Typing tool

Complete norovirus genomes

MH218689  GII.17
 GII.P17

Length: 7,562 | 3 CDS

ORF1: 5..5113
ORF2: 5094..6716
ORF3: 6716..7495
LOCUS       MH218689                7562 bp    RNA     linear   VRL 11-JUN-2018
DEFINITION  Norovirus GII isolate NORO_231_20_01_2016, complete genome.
ACCESSION   MH218689
VERSION     MH218689.1
KEYWORDS    .
SOURCE      Norovirus GII
  ORGANISM  Norovirus GII
            Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes;
            Picornavirales; Caliciviridae; Norovirus.
REFERENCE   1  (bases 1 to 7562)
  AUTHORS   Brown,J.R., Roy,S., Shah,D., Williams,C.A., Williams,R., Dunn,H.,
            Hartley,J., Harris,K. and Breuer,J.
  TITLE     Norovirus transmission dynamics in a paediatric hospital using full
            genome sequences
  JOURNAL   Clin. Infect. Dis. (2018) In press
   PUBMED   29800111
  REMARK    Publication Status: Available-Online prior to print
REFERENCE   2  (bases 1 to 7562)
  AUTHORS   Brown,J.R., Roy,S., Shah,D., Williams,C.A., Williams,R., Dunn,H.,
            Hartley,J., Harris,K. and Breuer,J.
  TITLE     Direct Submission
  JOURNAL   Submitted (17-APR-2018) Division of Infection and Immunity,
            University College London, 90 Gower St, London, London WC1E 6BT,
            United Kingdom
COMMENT     ##Assembly-Data-START##
            Assembly Method       :: CLC Genomics Workbench v. 10.1
            Sequencing Technology :: Illumina
            ##Assembly-Data-END##
FEATURES             Location/Qualifiers
     source          1..7562
                     /organism="Norovirus GII"
                     /mol_type="genomic RNA"
                     /isolate="NORO_231_20_01_2016"
                     /host="Homo sapiens"
                     /db_xref="taxon:122929"
                     /country="United Kingdom"
                     /collection_date="20-Jan-2016"
                     /note="genotype: GII.P17_GII.17"
     gene            5..5113
                     /gene="ORF1"
     CDS             5..5113
                     /gene="ORF1"
                     /codon_start=1
                     /product="nonstructural polyprotein"
                     /protein_id="AWR17725.1"
                     /translation="MKMASNDASAAVAGKNNNNDKEKSSSDSLFSNMTVTFKKALGAR
                     PKQPPPGETKQIQKPPRPPTPELVKRIPPPPPNGEDEPKIVYKVGEGVSGLPNLTTVA
                     QPDAQNTAYSVPPLSQREAGEAKEPLPGSILEMWDGEIYHYGLYVERGHVLGVHKPPA
                     AISLAKIELTPLSLYWRVVYTPQYLIAPETLKNLSGETFPYTAFDNNCYAFCCWVLDL
                     NDSWLSRRMIQRTTGFFRPYQEWNRKPLPTMDEPKIKKAANAVLCALSSLFTRPIKDI
                     IGKLRPLNILNILATCDWTFAGIVESMILLAELFGVFWTPPDVSAMIAPLLGDYEMQG
                     PEDLAVELVPVVMGGIGLVLGFTKEKIGKMLSSAATTLRACKDLGSYGLEILKLVMKW
                     FFPKKEEANELAMVRAIEDAVLDLEAIENNHMTTLLKDKDSLATYMRTLDLEEEKARK
                     LSTKSASPDIVGTINSLLARIAAARSLVHKAKEELSSRQRPVVVMISGKPGIGKTHLA
                     RELAKKVASTLSGDQRIGLIPRNGVDHWDAYKGERVVLWDDYGMSNPIQDALRLQELA
                     DTCPLTLNCDRIENKGKVFDSDAIIITTNLANPAPLDYVNFEACSRRIDFLVYADAPD
                     IEKAKRDFPGQPDMWKDHYRSDFTHIKLQLAPQGGFDKNGNTPHGKGVVKSLTIGSLI
                     ARASGLLHERMDEFELQGPDLPTFNFDRNKVAAFRQLAAENKYGLMDTLRVGNQLKSV
                     KTLDELKQAIKNISIKKCQIVYNGCTYTIESDGKNKVVVEKVQNATVQTNNELVGALH
                     HLRTARIRYYVKCFQEAIYSLLQIAGAAFVTSRIVKRMNISNLWSKPPIEEGDEPEDE
                     GGCPRPRDEGDLTIDSRDIKVEGKKGKNKSGRGKKHTAFSSKGLSDEEYDEYKRIREE
                     RNGKYSIEEYLQDRDRYYEELAIAKATEEDFCEEEEIKIRQRIFRPTRKQRKEERATL
                     GLVTGSEIRKRNPDDFKPKGKLWADDNRSVDYNERIDFEAPPSVWSRIVNFGTGWGFW
                     VSPSLFITSTHVIPKGTSEAFGVPINQIQIHKSGEFCRLRFPKPIRPDVSGMILEEGA
                     PEGTVVSILIKRTTGELMPLAVRMGTHATMKIQGRTVGGQMGMLLTGSNAKSMDLGTT
                     PGDCGCPYIYKRGNDFVVIGVHTAAARGGNTVICATQGSEGEATLEGGDNKGTYCGAP
                     ILGPGNSPKLSTKTKFWRSSNAPLPPGTYEPAYLGGRDPRVKGGPSLQQVMRDQLKPF
                     TEPRGKPPNPNVLESAKKTIINVLEQTIDPPQKWSYAQACASLDKTTSSGYPHHVRKN
                     DYWSGESFTGKLADQASKANLMYEEGKHMQPVYTAALKDELVKTDKIYGKIKKRLLWG
                     SDLSTMIRCARAFGGLMDELKANCITLPIRVGMNMNEDGPIIFEKHSRYRYHYDADYS
                     RWDSTQQRAVLEAALEIMVRFSAEPQLAQIVAEDLLSPSVVDVGDFKIAINEGLPSGV
                     PCTSQWNSIAHWLLTLCALSEVTGLGPDIIQANSMYSFYGDDEIVSTDIKLDPEKLTA
                     KLKEYGLKPTRPDKTEGPLVISEDLNGLTFLRRTVTRDPAGWFGKLDQNSILRQLYWT
                     RGPNHEDPSETMIPHAQRPVQLMALLGESSLHGPSFYSKVSKLVISELKEGGMDFYVP
                     RQESMFRWMRFSDLSTWEGDRNLAPSFVNEDGVE"
     mat_peptide     5..1003
                     /gene="ORF1"
                     /product="p48"
     mat_peptide     1004..2101
                     /gene="ORF1"
                     /product="NTPase"
     mat_peptide     2102..2638
                     /gene="ORF1"
                     /product="p22"
     mat_peptide     2639..3037
                     /gene="ORF1"
                     /product="VPg"
     mat_peptide     3038..3580
                     /gene="ORF1"
                     /product="Pro"
     mat_peptide     3581..5110
                     /gene="ORF1"
                     /product="RdRp"
     gene            5094..6716
                     /gene="ORF2"
     CDS             5094..6716
                     /gene="ORF2"
                     /codon_start=1
                     /product="VP1"
                     /protein_id="AWR17726.1"
                     /translation="MKMASNDAAPSNDGAAGLVPEDNNETLPLEPVAGAAIAAPVTGQ
                     NNIIDPWIRTNFVQAPNGEFTVSARNAPGEVLLNLELGPDLNPYLAHLSRMYNGYAGG
                     VEVQVLLAGNAFTAGKILFAAVPPNFPVEFLSPAQITMLPHLIVDVRTLEPIMIPLPD
                     VRNTFFHYNNQPTGRMRLVAMLYTPLRSNGSGDDVFTVSCRVLTRPTPDFQFTYLVPP
                     SVESKTKPFTLPILTLSELTNSRFPVPIDSLFTAQNNVLQVQCQNGRCTLDGELQGTT
                     QLLPSGICAFRGRVTAEPSRSDRWHMQLQNLNGTTYDPTDDVPAPLGTPDFKGFVFGV
                     ASQRNVGSDAPGSTRAHEVVISTYSPQFVPKLGSVNFKISSDDDFQLQPTKFTPVAIN
                     EEDDDHPFRQWELPDYSGVLTLNMNLAPPVAPNFPGEQLLFFRSFVPCAGGYNQGIVD
                     CLIPQEWIQHFYQESAPSQSDVALIRYVNPDTGRTLFEAKLHRSGYITVAHSGDYPLV
                     VPANGYFRFDSWVNQFYSLAPMGTGNGRRRAQ"
     gene            6716..7495
                     /gene="ORF3"
     CDS             6716..7495
                     /gene="ORF3"
                     /codon_start=1
                     /product="VP2"
                     /protein_id="AWR17727.1"
                     /translation="MAGALIAGLAGDMLTSSVGSLVNAGANAINQRIDFENNKQLQFA
                     SFQHDKEMLQAQVKATKQLQSEMIAIKQGVLAAGGFSPTDAARGAIGAPMTKVLDWSG
                     TRYWAPNSTKTTGYSGQFTSSPVHMPSPNVPQSKPAKPRSIAPSSSSSSVYSMSTQST
                     HLTSGSSSNASSASTKLTNLSSGSSQNRTVEWVNQQRSLSPFMSGALNISHVTPPSSR
                     ASSSGTVSTVPKEVLDSWTSAFNTHRQPLFAHLRVRGESRV"
ORIGIN      
        1 gtgaatgaag atggcgtcta acgacgcttc cgctgccgtt gctggcaaaa acaacaacaa
       61 cgacaaggag aaatcttcaa gtgacagctt gttttccaac atgactgtta cttttaagaa
      121 agccctcggg gcgcggccta aacaaccgcc cccgggagaa acaaaacaaa tacaaaaacc
      181 accaaggcca ccgacaccgg aattggtgaa gagaataccc ccacccccac ccaatggcga
      241 ggatgaacca aagatagtgt ataaggtggg agaaggtgtg tctgggctgc ccaacctaac
      301 gactgtggca cagcctgacg cacaaaacac agcttatagt gttcccccac ttagccagag
      361 agaagccggc gaagctaaag aaccgctgcc tggctccatt ctggaaatgt gggatggtga
      421 gatctaccac tatgggctgt atgttgagcg ggggcatgta ctcggagtgc ataaaccacc
      481 tgctgcaata agtcttgcca aaattgaatt aacacctctg tctctctact ggagagtggt
      541 ttacactccc cagtatttga tagctccaga aactcttaag aacttgagtg gggagacttt
      601 cccatacacg gcctttgaca acaactgtta tgccttctgt tgttgggttc tagacctcaa
      661 cgactcctgg ctcagcagga gaatgatcca aagaacaact ggcttcttca gaccgtatca
      721 ggagtggaac agaaaacctt taccaaccat ggatgaaccg aaaatcaaga aggccgcgaa
      781 tgctgttctg tgtgctctct cctcactctt cactagaccc atcaaggaca tcattggaaa
      841 gcttagacca ctgaatattc tcaatatact ggcaacttgt gactggactt ttgcaggcat
      901 agtggaatct atgatccttc ttgctgaact ctttggggtg ttctggaccc ccccagatgt
      961 gtctgcgatg attgctccct tactcggtga ctacgagatg caaggccccg aagacctagc
     1021 cgtggaactc gtgcccgtgg taatgggagg aataggtttg gtgttaggat tcaccaagga
     1081 aaagatcggc aagatgcttt catcagctgc gaccacgctt agggcctgta aggatctagg
     1141 atcttatgga ttggagatac tcaaattggt catgaagtgg ttcttcccca agaaggagga
     1201 ggctaatgaa ctagccatgg taagggccat tgaggacgca gtcctggatt tggaggcaat
     1261 agaaaacaat cacatgacca cccttctcaa ggataaagac agcttggcca catacatgag
     1321 aactcttgac ttggaagaag agaaagcaag gaaactgtcg accaaatcgg cgtcacctga
     1381 catcgtgggt acaataaact cattattggc aaggatagca gccgccaggt cactagtcca
     1441 caaggctaag gaggagctct cgagcagaca gagacctgtt gttgtaatga tatcaggtaa
     1501 accgggtata ggaaagaccc atctggccag agagctagcc aagaaagttg cgtcaacact
     1561 gtcaggcgac caaaggattg gactgatacc taggaatggc gtcgaccatt gggacgccta
     1621 caagggagaa agggtggttc tgtgggatga ttatggtatg agcaacccta tacaggacgc
     1681 actgaggctc caagaattgg ctgacacctg tcctctgacc ctaaattgtg acaggattga
     1741 aaacaaagga aaagtgttcg acagtgatgc cataattata acaaccaacc ttgcaaaccc
     1801 agcaccacta gattatgtca actttgaggc ctgctctaga cgcatagact tcttggtgta
     1861 tgcagacgca cctgacatag agaaggctaa gcgtgatttc cctggccaac cagatatgtg
     1921 gaaggaccat tacagatcag acttcacaca catcaaactt cagctggcac cacagggagg
     1981 ttttgataaa aatggcaaca ccccacacgg caaaggtgtg gtaaagtctc tgacgattgg
     2041 ttctctgatc gccagggctt ctggtttact ccacgagaga atggatgaat tcgagctcca
     2101 gggccctgac ttgccaacct tcaactttga ccgcaacaaa gtcgccgcct tcagacaatt
     2161 agcagctgaa aacaaatatg gtctcatgga cacactgagg gtcggcaacc aactgaaaag
     2221 tgtcaagacc ctggatgagc tgaagcaggc cataaagaac atcagtatca agaagtgcca
     2281 gatagtgtat aatggatgca cctataccat agaatctgat gggaagaaca aggttgtggt
     2341 tgaaaaggtg caaaatgcaa cagttcaaac taacaatgaa cttgtagggg cactccacca
     2401 cctgagaact gcaaggataa gatattatgt taaatgcttc caagaagcca tttattctct
     2461 actccaaatt gctggtgcag ccttcgtcac ctcacgcatc gtgaagcgca tgaacatctc
     2521 aaacctctgg tcgaagccac ccatcgagga gggtgatgag cctgaagatg aaggaggatg
     2581 ccccaggccc agggatgaag gtgacctcac tattgactct agggacatta aagtggaagg
     2641 gaaaaagggc aagaacaaat ctggccgggg caagaaacat acagccttct catccaaggg
     2701 tctcagtgat gaagagtacg acgagtacaa gagaatcaga gaggaaagga atggcaaata
     2761 ctcaatagag gaatacctcc aagataggga cagatactat gaagagcttg ccattgctaa
     2821 agccactgag gaggacttct gtgaagagga ggaaatcaaa attcgccaga gaatcttccg
     2881 acccaccagg aagcagcgga aagaggagag ggccacgctt gggcttgtca caggatcgga
     2941 aatcagaaag aggaatccag atgactttaa accaaaagga aaattgtggg ctgatgacaa
     3001 caggagcgtg gattacaatg agaggataga ttttgaggct cccccgagtg tttggtctag
     3061 gatagtcaac tttggcacag gctggggatt ctgggtttct ccaagtctct ttataacttc
     3121 aacacatgtc ataccaaaag gaaccagtga ggcctttgga gtgcccataa accaaatcca
     3181 aattcacaaa tctggagaat tttgccgctt gcggtttcca aaaccaatca gaccagacgt
     3241 gagtggaatg atcttggaag agggtgcccc tgaaggcact gttgtgtcta ttctcattaa
     3301 aaggacgaca ggggagctga tgcctctcgc agtcagaatg gggactcatg ccacaatgaa
     3361 aatccagggc agaacggtgg gtggtcagat gggtatgctt ctcactggct caaatgctaa
     3421 aagcatggat ctaggcacaa cgccaggtga ctgcgggtgt ccatacatat acaaaagggg
     3481 caatgacttc gtggtcattg gggtgcacac tgcagcagca cgtggaggca acacggtcat
     3541 atgtgccaca caaggaagtg aaggtgaagc cactcttgaa ggaggtgaca acaagggtac
     3601 ttactgtgga gcccccattt tgggacctgg caattcacca aaattgagca caaaaacaaa
     3661 attctggaga tcttctaacg caccgcttcc cccaggtact tatgaaccag catatcttgg
     3721 tgggagagac ccgcgtgtga agggaggccc atctctgcaa caagttatga gagatcaact
     3781 taaacctttt acagagccca gagggaagcc accaaaccca aatgtcctag agtcagcaaa
     3841 gaagactatc atcaatgttc tggaacaaac cattgacccc cctcaaaagt ggtcatatgc
     3901 tcaagcttgt gcatccctcg acaagacaac ttccagtggg tacccacacc acgtccggaa
     3961 gaatgactat tggagtggtg aatccttcac agggaaactt gcagaccagg cttcaaaagc
     4021 aaatctcatg tatgaggaag gcaaacacat gcaaccagtc tacaccgcag cactcaaaga
     4081 cgagctcgtg aaaactgaca aaatttatgg caagatcaag aaaagactcc tgtggggttc
     4141 tgacctctcc accatgattc gatgcgccag agcgtttggt ggtctcatgg atgagctcaa
     4201 agcaaattgt atcacactcc ctatcagagt tggtatgaat atgaatgaag atggccccat
     4261 aatatttgag aaacactcca ggtacaggta ccactatgac gctgattact cccgttggga
     4321 ctccacacaa cagcgggcag tgctggaagc agcacttgaa atcatggtga gattttctgc
     4381 tgagccacag ctggcacaaa tagtggcaga ggacctgcta tcaccaagtg tggttgatgt
     4441 gggcgatttc aaaatcgcta tcaatgaagg tttaccatca ggtgtgcctt gcacctcaca
     4501 atggaattct attgctcact ggttactcac cctgtgtgcc ctttctgaag tgactggatt
     4561 aggccctgac atcatacaag ccaactccat gtactctttc tatggtgatg atgagattgt
     4621 gagcacagat ataaaattgg acccagagaa attgactgca aaactcaaag aatatggcct
     4681 taaacccact cggcctgaca aaactgaggg gccgctggtg attagtgaag acctgaatgg
     4741 gttgactttc ctccgccgaa cagtcacccg tgatccagca ggttggtttg gaaagttgga
     4801 ccaaaactcc atcctcaggc aattgtactg gacaagagga cccaaccatg aagaccccag
     4861 tgagaccatg ataccacacg cacagaggcc tgtgcagctc atggcactac taggagaatc
     4921 ctccctacat ggaccctcat tttacagcaa ggtcagcaaa ctggtcatat ctgaacttaa
     4981 agagggggga atggattttt atgtgcccag acaagagtca atgttcaggt ggatgaggtt
     5041 ctcagatcta agcacatggg agggcgatcg caatctggct cccagttttg tgaatgaaga
     5101 tggcgtcgaa tgacgccgct ccatctaatg atggtgctgc tggtctcgta ccagaggaca
     5161 acaacgagac ccttccccta gaaccagttg cgggcgcagc tatagccgca cccgtcactg
     5221 gccaaaacaa cataattgac ccctggatta gaacaaattt tgtgcaagca ccaaatggag
     5281 agtttacagt gtcagccaga aacgctcctg gagaagtttt attaaatcta gagttgggcc
     5341 ctgatttaaa cccttattta gctcatttgt caaggatgta caatgggtat gctggtggag
     5401 tggaagttca ggttctcctg gcagggaacg cgttcactgc cggaaagatc ctcttcgccg
     5461 ccgtcccgcc aaatttccca gtggaattct taagcccagc ccagattact atgctcccac
     5521 atttaatagt agatgtcagg actcttgaac caattatgat cccactccct gatgttcgga
     5581 atacattctt ccattataac aatcagccca ccggccgtat gagattagtg gctatgctct
     5641 atacccctct tagatctaat ggctcaggtg atgatgtctt tactgtttct tgcagggttt
     5701 tgactaggcc cactcctgat tttcagttca cttatttagt gccaccttct gttgaatcta
     5761 agaccaagcc ttttacctta cctattttaa ccctttctga gctcacaaat tcgaggttcc
     5821 cagtccccat cgattcgctt ttcaccgccc agaataatgt gttgcaggtg cagtgtcaaa
     5881 atggcaggtg cacacttgat ggtgagttac aaggcacaac ccagttgctc ccatctggca
     5941 tctgtgcatt cagaggacgg gtgacagcag aacctagccg tagtgacagg tggcacatgc
     6001 aactgcaaaa tctcaatggc acaacatatg acccaactga tgatgtgcca gccccgctgg
     6061 gtacacctga cttcaagggc ttcgtgtttg gggtggcaag tcaaagaaat gtgggtagtg
     6121 atgcgcctgg ctcaaccagg gctcatgagg tggtgatttc aacctatagt ccccaatttg
     6181 tccccaaatt aggttctgtc aattttaaaa ttagcagtga tgatgatttc caattgcagc
     6241 cgacaaaatt cacaccagtg gccatcaatg aagaagatga tgaccacccg ttcagacaat
     6301 gggaactacc agactattca ggggtgctta ccttgaatat gaaccttgcc cccccggttg
     6361 cgccaaattt ccctggtgaa caattattat tcttcagatc ttttgtgcca tgcgcaggag
     6421 gttataacca aggtattgta gattgtctta ttccccaaga atggatccaa catttctatc
     6481 aggaatcagc gccctcccag tcagacgtgg ctctaatcag gtatgtcaac cccgacacgg
     6541 ggcgcacact gtttgaagca aaattgcaca gatctggtta cattactgtg gctcactctg
     6601 gagactatcc tcttgttgtt ccggctaatg gatactttag atttgattct tgggtaaatc
     6661 agttttactc actcgcccca atgggaactg ggaatgggcg aaggagggct cagtaatggc
     6721 tggagctttg attgcaggat tggcaggcga catgctcacg tcatctgtgg gctccctggt
     6781 gaacgcaggg gcaaacgcca tcaaccaaag gatagatttt gaaaacaaca aacaactcca
     6841 gtttgcttcc tttcagcatg ataaagagat gctccaagcg caggtgaagg caaccaagca
     6901 gctgcaatct gaaatgatag ccataaaaca aggggtttta gccgcaggcg gcttttcccc
     6961 cactgatgca gcaagggggg ccattggtgc acccatgaca aaggtgcttg attggtctgg
     7021 cactcgatac tgggcaccca attccacaaa gacaactggt tattcgggac aattcacctc
     7081 ttcacctgtg catatgccta gcccaaatgt tccacaatca aaacctgcaa agcctaggtc
     7141 tatagctcct tcctcttctt ctagtagtgt ctatagcatg tctactcaat caactcatct
     7201 aacatctggc tcctctagta atgcttcttc tgcctccaca aaattaacaa acttaagctc
     7261 tggctcctct caaaacagaa cagtagagtg ggtgaaccaa cagaggagtc ttagcccttt
     7321 catgagtggc gcactcaata tctcacatgt cacaccaccc tcaagtaggg cttccagttc
     7381 tgggacggtc tcaaccgtgc ccaaggaagt tttggactcc tggacgtctg cgtttaacac
     7441 acacagacag ccgctcttcg cacacctcag agtgaggggg gagtcacgtg tttagtgaaa
     7501 agaaataatt ggctataatg tgatttcttt aataaatttg gctaatttgt atcttttaaa
     7561 aa
//