Typing tool

Complete norovirus genomes

JX989074  GII.4 New Orleans
 GII.P4 New Orleans

Length: 7,559 | 3 CDS

ORF1: 5..5104
ORF2: 5085..6707
ORF3: 6707..7513
LOCUS       JX989074                7559 bp    RNA     linear   VRL 09-MAY-2014
DEFINITION  Norovirus Hu/GII.4/GZ2010-L87/Guangzhou/CHN/2011, complete genome.
ACCESSION   JX989074
VERSION     JX989074.1
KEYWORDS    .
SOURCE      Norovirus Hu/GII.4/GZ2010-L87/Guangzhou/CHN/2011
  ORGANISM  Norovirus Hu/GII.4/GZ2010-L87/Guangzhou/CHN/2011
            Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes;
            Picornavirales; Caliciviridae; Norovirus.
REFERENCE   1  (bases 1 to 7559)
  AUTHORS   Xue,L., Wu,Q., Kou,X., Zhang,J. and Guo,W.
  TITLE     A simple and novel method for GII norovirus genome clone with
            generic primers
  JOURNAL   J. Appl. Microbiol. 115 (2), 613-620 (2013)
   PUBMED   23647661
REFERENCE   2  (bases 1 to 7559)
  AUTHORS   Xue,L., Wu,Q., Kou,X. and Zhang,J.
  TITLE     Rational design of generic primers used for genome clone of GII
            Norovirus
  JOURNAL   Unpublished
REFERENCE   3  (bases 1 to 7559)
  AUTHORS   Xue,L., Wu,Q., Kou,X. and Zhang,J.
  TITLE     Direct Submission
  JOURNAL   Submitted (21-OCT-2012) State Key Laboratory of Applied
            Microbiology (Ministry-Guangdong Province Jointly Breeding Base),
            South China, Guangdong Provincial Key Laboratory of Microbial
            Culture Collection and Application, Guangdong Open Laboratory of
            Applied Microbiology, Guangdong Institute of Microbiology, No. 100,
            Xianliezhong Road, Yuexiu District, Guangzhou, Guangdong 510070,
            China
COMMENT     ##Assembly-Data-START##
            Assembly Method       :: seqman v. 7.1.0
            Sequencing Technology :: 454
            ##Assembly-Data-END##
FEATURES             Location/Qualifiers
     source          1..7559
                     /organism="Norovirus
                     Hu/GII.4/GZ2010-L87/Guangzhou/CHN/2011"
                     /mol_type="genomic RNA"
                     /isolate="Hu/GII.4/GZ2010-L87/Guangzhou/CHN/2011"
                     /isolation_source="stool"
                     /host="Homo sapiens"
                     /db_xref="taxon:1282425"
                     /country="China"
                     /collection_date="07-Jan-2011"
                     /note="genotype: GII.4"
     CDS             5..5104
                     /note="ORF1; contains NTPase, 3A-like protein, VPg,
                     protease, and RdRp"
                     /codon_start=1
                     /product="non-structural polyprotein"
                     /protein_id="AGC96531.1"
                     /translation="MKMASNDASAAAVANSNNDTAKSSSDGVLSSMAVTFKRALGARP
                     KQPPPREKPQRPPRPPTPELVKNIPPPPPNGEDEIVVSYSVKDGVSGLPDLSTVRQPE
                     ETNTAFSVPPLNQRENRDAKEPLTGTILEMWDGEIYHYGLYVERGLVLGVHKPPAAIS
                     LAKVELAPLSLYWRPVYTPQYLISPDTLKKLSGETFPYTAFDNNCYAFCCWVLDLNDS
                     WLSRRMIQRTTGFFRPYQDWNRKPLPTMDDSKIKKVANIFLCALSSLFTRPIKDIIGK
                     IRPLNILNILASCDWTFAGIVESLILLAELFGVFWTPPDVSAMIAPLLGDYELQGPED
                     LAVELVPVVMGGIGLVLGFTKEKIGKMLSSAASTLKACKDLGAYGLEILKLVMKWFFP
                     KKEEANELAIVRSIEDAVLDLEAIENNHMTTLLKDKDSLATYMRTLDLEEEKARKLST
                     KSASPDIVGTINALLARIAAARSLVHRAKEELSSRPRPVVLMISGRPGIGKTHLAREV
                     AKRIAASLTGDQRVGLIPRNGVDHWDAYKGERVVLWDDYGMSNPIHDALRLQELADTC
                     PLTLNCDRIENKGKVFDSDVIIITTNLANPAPLDYVNFEACSRRIDFLVYAEAPEVEK
                     AKRDFPGQPDMWKNAFSSDFSHIKLALAPQGGFDKNGNTPHGKGVMKTLTTGSLIARA
                     SGLLHERLDEFELQGPALTTFNFDRNKVLAFRQLAAENKYGLIDTMRVGKQLKDVRTM
                     PELKQALKDVSIKKCQIVYSGCTYILESDGKGNVKVDRIQSAAVQTNNELAGALHHLR
                     CARIRYYVKCVQEALYSIIQIAGAAFVTTRITKRMNIQDLWSKPQVENTEETTSKDGC
                     PKPKDDEEFVISSDDIKTEGKKGKNKTGRGKKHTAFSSKGLSDEEYDEYKRIREERNG
                     KYSIEEYLQDRDKYYEEVAIARATEEDFCEEEEAKIRQRIFRPTRKQRKEERASLGLV
                     TGSEIRKRNPDDFKPKGKLWADDDRSVDYNEKLSFEAPPSIWSRIVNFGSGWGFWVSP
                     SLFITSTHVIPQGAKEFFGVPIKQIQVHKSGEFCRLRFPKPIRTDVTGMILEEGAPEG
                     TVVTLLIKRSTGELMPLAARMGTHATMKIQGRTVGGQMGMLLTGSNAKSMDLGTTPGD
                     CGCPYIYKRGNDYVVIGVHTAAARGGNTVICATQGSEGEATLEGGDNKGTYCGAPILG
                     PGSAPTLSTKTKFWRSSTASLPPGTYEPAYLGGKDPRVKGGPSLQQVMREQLKPFTEP
                     RGKPPKPSVLEAAKKTIINVLEQTIDPPEKWSFAQACASLDKTTSSGHPHHMRKNDCW
                     NGESFTGKLADQASKANLMFEEGKSMTPVYTAALKDELVKTDKIYGKIKKRLLWGSDL
                     ATMIRCARAFGGLMDELKAHCVTLPIRVGMNMNEDGPIIFERHSRYTYHYDADYSRWD
                     STQQRAVLAAALEIMVKFSPEPHLAQVVAEDLLSPSVVDVGDFTISINEGLPSGVPCT
                     SQWNSIAHWLLTLCALSEVTNLSPDTIQANSLFSFYGDDEIVSTDIKLDPEKLTAKLR
                     EYGLKPTRPDKTEGPLVISEDLNGLTFLRRTVTRDPAGWFGKLEQSSILRQMYWTRGP
                     NHGDPSETMIPHSQRPIQLMSLLGEAALHGPAFYSKISKLVIAELKEGGMDFYVPRQE
                     PMFRWMRFSDLSTWEGDRNLAPSFVNEDGVE"
     gene            5085..6707
                     /gene="VP1"
     CDS             5085..6707
                     /gene="VP1"
                     /note="ORF2"
                     /codon_start=1
                     /product="major viral capsid protein"
                     /protein_id="AGC96532.1"
                     /translation="MKMASSDANPSDGSTANLVPEVNNEVMALEPVVGAAIAAPVAGQ
                     QNVIDPWIRNNFVQAPGGEFTVSPRNAPGEILWSAPLGPDLNPYLSHLARMYNGYAGG
                     FEVQVILAGNAFTAGKIIFAAVPPNFPTEGLSPSQVTMFPHIIVDVRQLEPVLIPLPD
                     VRNNFYHYNQSNDSTIKLIAMLYTPLRANNAGDDVFTVSCRVLTRPSPDFDFIFLVPP
                     TVESRTKPFSVPVLTVEEMTNSRFPIPLEKLFTGPSSAFVVQPQNGRCTTDGVLLGTT
                     QLSPVNICTFRGDVTHIPGSRNYTMNLASQNWNSYDPTEETPAPLGTPDFVGKIQGVL
                     TQTTRTNGSTRGHKATVYTGSADFSPKLGRVQFATDTDNDFETNQNTKFTPVGVIQDG
                     STTPRNEPQQWVLPSYSGRNIHNVHLAPAVAPTFPGEQLLFFRSTMPGCSGYPNMDLD
                     CLLPQEWVQYFYQEAAPAQSDVALLRFVNPDTGRVLFECKLHKSGYVTVAHTGQHDLV
                     IPPNGYFRFDSWVNQFYTLAPMGNGTGRRRAL"
     gene            6707..7513
                     /gene="VP2"
     CDS             6707..7513
                     /gene="VP2"
                     /note="ORF3"
                     /codon_start=1
                     /product="minor viral capsid protein"
                     /protein_id="AGC96533.1"
                     /translation="MAGAFFAGLASDVLGSGLGSLISAGAGAINQKVEFENNRKLQQA
                     SFQFSSNLQQASFQHDKEMLQAQIEATKKLQQEMMRVEQAMLLEGGSSETDAARGAIN
                     APKTKTLDWSGTRYWAPDARTTTYNAGRFSTPQPSGAPPGRANLRATVPARGSSSTSS
                     NSSIATSVYSNQTTSTRLGSTAGSGTSVSSLPSTARTRSWVEDQNRNLSPFMRGAHNI
                     SFVTPPSSRSSSQGTVSTVPKEVLDSWTGAFNTRRQPLFAHIRKRGESRV"
ORIGIN      
        1 gtgaatgaag atggcgtcta acgacgcttc cgctgccgct gttgctaaca gcaacaacga
       61 caccgcaaaa tcttcaagtg acggagtgct ttctagcatg gctgtcactt tcaaacgagc
      121 cctcggggcg cggcctaaac agcctccccc gagggaaaaa ccacaaagac ccccacgacc
      181 acctactcca gaactggtta aaaatattcc ccctccccca cccaacggag aggatgaaat
      241 agtggtttct tatagtgtca aagatggtgt ttccggcttg cctgaccttt ccaccgtcag
      301 gcaaccggaa gaaactaaca cggccttcag tgtccctcca ctcaatcaga gggagaatag
      361 agatgctaag gagccactta ctggaacaat tctggaaatg tgggacgggg aaatctacca
      421 ttatggcctg tatgtggagc gaggtcttgt actaggtgtg cacaaaccac cagctgccat
      481 cagcctcgct aaggttgagc tagcaccact ctccttgtac tggagacctg tgtacactcc
      541 tcagtacctc atctctccag acactctcaa gaaattatcc ggagaaacgt tcccctacac
      601 agcctttgac aacaactgtt atgccttttg ttgctgggtc ctggacctaa atgactcgtg
      661 gctgagcagg agaatgatcc agagaacaac tggtttcttc aggccctacc aagattggaa
      721 taggaaaccc cttcccacta tggatgactc caaaataaag aaggtagcta acatattcct
      781 gtgtgctctg tcctcgctgt tcaccagacc cataaaagat ataataggga agataaggcc
      841 tcttaacatc ctcaacatct tagcctcatg tgattggact tttgcaggca tagtggagtc
      901 cctgatactc ttggcagaac tctttggagt tttctggaca cccccagatg tgtctgcgat
      961 gattgccccc ttgcttggtg actacgagct acaaggacct gaggatcttg cagtggagct
     1021 cgtccccgtg gtgatggggg gaattggttt ggtgctagga ttcaccaaag agaagattgg
     1081 gaaaatgttg tcatctgctg cgtccacctt gaaagcttgt aaagaccttg gtgcatatgg
     1141 gttagagatc ctaaagttgg tcatgaagtg gttcttcccg aagaaggagg aggcaaacga
     1201 gctggctata gtgaggtcta tcgaggatgc agtcctggat ctcgaggcaa ttgaaaacaa
     1261 ccatatgacc accttgctca aagacaaaga cagcctggca acctatatga gaacacttga
     1321 ccttgaggag gagaaagcca ggaaactctc aaccaagtct gcctcacccg acatcgtggg
     1381 cacaatcaac gccctcctgg cgagaatcgc tgccgcacgt tctctggtgc atcgagcgaa
     1441 ggaagagctt tccagcagac caagacctgt ggtgttgatg atatcaggca ggccaggaat
     1501 agggaagacc cacctcgcta gggaagtggc taagagaatc gcagcctccc ttacaggaga
     1561 ccagcgtgtg ggcctcatcc cgcgcaatgg cgtcgaccat tgggacgcgt acaaggggga
     1621 gagggtcgtc ctatgggacg attacggaat gagcaaccct attcacgatg ccctcaggct
     1681 gcaagaactc gctgacactt gccccctcac tctaaactgt gacaggattg aaaataaagg
     1741 aaaggtcttt gacagcgatg tcatcattat caccactaat ctggccaacc cagcaccact
     1801 ggactatgtc aactttgaag catgctcgag gcgcatcgac ttcctcgtgt atgcagaagc
     1861 tcctgaagtc gaaaaggcga agcgtgactt cccaggccag cctgacatgt ggaagaacgc
     1921 tttcagttct gatttctcac acataaaact agcactggcc ccacagggtg gtttcgacaa
     1981 gaacgggaac accccacacg gaaagggcgt catgaagact ctcaccactg gctcccttat
     2041 tgcccgggca tcagggctac tccatgagag gttagatgaa tttgaactac agggcccagc
     2101 tctcaccacc tttaattttg atcgcaataa agtgcttgcc tttagacagc ttgctgctga
     2161 aaataaatat gggttgatag acacaatgag agttgggaaa cagctcaagg atgtcagaac
     2221 catgccagaa ctcaaacaag cactcaagga tgtctcaatc aagaagtgcc aaatagtgta
     2281 tagtggttgc acctacatac ttgagtctga tggcaagggc aatgtgaaag ttgacaggat
     2341 ccaaagcgcc gccgtgcaga ccaacaatga gctggctggt gccctgcacc atttgaggtg
     2401 cgccagaatc agatactacg tcaagtgtgt ccaggaggcc ctgtattcca tcattcaaat
     2461 tgctggggct gcatttgtca ctacgcgcat taccaagcgc atgaacatac aagacctatg
     2521 gtccaagcca caagtggaaa acacagagga gactaccagc aaggacgggt gcccaaaacc
     2581 caaggatgat gaggagtttg tcatttcatc cgacgacatc aaaactgagg gcaagaaagg
     2641 gaagaacaaa actggccgcg gcaagaagca cacagcattt tcaagcaaag gcctcagtga
     2701 tgaagagtac gatgagtaca agaggattag agaagaaagg aatggcaagt actccataga
     2761 agagtacctt caggacaggg acaaatacta tgaggaggtg gccattgcca gggcgactga
     2821 ggaagacttc tgtgaagagg aggaagccaa gatccggcaa aggatcttta ggccaacaag
     2881 gaaacaacgc aaggaggaaa gagcctctct cggtctggtc acaggctctg aaattaggaa
     2941 aagaaaccca gatgacttca aacccaaggg gaaattgtgg gctgacgatg acaggagtgt
     3001 ggactacaat gagaaactca gttttgaggc cccaccaagc atctggtcga gaatagtcaa
     3061 ctttggttca ggatggggat tctgggtctc ccccagtctg ttcataacat caacccatgt
     3121 cataccccag ggcgcaaagg agttctttgg agtccccatc aaacaaatac aggtacacaa
     3181 gtcaggcgag ttctgtcgct tgagattccc aaaaccaatc aggactgatg tgacgggcat
     3241 gatcttagaa gaaggcgcac ctgagggcac cgtggtcaca ctactcatca aaaggtccac
     3301 tggggaactc atgcccctag cagctaggat ggggacccat gcgaccatga agatccaagg
     3361 gcgcaccgtt ggaggccaga tgggcatgct tctgacagga tccaacgcca agagcatgga
     3421 cctgggtact acaccaggtg attgtggctg cccctatatt tacaagagag gcaatgacta
     3481 tgtggtcatt ggagtccaca cggctgccgc acgtggggga aacactgtca tatgtgccac
     3541 ccaggggagt gaaggagagg ctacacttga aggtggtgac aacaagggga catactgtgg
     3601 tgcaccaatc ctaggcccag ggagtgcccc aacacttagc accaagacca aattctggag
     3661 atcgtccaca gcatcactcc cacctggcac ctatgaacca gcctatcttg gtggcaagga
     3721 ccctagagtc aagggtggcc cctcactgca gcaagtcatg agggagcagt tgaagccatt
     3781 cacagagcca aggggcaagc caccaaaacc aagtgtatta gaagctgcca agaagaccat
     3841 catcaatgtc cttgagcaaa caattgatcc acctgagaaa tggtcgttcg cacaagcttg
     3901 cgcgtccctt gacaagacaa cttccagtgg tcatccgcac cacatgcgga agaacgactg
     3961 ctggaacggg gagtccttca caggcaagct ggcagaccag gcttccaagg ccaacctgat
     4021 gtttgaagaa gggaagagca tgaccccagt ctacacagct gcgctcaagg atgagttagt
     4081 taaaactgac aaaatttatg gtaagatcaa gaagaggctt ctctggggct cggacttggc
     4141 gaccatgatc cggtgtgctc gggcattcgg aggcctaatg gatgaactca aagcacactg
     4201 tgtcacactt cctattagag ttggcatgaa catgaatgag gatggtccca tcatcttcga
     4261 gaggcattcc aggtacacat atcactatga tgctgattac tctcgatggg attcaacaca
     4321 acagagagcc gtgttggcag cagctctgga aatcatggtt aaattctccc cagaaccaca
     4381 tttggctcag gtagtcgcgg aagaccttct ttctcctagc gtggtggacg tgggcgactt
     4441 cacaatatca atcaacgagg gtcttccctc tggggtgccc tgtacctccc aatggaactc
     4501 catcgcccac tggcttctca ctctctgtgc gctctctgaa gtcacaaacc tatcccctga
     4561 taccatacag gccaactccc tcttctcttt ttatggtgat gatgaaattg ttagcacaga
     4621 cataaaattg gacccagaga aattgacagc aaagctcaga gaatatgggt taaaaccaac
     4681 ccgccctgac aaaactgaag gaccccttgt catctctgaa gacctgaatg gcctaacttt
     4741 cctgcggaga accgtgaccc gcgacccagc tggttggttt ggaaaactgg agcagagttc
     4801 aatactcagg caaatgtact ggactagggg tcccaaccat ggagacccat ctgaaacaat
     4861 gattccacac tcccaaagac ccatacaact gatgtcccta ctgggggagg ccgctctcca
     4921 cggcccagca ttttacagta aaatcagcaa attggtcatt gcagagctta aagaaggtgg
     4981 catggatttt tacgtgccca gacaggagcc aatgttcaga tggatgagat tctcagatct
     5041 gagcacgtgg gagggcgatc gcaatctggc tcccagtttt gtgaatgaag atggcgtcga
     5101 gtgacgccaa cccatctgat gggtccacag ccaacctcgt cccagaggtc aacaatgagg
     5161 ttatggcttt ggagcccgta gttggtgccg ctattgcggc acctgtagcg ggccaacaaa
     5221 atgtaattga cccctggatt agaaacaatt ttgtacaagc ccctggtgga gagtttacag
     5281 tatcccctag aaacgctcca ggtgaaatac tatggagcgc gcccttaggc cctgatttga
     5341 atccctacct ttcccatttg gccagaatgt acaatggtta tgcaggtggt tttgaagtgc
     5401 aggtaatcct cgcggggaac gcgttcaccg ccgggaaaat catatttgca gcagtcccac
     5461 caaatttccc aactgaaggt ttgagcccca gccaagtcac tatgttcccc cacataatag
     5521 tagatgttag gcaattggaa cctgtgttga tccccttacc cgatgttagg aataacttct
     5581 accattataa tcaatcaaat gactccacca tcaagttgat agcaatgttg tacacaccac
     5641 ttagggctaa taatgccggg gacgatgtct tcacagtttc ttgtcgagtt ctcacgagac
     5701 catcccccga ttttgatttc atatttttgg tgccacccac agttgaatca agaactaaac
     5761 cattctctgt cccagtttta actgttgagg agatgaccaa ctcaaggttc cccattcctt
     5821 tggaaaaatt gttcacaggc cccagtagtg cctttgttgt tcaaccacaa aacggcaggt
     5881 gcacgactga tggcgtgctc ctaggtacta cccaactgtc tcctgtcaac atctgcacct
     5941 tcagagggga tgtcacccat attccaggca gtcgtaacta cacaatgaat ttggcctccc
     6001 aaaattggaa cagttacgat ccaacagaag aaaccccagc ccctctagga actccagatt
     6061 tcgtggggaa gattcaaggt gtgctcaccc aaaccacaag gacaaatggc tcgacccgcg
     6121 gccacaaagc tacagtgtac actgggagcg ccgacttttc tccaaaactg ggtagagttc
     6181 agtttgccac tgacacagac aatgattttg aaactaacca aaacacaaag ttcaccccag
     6241 tcggtgttat ccaggatggt agtactaccc cccgaaatga accccaacaa tgggtgctcc
     6301 caagttactc aggcagaaat attcataatg tgcacctggc ccccgctgta gcccccactt
     6361 tcccgggcga gcagcttctc ttctttagat ctactatgcc cggatgcagc gggtacccca
     6421 acatggactt ggactgtctg ctcccccagg aatgggtgca gtacttctac caggaggcag
     6481 ccccagcaca atctgatgtg gctctgttaa gatttgtgaa tccagacaca ggtagggttt
     6541 tgtttgagtg taagcttcat aaatcaggct atgttacagt ggctcacact ggccaacatg
     6601 atttggttat cccccccaat ggttatttta gatttgattc ctgggtcaac cagttctaca
     6661 cacttgcccc catgggaaat gggacggggc gtagacgtgc attataatgg ctggagcttt
     6721 ctttgctgga ttggcatctg acgtccttgg ctctggactt ggttccctaa tcagtgctgg
     6781 ggctggggcc atcaaccaaa aagttgaatt tgaaaataac agaaaattgc aacaggcttc
     6841 cttccaattt agtagcaatc tacaacaggc ttcctttcaa catgacaaag agatgctcca
     6901 agcacaaatt gaggccacaa aaaagttgca acaggaaatg atgagagtcg aacaagcaat
     6961 gctcctagag ggtggatcct ctgagacaga tgcagcccgt ggggcaatca acgcccccaa
     7021 gacaaaaact ttggactgga gcgggacgag gtactgggct cccgatgcta ggactacaac
     7081 atataatgca ggccgctttt ccacccctca accctcgggg gcaccaccag ggagagctaa
     7141 tcttagggct actgtccccg cccggggttc ctctagcacg tcttctaact cttctattgc
     7201 tacttctgtg tattcaaatc aaaccacctc aacgagactt ggttctacag ctggttctgg
     7261 taccagtgtc tcgagcctcc cgtcaactgc aaggactagg agctgggttg aggatcaaaa
     7321 taggaatttg tcacctttca tgaggggggc ccacaacatc tcgtttgtca ccccaccatc
     7381 tagcagatcc tctagccaag gcacagtctc gaccgtgccc aaagaagttt tggactcctg
     7441 gactggcgct ttcaacacgc gcaggcagcc tctcttcgct cacattcgca agcgagggga
     7501 gtcacgggtg taatgtgaaa agacaaaatt gatcatcttt cttttcttta gtgtcttct
//