Typing tool

Complete norovirus genomes

KP784691  GII.4 Farmington Hills
 GII.P4 New Orleans

Length: 7,570 | 3 CDS

ORF1: 5..5104
ORF2: 5085..6707
ORF3: 6707..7513
LOCUS       KP784691                7570 bp    RNA     linear   VRL 22-NOV-2016
DEFINITION  Norovirus GII/Hu/ZAF/2009/GII.P4_GII.4/Johannesburg/4175, complete
            genome.
ACCESSION   KP784691
VERSION     KP784691.1
KEYWORDS    .
SOURCE      Norovirus GII/Hu/ZAF/2009/GII.P4_GII.4/Johannesburg/4175
  ORGANISM  Norovirus GII/Hu/ZAF/2009/GII.P4_GII.4/Johannesburg/4175
            Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes;
            Picornavirales; Caliciviridae; Norovirus.
REFERENCE   1  (bases 1 to 7570)
  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  JOURNAL   Unpublished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 7570)
  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..7570
                     /organism="Norovirus
                     GII/Hu/ZAF/2009/GII.P4_GII.4/Johannesburg/4175"
                     /mol_type="genomic RNA"
                     /isolate="GII/Hu/ZAF/2009/GII.P4_GII.4/Johannesburg/4175"
                     /host="Homo sapiens"
                     /db_xref="taxon:1777882"
                     /country="South Africa"
                     /collection_date="2009"
                     /note="genotype:
                     GII.P4_New_Orleans_2009/GII.4_Hunter_2004"
     5'UTR           1..4
     gene            5..5104
                     /gene="POL"
     CDS             5..5104
                     /gene="POL"
                     /codon_start=1
                     /product="polyprotein"
                     /protein_id="ALX87341.1"
                     /translation="MKMASNDASAAAVANSNNDTAKSSSDGVLSSMAVTFKRALGARP
                     KQPPPREKPQRPPRPPTPELVKNIPPPPPNGEDEIVVSYSVRDGVSGLPDLSTVRQPE
                     ESNTAFSVPPLNQRENRDAKEPLTGTILEMWDGEIYHYGLYVERGLVLGVHKPPAAIS
                     LARVELTPLSLYWRPVYTPQYLISPDSLKKLHGETFPYTAFDNNCYAFCCWVLDLNDS
                     WLSRRMIQRTTGFFRPYQDWNKKPLPTMDDSKLKKVANIFLCALSSLFTRPIKDIIGK
                     IRPLNILNILASCDWTFAGIVESLILLAELFGVFWTPPDVSAMIAPLLGDYELQGPED
                     LAVELVPVVMGGIGLVLGFTKEKIGKMLSSAASTLRACKDLGAYGLEILKLIMKWFFP
                     KKEEANELAIVRSIEDAVLDLEAIENNHMTTLLKDKDSLATYMRTLDLEEEKARKLST
                     KSASPDIVGTINALLARIAAARSLVHRAKEELSSRPRPVVLMISGRPGIGKTHLAREV
                     AKRIAASLTGDQRVGLIPRNGVDHWDAYKGERVVLWDDYGMSNPIHDALRLQELADTC
                     PLTLNCDRIENKGKVFDSDVIIITTNLANPAPLDYVNFEACSRRIDFLVYAEAPEVEK
                     AKRDFPGQPDMWKNAFSSDFSHIKLALAPQGGFDKNGNTPHGKGVMKTLTTGSLIARA
                     SGLLHERLDEFELQGPALTTFNFDRNKVLAFRQLAAENKYGLMDTMRVGKQLKDVRTM
                     PELKQALKNVSIKKCQIVYSGCTYILESDGKGNVKVDRIQSASVQTNNELAGALHHLR
                     CARIRYYVKCVQEALYSIIQIAGAAFVTARIVKRMNIQDLWSKPQVENTEETTSKDGC
                     PKPKDDEEFVISSDDIKTEGKKGKNKTGRGKKHTAFSSKGLSDEEYDEYKRIREERNG
                     KYSIEEYLQDRDKYYEEVAIARATEEDFCEEEEAKIRQRIFRPTRKQRKEERASLGLV
                     TGSEIRKRNPDDFKPKGKLWADDDRSVDYNEKLSFEAPPSIWSRIVNFGSGWGFWVSP
                     SLFITSTHVIPQGAKEFFGVPIKQIQVHKSGEFCRLRFPKPIRTDVTGMILEEGAPEG
                     TVVTLLIKRSTGELMPLAARMGTHATMKIQGRTVGGQMGMLLTGSNAKSMDLGTTPGD
                     CGCPYIYKRGNDYVVIGVHTAAARGGNTVICATQGSEGEATLEGGDNKGTYCGAPILG
                     PGSAPTLSTKTKFWRSSTAPLPPGTYEPAYLGGKDPRVKGGPSLQQVMREQLKPFTEP
                     RGKPPKPSVLEAAKKTIINVLEQTIDPPEKWSFAQACASLDKTTSSGHPHHMRKNDCW
                     NGESFTGKLADQASKANLMFEEGKSMTPVYTAALKDELVKTDKIYGKIKKRLLWGSDL
                     ATMIRCARAFGGLMDELKAHCVTLPIRVGMNMNEDGPIIFERHSRYTYHYDADYSRWD
                     STQQRAVLAAALEIMVKFSPEPHLAQVVAEDLLSPSVVDVGDFTISINEGLPSGVPCT
                     SQWNSIAHWLLTLCALSEVTNLSPDTIQANSLFSFYGDDEIVSTDIKLDPEKLTTKLR
                     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="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="ALX87342.1"
                     /translation="MKMASNDATPSDGSTANLVPEVNNEVMALEPVVGAAIAAPVAGQ
                     QNVIDPWIRNNFVQAPGGEFTVSPRNAPGEILWSAPLGPDLNPYLSHLARMYNGYAGG
                     FEVQVILAGNAFTAGKIIFAAVPPNFPTEGLSPSQVTMFPHIIVDVRQLEPVLIPLPD
                     VRNNFYHYNQSNDPTIKLIAMLYTPLRANNAGDDVFTVSCRVLTRPSPDFDFIFLVPP
                     TVESRTKPFSVPILTVEEMTNSRFPIPLEKLFTGPSSAFVVQPQNGRCTTDGVLLGTT
                     QLSPVNICTFRGDVTHIAGTHNYTMNLASQNWNNYDPTEEIPAPLGTPDFVGKIQGVL
                     TQTTRGDGSTRGHKATVSTGDAHFTPKLGSVMFSTDTNNDFETGQNTRFTPVGVVQDG
                     STTHQNEPQQWVLPSYLGRDSHNVHLAPAVAPSFPGEQLLFFRSTMPGCSGYPNMNMD
                     CLLPQEWVQHFYQEAAPAQSDVALLRFVNPDTGRVLFECKLHKSGYVTVAHTGQHDLV
                     IPPNGYFRFDSWVNQFYTLAPMGNGTGRRRAL"
     gene            6705..7513
                     /gene="VP2"
     CDS             6707..7513
                     /gene="VP2"
                     /note="minor capsid protein"
                     /codon_start=1
                     /product="capsid protein VP2"
                     /protein_id="ALX87343.1"
                     /translation="MAGAFFAGLASDVLGSGLGSLINAGAGAINQKIDFENNRKLQQA
                     SFQFSSNLQQASFQHDKEMLQAQIEATKKLQQEMMKVKQAMLLEGGFSETDAARGAIN
                     APMTKALDWSGTRYWAPDARTTTYNAGRFSTPQPSGALPGRTNPRATVPARGSSSIPS
                     NTSTATSVYSNQTASTRLGSTAGSGTSVSSLPSTARTRSWVEDQNRNLSPFMRGAHNI
                     SFVTPPSSRSSSQGTVSTVPKEVLDSWTGAFNTRRQPLFAHIRKRGESRV"
     3'UTR           7513..7570
ORIGIN      
        1 gtgaatgaag atggcctcta acgacgcttc cgctgccgct gttgctaaca gcaacaacga
       61 caccgcaaaa tcttcaagtg acggagtgct ttctagcatg gctgtcactt ttaaacgagc
      121 cctcggggcg cggcctaaac agcctccccc gagggaaaaa ccacaaagac ccccacgacc
      181 acctactcca gaactggtta aaaatattcc ccctcccccg cccaacggag aggatgaaat
      241 agtggtttct tatagtgtca gagatggtgt ttccggtttg cctgatcttt ccaccgtcag
      301 acaaccggaa gaatccaaca cggccttcag tgtccctcca ctcaatcaga gggagaatag
      361 agatgcaaag gagccactta ctggaacaat tctggaaatg tgggatgggg aaatctacca
      421 ttatggcctg tatgtggagc gaggtcttgt actaggtgtg cacaaaccac cagccgccat
      481 cagcctcgct agggttgagc taacaccact ctccttgtac tggagacctg tgtacacccc
      541 tcagtacctc atctctccag actctctcaa gaaattacac ggagaaacgt tcccctacac
      601 agcctttgac aacaactgtt atgccttttg ttgctgggtc ctggatctaa atgactcgtg
      661 gctgagcagg aggatgatcc agagaacaac tggtttcttc aggccctacc aagactggaa
      721 taagaaaccc cttcccacta tggatgactc caaattaaag aaggtagcta atatattctt
      781 gtgtgctctg tcctcgctgt tcaccagacc cataaaagat ataataggga agataaggcc
      841 tcttaacatc ctcaacatct tagcctcatg tgattggact tttgcaggca tagtggagtc
      901 cctgatactc ttggcagaac tctttggagt tttctggaca cccccagatg tgtctgcgat
      961 gattgccccc ttactcggtg actacgagct acaaggacct gaggaccttg cagtggagct
     1021 cgtccccgtg gtgatggggg gaattggttt ggtgctagga ttcaccaaag agaagattgg
     1081 aaaaatgttg tcatctgctg cgtccacctt gagagcttgt aaagatcttg gtgcatatgg
     1141 gctagagatc ctaaagttga tcatgaagtg gttcttcccg aagaaggagg aagcaaatga
     1201 gctggctata gtgaggtcta ttgaggatgc agtcctggat ctcgaggcaa ttgaaaacaa
     1261 ccatatgacc accttgctca aagacaaaga cagtctggca acctacatga gaacacttga
     1321 ccttgaggag gagaaagcca ggaaactttc aaccaagtct gcctcacctg acatcgtggg
     1381 cacaatcaac gccctcctgg cgagaatcgc tgccgcacgt tctctggtgc accgagcgaa
     1441 ggaggagctt tccagcagac caagacctgt ggtgttgatg atatcaggca gaccaggaat
     1501 agggaagacc cacctcgcta gggaagtggc taagagaatc gcagcctccc ttacaggaga
     1561 ccagcgtgtg ggcctcatcc cacgcaatgg cgtcgaccat tgggatgcgt acaaggggga
     1621 gagggtcgtc ctatgggacg attatggaat gagtaaccct attcacgatg ccctcaggct
     1681 gcaagaactc gctgacactt gccccctcac tctaaactgt gacaggatag agaataaagg
     1741 aaaggtcttt gacagcgatg tcatcatcat caccactaat ctggccaacc cagcaccact
     1801 ggactatgtc aactttgaag catgttcgag gcgcatcgac ttcctcgtgt atgcagaagc
     1861 ccctgaagtc gaaaaggcga agcgtgactt cccaggccag cctgacatgt ggaagaacgc
     1921 cttcagttct gatttctcac acataaaact agcactggcc ccacagggtg gtttcgacaa
     1981 gaacgggaac accccacacg gaaagggcgt catgaagact ctcaccactg gctcccttat
     2041 cgcccgggca tcagggctac tccatgagag gttagatgaa tttgaactac agggcccagc
     2101 tctcaccacc ttcaatttcg atcgcaataa agtgcttgcc tttagacaac ttgctgctga
     2161 aaataaatat ggattgatgg acacaatgag agttgggaaa cagctcaagg atgttagaac
     2221 catgccagaa ctcaaacaag cactcaagaa tgtctcaatc aagaagtgcc aaatagtgta
     2281 tagtggttgc acctacatac ttgagtctga cggcaagggc aatgtgaaag ttgacagaat
     2341 ccaaagcgcc tccgtgcaaa ccaacaatga gctggctggc gccctgcacc atttgaggtg
     2401 cgccagaatc agatactatg tcaagtgtgt ccaggaggcc ctgtattcca tcattcaaat
     2461 tgctggggct gcatttgtca ccgcgcgcat cgtcaagcgc atgaacatac aggacctatg
     2521 gtccaagcca caagtggaaa acacagagga gaccaccagc aaggacgggt gcccaaaacc
     2581 caaggatgat gaggagtttg tcatttcatc cgacgacatc aaaactgagg gcaagaaagg
     2641 gaagaacaag actggccgtg gcaagaagca cacagccttt tcaagcaaag gcctcagtga
     2701 tgaagagtac gatgagtaca agaggattag agaagaaagg aatggcaagt actccataga
     2761 agagtacctt caggacaggg acaaatacta tgaggaggtg gccattgcca gggcgactga
     2821 ggaagacttc tgtgaagagg aggaggccaa gatccggcaa aggatcttta ggccaacaag
     2881 gaaacaacgc aaggaggaaa gagcttctct cggtctggtc acaggctctg aaattaggaa
     2941 aagaaaccca gatgacttca aacccaaggg taaattgtgg gctgacgatg acagaagtgt
     3001 ggactacaat gagaaactca gttttgaggc cccaccaagc atctggtcga gaatagtcaa
     3061 ctttggttca ggctggggat tctgggtctc ccccagtctg ttcataacat caacccatgt
     3121 cataccccag ggtgcaaagg agttctttgg agtccccatc aaacaaatac aggtacacaa
     3181 gtcaggcgag ttctgtcgct tgagattccc aaaaccaatc aggactgatg tgacgggcat
     3241 gatcttagaa gaaggcgcac ctgagggcac cgtggtcaca ctactcatca aaaggtccac
     3301 cggggaactc atgcccctag cagctaggat ggggacccat gcaaccatga agatccaagg
     3361 gcgcactgtc ggaggccaga tgggcatgct tctgacagga tccaatgcca agagcatgga
     3421 cctgggtact acaccaggtg attgtggctg tccctatatc tacaagagag gcaatgacta
     3481 tgtggtcatt ggagtccaca cggctgccgc acgtggggga aacactgtca tatgtgccac
     3541 ccaggggagt gaaggggagg ccacacttga aggtggtgac aacaagggga catactgcgg
     3601 tgcaccaatc ctaggaccag ggagtgcccc aacccttagc accaagacca aattctggag
     3661 atcgtccaca gcaccgctcc cacctggcac ctatgaacca gcctatcttg gtggcaagga
     3721 ccctagagtc aagggtggcc cttcactgca gcaagtcatg agggaacagt tgaaaccatt
     3781 cacagagcca aggggcaaac caccaaagcc aagtgtatta gaggctgcca agaagaccat
     3841 catcaatgtc cttgagcaaa caattgatcc acctgagaaa tggtcattcg cacaagcttg
     3901 cgcgtccctt gacaagacca cttccagtgg tcatccgcac cacatgcgga aaaacgactg
     3961 ctggaacggg gagtccttca caggcaagct ggcagaccag gcttccaagg ccaacctgat
     4021 gtttgaagaa gggaagagca tgaccccagt ctacacagct gcgctcaagg atgagttagt
     4081 taaaactgac aaaatttatg gtaagatcaa gaagaggctt ctctggggtt cggacttggc
     4141 gaccatgatc cggtgtgctc gagcattcgg aggcctaatg gatgaactca aagcacactg
     4201 tgtcacactt cccattagag ttggtatgaa tatgaatgag gatggcccca tcatcttcga
     4261 gaggcattcc aggtacacat atcactatga tgctgattac tctcgatggg attcaacaca
     4321 acagagagcc gtgctggcag cagctctaga aatcatggtt aaattctccc cagaaccaca
     4381 tttggctcag gtagtcgcgg aagaccttct ttctcctagc gtggtggacg tgggcgactt
     4441 cacaatatca atcaacgagg gccttccctc tggggtgccc tgcacctccc aatggaattc
     4501 catcgcccac tggcttctca ctctctgcgc gctctctgaa gtcacaaact tgtcccctga
     4561 taccatacag gctaattccc tcttctcttt ttatggtgat gatgaaattg ttagcacaga
     4621 cataaaattg gacccagaga aattaactac aaagctcagg gaatatgggt taaaaccaac
     4681 ccgccctgac aaaactgaag gaccccttgt catttctgaa gacttgaatg gcctaacttt
     4741 cctgcggaga actgtgaccc gcgacccagc tggttggttt ggaaaactgg agcagagctc
     4801 aatactcagg caaatgtact ggactagggg ccccaaccat ggagacccat ctgaaacaat
     4861 gattccacac tcccaaagac ccatacaatt gatgtccctg ctgggggagg ctgctctcca
     4921 cggcccagca ttttacagca aaatcagcaa attggtcatt gcagagctaa aagaaggtgg
     4981 catggatttt tacgtgccca gacaagagcc aatgttcaga tggatgagat tctcagatct
     5041 gagcacgtgg gagggcgatc gcaatctggc tcccagtttt gtgaatgaag atggcgtcga
     5101 atgacgccac cccatctgat gggtccacag ccaacctcgt cccagaggtc aacaatgagg
     5161 ttatggcttt ggagcccgtt gttggtgccg ctattgcggc acctgtagcg ggccaacaaa
     5221 atgtaattga cccctggatt agaaacaatt ttgtacaagc ccctggtggt gagtttacag
     5281 tatcccctag aaacgctcca ggtgaaatac tatggagcgc gcccttgggc cctgatttga
     5341 acccctacct ttcccattta gccaggatgt acaatggcta cgcaggtggt tttgaagtgc
     5401 aggtaatcct cgcggggaat gcgttcaccg ccggaaaaat tatatttgca gcagtcccac
     5461 caaacttccc aactgaaggc ttgagcccca gccaggtcac tatgtttccc catataatag
     5521 tagatgttag gcaattggaa cctgtgctga tccccttacc tgatgttagg aacaatttct
     5581 atcattacaa tcaatcaaat gaccccacca tcaaattgat agcaatgctg tacacaccac
     5641 ttagggcaaa caatgctgga gatgatgtct ttacagtctc ttgtcgagtc ctcacgagac
     5701 catcccccga ttttgatttc atatttctgg tgccacccac agttgagtca agaactaaac
     5761 cattctctgt cccaatttta actgttgaag agatgaccaa ttcaagattc cccatccctt
     5821 tggaaaagtt gtttacgggt cccagcagtg cctttgttgt tcaaccacaa aatggcagat
     5881 gcacgactga tggcgtgctc ttaggtacta cccaactgtc tcctgtcaac atctgcacct
     5941 tcagagggga tgtcacccac attgcaggta cccacaatta cacaatgaat ctggcctccc
     6001 aaaattggaa caattatgac ccaacagaag aaatcccagc tcctctggga actccagatt
     6061 tcgtgggaaa gatccaaggc gtactcaccc aaaccacaag gggggatggc tcgacccgcg
     6121 gtcacaaggc tacagtgagc actggggacg cccacttcac cccaaagctg ggcagtgtta
     6181 tgttctccac tgatacaaac aatgactttg aaactggcca aaacacgaga ttcaccccag
     6241 tcggtgtcgt ccaggacggt agcaccaccc accaaaatga accccaacaa tgggttctcc
     6301 caagctactt aggtagagac agtcacaatg tgcatttagc ccctgccgtg gccccctctt
     6361 tcccgggtga gcaacttctt ttcttcaggt ccactatgcc cggatgcagc gggtatccca
     6421 acatgaacat ggattgccta ctcccccaag agtgggtgca gcacttctat caagaggcag
     6481 ccccagcgca atctgatgtg gctctactga gatttgtgaa tccagacaca ggtagggttc
     6541 tgtttgagtg caagcttcat aaatcaggtt atgtcacagt ggcccacact ggccaacatg
     6601 atttagttat tccccccaat ggttatttta gatttgattc ttgggtcaac caattctaca
     6661 ctcttgcccc catgggaaat ggaacggggc gcagacgagc attataatgg ctggagcttt
     6721 ctttgctgga ttggcatctg atgtccttgg ctctggactt ggttccctaa tcaatgctgg
     6781 ggctggggcc atcaaccaaa agattgactt tgaaaataat agaaaattgc aacaagcttc
     6841 cttccaattt agcagcaacc tacaacaggc ttcttttcag catgataaag agatgctcca
     6901 agcacaaatt gaggccacca aaaagttgca acaggagatg atgaaagtta aacaggcaat
     6961 gctcctagag ggcgggttct ctgagacaga tgcagcccgt ggggcaatca acgcccccat
     7021 gacaaaggct ttggactgga gcggaacaag gtactgggct cctgatgcta ggactacaac
     7081 atacaatgca ggccgctttt ccacccccca accctcaggg gcactgccag gaagaactaa
     7141 tcccagggct acagtccccg ctcgtggctc ctccagtata ccttctaaca cttctactgc
     7201 tacttctgtg tactcaaatc aaactgcttc aacgagactt ggttctacag ctggttctgg
     7261 aactagtgtc tcgagcctcc cgtcaactgc aagaactagg agctgggttg aggatcaaaa
     7321 ccggaatttg tcacctttca tgaggggggc ccacaacata tcgttcgtca ccccaccatc
     7381 tagcaggtcc tctagccaag gcacagtctc aaccgtgcct aaagaagttt tggactcctg
     7441 gactggcgct ttcaacacgc gcaggcagcc tctcttcgct cacatacgta agcgagggga
     7501 gtcacgggtg taatgtgaaa agacaaaatt gattatcttt cttttcttta gtgtctttga
     7561 aaaaaaaaaa
//