Typing tool

Complete norovirus genomes

MH218668  GII.3
 GII.P21

Length: 7,548 | 3 CDS

ORF1: 5..5104
ORF2: 5085..6731
ORF3: 6731..7495
LOCUS       MH218668                7548 bp    RNA     linear   VRL 11-JUN-2018
DEFINITION  Norovirus GII isolate NORO_210_16_12_2015, complete genome.
ACCESSION   MH218668
VERSION     MH218668.1
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_210_16_12_2015"
                     /host="Homo sapiens"
                     /db_xref="taxon:122929"
                     /country="United Kingdom"
                     /collection_date="16-Dec-2015"
                     /note="genotype: GII.P21_GII.3"
     gene            5..5104
                     /gene="ORF1"
     CDS             5..5104
                     /gene="ORF1"
                     /codon_start=1
                     /product="nonstructural polyprotein"
                     /protein_id="AWR17662.1"
                     /translation="MKMASNDASAAAAAKSNNDNAKSSSDGVLSNMAVTFKRALGARP
                     KQPPPSDKPPKPPRPPTPELVKAIPPPPPNGEDEPIISYNVKGGVSGLPELSTVTQLE
                     ENSTAFSVPPLSQRENRDAKEPLTGTILEMWDGEIYHYGLYVERGLVLGVHKPPAAIS
                     LAKIELTPLSLYWRPVYTPQYLISPDTLRKLHGETFPYTAFDNNCYAFCCWVLDLNDS
                     WLNRRMIQRTTGFFRPYQDWNRKPLPTMDDSKVKKVANVVLCALSSLFTRPIKDIIGK
                     LKPLNILNILATCDWTFAGIVESLILLAELFGVFWTPPDVSAMIAPLLGDYELQGPED
                     LAVELVPVVMGGIGLVLGFTKEKIGKMLSSAASTLRACKDLGAYGLEILKLVMKWFFP
                     KKEEKNELAMVRSIEDAVLDLEAIENNHMTALLKDKDSLATYMRTLDMEEEKARKLST
                     KSASPDIVGTINALLSRIAAARSLVHRAKEELSSRPRPVVLMISGKPGIGKTHLAREL
                     AKKIASTLTGDQRVGLIPRNGVDHWDAYKGERVVLWDDYGMSSPVHDALRLQELADTC
                     PLTLNCDRIENKGKVFDSDVIIITTNLANPAPLDYVNFEACSRRIDFLVYADAPEVEK
                     AKRDFPGQPDMWKDTFKPDFSHIKLALAPQGGFDKNGNTPHGKGVMKTLTASSLVARA
                     SGLLHERLDEYELQGPTPTTFNFDRNKVLAFRQLAAENKYGLVDTMRVGSQLKNVKTM
                     TELKQALKNISVKKCQLVYGGGTYTLESDGKGNVHVEKVNNTSVQTNNELSGVLHHLR
                     CARIRYYVKCVQEALYSILQIAGAAFITTRIAKRTNIQNLWSKPQAEDLEETNNEEGC
                     PKPKNDEEFVVSSDDIKSEGKKGKNKTGRGKKHTAFSSKGLSDEEYDEYKRIREERNG
                     KYSIEEYLQDRDKYYEEVAIARATEEDFCEEEEAKIRQRIFRPTRKQRKEERASLGLV
                     TGSEIRKRNPDDFKPKGKLWADDDRSVDYNEKLSFEAPPSIWSRIVNFGSGWGFWVSP
                     SLFITSTHVIPQGAQEFFGVPIKQIQIHKSGEFCRLRFPKPIRTDVTGMILEEGAPEG
                     TVATLLIKRPTGELMPLAARMGTHATMKIQGRTVGGQMGMLLTGSNAKSMDLGTTPGD
                     CGCPYIYKRGNDYVVIGVHTAAARGGNTVICATQGNEGEAMLEGGDNKGTYCGAPILG
                     PGNAPKLSTKTKFWRSSTTPLPPGTYEPAYLGGKDPRVKGGPSLQQVMRDQLKPFTEP
                     RGKPPKPSVLEAAKKTIINVLEQTIDPPQKWTYAQACASLDKTTSSGHPHHMRKNDCW
                     NGESFTGKLADQASKANLMFEEGKNMTPVYTGALKDELVKTDKIYGVVKKRLLWGSDL
                     STMIRCARAFGGLMDELKAHCVTLPVRVGMNMNEDGPIIFEKHSRYKYHYDADYSRWD
                     STQQRAVLAAALEIMVKFSPEPHLAQVVAEDLLSPSVMDVGDFRISINEGLPSGVPCT
                     SQWNSIAHWLLTLCALSEVTDLSPDIIQANSLFSFYGDDEIVSTDIKLDPEKLTAKLR
                     EYGLKPTRPDKTEGPLIISEDLNGLTFLRRTVTRDPAGWFGKLDQSSILRQMYWTKGP
                     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="AWR17663.1"
                     /translation="MKMASNDAAPSNDGAAGLVPEINNEAMALEPVAGAAIAAPLTGQ
                     QNIIDPWIMNNFVQAPGGEFTVSPRNSPGEVLLNLELGPEINPYLAHLARMYNGYAGG
                     FEVQVVLAGNAFTAGKIIFAAIPPNFPVDNLSAAQITMCPHVIVDVRQLEPVNLPMPD
                     VRNNFFHYNQGSDSRLRLIAMLYTPLRANNSGDDVFTVSCRVLTRPSPDFSFNFLVPP
                     TVESKTKPFSLPILTISEMSNSRFPVPIDSLHTSPTENVVVQCQNGRVTLDGELMGTT
                     QLLPSQICAFRGVLTRSTSRASDQADTATPRLFNYYWHIQLDNLNGTPYDPAEDIPGP
                     LGTPDFRGKVFGVASQRNPDATTRAHEAKIDTTSGRFTPKLGSLEISTESSDFDQSQP
                     TRFTPVGIGVDHEADFQQWALPDYAGQFTHNMNLAPAVAPNFPGEQLLFFRSHLPSSG
                     GRSNGILDCLVPQEWVQHFYQESAPSQSQVALVRYVNPDTGRVLFEAKLHKLGFMTIA
                     KNGDSPITVPPNGYFRFESWVNPFYTLAPMGTGNGRRRIQ"
     gene            6731..7495
                     /gene="ORF3"
     CDS             6731..7495
                     /gene="ORF3"
                     /codon_start=1
                     /product="VP2"
                     /protein_id="AWR17664.1"
                     /translation="MAGAFIAGLAGDMLTNTVGSLVNAGANAINQTIDFENNKYLQNA
                     SFNHDKEMLNAQIEATKKLQADMIAIKQGVLTAGGFSPTDAARGAINAPMTKVLDWSG
                     TRNWAPGATSTTSMSGGFTHQTVHRSTPNFKTNQAPKSTPSSGSSVRSNSTQITSLSS
                     HSSGSSRSSGSTVISSIPSSNRTRDWVNQQNFNLEPHMPGSLRTAFVTPPSSTASSSG
                     TVSTVPKNVLDSWTSAFNTRRQPLFAHLRRRGESNV"
ORIGIN      
        1 gtgaatgaag atggcgtcta acgacgcttc cgctgccgct gctgccaaaa gcaacaacga
       61 caacgcaaaa tcttcaagtg acggagtatt atctaatatg gctgtcactt ttaaacgagc
      121 cctcggggcg cggcctaaac agccgccccc gagtgacaaa ccaccaaaac ccccaagacc
      181 acccacacca gagttggtta aggcaattcc ccctccccca cccaacgggg aggacgaacc
      241 aatcatctct tacaacgtca aagggggtgt ttctggtttg cctgagctct caactgtcac
      301 ccaactggaa gagaactcta cagcattcag cgtcccccct cttagtcaga gggagaacag
      361 agatgcaaag gaaccattga ctggaaccat cctggagatg tgggacgggg agatctacca
      421 ttatggctta tacgtagaac gagggttagt gctcggtgta cacaaaccac cagcagccat
      481 cagccttgct aagattgagc tgaccccttt gtctttgtat tggagaccag tgtacacccc
      541 acagtacctc atctcccctg acactctcag aaagttgcat ggggagacgt tcccttatac
      601 agcctttgac aacaactgtt atgccttctg ctgttgggtg cttgacttga acgattcatg
      661 gctgaacaga aggatgatac agaggacaac aggcttcttc cgaccctacc aggattggaa
      721 caggaaaccc ctccccacga tggatgactc taaagtgaaa aaggtggcca atgttgttct
      781 atgtgctctc tcatcattgt tcacaagacc aattaaggac attattggga agttaaaacc
      841 cctaaacatt ctcaacatct 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 tcgaggacgc agtgctagat cttgaagcca ttgagaacaa
     1261 ccatatgaca gctctactca aggataaaga cagccttgca acctacatga ggactcttga
     1321 catggaagag gagaaggcga gaaaactttc caccaagtct gcctctccgg atattgtggg
     1381 cacgataaat gccctactgt caaggattgc agctgcccgg tctctagtgc acagggctaa
     1441 ggaggagctg tcaagcaggc cccgaccggt cgtcttaatg atttcaggga aaccgggtat
     1501 aggaaaaacc catctagcta gagagttggc aaagaagatc gcctccacac tcacaggtga
     1561 ccagagggtg ggtcttatcc cacgtaacgg ggtcgaccac tgggatgcat acaaaggtga
     1621 aagagtcgtt ctctgggacg actacgggat gagcagccct gtccacgacg ccctcagact
     1681 ccaggagctc gctgatacct gtcctctcac actcaactgt gacaggattg agaacaaagg
     1741 taaagtcttt gacagtgacg tcataataat aaccaccaat ttagccaacc cagcaccact
     1801 ggattatgtc aactttgaag cttgctcgag acgcatagac ttcctcgtct atgctgatgc
     1861 tcctgaagtt gagaaggcta agcgggactt cccaggccaa ccagacatgt ggaaagacac
     1921 cttcaaaccc gacttctcac atataaaatt ggcattggcc ccgcaaggag gttttgacaa
     1981 gaatggtaac actcctcacg ggaagggagt catgaagacc ctcactgcca gttccctcgt
     2041 tgcccgagca tcagggctcc tccacgagag attagacgag tatgagctgc agggcccaac
     2101 tcccacaaca ttcaacttcg accgcaacaa ggtgcttgct tttaggcagc ttgctgctga
     2161 aaacaagtac ggtcttgttg acacaatgag ggtcgggtca caactcaaga atgtcaaaac
     2221 tatgacagaa ctcaagcagg ccctcaagaa catctcagtc aagaaatgtc agcttgtgta
     2281 cggtgggggc acatacacac ttgaatctga tggtaaaggc aatgtacacg tcgaaaaggt
     2341 gaacaacacc agtgtacaaa ctaacaacga gctctccggg gttttgcacc atctcaggtg
     2401 tgctagaatc aggtactatg ttaagtgtgt tcaggaagct ctctactcca tcttacaaat
     2461 tgccggggct gcattcataa ccacgcgcat tgcaaagcgc acaaacatac aaaacctctg
     2521 gtctaaacca caagcagaag atctagagga gactaacaac gaggagggtt gtccaaaacc
     2581 taaaaatgat gaagaatttg tcgtctcctc tgatgacatc aaatctgagg gtaagaaagg
     2641 aaagaacaag actggccgtg gtaagaagca cacagccttt tccagcaaag gactcagtga
     2701 tgaggagtac gatgagtata agagaatcag ggaagagaga aatggtaagt actccataga
     2761 ggaataccta caggacagag acaaatacta tgaggaggtg gccatagcca gggcaactga
     2821 ggaagatttc tgtgaagaag aggaggccaa gatccgacag aggatattca gaccaacaag
     2881 gaaacaacgc aaagaggaaa gagcttctct tggtttggtt acaggctctg agatcaggaa
     2941 gagaaaccca gatgacttca agcccaaagg gaaactatgg gctgatgatg acaggagtgt
     3001 tgactacaat gagaaactta gtttcgaggc tccaccaagc atttggtcac gaatagtcaa
     3061 ctttggctca gggtggggct tttgggtctc gcccagcctc ttcataacat caacccatgt
     3121 cattccccaa ggcgcgcagg agttctttgg agtgcccatc aaacaaatac aaatccacaa
     3181 gtcaggtgag ttctgccggc ttaggttccc gaaaccaatc aggacagatg ttacaggcat
     3241 gatcttggag gaaggtgctc cagaaggcac tgttgccaca cttctcatca agagaccaac
     3301 tggggaactc atgcccttgg cagccaggat gggcacccac gctaccatga aaattcaggg
     3361 tcgcactgtt ggtggacaga tgggcatgct actcacaggg tctaacgcta agagcatgga
     3421 tttgggcaca actcctggcg attgtggttg tccctatatc tacaagagag ggaacgacta
     3481 cgtggtcatt ggagttcaca ctgccgccgc tcgtggagga aacaccgtca tctgtgcaac
     3541 ccaaggaaac gagggtgagg ccatgctaga aggtggtgac aacaagggaa cttattgtgg
     3601 ggcaccaata ttaggccctg gaaatgcccc caaactcagc accaaaacca aattttggag
     3661 gtcttccacc acccccctgc cacccggaac ctatgagcca gcttatctgg gtggcaagga
     3721 ccctagagtg aaaggtggtc cctcactgca acaggttatg agagaccaac taaaaccatt
     3781 cactgagccc agaggcaaac cacccaaacc aagtgtgcta gaagctgcca agaagactat
     3841 aatcaatgtg cttgaacaaa caatagaccc acctcaaaaa tggacatacg cacaagcgtg
     3901 tgcatcacta gacaaaacca cttccagcgg tcaccctcac cacatgcgga agaacgattg
     3961 ctggaatggg gaatctttca caggaaaact ggcagaccaa gcatcaaagg ccaacctaat
     4021 gtttgaggaa ggaaagaaca tgactccagt atacacagga gctctgaaag atgagctagt
     4081 caagactgac aagatctatg gggtagtcaa gaagaggctc ctgtggggtt cagacctatc
     4141 aaccatgata cggtgtgcac gagccttcgg tgggctaatg gacgagctca aggcccattg
     4201 cgtcacacta ccagtcaggg ttggtatgaa catgaatgag gatggaccca taatatttga
     4261 gaaacactcc agatacaaat accattatga tgcagattac tcccgctggg actcaacaca
     4321 acaaagagca gtgctagccg cagccctgga aataatggtt aaattctcac cagaacccca
     4381 cctggcccag gtggttgcag aagacctttt gtcccccagt gtgatggacg tgggtgattt
     4441 caggatatca atcaacgagg gattgccctc tggtgttccc tgtacttcac aatggaactc
     4501 cattgctcac tggctcctca cactatgtgc actgtctgaa gtcacagacc tgtcccctga
     4561 catcatccag gcgaattccc tgttttcctt ttatggtgat gatgaaatag tgagcacaga
     4621 catcaaatta gacccagaga aactgacagc aaagctgagg gaatacgggc ttaaaccaac
     4681 tcgccctgac aaaacagagg gacccttaat tatctctgaa gatttgaatg gcctgacctt
     4741 cttgcggaga acagtgaccc gcgatccggc cggatggttt ggcaaactgg accaaagttc
     4801 aatactcagg cagatgtact ggaccaaggg gccaaaccat gaagacccct ttgaaacaat
     4861 gataccacac tcccaaagac ccatacaact gatgtcatta cttggtgaag ctgcattgca
     4921 tggtccatca ttctacagta aaatcagcaa attggtcatc tcagaattga aagagggtgg
     4981 aatggatttt tacgtgccca gacaagaacc aatgttcagg tggatgagat tctcagattt
     5041 gagcacgtgg gagggcgatc gcaatctggc tcccagtttt gtgaatgaag atggcgtcga
     5101 atgacgccgc tccatctaat gatggtgccg ccggcctcgt cccagagatc aacaatgagg
     5161 caatggcgct agagccagtg gcgggtgcag cgatagcagc acccctcact ggtcagcaaa
     5221 atataattga tccctggatt atgaataatt ttgtgcaagc tcctggtggt gagtttacag
     5281 tgtcccccag aaattcccct ggtgaagtcc ttcttaattt ggaattgggc ccagaaataa
     5341 atccctactt ggcccatctt gctagaatgt ataatggtta tgcaggtgga tttgaagtgc
     5401 aggtggtcct agctggaaat gcgtttacag caggaaagat aatctttgca gctattcccc
     5461 ccaactttcc agttgacaat ttgagtgcag cacagatcac aatgtgccca catgtgattg
     5521 tggatgtcag acagttggaa ccagtcaacc tcccgatgcc tgacgttcgc aataacttct
     5581 ttcattataa tcaagggtct gattcgaggt tacgcctaat tgcaatgcta tatacacctc
     5641 ttagagcaaa caattctggg gatgatgttt ttactgtatc ttgtagagtg ctaactagac
     5701 ctagtcctga tttctcattc aatttccttg tgccacctac tgtggagtca aagacaaaac
     5761 ccttctccct ccctatcctg actatctctg aaatgtctaa ttctaggttc ccagtaccaa
     5821 ttgattctct gcacaccagt cctactgaga atgttgttgt tcagtgccaa aatgggcgcg
     5881 tcacccttga tggtgagttg atgggcacca cccaactctt gcctagccaa atctgtgctt
     5941 tcaggggcgt tctcaccaga tcaacaagca gggccagtga ccaggccgat acagcaactc
     6001 ctagattgtt taattattat tggcatatac aattggataa tctaaatgga accccttatg
     6061 atcctgcaga agacatacca ggccccctag ggacaccaga tttccgtggc aaagtctttg
     6121 gcgtggccag ccagagaaat cctgatgcca cgactagggc acatgaagca aagatagaca
     6181 ccacatctgg ccgcttcacc cctaagttag gctcattaga gatatccact gaatctagtg
     6241 attttgacca aagccaacca acaagattca ccccagttgg cattggagtt gaccatgagg
     6301 cagactttca acaatgggcc ctacccgatt acgctggtca gttcacacac aacatgaact
     6361 tagccccagc tgttgctccc aactttcctg gtgagcagct ccttttcttc cgctcacatt
     6421 tgccatcttc tggtgggcga tccaacggga ttctagattg cctggtcccc caagaatggg
     6481 tacagcactt ctaccaagag tcagccccct ctcagtctca agtggccctg gttaggtatg
     6541 ttaatcctga cactggtaga gtgttatttg aggccaagct acacaaatta ggtttcatga
     6601 ctatagctaa gaatggtgat tctccaataa ctgttcctcc aaatggatac tttaggtttg
     6661 aatcttgggt gaaccccttt tacacacttg cccccatggg aactgggaat gggcgtagaa
     6721 ggattcaata atggctggag cttttatagc aggattggct ggtgacatgc tcacaaatac
     6781 tgtaggatct ttagttaatg caggggctaa tgctattaat caaacaattg attttgaaaa
     6841 taataaatat ttgcaaaatg cttcttttaa tcatgataag gagatgttga atgcacaaat
     6901 tgaggcaaca aagaagttac aggctgacat gattgctatc aagcaagggg tcttgaccgc
     6961 tggcggcttc tcccctactg atgcagcccg tggggcaatt aatgccccca tgacaaaagt
     7021 cctagattgg agtggaacga gaaactgggc accaggtgcc acctccacaa cctcgatgtc
     7081 gggtggcttt acacatcaaa ctgtacacag atccacacca aattttaaaa cgaaccaggc
     7141 tcccaaatcc acacccagca gtgggtcttc agtgaggtca aactcaaccc aaatcactag
     7201 cctgagctca cactcgtccg ggtcgtctcg atccagcggg tctacagtta tcagctcaat
     7261 accatcctct aacaggacta gggactgggt caaccaacaa aattttaatt tggaaccaca
     7321 catgcctgga tctcttagga cagcttttgt cactccacca tctagtacag cctctagctc
     7381 aggcacagtc tcaactgtgc ccaaaaatgt tttggactcc tggacatctg cgtttaacac
     7441 gcgcagacag ccgctattcg cacaccttcg cagaaggggg gagtcaaatg tttagtgaaa
     7501 agattatttt aaatttggtt taaaattaga tttaatttgg aatctttt
//