Typing tool

Complete norovirus genomes

JN400618  GII.4 New Orleans
 GII.P4 New Orleans

Length: 7,479 | 3 CDS

ORF1: 1..5100
ORF2: 5081..6673
ORF3: 6673..7479
LOCUS       JN400618                7479 bp    RNA     linear   VRL 14-JAN-2014
DEFINITION  Norovirus Hu/GII-4/CGMH20/2009/TW, complete genome.
ACCESSION   JN400618
VERSION     JN400618.2
KEYWORDS    .
SOURCE      Norovirus Hu/GII-4/CGMH20/2009/TW
  ORGANISM  Norovirus Hu/GII-4/CGMH20/2009/TW
            Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes;
            Picornavirales; Caliciviridae; Norovirus.
REFERENCE   1  (bases 1 to 7479)
  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 7479)
  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
REFERENCE   3  (bases 1 to 7479)
  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 (14-JAN-2014) Graduate Institute of clinical medical
            sciences, 259, Wen-Hwa 1st Rd, Kwei-Shan, Taoyuan, Taiwan
  REMARK    Sequence update by submitter
COMMENT     On Jan 14, 2014 this sequence version replaced JN400618.1.
FEATURES             Location/Qualifiers
     source          1..7479
                     /organism="Norovirus Hu/GII-4/CGMH20/2009/TW"
                     /mol_type="genomic RNA"
                     /isolation_source="stool"
                     /host="Homo sapiens"
                     /db_xref="taxon:1195632"
                     /country="Taiwan"
                     /collection_date="31-Dec-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="AFN09974.2"
                     /translation="MKVASNDASAAAVANSNNDTAKSSSDGMLSSMAVTFKRALGARP
                     KQPPPREKPQRPPRPPTPELVKNIPPPPPNGEDGIVVSYSVKDGVSGLPDLSTVRQPE
                     ESNTAFSVPPLNQRENRDAKEPLTGTILEMWDGEIYHYGLYVERGLVLGVHKPPAAIS
                     LAKVELAPLSLYWRPVYTPQYLISPDTLKKLSGETFPYTAFDNNCYAFCCWVLDLNDS
                     WLSRRMIQRTTGFFRPYQDWNRKPLPTMDDSKIKKVANIFLCALSSLFTRPIKDIIGK
                     IRPLNILNILASCDWTFAGIVESLILLAELFGVFWTPPDVSAMIAPLLGDYELQGPED
                     LAVELVPVVMGGIGLVLGFTKEKIGKMLSSAASTLRACKDLGAYGLEILKLVMKWFFP
                     KKEEANELAIVRSIEDAVLDLEAIENNHMTTLLKDKDGLATYMRTLDLEEEKARKLST
                     KSASPDIVGTINALLARIAAARSLVHREKEELSSRPRPVVLMISGKPGIGKTHLAREV
                     AKRIAASLTGDQRVGLIPRNGVDHWDAYKGERVVLWDDYGMSNPIHDALRLQELADTC
                     PLTLNCDRIENKGKVFDSDVIIITTNLANPAPLDYVNFEACSRRIDFLVYAEAPEVEK
                     AKRDFPGQPDMWKNAFSSDFSHIKLALAPQGGFDKNGNTPHGKGVMKTLTTGSLIARA
                     SGLLHERLDEFELQGPAITTFNFDRNKVLAFRQLAAENKYGLMDTMRVGKQLKDVRTM
                     PELKQALKNVSIKKCQIVYSGCTYILESDGKGNVKVDRIQSAAVQTNNELAGALHHLR
                     CARIRYYVKCVQEALYSIIQIAGAAFVTTRIAKRMNIQDLWSKPQVENTEETTSKDGC
                     PKPKDDEEFVISSDDIKTEGKKGKNKTGRGKKHTAFSSKGLSDEEYDEYKRIREERNG
                     KYSIEEYLQDRDKYYEEVAIARATEEDFCEEEEAKIRQRIFRPTRKQRKEERASLGLV
                     TGSEIRKRNPDDFKPKGKLWADDDRSVDYNEKLSFEAPPSIWSRIVNFGSGWGFWVSP
                     SLFITSTHVIPQGAKEFFGVPIKQIQVHKSGEFCRLRFPKPIRTDVTGMILEEGAPEG
                     TVVTLLIKRSTGELMPLAARMGTHATMKIQGRTVGGQMGMLLTGSNAKSMDLGTTPGD
                     CGCPYIYKRGNDYVVIGVHTAAARGGNTVICATQGSEGEATLEGGDNKGTYCGAPILG
                     PGSAPTLSTKTKFWRSSTASLPPGTYEPAYLGGKDPRVKGGPSLQQVMREQLKPFTEP
                     RGKPPKPSVLEAAKKTIINVLEQTIDPPEKWSFAQACASLDKTTSSGHPHHMRKNDCW
                     NGESFTGKLADQASKANLMFEEGKNMTPVYTAALKDELVKTDKIYGKIKKRLLWGSDL
                     ATMIRCARAFGGLMDELKAHCVTLPIRVGMNMNEDGPIIFERHSRYTYHYDADYSRWD
                     STQQRAVLAAALEIMVKFSPEPHLAQVVAEDLLSPSVVDVGDFTISINEGLPSGVPCT
                     SQWNSIAHWLLTLCALSEVTNLSPDTIQANSLFSFYGDDEIVSTDIKLDPEKLTAKLR
                     EYGLKPTRPDKTEGPLVISEDLNGLTFLRRTVTRDPAGWFGKLEQSSILRQMYWTRGP
                     NHGDPSETMIPHSQRPIQLMSLLGEAALHGPAFYSKISKLVIAELKEGGMDFYVPRQE
                     PMFRWMRFSDLSTWEGDRNLAPSFVNEDGVE"
     gene            5081..6673
                     /gene="VP1"
     CDS             5081..6673
                     /gene="VP1"
                     /note="ORF2"
                     /codon_start=1
                     /product="major viral capsid protein"
                     /protein_id="AFN09975.1"
                     /translation="MKMASSDANPSDGSTANLVPEVNNEVMALEPVVGAAIAAPVAGQ
                     QNVIDPWIRNNFVQAPGGEFTVSPRNAPGEILWSAPLGPDLNPYLSHLARMYNGYAGG
                     FEVQVILAGNAFTAGKIIFAAVPPNFPTEGLSPSQVTMFPHIIVDVRQLEPVLIPLPD
                     VRNNFYHYNQSNDSTIKLIAMLYTPLRANNAGDDVFTVSCRVLTRPSPRFESRTKPFS
                     VPVLTVEEMTNSRFPIPLEKLFTGPSSAFVVQPQNGRCTTDGVLLGTTQLSPVNICTF
                     RGDVTHIPGSRNYTMNLASQNWNSYGPTEEIPAPLGTPDFVGKIQGVLTQTTRTNGST
                     RGHKATVYTGSADFSPKLGRVQFATDTDNDFETNQNTKFTPVGVIQDGSTTPRNEPQQ
                     WVLPSYSGRNIHNVHLAPAVAPTFPGEQLLFFRSTMPGCSGYPNMDLDCLLPQEWVQY
                     FYQEAAPAQSDVALLRFVNPDTGRVLFECKLHKSGYVTVAHTGQHDLVIPPNGYFRFD
                     SWVNQFYTLAPMGNGTGRRRAL"
     gene            6673..7479
                     /gene="VP2"
     CDS             6673..7479
                     /gene="VP2"
                     /note="ORF3"
                     /codon_start=1
                     /product="minor viral capsid protein"
                     /protein_id="AFN09976.1"
                     /translation="MAGAFFAGLASDVLGSGLGSLINAGAGAINQKVEFENNRKLQQA
                     SFQFSSNLQQASFQHDKEMLQAQIEATKKLQQEMMRVKQAVLLEGGFSETDAARGAIN
                     APMTKTLDWSGTRYWAPDARTTTYNAGRFSTPQPSGALPGRANLRATVPARGSSSTSS
                     NSSIATSVYSNQTTSTRLGSTAGSGTSVSSLPSTARTRSGVEDQKRNLSPFMGGAHNI
                     SFFPPLFSRSFSQGTVSTVPKKVLDSWTGAFNTGRQPFFAHICKGGESRG"
ORIGIN      
        1 atgaaagtgg cgtctaacga cgcttccgct gccgctgttg ctaacagcaa caacgacacc
       61 gcaaaatctt caagtgacgg aatgctttct agcatggctg tcacttttaa acgagccctc
      121 ggggcgcggc ctaaacagcc tcccccgagg gaaaaaccac aaagaccccc acgaccacct
      181 actccagaac tggttaaaaa tattccccct cccccaccca acggagagga tggaatagtg
      241 gtttcttata gtgtcaaaga tggtgtttcc ggcttgcctg acctttccac cgtcaggcaa
      301 ccggaagaat ctaacacggc cttcagtgtc cctccactca atcagaggga gaatagagat
      361 gctaaggagc cacttactgg aacaattctg gaaatgtggg acggggaaat ctaccactat
      421 ggcctgtatg tggagcgagg tcttgtacta ggtgtgcaca aaccaccagc tgctatcagc
      481 ctcgctaagg ttgagctagc accactctcc ttgtactgga gacctgtgta cactcctcag
      541 tacctcatct ctccagacac tctcaagaaa ttatccggag aaacgttccc ctacacagcc
      601 tttgacaaca actgttatgc cttttgttgc tgggtcctgg acctaaatga ctcgtggctg
      661 agcaggagaa tgatccagag gacaactggt ttcttcaggc cctaccaaga ctggaatagg
      721 aaaccccttc ccactatgga tgactccaaa ataaagaagg tagctaacat attcctgtgt
      781 gctctgtcct cgctgttcac cagacccata aaagatataa tagggaagat aaggcctctt
      841 aacatcctca acatcttagc ctcatgtgat tggacttttg caggcatagt ggagtccctg
      901 atactcttgg cagaactctt tggagttttc tggacacccc cagatgtgtc tgcgatgatt
      961 gcccccttac ttggtgacta cgagctacaa ggacctgagg accttgcagt ggagctcgtc
     1021 cccgtggtga tggggggaat tggtttggtg ttaggattca ccaaagagaa gattgggaaa
     1081 atgttgtcat ctgctgcgtc caccttgaga gcttgtaaag accttggtgc atatgggcta
     1141 gagatcctaa agttggtcat gaagtggttc ttcccgaaga aggaggaggc aaatgagctg
     1201 gctatagtga ggtctatcga ggatgcagtc ctggatctcg aggcaattga aaacaaccat
     1261 atgaccacct tgctcaaaga caaagacggc ctggcaacct atatgagaac acttgacctt
     1321 gaggaggaga aagccaggaa actctcaacc aagtctgcct cacccgacat cgtgggcaca
     1381 atcaacgccc tcctggcgag aatcgctgcc gcacgttctc tggtgcatcg agagaaggag
     1441 gaactttcca gcagaccaag acctgtggtg ttgatgatat caggcaagcc aggaataggg
     1501 aagacccacc tcgctaggga agtggctaag agaatcgcag cctcccttac aggagaccag
     1561 cgtgtgggcc tcatcccacg caatggcgtc gaccattggg atgcgtacaa gggggagagg
     1621 gtcgttctat gggacgatta tggaatgagc aaccctattc acgatgccct caggctgcaa
     1681 gaactcgctg acacttgccc cctcactcta aactgtgaca ggattgaaaa taaaggaaag
     1741 gtctttgaca gcgatgtcat cattatcacc actaatctgg ccaacccagc accactggac
     1801 tatgtcaact ttgaagcatg ctcgaggcgc atcgacttcc tcgtgtatgc agaagcccct
     1861 gaagtcgaaa aggcgaagcg tgacttccca ggccagcctg acatgtggaa gaacgctttc
     1921 agttctgatt tctcacacat aaaactagca ctggccccac agggtggttt cgacaagaac
     1981 gggaacaccc cacacggaaa gggcgtcatg aagactctca ccactggctc ccttattgcc
     2041 cgggcatcag ggctactcca tgagaggtta gatgaatttg aactacaggg cccagctatc
     2101 accaccttca atttcgatcg caataaagtg cttgccttta gacagcttgc tgctgaaaat
     2161 aaatatgggt tgatggacac aatgagagtt gggaaacagc tcaaggatgt cagaaccatg
     2221 ccagaactca aacaagcact caagaatgtc tcaatcaaga agtgccaaat agtgtatagt
     2281 ggttgcacct acatacttga gtctgatggc aagggcaatg tgaaagttga cagaatccaa
     2341 agcgccgccg tgcagaccaa caatgagctg gctggtgccc tgcaccatct gaggtgcgcc
     2401 agaatcagat actatgtcaa gtgtgtccag gaggccctgt attccatcat tcaaattgct
     2461 ggggctgcat ttgtcaccac gcgcattgcc aagcgcatga acatacaaga cctatggtcc
     2521 aagccacaag tggaaaacac agaggagacc accagcaagg acgggtgccc aaaacctaag
     2581 gatgatgagg agtttgtcat ttcatctgac gacatcaaaa ctgagggtaa gaaagggaag
     2641 aacaaaactg gccgcggcaa gaagcacaca gcattttcaa gcaaaggcct cagtgatgaa
     2701 gagtacgatg agtacaagag gattagagaa gaaaggaatg gcaagtactc catagaagag
     2761 taccttcagg acagggacaa atattatgag gaggtggcca ttgccagggc gactgaggaa
     2821 gacttctgtg aagaggagga ggccaagatc cggcaaagga tctttaggcc aacaaggaaa
     2881 caacgcaagg aggaaagagc ctctctcggt ctggtcacag gctctgaaat taggaaaaga
     2941 aacccagatg acttcaaacc caaggggaaa ttgtgggctg acgatgacag gagtgtggac
     3001 tacaatgaga aactcagttt tgaggcccca ccaagcatct ggtcgagaat agtcaacttt
     3061 ggttcaggct ggggattctg ggtctccccc agtctgttca taacatcaac ccatgtcata
     3121 ccccagggcg caaaggagtt ctttggagtc cccatcaaac aaatacaggt acacaagtca
     3181 ggcgagttct gtcgcttgag attcccaaaa ccaatcagga ctgatgtgac gggcatgatc
     3241 ttagaagaag gcgcacctga gggcaccgtg gtcacactac tcatcaaaag gtccactggg
     3301 gaactcatgc ccctagcagc taggatgggg acccatgcga ccatgaagat ccaagggcgc
     3361 actgttggag gccagatggg catgcttctg acaggatcca acgccaagag catggacctg
     3421 ggtactacac caggtgattg tggctgcccc tatatctaca agagaggtaa tgactatgtg
     3481 gtcattggag tccacacggc tgccgcacgt gggggaaaca ctgtcatatg tgccacccag
     3541 gggagtgaag gagaggctac acttgaaggt ggtgacaaca aggggacata ctgtggtgca
     3601 ccaatcctag gcccagggag tgccccaaca ctcagcacca agaccaaatt ctggagatcg
     3661 tccacagcat cactcccacc tggcacctat gaaccagcct atcttggtgg caaggaccct
     3721 agagtcaagg gtggcccttc actgcagcaa gtcatgaggg aacagttgaa gccattcaca
     3781 gagccaaggg gcaagccacc aaaaccaagt gtattagaag ctgccaagaa gaccatcatc
     3841 aatgtccttg agcaaacaat tgatccacct gagaaatggt cgttcgcaca agcttgcgcg
     3901 tcccttgaca agaccacttc cagtggtcat ccgcaccaca tgcggaaaaa cgactgctgg
     3961 aacggggagt ccttcacagg caagctggca gaccaggctt ccaaggccaa cctgatgttt
     4021 gaggaaggga agaacatgac cccagtctac acagctgcgc tcaaggatga gttagttaaa
     4081 actgacaaaa tttatggtaa gatcaagaag aggcttctct ggggctcgga cttggcgacc
     4141 atgatccggt gcgctcgagc attcggaggc ctcatggatg aactcaaagc acactgtgtc
     4201 acacttccca ttagagttgg catgaatatg aatgaggatg gccccatcat cttcgagagg
     4261 cattccaggt acacatatca ctatgatgct gattactctc gatgggattc aacacaacag
     4321 agagccgtgt tggcagcagc tctggaaatc atggttaaat tctccccaga accacatttg
     4381 gctcaggtag tcgcggaaga ccttctttct cctagcgtgg tggacgtggg cgatttcaca
     4441 atatcaatca acgagggtct tccctctggg gtgccctgca cctcccaatg gaactccatc
     4501 gcccactggc ttctcactct ctgtgcgctc tctgaagtca caaacctatc ccctgatacc
     4561 atacaggcta actccctctt ctctttttat ggtgatgatg aaattgttag cacagacata
     4621 aaattggacc cagagaaatt gacagcaaag ctcagggagt atgggttaaa accaacccgc
     4681 cctgacaaaa ctgaaggacc ccttgtcatc tctgaagacc tgaatggcct aactttcctg
     4741 cggagaactg tgacccgcga cccagctggt tggtttggaa aattggagca gagttcaata
     4801 ctcaggcaaa tgtattggac taggggtccc aaccatggag acccttctga aacaatgatt
     4861 ccacactccc aaagacccat acaattgatg tccctactgg gggaggccgc tctccacggc
     4921 ccagcatttt acagtaaaat cagcaaattg gtcattgcag aacttaaaga aggtggcatg
     4981 gatttttacg tgcccagaca agagccaatg ttcagatgga tgagattctc agatctgagc
     5041 acgtgggagg gcgatcgcaa tctggctccc agttttgtga atgaagatgg cgtcgagtga
     5101 cgccaaccca tctgatgggt ccacagccaa cctcgtccca gaggtcaaca atgaggttat
     5161 ggctttggag cccgtagttg gtgccgccat tgcggcacct gtagcgggcc aacaaaatgt
     5221 aattgacccc tggattagaa acaattttgt acaagcccct ggtggagagt ttacagtatc
     5281 ccctagaaac gctccaggtg aaatactatg gagcgcgccc ttaggccctg atttgaatcc
     5341 ctacctttcc catttggcca gaatgtacaa tggttatgca ggtggttttg aagtgcaggt
     5401 aatcctcgcg gggaacgcgt tcaccgccgg gaaaatcata tttgcagcag tcccaccaaa
     5461 tttcccaact gaaggtttga gccccagcca ggtcactatg ttcccccaca taatagtaga
     5521 tgttaggcaa ttggaacctg tgttgatccc cttacccgat gttaggaata atttctatca
     5581 ttataatcaa tcaaatgact ccaccatcaa attgatagca atgttgtaca caccacttag
     5641 ggctaataat gccggggacg atgtcttcac agtttcttgt cgagttctca cgagaccatc
     5701 cccccgattt gaatcaagaa ctaaaccatt ctctgtccca gttttaactg ttgaggagat
     5761 gaccaattca aggttcccca ttcctttgga aaagttgttc acgggcccca gtagtgcctt
     5821 tgttgttcaa ccacaaaacg gcaggtgcac gactgatggc gtgctcctag gtaccaccca
     5881 actgtctcct gtcaacatct gcaccttcag aggggatgtc acccatattc caggcagtcg
     5941 taactacaca atgaatttgg cctcccaaaa ttggaacagt tacggtccaa cagaagaaat
     6001 cccagcccct ctaggaactc cagatttcgt ggggaaaatt caaggtgtgc tcacccaaac
     6061 cacaaggaca aatggctcga cccgcggcca caaagctaca gtgtacactg ggagcgccga
     6121 cttttctcca aaactgggta gagttcaatt tgccactgac acagacaatg attttgaaac
     6181 taaccaaaac acaaagttca ccccagtcgg cgttatccag gatggtagta ctaccccccg
     6241 aaatgaaccc caacaatggg tgctcccaag ttactcaggc aggaacattc acaatgtgca
     6301 cctggccccc gctgtagccc ccactttccc gggcgagcag ctcctctttt tcagatctac
     6361 tatgcccgga tgcagtgggt accccaacat ggacttggac tgtctgctcc cccaggaatg
     6421 ggtgcagtac ttctaccagg aggcagcccc agcacaatct gatgtggctc tgttaagatt
     6481 tgtgaatcca gacacaggta gggttttgtt tgagtgtaag cttcataaat caggctatgt
     6541 tacagtggct catactggcc aacatgattt ggttatcccc cccaatggtt attttagatt
     6601 tgattcctgg gtcaaccagt tctacacact tgcccccatg ggaaatggga cggggcgtag
     6661 acgtgcatta taatggctgg agctttcttt gctggattgg catctgacgt ccttggctct
     6721 ggacttggtt ccctaatcaa tgctggggct ggggccatca accaaaaagt tgaatttgaa
     6781 aataacagaa aattgcaaca agcttccttc caatttagta gcaatctaca acaggcttcc
     6841 tttcaacatg acaaagagat gctccaagca caaattgagg ccaccaaaaa gttgcaacag
     6901 gaaatgatga gagttaaaca agcagtgctc ctagagggtg gattctctga gacagatgca
     6961 gcccgtgggg caatcaacgc ccccatgaca aaaactttgg actggagcgg gacaaggtac
     7021 tgggctcccg atgctaggac tacaacatat aatgcaggcc gcttttccac ccctcaaccc
     7081 tcgggggcac taccaggaag agctaatctt agggctactg tccccgcccg gggttcctcc
     7141 agcacgtctt ctaattcttc tattgctact tctgtgtatt caaatcaaac cacctcaacg
     7201 agacttggtt ctacagctgg ttctggtacc agtgtctcga gcctcccgtc aactgcaagg
     7261 actaggagcg gggttgagga tcaaaaaagg aatttgtccc ctttcatggg gggggctcac
     7321 aacatttctt ttttcccccc cctatttagc agatccttta gccaaggcac agtttcaacc
     7381 gtgcccaaaa aagttttgga ctcctggacg ggggctttca acacgggcag gcagcctttt
     7441 tttgctcaca tttgcaaggg aggggagtca cgggggtaa
//