Typing tool

Complete norovirus genomes

MH218580  GII.3
 GII.P21

Length: 7,548 | 3 CDS

ORF1: 5..5104
ORF2: 5085..6731
ORF3: 6731..7495
LOCUS       MH218580                7548 bp    RNA     linear   VRL 11-JUN-2018
DEFINITION  Norovirus GII isolate NORO_110_06_08_2014, complete genome.
ACCESSION   MH218580
VERSION     MH218580.1
KEYWORDS    .
SOURCE      Norovirus GII
  ORGANISM  Norovirus GII
            Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes;
            Picornavirales; Caliciviridae; Norovirus.
REFERENCE   1  (bases 1 to 7548)
  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 7548)
  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..7548
                     /organism="Norovirus GII"
                     /mol_type="genomic RNA"
                     /isolate="NORO_110_06_08_2014"
                     /host="Homo sapiens"
                     /db_xref="taxon:122929"
                     /country="United Kingdom"
                     /collection_date="06-Aug-2014"
                     /note="genotype: GII.P21_GII.3"
     gene            5..5104
                     /gene="ORF1"
     CDS             5..5104
                     /gene="ORF1"
                     /codon_start=1
                     /product="nonstructural polyprotein"
                     /protein_id="AWR17398.1"
                     /translation="MKMASNDASAAAAAKSNNDNAKSSSDGVLSNMAVTFKRALGARP
                     KQPPPSDKPPKPPRPPTPELVKAIPPPPPNGEDEPIISYNVKGGVSGLPELSTVTQLE
                     ENSTAFSVPPLSQRENRDAKEPLTGTILEMWDGEIYHYGLYVERGLVLGVHKPPAAIS
                     LAKIELTPLSLYWRPVYTPQYLISPDTLRKLHGETFPYTAFDNNCYAFCCWVLDLNDS
                     WLNRRMIQRTTGFFRPYQDWNRKPLPTMDDSKVKKVANVVLCALSSLFTRPIKDIIGK
                     LKPLNILNILATCDWTFAGIVESLILLAELFGVFWTPPDVSAMIAPLLGDYELQGPED
                     LAVELVPVVMGGIGLVLGFTKEKIGKMLSSAASTLRACKDLGAYGLEILKLVMKWFFP
                     KKEEKNELAMVRSIEDAVLDLEAIENNHMTALLKDKDSLATYMRTLDMEEEKARKLST
                     KSASPDIVGTINALLSRIAAARSLVHRAKEELSSRPRPVVVMISGKPGIGKTHLAREL
                     AKKIASTLTGDQRVGLIPRNGVDHWDAYKGERVVLWDDYGMSSPVHDALRLQELADTC
                     PLTLNCDRIENKGKVFDSDVIIITTNLANPAPLDYVNFEACSRRIDFLVYADAPEVEK
                     AKRDFPGQPDMWKDTFKPDFSHIKLALAPQGGFDKNGNTPHGKGVMKTLTAGSLVARA
                     SGLLHERLDEYELQGPTPTTFNFDRNKVLAFRQLAAENKYGLVDTMRVGSQLKNVKTM
                     TELKQALKNISVKKCQLVYGGGTYTLESDGKGNVHVEKVNNTSVQTNNELSGVLHHLR
                     CARIRYYVKCVQEALYSILQIAGAAFITTRIAKRTNIQNLWSKPQAEDLEETNNEEGC
                     PKPKSDEEFVVSSDDIKTEGKKGKNKTGRGKKHTAFSGKGLSDEEYDEYKRIREERNG
                     KYSIEEYLQDRDKYYEEVAIARATEEDFCEEEEAKIRQRIFRPTRKQRKEERASLGLV
                     TGSEIRKRNPDDFKPKGKLWADDDRSVDYNEKLSFEAPPSIWSRIVNFGSGWGFWVSP
                     SLFITSTHVIPQGAQEFYGVPIKQIQIHKSGEFCRLRFPKPIRTDVTGMILEEGAPEG
                     TVATLLIKRPTGELMPLAARMGTHATMKIQGRTVGGQMGMLLTGSNAKSMDLGTTPGD
                     CGCPYIYKRGNDYVVIGVHTAAARGGNTVICATQGNEGEAMLEGGDNKGTYCGAPILG
                     PGNAPKLSTKTKFWRSSTTPLPPGTYEPAYLGGKDPRVKGGPSLQQVMRDQLKPFTEP
                     RGKPPKPSVLEAAKKTIINVLEQTIDPPQKWTYAQACASLDKTTSSGHPHHMRKNDCW
                     NGESFTGKLADQASKANLMFEEGKNMTPVYTGALKDELVKTDKIYGVVKKRLLWGSDL
                     STMIRCARAFGGLMDELKAHCVTLPVRVGMNMNEDGPIIFEKHSRYKYHYDADYSRWD
                     STQQRAVLAAALEIMVKFSPEPHLAQVVAEDLLSPSVMDVGDFKISINEGLPSGVPCT
                     SQWNSIAHWLLTLCALSEVTDLSPDIIQANSLFSFYGDDEIVSTDIKLDPEKLTAKLR
                     EYGLKPTRPDKTEGPLIVSEDLNGLTFLRRTVTRDPAGWFGKLDQSSILRQMYWTRGP
                     NHEDPFETMIPHSQRPIQLMSLLGEAALHGPSFYSKISKLVISELKEGGMDFYVPRQE
                     PMFRWMRFSDLSTWEGDRNLAPSFVNEDGVE"
     mat_peptide     5..994
                     /gene="ORF1"
                     /product="p48"
     mat_peptide     995..2092
                     /gene="ORF1"
                     /product="NTPase"
     mat_peptide     2093..2629
                     /gene="ORF1"
                     /product="p22"
     mat_peptide     2630..3028
                     /gene="ORF1"
                     /product="VPg"
     mat_peptide     3029..3571
                     /gene="ORF1"
                     /product="Pro"
     mat_peptide     3572..5101
                     /gene="ORF1"
                     /product="RdRp"
     gene            5085..6731
                     /gene="ORF2"
     CDS             5085..6731
                     /gene="ORF2"
                     /codon_start=1
                     /product="VP1"
                     /protein_id="AWR17399.1"
                     /translation="MKMASNDAAPSNDGAAGLVPEINNEAMALEPVAGAAIAAPLTGQ
                     QNIIDPWIMNNFVQAPGGEFTVSPRNSPGEVLLNLELGPEINPYLAHLARMYNGYAGG
                     FEVQVVLAGNAFTAGKIIFAAIPPNFPIDNLSAAQITMCPHVIVDVRQLEPVNLPMPD
                     VRNNFFHYNQGSDSRLRLIAMLYTPLRANNSGDDVFTVSCRVLTRPSPDFSFNFLVPP
                     TVESKTKPFSLPILTISEMSNSRFPVPIDSLHTSPTENIVVQCQNGRVTLDGELMGTT
                     QLLPSQICAFRGVLTRSTSRASDQADTATPRLFDYYWHIQLDNLNGTPYDPAEDIPGP
                     LGTPDFRGKVFGVASQRNPDTTTRAHEAKIDTTSGRFTPKLGSLEISTESSDFDQNQP
                     TRFTPVGIGVDHEADFQQWTLPDYAGQFTHNMNLAPAVAPNFPGEQLLFFRSHLPSSG
                     GRSNGILDCLVPQEWVQHFYQESAPSQSQVALVRYVNPDTGRVLFEAKLHKLGFMTIA
                     KNGDSPITVPPNGYFRFESWVNPFYTLAPMGTGNGRRRIQ"
     gene            6731..7495
                     /gene="ORF3"
     CDS             6731..7495
                     /gene="ORF3"
                     /codon_start=1
                     /product="VP2"
                     /protein_id="AWR17400.1"
                     /translation="MAGAFIAGLAGDMLTNTVGSLVNAGANAINQTIDFENNKYLQNA
                     SFNHDKEMLNAQIEATKKLQADMIAIKQGVLTAGGFSPTDAARGAINAPMTKVLDWNG
                     TRYWAPGATSTTSMSGGFTHQTVHRSTPNFKTNQAPKSTPSSGSSVRSNSTQITSLSS
                     HSSGSSRSSGSTVISSIPSSNRTRDWVNQQNFNLEPHMPGSLRTAFVTPPSSTASSSG
                     TVSTVPKNVLDSWTSAFNTRRQPLFAHLRRRGESNV"
ORIGIN      
        1 gtgaatgaag atggcgtcta acgacgcttc cgctgccgct gctgccaaaa gcaacaacga
       61 caacgcaaaa tcttcaagtg acggagtatt atctaatatg gctgtcactt ttaaacgagc
      121 cctcggggcg cggcctaaac agccgccccc gagtgacaaa ccaccaaaac ccccaaggcc
      181 acccacacca gagttggtta aggcaattcc ccctccccca cccaacgggg aagacgaacc
      241 aatcatttct tacaacgtca aagggggtgt ttctggtttg cctgagctct caactgtcac
      301 ccaactggaa gagaactcta cagcattcag cgttccccct cttagtcaga gggagaacag
      361 agatgcaaag gaaccattga ctggaaccat cctggagatg tgggacgggg agatctacca
      421 ttatggctta tacgtagaac gagggttagt gctcggcgtg cacaaaccac cagcagcaat
      481 cagccttgct aagattgagc tgaccccctt gtctttgtat tggagaccag tgtacacccc
      541 acagtacctc atttcccctg acactctcag aaagttgcat ggggagacat tcccttatac
      601 agcctttgac aacaactgtt atgccttctg ctgttgggtg cttgacttga acgattcatg
      661 gctgaacaga aggatgatac agaggacaac aggcttcttc cgaccctatc aggattggaa
      721 caggaaaccc ctccccacga tggatgattc caaagtgaaa aaggtggcca atgttgtcct
      781 atgtgctctc tcatcattgt tcacaagacc aattaaggac attattggga agttaaaacc
      841 cctaaacatt ctcaatatct tagccacatg tgattggact tttgcaggca tagtagaatc
      901 cctgatcctt ttggctgaac tttttggagt tttctggaca cccccagatg tgtctgcgat
      961 gatcgctccc ttactgggtg attatgaact acagggaccc gaggacctcg ctgtggaact
     1021 cgtacccgta gtaatgggag ggataggttt ggtgctggga ttcaccaaag agaaaatcgg
     1081 caagatgctt tcttctgctg cttcaaccct gagggcatgt aaagatctcg gtgcatatgg
     1141 gttggagatc ctcaaattgg ttatgaaatg gtttttccca aagaaagaag agaaaaacga
     1201 attggcaatg gtgagatcca tcgaggatgc agtgctagac cttgaagcca ttgagaacaa
     1261 ccatatgaca gctctactca aggataaaga cagccttgca acctacatga ggactcttga
     1321 catggaggag gagaaggcga gaaaactttc caccaagtct gcctctccgg atattgtggg
     1381 tacgataaat gccctactgt caaggattgc agctgcccgg tctctagtgc acagggctaa
     1441 ggaagagctg tcaagcaggc cccgaccggt cgttgtaatg atttcaggga aaccgggtat
     1501 agggaaaacc catctagcta gagagttggc gaagaagatc gcctccacac tcacgggtga
     1561 ccagagggtg ggtcttatcc cacgtaacgg ggtcgaccac tgggatgcat acaaaggtga
     1621 aagagtcgtt ctctgggacg actacgggat gagcagccct gtccacgacg ccctcagact
     1681 ccaggagctc gctgacacct gtcctctcac actcaactgc gacaggattg agaacaaagg
     1741 taaagtcttt gacagtgacg tcataataat aaccaccaat ttggccaacc cagcgccact
     1801 ggattatgtc aactttgaag cttgctcgag acgcatagac ttcctcgtct atgctgatgc
     1861 tcccgaagtt gagaaggcta agcgggactt cccaggccaa ccagacatgt ggaaagacac
     1921 cttcaaacct gacttctcac acataaaatt ggcattagcc ccgcaaggag gttttgacaa
     1981 gaatggtaac actcctcatg ggaagggagt catgaagacc ctcactgccg gttccctcgt
     2041 tgcccgagca tcagggctcc tccacgagag attggacgag tatgagctgc agggcccaac
     2101 tcccacaaca ttcaacttcg accgcaacaa ggtgcttgct tttaggcagc ttgctgctga
     2161 aaacaagtac ggtctagttg acacaatgag ggtcgggtca caactcaaga atgtcaaaac
     2221 tatgacagaa ctcaaacagg ccctcaagaa catctcagtc aagaaatgtc agcttgtgta
     2281 cggtgggggc acatacacac tcgaatctga tggcaaaggc aatgtgcatg tcgaaaaggt
     2341 gaacaacacc agtgtgcaaa ctaacaacga gctctccggg gttttgcacc atctcaggtg
     2401 tgctagaatc aggtactatg ttaagtgtgt tcaggaagct ctctactcca tcttacaaat
     2461 tgccggggct gcattcatca ccacgcgcat tgctaagcgc acgaacatac aaaacctctg
     2521 gtccaaacca caagcagaag atctagagga gactaacaac gaggagggtt gtccaaaacc
     2581 taaaagtgat gaagaatttg tcgtctcctc tgatgacatc aaaactgagg gtaagaaagg
     2641 aaagaacaag actggccgtg gtaagaagca cacggccttt tccggcaaag gactcagtga
     2701 tgaggagtac gatgagtata agagaatcag ggaagagaga aatggtaagt actccataga
     2761 ggaataccta caggacagag acaaatacta tgaggaggtg gccatagcca gggcaactga
     2821 ggaagatttc tgtgaagaag aggaggccaa aatccggcag aggatattca gaccaacaag
     2881 gaaacaacgc aaagaggaaa gagcttctct tggtttggtt acaggttctg agatcaggaa
     2941 gagaaaccca gatgacttca agcccaaagg gaaactatgg gccgatgatg acaggagtgt
     3001 tgactacaat gagaaactta gtttcgaggc tccaccaagc atttggtcac gaatagtcaa
     3061 ctttggatca gggtggggct tttgggtctc gcccagcctc ttcataacat caacccatgt
     3121 cattccccag ggcgcgcagg agttctatgg agtgcccatc aaacaaatac aaattcacaa
     3181 gtcaggtgag ttctgccggc ttaggttccc aaaaccaatc aggacagatg ttacaggtat
     3241 gatcttggag gaaggtgctc cagaaggcac tgttgccaca cttctcatca agagaccaac
     3301 tggggaactc atgcccttgg cagccaggat gggcacccac gctaccatga aaattcaggg
     3361 tcgcactgtt ggtggacaga tgggcatgct actcacaggg tctaacgcta agagcatgga
     3421 tttgggcaca actcctggcg attgtggctg tccctacatc tacaagagag ggaacgacta
     3481 cgtggtcatt ggagttcaca ctgccgccgc gcgtggagga aacaccgtca tctgtgcaac
     3541 ccaaggaaac gagggtgagg ccatgctaga gggtggtgac aacaagggaa cttattgtgg
     3601 agcaccaata ttaggccctg gaaatgcccc caaactcagc accaaaacca aattctggag
     3661 gtcttccacc acccccctgc cacccggaac ctatgagcca gcctatctgg gtggcaagga
     3721 ccctagagtg aaaggtggcc cctcactgca acaggtaatg agagaccaac taaaaccatt
     3781 cactgagccc agaggcaaac cacccaaacc aagtgtgcta gaagctgcca agaagactat
     3841 aatcaatgtg cttgaacaaa caatagaccc acctcaaaaa tggacatacg cacaagcgtg
     3901 tgcatcacta gacaagacca cttccagcgg tcaccctcac cacatgcgga agaacgattg
     3961 ctggaatggg gaatctttca caggaaaact ggcagaccaa gcatcaaagg ccaacctaat
     4021 gtttgaggaa ggaaagaaca tgactccagt atacacagga gctctgaaag atgagctagt
     4081 caaaactgac aagatctatg gggtagtcaa gaagaggctc ctgtggggtt cagacctatc
     4141 aaccatgata cggtgtgcac gagccttcgg tgggctaatg gacgagctca aggcccattg
     4201 cgtcacacta ccagtcaggg ttggtatgaa catgaatgag gatggaccca taatatttga
     4261 gaaacactcc agatacaaat atcattatga tgcagattac tcccgctggg actcaacaca
     4321 acaaagagca gtgctagccg cagccctgga aataatggtc aaattctcac cagaacccca
     4381 tctggcccaa gtggttgcag aagacctttt gtcccccagt gtgatggatg tgggtgattt
     4441 caagatatca atcaacgagg gattgccctc tggtgtccct tgcacttcac aatggaactc
     4501 cattgctcac tggctcctca cactatgtgc actgtctgaa gtcacagacc tgtcccctga
     4561 catcatccag gcgaattccc tgttctcctt ttatggtgat gatgaaatag tgagcacaga
     4621 catcaaatta gacccagaga aattgacagc aaaactgagg gaatacgggc ttaaaccaac
     4681 ccgccctgac aaaacggagg gacccttaat tgtctctgaa gatttgaatg gcctgacctt
     4741 cctgcggaga acagtgaccc gcgacccggc cggatggttt ggcaaactgg accaaagttc
     4801 aatactcagg cagatgtact ggaccagggg gccaaaccat gaagacccct ttgaaacaat
     4861 gataccacac tcccaaagac ccatacaact gatgtcatta cttggtgaag ctgcattgca
     4921 tggtccatca ttctacagta aaatcagcaa attggtcatc tcggaactga aagagggtgg
     4981 aatggatttc tacgtgccca gacaagaacc aatgttcagg tggatgagat tctcagattt
     5041 gagcacgtgg gagggcgatc gcaatctggc tcccagtttc gtgaatgaag atggcgtcga
     5101 atgacgccgc tccatctaat gatggtgccg ccggcctcgt cccagagatc aacaatgagg
     5161 caatggcgct agagccagtg gcgggtgcag cgatagcagc acccctcact ggtcagcaaa
     5221 atataattga tccctggatt atgaataatt ttgtacaagc acctggtggt gaatttacag
     5281 tgtcccccag aaattcccct ggtgaagtcc ttcttaattt ggaattgggc ccagaaataa
     5341 atccctattt ggcccatctt gctagaatgt ataatggtta tgcaggtgga tttgaagtgc
     5401 aggtggtcct agctggaaat gcgtttacag caggaaagat aatctttgca gccatccccc
     5461 ccaattttcc aattgacaat ttaagtgcag cacagatcac aatgtgccca catgtgattg
     5521 tggatgtcag acagttggaa ccagtcaacc tcccgatgcc tgacgttcgc aataacttct
     5581 ttcattataa tcaagggtct gattcgaggt tacgcctaat tgcaatgcta tacacacctc
     5641 ttagggcaaa caattctggg gatgatgtct ttactgtgtc ttgtagagtg ctaactagac
     5701 ctagtcctga tttctcattt aatttccttg tgccacccac tgtggagtca aagacaaaac
     5761 ccttttccct ccctatcctg actatctctg aaatgtccaa ttctaggttc ccagtaccaa
     5821 ttgattccct acacaccagt cctactgaga atattgttgt tcagtgccaa aatgggcgcg
     5881 tcacccttga tggtgagctg atgggcacca cccaactctt gcctagccaa atctgtgctt
     5941 tcaggggcgt tctcaccaga tcaacaagca gggccagtga ccaggccgac acagcaaccc
     6001 ctagattgtt tgattattat tggcatatac aattggataa tctaaatgga accccttatg
     6061 atcctgcaga agacatacca ggccccctag ggacaccaga cttccgtggc aaagtctttg
     6121 gcgtggccag ccagagaaat cctgatacca cgactagggc acatgaagca aagatagaca
     6181 ccacatctgg ccgcttcacc ccaaagctag gctcattaga gatatccact gaatctagtg
     6241 attttgatca aaaccaacca acaagattca ccccagttgg cattggagtt gaccatgagg
     6301 cagactttca gcaatggacc ctacccgact acgctggtca gttcacacac aacatgaact
     6361 tagccccagc tgttgctccc aacttccctg gtgagcagct ccttttcttc cgctcacatt
     6421 tgccatcttc tggtgggcga tccaacggga ttctagactg cctggttccc caagaatggg
     6481 tacagcactt ctaccaagag tcagccccct ctcagtctca agtggccctg gttaggtatg
     6541 ttaatcctga cactggtaga gtgttatttg aggccaagct acacaaatta ggtttcatga
     6601 ctatagccaa gaatggtgat tctccaataa ctgtccctcc aaatggatac tttaggtttg
     6661 aatcttgggt gaaccccttt tacacacttg cccccatggg aactgggaat gggcgtagaa
     6721 ggattcaata atggctggag cttttatagc aggattggct ggtgatatgc taacaaatac
     6781 tgtaggatct ttagttaatg caggagctaa tgctattaat caaacaattg attttgaaaa
     6841 taataaatat ttgcaaaatg cttcttttaa tcatgataag gagatgttaa atgcgcaaat
     6901 tgaggcaaca aagaagttac aggctgacat gattgctatc aaacaagggg ttttgaccgc
     6961 tggcggcttc tctcctactg atgcagcccg tggggcaatt aatgccccca tgacaaaagt
     7021 cctagattgg aatggaacga gatactgggc accaggtgcc acctccacaa cttcgatgtc
     7081 gggtggcttt acacatcaaa ctgtgcacag atccacacca aattttaaaa cgaaccaggc
     7141 ccccaaatcc acacccagca gtgggtcttc agtgaggtca aactcaaccc aaatcactag
     7201 cctgagctca cactcgtccg ggtcgtctcg atccagcggg tctacagtca tcagctcaat
     7261 accatcctct aacaggacta gggactgggt caaccaacaa aattttaatt tggaaccaca
     7321 catgcctggg tctcttagga cagcttttgt cactccacca tctagtacgg cctctagctc
     7381 aggcacagtc tcaactgtgc ccaaaaatgt tttggactcc tggacatctg cgtttaacac
     7441 gcgcagacag ccgctattcg cacaccttcg cagaaggggg gagtcaaatg tttagtgaaa
     7501 agattatttt aaatttggtt taaaattagg tttaatttgg aatctttt
//