Typing tool

Complete norovirus genomes

JN400617  GII.4 Den Haag
 GII.P4 Den Haag

Length: 7,509 | 3 CDS

ORF1: 1..5100
ORF2: 5081..6703
ORF3: 6703..7509
LOCUS       JN400617                7509 bp    RNA     linear   VRL 19-DEC-2013
DEFINITION  Norovirus Hu/GII-4/CGMH19/2009/TW, complete genome.
ACCESSION   JN400617
VERSION     JN400617.1
KEYWORDS    .
SOURCE      Norovirus Hu/GII-4/CGMH19/2009/TW
  ORGANISM  Norovirus Hu/GII-4/CGMH19/2009/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/CGMH19/2009/TW"
                     /mol_type="genomic RNA"
                     /isolation_source="stool"
                     /host="Homo sapiens"
                     /db_xref="taxon:1195631"
                     /country="Taiwan"
                     /collection_date="16-May-2009"
                     /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="AFN09971.1"
                     /translation="MKMASNDASAAAVANSNNDTAKSSSDKMFSSMAVTFKRALGARP
                     KQPPPREIPQRPPRPPTPELVKKIPPPPPNGEDEVVVSYNAKDGISGLPELSTVRQPE
                     ETNTAFSVPPLNQRENRDAKEPLTGTILEMWDGEIYHYGLYVERGLVLGVHKPPAAIS
                     LAKVELTPLSLFWRPVYTPQYLISPDTLKKLHGETFPYTAFDNNCYAFCCWVLDLNDS
                     WLSRRMIQRTTGFFRPYQDWNRKPLPTTDDSKLKKVANIFLCTLSSLFTRPIKDIIGK
                     LRPLNIINILASCDWTFAGIVESLILLAELFGVFWTPPDVSAMIAPLLGDFELQGPED
                     LVVELVPVVMGGIGLVLGFTKEKIGKMLSSAASTLRACKDLGAYGLEILKLVMKWFFP
                     KKEEANELAMVRSIEDAVLDLEAIENNHMTTLLKDKDSLATYMRTLDLEEEKARKLST
                     KSASPDIVGTINALLARIAAARSLVHRAKEELSSRPRPVVLMISGRPGIGKTHLAREV
                     AKRIAASLTGDQRVGLIPRNGVDHWDAYKGERVVLWDDYGMSNPIHDALRLQELADTC
                     PLTLNCDRIENKGKVFDSDVIIITTNLANPAPLDYVNFEACSRRIDFLVYAEAPEVEK
                     AKRDFPGQPDMWKNAFSSDFSHIKLALAPQGGFDKNGNTPHGKGVMKTLTTGSLIARA
                     SGLLHERLDEFELQGPALTTFNFDRNKVLAFRQLAAENKYGLIDTMKVGRQLKDVTTM
                     PELKQALKNISIKKCQIVYSGCTYTLESDGKGNVKVDRVQSTSVQTNNELAGALHHLR
                     CARIRYYVKCVQEALYSIIQIAGAAFVTTRIIKRVNIQDLWSKPQVEDTEEATNKDGC
                     LKPKDDEEFVISSDDIKTEGKKGKNKTGRGKKHTAFSSKGLSDEEYDEYKRIREERNG
                     KYSIEEYLQDRDKYYEEVAIARATEEDFCEEEEAKIRQRIFRPTRKQRKEERASLGLV
                     TGSEIRKRNPEDFKPKGKLWADDDRSVDYNEKLSFEAPPSIWSRIVNFGSGWGFWVSP
                     SLFITSTHVIPQGAKEFFGVPIKQIQVHKSGEFCRLRFPKPIRTDVTGMILEEGAPEG
                     TVATLLIKRSTGELMPLAARMGTHATMKIQGRTVGGQMGMLLTGSNAKSMDLGTTPGD
                     CGCPYIYKRGNDYVVIGVHTAAARGGNTVICATQGGEGEATLEGGDSKGTYCGAPILG
                     PGSAPKLSTKTKFWRSSTVPLPPGTYEPAYLGGKDPRVKGGPSLQQVMREQLKPFTEP
                     RGKPPKPSVLEAAKKTIINVLEQTIDPPEKWSFAQACASLDKTTSSGHPHHMRKNDCW
                     NGESFTGKLADQASKANLMFEEGKNMTPVYTGALKDELVKTDKIYGKIKKRLLWGSDL
                     ATMIRCARAFGGLMDELKAHCVTLPIRVGMNMNEDGPIIFEKHSRFRYHYDADYSRWD
                     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="AFN09972.1"
                     /translation="MKMASNDASPSDGSAANLVPEVNNEVMALEPVVGAAIAAPVAGQ
                     QNVIDPWIRNNFVQAPGGEFTVSPRNAPGEILWSAPLGPDLNPYLSHLARMYNGYAGG
                     FEVQVILAGNAFTAGKIIFAAVPPNFPTEGLSPSQVTMFPHIIVDVRQLEPVLIPLPD
                     VRNNFYHYNQSNDSTIKLIAMLYTPLRANNAGEDVFTVSCRVLTRPSPDFDFIFLVPP
                     TVESRTKPFTVPILTVEEMTNSRFPIPLEKLFTGPSGAFVVQPQNGRCTTDGVLLGTT
                     QLSPVNICTFRGDVTHIAGSRNYTMNLAALNWNNYDPTEEIPAPLGTPDFVGKIQGVL
                     TQTTKADGSTRGHKATVYTGSADFTPKLGSVQFSTDTENDFETHQNTKFTPVGVIQDG
                     STTHRNEPQQWVLPSYSGRNVQNVHLAPAVAPTFPGEQLLFFRSTMPGCSGYPNMDLD
                     CLLPQEWVQHFYQEAAPAQSDVALLRFVNPDTGRVLFECKLHKSGYVTVAHTGQHDLV
                     IPPNGYFRFDSWVNQFYTLAPMGNGTGRRRAL"
     gene            6703..7509
                     /gene="VP2"
     CDS             6703..7509
                     /gene="VP2"
                     /note="ORF3"
                     /codon_start=1
                     /product="minor viral capsid protein"
                     /protein_id="AFN09973.1"
                     /translation="MAGAFFAGLASDVLGSGLGSLINAGAGAINQKIDFENNRKLQQA
                     SFQFSSNLQQASFQHDKETLQAQIEATKKLQQEMMRVKQAMLLEGGFSETDAARGAIN
                     APMTKALDWSGTRYWAPDARTTTYNAGRFSSPQPSGALPGRINPRAPTPARGSSSTSS
                     NASTATSIYSNQTASTRLGSTAGSGTNVSSLPSTARTRSWVEDQNRNLSPFMRGAHDI
                     SFVTPPSSRSSSQGTVSTVPKEVLDSWTGAFNTRRQPLFAHIRRRGESRV"
ORIGIN      
        1 atgaagatgg cgtctaacga cgcttccgct gccgctgttg ctaacagcaa caacgacacc
       61 gcaaaatctt caagtgacaa aatgttttct agcatggctg tcacttttaa acgagccctc
      121 ggggcgcggc ccaaacagcc ccccccgagg gaaataccac aaagaccccc acgaccacct
      181 actccagaac tggtcaagaa gatccctcct cccccgccca acggagagga tgaagtagtg
      241 gtttcttata atgccaaaga tggcatttcc ggtttacctg agctctccac cgtcagacaa
      301 ccagaagaaa 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 tacctcatct ctccagacac tctcaagaaa ttgcacggag aaacatttcc ctacacagcc
      601 tttgacaaca attgctatgc cttttgttgc tgggtcctgg acctaaacga ctcgtggctg
      661 agtaggagaa tgatccagag aacaactggc ttcttcagac cctaccaaga ttggaatagg
      721 aaacccctcc ctactacgga tgattccaaa ttaaagaagg tagctaacat attcctgtgt
      781 accctgtctt cgctattcac caggcccata aaagacataa taggaaagct aaggcctctc
      841 aacatcatca acatcctagc ttcatgtgat tggactttcg cgggcatagt ggagtccttg
      901 atactcttgg cagagctctt tggagtcttc tggacacccc cagatgtgtc tgcgatgatc
      961 gcccccttac tcggtgattt cgagttacaa ggacctgagg accttgtagt ggagctcgtc
     1021 cctgtagtaa tgggggggat tggtttggtg ctaggattca ccaaagagaa gattggaaaa
     1081 atgttgtcat ctgctgcatc caccttgaga gcttgcaaag atcttggtgc atatgggcta
     1141 gagatcctaa agttagtcat gaagtggttc ttcccgaaga aagaggaggc aaatgaactg
     1201 gctatggtga gatctatcga ggatgcagta ctggaccttg aggcaattga aaacaaccat
     1261 atgaccaccc tgctcaaaga taaagacagc ctggcaacct acatgagaac ccttgacctc
     1321 gaggaagaga aagccaggaa actctcaacc aagtccgctt cacctgacat cgtgggcaca
     1381 atcaacgccc ttctggcgag aatcgccgct gcacgctccc tggtgcaccg agcgaaggag
     1441 gagctttcca gcagaccaag acctgtagtc ttgatgatat caggcagacc agggataggg
     1501 aagacccacc ttgctaggga agtggctaag agaattgcag cctccctcac aggagaccag
     1561 cgtgtaggcc tcatcccacg caatggcgtc gatcactggg atgcgtacaa gggggagagg
     1621 gtcgtcctat gggacgacta tggaatgagc aatcccatcc acgacgccct caggctgcaa
     1681 gaactcgctg acacttgccc cctcacccta aattgtgaca ggatcgagaa taaaggaaag
     1741 gtctttgaca gcgatgtcat cattatcact actaatctgg ccaacccagc accactggac
     1801 tatgtcaact ttgaagcgtg ctcgaggcgc atcgatttcc tcgtgtatgc ggaagccccc
     1861 gaggtcgaaa aggcgaagcg tgacttcccg ggccaacctg acatgtggaa aaacgctttt
     1921 agttctgatt tctcacacat aaaattggcc ctggctccac aaggtggctt tgacaagaac
     1981 gggaacaccc cacacgggaa gggcgtcatg aagactctca ccactggctc cctcattgcc
     2041 cgggcatcag ggctgctcca tgagagattg gatgagtttg aactacaggg cccagctctt
     2101 accaccttca actttgatcg caacaaagtg cttgccttca ggcagcttgc tgctgaaaat
     2161 aaatatgggt tgatagatac aatgaaagtt gggaggcagc tcaaggatgt cacaaccatg
     2221 ccagaactta aacaagcact caaaaatatc tcaatcaaga agtgccagat tgtgtacagt
     2281 ggttgcactt acacacttga gtctgatggc aagggcaatg tgaaagttga cagagttcag
     2341 agcacctccg tacagaccaa caatgagctg gctggcgccc tgcaccatct aaggtgcgcc
     2401 agaatcaggt actatgtcaa gtgtgtccag gaggccctgt attctatcat ccagattgct
     2461 ggggctgcat ttgtcaccac acgcatcatc aagcgtgtga acattcaaga cctgtggtcc
     2521 aagccacaag tggaagacac agaggaggct accaacaagg acgggtgcct aaaacccaaa
     2581 gatgatgagg agttcgtcat ttcatctgac gacattaaaa ctgagggtaa gaaagggaag
     2641 aacaagactg gccgtggcaa gaagcacaca gccttctcaa gtaaaggtct cagtgatgaa
     2701 gagtatgatg agtacaagag gattagagag gaaaggaatg gcaagtactc catagaagag
     2761 taccttcagg acagggacaa atactatgag gaggtggcca ttgctagggc gaccgaggaa
     2821 gacttctgtg aagaggagga ggccaagatc cggcaaagga ttttcagacc aacaaggaaa
     2881 caacgcaagg aagaaagagc ttctctcggt ttagtcacag gttctgaaat taggaaaaga
     2941 aacccagaag acttcaagcc caaggggaaa ctatgggctg atgatgacag aagtgtggac
     3001 tacaatgaga aactcagttt tgaggccccg ccaagcatct ggtcaaggat agtcaacttt
     3061 ggctcaggtt ggggcttctg ggtctccccc agcttgttca taacatcaac ccacgtcata
     3121 ccccagggcg caaaggagtt ctttggagtc cccatcaaac aaattcaggt acacaagtca
     3181 ggcgaattct gtcgcttgag attcccaaaa ccaatcagga ctgatgtgac tggcatgatc
     3241 ttggaagaag gcgcgcccga aggcaccgtg gccacactac tcatcaaaag gtccactgga
     3301 gaactcatgc ccctagcagc cagaatgggg acccatgcaa ccatgaaaat tcaagggcgc
     3361 actgttggag gtcagatggg catgcttctg acaggatcca acgccaaaag catggaccta
     3421 ggcaccacac caggtgattg cggctgtccc tacatctaca agagaggaaa tgactatgtg
     3481 gtcattggag tccacacggc tgccgctcgt ggtggaaaca ctgtcatatg tgccacccag
     3541 gggggtgagg gggaagctac acttgaaggt ggtgacagta agggaacata ctgtggtgca
     3601 ccaatcctag gcccagggag cgccccaaaa cttagcacca aaaccaaatt ctggaggtcg
     3661 tccacagtac cgctcccacc tggcacctat gaaccagcct accttggtgg caaggacccc
     3721 agagtcaagg gtggcccctc gttgcagcaa gtcatgagag aacagctgaa accatttaca
     3781 gagcccaggg gaaagccacc aaagccaagt gtgttagaag ctgccaagaa aaccatcatc
     3841 aatgtccttg aacaaacaat tgacccacct gagaagtggt cgttcgcaca agcttgcgcg
     3901 tcccttgaca agaccacttc tagcggccat ccgcaccaca tgcggaaaaa cgactgctgg
     3961 aacggggagt ccttcacagg caagctggca gaccaggctt ccaaagccaa cctgatgttt
     4021 gaagaaggga agaacatgac cccagtttac acaggtgcac ttaaggatga attagtcaaa
     4081 actgacaaaa tttatggtaa gatcaagaag aggcttctct ggggctcgga tttagcaacc
     4141 atgatccggt gtgctcgagc attcggaggc ctaatggatg aactcaaagc acactgtgtc
     4201 acactgccta tcagagttgg tatgaatatg aatgaggatg gccccatcat cttcgagaag
     4261 cattccaggt tcagatacca ctatgatgct gactactctc ggtgggattc aacacaacag
     4321 agagccgtgc tggcagctgc tctagaaatc atggtcaaat tctcctcgga accgcatttg
     4381 gctcaggtag tcgcagaaga ccttctttct cctagcgtgg tggatgtggg tgacttcaca
     4441 atatcaatca acgagggtct tccctctggg gtgccctgca cctcccaatg gaactccatc
     4501 gcccactggc ttctcactct ctgtgcgctc tccgaagtta caaatttgtc cccagacatc
     4561 atacaggcta attctctctt ctccttctat ggtgatgatg aaattgttag tacagacata
     4621 aaactagacc cggagaagtt gacagcaaag cttaaggaat atgggttgaa accaacccgc
     4681 cctgataaaa ctgaagggcc tcttgttatt tctgaagact tggatggttt gactttcctg
     4741 cggagaactg tgacccgcga cccagctggt tggtttggaa aactggagca gagctcaata
     4801 ctcaggcaaa tgtactggac caggggccct aaccatgaag atccatctga atcaatgatt
     4861 ccacactctc agagacccat 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 cgccagccca tctgatgggt ccgcagccaa cctcgtccca gaggtcaaca atgaggttat
     5161 ggctttggag cccgttgtcg gtgccgctat tgcggcgcct gtagcgggcc aacaaaatgt
     5221 aattgacccc tggattagaa ataattttgt acaagcccct ggtggggagt tcacagtatc
     5281 ccctagaaac gctccaggtg aaatattgtg gagcgcgccc ttaggccctg atctgaatcc
     5341 ctacctatct catttggcca gaatgtataa tggttatgca ggtggttttg aagtgcaggt
     5401 gatcctcgcg gggaacgcgt tcaccgccgg aaaaattata tttgcagcag tcccaccaaa
     5461 ttttccaact gaaggcttga gccccagcca ggtcaccatg ttcccccaca taatagtaga
     5521 tgttaggcaa ttggaacctg tgttgatccc cttacctgat gttaggaata acttctatca
     5581 ttataatcag tcaaacgatt ctaccattaa attgatagca atgctgtata caccacttag
     5641 ggctaataat gctggggaag atgtcttcac agtctcttgt cgagtcctca cgaggccatc
     5701 ccccgatttt gattttatat ttttggtgcc acctacagtt gagtcaagaa ctaaaccatt
     5761 tactgtccca atcttaactg ttgaagaaat gactaattca agattcccca ttcctttgga
     5821 aaagttgttc acgggtccca gcggtgcctt tgttgttcaa ccacaaaatg gcagatgcac
     5881 gactgatggc gtgctcctag gcaccaccca actgtctcct gtcaacatct gcaccttcag
     5941 aggggatgtc acccacattg caggttctcg taattacaca atgaatttgg ctgctctgaa
     6001 ttggaacaat tatgacccaa cagaagaaat tccagcccct ctaggaaccc cagatttcgt
     6061 gggaaagatc caaggtgtgc ttactcaaac cacaaaggca gatggctcga cccgtggcca
     6121 taaagctaca gtttacactg ggagtgccga ctttactcca aagctgggca gtgttcaatt
     6181 cagtactgat acagaaaatg attttgaaac tcaccaaaac acaaaattca ccccagtcgg
     6241 tgtcatccag gatggtagca ccacccaccg aaatgaaccc caacaatggg tgctcccaag
     6301 ttattcaggt agaaatgtcc aaaatgtaca cctagcccct gctgtagccc ccaccttccc
     6361 gggtgaacaa cttcttttct tcaggtccac tatgcccgga tgcagcgggt atcccaacat
     6421 ggatttggat tgcctactcc cccaagagtg ggtgcagcac ttctaccaag aggcagctcc
     6481 agcacaatct gatgtggctc tattgagatt tgtgaatcca gacacgggta gggtcctgtt
     6541 tgagtgcaaa cttcataaat caggctatgt cacagtggct cacaccggcc agcatgactt
     6601 ggtcatcccc cccaatggct attttaggtt tgattcctgg gttaatcaat tctacacact
     6661 tgcccccatg ggaaatggaa cggggcgtag acgtgcttta taatggctgg agctttcttt
     6721 gctggattgg catctgatgt ccttggctct ggacttggtt ccctgattaa tgctggggct
     6781 ggggctatca accaaaagat tgattttgaa aataacagaa aattgcagca agcttccttc
     6841 cagtttagca gtaatctaca acaggcttcc tttcaacatg acaaagagac gctccaagca
     6901 caaattgagg ccactaaaaa gttgcaacag gaaatgatga gagtcaaaca ggcaatgctc
     6961 ttagaaggtg gattctctga aacagatgca gcccgtgggg caatcaacgc ccccatgaca
     7021 aaggctttgg actggagcgg aacaaggtac tgggcccctg atgctaggac tacaacatac
     7081 aatgcaggcc gcttttcctc ccctcaacct tcgggggcac tgccaggaag aatcaatccc
     7141 agggctccca cccccgctcg gggctcctct agcacatctt ctaatgcttc tactgctact
     7201 tctatatatt caaatcaaac cgcttcaacg agacttggtt ctacagctgg ttctggcacc
     7261 aatgtctcga gtctcccgtc aactgcaagg actaggagtt gggttgagga tcaaaacaga
     7321 aatttgtcac ctttcatgag gggggctcac gacatatcgt ttgtcactcc accatctagt
     7381 agatcctcta gccaaggcac agtctcaacc gtgcctaaag aagttttgga ctcctggact
     7441 ggcgctttca acacgcgcag gcagcctctc ttcgctcaca ttcgtaggcg aggggagtca
     7501 cgggtgtaa
//