Typing tool

Complete norovirus genomes

KP784696  GII.4 Sydney
 GII.P31

Length: 7,570 | 3 CDS

ORF1: 5..5104
ORF2: 5085..6707
ORF3: 6707..7513
LOCUS       KP784696                7570 bp    RNA     linear   VRL 22-NOV-2016
DEFINITION  Norovirus GII/Hu/ZAF/2012/GII.P4_GII.4/CapeTown/9772, complete
            genome.
ACCESSION   KP784696
VERSION     KP784696.1
KEYWORDS    .
SOURCE      Norovirus GII/Hu/ZAF/2012/GII.P4_GII.4/CapeTown/9772
  ORGANISM  Norovirus GII/Hu/ZAF/2012/GII.P4_GII.4/CapeTown/9772
            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  JOURNAL   Unpublished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/CapeTown/9772"
                     /mol_type="genomic RNA"
                     /isolate="GII/Hu/ZAF/2012/GII.P4_GII.4/CapeTown/9772"
                     /host="Homo sapiens"
                     /db_xref="taxon:1777886"
                     /country="South Africa"
                     /collection_date="2012"
                     /note="genotype: GII.Pe/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="ALX87356.1"
                     /translation="MKMASNDASAAAVANSNNDIAKSSSDGVFSNMAVTFKRALGARP
                     KQPPPKEIPPRPPRPPTPELVKKILPPPPNGEDELVVSYSARDGVSGLPELTTVRQPE
                     ETNTAFSVPPLKQRESRDAKEPLTGTIIEMWDGEIYHYGLYVERGLILGVHKPPAAIS
                     LAKVELTPLSLFWRPVYTPQYLISPDTLRRLHGESFPYTAFDNNCYAFCCWVLDLNDS
                     WLSRRMIQRTTGFFRPYQDWNRKPLPTMDDSKLKKVANIFLCTLSSLFTRPIKDIVGK
                     LKPLNILNILATCDWTFAGIVESLILLAELFGVFWTPPDVSAMIAPLLGDYELQGPED
                     LAVELVPIVMGGIGLVPGFTKEKIGKMLSSAASTLRACKDLGAYGLEILKLVMKWFFP
                     KKEEANELAMVRSIEDAVLDLEAIENNHMTTLLKDKDSLATYMRTLDLEEEKARKLST
                     KSASPDIVGTINSLLARIAAARSLVHRAKEELSSRPRPVVVMISGKPGIGKTHLAREL
                     AKKIAASLTGDQRVGLIPRNGVDHWDAYKGERVVLWDDYGMSNPIHDALRLQELADTC
                     PLTLNCDRIENKGKVFDSDAIIITTNLANPAPLDYVNFEACSRRIDFLVYAEAPEVEK
                     AERDFPGQPDMWKNAFSPDFSHIKLSLAPQGGFDKNGNTPHGKGVMKTLTTGSLIARA
                     SGLLHERLDEYELQGPALTTFNFDRNKILAFRQLAAENKYGLMDTMRVGKQLKDVKTM
                     SDLKQALKNIAIKKCQIVYNGGTYTLEADGKGSVKVDKVQSATVQTNNELAGALHHLR
                     CARIRYYVKCVQEALYSIIQIAGAAFVTTRIAKRMNIQNLWSKPQVEDTEEVANKEGL
                     LKPKDDEEFVVSSDDIKTEGKKGKNKSGRGKKHTAFSSKGLSDEEYDEYKRIREERNG
                     KYSIEEYLQDRDRYYEEVAIARATEEDFCEEEEAKIRQRIFRPTRKQRKEERASLGLV
                     TGSEIRKRNPEDFKPKGKLWADDDRSVDYNEKLNFEAPPSIWSRIVNFGSGWGFWVSP
                     SLFITSTHVIPQGAKEFFGVPIKQIQIHKSGEFCRLRFPKPIRTDVTGMILEEGAPEG
                     TVATLLIKRPTGELMPLAARMGTHATMRIQGRTVGGQMGMLLTGSNAKSMDLGTTPGD
                     CGCPYIYKRGNDYVVIGVHTAAARGGNTVICATQGSEGEATLEGGDSKGTYCGAPILG
                     PGSAPKLSAKTKFWRSSTTPLPPGTYEPAYLGGKDPRVKGGPSLQQVMRDQLKPFTEP
                     RGKPPRPNVLEAAKKTIINVLEQTIDPPQKWSFAQACASLDKTTSSGHPHHMRKNDCW
                     NGESFTGKLADQASKANLMFEEGKNMTPVYTGALKDELVKTDKVYGKIKKRLLWGSDL
                     ATMIRCARAFGGLMDELKAHCVTLPVRVGMNMNEDGPIIFEKHSRYRYHYDADYSRWD
                     STQQRDVLAAALEIMVKFSPEPHLAQIVAEDLLSPSVMDVGDFQISISEGLPSGVPCT
                     SQWNSIAHWLLTLCALSEVTDLSPDIIQANSLFSFYGDDEIVSTDIKLDPEKLTAKLK
                     EYGLKPTRPDKTEGPLVISEDLDGLTFLRRTVTRDPAGWFGKLEQSSILRQMYWIRGP
                     NHEDPFETMIPHSQRPIQLMSLLGEAALRGPAFYSKISKLVIAELKEGGMDFYVPRQE
                     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="ALX87357.1"
                     /translation="MKMASSDANPSDGSAANLVPEVNNEVMALEPVVGAAIAAPVAGQ
                     QNVIDPWIRNNFVQAPGGEFTVSPRNAPGEILWSAPLGPDLNPYLSHLARMYNGYAGG
                     FEVQVILAGNAFTAGKVIFAAVPPNFPTEGLSPSQVTMFPHIVVDVRQLEPVLIPLPD
                     VRNNFYHYNQSNDPTIKLIAMLYTPLRANNAGDDVFTVSCRVLTRPSPDFDFIFLVPP
                     TVESRTKPFSVPVLTVEEMTNSRFPIPLEKLFTGPSSAFVVQPQNGRCTTDGVLLGTT
                     QLSPVNICTFRGDVTHITGSRNYTMNLASQNWNNYDPTEEIPAPLGTPDFVGEIQGVL
                     TQTTRTDGSTRGHKATVYTGSADFAPKLGRIQFETDTDHDFEANQNTKFTPVGVIQDG
                     STTHRNEPQQWVLPSYSGRNTHNVHLAPAVAPTFPGEQLLFFRSTMPGCSGYPNMDLD
                     CLLPQEWVQYFYQEAAPSQSDVALLRFVNPDTGRVLFECKLHKSGYVTVAHTGQHDLV
                     IPPNGYFRFDSWVNQFYTLAPMGNGTGRRRVV"
     gene            6705..7513
                     /gene="VP2"
     CDS             6707..7513
                     /gene="VP2"
                     /note="minor capsid protein"
                     /codon_start=1
                     /product="capsid protein VP2"
                     /protein_id="ALX87358.1"
                     /translation="MAGAFFAGLASDVLGSGLGSLINAGAGAINQKVEFENNRKLQQA
                     SFQFSSNLQQASFQHDKEMLQAQIEATKKLQQEMMKVKQAMLLEGRFSETDAARGAIN
                     APMTKALDWSGTRYWAPDARTTTYNAGRFSTPQPSGALPGRANLRDAVPARGSSSKSS
                     NSFTATSVHSNQTTSTRLGSTAGSGTSVSSLPSTARTRSWVEDQSRNLSPFMRGAHNI
                     SFVTPPSSRSSSQGTVSTVPKEVLDSWTGAFNTRRQPLFAHIRKRGESRV"
     3'UTR           7514..7570
ORIGIN      
        1 gtgaatgaag atggcgtcta acgacgcttc cgctgccgct gttgccaaca gcaacaacga
       61 catcgcaaaa tcttcaagtg acggtgtgtt ttctaacatg gctgtcactt ttaagcgggc
      121 cctcggggcg cggcctaaac agccgccccc gaaggaaata ccacccagac ccccgcgacc
      181 acccacacca gaattggtca aaaagatcct tcctcctcca cccaacgggg aggatgaact
      241 agtggtatcc tacagcgcca gagatggcgt ttccggactg cctgagctca ccactgtcag
      301 acaaccggaa gaaaccaaca cggcgttcag tgttcctcca ctcaaacaaa gggagagcag
      361 ggacgccaag gagccactaa ctggaacaat tattgaaatg tgggatggag aaatttacca
      421 ttacggcctg tacgtggaac gaggtcttat acttggtgtg cacaagccac cggcagccat
      481 cagccttgcc aaggtcgagc taacaccgct ctctttgttc tggagacctg tatacacccc
      541 ccagtatctc atctctccag acactcttag aagactacat ggagagtcat tcccctacac
      601 tgcatttgac aacaattgct acgccttttg ttgttgggta ttagacctaa acgactcatg
      661 gctaagcagg agaatgattc agagaacaac aggtttcttc aggccgtacc aggattggaa
      721 caggaaaccc ctccccacta tggatgattc caaattaaag aaggtagcca acatattctt
      781 gtgcactttg tcctcactat tcaccagacc cattaaggac atagtaggga agttgaaacc
      841 tcttaacatc cttaacattc tggctacatg tgattggacc ttcgcaggca tagtggaatc
      901 cttaatactc ttggcagaac tctttggagt tttctggaca cccccagatg tgtctgcgat
      961 gatcgccccc ttgctaggcg attatgaact gcaaggacct gaggaccttg cagtggaatt
     1021 ggtcccaata gtgatggggg ggataggttt ggtgccagga tttaccaaag agaaaattgg
     1081 aaagatgcta tcatccgctg catccacttt aagagcttgt aaagaccttg gtgcatacgg
     1141 actggaaatc ttaaaattgg tcatgaagtg gttcttccca aagaaagagg aagcaaacga
     1201 actggctatg gtgagatcca tcgaggatgc agtgttagac ctcgaggcga ttgaaaacaa
     1261 ccacatgacc accctactca aagacaaaga tagcttggca acttacatga gaacccttga
     1321 ccttgaggag gagaaagcca gaaaactctc aaccaaatct gcttcacccg atattgtggg
     1381 cacaatcaac tctcttctgg caagaatcgc tgctgcacgc tccctagtgc atcgtgcgaa
     1441 agaagagctc tccagcaggc cgagacctgt cgttgtgatg atatcgggaa aaccagggat
     1501 agggaaaact caccttgcca gggagctggc caagaagatc gcggcctccc tcacagggga
     1561 ccagcgtgtg ggtcttatcc cgcgcaatgg tgtcgaccac tgggacgcat acaagggcga
     1621 aagagttgtc ctatgggacg actatggaat gagcaacccc atccatgatg ccctcaggtt
     1681 gcaggagctt gctgacactt gccccctcac gctaaattgt gacagaattg agaacaaagg
     1741 gaaagtcttt gacagtgatg ccataattat caccaccaat ctggccaacc cagcaccact
     1801 ggattatgta aactttgaag cgtgctcgag acgcattgac ttcctcgttt acgcagaagc
     1861 ccctgaggtg gagaaggcag agcgcgactt cccaggtcaa cctgacatgt ggaagaacgc
     1921 tttcagtcct gacttctcac acataaaact gtcattggct ccacagggtg gttttgacaa
     1981 gaacggcaac accccgcatg gaaaaggggt catgaagacc ctcactactg gttccctcat
     2041 cgcccgagca tcagggttac tccatgagag gctagatgaa tatgaactgc aaggcccagc
     2101 cctcaccact ttcaactttg accgcaacaa gatacttgct tttagacagc ttgctgctga
     2161 aaacaagtat gggctgatgg acacaatgag agttggaaaa cagctcaagg atgtcaagac
     2221 catgtcagac ctcaaacaag cactcaagaa tattgcgatc aagaagtgcc agatagtata
     2281 caatggtggc acctacacac ttgaggccga tggcaagggt agtgtgaaag ttgacaaagt
     2341 gcaaagtgcc actgtgcaga ccaacaatga actagccggt gccctacacc acctaaggtg
     2401 cgctagaatt agatactatg ttaagtgcgt ccaggaggca ctgtattcca tcatccaaat
     2461 cgctggggct gcattcgtca ccacgcgcat cgctaagcgc atgaatatac agaatctctg
     2521 gtccaagcca caggtggaag acacagaaga ggtggccaac aaagaaggtc tcctaaaacc
     2581 caaagatgat gaagagtttg tcgtctcatc cgacgacatc aaaactgagg gcaagaaagg
     2641 gaagaacaag tccggccgtg gcaagaagca cacagccttt tcaagcaaag ggctcagtga
     2701 tgaggagtac gatgagtaca agagaatcag agaagaaagg aatggtaagt actccataga
     2761 agagtacctt caggacagag acaggtatta cgaggaggtg gccattgcca gggcaaccga
     2821 agaggacttc tgtgaagaag aagaggccaa aatccggcag agaattttta gaccaacaag
     2881 gaaacaacgc aaagaagaga gggcctctct cggcttggtc acaggctctg aaatcaggaa
     2941 gagaaaccca gaagacttca aacccaaggg aaagctgtgg gctgatgatg acagaagtgt
     3001 tgactacaat gagaaactca actttgaggc cccaccaagc atctggtcgc ggatagtcaa
     3061 ctttggttca ggttggggct tctgggtctc ccccagtctg tttataacat caacccatgt
     3121 cataccccaa ggtgcaaaag agttcttcgg agtccctatc aagcaaatcc agatacacaa
     3181 atcaggtgaa ttctgccggt tgagattccc aaagccaatc agaactgatg tgacgggcat
     3241 gattctagaa gaaggtgcgc ccgaggggac tgtggccaca ctgctcatca agagaccaac
     3301 tggagagctc atgcctctgg cagccagaat ggggacccat gcaaccatga gaattcaggg
     3361 gcgcacagtt ggagggcaaa tgggtatgct cctgacagga tccaacgcca agagtatgga
     3421 cctaggcaca acaccaggcg actgcggctg cccctacatc tacaagaggg ggaatgacta
     3481 cgtggtcata ggagtccata cggccgctgc ccgtggagga aacactgtca tatgtgccac
     3541 ccaggggagt gagggagaag ccacacttga aggaggtgac agtaaaggaa catactgcgg
     3601 cgcaccaatc ttgggcccag ggagcgctcc aaagctcagt gccaagacta agttttggag
     3661 atcatccaca acaccactcc cacctggcac ctatgaacca gcctacctcg gtggcaaaga
     3721 ccccagagtc aaaggtggcc cttcattgca acaagttatg agggatcagc taaagccatt
     3781 cacagaaccc agaggcaaac caccaagacc aaatgtgttg gaagctgcca agaaaaccat
     3841 catcaatgtc cttgagcaaa caattgatcc accccaaaaa tggtcatttg cgcaagcttg
     3901 cgcatccctt gacaaaacca cctccagcgg ccacccgcac cacatgcgga aaaacgattg
     3961 ttggaatggg gagtccttca caggaaaatt ggctgatcag gcctccaagg ccaacctaat
     4021 gtttgaagag gggaagaaca tgactccagt ctacacaggt gcacttaaag atgagttggt
     4081 aaagaccgat aaagtttatg gtaagatcaa aaagaggctc ctgtggggtt cagatctggc
     4141 aaccatgata cggtgcgccc gagcttttgg aggccttatg gatgaactca aggcacactg
     4201 tgtcacactt cctgtcagag ttggtatgaa catgaatgag gatggcccca tcatctttga
     4261 gaagcactcc agatataggt atcactatga tgctgattat tcccggtggg actcaacaca
     4321 acaaagggat gtgctagcag cagcactaga aatcatggtt aagttctctc cagaaccaca
     4381 cctggcccag atagttgcag aagacctcct ttcccctagc gtaatggatg taggtgactt
     4441 tcaaatatca ataagtgagg gtcttccctc tggggtacct tgtacctccc agtggaattc
     4501 catcgcccac tggctcctca ctctttgtgc actctctgaa gtcacggacc tgtcccctga
     4561 catcattcag gccaactccc ttttctcctt ctatggtgat gatgagattg taagcacaga
     4621 cataaagttg gacccagaga agctgacagc aaaactcaag gagtacgggc tgaaaccaac
     4681 ccgccccgac aaaactgaag gaccccttgt tatctctgaa gaccttgatg gcctgacatt
     4741 cctccggaga actgtgaccc gtgatccagc tggctggttt ggaaaattgg aacaaagttc
     4801 aattcttagg caaatgtact ggatcagggg tcccaaccat gaagacccat ttgaaacaat
     4861 gataccacac tcccaaagac ccatacaatt gatgtccttg ctgggcgagg ctgcactccg
     4921 cggcccggca ttttatagca aaattagcaa attagtcatt gcagagttga aggaaggtgg
     4981 catggatttt tacgtgccca gacaagagcc aatgttcaga tggatgagat tctcagatct
     5041 gagcacgtgg gagggcgatc gcaatctggc tcccagtttt gtgaatgaag atggcgtcga
     5101 gtgacgccaa cccatctgat gggtccgcag ccaacctcgt cccagaggtc aacaatgagg
     5161 ttatggctct ggagcccgtt gttggtgccg ccattgcggc acctgtagcg ggccaacaaa
     5221 atgtaattga cccctggatt agaaacaatt ttgtacaagc ccctggtgga gagtttacag
     5281 tatcccctag aaacgctcca ggtgaaatac tatggagcgc gcccttgggc cctgatctaa
     5341 atccctacct atcccatttg gccagaatgt acaatggtta tgcaggtggt tttgaagtgc
     5401 aggtaattct cgcggggaac gcgttcaccg ccgggaaggt catatttgca gcagtcccac
     5461 caaactttcc aactgaaggc ttgagcccca gccaggtcac tatgttcccc catatagtag
     5521 tagatgttag gcaactagaa cctgtgttga ttcccttacc tgatgttagg aataacttct
     5581 atcattacaa tcaatcaaat gaccccacca ttaagttgat agcaatgttg tatacaccac
     5641 ttagggctaa taatgctggg gatgatgtct tcacagtttc ttgccgagtt ctcacgagac
     5701 catcccccga ttttgatttc atatttctag tgccacccac agttgagtca agaactaaac
     5761 cattctctgt cccagtttta actgttgagg agatgactaa ttcaagattc cccattcctt
     5821 tggaaaagct gttcacgggt cccagcagtg cctttgttgt tcaaccacaa aacggcaggt
     5881 gcacgactga tggcgtgctc ctaggcacca cccaactgtc tcctgtcaac atctgcacct
     5941 tcagaggaga tgtcacccat atcactggta gtcgtaacta cacaatgaat ttggcttctc
     6001 aaaattggaa taattatgac ccaacagaag aaatcccagc ccctctagga actccagatt
     6061 ttgtggggga gattcaaggc gtactcaccc aaaccacaag gacagatggc tcaacacgcg
     6121 gccacaaagc cacagtgtac actgggagcg ccgactttgc tccaaaactg ggtagaattc
     6181 aatttgaaac tgacacagac catgattttg aagctaacca aaacacaaag ttcaccccag
     6241 tcggtgtcat ccaagatggt agcaccaccc accgaaatga accccaacaa tgggtgctcc
     6301 caagttactc aggcagaaat actcataatg tgcatctggc ccccgctgta gcccccactt
     6361 ttccgggtga gcaacttctc ttcttcagat ccaccatgcc cggatgcagc gggtacccca
     6421 acatggattt ggactgtctg ctcccccagg aatgggtgca gtatttctac caagaggcag
     6481 ccccatcaca atctgatgtg gctctgctaa gatttgtgaa tccagacaca ggtagggttt
     6541 tgtttgagtg taagcttcac aaatcaggct atgttacagt ggctcacact ggccaacatg
     6601 atttggttat cccccccaat ggttatttta ggtttgattc ctgggtcaac cagttctaca
     6661 cgcttgcccc catgggaaat ggaacggggc gtagacgcgt agtataatgg ctggagcttt
     6721 ctttgctgga ttggcatctg atgtccttgg ctctggtctt ggttccctta tcaatgctgg
     6781 ggctggggcc atcaaccaaa aagttgagtt tgaaaataac agaaaattgc aacaagcatc
     6841 cttccaattt agcagcaatc tacaacaggc ttcctttcaa catgacaaag agatgctcca
     6901 agcacaaatt gaggccacca aaaagctaca acaggaaatg atgaaagtta agcaggcaat
     6961 gctcctagag ggtaggttct ctgagacaga tgcagcccgc ggggcaatca atgcccccat
     7021 gacaaaagct ttggactgga gcgggacaag gtactgggct cccgatgcta ggactacaac
     7081 atacaatgca ggccgctttt ccacccctca accatcgggg gcactgccag gaagagctaa
     7141 tcttagggat gctgtccctg ctcggggctc ctccagcaaa tcttctaatt cttttactgc
     7201 tacttctgtg cattcaaatc aaaccacttc aacgagactt ggttctacag ctggttctgg
     7261 taccagtgtc tcgagcctcc cgtcaactgc aaggactagg agctgggttg aggatcaaag
     7321 taggaatttg tcacctttca tgaggggggc ccacaacata tcgtttgtca ccccaccatc
     7381 tagcagatcc tccagccaag gcacagtctc aaccgtgcct aaagaggtct tggactcctg
     7441 gactggcgct ttcaacacgc gcaggcagcc actcttcgct cacattcgta agcgagggga
     7501 gtcacgggtg taatgtgaaa agacaaaatt gattattttt ctttttcttt agtgtctttg
     7561 aaaaaaaaaa
//