Typing tool

Complete norovirus genomes

KJ710245  GII.4 New Orleans
 GII.P4 Yerseke

Length: 7,570 | 3 CDS

ORF1: 5..5104
ORF2: 5085..6707
ORF3: 6707..7513
LOCUS       KJ710245                7570 bp    RNA     linear   VRL 21-APR-2015
DEFINITION  Norovirus GII strain GII/Hu/ZAF/2011/GII.P4_GII.4/CapeTown/6745,
            partial genome.
ACCESSION   KJ710245
VERSION     KJ710245.2
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     Norovirus recombinants in South Africa
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 7570)
  AUTHORS   Mans,J.
  TITLE     Direct Submission
  JOURNAL   Submitted (16-APR-2014) Department of Medical Virology, University
            of Pretoria, Bophelo Road, Pretoria, Gauteng 0001, South Africa
REFERENCE   3  (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 KJ710245.1.
FEATURES             Location/Qualifiers
     source          1..7570
                     /organism="Norovirus GII"
                     /mol_type="genomic RNA"
                     /strain="GII/Hu/ZAF/2011/GII.P4_GII.4/CapeTown/6745"
                     /isolation_source="stool"
                     /host="Homo sapiens"
                     /db_xref="taxon:122929"
                     /country="South Africa"
                     /collection_date="07-Jan-2011"
                     /collected_by="J. Mans"
                     /note="genotype:
                     GII.P4_Yerseke_2006a/GII.4_Apeldoorn_2007"
     5'UTR           <1..4
     gene            5..5104
                     /gene="POL"
     CDS             5..5104
                     /gene="POL"
                     /codon_start=1
                     /product="polyprotein"
                     /protein_id="AKE07105.1"
                     /translation="MKMAANDASAAAVANGNNDIAKSSSDRVLSSMAVTFKRALGARS
                     KQPPPREIPQKPPRPPTPELVKNIPPPPPNGEDEIVVSYSVKDGVSGLPDLSTVRQPE
                     ESNTAFSVPPLHQRENRDAKEPLTGTILEMWDGEIYHYGLYVERGLVLGVHKPPAAIS
                     LARIELSPLSLYWRPVYTPQYLISPDTLKKLHGETFPYTAFDNNCYALCCWVLDLNDS
                     WLSRRMIQRTTGFFRPYQDWNRKPLPTMDDSKLKKVANIFLCALSSLFTRPIKDIIGK
                     LRPLNILNILASCDWTFAGIVESLILLAELFGVFWTPPDVSAMIAPLLGDYELQGPED
                     LAVELVPVVMGGIGLVLGFTKEKIGKMLSSAATTLRACKDLGAYGLEILKLVMKWFFP
                     KKEEANELAIVRSIEDAVLDLEAIENNHMTTLLKDKDSLATYMRTLDLEEEKARKLST
                     KSASPDIVGTINALLARIAAARSLVHRAKEELSSRPRPVVLMISGRPGIGKTHLAREV
                     AKRIASSLTGDQRVGLIPRNGVDHWDAYKGERVVLWDDYGMSNPVHDALRLQELADTC
                     PLTLNCDRIENKGKVFDSDVIIITTNLANPAPLDYVNFEACSRRIDFLVYAEAPEVEK
                     SKRDFPGQPDMWKNAFSSDFSHMKLTLAPQGGFDKNGNTPHGKGVMKSLTTGSLIARA
                     SGLLHERLDEFELQGPTLTTFNFDRNKVLAFRQLAAENKYGLMDTMRVGRQLKDVRTM
                     TELKQALKNIAIKKCQIVYSGYTYILESDGKGDVKVDKIQNTSVQTNNELTGALHHLR
                     CARIRYYVKCVQEALYSIIQIAGAAFVTTRIVKRMNIQDLWSKPQVEDTEETTSKDGC
                     PKPKDDEEFVISSDDIKTEGKKGKNKTGRGKKHTAFSSKGLSDEEYDEYKRIREERNG
                     KYSIEEYLQDRDKYYEEVTIARATEEDFCEEEEAKIRQRIFRPTRKQRKEERASLGLV
                     TGSEIRKRNPDDFKPKGKLWADDDRSVDYNEKLSFEAPPSIWSRIVNFGSGWGFWVSP
                     SLFITSTHVIPQGAKEFFGVPIKQIQVHKSGEFCRLRFPKPIRTDVTGMILEEGAPEG
                     TVVTLLIKRSTGELMPLAARMGTHATMKIQGRTVGGQMGMLLTGSNAKSMDLGTTPGD
                     CGCPYIYKRGNDYVVIGVHTAAARGGNTVICATQGSEGEAVLEGGDNKGTYCGAPILG
                     PGNAPTLSTKTKFWRSSTAPLPPGTYEPAYLGGKDPRVKSGPSLQQVMREQLKPFTEP
                     RGKPPKPSVLEAAKKTIINVLEQTIDPPEKWTFAQACASLDKTTSSGHPHHMRKNDCW
                     NGENFTGKLADQASKANLMFEEGKNMTPVYTAALKDELVKTDKIYSKIKKRLLWGSDL
                     ATMVRCARAFGGLMDELKAHCVTLPIRVGMNMNEDGPIIFEKHSRYTYHYDADYSRWD
                     STQQRAVLAAALEIMVKFSPEPRLAQVVAEDLLSPSVVDVGDFTISINEGLPSGVPCT
                     SQWNSIAHWLLTLCALSEVTNLSPDTIQANSLFSFYGDDEIVSTDIKLDPEKLTAKLR
                     EYGLKPTRPDKTEGPLVISEDLDGLTFLRRTVTRDPAGWFGKLEQSSILRQMYWTRGP
                     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            5084..6707
                     /gene="VP1"
     CDS             5085..6707
                     /gene="VP1"
                     /note="major capsid protein"
                     /codon_start=1
                     /product="capsid protein VP1"
                     /protein_id="AKE07106.1"
                     /translation="MKMASSDANPSDGSTANLVPEVNDEVMALEPVVGAALAAPVAGQ
                     QNVIDPWIRNNFVQAPGGEFTVSPRNAPGEILWSAPLGPDLNPYLSHLARMYNGYAGG
                     FEVQVILAGNAFTAGKVIFAAVPPNFPTEGLSPSQVTMFPHIIVDVRQLEPVLIPLPD
                     ARNNFYHYNQSNESTIKLIAMLYTPLRANNAGDDVFTVSCRVLTRPSLDFDFIFLVPP
                     TVESRTKPFSVPILTVEEMTNSRFPIPLERLFTGPSSAFAVQPQNGRCTTDGVLLGTT
                     QLSPVNICTFRGDVTHTTGSHNYTMNLASQNRSNYDPTEEIPAPLGTPDFVGKIQGAL
                     TQTTRADGSTRGHKATVYTGSADFTPKLGRVQFATDTDHDFDTNQNTKFTPVGVIQDG
                     STTHRNEPQQWVLPSYSGRNTHNVHLAPAVAPTFPGEQLLFFRSTMPGCSGYPNMDLD
                     CLLPQEWVAHFYQEAAPAQSDVALLRFVNPDTGRVLFECKLHKSGYVTVAHTGQHDLV
                     IPPNGYFRFDSWVNQFYTLAPMGNGTGRRRAL"
     gene            6707..7513
                     /gene="VP2"
     CDS             6707..7513
                     /gene="VP2"
                     /note="minor capsid protein"
                     /codon_start=1
                     /product="capsid protein VP2"
                     /protein_id="AKE07107.1"
                     /translation="MAGAFFAGLASDVLGSGLGSLINAGAGAINQKVEFENNRKLQQA
                     SFQFSSNLQQASFQHDKDMLQAQIEATKKLQQEMMRVKQAMLLEGGFSETDAARGAIN
                     APMTKALDWSGTRYWAPDARTTTYNAGHFSTPQPSGALPGRANLRAAVPARGPSSTSS
                     NSSTATSVYSNQTTSTRLGSTAGSGASVSSLPSTARTVNWVRDQNRSLSPFMRGAHNT
                     SFVTPPSSRSSSQGTVSTVPKEVLDSWTGAFNTRRQPLFAHIRTRGESRV"
     3'UTR           7514..7570
ORIGIN      
        1 gtgaatgaag atggcggcta acgacgcttc cgctgccgct gttgctaacg gcaacaacga
       61 catcgcaaaa tcttcaagtg accgagtgct ttctagcatg gctgtcactt ttaaacgagc
      121 cctcggggcg cggtctaaac agcctccccc gagggaaata ccacaaaagc ccccacgacc
      181 acctactcca gaactggtta aaaacattcc ccctcccccg cccaacggag aggatgaaat
      241 agtggtttct tatagtgtca aagatggtgt ttccgggttg cccgaccttt ccaccgtcag
      301 gcaaccggaa gaatctaaca cggcctttag tgtccctcca ctccatcaga gggagaatag
      361 agatgctaag gagccactta ctggaacaat tctggaaatg tgggatggag aaatctacca
      421 ttatggcctg tatgtggagc gaggccttgt actgggtgta cacaaaccgc cagctgccat
      481 cagcctcgct aggattgagc tatcaccact ctccttgtac tggagacctg tgtacactcc
      541 tcagtacctc atctctccag acaccctcaa gaagttacac ggagaaacgt tcccctacac
      601 agcctttgac aacaattgtt atgccctttg ttgttgggtc ctggacctaa atgactcgtg
      661 gctgagcagg agaatgatcc agaggacaac tggtttcttc aggccctacc aagactggaa
      721 taggaaaccc cttcccacta tggatgactc caaattaaag aaggtagcta acatattcct
      781 gtgtgctctg tcttcgctat tcaccaggcc cataaaagat ataataggta agctaaggcc
      841 tcttaacatc ctcaacatct tagcctcatg tgattggact tttgcaggca tagtggaatc
      901 cctgatactc ttggcagagc tctttggagt gttctggaca cccccagatg tgtctgcgat
      961 gattgccccc ttactcggtg actacgagct acaaggacct gaggaccttg cagtggagct
     1021 cgtccctgta gtgatggggg gaattggttt ggtgctagga ttcaccaaag agaagattgg
     1081 gaagatgttg tcatctgctg cgaccacttt gagggcttgt aaagaccttg gtgcatatgg
     1141 gctagagatc ctaaagttgg tcatgaagtg gttcttcccg aagaaggagg aagcaaacga
     1201 actggctata gtgagatcta tcgaggacgc agtcctagat ctcgaggcaa ttgaaaacaa
     1261 ccatatgacc accttgctca aagacaaaga cagcttggca acctacatga gaacccttga
     1321 cctcgaggag gagaaagcca ggaaactctc aaccaagtct gcctcacctg acatcgtggg
     1381 cacaatcaat gcccttctgg cgagaatcgc tgctgcacgt tctctggtgc atcgagcgaa
     1441 ggaggaactt tccagcaggc caagaccagt agtattgatg atatcgggca gaccaggaat
     1501 agggaagacc cacctcgcta gagaagtggc caagagaatc gcgtcctccc tcacaggaga
     1561 ccagcgtgtg ggcctcatcc cacgcaatgg cgtcgaccat tgggatgcgt acaaggggga
     1621 gagggtcgtc ctatgggacg attatggaat gagtaaccct gttcatgatg ccctcaggtt
     1681 gcaagaactc gctgacactt gcccccttac tctaaactgt gacaggattg agaacaaagg
     1741 aaaagtcttt gatagcgatg tcatcattat caccactaat ctggccaacc cagcaccact
     1801 ggactatgtc aactttgaag catgctcgag gcgcatcgac ttcctcgtgt atgcagaagc
     1861 ccctgaagtc gaaaagtcaa agcgtgactt cccaggccag cctgacatgt ggaagaacgc
     1921 cttcagttct gatttctcac acatgaaact aacattggcc ccacagggtg gcttcgacaa
     1981 gaacggaaac accccacacg gcaagggcgt catgaagtct ctcaccactg gctcccttat
     2041 tgcccgggca tcaggactac tccatgagag gttagatgaa tttgaactac agggcccaac
     2101 cctcaccacc ttcaattttg atcgcaataa agtacttgcc tttagacaac ttgctgctga
     2161 gaacaaatat gggttgatgg acacaatgag ggttgggaga cagctcaagg atgtcagaac
     2221 catgacagaa ctcaaacaag cactcaagaa tatcgcaatc aagaagtgcc agatagtgta
     2281 tagtggttac acctacatac ttgagtctga tggtaagggc gatgtgaaag ttgacaaaat
     2341 tcagaacacc tccgtgcaga ccaacaatga gctgactggt gctctgcacc atctgaggtg
     2401 cgccagaatc agatactatg tcaagtgtgt tcaggaggcc ctgtattcca tcattcaaat
     2461 tgctggggct gcatttgtca ccacgcgcat cgtcaagcgc atgaacatac aagacctatg
     2521 gtccaaacca caagtggaag acacagagga gaccaccagc aaggatgggt gcccaaaacc
     2581 caaagatgat gaggagtttg tcatttcatc cgacgacatc aaaactgagg gtaagaaagg
     2641 gaagaacaag actggccgcg gcaagaagca cacagccttc tcaagcaaag gcctcagtga
     2701 tgaagagtac gacgagtaca agaggattag agaagagagg aatggcaagt actccataga
     2761 agagtacctt caggacaggg acaaatacta tgaggaggtg accattgcca gggcaactga
     2821 ggaagacttc tgtgaagagg aggaggccaa gatccgacaa aggatcttca ggccaacaag
     2881 gaaacaacgc aaggaggaaa gagcttcgct cggtctggtc acaggttctg aaattaggaa
     2941 aagaaaccca gatgatttca aacccaaggg gaaactgtgg gctgacgatg acagaagtgt
     3001 ggactacaat gagaaactca gttttgaggc cccaccaagc atctggtcaa ggatagtcaa
     3061 ctttggttca ggttggggat tctgggtctc ccccagtctg ttcataacat caacccacgt
     3121 tataccccag ggcgcaaagg agttctttgg agtccccatc aaacaaattc aggtgcacaa
     3181 gtcaggcgag ttctgtcgct tgagattccc aaaaccaatc aggactgatg tgacgggcat
     3241 gatcttagaa gaaggcgcac ctgagggcac cgtggtcaca ctactcatca aaaggtccac
     3301 tggggaactc atgcccctag cagctagaat ggggacccat gcaaccatga agatccaagg
     3361 gcgcactgtt ggaggccaaa tgggcatgct tctgacagga tccaacgcca aaagcatgga
     3421 tctgggcact acaccaggtg attgtggctg tccctacatc tacaagagag gcaatgacta
     3481 tgtagtcatt ggagtccaca cagccgccgc tcgtggagga aacactgtca tatgtgccac
     3541 ccaggggagt gaaggagagg ctgtgcttga aggtggtgac aacaagggga cgtactgtgg
     3601 tgcaccaatc ctaggcccag ggaatgcccc aacacttagc accaagacca aattttggag
     3661 atcgtccacg gcaccactcc cacctggcac ctatgaacca gcctaccttg gtggcaagga
     3721 ccctagagtc aagagtggcc cttcactgca gcaagtcatg agggaacagt tgaagccatt
     3781 cacagagccc aggggcaagc caccaaagcc aagtgtgtta gaagctgcca agaaaaccat
     3841 catcaatgtc cttgaacaaa caattgatcc acctgagaaa tggacatttg cacaagcttg
     3901 cgcgtccctt gacaagacca cttccagtgg ccacccgcac cacatgcgga aaaacgactg
     3961 ctggaacggg gagaacttca caggcaagct ggcagaccag gcttccaagg ccaacttgat
     4021 gtttgaagaa ggaaagaaca tgaccccagt ctatacagct gcgctcaagg atgagctagt
     4081 taaaactgat aaaatttata gcaagatcaa gaagaggctt ctctggggtt cggacttggc
     4141 gaccatggtc cggtgtgctc gagcattcgg aggcctaatg gacgaactca aagcacactg
     4201 tgtcacactt cccattagag ttggtatgaa catgaacgag gatggcccca tcatcttcga
     4261 gaaacattcc aggtacacat atcactatga tgctgattac tctcgatggg attcgacaca
     4321 acagagagcc gtgttggcag cagctctaga aatcatggtt aaattctctc cagaaccacg
     4381 cttggctcag gtagttgcgg aagatcttct ttctcctagc gtggtggacg tgggcgactt
     4441 cacaatatca atcaacgagg gtcttccctc tggggtgccc tgcacctccc aatggaattc
     4501 catcgcccac tggcttctca ctctctgcgc gctctctgaa gtcacaaact tgtcccctga
     4561 caccatacag gctaactccc tcttctcttt ttatggtgat gatgaaattg ttagcacaga
     4621 tataaaattg gacccagaga aattgacagc aaagcttagg gaatatggat tgaaaccaac
     4681 ccgccctgac aaaactgaag gaccccttgt catctctgag gacttggatg gcctaacctt
     4741 cctgcggaga actgtgaccc gtgacccagc tggttggttt ggaaaactgg agcagagctc
     4801 aatactcagg caaatgtact ggacaagggg ccccaaccat ggagacccat ctgaaacaat
     4861 gattccacac tcccaaagac ccatacaatt gatgtcccta ttgggggagg ccgctctcca
     4921 cggcccagca ttctacagca aaatcagcaa gttagtcatt gcagagctaa aagaaggtgg
     4981 catggatttt tacgtgccca gacaagagcc aatgttcaga tggatgagat tctcagatct
     5041 gagcacgtgg gagggcgatc gcaatctggc tcccagtttt gtgaatgaag atggcgtcga
     5101 gtgacgccaa cccatctgat gggtccacag ccaacctcgt cccagaggtc aacgatgagg
     5161 ttatggcttt ggagcccgtt gttggtgccg cccttgcggc acctgtagcg ggccaacaaa
     5221 atgtaattga cccctggatt agaaacaatt ttgtacaagc ccctggtgga gagttcacag
     5281 tatcccctag aaacgctcca ggtgaaatac tatggagcgc gcccttaggc cccgatttga
     5341 atccctacct ttctcatttg gccagaatgt acaatggtta tgcaggtggt tttgaagtgc
     5401 aggtgatcct cgcggggaat gcgttcaccg ccggaaaggt catatttgca gcagtcccac
     5461 caaatttccc aactgaaggc ttgagcccca gccaggtcac tatgttcccc cacataatag
     5521 tagatgttag gcaattggaa cctgtgttga tccccttacc cgatgctagg aataatttct
     5581 accactacaa tcaatcaaat gaatccacca tcaaattgat agcaatgttg tatacaccac
     5641 ttagggctaa caatgctggg gacgatgtct tcacagtctc ttgtcgagtc ctcacgagac
     5701 catccctcga ttttgatttc atatttttag tgccacccac agttgagtca agaactaaac
     5761 cattctctgt cccaatttta actgttgagg aaatgaccaa ttcaagattc cccattcctt
     5821 tggaaagatt gttcacgggt cccagcagtg cctttgccgt tcaaccacaa aacggcaggt
     5881 gcacgactga tggcgtgctc ctaggtacta ctcaactgtc tcctgtcaac atctgcacct
     5941 tcagaggaga tgtcacccac accacaggta gtcacaacta cacaatgaat ttggcttccc
     6001 aaaatcggag caattatgac ccaacagaag aaatcccagc ccctctagga actccagact
     6061 tcgtggggaa gattcaaggt gcgctcaccc aaaccacaag ggcagatggc tcgacccgcg
     6121 gccacaaagc tacagtgtac actgggagcg ccgactttac tccaaaactg ggtagagttc
     6181 aatttgccac tgatacagac catgattttg atactaacca aaacacaaag ttcaccccag
     6241 tcggtgtcat ccaggatggt tctactaccc accggaatga accccaacaa tgggtgctcc
     6301 caagttactc aggcagaaat actcataatg tgcacctggc ccccgctgtg gcccccactt
     6361 ttccgggtga acagcttctc ttctttaggt ccactatgcc cggatgtagt gggtacccca
     6421 acatggattt ggactgcctg ctcccccaag aatgggtggc gcacttctac caagaggcag
     6481 cccccgcaca atctgatgtg gctctgctaa gatttgtgaa tccagataca ggcagggttt
     6541 tgtttgagtg taagcttcat aaatcaggct atgttacagt ggctcacact ggccaacatg
     6601 atttggttat cccccccaat ggttacttta gatttgattc ctgggtcaac cagttctaca
     6661 cacttgcccc catgggaaat ggaacggggc gtagacgtgc attgtaatgg ctggagcttt
     6721 ctttgctgga ttggcatctg acgtccttgg ctctggactt ggttccctga tcaatgctgg
     6781 ggctggggcc atcaaccaaa aagttgaatt tgaaaataac agaaaattgc aacaagcttc
     6841 cttccaattt agcagcaatc tacaacaggc ttcctttcaa catgataaag atatgctcca
     6901 agcacaaatt gaggccacca aaaagttgca acaggaaatg atgagagtta aacaggcaat
     6961 gctcctagag ggtggattct ctgagacaga tgcagcccgt ggggcaatca acgcccccat
     7021 gacaaaggct ttggactgga gcgggacaag gtactgggct cccgatgcta ggactacaac
     7081 atacaatgca ggccactttt ccacccctca accctcgggg gcgctgccag ggagagctaa
     7141 tctcagggct gctgtccccg ctcggggtcc ctccagcaca tcttctaatt cttctactgc
     7201 tacttctgtg tactcaaatc aaaccacttc aacgagactt ggttctacag ctggttctgg
     7261 tgccagtgtc tcgagcctcc cgtcaactgc aaggaccgtg aactgggtta gggatcaaaa
     7321 caggagtttg tcacctttca tgaggggggc ccacaacaca tcgtttgtca ccccaccgtc
     7381 tagcagatcc tctagtcaag gcacagtctc aaccgtgccc aaagaagttt tggactcctg
     7441 gactggcgct ttcaacacgc gcaggcagcc tctcttcgct cacattcgca cgcgagggga
     7501 gtcacgggtg taatgtgaaa agacaaaatt gattatcttt cttttcttta gtgtctttga
     7561 aaaaaaaaaa
//