Typing tool

Complete norovirus genomes

JX989073  GII.4 Den Haag
 GII.P4 Den Haag

Length: 7,557 | 3 CDS

ORF1: 3..5102
ORF2: 5083..6705
ORF3: 6705..7511
LOCUS       JX989073                7557 bp    RNA     linear   VRL 09-MAY-2014
DEFINITION  Norovirus Hu/GII.4/GZ2010-L26/Guangzhou/CHN/2010, complete genome.
ACCESSION   JX989073
VERSION     JX989073.1
KEYWORDS    .
SOURCE      Norovirus Hu/GII.4/GZ2010-L26/Guangzhou/CHN/2010
  ORGANISM  Norovirus Hu/GII.4/GZ2010-L26/Guangzhou/CHN/2010
            Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes;
            Picornavirales; Caliciviridae; Norovirus.
REFERENCE   1  (bases 1 to 7557)
  AUTHORS   Xue,L., Wu,Q., Dong,R., Kou,X., Li,Y., Zhang,J. and Guo,W.
  TITLE     Genetic analysis of noroviruses associated with sporadic
            gastroenteritis during winter in Guangzhou, China
  JOURNAL   Foodborne Pathog. Dis. 10 (10), 888-895 (2013)
   PUBMED   23947818
REFERENCE   2  (bases 1 to 7557)
  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  JOURNAL   Unpublished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 7557)
  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..7557
                     /organism="Norovirus
                     Hu/GII.4/GZ2010-L26/Guangzhou/CHN/2010"
                     /mol_type="genomic RNA"
                     /isolate="Hu/GII.4/GZ2010-L26/Guangzhou/CHN/2010"
                     /isolation_source="stool"
                     /host="Homo sapiens"
                     /db_xref="taxon:1282423"
                     /country="China"
                     /collection_date="26-Nov-2010"
                     /note="genotype: GII.4"
     CDS             3..5102
                     /note="ORF1; contains NTPase, 3A-like protein, VPg,
                     protease, and RdRp"
                     /codon_start=1
                     /product="non-structural polyprotein"
                     /protein_id="AGC96528.1"
                     /translation="MKMASNDASAAAVANSNNDTAKSSSDKMFSSMAVTFKRALGARP
                     KQPPPRETPQGPPRPTTPELVKKIPPPPPNGEDEVVVSYSAKDGVSGLPELSTVRQPE
                     ETNTAFSVPPLNQRESRDAKEPLTGTILEMWDGEIYHYGLYVERGLVLGVHKPPAAIS
                     LAKVELTPLSLFWRPVYTPQYLISPDTLKKLHGETFPYTAFDNNCYAFCCWVLDLNDS
                     WLSRRMIQRTTGFFRPYQDWNRKPLPTMDDSKLKKVANIFLCTLSSLFTRPIKDIIGK
                     LRPLNIINILASCDWTFAGIVESLILLAELFGVFWTPPDVSAMIAPLLGDFELQGPGD
                     LVVELVPVVMGGIGLVLGFTKEKIGKMLSSAASTLRACKDLGAYGLEILKLVMKWFFP
                     KKEEANELAMVRSIEDAVLDLEAIENNHMTTLLKDKDSLATYMRTLDLEEEKARKLST
                     KSASPDIVGTINALLARIAAARSLVHRAKEELSSRPRPVVLMISGRPGIGKTHLAREV
                     AKRIAASLTGDQRVGLIPRNGVDHWDAYKGERVVLWDDYGMSNPIHDALRLQELADTC
                     PLTLTGDRIENKGKVFDSDVIIITTNLANPAPLDYVNFEACSRRIDFLVYAEAPEVEK
                     AKRDFPGQPDMWKNAFSPDFSHIKLALAPQGGFDKNGNTPHGKGVMKTLTTGSLIARA
                     SGLLHERLDEFELQGPALTTFNFDRNKVLAFRQLAAENKYGLMDTMKVGRQLKDVKTM
                     PELKQALKNISIKKCQIVYSGCTYTLESDGKGNVKVDRVQSTSVQTNNELAGALHHLR
                     CARIRYYVKCVQEALYSIIQIAGAAFVTTRIIKRVNIQDLWSKPQVENTEEATNKDGC
                     PKPKDNEEFVISSDDIKTEGKKGKNKTGRGKKHTAFSSKGLSDEEYDEYKRIREERNG
                     KYSIEEYLQDRDKYYEEVAIARATEEDFCEEEEAKIRQRIFRPTRKQRKEERASLGLV
                     TGSEIRKRNPDDFKPKGKLWADDDRSVDYNEKLSFEAPPSIWSRIVNFGSGWGFWVSP
                     SLFITSTHVIPQGAKEFFGVPIKQIQVHKSGEFCRLRFPKPIRTDVTGMILEEGAPEG
                     TVVTLLIKRSTGELMPLAARMGTHATMKIQGRTVGGQMGMLLTGSNAKSMDLGTTPGD
                     CGCPYIYKRGNDYVVIGVHTAAARGGNTVICATQGGEGEATLEGGDNKGTYCGAPILG
                     PGSAPKLSTKTKFWRSSTAPLPPGTYEPAYLGGKDPRVKGGPSLQQVMRDQLKPFTEP
                     RGKPPKPSVLEAAKKTIINVLEQTIDPPEKWSFAQACASLDKTTSSGHPHHMRKNDCW
                     NGESFTGKLADQASKANLMFEEGKNMTPVYTGALKDELVKTDKIYGKIKKRLLWGSDL
                     ATMIRCARAFGGLMDELKAHCVTLPIRVGMNMNEDGPIIFEKHSRYRYHYDADYSRWD
                     STQQRAVLAAALEIMVKFSSEPHLAQVVAEDLLSPSVVDVGDFTISINEGLPSGVPCT
                     SQWNSIAHWLLTLCALSEVTNLSPDIIQANSLFSFYGDDEIVSTDIKLDPEKLTAKLK
                     EYGLKPTRPDKTEGPLVISEDLDGLTFLRRTVTRDPAGWFGKLEQSSILRQMYWTRGP
                     NHEDPSESMIPHSQRPIQLMSLLGEAALHGPTFYSKISKLVIAELKEGGMDFYVPRQE
                     PMFRWMRFSDLSTWEGDRNLAPSFVNEDGVE"
     gene            5083..6705
                     /gene="VP1"
     CDS             5083..6705
                     /gene="VP1"
                     /note="ORF2"
                     /codon_start=1
                     /product="major viral capsid protein"
                     /protein_id="AGC96529.1"
                     /translation="MKMASNDANPSDGSAANLVPEVNNEVMALEPVVGAAIAAPVAGQ
                     QNVIDPWIRNNFVQAPGGEFTVSPRNAPGEILWSAPLGPDLNPYLSHLARMYNGYAGG
                     FEVQVILAGNAFTAGKIIFAAVPPNFPTEGLSPSQVTMFPHIIVDVRQLEPVLIPLPD
                     VRNNFYHYNQSNDSTIKLIAMLYTPLRANNAGEDVFTVSCRVLTRPSPDFDFIFLVPP
                     TVESRTKPFTVPILTVEEMTNSRFPIPLEKLFTGPSSAFVVQPQNGRCTTDGVLLGTT
                     QLSPVNICTFRGDVTHIAGSRNYTMNLASLNWNNYDPTEEIPAPLGTPDFVGKIQGML
                     TQTTKGDGSTRGHKATVYTGSAPFTPKLGSVQFSTDTENDFETHQNTKFTPVGVIQDG
                     STTHRNEPQQWVLPSYSGRDIPNVHLAPAVAPTFPGEQLLFFRSTMPGCSGYPNMDLD
                     CLLPQEWVQHFYQEAAPAQSDVALLRFVNPDTGRVLFECKLHKSGYVTVAHTGQHDLV
                     IPPNGYFRFDSWVNQFYTLAPMGNGTGRRRAL"
     gene            6705..7511
                     /gene="VP2"
     CDS             6705..7511
                     /gene="VP2"
                     /note="ORF3"
                     /codon_start=1
                     /product="minor viral capsid protein"
                     /protein_id="AGC96530.1"
                     /translation="MAGAFFAGLASDVLSSGLGSLINAGAGAINQKIDFENNRKLQQA
                     SFQFSSNLQQASFQHDKEMLQAQIEATKKLQQEMMKVKQAVLLEGGFAETDAARGAIN
                     APMTKALDWSGTRYWAPDARTTTYNAGRFSTPQSPGVLLGRANPRTPTPARGSPSTSS
                     NASTATSIYSNQTVSTRLGSTAGSGTSVSSLPSTARTRSWVEDQNRNLSPFMRGAHNI
                     SFVTPPSSRSSSQGTVSTVPKEVLDSWAGAFNTRRQPLFAHIRRRGESRV"
ORIGIN      
        1 gaatgaagat ggcgtctaac gacgcttccg ctgccgctgt tgctaacagc aacaacgaca
       61 ccgcaaaatc ttcaagtgac aaaatgtttt ctagcatggc tgtcactttc aaacgagccc
      121 tcggggcgcg gcctaaacag ccccccccga gggaaacacc acaaggaccc ccacgaccaa
      181 ctactccaga actggtcaaa aagatccctc cccccccgcc caacggagag gatgaagtag
      241 tggtttctta tagtgccaaa gatggtgttt ccggtttacc tgaactttcc accgtcaggc
      301 aaccggaaga aaccaatacg gctttcagtg tccctcccct caatcagagg gagagtaggg
      361 atgctaagga accactgact ggaacaattc tggaaatgtg ggatggagaa atctaccatt
      421 atggcctgta tgttgagcga ggtcttgtgc tgggtgtgca caaaccacca gctgccatta
      481 gcctcgccaa ggtcgaacta acaccactct ccctgttctg gagacctgtg tacactcctc
      541 agtacctcat ctctccagac actctcaaga aattacacgg agaaacattt ccctacacag
      601 ccttcgacaa caattgctat gccttctgtt gctgggtcct ggacctaaat gactcgtggc
      661 tgagtaggag aatgatccag agaacaactg gcttcttcag accctaccaa gattggaata
      721 ggaaacccct ccccactatg gatgattcca aattaaagaa ggtagctaac atattcctgt
      781 gcaccctgtc ttcgctattc accagaccca taaaagacat aatagggaag ttaaggcctc
      841 tcaacatcat caacatcctg gcttcatgtg attggacctt cgcaggcata gtggagtcct
      901 tgatactctt ggcagagctc tttggagtct tctggacacc cccagatgtg tctgcgatga
      961 ttgccccctt actcggtgat ttcgagttac aagggcctgg ggaccttgta gtggagctcg
     1021 tccctgtagt aatgggggga attggtttgg tgctaggatt cactaaagag aagattggaa
     1081 aaatgttgtc atctgctgca tctaccttaa gagcttgtaa agatcttggt gcgtatgggc
     1141 tagagatcct aaagttagtc atgaagtggt tcttcccgaa gaaagaggaa gcaaatgaac
     1201 tggctatggt gagatccatc gaggatgcag tgctagacct tgaggcaatt gaaaacaacc
     1261 atatgaccac cttgctcaaa gacaaagaca gcctggcaac ctatatgaga acccttgacc
     1321 tcgaggaaga gaaagccaga aaactctcaa ccaagtctgc ttcacctgac atcgtgggca
     1381 caatcaacgc ccttctggcg aggatcgccg ctgcacgctc cctggtgcac cgagcgaaag
     1441 aggagctttc tagcagacca agacctgtag tcttgatgat atcaggcaga ccaggaatag
     1501 ggaagaccca ccttgctagg gaagtggcta agagaattgc agcctccctc acaggagatc
     1561 agcgtgtagg cctcatccca cgcaatggcg tcgatcactg ggacgcgtac aagggggaga
     1621 gggtcgtcct atgggacgac tatggaatga gcaaccccat ccacgacgcc ctcaggctgc
     1681 aagaactcgc tgacacttgc cccctcactc taactggtga caggattgag aataaaggaa
     1741 aggtctttga cagcgatgtc atcatcatca ccactaacct ggccaaccca gcaccactgg
     1801 actatgtcaa ctttgaagcg tgctcgaggc gcattgattt cctcgtgtat gcagaagccc
     1861 ccgaggtcga aaaggcgaag cgtgacttcc cgggccaacc tgacatgtgg aaaaacgctt
     1921 ttagtcctga tttctcacac ataaaattgg cactggctcc acaaggtggc tttgataaga
     1981 acgggaacac cccacatggg aagggcgtca tgaagactct caccactggc tccctcatcg
     2041 ccagggcatc agggctgctc catgagagat tggatgagtt tgaactacag ggcccagctc
     2101 ttaccacctt caactttgac cgcaacaaag tgcttgcctt caggcagctt gctgctgaaa
     2161 ataagtacgg gttgatggac acaatgaaag ttggaaggca gctcaaggat gtcaaaacca
     2221 tgccggaact taaacaagca ctcaagaata tctcaatcaa gaagtgccag attgtgtata
     2281 gtggttgtac ctacacactt gagtctgatg gcaagggcaa tgtgaaagtt gacagagttc
     2341 agagcacctc cgttcagacc aacaatgagc tggctggcgc cctgcaccac ctgaggtgcg
     2401 ccagaatcag gtactacgtc aagtgtgttc aggaggccct gtattctatc atccagattg
     2461 ctggggctgc atttgtcacc acgcgcatca tcaagcgtgt gaacattcaa gacttatggt
     2521 ccaagccaca agtggaaaac acagaggagg ccaccaacaa ggacgggtgc ccaaaaccca
     2581 aagataatga ggagttcgtc atttcatctg acgacattaa aactgagggt aagaaaggga
     2641 agaacaagac tggccgtggc aagaagcaca cagccttctc aagtaaaggt ctcagtgatg
     2701 aagagtatga tgagtacaag agaattagag aggaaaggaa tggtaagtac tccatagaag
     2761 agtatcttca ggacagggac aaatactatg aggaggtggc cattgccagg gcgaccgagg
     2821 aagacttctg tgaagaggag gaggccaaga tccggcaaag gatcttcaga ccaacaagga
     2881 agcaacgcaa ggaagaaaga gcttctctcg gtttagtcac aggttctgaa attaggaaaa
     2941 ggaacccaga cgacttcaag cctaagggga aactatgggc tgatgatgac agaagtgtgg
     3001 actacaatga aaaactcagt tttgaggctc caccaagcat ctggtcaagg atagtcaact
     3061 ttggctcagg ttggggcttc tgggtctccc ccagcctgtt tataacatca acccacgtca
     3121 taccccaggg cgcaaaggag ttctttggag tccccatcaa acaaattcag gtacacaagt
     3181 caggcgaatt ctgtcgcttg aggttcccaa agccaatcag gactgatgtg actggcatga
     3241 tcttggaaga aggtgccccc gaaggcaccg tggtcacact actcatcaaa aggtctactg
     3301 gagaactcat gcccttagca gctagaatgg ggacccatgc aaccatgaaa attcaagggc
     3361 gcactgttgg aggtcagatg ggcatgcttc tgacaggatc caacgccaaa agcatggatc
     3421 taggcaccac accaggtgat tgcggctgtc cctacatcta caagagagga aatgactatg
     3481 tggtcattgg agtccacacg gctgccgctc gtgggggaaa cactgtcata tgtgccaccc
     3541 aggggggtga gggggaagct acacttgaag gtggtgacaa taagggaaca tactgtggcg
     3601 caccaatcct aggcccaggg agcgccccaa aacttagcac caaaaccaaa ttctggagat
     3661 catccacagc accactccca cctggcacct acgaaccagc ctaccttggt ggcaaggacc
     3721 ccagagtcaa gggtggcccc tcgttgcagc aagttatgag ggaccagctg aaaccattta
     3781 cagagcctag gggtaagcca ccaaagccaa gtgtgttaga agctgccaag aaaaccatca
     3841 tcaatgtcct tgaacaaaca atcgacccac ctgagaagtg gtcgttcgca caagcttgcg
     3901 cgtcccttga caagaccact tctagcggcc atccgcacca catgcggaaa aacgactgct
     3961 ggaacgggga atctttcaca ggcaagctgg cggaccaggc ttccaaggcc aacctgatgt
     4021 ttgaagaagg gaagaacatg accccagtct acacaggtgc acttaaggat gaattagtca
     4081 aaactgacaa aatttatggt aagatcaaga agaggcttct ctggggctcg gatttggcaa
     4141 ccatgatccg gtgtgctcga gcattcggag gcctaatgga tgaactcaaa gcacactgtg
     4201 tcaccctccc tatcagagtt ggtatgaata tgaatgagga tggccccatc atcttcgaga
     4261 agcattccag gtacagatac cactatgatg ctgattactc tcggtgggat tcaacacaac
     4321 agagagccgt gctggcagct gctctagaaa tcatggttaa attctcctca gaaccacatt
     4381 tggctcaggt agtagcagag gaccttcttt ctcctagcgt ggtggacgtg ggtgacttca
     4441 caatatcaat caacgagggt cttccctctg gggtgccctg cacctcccaa tggaactcca
     4501 tcgcccactg gcttctcact ctctgtgcac tctccgaagt tacaaatttg tccccagaca
     4561 tcatacaggc taattctctc ttctccttct atggtgatga tgaaattgtt agtacggaca
     4621 taaaattaga cccagagaag ttgacagcaa agcttaagga atacgggttg aaaccaaccc
     4681 gccctgataa gactgaggga cctcttgtta tttctgaaga tttagatggc ttgaccttcc
     4741 tgcggaggac tgtgacccgc gacccagctg gttggtttgg aaaactggag cagagctcaa
     4801 tactcaggca aatgtactgg actaggggtc ctaaccatga agatccatct gaatcaatga
     4861 tcccacactc tcaaagaccc atacaattga tgtccttact gggagaggcc gcactccacg
     4921 gcccaacatt ctacagtaaa atcagcaaat tagtcattgc agagttaaaa gaaggtggta
     4981 tggattttta cgtgcccagg caagagccaa tgttcagatg gatgagattc tcagatctga
     5041 gcacgtggga gggcgatcgc aatctggctc ccagttttgt gaatgaagat ggcgtcgaat
     5101 gacgccaacc catctgatgg gtccgcagcc aacctcgtcc cagaggtcaa caatgaggtt
     5161 atggctttgg agcccgttgt cggcgccgct attgcggcgc ctgtagcggg ccaacaaaat
     5221 gtaattgacc cctggattag aaataatttt gtacaagccc ctggtggaga gttcacagta
     5281 tcccctagaa acgctccagg tgaaatacta tggagcgcac ccttaggccc tgatctgaat
     5341 ccctacctat ctcatttggc cagaatgtat aatggttatg caggtggttt tgaagtgcag
     5401 gtgatccttg cggggaacgc gttcaccgcc ggaaaaatta tatttgcagc agtcccacca
     5461 aattttccaa ctgaaggctt gagccccagc caggtcacta tgttccccca cataatagtg
     5521 gatgttaggc aattggaacc tgtgttgatc cccttacctg atgttaggaa taacttctat
     5581 cactataacc aatcaaatga ttctaccatt aaattgatag caatgctgta tacaccactt
     5641 agggctaata atgctgggga agatgtcttc acagtctctt gtcgagttct cacgaggcca
     5701 tcccctgatt ttgattttat atttttggtg ccacctacag ttgagtcaag aaccaaacca
     5761 tttactgtcc caatcttaac tgttgaggaa atgaccaatt caagattccc cattcctttg
     5821 gaaaagttgt tcacgggtcc cagcagtgcc tttgttgtcc aaccacaaaa tggcagatgc
     5881 acgactgatg gcgtgctctt aggcaccacc caactgtctc ctgtcaacat ctgcaccttc
     5941 agaggggatg tcacccacat tgcaggttct cgtaattaca caatgaattt ggcttctcta
     6001 aattggaaca attatgaccc aacagaagaa attccagccc ctctaggaac tccagatttc
     6061 gtgggaaaga tccaaggtat gctcactcaa accacgaaag gagatggttc gacccgtggc
     6121 cataaagcta cagtttatac tgggagtgcc ccctttactc caaagctggg cagtgttcaa
     6181 ttcagtactg acacagaaaa tgattttgaa actcaccaaa acacaaaatt caccccagtc
     6241 ggtgtcatcc aggatggtag caccacccac cgaaatgaac cccaacaatg ggtgctccca
     6301 agctattcag gtagagatat ccctaatgta cacctagccc ctgctgtagc ccccactttc
     6361 ccgggtgaac aacttctttt ctttaggtct actatgcccg gatgcagcgg gtatcccaac
     6421 atggatttgg attgcctgct cccccaggag tgggtgcagc acttctacca agaggcagct
     6481 ccagcacaat ctgatgtggc tctattgagg tttgtgaatc cagacacggg cagggtcctg
     6541 tttgagtgca aacttcataa atcaggctat gtcacagtgg ctcacaccgg ccagcatgat
     6601 ttggtcatcc cccccaatgg ttattttagg tttgattcct gggttaatca attctacaca
     6661 cttgccccca tgggaaatgg aacggggcgt agacgtgctt tataatggct ggagctttct
     6721 ttgctggatt ggcatctgat gtccttagct ctggacttgg ttccctaatc aatgctgggg
     6781 ctggggctat caaccaaaag attgattttg aaaataacag aaaattgcag caagcttcct
     6841 ttcagtttag cagtaatcta caacaggctt cctttcaaca tgataaagaa atgctccaag
     6901 cacaaattga ggccactaaa aagttgcaac aggaaatgat gaaagtcaaa caggcagtgc
     6961 tcttagaagg tggattcgct gaaacagatg cagcccgtgg ggcaatcaac gcccctatga
     7021 caaaggcttt ggactggagc ggaacaaggt actgggcccc tgatgctagg actacaacat
     7081 acaacgcagg ccgcttttcc acccctcaat ctccgggggt actgctagga agagccaatc
     7141 ccagaactcc tacccccgct cggggctctc ccagcacatc ttctaatgct tctactgcta
     7201 cttctatata ttcaaatcaa actgtttcaa cgagacttgg ttctacagct ggttctggca
     7261 ccagtgtttc gagtctcccg tcaactgcaa ggactaggag ttgggttgag gaccaaaaca
     7321 gaaatttgtc acctttcatg aggggggctc acaacatatc gttcgtcacc ccaccatcta
     7381 gcagatcctc tagccaaggc acagtctcaa ccgtgcctaa agaagttttg gactcctggg
     7441 ctggcgcttt caacacgcgc aggcagcctc tcttcgctca cattcgtagg cgaggggagt
     7501 cacgggtgta atgtgaaaag acaaaattga ttatctttcc ttttctttag tgtcttt
//