Typing tool

Complete norovirus genomes

KP784695  GII.4 New Orleans
 GII.P4 New Orleans

Length: 7,570 | 3 CDS

ORF1: 5..5104
ORF2: 5085..6707
ORF3: 6707..7513
LOCUS       KP784695                7570 bp    RNA     linear   VRL 22-NOV-2016
DEFINITION  Norovirus GII/Hu/ZAF/2012/GII.P4_GII.4/Empangeni/9693, complete
            genome.
ACCESSION   KP784695
VERSION     KP784695.1
KEYWORDS    .
SOURCE      Norovirus GII/Hu/ZAF/2012/GII.P4_GII.4/Empangeni/9693
  ORGANISM  Norovirus GII/Hu/ZAF/2012/GII.P4_GII.4/Empangeni/9693
            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  JOURNAL   Unpublished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/2012/GII.P4_GII.4/Empangeni/9693"
                     /mol_type="genomic RNA"
                     /isolate="GII/Hu/ZAF/2012/GII.P4_GII.4/Empangeni/9693"
                     /host="Homo sapiens"
                     /db_xref="taxon:1777888"
                     /country="South Africa"
                     /collection_date="2012"
                     /note="genotype: GII.P4_GII.4_New_Orleans_2009"
     5'UTR           1..4
     gene            5..5104
                     /gene="POL"
     CDS             5..5104
                     /gene="POL"
                     /codon_start=1
                     /product="polyprotein"
                     /protein_id="ALX87353.1"
                     /translation="MKMASNDASAAAVANSNNDTAKSSSDGVLSSMAVTFKRALGARP
                     KQPPPREKPQRPPRPPTPELVKNTPPPPPNGEDEIVVSYSVKDGVSGLPDLSTVRQPE
                     ESNTAFSVPPLNQRENRDAKEPLTGTILEMWDGEIYHYGLYVERGLVLGVHKPPAAIS
                     LAKVELAPLSLYWRPVYTPQYLISPDTLKKLSGETFPYTAFDNNCYAFCCWVLDLNDS
                     WLSRRMIQRTTGFFRPYQDWNRKPLPTMDDSKIKKVANIFLCALSSLFTRPIKDIIGK
                     IRPLNILNILASCDWTFAGLVESLILLAELFGVFWTPPDVSAMIAPLLGDYELQGPED
                     LAVELVPVVMGGIGLVLGFTKEKIGKMLSSAASTLRACKDLGAYGLEILKLVMKRFFP
                     KKEEANELAIVRSIEDAVLDLEAIENNHMTTLLKDKDSLATYMRTLDLEEEKARKLST
                     KSASPDIVGTINALLARIAAARSLVHRAKEELSSRPRPVVLMISGRPGIGKTHLAREV
                     AKRIAASLTGDQRVGLIPRNGVDHWDAYKGERVVLWDDYGMSNPIHDALRLQELADTC
                     PLTLNCDRIENKGKVFDSDVIIITTNLANPAPLDYVNFEACSRRIDFLVYAEAPEVEK
                     AKRDFPGQPDMWKNAFSSDFSHIKLALAPQGGFDKNGNTPHGKGVMKTLTTGSLIARA
                     SGLLHERLDEFELQGPALTTFNFDRNKVLAFRQLAAENKYGLMDTMRVGKQLKDVRTM
                     PELKQALKNVSIKKCQIVYSGCTYMLESDGKGNVKVDRIQSAAVQTNNELAGALHHLR
                     CARIRYYVKCVQEALYSIIQIAGAAFVTTRIAKRMNIQDLWSKPQVENTEETTSKDGC
                     PKPKDDEEFVISSDDIKTEGKKGKNKTGRGKKHTAFSSKGLSDEEYDEYKRIREERNG
                     KYSIEEYLQDRDKYYEEVAIARATEEDFCEEEEAKIRQRIFRPTRKQRKEERVSLGLV
                     TGSEIRKRNPDDFKPKGKLWADDDRSVDYNEKLSFEAPPSIWSRIVNFGSGWGFWVSP
                     SLFITSTHVIPQGAKEFFGVPIKQIQVHKSGEFCRLRFPKPIRTDVTGMILEEGAPEG
                     TVVTLLIKRSTGELMPLAARMGTHATMKIQGRTVGGQMGMLLTGSNAKSMDLGTTPGD
                     CGCPYIYKRGNDYVVIGVHTAAARGGNTVICATQGSEGEATLEGGDNKGTYCGAPILG
                     PGSAPTLSTKTKFWRSSTASLPPGTYEPAYLGGKDPRVKGGPSLQQVMREQLKPFTEP
                     RGKPPKPSVLEAAKKTIINVLEQTIDPPEKWSFAQACASLDKTTSSGHPHHMRKNDCW
                     NGESFTGKLADQASKANLMFEEGKNMTPVYTAALKDELVKTDKIYGKIKKRLLWGSDL
                     ATMIRCARAFGGLMDELKAHCVTLPIRVGMNMNEDGPIIFERHSRYTYHYDADYSRWD
                     STQQRAVLAAALEIMVKFSPEPHLAQVVAEDLLSPSVVDVGDFTISINEGLPSGVPCT
                     SQWNSIAHWLLTLCALSEVTNLSPDTIQANSLFSFYGDDEIVSTDIKLDPEKLTAKLR
                     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="ALX87354.1"
                     /translation="MKMASSDANPSDGSTANLVPEVNNEVMALEPVVGAAIAAPVAGQ
                     QNVIDPWIRNNFVQAPGGEFTVSPRNAPGEILWSAPLGPDLNPYLSHLARMYNGYAGG
                     FEVQVILAGNAFTAGKIIFAAVPPNFPTEGLSPSQVTMFPHIIVDVRQLEPVLIPLPD
                     VRNNFYHYNQSNDSTIKLIAMLYTPLRANNAGDDVFTVSCRVLTRPSPDFDFIFLVPP
                     TVESRTKPFSVPVLTVEEMTNSRFPIPLEKLFTGPSSAFVVQPQNGRCTTDGVLLGTT
                     QLSPVNICTFRGDVTHISGSRNYTMNLASQNWNSYDPTEEIPAPLGTPDFVGKIQGVL
                     TQTTRTDGSTRGHKATVYTGSADFSPKLGRVQFATDTDNDFVTNQNTKFTPVGVIQDG
                     NTTPRNEPQQWVLPSYSGRNTHNVHLAPAVAPTFPGEQLLFFRSTMPGCSGYPNMDLD
                     CLLPQEWVQYFYQEAAPAQSDVALLRFVNPDTGRVLFECKLHKSGYVTVAHTGQHDLV
                     IPPNGYFRFDSWVNQFYTLAPMGNGTGRRRAL"
     gene            6705..7513
                     /gene="VP2"
     CDS             6707..7513
                     /gene="VP2"
                     /note="minor capsid protein"
                     /codon_start=1
                     /product="capsid protein VP2"
                     /protein_id="ALX87355.1"
                     /translation="MAGAFFAGLASDVLGSGLGFLINAGAGAINQKVEYENNRKLQQA
                     SFQFSSNLQQASFQHDKEMLQAQIEATKKLQQEMMRVKQAMLLEGGFSETDAARGAIN
                     APMTKTLDWSGTRYWAPDARTTTYNAGRFSTPQPSGAPPGRANLRATVPARGSSSTSS
                     NSSIATSVYSNQTTSTRLGSTAGSGTNVSSLPSTARTRSWVEDQNRNLSPFMRGAHNI
                     SFVTPPSSRSSSQGTVSTVPKEVLDSWTGAFNTRRQPLFAHFRKRGESRV"
     3'UTR           7514..7570
ORIGIN      
        1 gtgaatgaag atggcctcta acgacgcttc cgctgccgct gttgctaaca gcaacaacga
       61 caccgcaaaa tcttcaagtg acggagtgct ttctagcatg gctgtcactt tcaaacgagc
      121 cctcggggcg cggcctaaac agcctccccc gagggaaaaa ccacaaagac ccccacgacc
      181 acccactcca gaactggtta aaaacacccc ccctccccca cccaacggag aggatgaaat
      241 agtggtttct tatagtgtca aagatggtgt ttccggtttg cctgacctct ccaccgtcag
      301 gcaaccggaa gaatccaaca cggccttcag tgtccctcca ctcaatcaga gggagaatag
      361 agatgctaag gagccactca ctggaacaat tctggaaatg tgggacgggg aaatctacca
      421 ttatggcctg tatgtggagc gaggtcttgt actaggtgtg cacaaaccgc cagctgccat
      481 cagcctcgct aaggttgagc tagcaccact ctccttgtac tggagacctg tgtacactcc
      541 tcagtacctc atctctccag acactctcaa gaaattgtcc ggagaaacgt tcccctacac
      601 agcctttgac aacaactgtt atgccttttg ttgctgggtc ctggacctaa atgactcgtg
      661 gctgagcagg agaatgatcc agagaacaac tggtttcttc aggccctacc aagactggaa
      721 taggaaaccc cttcccacta tggatgactc caaaataaag aaggtagcta acatatttct
      781 gtgtgctttg tcctcgctat tcactagacc cataaaagat ataataggga agataaggcc
      841 tcttaacatc ctcaacatct tagcctcatg tgattggacc tttgcgggct tagtggagtc
      901 cctaatactc ttggcagaac tctttggagt tttctggaca cccccagatg tgtctgcgat
      961 gattgccccc ttactcggtg actacgagct acaaggacct gaggaccttg cagtggagct
     1021 cgtccccgtg gtgatggggg gaattggttt ggtgttagga ttcaccaaag aaaagattgg
     1081 gaaaatgttg tcatccgctg cgtccacttt gagagcttgc aaagaccttg gtgcatatgg
     1141 gctagagatc ctaaagttag tcatgaagcg gttcttcccg aagaaggagg aggcaaatga
     1201 gctggctata gtgaggtcca tcgaggatgc agtcctggat ctcgaggcaa ttgaaaacaa
     1261 tcatatgacc accctgctta aagataaaga cagtctggca acctacatga gaacacttga
     1321 ccttgaagag gagaaagcca ggaaactctc aaccaagtct gcctcacccg acatcgtggg
     1381 cacaatcaat gccctcctgg cgagaatcgc tgccgcacgt tctctggtgc atcgagcgaa
     1441 ggaggagctt tccagcagac caagacctgt ggtattgatg atatcaggca ggccaggaat
     1501 agggaagacc cacctcgcta gggaagtggc taagagaatc gcagcctccc ttacaggaga
     1561 ccagcgtgtg ggcctcatcc cacgcaatgg cgtcgaccat tgggatgcgt acaaggggga
     1621 gagggtcgtc ctatgggacg attatggaat gagcaaccct attcacgatg ccctcaggct
     1681 gcaagaactc gctgacactt gccccctcac tctgaactgt gacaggattg aaaataaagg
     1741 aaaggtcttt gacagcgatg tcatcattat caccactaat ctggccaacc cagcaccact
     1801 ggactatgtc aactttgaag catgctcgag gcgcattgac ttcctcgtgt atgcagaagc
     1861 ccctgaagtc gaaaaggcga agcgtgactt cccaggccag cctgacatgt ggaagaacgc
     1921 tttcagttct gatttctcac acataaaact agcactggcc ccacagggtg gtttcgacaa
     1981 gaacgggaac accccacacg gaaagggcgt catgaagact ctcaccactg gctcccttat
     2041 tgcccgggca tcagggctac tccatgagag gttagatgag tttgaactgc agggcccagc
     2101 tctcaccacc ttcaatttcg atcgtaataa agtgcttgcc tttagacagc ttgctgctga
     2161 aaataaatat ggattgatgg acacaatgag ggttgggaaa cagctcaagg atgtcagaac
     2221 catgccagaa ctcaaacaag cactcaagaa tgtctcaatc aagaagtgtc aaatagtgta
     2281 tagtggttgc acctacatgc ttgagtctga tggcaagggc aatgtgaaag ttgacagaat
     2341 ccaaagtgcc gccgtgcaga ccaacaatga gctggctggt gccctgcacc acttgaggtg
     2401 cgccagaatc agatactatg tcaaatgtgt ccaggaagcc ctgtactcca tcatccaaat
     2461 cgctggggct gcatttgtca ccacgcgcat tgccaagcgc atgaacatac aagacctatg
     2521 gtccaagcca caagtggaaa acacagagga gactaccagc aaggacgggt gcccaaaacc
     2581 taaggatgat gaggagtttg tcatttcatc cgacgacatc aaaactgagg gcaagaaggg
     2641 gaagaacaag actggtcgtg gcaagaagca cacagcattt tcaagcaaag gcctcagtga
     2701 tgaagagtac gatgaataca agaggattag agaagaaagg aatggcaagt actctataga
     2761 agagtacctt caggacaggg acaaatacta tgaggaggtg gccattgcta gggcgactga
     2821 ggaagacttc tgtgaagagg aggaggccaa gatccggcaa aggatcttta ggccaacaag
     2881 gaaacaacgc aaggaggaaa gagtctctct cggtttggtc acaggctctg aaattaggaa
     2941 aagaaaccca gatgacttca aacccaaggg gaaattgtgg gctgacgatg acaggagtgt
     3001 ggactacaat gaaaaactca gctttgaggc cccgccaagc atttggtcga gaatagtcaa
     3061 ctttggttca ggctggggat tctgggtctc ccccagtctg ttcataacat caacccatgt
     3121 cataccccag ggcgcaaagg agttctttgg agtccccatc aaacaaatac aggtgcataa
     3181 gtcaggcgag ttctgtcgct tgagattccc taaaccaatc aggactgatg tgacgggcat
     3241 gatcttagaa gaaggcgcac ctgagggcac tgtggtcacg ctactcatca aaaggtccac
     3301 tggggaactc atgcccctag cagctaggat ggggacccat gcgaccatga agatccaagg
     3361 gcgcaccgtt gggggccaga tgggcatgct tctgacagga tccaacgcca agagcatgga
     3421 cctgggtact acaccaggtg attgtggctg cccctatatc tacaagagag gtaatgacta
     3481 tgtggtcatt ggagtccaca cggctgccgc acgtggggga aacactgtca tatgtgccac
     3541 ccaggggagt gagggagagg ctacacttga gggtggtgac aacaagggga catactgtgg
     3601 tgcaccaatc ctaggcccag ggagtgcccc aacacttagc accaagacca aattctggag
     3661 atcgtccaca gcatcactcc cacctggcac ctatgaacca gcttatcttg gtggaaagga
     3721 ccctagagtc aagggtggcc cttcactgca gcaagtcatg agggaacagc tgaagccatt
     3781 cacagagccc aggggcaagc caccaaaacc aagtgtgtta gaagctgcca agaagaccat
     3841 cattaatgtc cttgagcaaa caattgatcc acctgaaaaa tggtcgttcg cacaagcttg
     3901 cgcgtccctt gacaagacca cttccagtgg tcatccgcac cacatgcgga aaaacgactg
     3961 ctggaacggg gagtccttca caggcaagct agcagaccag gcttccaagg ccaacctgat
     4021 gtttgaagaa gggaagaaca tgaccccagt ctacacagct gcgctcaagg atgagttagt
     4081 taaaactgac aaaatttatg gtaagatcaa gaagaggctt ctctggggct cggacttggc
     4141 gaccatgatc cggtgtgctc gagcgttcgg aggcctaatg gatgaactca aagcgcactg
     4201 tgtcacactt cccattagag ttggcatgaa tatgaatgag gatggtccca tcatcttcga
     4261 gaggcattcc aggtacacgt accactatga tgctgattac tctcgatggg attcaacaca
     4321 acagagagcc gtgttggcag cagctctaga aatcatggtt aaattctccc cagaaccaca
     4381 tttggctcag gtagtcgcag aagaccttct ttctcctagc gtggtggacg tgggcgactt
     4441 cacaatatca atcaatgagg gtcttccctc tggggtgccc tgcacctccc aatggaactc
     4501 catcgcccac tggctcctca ctctctgtgc gctctctgaa gtcacaaacc tgtctcctga
     4561 taccatacag gccaattccc tcttctcttt ctatggtgat gatgaaattg ttagcacaga
     4621 cataaaattg gacccagaga aattgacagc aaagctcaga gagtatgggt taaaaccaac
     4681 ccgccctgac aaaactgaag gaccccttgt catctctgaa gacctgaatg gcctaacttt
     4741 cctgcggagg actgtgaccc gcgacccagc tggttggttt ggaaaactgg agcagagttc
     4801 aatactcagg caaatgtact ggactagggg tcccaaccat ggagacccat ctgaaacaat
     4861 gattccacac tcccaaagac ccatacaatt gatgtcccta ttgggggagg ccgctctcca
     4921 cggcccagca ttttacagca aaatcagtaa attggtcatt gcagagctaa aagaaggtgg
     4981 tatggatttt tacgtgccca gacaagagcc aatgttcaga tggatgagat tctcagatct
     5041 gagcacgtgg gagggcgatc gcaatctggc tcccagtttt gtgaatgaag atggcgtcga
     5101 gtgacgccaa cccatctgat gggtccacag ccaacctcgt cccagaggtc aacaatgagg
     5161 ttatggcttt ggagcccgtg gttggtgccg ctattgcggc acctgtagcg ggccagcaaa
     5221 atgtaattga cccctggatt agaaacaatt ttgtacaagc ccctggtgga gagtttacag
     5281 tatcccctag aaacgctcca ggtgaaatac tatggagcgc gcccttaggc cctgatctga
     5341 acccctacct ttcccatttg gccagaatgt acaatggtta tgcaggtggt tttgaagtgc
     5401 aggtaatcct cgcggggaat gcgttcaccg ccgggaaaat catatttgca gcagtcccac
     5461 caaatttccc aactgaaggt ttgagcccca gccaagtcac tatgttcccc cacataatag
     5521 tagatgttag gcaattggaa cctgtgttga tccccttacc cgatgttagg aataatttct
     5581 accattataa tcagtcaaat gactccacca tcaaattgat agcaatgttg tacacaccac
     5641 ttagggctaa caatgccggg gacgatgtct tcacagtctc ttgtcgagtt ctcacgagac
     5701 catcccccga ttttgatttc atatttttgg tgccacccac agttgaatca agaactaaac
     5761 cattttctgt cccagtttta actgttgagg agatgaccaa ttcaaggttc cccattcctt
     5821 tggaaaagtt gttcacgggt cccagtagtg cctttgttgt tcaaccacaa aatggcaggt
     5881 gcacgactga tggcgtgctc ctaggtacta cccaactgtc tcctgtcaac atctgcacct
     5941 tcagagggga tgtcacccac atttcaggca gtcgtaacta cacaatgaat ttggcctccc
     6001 aaaattggaa cagttacgat ccaacagaag aaatcccggc ccccctagga actccagatt
     6061 tcgtggggaa gatccaaggt gtgctcaccc agaccacaag gacagatggc tcgacccgcg
     6121 gccacaaagc tacagtgtac actgggagcg ccgacttttc tccaaaactg ggtagggttc
     6181 aatttgctac tgacacagac aatgattttg taactaatca aaacacaaag ttcaccccag
     6241 tcggtgttat ccaggatggt aatactaccc cccgaaatga accccaacaa tgggtgctcc
     6301 caagttactc aggtagaaac actcataatg tgcacctggc ccccgctgta gcccccactt
     6361 tcccgggcga gcagctcctc ttcttcagat ctaccatgcc cggatgcagc gggtacccca
     6421 acatggattt ggactgtctg ctcccccagg aatgggtgca gtatttctac caggaggcag
     6481 ccccagcaca atctgatgtg gcactattaa gatttgtgaa tccagacaca ggtagggttt
     6541 tgtttgagtg taagcttcat aaatcaggct atgttacagt ggctcacact ggccaacatg
     6601 atttagttat cccccccaat ggttatttta gatttgattc ctgggtcaac cagttctaca
     6661 cacttgcccc catgggaaat gggacggggc gtagacgtgc attataatgg ctggagcctt
     6721 ctttgctgga ttggcatctg acgtccttgg ctctggactt ggtttcctaa tcaatgctgg
     6781 ggctggggcc atcaaccaaa aagttgaata tgaaaacaac agaaaattgc aacaagcttc
     6841 cttccaattt agtagcaatc tacaacaggc ttcctttcaa catgacaagg agatgctcca
     6901 agcacaaatt gaggccacca aaaagttgca acaggaaatg atgagagtta agcaagcaat
     6961 gctcctagag ggtgggttct ctgagacaga tgcagcccgt ggggcaatca acgcccccat
     7021 gacaaaaact ttggactgga gcggaacaag gtactgggct cccgatgcta ggactacaac
     7081 atacaatgca ggccgctttt ccacccctca accctcgggg gcaccaccag gaagagctaa
     7141 tcttagggct actgtccccg cccggggttc ctccagcacg tcttctaact cttctattgc
     7201 cacttctgtg tattcaaatc aaaccacctc aacgagactt ggttctacag ctggttctgg
     7261 caccaacgtc tcgagcctcc cgtcaactgc aaggactagg agctgggttg aggatcaaaa
     7321 taggaatttg tcacctttca tgaggggggc ccacaacatc tcgtttgtca ccccaccatc
     7381 tagcagatcc tctagccaag gcacagtctc aaccgtgccc aaagaagttt tggactcctg
     7441 gactggcgct tttaacacgc gcaggcagcc tctcttcgct cactttcgca aacgagggga
     7501 gtcacgggtg taatgtgaaa agacaaaatt gatcactttt ctcttctttt gtgtctttta
     7561 aaaaaaaaaa
//