacttgcc tttagacaac ttgctgctga
2161 gaacaaatat ggactagtgg acacaatgaa agttgggaga cagctcaagg atgtcaaaac
2221 catgccagaa ctcaaacaag cactcaagag tgtctcaatc aagaagtgcc agatagtgta
2281 tagtggttcc acctacacac ttgagtctga tggcaagggc agtgtgaaag ttgacagaat
2341 ccagagcgcg tccgtgcaga ccaacaatga gctgaccggt gccctgcacc atttgaggtg
2401 cgccagaatc agatattatg tcaagtgtgt ccaggaggcc ctgtactcca tcatccaaat
2461 tgctggggct gcatttgtca ccacgcgcat cgtcaagcgc atgaacatac aagacctgtg
2521 gtccaagcca caagtggaaa acacagagga gaccaccaac aaagacgggt gcccaaaacc
2581 caaagatgat gaggagttcg tcatttcatc tgacgacatc aaaactgagg gtaagaaggg
2641 gaagaacaag actggccgcg gcaagaagca cacagccttt tcaagcaaag gcctcagtga
2701 tgaagagtac gatgagtaca agagaattag ggaagaaagg aatggcaagt actccataga
2761 agagtacctc caggacaggg acaaatacta tgaggaggtg gccattgcca gggcgactga
2821 ggaagacttc tgtgaagagg aggaggccaa gatccggcaa agaatcttca ggccaacaag
2881 gaaacaacgc aaggaggaaa gagcttctct cggtctagtt acaggttctg aaattaggaa
2941 aagaaaccca gatgatttca aacccaaggg gaaattgtgg gctgacgatg acagaagtgt
3001 ggactacaat gagaaactca gttttgaggc cccaccaagc atctggtcga ggatagtcaa
3061 ctttggttcg ggttggggat tttgggtctc ccccagtctg ttcataacat caacccatgt
3121 cataccccag ggcgcaaagg agttctttgg agtccccatc aaacaaattc aggtacacaa
3181 atcaggcgag ttctgtcgcc tgagattccc aaaaccaatc aggactgatg tgacgggcat
3241 gatcttggaa gaaggcgcac ctgagggcac cgtggtctca ctactcatca aaaggcccac
3301 tggggagctc atgcccctag cagctagaat ggggacccat gcaactatga agatccaagg
3361 gcgtactgtt ggaggccaga tgggcatgct tctgacagga tccaacgcca aaagcatgga
3421 tctgggtact acaccaggtg attgtggctg tccctacatc tataagagag gtaatgacta
3481 tgtagtcatt ggagtccaca cagctgccgc tcgtggggga aacactgtca tatgtgccac
3541 ccaggggagt gaaggagagg ctacacttga aggaggtgac aacaaaggga catactgtgg
3601 tgcaccaatc ctaggcccag ggagtgcccc aacacttagc accaagacca aattctggag
3661 atcgtccaca gcatcactcc cacctggcac ctatgaacca gcctatcttg gtggcaagga
3721 ccctagagtc aagggtggcc cttcactaca gcaagtcatg agggaacagt tgaagccatt
3781 cacagagccc aggggcaagc caccaaagcc aagtgtgtta gaagctgcca agaagaccat
3841 catcaatgtc cttgagcaaa caattgatcc gcctgagaaa tggtcattcg cgcaagcttg
3901 cgcgtccctt gacaagacca cttccagcgg tcacccgcac cacatacgga aaaatgatgg
3961 ttggaacggg gagtccttca caggcaagct ggcagaccag gcttccaagg ccaacctgat
4021 gtttgaggaa gggaagaaca tgaccccagt ctacacagct gcgcttaaag atgaattggt
4081 caaaactgac aaaatttatg gtaagatcaa aaagaggctt ctctggggct cggacttggg
4141 aaccatgatc cggtgtgctc gggcattcgg aggcctaatg gatgaactca aagcgcactg
4201 tgtcacactc cccattagag ttggtatgaa tatgaatgag gatggcccca tcatcttcga
4261 gaggcactcc aggtacgcat atcactatga tgctgattac tctcgatggg attcgacaca
4321 acagagagcc gtattggcag cagctctaga aatcatggtt aaattctccc cagaaccaca
4381 tttggctcag gtagtcgcgg aggacctcct ttcccctagc gtggtggacg tgggcgactt
4441 cacaatatcg atcaacgagg gtcttccctc tggggtgcct tgcacctccc aatggaattc
4501 catcgcccac tggctactca ctctctgtgc gctctctgaa gtcacaaatt tgtcccctga
4561 caccatacag acaaattccc tcttctcttt ttatggtgat gatgaaattg ttagcacaga
4621 tataaaattg gacccagaga aattgacagc aaagctcagg gaatatgggt taaaaccaac
4681 ccgccctgat aaaactgaag gaccccttgt catctccgaa gacttgaatg gcctaacttt
4741 cctgcggaga actgtgaccc gcgacccagc tggttggttt ggaaaactgg agcagagttc
4801 aatactcagg caaatgtact ggactagggg ccccaaccat ggagacccat ctgaaacaat
4861 gattccacac tcccaaagac ccatacaatt gatgtcccta ctgggggagg ccgctctcca
4921 cggcccagca ttctacagca aaatcagcaa gttggttatt gcagagctaa aagaaggtgg
4981 catggatttt tacgtgccca gacaagagcc aatgttcaga tggatgagat tctcagatct
5041 gagcacgtgg gagggcgatc gcaatctggc tcccagcttt gtgaatgaag atggcgtcga
5101 gtgacgccaa cccatctgat gggtccgcag ccaacctcgt cccagaggtc aacaatgagg
5161 ttatggctct ggagcccgtt gttggtgccg ccattgcggc acctgtagcg ggccaacaaa
5221 atgtaattga cccctggatt agaaacaatt ttgtacaagc ccctggtgga gagtttacag
5281 tgtcccctag gaacgctcca ggtgaaatac tatggagcgc gcccttaggc cctgatctaa
5341 acccctacct atcccacttg gccagaatgt acaatggtta tgcaggtggt tttgaagtgc
5401 aggtgatcct tgcggggaac gcgttcaccg ccgggaagat catatttgca gcagtcccac
5461 caaatttccc aactgaaagc ttgagcccca gtcaggtcac tatgttcccc catataatag
5521 tagatgttag gcaactagaa cctgtgttga ttcccttacc cgatgttagg aacaatttct
5581 accattataa tcaatcaaat gaccccacta tcaagttgat agcaatgttg tacacaccac
5641 ttagggctaa taatgctggg gacgatgtct tcacagtttc ttgccgagtt ctcacgaggc
5701 catcccccga ttttgacttc atatttttag tgccacccac agttgagtca agaactaaac
5761 cattctctgt cccaatttta actgttgagg agatgaccaa ttcaagattc cccattcctt
5821 tggaaaagtt gttcacgggt cccagcagtg cctttgttgt tcaaccacaa aacggcaggt
5881 gcacgattga cggcgtgctc ctaggtacta cccaactgtc tcctgtcaac atctgcacct
5941 tcagagggga tgtcactcat attgcaggta ctcacaacta cacaatgaat ttggccactc
6001 aaaattggaa cagttatgac ccaacagaag aaatcccagc ccctctagga actccagatt
6061 tcgtggggaa gattcaaggt gtactcaccc aaaccacaaa gacagatggc tcgacacgcg
6121 gccacaaagc tacagtgtgc attgggagcg ccgactttgc tccaaaattg ggtagagttc
6181 aatttgaaac tgacacaaac aatgatcttg aaactaacca aaacacaaag ttcaccccag
6241 tcggtgtcat ccagaatggt gaaactgccc acaggaatga accccaacag tgggtgctcc
6301 cgagttactc aggcagaaat actcccaatg tgcatttggc ccccgctgta gcccccactt
6361 ttccgggtga acaacttctc ttcttcagat ccactatgcc cggatgcagc gggtatccca
6421 acatggattt ggactgcctg ctcccccagg aatgggtgca gtacttctac caagaggcag
6481 ccccagcaca atctgatgtg gctctactaa gatttgtgaa cccagacaca ggtagggttt
6541 tgtttgagtg taagcttcat aaatcaggct atgttacagt ggctcacact ggttcacatg
6601 atttggttat cccccctaat ggttatttta ggtttgattc ctgggtcaac cagttctaca
6661 cacttgcccc catgggaaat gggacggggc gtagacgtgc aacataatgg ctggagcctt
6721 ctttgctgga ttggcatctg acgtccttgg ctctgggctt ggttctctga tcaatgctgg
6781 ggctggggcc atcaaccaaa aagttgaatt tgaaaataac agaaaattgc aacaagcttc
6841 cttccaattt agcagcaatc tacaacaagc ttcttttcaa catgataaag agatgctcca
6901 agcacaaatt gaggccacca aaaagttgca gcaggaaatg atgaaagtta aacaggcagt
6961 gctcctagag ggtgggttct ctgagacaga tgcagcccgt ggggcgatca acgcccccat
7021 gacaaaggct ttggactgga gcgggacaag gtactgggct cctgatgcta ggactacaac
7081 atacaatgca ggccgctttt ccacccctca accatcgggg atactgccgg gaagagctaa
7141 tcttagggat actgtccccg ctcggggttc ctccagcaca tcttctaaat cttctattgc
7201 tacttctttg tattcaaatc aaactgctac aacgagactt ggttctacag ctggttctgg
7261 taccagtgtc tcgagcctcc cgtcaactgc aaggactagg agctgggttg aggatcaaaa
7321 taggaatttg tcacctttca tgaggggggc ccacaacata tcgtttgtca ccccaccatc
7381 tagcagatcc tctagccaag gcacagtctc aaccgtgcct aaagaagttt tggactcctg
7441 gactggcgct ttcaacacgc gcaggcagcc tctcttcgct cacattcgta agcgagggga
7501 gtcacgggtg taatgtgaaa agacaaaatt gattatcttt cttttcttta gagtctttga
7561 aaaaaaaaaa
//