Typing tool

Complete norovirus genomes

KP784692  GII.4 New Orleans
 GII.P4 Yerseke

Length: 7,569 | 3 CDS

ORF1: 5..5104
ORF2: 5085..6707
ORF3: 6707..7513
LOCUS       KP784692                7569 bp    RNA     linear   VRL 22-NOV-2016
DEFINITION  Norovirus GII/Hu/ZAF/2011/GII.P4_GII.4/Johannesburg/7028, complete
            genome.
ACCESSION   KP784692
VERSION     KP784692.1
KEYWORDS    .
SOURCE      Norovirus GII/Hu/ZAF/2011/GII.P4_GII.4/Johannesburg/7028
  ORGANISM  Norovirus GII/Hu/ZAF/2011/GII.P4_GII.4/Johannesburg/7028
            Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes;
            Picornavirales; Caliciviridae; Norovirus.
REFERENCE   1  (bases 1 to 7569)
  AUTHORS   Botha,J.C., Mans,J. and Taylor,M.B.
  TITLE     Comparative analysis of South African norovirus GII.4 strains
            identifies minor recombinant variants
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 7569)
  AUTHORS   Botha,J.C., Mans,J. and Taylor,M.B.
  TITLE     Direct Submission
  JOURNAL   Submitted (13-FEB-2015) Medical Virology, University of Pretoria,
            Pretoria, Gauteng, South Africa
COMMENT     ##Assembly-Data-START##
            Assembly Method       :: Sequencher v. 4.10.1
            Sequencing Technology :: Sanger dideoxy sequencing
            ##Assembly-Data-END##
FEATURES             Location/Qualifiers
     source          1..7569
                     /organism="Norovirus
                     GII/Hu/ZAF/2011/GII.P4_GII.4/Johannesburg/7028"
                     /mol_type="genomic RNA"
                     /isolate="GII/Hu/ZAF/2011/GII.P4_GII.4/Johannesburg/7028"
                     /host="Homo sapiens"
                     /db_xref="taxon:1777884"
                     /country="South Africa"
                     /collection_date="2011"
                     /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="ALX87344.1"
                     /translation="MKMASNDASAAAVANGNNDTAKSSSDRVLSSMAVTFKRALGARS
                     KQPPPREISQKPPRPPTPELVKNIPPPPPNGEDEIVVSYSVKDGVSGLPDLSTVRQPE
                     ESNTAFSVPPLHQRENRDAKEPLTGTILEMWDGEIYHYGLYVDRGLVLGVHKPPAAIS
                     LARIELSPLSLYWRPVYTPQYLISPDTLKKLHGETFPCTAFDNNCYAFCCWVLDLNDS
                     WLSRRMIQRTTGFFRPYQDWNRKPLPTMDDSKLKKVANIFLCALSSLFTRPIKDIIGK
                     LRPLNILNILASCDWTFAGVVESLILLAELFGVFWTPPDVSAMIAPLLGDYELQGPED
                     LAVELVPVVMGGIGLVLGFTKEKIGKMLSSAASTLRACKDLGAYGLEILKLVMKWFFP
                     RKEEANELAIVRSIEDAVLDLEAIENNHMTTLLKDKDSLATYMRTLDLEEEKARKLST
                     KSASPDIVGTINALLARIAAARSLVHRAKEELSSRPRPVVMMISGRPGIGKTHLAREV
                     AKRIASSLTGDQRVGLIPRNGVDHWDAYKGERVVLWDDYGMSNPVHDALRLQELADTC
                     PLTLNCDRIESKGKVFDSDVIIITTNLANPAPLDYVNFEACSRRIDFLVYAEAPEVEK
                     SKREFPGQPDMWKNAFSSDFSHMKLTLAPQGGFDKNGNTPHGKGVMKSLTTGSLIARA
                     SGLLHERLDEFELQGPTLTTFNFDRNKVLAFRQLAAENKYGLMDTMRVGRQLKDVRTM
                     TELKQALKNIAIKKCQIVYSGCTYILESDGKGDVKVDKIQNTSVQTNNELTGALHHLR
                     SARIRYYVKCVQEALYSIIQIAGAAFVTTRIVKRMNIQDLWSKPQVEDTEETTSKDGC
                     PKPKDDEEFVISSDDIKTEGKKGKNKTGRGKKHTAFSSKGLSDEEYDEYKRIREERNG
                     KYSIEEYLQDRDKYYEEVAIARATEEDFCEEEEAKIRQRIFRPTRKQRKEERASLGLV
                     TGSEIRRRNPDDFKPKGKLWADDDRSVDYNEKLSFEAPPSIWSRIVNFGSGWGFWVSP
                     SLFITSTHVIPQGAKEFFGVPIKQIQVHKSGEFCRLRFPKPIRTDVTGMILEEGAPEG
                     TVVTLLIKRSTGELMPLAARMGTHATMKIQGRTVGGQMGMLLTGSNAKSMDLGTTPGD
                     WGCPYIYKRGNDYVVIGVHTAAARGGNTVICATQGSEGEAVLEGGDNKGTYCGAPILG
                     PGNAPTLSTKTKFWRSSTAPLPPGTYEPAYLGGKDPRVKGGPSLQQVMREQLKPFTEP
                     RGKPPKPSVLEAAKKTIINVLEQTIDPPEKWTFAQACASLEKTTSSGHPHHMRKNDCW
                     NGESFTGKLADQASKANLMFEEGKNMTPVYTAALKDELVKTDKIYSKIKKRLLWGSDL
                     ATMVRCARAFGGLMDELKAHCVTLPIRVGMNMNEDGPIIFEKHSRYTYHYDADYSRWD
                     STQQRAVLAAALEIMVKFSPEPHLAQVVAEDLLSPSVVDVGDFTISINEGLPSGVPCT
                     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="VPg"
     mat_peptide     3029..3571
                     /gene="POL"
                     /product="3C-like protease"
     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="ALX87345.1"
                     /translation="MKMASSDANPSDGSTANLVPEVNNEVMALEPVVGAALAAPVAGQ
                     QNVIDPWIRSNFVQAPGGEFTVSPRNAPGEILWSAPLGPDLNPYLSHLARMYNGYAGG
                     FEVQVILAGNAFTAGKVIFAAVPPNFPTEGLSPSQVTMFPHIIVDVRQLEPVLIPLPD
                     VRNNFYHYNQSNESTIKLIAMLYTPLRANNAGDDVFTVSCRVLTRPSPDFDFIFLVPP
                     TVESRTKPFSVPILTVEEMTNSRFPIPLERLFTGPSSAFVVQPQNGRCTTDGVLLGTT
                     QLSPVNICTFRGDVTHTTGSHNYTMNLASQNWSNYDPTEEIPAPLGTPDFVGKIQGVL
                     TQTTRADGSTRGHKATVYTGSADFTPKLGRVQFATDTDHDFDTNQNTKFTPVGVIQDG
                     STTHRNEPQQWVLPSYSGRNTHNVHLAPAVAPTFPGEQLLFFRSTMPGCSGYPNMDLD
                     CLLPQEWVAHFYQEAAPAQSDVALLRFVNPDTGRVLFECKLHKSGYVTVAHTGQHDLV
                     IPPNGYFRFDSWVNQFYTLAPMGNGTGRRRAL"
     gene            6705..7513
                     /gene="VP2"
     CDS             6707..7513
                     /gene="VP2"
                     /note="minor capsid protein"
                     /codon_start=1
                     /product="capsid protein VP2"
                     /protein_id="ALX87346.1"
                     /translation="MAGAFFAGLASDVLGSGLGSLINAGAGAINQKVEFDNNRKLQQA
                     SFQFSSNLQQASFQHDKDMLQAQIEATKKLQQEMMRIKQAMLLEGGFSETDAARGAIN
                     APMTKALDWSGTRYWAPDARTTTYNAGHFSTPQPSGALPGRANLRAAVPARGPSSTSS
                     NSSTATSVYSNQTTSTRLGSTAGSGASVSSLPSTARTMNWVRDQNRSLSPFMRGAHNI
                     SFVTPPSSRSSSQGTVSTVPKEVLDSWTGAFNTRRQPLFAHIRKRGESRV"
     3'UTR           7514..7569
ORIGIN      
        1 gtgaatgaag atggcgtcta acgacgcttc cgctgccgct gttgctaacg gcaacaacga
       61 caccgcaaaa tcttcaagtg accgagtgct ttctagcatg gctgtcactt ttaaacgagc
      121 cctcggggcg cggtctaaac agcccccccc gagggaaata tcacaaaagc ccccacgacc
      181 acctactcca gaactggtta aaaacattcc ccctcccccg cccaacggag aggatgaaat
      241 agtggtttct tatagtgtca aagatggtgt ttccgggttg cctgaccttt ccaccgtcag
      301 gcaaccggaa gaatctaaca cggcctttag tgtccctcca ctccatcaga gggagaatag
      361 agatgctaag gagccactta ctggaacaat tctggaaatg tgggatggag aaatctacca
      421 ttatggtctg tatgtggatc gaggccttgt actgggtgta cacaaaccgc cagctgccat
      481 cagcctcgct aggattgagc tatcaccact ctccttgtac tggagacctg tgtacactcc
      541 tcagtacctc atctctccag acaccctcaa gaagttacac ggagaaacgt tcccctgcac
      601 agcctttgac aacaattgtt atgccttttg ttgttgggtc ctggacctaa atgactcgtg
      661 gctgagtagg aggatgatcc agaggacaac tggtttcttc aggccctacc aagactggaa
      721 taggaaaccc cttcccacta tggatgactc caaattaaag aaggtagcta acatattcct
      781 gtgtgctctg tcttcgttat tcaccaggcc cataaaggat ataataggga agctaaggcc
      841 tcttaacatc ctcaacatct tagcctcatg tgattggact tttgcaggcg tagtggaatc
      901 cctgatactc ttggcagagc tctttggagt gttctggaca cccccagatg tgtctgcgat
      961 gattgccccc ttactcggtg actacgaact gcaaggacct gaggaccttg cagtggagct
     1021 cgtccctgta gtgatggggg gaattggttt ggtgctagga ttcaccaaag agaagattgg
     1081 gaaaatgttg tcatctgctg cgtccacttt gagggcttgt aaagaccttg gtgcatatgg
     1141 gctagagatc ctaaagttgg tcatgaagtg gttcttcccg aggaaggagg aagcaaacga
     1201 actggctata gtgagatcta tcgaggacgc agtcctagat ctcgaggcaa ttgaaaacaa
     1261 ccatatgacc accttgctca aagacaaaga cagcctggca acctacatga gaacccttga
     1321 cctcgaggag gagaaagcca ggaaactctc aaccaagtct gcctcacctg acatcgtggg
     1381 cacaatcaat gcccttctgg cgagaatcgc tgctgcacgc tctctggtgc atcgagcgaa
     1441 ggaggaactt tccagcaggc caagaccagt ggtaatgatg atatcgggca gaccaggaat
     1501 agggaagacc cacctcgcta gggaagtggc caaaagaatc gcgtcctccc tcacaggaga
     1561 ccagcgtgtg ggcctcatcc cacgcaatgg cgtcgaccat tgggatgcgt acaaggggga
     1621 gagggtcgtc ctatgggacg attatggaat gagtaaccct gttcatgatg ccctcaggtt
     1681 gcaagaactc gctgacactt gcccccttac tctaaactgt gacaggattg agagcaaagg
     1741 aaaagtcttt gatagcgatg tcatcattat caccactaat ctggccaacc cagcaccact
     1801 ggactatgtc aactttgaag catgctcgag gcgcatcgac ttcctcgtgt atgcagaagc
     1861 ccctgaagtc gaaaagtcaa agcgtgaatt cccaggccag cctgacatgt ggaagaacgc
     1921 cttcagttct gatttctcac acatgaaact aacattggcc ccacagggtg gcttcgacaa
     1981 gaacgggaac accccacacg gcaaaggcgt catgaagtct ctcaccactg gctcccttat
     2041 tgcccgggca tcaggactac tccatgagag gttagatgaa tttgaactac agggcccaac
     2101 tctcaccacc ttcaatttcg atcgcaataa agtacttgcc tttagacaac ttgctgctga
     2161 gaacaaatat gggttgatgg acacaatgag agttgggaga cagctcaagg atgtcagaac
     2221 catgacagaa ctcaaacaag cactcaagaa catcgcaatc aagaagtgcc agatagtgta
     2281 tagtggttgc acctacatac ttgagtctga tggcaagggc gatgtgaaag ttgacaaaat
     2341 tcagaacacc tccgtgcaga ccaacaatga gctgactggt gctctgcacc atctgaggag
     2401 cgccagaatc agatactatg tcaagtgtgt tcaggaggcc ctgtattcca tcattcaaat
     2461 tgctggggct gcgtttgtca ccacgcgcat cgtcaagcgc atgaacatac aagacctgtg
     2521 gtccaaacca caagtggaag acacagagga gaccaccagc aaggacgggt 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 ataaatacta tgaggaggtg gccattgcca gggcaactga
     2821 ggaagacttc tgtgaagagg aggaagccaa gatccgacaa aggatcttca ggccaacaag
     2881 gaaacaacgc aaggaggaaa gagcttcgct cggtctggtc acaggttctg aaattaggag
     2941 aagaaaccca gatgatttca aacccaaggg gaagctgtgg 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 ctgagggtac cgtggtcaca ctactcatca aaaggtccac
     3301 tggggaactc atgcccctag cagctagaat ggggacccat gcaaccatga agatccaagg
     3361 gcgcactgtt ggaggccaaa tgggcatgct tctgacagga tccaacgcca aaagcatgga
     3421 tctgggcact acaccaggtg attggggctg tccctacatc tataagagag 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 gcctatcttg gtggcaagga
     3721 ccctagagtc aagggtggcc cttcactgca gcaagtcatg agggaacagt tgaagccatt
     3781 cacagagccc aggggcaagc caccaaagcc aagtgtgtta gaagctgcca agaagaccat
     3841 catcaatgtc cttgaacaaa caattgatcc acctgagaaa tggacatttg cacaagcttg
     3901 cgcgtccctt gagaagacca cttccagtgg ccacccgcac cacatgcgga aaaacgactg
     3961 ctggaacgga gagtccttca caggcaagct ggcagaccag gcttccaagg ccaacttgat
     4021 gtttgaagaa ggaaaaaaca tgaccccagt ctatacagct gcgctcaagg atgagctagt
     4081 taaaactgac aaaatttata gcaagatcaa gaagaggctt ctttggggtt cggacttggc
     4141 gactatggtc cggtgtgctc gagcattcgg aggcttaatg gatgaactca aagcacattg
     4201 tgtcacactt cccattagag ttggtatgaa catgaacgag gatggcccca tcatcttcga
     4261 gaaacattcc aggtacacat atcactatga tgctgattac tctcgatggg attcgacaca
     4321 acagagagcc gtgttggcag cagctctaga aatcatggtt aaattctctc cagaaccaca
     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 gacgaaattg ttagcacaga
     4621 tataaaattg gacccagaga aattgacagc aaagcttagg gaatatggat tgaaaccaac
     4681 ccgccctgac aaaactgaag gaccccttgt catctctgag gatttggacg gcctaacctt
     4741 cctgcggaga actgtgaccc gtgacccagc tggttggttt ggaaaactgg agcagagctc
     4801 aatactcagg caaatgtact ggacaagggg ccccaaccat ggagacccat ctgaaacaat
     4861 gattccacac tctcaaagac ccatacaatt gatgtcccta ctgggggagg 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 aacaatgagg
     5161 ttatggcttt ggagcccgtt gttggtgccg cccttgcggc acctgtagcg ggccaacaaa
     5221 atgtaattga cccctggatt agaagcaatt ttgtacaagc ccctggtgga gagttcacag
     5281 tatcccctag aaacgctcca ggtgaaatac tatggagcgc gcccttaggc cccgatttga
     5341 acccctacct ttctcatttg gccagaatgt acaatggtta tgcaggtggt tttgaagtgc
     5401 aggtgatcct cgcggggaat gcgttcaccg ccggaaaagt catatttgca gcagtcccac
     5461 caaatttccc aactgaaggc ttgagcccca gccaggtcac tatgttcccc cacataatag
     5521 tagatgttag gcaattggaa cctgtgttga tccccctacc cgatgttagg aataatttct
     5581 accactacaa tcaatcaaat gaatccacca tcaaattgat agcaatgttg tatacaccac
     5641 ttagggctaa caatgctggg gacgatgtct tcacagtctc ttgtcgagtc ctcacgagac
     5701 catcccccga ttttgatttt atatttttag tgccacccac agttgagtca agaactaaac
     5761 cattctctgt cccaatttta actgttgagg aaatgaccaa ttcaagattc cccattcctt
     5821 tggaaaggtt gttcacgggt cccagcagtg cctttgtcgt tcaaccacaa aacggcaggt
     5881 gcacgactga tggcgtgctc ctaggtacta ctcaactgtc tcctgtcaac atctgcacct
     5941 tcagaggaga tgtcacccac accacaggta gtcacaacta cacaatgaat ttggcttccc
     6001 aaaattggag caattatgac ccaacagaag aaatcccagc ccctctagga actccagatt
     6061 tcgtggggaa gattcaaggt gtgctcaccc 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 aggcaggaat actcataatg tgcacctggc ccccgctgtg gcccccactt
     6361 ttccgggtga acagcttctc ttctttagat ccaccatgcc cggatgtagt gggtacccca
     6421 acatggattt ggactgcctg ctcccccaag aatgggtggc gcatttctac caggaggcag
     6481 ccccagcaca atctgatgtg gctctgctaa gatttgtgaa tccagataca ggcagggttt
     6541 tgtttgagtg taagctccat aaatcaggct atgttacagt ggctcacact ggccaacatg
     6601 atttggttat cccccccaat ggttatttta gatttgattc ctgggtcaac cagttctaca
     6661 cacttgcccc catgggaaat ggaacggggc gtagacgtgc attgtaatgg ctggagcttt
     6721 ctttgctgga ttggcatctg acgtccttgg ctctggactt ggttccctga tcaatgctgg
     6781 ggctggagcc atcaaccaaa aagttgaatt tgataataac agaaaattgc aacaagcttc
     6841 cttccaattt agcagcaatc tacaacaggc ttcctttcaa catgataaag atatgctcca
     6901 agcacaaatt gaggccacca aaaagttgca acaggaaatg atgagaatta aacaggcaat
     6961 gctcctagag ggtggattct ctgagacaga tgcagcccgt ggggcaatca acgcccccat
     7021 gacaaaggct ttggactgga gcgggacaag gtactgggct cccgacgcta ggactacaac
     7081 atacaatgca ggccactttt ccacccctca accctcgggg gcgctgccag gaagagctaa
     7141 tctcagggct gctgtccccg ctcggggtcc ctccagcaca tcttctaatt cttctactgc
     7201 tacttctgtg tactcaaatc aaaccacttc aacgagactt ggttctacag ctggttctgg
     7261 tgccagtgtc tcgagcctcc cgtcaactgc aaggaccatg aactgggtta gggatcaaaa
     7321 taggagtttg tcacctttca tgaggggggc ccacaatata tcgtttgtca ccccaccatc
     7381 tagcagatcc tctagccaag gcacagtctc aaccgtgccc aaagaagttt tggactcctg
     7441 gactggcgct ttcaacacgc gcaggcagcc tctcttcgct cacattcgta agcgagggga
     7501 gtcacgggtg taatgtgaaa agacaaaaat tgattatctt tcttttcttt agtgtctttt
     7561 aaaaaaaaa
//