Typing tool

Complete norovirus genomes

JN400602  GII.4 Den Haag
 GII.P4 Den Haag

Length: 7,509 | 3 CDS

ORF1: 1..5100
ORF2: 5081..6703
ORF3: 6703..7509
LOCUS       JN400602                7509 bp    RNA     linear   VRL 19-DEC-2013
DEFINITION  Norovirus Hu/GII-4/CGMH04/2006/TW, complete genome.
ACCESSION   JN400602
VERSION     JN400602.1
KEYWORDS    .
SOURCE      Norovirus Hu/GII-4/CGMH04/2006/TW
  ORGANISM  Norovirus Hu/GII-4/CGMH04/2006/TW
            Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes;
            Picornavirales; Caliciviridae; Norovirus.
REFERENCE   1  (bases 1 to 7509)
  AUTHORS   Tsai,C.N., Lin,C.Y., Lin,C.W., Shih,K.C., Chiu,C.H. and Chen,S.Y.
  TITLE     Clinical relevance and genotypes of circulating noroviruses in
            northern Taiwan, 2006-2011
  JOURNAL   J. Med. Virol. 86 (2), 335-346 (2014)
   PUBMED   24009100
REFERENCE   2  (bases 1 to 7509)
  AUTHORS   Tsai,C.-N., Lin,C.-Y., Lin,C.-W., Shih,K.-C., Chi,H.-C.,
            Chao,H.-C., Lai,M.-W., Yu,T.-H., Chen,S.-Y. and Chiu,C.-H.
  TITLE     Direct Submission
  JOURNAL   Submitted (27-JUL-2011) Graduate Institute of clinical medical
            sciences, 259, Wen-Hwa 1st Rd, Kwei-Shan, Taoyuan, Taiwan
FEATURES             Location/Qualifiers
     source          1..7509
                     /organism="Norovirus Hu/GII-4/CGMH04/2006/TW"
                     /mol_type="genomic RNA"
                     /isolation_source="stool"
                     /host="Homo sapiens"
                     /db_xref="taxon:1195616"
                     /country="Taiwan"
                     /collection_date="18-Oct-2006"
                     /note="serogroup: GII-4"
     CDS             1..5100
                     /note="ORF1; encodes NTPase, 3A, VPg, 3Cpro and 3Dpol"
                     /codon_start=1
                     /product="non-structural polyprotein"
                     /protein_id="AFN09926.1"
                     /translation="MKMASNDASAAAVANSNNDTAKSSSDKMFSSMAVTFKRALGARP
                     KQPPPREIPQRPPRPPTPELVKKIPPPPPNGEDEVVVSYSAKDGVSGLPELSTVRQPE
                     ETNTAFSVPPLNQRENRDAKEPLTGTILEMWDGEIYHYGLYVERGLVLGVHKPPAAIS
                     LAKVELTPLSLFWRPVYTPQYLTSPDTLKKLHGETFPYTAFDNNCYAFCCWVLDLNDS
                     WLSRRMIQRTTGFFRPYQDWNRKPLPTMDDSKLKKVANIFLCTLSSLFTRPIKDIIGK
                     LRPLNIINILASCDWTFAGIVESLILLAELFGVFWTPPDVSAMIAPLLGDFELQGPED
                     LVVELVPVVMGGIGLVLGFTKEKIGKMLSSAASTLRACKDLGAYGLEILKLVMKWFFP
                     KKEEANELAMVRSIEDAVLDLEAIENNHMTTLLKDKDSLATYMRTLDLEEEKARKLST
                     KSASPDIVGTINALLARIAAARSLVHRAKEELSSRPRPVVLMISGRPGIGKTHLAREV
                     AKRIAASLTGDQRVGLIPRNGVDHWDAYKGERVVLWDDYGMSNPIHDALRLQELADTC
                     PLTLNCDRIENKGKVFDSDVIIITTNLANPAPLDYVNFEACSRRIDFLVYAEAPEVEK
                     AKRDFPGQPDMWKNAFSSDFSHIKLALAPQGGFDKNGNTPHGKGVMKTLTTGSLIARA
                     SGLLHERLDEFELQGPALTTFNFDRNKVLAFRQLAAENKYGLMDTMKVGRQLKDVKTM
                     PELKQALKNISIKKCQIVYSGCTYTLESDGKGNVKVDRVQSTSVQTNNELAGALHHLR
                     CARIRYYVKCVQEALYSIIQIAGAAFVTTRIIKRVNIQGLWSKPQVEDTEEATNKDGC
                     PKPKDDEEFVISSDDIKTEGKKGKNKTGRGKKHTAFSSKGLSDEEYDEYKRIREERNG
                     KYSIEEYLQDRDKYYEEVAIARATEEDFCEEEEAKIRQRIFRPTRKQRKEERASLGLV
                     TGSEIRKRNPEDFKPKGKLWADDDRSVDYNEKLSFEAPPSIWSRIVNFGSGWGFWVSP
                     SLFITSTHVIPQGAKEFFGVPIKQIQVHKSGEFCRLRFPKPIRTDVTGMILEEGAPEG
                     TVVTLLIKRSTGELMPLAARMGTHATMKIQGRTVGGQMGMLLTGSNAKSMDLGTTPGD
                     CGCPYIYKRGNDYVVIGVHTAAARGGNTVICATQGGEGEATLEGGDSKGTYCGAPILG
                     PGSAPKLSTKTKFWRSSTAPLPPGTYEPAYLGGKDPRVKGGPSLQQVMRDQLKPFTEP
                     RGKPPKPSVLEAAKKTIINVLEQTIDPPEKWSFAQACASLDKTTSSGHPHHMRKNDCW
                     NGESFTGKLADQASKANLMFEEGKNMTPVYTGALKDELVKTDKIYGKIKKRLLWGSDL
                     ATMIRCARAFGGLMDELKAHCVTLPIRVGMNMNEDGPIIFEKHSRYRYHYDADYSRWD
                     STQQRAVLAAALEIMVKFSSEPHLAQVVAEDLLSPSVVDVGDFTISINEGLPSGVPCT
                     SQWNSIAHWLLTLCALSEVTNLSPDIIQANSLFSFYGDDEIVSTDIKLDPEKLTAKLK
                     EYGLKPTRPDKTEGPLVISEDLDGLTFLRRTVTRDPAGWFGKLEQSSILRQMYWTRGP
                     NHEDPSESMIPHSQRPIQLMSLLGEAALHGPTFYSKISKLVIAELKEGGMDFYVPRQE
                     PMFRWMRFSDLSTWEGDRNLAPSFVNEDGVE"
     gene            5081..6703
                     /gene="VP1"
     CDS             5081..6703
                     /gene="VP1"
                     /note="ORF2"
                     /codon_start=1
                     /product="major viral capsid protein"
                     /protein_id="AFN09927.1"
                     /translation="MKMASNDANPSDGSAANLVPEVNNEVMALEPVVGAAIAAPVAGQ
                     QNVIDPWIRNNFVQAPGGEFTVSPRNAPGEILWSAPLGPDLNPYLSHLARMYNGYAGG
                     FEVQVILAGNAFTAGKIIFAAVPPNFPTEGLSPSQVTMFPHIIVDVRQLEPVLIPLPD
                     VRNNFYHYNQSNDSTIKLIAMLYTPLRANNAGEDVFTVSCRVLTRPSPDFDFIFLVPP
                     TVESRTKPFTVPILTVEEMTNSRFPIPLEKLFTGPSGAFVVQPQNGRCTTDGVLLGTT
                     QLSPVNICTFRGDVTHIAGSRNYTMNLASLNWNNYDPTEEIPAPLGTPDFVGKIQGVL
                     TQTTKGDGSTRGHKATVYTGSAPFTPKLGSVQFSTDTENDFETHQNTKFTPVGVIQDG
                     STTHRNEPQQWVLPSYSGRNVHNVHLAPAVAPTFPGEQLLFFRSTMPGCSGYPNMDLD
                     CLLPQEWVQHFYQEAAPAQSDVALLRFVNPDTGRVLFECKLHKSGYVTVAHTGQHDLV
                     IPPNGYFRFDSWVNQFYTLAPMGNGTGRRRAL"
     gene            6703..7509
                     /gene="VP2"
     CDS             6703..7509
                     /gene="VP2"
                     /note="ORF3"
                     /codon_start=1
                     /product="minor viral capsid protein"
                     /protein_id="AFN09928.1"
                     /translation="MAGAFFAGLASDVLGSGLGSLINAGAGAINQKIDFENNRKLQQA
                     SFQFSSNLQQASFQHDKEMLQAQIEATKRLQQEMMKVKQAMLLEGGFSETDAARGAIN
                     APMTKALDWSGTRYWAPDAGTTTYNAGRFSTPQPSGALPGRINPRIPTPARGSPSTSS
                     NASIATSIYSNQTVSTRLGSTAGSGTNASSFPSTARTRSWVEDQNRNLSPFMRGAHNI
                     SFVTPPSSRSSSQGTVSTVPKEVLDSWTGAFNTRRQPLFAHIRKRGESRV"
ORIGIN      
        1 atgaagatgg cgtctaacga cgcttccgct gccgctgttg ctaacagcaa caacgacacc
       61 gcaaaatctt caagtgacaa aatgttttct agcatggctg tcacttttaa acgagccctc
      121 ggggcgcggc ctaaacagcc ccccccgagg gaaataccac aaagaccccc acgaccacct
      181 actccagaac tggtcaaaaa gatccctcct cccccgccca acggagagga tgaagtggtg
      241 gtttcttata gtgccaaaga tggcgtttcc ggtttacctg agctttccac cgtcaggcaa
      301 ccggaagaaa ccaatacggc cttcagtgtc cctccactca atcagaggga gaatagggat
      361 gctaaggaac cactgactgg aacaattctg gaaatgtggg atggagaaat ctaccattat
      421 ggcctgtatg ttgagcgagg tcttgtgctg ggtgtgcaca aaccaccagc tgccattagc
      481 ctcgccaagg tcgaactaac accactctcc ttgttctgga gacctgtgta cactcctcag
      541 tacctcacct ctccagacac tctcaagaaa ttacacggag aaacatttcc ctacacagcc
      601 tttgacaaca attgctatgc cttttgttgc tgggtcctgg atctaaacga ctcgtggctg
      661 agtaggagaa tgatccagag aacaactggc ttcttcagac cctatcaaga ttggaatagg
      721 aaacccctcc ccactatgga tgattccaaa ttaaagaagg tagctaacat attcctgtgc
      781 accctgtctt cgctattcac caggcccata aaagacataa taggaaagtt gaggcctctc
      841 aacatcatca acatcctggc ttcatgtgat tggactttcg caggcatagt ggagtccttg
      901 atactcttgg cagagctctt tggagtcttc tggacacccc cagatgtgtc tgcgatgatt
      961 gcccccttac tcggtgattt cgagttgcaa ggacctgagg accttgtagt ggagctcgtc
     1021 cctgtagtaa tggggggaat tggtttggtg ttaggattca ccaaagagaa gattggaaaa
     1081 atgttgtcat ctgctgcatc caccttgaga gcttgtaaag atcttggtgc atatggacta
     1141 gagatcctga aattagtcat gaagtggttc ttcccgaaga aagaggaggc aaatgaactg
     1201 gctatggtga gatccatcga ggatgcagta ctggaccttg aggcaattga aaacaaccat
     1261 atgaccacct tgctcaaaga caaagacagc ctggcaacct acatgagaac ccttgacctc
     1321 gaggaagaga aagccagaaa actctcaacc aagtctgctt cacctgacat cgtgggcaca
     1381 atcaacgccc ttctggcgag aatcgccgct gcacgctccc tggtgcaccg agcgaaggag
     1441 gagctttcca gcagaccaag acctgtagtc ttgatgatat caggcagacc agggataggg
     1501 aagacccacc ttgctaggga agtggctaag agaatcgcag cctccctcac aggagaccag
     1561 cgtgtaggcc tcatcccacg caatggcgtc gatcactggg atgcgtacaa gggggagagg
     1621 gtcgtcctat gggacgacta tggaatgagc aatcccatcc acgacgccct caggctgcaa
     1681 gaactcgctg acacttgccc cctcactcta aattgtgaca ggattgagaa taaaggaaag
     1741 gtctttgaca gcgatgtcat cattatcacc actaatctgg ccaacccagc accactggac
     1801 tatgtcaact ttgaagcgtg ctcgaggcgc atcgatttcc tcgtgtatgc agaagccccc
     1861 gaggtcgaaa aggcgaagcg tgacttcccg ggccaacctg acatgtggaa aaacgctttt
     1921 agttctgatt tctcacacat aaaattggca ctggctccac aaggtggctt tgataagaac
     1981 gggaacaccc cacacgggaa gggcgtcatg aagactctca ccactggctc cctcattgcc
     2041 cgggcatcag ggctgctcca tgagagattg gatgagtttg aactacaggg cccagctctt
     2101 accaccttca actttgaccg caacaaagtg cttgccttca ggcagcttgc tgctgaaaac
     2161 aagtatgggt tgatggacac aatgaaagtt gggaggcagc tcaaggatgt caaaaccatg
     2221 ccagaactta aacaagcact caagaatatt tcaatcaaga agtgccagat tgtgtatagt
     2281 ggttgcacct acacacttga gtctgatggc aagggcaatg tgaaagttga cagagttcag
     2341 agcacctccg tacagaccaa caatgagctg gctggcgccc tgcaccacct aaggtgcgcc
     2401 agaatcaggt actatgtcaa gtgtgtccag gaggccctgt attctatcat ccagattgct
     2461 ggggctgcat ttgtcaccac gcgcatcatc aagcgtgtga acattcaagg cttatggtcc
     2521 aagccacaag tggaagacac agaggaggct accaacaagg acgggtgccc aaaacccaaa
     2581 gatgatgagg agttcgtcat ttcatctgac gacattaaaa ctgagggtaa gaaagggaag
     2641 aacaagactg gccgtggcaa gaagcacaca gccttctcaa gtaaaggtct cagtgatgaa
     2701 gagtatgatg agtacaagag aattagagag gaaaggaatg gcaagtactc catagaagag
     2761 taccttcagg acagggacaa atactatgag gaggtggcca ttgccagggc gaccgaggaa
     2821 gacttttgtg aagaggagga ggccaagatc cggcaaagga tcttcagacc aacaaggaaa
     2881 caacgcaagg aagaaagagc ttctctcggt ttagtcacag gttctgaaat taggaaaaga
     2941 aacccagaag acttcaagcc caaggggaaa ctatgggctg acgatgacag aagtgtggac
     3001 tacaatgaaa aactcagttt tgaggcccca ccaagcatct ggtcaaggat agtcaacttt
     3061 ggctcaggtt ggggcttctg ggtctccccc agcctgttca taacatcaac ccacgtcata
     3121 ccccagggcg caaaggagtt ctttggagtc cccatcaaac aaattcaggt acacaagtca
     3181 ggcgaattct gtcgcttgag gttcccaaaa ccaatcagga ctgatgtgac tggcatgatc
     3241 ttggaagaag gtgcgcccga aggcaccgtg gtcacactac tcatcaaaag gtctactgga
     3301 gaactcatgc ccctagcagc tagaatgggg acccatgcaa ccatgaaaat tcaagggcgc
     3361 actgttggag gtcagatggg catgcttctg acaggatcca acgccaaaag catggatcta
     3421 ggcaccacac caggtgattg cggctgtccc tacatctaca agagaggaaa tgactatgtg
     3481 gttattggag tccacacggc tgccgcccgt gggggaaaca ctgtcatatg tgccacccag
     3541 gggggtgagg gtgaagctac acttgaaggt ggtgacagta agggaacata ctgtggtgca
     3601 ccaatcctag gcccagggag tgccccaaaa cttagcacca aaaccaaatt ctggagatca
     3661 tccacagcac cgctcccacc tggcacctat gaaccagcct accttggtgg caaggacccc
     3721 agagtcaagg gtggcccctc gttgcagcaa gtcatgaggg accagctgaa accatttaca
     3781 gagcctaggg gtaagccacc aaagccaagt gtgttagaag ctgccaagaa aaccatcatc
     3841 aatgtccttg aacaaacaat tgacccacct gagaagtggt cgttcgcaca agcttgcgcg
     3901 tcccttgaca agaccacttc tagcggccat ccgcaccaca tgcggaaaaa cgactgctgg
     3961 aacggggaat ccttcacagg caagctggca gaccaggctt ccaaggccaa cctgatgttt
     4021 gaagaaggga agaacatgac cccagtctac acaggtgcac ttaaggatga attagtcaaa
     4081 actgataaaa tttatggtaa gatcaagaag aggcttctct ggggctcgga tttagcaacc
     4141 atgatccggt gtgctcgggc attcggaggc ctaatggatg aactcaaagc acactgtgtc
     4201 acacttccta tcagagttgg tatgaatatg aatgaggatg gccccatcat cttcgagaag
     4261 cattccaggt acagatacca ctatgatgct gattactctc ggtgggattc aacacaacag
     4321 agagccgtgc tggcagctgc tctagaaatc atggttaaat tctcctcaga accacatttg
     4381 gctcaggtag tcgcagaaga cctcctttct cctagcgtgg tggatgtggg tgacttcaca
     4441 atatcaatca acgagggtct tccctctggg gtgccttgca cctcccaatg gaactccatt
     4501 gcccactggc ttctcactct ctgtgcactc tccgaagtta caaatttgtc cccagacatc
     4561 atacaggcta attctctctt ctccttctat ggtgatgatg aaattgttag tacagacata
     4621 aaattagacc cagagaagtt gacagcaaag cttaaggaat atgggttgaa accaacccgc
     4681 cctgataaaa ctgaaggacc tcttgttatt tctgaagact tagatggttt gactttcctg
     4741 cggagaactg tgacccgcga cccagctggt tggtttggaa aactggagca gagctcaata
     4801 ctcaggcaaa tgtactggac taggggcccc aaccatgaag atccatctga atcaatgatt
     4861 ccacactctc aaagacccat acaattgatg tccttactgg gagaggccgc actccacggc
     4921 ccaacattct acagtaaaat cagcaaatta gtcattgcag agctaaaaga aggtggtatg
     4981 gatttttacg tgcccaggca agagccaatg ttcagatgga tgagattctc agatctgagc
     5041 acgtgggagg gcgatcgcaa tctggctccc agttttgtga atgaagatgg cgtcgaatga
     5101 cgccaaccca tctgatgggt ccgcagccaa cctcgtccca gaggtcaaca atgaggttat
     5161 ggctttggag cccgttgttg gtgccgctat tgcggcgcct gtggcgggcc aacaaaatgt
     5221 aattgacccc tggattagaa ataattttgt acaagcccct ggtggagagt tcacagtgtc
     5281 ccctagaaac gctccaggtg aaatactatg gagcgcgccc ttaggccctg atctgaatcc
     5341 ctacctatct catttggcca gaatgtataa tggttatgca ggtggttttg aagtgcaggt
     5401 gatcctcgcg gggaacgcgt tcaccgccgg aaaaattata tttgcagcag tcccaccgaa
     5461 ttttccaact gaaggcttga gtcccagcca ggtcactatg ttcccccaca taatagtaga
     5521 tgttaggcaa ttggaacctg tgttgatccc cttacctgat gttaggaata acttctatca
     5581 ctataatcag tcaaatgatt ccaccattaa attgatagca atgctgtata caccactcag
     5641 ggctaataat gctggggaag atgtcttcac agtctcttgt cgagtcctca cgaggccatc
     5701 ccctgatttt gattttatat ttttggtgcc acctacagtt gagtcaagaa ctaaaccatt
     5761 tactgtccca atcttaactg ttgaagaaat gaccaattca agattcccca ttcctttgga
     5821 aaagttgttc acgggtccca gcggtgcctt tgttgttcaa ccacaaaatg gcagatgcac
     5881 gactgatggc gtgctcttag gcaccaccca actgtctcct gtcaacatct gcaccttcag
     5941 aggggatgtc acccacattg caggttctcg taattacaca atgaatttgg cttctctaaa
     6001 ttggaacaat tatgacccaa cagaagaaat tccagcccct ctaggaactc cagatttcgt
     6061 gggaaagatc caaggtgtgc tcactcaaac cacaaaggga gatggctcga cccgtggcca
     6121 taaagctaca gtttacactg ggagtgcccc ctttactcca aagctgggca gtgttcaatt
     6181 cagtactgat acagaaaatg attttgaaac tcaccaaaac acaaaattca ccccagtcgg
     6241 tgtcatccag gatggtagca ccacccaccg aaatgaaccc caacaatggg tgctcccaag
     6301 ttattcaggt agaaatgtcc ataatgtaca cctagcccct gctgtagccc ccacttttcc
     6361 gggtgaacaa cttcttttct tcaggtccac tatgcccgga tgcagcgggt atcccaacat
     6421 ggatttggat tgcctactcc cccaggagtg ggtgcagcac ttctaccaag aggcagctcc
     6481 agcacaatct gatgtggctc tattgagatt tgtgaatcca gacacgggta gggtcctgtt
     6541 tgagtgcaaa ctccataagt caggctatgt cacagtggct cacaccggcc agcatgattt
     6601 ggtcatcccc cccaatggct attttaggtt tgattcctgg gttaatcaat tctacacact
     6661 tgcccccatg ggaaatggaa cggggcgtag acgtgcttta taatggctgg agctttcttt
     6721 gctggattgg catctgatgt ccttggctct gggcttggct ccctaatcaa tgctggggct
     6781 ggggctatca accaaaagat tgattttgaa aataacagaa aattgcagca agcttctttc
     6841 cagttcagta gtaatctaca acaggcttcc tttcaacatg ataaagagat gctccaagca
     6901 caaattgagg ccactaaaag gttgcaacag gaaatgatga aagtcaaaca ggcaatgctc
     6961 ttagaaggtg gattctctga aacagatgca gcccgtgggg caatcaacgc ccccatgaca
     7021 aaggctttgg actggagcgg aacaaggtac tgggcccctg atgctgggac tacaacatac
     7081 aatgcaggcc gcttttccac ccctcaacct tcgggggcat tgccaggaag aatcaatccc
     7141 aggattccta cccccgctcg gggctccccc agcacatctt ctaatgcttc tattgctact
     7201 tctatatatt caaatcaaac tgtttcaacg agacttggtt ctacagctgg ttctggcacc
     7261 aatgcctcga gtttcccgtc aactgcaagg actaggagtt gggttgagga tcaaaacaga
     7321 aatttgtcac ctttcatgag gggggctcac aacatatcgt ttgtcacccc accatccagc
     7381 agatcctcta gccaaggcac agtctcaacc gtgcctaaag aagttttgga ctcctggact
     7441 ggcgctttca acacgcgcag gcagcctctc ttcgctcaca ttcgtaagcg aggggagtca
     7501 cgggtgtaa
//