Typing tool

Complete norovirus genomes

LN854565  GII.4 Den Haag
 GII.P4 Den Haag

Length: 7,511 | 3 CDS

ORF1: 3..5102
ORF2: 5083..6705
ORF3: 6705..7511
LOCUS       LN854565                7511 bp    RNA     linear   VRL 12-JUN-2015
DEFINITION  Norovirus GII/Hu/NL/2012/GII.4/Groningen, complete genome.
ACCESSION   LN854565
VERSION     LN854565.1
KEYWORDS    complete genome.
SOURCE      Norovirus GII/Hu/NL/2012/GII.4/Groningen
  ORGANISM  Norovirus GII/Hu/NL/2012/GII.4/Groningen
            Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes;
            Picornavirales; Caliciviridae; Norovirus.
REFERENCE   1
  AUTHORS   Bavelaar,H., Rahamat-Langendoen,J., Niesters,H.G.M., Zoll,J. and
            Melchers,W.J.G.
  TITLE     Whole genome sequencing of faecal samples as a tool for the
            diagnosis and genetic characterization of norovirus
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 7511)
  AUTHORS   Zoll,J.
  TITLE     Direct Submission
  JOURNAL   Submitted (18-MAY-2015) Medical Microbiology, RADBOUDUMC, PO Box
            9101, 6500 HB Nijmegen, NETHERLANDS
FEATURES             Location/Qualifiers
     source          1..7511
                     /organism="Norovirus GII/Hu/NL/2012/GII.4/Groningen"
                     /mol_type="genomic RNA"
                     /strain="GII/Hu/NL/2012/GII.4/Groningen"
                     /host="Homo sapiens"
                     /db_xref="taxon:1665646"
                     /note="genotype:GII.4"
     gene            3..5102
                     /gene="POL"
     CDS             3..5102
                     /gene="POL"
                     /note="ORF1"
                     /codon_start=1
                     /product="nonstructural polyprotein"
                     /protein_id="CRL46957.1"
                     /translation="MKMASNDASAAAVANSNNVTAKSSSDKMLSSMAVTFKRALGARP
                     KQPPPREIPQRPPRPPTPELVKKIPPPPPNGEDEVVVSYSAKNGVSGLPELSTVRRPE
                     EHNTAFSVPPLNQRENRDAKEPLTGTILEMWDGEIYHYGLYVERGLVLGVHKPPAAIS
                     LAKVELTPLSLFWRPVYTPQYLIAPDTLKKLHNETFPYTAFDNNCYAFCCWVLDLNDS
                     WLSRRMIQRTTGFFRPYQDWNRKPLPTMDDSKLKKVANIFLCALSSLFTRPIKDIIGK
                     LRPLNIINILASCDWTFAGIVESLILLAELFGVFWTPPDVSAMIAPLLGDFELQGPED
                     LAVELVPVVMGGIGLVLGFTKEKIGKMLSSAASTLRACKDLGAYGLEILKLVMKWFFP
                     KKEEANELAIVRSIEDAVLDLEAIENNHMTTLLKDKDSLATYMRTLDLEEEKARKLST
                     KSASPDIVGTINALLARIAAARSLVHRAKEELSSRPRPVVLMISGRPGIGKTHLAREV
                     AKKIAASLTGDQRVGLIPRNGVDHWDAYKGERVVLWDDYGMSNPIHDALRLQELADTC
                     PLTLNCDRIENKGKVFDSDVIIITTNLANPAPLDYVNFEACSRRIDFLVYAEAPEVEK
                     VKRDFPGQPDMWKNAFSSDFSHIKLALAPQGGFDKNGNTPHGKGVMKTLTTGSLIARA
                     SGLLHERLDEFELQGPALATFNFDRNKVLAFRQLAAENKYGLMDTMRVGRQLKDVKTM
                     PELKQALKNISIKKCQIVHGGCTYTLESDGKGNVEVNRVQSTTVQTNNELAGALHHLR
                     CARIRYYVKCVQEALYSVIQIAGAAFVTTRIIKRVNIQDLWSKPQVENTEEAANKEGC
                     PKIRDDEEFVISSDDIKAEGKKGKNKTGRGKKHTAFSSKGLSDEEYDEYKRIREERNG
                     KYSIEEYLQDRDKYYEEVAIARATEEDFCEEEEAKIRQRIFRPTRKQRKEERASLGLV
                     TGSEIRKRNPEDFKPKGKLWADDDRSVDYNEKLSFEAPPSIWSRIVNFGSGWGFWVSP
                     SLFITSTHVIPQGAKEFFGVPVKQIQVHKSGEFCRLRFPKPIRTDVAGMILEEGAPEG
                     TVVTLLIKRSTGELMPLAARMGTHATMKIQGRTVGGQMGMLLTGSNAKSMDLGTTPGD
                     CGCPYIYKRGNDYVVIGVHTAAARGGNTVICATQGSEGEATLEGGDSKGTYCGAPILG
                     PGSAPKLSTKTKFWRSSTAPLPPGTYEPAYLGGKDPRVKGGPSLQQVMRDQLKPFTEP
                     RGKPPKPSVLEAAKKTIINVLEQTIDPPEKWSFAQACASLDKTTSSGHPHHMRKNDCW
                     NGESFTGKLADQASKANLMFEEGKNMTPVYTGALKDELVKTDKIYGKIKKRLLWGSDL
                     ATMIRCARAFGGLMDELKTHCVTLPIRVGMNMNEDGPIIFEKHSRYKYHYDADYSRWD
                     STQQRAVLAAALEIMVKFSSEPHLAQVVAEDLLSPSVVDVGDFTISINEGLPSGVPCT
                     SQWNSIAHWLLTLCALSEVTNLSPDIVQANSIFSFYGDDEIVSTDIKLDPEKLTAKLK
                     EYGLKPTRPDKTEGPLVISEDLDGLTFLRRTVTRDPAGWFGKLEQSSILRQMYWTRGP
                     NHEDPSETMIPHSQRPIQLMSLLGEAALHGPTFYSKISKLVITELKEGGMDFYVPRQE
                     PMFRWMRFSDLSTWEGDRNLAPSFVNEDGVE"
     gene            5083..6705
                     /gene="VP1"
     CDS             5083..6705
                     /gene="VP1"
                     /note="ORF2"
                     /codon_start=1
                     /product="capsid protein VP1"
                     /protein_id="CRL46958.1"
                     /translation="MKMASNDANPSDGSAANLVPEVNNEVMALEPVVGAAIAAPVAGQ
                     QNIIDPWIRNNFVQAPGGEFTVSPRNAPGEILWSAPLGPDLNPYLSHLARMYNGYAGG
                     FEVQVILAGNAFTAGKIIFAAVPPNFPTEGLSPSQVTMFPHIIVDVRQLEPVLIPLPD
                     VRNNFYHYNQSNDSTIKLIAMLYTPLRANNAGDDVFTVSCRVLTRPSPDFDFIFLVPP
                     TVESRTKPFTIPILTVEEMTNSRFPIPLEKLYTGPSSAFVVQPQNGRCTTDGVLLGTT
                     QLSPVNICTFRGDVTNIQGSHTYTMNLASLNWNNYDPTEETPAPLGTPDFVGKIQGVL
                     TQTTKGQGSTRGHKATVYTGSASFTPKLGSVQFRTDTQNDFVTHQNTKFTPVGVIQDG
                     DTTHRNEPQQWVLPNYSGVNTHNVHLAPAVAPTIPGEQLLFFRSSMPGCSGYPNMDLD
                     CLVPQEWVQHFYQEAAPALSDVALLRFVNPDTGRVLFECKLHKSGYVTVAHTGHHDLV
                     IPPNGYFRFDSWVNQFYTLAPMGNGTGRRRVL"
     gene            6705..7511
                     /gene="VP2"
     CDS             6705..7511
                     /gene="VP2"
                     /note="ORF3"
                     /codon_start=1
                     /product="capsid protein VP2"
                     /protein_id="CRL46959.1"
                     /translation="MAGAFFAGLASDVLGSGLSSLINAGAGAINQKIDFENNRKLQQA
                     SFQFSSNLQQASFQHDKEMLQAQVEATKKLQQEMMKVKQAILLEGGFSATDAARGAIN
                     APMTKVLDWNGTRYWAPDARTTTYNTGHFSTPQSSGALPGRTNPRIPTPARASSSTSS
                     NASTATSISSNQTVSTRLGSTAGSGTNVSSLPSTARTRSWVEDQNRNLSPFMRGAHNI
                     SFVTPPSSRSSSQGTVSTVPKGVLDSWTGAFNTRRQPLFAYTHRRGESRV"
ORIGIN      
        1 gaatgaagat ggcgtctaac gacgcttccg ctgccgctgt tgctaacagc aacaacgtca
       61 ccgcaaaatc ttcaagtgac aaaatgcttt ccagcatggc tgtcactttt aaacgagccc
      121 tcggggcgcg gcctaaacag ccccccccga gggaaatacc acaaagaccc ccacgaccac
      181 ctactccaga actggtcaaa aagatccctc ctcccccgcc caacggagag gatgaggtag
      241 tggtttctta cagtgccaaa aatggcgttt ccggtttgcc tgagctttcc actgtcaggc
      301 gaccggaaga acacaacacg gccttcagtg tccctccact caatcagagg gagaataggg
      361 atgctaagga accgttgact ggaacaattc tggaaatgtg ggatggagag atctaccatt
      421 atggcctgta tgttgagcga ggtcttgtgc tgggtgtaca caaaccacca gctgccatca
      481 gcctcgccaa ggtcgaacta acaccactct ccttgttctg gaggcctgtg tacactcctc
      541 agtacctcat cgctccagac accctcaaga aattacacaa tgaaacattt ccctacacag
      601 cctttgacaa caattgctat gccttttgtt gctgggtcct ggatctaaac gactcgtggc
      661 tgagtaggag aatgatccag agaacaactg gcttctttag accctaccaa gattggaata
      721 ggaaacccct ccccactatg gatgactcca aattaaagaa ggtagctaac atattcctgt
      781 gcgccctgtc ttcgctattc accagaccca taaaggacat aataggaaag ttaaggcctc
      841 tcaacatcat caatatcctg gcttcatgtg attggacttt tgcaggcata gtggagtcct
      901 tgatactctt ggcagaactc tttggagtct tctggacacc cccagatgtg tctgcgatga
      961 ttgccccctt actcggtgat ttcgagttac aagggcctga ggaccttgca gtggagctcg
     1021 tccctgtggt aatgggggga attggtttgg tgctgggatt caccaaagag aagattggaa
     1081 aaatgttgtc atctgctgca tccaccttga gagcttgtaa agatcttggc gcatatgggc
     1141 tagagatcct aaagttggtc atgaagtggt tcttcccgaa gaaagaggag gcgaacgaac
     1201 tggctatagt gagatccatc gaggatgcag tactggacct tgaggcaatt gaaaacaacc
     1261 atatgaccac cttgctcaaa gacaaagaca gcctggcaac ctacatgaga acccttgacc
     1321 tcgaggaaga gaaagccaga aaactctcaa ccaagtctgc ctcgcctgac atcgtaggca
     1381 caatcaacgc ccttctggcg agaatcgccg ctgcacgctc cctggtgcac cgagcgaagg
     1441 aggagctttc tagcagacca agacctgtag tcttgatgat atcaggcaga ccagggatag
     1501 gaaagaccca ccttgctaga gaggtggcta agaaaatcgc agcctctctc acaggagacc
     1561 aacgtgtggg cctcatccca cgcaatggtg tcgatcactg ggatgcatac aagggggaga
     1621 gggttgtcct atgggacgac tatggaatga gcaatcccat ccatgacgcc ctcaggttgc
     1681 aagaactcgc tgacacttgc cccctcactc taaattgtga caggattgag aacaaaggaa
     1741 aggtctttga cagcgacgtc atcatcatca ctaccaatct ggccaaccca gcaccactgg
     1801 actatgtcaa ttttgaagcg tgctcgaggc gtatcgattt cctcgtgtat gctgaagccc
     1861 ctgaggtcga aaaggtgaaa cgtgatttcc cgggtcaacc tgacatgtgg aaaaatgctt
     1921 ttagttctga tttctcacac ataaaattgg cactggctcc acaaggtggc tttgataaga
     1981 acggaaacac cccacacgga aagggcgtca tgaagaccct caccactggc tccctcattg
     2041 cccgggcatc agggttgctc catgagagat tggatgagtt tgaactacag ggcccagccc
     2101 ttgccacctt caactttgac cgcaacaaag tgctcgcctt taggcagctt gccgctgaaa
     2161 ataaatatgg gttgatggac acaatgagag ttgggaggca gctcaaggat gtcaaaacaa
     2221 tgccagaact caaacaagca ctcaagaaca tctcaatcaa gaagtgccag attgtgcatg
     2281 gtggttgcac ctacacactt gagtctgatg gcaagggcaa tgtggaagtg aacagagttc
     2341 agagcaccac cgtacagacc aacaatgagc tagctggcgc tctgcaccat ctaaggtgcg
     2401 ccagaatcag gtactatgtc aagtgtgtcc aggaggccct gtattctgtc atccagattg
     2461 ctggggctgc atttgtcacc acgcgcatca tcaagcgtgt gaacatccaa gacttatggt
     2521 ccaagccaca agtggaaaac acagaggagg ctgccaacaa ggaagggtgc ccgaaaatca
     2581 gagatgatga ggagttcgtc atttcatctg acgacattaa agctgagggt aagaaaggga
     2641 aaaacaagac tggccgtggc aagaagcaca cagccttctc aagtaaaggt ctcagtgatg
     2701 aagagtatga tgagtacaag agaattagag aggaaaggaa tggcaagtac tccatagaag
     2761 agtaccttca ggacagggac aaatactacg aggaggtggc cattgccagg gcgaccgagg
     2821 aagacttctg cgaagaggag gaggccaaga tccggcagag gatcttcaga ccaacaagga
     2881 aacaacgcaa ggaagaaaga gcttctctcg gtttagtcac aggttctgaa attaggaaaa
     2941 gaaacccaga agacttcaag cccaagggga aactatgggc tgacgatgac agaagtgtgg
     3001 actacaatga gaaactcagt tttgaggccc caccaagcat atggtcaagg atagtcaact
     3061 ttggctcagg ttggggcttc tgggtctccc ccagcctgtt cataacatca acccacgtca
     3121 tacctcaagg cgcaaaggag ttctttggag tccctgtcaa acaaatccag gtgcacaagt
     3181 caggcgaatt ctgtcgcttg aggttcccaa aaccaatcag gactgatgtg gctggcatga
     3241 tcttggaaga aggtgcaccc gaaggcaccg tggtcacact actcatcaaa aggtccactg
     3301 gagaactcat gcccctagcg gctagaatgg ggacccatgc aaccatgaaa attcaagggc
     3361 gcactgtcgg aggccagatg ggcatgcttc tgacaggatc caacgccaaa agcatggatc
     3421 taggcaccac accaggtgac tgcggctgcc cctacatcta caagagagga aatgattatg
     3481 tggtcattgg agtccacacg gctgccgctc gtgggggaaa cactgtcata tgtgccaccc
     3541 aggggagcga gggggaagcc acacttgaag gtggtgacag taaaggaaca tactgtggtg
     3601 caccaatcct aggcccaggg agtgctccaa aacttagcac caaaaccaaa ttctggagat
     3661 catccacagc acccctccca cctggcacct atgaaccagc ctaccttggt ggtaaggacc
     3721 ccagagtcaa gggaggcccc tcgttgcagc aagtcatgag ggaccagctg aaaccattta
     3781 cagagcccag gggtaagcca ccaaagccaa gtgtgttaga agctgccaag aaaactatta
     3841 ttaatgtcct tgaacaaaca attgacccac ctgagaagtg gtcgttcgca caagcttgcg
     3901 cgtcccttga caaaaccact tccagcggcc acccgcacca catgcggaaa aacgactgct
     3961 ggaacgggga atccttcaca ggcaagctgg cagaccaggc ttccaaggcc aacctaatgt
     4021 ttgaggaagg gaagaacatg accccagtct acacaggtgc acttaaagat gaattagtca
     4081 aaactgacaa aatttatggt aagatcaaga agaggcttct ctggggctcg gacttagcaa
     4141 ccatgatccg gtgtgcccga gcattcggag gcctaatgga tgaactcaaa acacattgtg
     4201 tcacacttcc catcagagtt ggtatgaata tgaatgagga tggccctatc atcttcgaga
     4261 agcattccag gtataagtac cactatgatg ctgattactc tcggtgggat tcaacacaac
     4321 agagagccgt gttggcagct gctctagaaa tcatggtaaa attttcctca gaaccacatt
     4381 tggctcaggt agtcgcagaa gaccttcttt ctcctagcgt ggtggatgtg ggtgacttca
     4441 caatatcaat caacgagggt cttccctctg gggtgccatg cacctcccaa tggaactcca
     4501 tcgcccactg gcttctcact ctctgtgcac tctccgaagt tacgaatttg tccccagaca
     4561 ttgtacaggc taactctatc ttttccttct atggtgatga tgaaattgtt agtacagaca
     4621 taaaattaga cccagagaag ttgacagcaa agcttaagga atatgggttg aaaccaaccc
     4681 gccctgacaa aactgaagga cctcttgtta tttctgaaga cttagatggt ttgacttttc
     4741 tgcggagaac cgtgacccgt gacccagctg gttggtttgg aaaactggag cagagctcaa
     4801 tactcaggca aatgtactgg actaggggcc ctaaccatga agatccatct gaaacaatga
     4861 tcccacactc tcaaagaccc atacaactga tgtccttact gggagaggcc gcactccatg
     4921 gcccaacatt ctacagtaaa atcagcaaat tagtcattac ggagctaaaa 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 cggtgccgct attgcggcgc ctgtagcggg ccaacaaaat
     5221 ataattgacc cctggattag aaacaatttt gtacaagccc ctggtggaga gttcacagta
     5281 tcccctagaa acgctccagg cgaaatacta tggagcgcgc ccttaggacc tgatttgaat
     5341 ccctacctat ctcatttggc cagaatgtat aatggttatg caggtggttt tgaagtgcag
     5401 gtgatccttg cggggaacgc gttcaccgct ggaaaaatta tatttgcagc agtcccacca
     5461 aattttccaa ctgaaggctt gagtcccagc caggtcacta tgttccccca cataatagta
     5521 gatgttaggc aattggaacc tgtgttgatc cccttacctg atgttaggaa taacttctac
     5581 cattataatc agtcaaatga ctctactatt aaattgatag caatgttgta tacaccactt
     5641 agggctaaca atgctgggga tgatgttttc acagtctctt gtcgagtact cacgaggcca
     5701 tcccctgatt ttgattttat atttttggta ccacccacag ttgagtcaag aactaaacca
     5761 tttactatcc caatcttaac tgttgaagaa atgaccaatt caagattccc cattcctttg
     5821 gaaaagttgt acacgggtcc cagcagtgcc ttcgttgtcc aaccacaaaa cggcagatgc
     5881 acgactgatg gcgtgctctt aggcaccact caactgtctc ctgtcaacat ctgcaccttc
     5941 agaggggatg tcaccaacat tcaaggttcc cacacttaca caatgaattt ggcttctcta
     6001 aattggaaca attatgaccc aacagaagaa actccagccc ctctaggaac tccagatttc
     6061 gtgggaaaga tccaaggtgt gctcactcaa accacaaagg gacaaggctc gacccgtggc
     6121 cataaagcca cagtatacac tgggagtgcc tcctttactc caaagctagg cagtgttcaa
     6181 tttagaactg atacacaaaa tgattttgta actcaccaaa acacaaaatt caccccagtc
     6241 ggtgttatcc aggatggtga caccacccac cgaaatgaac cccaacaatg ggtgctccca
     6301 aattattcag gtgtaaatac ccataatgtg cacctagccc ctgctgtagc tcccaccatc
     6361 ccgggtgaac aacttctctt cttcaggtcc agtatgcccg gatgcagcgg gtatcccaac
     6421 atggatttgg attgcctagt cccccaggaa tgggtgcagc acttctacca ggaggcagct
     6481 ccagcactat ctgatgtggc tctattgaga tttgtgaatc cagacactgg tagggtcctg
     6541 tttgagtgta aacttcataa atcaggctat gttacagtgg cccacaccgg ccatcatgat
     6601 ttggtcatcc ctcccaatgg ctattttagg tttgattcct gggttaacca attttacaca
     6661 cttgccccca tgggaaatgg aacggggcgt agacgtgttt tataatggct ggagctttct
     6721 ttgctggatt ggcatctgac gtccttggct ctggacttag ttccctaatc aatgctgggg
     6781 ctggggctat caaccaaaag attgattttg aaaataacag aaaattgcag caagcttcct
     6841 tccagtttag cagcaaccta caacaggctt cctttcaaca tgataaagag atgctccaag
     6901 cacaagttga ggctactaaa aagttgcaac aggaaatgat gaaagtcaaa caagcaatac
     6961 tcttagaagg tggattctct gcaacagatg cagcccgtgg ggcaatcaat gcccccatga
     7021 caaaggtttt ggactggaat ggaacaaggt attgggcccc tgatgctagg accacaacat
     7081 acaatacagg ccacttttcc acccctcaat cctcgggggc actgccagga agaactaatc
     7141 ccagaattcc cacccccgct cgggcttcct ctagtacatc ttctaatgct tctactgcta
     7201 cttctataag ttcaaatcaa actgtttcaa cgagacttgg ttctacagct ggttctggca
     7261 ccaatgtctc gagtctcccg tcaactgcaa ggaccaggag ttgggttgag gatcaaaata
     7321 gaaatttgtc acctttcatg aggggagctc acaacatatc gtttgtcacc ccaccatcta
     7381 gcagatcctc tagtcaaggc acagtctcaa ccgtgcctaa aggagttttg gactcctgga
     7441 ctggcgcttt caacacgcgc aggcagcctc tcttcgctta cactcatagg cgaggggagt
     7501 cacgggtgta a
//