Typing tool

Complete norovirus genomes

KC962462  GII.4 Sydney
 GII.P4 Yerseke

Length: 7,570 | 3 CDS

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.
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"
                     /country="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
//