Typing tool

Complete norovirus genomes

KC962453  GII.4 New Orleans
 GII.P4 Yerseke

Length: 7,567 | 3 CDS

ORF1: 5..5104
ORF2: 5085..6707
ORF3: 6707..7510
LOCUS       KC962453                7567 bp    RNA     linear   VRL 21-APR-2015
DEFINITION  Norovirus GII strain
            GII/Hu/ZAF/2010/GII.P4_GII.4/Bushbuckridge/5928, partial genome.
ACCESSION   KC962453
VERSION     KC962453.2
KEYWORDS    .
SOURCE      Norovirus GII
  ORGANISM  Norovirus GII
            Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes;
            Picornavirales; Caliciviridae; Norovirus.
REFERENCE   1  (bases 1 to 7567)
  AUTHORS   Murray,T.Y., Mans,J. and Taylor,M.B.
  TITLE     Noroviruses detected in paediatric patients with gastroenteritis in
            South Africa
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 7567)
  AUTHORS   Murray,T.Y.
  TITLE     Direct Submission
  JOURNAL   Submitted (24-APR-2013) Department of Medical Virology, University
            of Pretoria, Bophelo Road, Pretoria, Gauteng 0001, South Africa
REFERENCE   3  (bases 1 to 7567)
  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 KC962453.1.
FEATURES             Location/Qualifiers
     source          1..7567
                     /organism="Norovirus GII"
                     /mol_type="genomic RNA"
                     /strain="GII/Hu/ZAF/2010/GII.P4_GII.4/Bushbuckridge/5928"
                     /isolation_source="stool"
                     /host="Homo sapiens"
                     /db_xref="taxon:122929"
                     /country="South Africa"
                     /collection_date="Jul-2010"
                     /collected_by="T.Y. Murray"
                     /identified_by="T.Y. Murray"
                     /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="AGX93463.2"
                     /translation="MKMASNDASAAAVANSNNDTAKSSSDGVLSSMAVTFKRALGARS
                     KQPPPREIPQRPPRPPTPELIKNVPPPPPNGEDEIVVSYSVKDGVSGLPDLSTVRQPE
                     ESNTAFSVPPLNQRENRDAKEPLTGSILEMWDGEIYHYGLYVERGLVLGVHKPPAAIS
                     LARVELAPLSLYWRSVYTPQYLISPDTLKKLHGETFPYTAFDNNCYAFCCWVLDLNDS
                     WLSRRMIQRTTGFFRPYQDWNRKPLPTMDDSKLKKVANIFLCALSSLFTRPIKDIIGK
                     LRPLNILNILASCDWTFAGIVESLILLAELFGVFWTPPDVSAMIAPLLGDYELQGPED
                     LAVELVPVVMGGIGLVLGFTKEKIGKMLSSAASTLRACKDLGAYGLEILKLVMKWFFP
                     KKEEANELAIVRSIEDAVLDLEAIENNHMTTLLKDKDSLATYMRTLDLEEEKARKLST
                     KSASPDIVGTINALLARIAAARSLVHRAKEELSSRPRPVVLMISGRPGIGKTHLAREV
                     AKRIAASLTGDQRVGLVPRNGVDHWDAYKGERVVLWDDYGMSNPIHDALRLQELADTC
                     PLTLNCDRIENKGKVFDSDVIIITTNLANPAPLDYVNFEACSRRIDFLVYAEAREVEK
                     AKRDFPGQPDMWKNAFSSDFSHIKLTLAPQGGFDKNGNTPHGKGVTKSLTTGSLIARA
                     TGLLHERLDEFELQGPTLTTFNFDRNKVLAFRQLAAENKYGLMDTMRVGRQLKDVRTM
                     PELKQALKNVSIKKCQIVYSGCTYILESDGKGNVKVDKIQSASVQTNNELTGALHHLR
                     CARIRYYVKCIQEALYSIIQIAGAAFVTTRIVKRMNIQDLWSKPQVEDTEETTSKDGC
                     PKPKDDEEFVISSDDIKTEGKKGKNKTGRGKKHTAFSSKGLSDEEYDEYKRIREERNG
                     KYSVKEYLQDRDKYYEEVAIARATEEDFCEEGEAKIRQRIFRPTRKQRKEERASLGLV
                     TGSEIRKRNPDDFKPKGKLWADDDRSVDYNEKLSFEAPPSIWSRIVNFGSGWGFWVSP
                     SLFITSTHVIPQGAKEFFGVPIKQIQIHKSGEFCRLRFPKPIRTDVTGMILEEGAPEG
                     TVVTLLIKRPTGELMPLAVRMGTHATMKIQGRTVGGQMGMLLTGSNAKSMDLGTTPGD
                     CGCPYIYKRGNDYVAIGVHTAAARGGNTVICATQGSEGEATLEGGDDKGTYCGAPILG
                     PGSAPALSTKTKFWRSSTAPLPPGTYEPAYLGGKDPRIKGGPSLQQVMREQLKPFTEP
                     RGKPPKPSVLEAAKKTIVNVLEQTIDPPEKWSFAQACASLDKTTSSGHPHHMRKNDCW
                     NGESFTGKLADQASKANLMYEEGKNMTPVFTASLKDELVKTDKIYGKIRKRLLWGSDL
                     ATMIRCARAFGGLMDEFKAHCVTLPIRVGMNMNEDGPIIFEKHSRYKYHYDADYSRWD
                     STQQRAVLAAALEIMVKFSPEPHLAQVVAEDLLSPSVMDVGDFTVSINEGLPSGVPCT
                     SQWNSIAHWLLTLCALSEVTNLSPDIIQANSLFSFYGDDEIVSTDIKLDSEKLTAKLR
                     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="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            5085..6707
                     /gene="VP1"
     CDS             5085..6707
                     /gene="VP1"
                     /note="major capsid protein"
                     /codon_start=1
                     /product="capsid protein VP1"
                     /protein_id="AKE07100.1"
                     /translation="MKMASSDANPSDGSTANLVPEVNNEVMALEPVVGAAIAAPVAGQ
                     QNVIDPWIRNNFVQAPGGEFTISPRNAPGEILWSAPLGPDLNPYLSHLARMYNGYAGG
                     FEVQVILAGNAFTAGKVIFAAVPPNFPTEGLSPSQVTMFPHIVVDVRQLEPVLIPLPD
                     VRNNFYHYNQSNDPTIKLIAMLYTPLRANNAGDDVFTVSCRVLTRPSPDFDFIFLVPP
                     TVESRTKPFSIPVLTIEEMTNSRFPIPLEKLFTGPSSAFVVQPQNGRCSTDGVLLGTT
                     QLSPVNICTFRGDVTHIAGSHNYTMNLASQNWNSYDPTEEIPAPLGTPDFVGKIQGVL
                     TQTTRADGSTRGHKATVLTGSANFTPKLGRIQFATDTDNDFETNQNTKFTPVGVIQDG
                     DTAHRNEPQQWVLPSYSGRNTHNVHLAPAVAPTFPGEQLLFFRSTIPGCSGYPNMDLD
                     CLLPQEWVQFFYQEAAPAQSDVALLRFVNPDTGRVLFECKLHKSGYITVAHTGQHDLV
                     IPPNGYFRFDSWVNQFYTLAPMGNGTGRRRAL"
     gene            6707..7510
                     /gene="VP2"
     CDS             6707..7510
                     /gene="VP2"
                     /note="minor capsid protein"
                     /codon_start=1
                     /product="capsid protein VP2"
                     /protein_id="AKE07101.1"
                     /translation="MAGAFFAGLASDVLGSGLGSLINAGAGAINQKVEFENNRKLQQA
                     SFQFSSNLQQASFQHDKEMLQAQIEATKKLQQEMMKVKQAVLLEGGFSETDAARGAIN
                     APMTKALDWSGTRYWAPDARTTTYNAGHFSTPQPSGAPLGRANLRAAVPTRGSSSTSS
                     NSSIATSVYSNQTASTRLGSTAGSGASVSSLPSTARTRSWVEDQRNLSPFMRGAHNIS
                     FVTPPSSRSSSQGTVSTVPKEVLDSWTGAFNTRRQPLFAHIRKRGESRV"
     3'UTR           7511..7567
ORIGIN      
        1 gtgaatgaag atggcctcta acgacgcttc cgctgccgct gttgctaaca gcaacaacga
       61 caccgcaaaa tcttcaagtg acggagtgct ttctagcatg gctgtcactt ttaaacgagc
      121 cctcggggcg cggtctaaac agcctccccc gagggaaata ccacagagac ccccacgacc
      181 acctactcca gaactgatta agaatgttcc cccccccccg cccaacgggg aggatgaaat
      241 agtggtttct tatagtgtca aagatggtgt ttccggtttg cctgaccttt ccaccgtcag
      301 gcaaccggaa gaatccaaca cggctttcag tgtccctcca ctcaatcaga gggagaatag
      361 agatgctaag gagccactta ccggatcaat tctggaaatg tgggatggag aaatctacca
      421 ttatggcctg tatgtggagc gaggtcttgt actaggtgtg cacaaaccac cagctgccat
      481 cagcctcgct agggttgagc tagcaccact ctccttgtac tggagatctg tgtacactcc
      541 tcaatacctc atctccccag acactctcaa gaaattacac ggagaaacgt tcccctacac
      601 agcctttgac aacaattgtt atgccttttg ttgctgggtc ctggacctaa atgactcgtg
      661 gctgagtagg agaatgatcc agagaacaac tggtttcttc aggccctacc aagattggaa
      721 taggaaaccc cttcccacta tggatgactc taaattaaag aaggtagcca acatattctt
      781 gtgtgctctg tcttcgctat tcaccaggcc cataaaagac ataataggga agctaaggcc
      841 tcttaacatc ctcaacatct tagcctcatg tgattggact tttgcaggca tagtggagtc
      901 cctgatactc ttggcagagc tctttggagt cttctggaca cccccagatg tgtctgcgat
      961 gatcgctccc ttactcggtg actacgagct gcaaggacct gaggaccttg cagtggagct
     1021 cgtccccgta gtgatgggtg ggattggttt ggtgctagga ttcaccaaag agaaaattgg
     1081 gaaaatgttg tcatctgctg catccacctt gagagcttgt aaagacctcg gtgcatatgg
     1141 gctagagatc ctaaagttgg tcatgaagtg gttcttcccg aagaaggagg aagcaaatga
     1201 actggctata gtgagatcta tcgaggatgc agtcttagat ctcgaggcaa ttgaaaacaa
     1261 ccatatgacc accttgctca aagacaaaga cagtttggca acctatatga gaacccttga
     1321 ccttgaggag gagaaagcca ggaaactctc aaccaagtct gcctcacctg acatcgtggg
     1381 cacaatcaac gctcttctgg cgagaatcgc cgctgcacgc tctttggttc atcgagcaaa
     1441 ggaggaactt tccagcagac caaggcctgt agtgttgatg atatcaggta gaccaggaat
     1501 agggaagacc caccttgcta gggaagtggc taagagaatc gcagcctccc tcacaggaga
     1561 ccagcgtgta ggcctcgtcc cacgcaatgg cgttgaccat tgggatgcgt acaaggggga
     1621 gagggtcgtc ctttgggacg attatggaat gagcaaccct attcacgatg ccctcaggtt
     1681 gcaagaactc gctgacactt gccccctcac tctaaactgt gacaggattg agaataaagg
     1741 aaaggtcttt gacagcgatg tcatcatcat caccactaat ctggccaacc cagcaccact
     1801 ggactatgtc aactttgaag catgctcgag gcgcatcgac ttcctcgtgt atgcagaagc
     1861 ccgtgaagtt gaaaaggcga agcgtgactt cccaggccag cctgacatgt ggaagaacgc
     1921 tttcagttct gacttctcac acataaaact aacattggct ccacagggtg gcttcgacaa
     1981 gaacgggaac accccacacg gaaagggcgt cacgaagtct ctcaccactg gctcccttat
     2041 tgcccgggca accgggttgc tccatgagag gttagatgaa tttgaactac agggcccaac
     2101 actcaccacc tttaacttcg atcgcaataa agtgcttgcc tttagacaac tagctgctga
     2161 gaacaaatat ggactgatgg acacaatgag agttgggaga cagctcaagg atgtcagaac
     2221 catgccagaa ctcaaacaag cactcaagaa tgtctcaatc aagaagtgcc agatagtgta
     2281 tagtggttgc acctacatac ttgagtctga tggcaagggc aatgtgaaag ttgacaaaat
     2341 tcagagcgcc tccgtgcaga ctaacaacga gctgaccggt gccctgcacc atttgaggtg
     2401 cgccaggatt agatactatg tcaagtgcat ccaggaagcc ctgtattcca tcatccaaat
     2461 tgctggagct gcatttgtca ccacgcgcat cgtcaagcgc atgaacatac aagacctgtg
     2521 gtctaagcca caagtggaag acacagagga gaccaccagc aaggacgggt gtccaaaacc
     2581 caaagatgat gaggagtttg tcatttcatc tgacgacatc aaaactgaag gtaagaaagg
     2641 gaagaacaag actggccgcg gcaagaagca cacagccttt tcaagcaaag gcctcagtga
     2701 tgaagagtac gatgagtaca agaggattag ggaagaaagg aatggtaagt attccgtaaa
     2761 agagtacctt caggacaggg acaaatacta tgaggaggtg gccattgcca gggcaactga
     2821 ggaagacttc tgtgaagagg gggaggccaa aatccggcaa aggatcttca ggccaacaag
     2881 gaaacaacgc aaggaggaaa gagcttctct cggtctggtt acaggttctg aaattaggaa
     2941 aagaaaccca gatgatttca aacccaaggg gaaactgtgg gctgacgatg acagaagtgt
     3001 ggactataat gagaaactca gttttgaggc cccaccaagc atctggtcaa ggatagtcaa
     3061 ctttggttca ggttggggat tctgggtctc ccccagtctg ttcataacat caacccatgt
     3121 tataccccag ggcgcaaagg agttctttgg agtccccatc aaacaaattc aaatacacaa
     3181 gtcaggcgag ttctgccgct tgagattccc aaagccaatc aggactgatg tgacgggcat
     3241 gatcttagaa gaaggcgcac ctgagggcac tgtagtcaca ctacttatca aaaggcccac
     3301 tggggaactc atgcccctag cagttaggat ggggacccat gcaaccatga agatccaagg
     3361 gcgcactgtt ggaggccaaa tgggcatgct cctgacaggg tccaacgcca aaagcatgga
     3421 cctgggtact acaccaggtg attgtggctg tccctacatc tacaagagag gcaatgacta
     3481 tgtggccatt ggagtccaca cggctgctgc tcgtggggga aacaccgtca tatgtgccac
     3541 ccaggggagt gaaggagagg ctacacttga gggtggtgac gacaagggga catactgtgg
     3601 tgcaccaata ttaggcccag ggagtgcccc agcacttagc accaagacca aattctggag
     3661 atcatccaca gcaccactcc cacctggcac ctatgaacca gcctaccttg gtggcaagga
     3721 ccctagaatc aagggtggcc cttcactaca gcaagtcatg agggaacagt tgaagccatt
     3781 cacagagccc aggggcaagc caccaaagcc aagtgtgtta gaagctgcca agaaaaccat
     3841 cgtcaatgtc cttgagcaaa caattgatcc acctgagaag tggtcattcg cacaagcttg
     3901 cgcgtccctc gacaagacca cttccagtgg tcatccgcac cacatgcgga aaaacgactg
     3961 ctggaatggg gagtccttca caggcaagct ggcagaccaa gcttccaaag ccaacctgat
     4021 gtatgaagaa gggaagaata tgaccccagt cttcacagct tcgctcaagg atgaactagt
     4081 taagactgac aaaatttatg gtaagatcag gaagaggctt ctctggggct cggacttagc
     4141 gaccatgatc cggtgcgctc gagctttcgg aggcctaatg gatgaattca aagcacactg
     4201 tgtcacactt cccattagag ttggtatgaa tatgaatgag gatggcccca tcatcttcga
     4261 gaagcattcc aggtacaaat atcactatga tgctgattac tctcgatggg attcaacaca
     4321 acagagagcc gtgttggcag cagctctaga aatcatggtc aaattctccc cagaaccaca
     4381 tttggctcag gtagtcgcgg aagaccttct ttctcctagc gtgatggacg tgggcgactt
     4441 cacagtatca atcaatgagg gtcttccctc cggggtgccc tgcacctccc aatggaactc
     4501 catcgcccat tggcttctca ctctctgtgc gctctctgaa gtcacaaact tgtcccctga
     4561 tatcatacag gctaattccc tcttctcttt ttatggtgat gatgaaattg ttagcacaga
     4621 tataaaattg gactcagaga aattgacagc aaagctcagg gaatatgggt taaaaccaac
     4681 ccgccctgac aaaactgaag gaccccttgt catctctgaa gacttaaatg gcctgacttt
     4741 cctgcggaga actgtgaccc gcgacccagc tggttggttt ggaaaactgg agcagagttc
     4801 aatactcagg caaatgtact ggactagggg ccccaaccat ggagacccat ctgaaacaat
     4861 gattccacat tcccaaagac ccatacaatt gatgtcccta ctgggggagg ccgctctcca
     4921 cggcccagca ttctacagca aaattagcaa attggtcatt 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 ccattgcggc acctgtagcg ggccaacaaa
     5221 atgtaattga cccctggatt agaaacaatt ttgtacaagc ccctggtgga gagttcacaa
     5281 tatcccctag aaacgctcca ggtgaaatac tatggagcgc gcccttaggc cctgatttga
     5341 atccctacct ttcccatttg gccagaatgt acaatggtta tgcaggtggt tttgaagtgc
     5401 aggtaatcct tgcggggaat gcgttcaccg ccggaaaagt catatttgca gcagtcccac
     5461 caaatttccc aactgaaggc ttgagcccca gccaggtcac tatgtttccc catatagtag
     5521 tagatgttag gcaactggag cctgtgttga tccccttacc cgatgttagg aataatttct
     5581 accactacaa tcaatcaaat gaccccacca tcaaattgat agcaatgttg tatacaccac
     5641 ttagggctaa caatgctggg gacgatgtct tcacagtttc ttgtcgcgtt ctcacgagac
     5701 catcccccga ctttgatttc atatttctag tgccacccac agttgaatca agaactaaac
     5761 cattctctat cccagtttta actattgagg agatgaccaa ttcaagattc cccattcctc
     5821 tggaaaagtt gttcacgggt cccagcagcg cctttgttgt tcaaccacaa aacggcaggt
     5881 gctcgactga tggcgtgctc ctaggtacta cccaactgtc tcctgtcaac atctgcacct
     5941 tcagagggga tgtcacccac atcgcaggta gccacaacta cacaatgaat ttggcttctc
     6001 aaaattggaa cagttatgat ccaacggaag aaatcccagc ccctttagga actccagatt
     6061 tcgtgggcaa gattcaaggt gtgctcaccc aaaccacaag ggcagatggc tcgacccgcg
     6121 gccacaaagc tacagtactc actgggagcg ccaactttac tccaaagctg ggtagaattc
     6181 aatttgccac tgacacagac aatgattttg aaactaacca aaacacaaaa ttcaccccag
     6241 tcggtgtcat ccaggatggt gatactgccc accgaaatga accccaacag tgggtgctcc
     6301 caagttactc aggtagaaac actcataatg tgcatctggc ccccgctgta gcccccactt
     6361 ttccgggtga acaacttctt ttcttcaggt ccaccatacc cggatgcagc gggtacccca
     6421 atatggattt ggactgtctg ctcccccagg aatgggtgca gttcttctac caagaggcag
     6481 ccccagcaca atctgatgtg gctctgctaa gatttgtgaa tccagacaca ggtagggttt
     6541 tgtttgaatg caagcttcat aaatcaggct acattacagt ggcccacaca ggccaacatg
     6601 atttggttat cccccccaat ggttatttta gatttgattc ctgggtcaac cagttctaca
     6661 cgcttgcccc catgggaaat ggaacggggc gtagacgtgc attataatgg ctggagcttt
     6721 ctttgctgga ttggcatctg acgtccttgg ctctggactt ggttccctga tcaatgctgg
     6781 ggctggggcc atcaaccaaa aagttgaatt tgaaaataac agaaaattgc aacaagcttc
     6841 ctttcaattt agcagcaatt tacaacaggc ttcctttcaa catgataagg agatgctcca
     6901 agcacaaatt gaggccacca aaaagttgca acaggaaatg atgaaagtta aacaggcagt
     6961 gctcctagag ggtggattct ctgagacaga cgcagcccgt ggggcaatca acgcccccat
     7021 gacaaaggct ttggactgga gcgggacaag gtactgggct cccgatgcta ggactacaac
     7081 atacaatgca ggccactttt ccacccctca accctcgggg gcaccgctag ggagggctaa
     7141 tcttagggct gctgtcccca ctcggggttc ctccagcaca tcttctaact cttctattgc
     7201 tacttctgtg tattcaaatc aaactgcttc aacgagactt ggttctacag ctggttctgg
     7261 tgccagtgtc tcgagcctcc cgtcaactgc aaggactagg agctgggttg aggatcaaag
     7321 gaacttgtca cctttcatga ggggggccca caacatatcg tttgtcaccc caccatctag
     7381 cagatcctct agccaaggca cagtctcaac cgtgcctaaa gaagttttgg actcctggac
     7441 tggcgctttc aacacgcgca ggcagcctct cttcgctcac attcgtaagc gaggggagtc
     7501 acgggtgtaa tgtgaaaaga caaaattgat tatctttctt tttctttact gtcttttaaa
     7561 aaaaaaa
//