Typing tool

Complete norovirus genomes

MH218590  GII.3
 GII.P21

Length: 7,548 | 3 CDS

ORF1: 5..5104
ORF2: 5085..6731
ORF3: 6731..7495
LOCUS       MH218590                7548 bp    RNA     linear   VRL 11-JUN-2018
DEFINITION  Norovirus GII isolate NORO_120_28_11_2014, complete genome.
ACCESSION   MH218590
VERSION     MH218590.1
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_120_28_11_2014"
                     /host="Homo sapiens"
                     /db_xref="taxon:122929"
                     /country="United Kingdom"
                     /collection_date="28-Nov-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="AWR17428.1"
                     /translation="MKMASNDASAAAAAKSNNDNAKSSSDGVLSNMAVTFKRALGARP
                     KQPPPSDKPPKPPRPPTPELVKAIPPPPPNGEDEPIISYNVKGGVSGLPELSTVTQLE
                     ENSTAFSVPPLSQRENKDAKEPLTGTILEMWDGEIYHYGLYVERGLVLGVHKPPAAIS
                     LAKVELTPLSLYWRPVYTPQYLISPDTLRKLHGETFPYTAFDNNCYAFCCWVLDLNDS
                     WLNRRMIQRTTGFFRPYQDWNRKPLPTMDDSKVKKVANVVLCALSSLFTRPIKDIIGK
                     LKPLNILNILATCDWTFAGIVESLILLAELFGVFWTPPDVSAMIAPLLGNYELQGPED
                     LAVELVPVVMGGIGLVLGFTKEKIGKMLSSAASTLRACKDLGAYGLEILKLVMKWFFP
                     KKEEKNELAMVRSIEDAVLDLEAIENNHMTALLKDKDSLATYMRTLDMEEEKARKLST
                     KSASPDIVGTINALLSRIAAARSLVHRAKEELSSRPRPVVVMISGKPGIGKTHLAREL
                     AKKIASTLTGDQRVGLIPRNGVDHWDAYKGERVVLWDDYGMSSPVHDALRLQELADTC
                     PLTLNCDRIENKGKVFDSDVIIITTNLANPAPLDYVNFEACSRRIDFLVYADAPEVEK
                     AKRDFPGQPDMWKDTFKPDFSHIKLALAPQGGFDKNGNTPHGKGVMKTLTASSLVARA
                     SGLLHERLDEYELQGPTPTTFNFDRNKVLAFRQLAAENKYGLVDTMRVGSQLKNVKTM
                     TELKQALRNISVKKCQLVYGGGTYTLESDGKGNVHVEKVNNTSVQTNNELSGVLHHLR
                     CARIRYYVKCVQEALYSILQIAGAAFITTRIAKRTNIQSLWSKPQVEDLEETNNEEGC
                     PKPKNDEEFVVSSDDIKTEGKKGKNKTGRGKKHTAFSSKGLSDEEYDEYKRIREERNG
                     KYSIEEYLQDRDKYYEEVAIARATEEDFCEEEEAKIRQRIFRPTRKQRKEERASLGLV
                     TGSEIRKRNPDDFKPKGKLWADDDRSVDYNEKLSFEAPPSIWSRIVNFGSGWGFWVSP
                     SLFITSTHVIPQGAQEFFGVPIKQIQIHKSGEFCRLRFPKPIRTDVTGMILEEGAPEG
                     TVATLLIKRPTGELMPLAARMGTHATMKIQGRTVGGQMGMLLTGSNAKSMDLGTTPGD
                     CGCPYIYKRGNDYVVIGVHTAAARGGNTVICATQGNEGEAMLEGGDNKGTYCGAPILG
                     PGNAPKLSTKTKFWRSSTTPLPPGTYEPAYLGGKDPRVKGGPSLQQVMRDQLKPFTEP
                     RGKPPKPSVLEAAKKTIINVLEQTIDPPQKWTYAQACASLDKTTSSGHPHHMRKNDCW
                     NGDSFTGKLADQASRANLMFEEGKNMTPVYTGALKDELVKTDKIYGVVKKRLLWGSDL
                     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="AWR17429.1"
                     /translation="MKMASNDAAPSNDGAAGLVPEINNEAMALEPVAGAAIAAPLTGQ
                     QNIIDPWIMNNFVQAPGGEFTVSPRNSPGEVLLNLELGPEINPYLAHLARMYNGYAGG
                     FEVQVVLAGNAFTAGKIIFAAIPPNFPIDNLSAAQITMCPHVIVDVRQLEPVNLPMPD
                     VRNNFFHYNQGSDSRLRLIAMLYTPLRANNSGDDVFTVSCRVLTRPSPDFSFNFLVPP
                     TVESKTKPFSLPILTISEMSNSRFPVPIDSLHTSPTENIVVQCQNGRVTLDGELMGTT
                     QILPSQICAFRGVLTRSTSRASDQADTATPRLFNYYWHIQLDNLNGTPYDPAEDIPGP
                     LGTPDFRGKVFGVASQRNPDATTRAHEAKIDTTSGRFTPKLGSLEMSTESSDFDQNQP
                     TRFTPVGIGVDHEADFQQWTLPDYAGQFTHNMNLAPAVAPNFPGEQLLFFRSHLPSSG
                     GRSNGILDCLVPQEWVQHFYQESAPSQSQVALVRYVNPDTGRVLFEAKLHKLGFMTIA
                     KNGDSPITVPPNGYFRFESWVNPFYTLAPMGTGNGRRRIQ"
     gene            6731..7495
                     /gene="ORF3"
     CDS             6731..7495
                     /gene="ORF3"
                     /codon_start=1
                     /product="VP2"
                     /protein_id="AWR17430.1"
                     /translation="MAGAFIAGLAGDMLTNTVGSLVNAGANVINQTIDFENNKYLQNA
                     SFNHDKEMLNAQIEATKKLQADMIAIKQGVLTAGGFSPTDAARGAINAPMTKVLDWNG
                     TRYWAPGATSTTSMSGGFTHQTVHRSTPNFKTNQAPKPTPSSGSSVRSNSTQITSLSS
                     HSSGSSRSSGSTVVSSIPSSNRTRDWVNQQNFNLEPHMPGSLRTAFVTPPSSTASSSG
                     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 aatcatttct tacaacgtca aagggggtgt ttctggtttg cctgagctct caactgtcac
      301 ccaactggaa gagaactcta cagcattcag cgttccccct cttagtcaga gggagaacaa
      361 agatgcaaag gaacctttga ctggaaccat cctggagatg tgggacgggg agatctacca
      421 ttatggctta tacgtagaac gggggttagt gctcggcgta cacaaaccac cagcagccat
      481 cagccttgct aaggttgagc tgaccccctt gtctttgtat tggagaccag tgtacacccc
      541 acagtacctc atttcccctg acactctcag aaagttgcat ggggagacgt tcccttatac
      601 agcctttgac aacaactgtt atgccttctg ctgttgggtg cttgacttga acgattcatg
      661 gctgaacaga aggatgatac agaggacaac aggcttcttc cgaccctacc aggattggaa
      721 caggaaaccc ctccccacga tggatgactc caaagtgaaa aaggtggcca atgttgtcct
      781 atgtgctctc tcatcattgt tcacaagacc aattaaggac attattggaa aattaaaacc
      841 cctaaacatt ctcaacatct tagccacatg tgactggact tttgcaggca tagtagaatc
      901 cctgatcctt ttggctgaac tttttggagt tttctggaca cccccagacg tgtctgcgat
      961 gatcgctccc ttactgggta attatgaact acagggaccc gaggacctcg ctgtggaact
     1021 cgtacccgta gtaatgggag ggataggttt ggtgctggga ttcaccaaag agaaaatcgg
     1081 caagatgctt tcttctgctg cttcaaccct gagagcatgt aaagatctcg gtgcatatgg
     1141 gttggagatc ctcaaattgg ttatgaaatg gtttttccca aagaaagaag agaaaaacga
     1201 attggcaatg gtgagatcca tcgaggatgc agtgctagac cttgaagcca ttgagaacaa
     1261 ccacatgaca gctctactca aggataaaga tagccttgca acctacatga ggactcttga
     1321 catggaggag gagaaggcga gaaaactttc caccaagtct gcctctccgg atattgtggg
     1381 cacgataaat gccctgctgt caaggattgc agctgcccgg tctctagtgc acagggctaa
     1441 ggaggagctg tcaagtagac cccgaccggt cgttgtaatg atttcaggga aaccgggtat
     1501 agggaaaacc catctagcta gagaactggc aaagaagatc gcctccacac tcacaggtga
     1561 ccagagggtg ggcctaatcc cacgcaacgg ggtcgaccac tgggatgcat acaaaggtga
     1621 aagagtcgtt ctctgggacg actacgggat gagcagcccc gtccacgacg ccctcagact
     1681 ccaggagctc gctgacacct gtcctctcac actcaactgt gacaggattg agaacaaagg
     1741 taaagttttt gacagtgacg tcataataat aaccaccaat ttagccaacc cagcaccact
     1801 ggattatgtc aacttcgaag cttgctcgag acgcatagac ttcctcgtct atgctgatgc
     1861 tcctgaagtt gagaaggcta agcgggactt cccaggccaa ccagacatgt ggaaagacac
     1921 cttcaaaccc gacttctcac atataaaatt ggcattagcc ccgcaaggag gttttgacaa
     1981 gaatggcaac actcctcatg ggaagggagt catgaagacc ctcactgcca gttccctcgt
     2041 tgcccgagca tcagggctcc tccacgagag gttagacgag tatgagctgc agggcccaac
     2101 tcccacaaca ttcaacttcg accgcaacaa ggtgcttgct tttaggcagc ttgctgctga
     2161 aaacaagtac ggtcttgttg acacaatgag ggtcgggtca caactcaaga atgttaaaac
     2221 tatgactgaa ctcaagcagg ccctcaggaa catctcagta aaaaaatgtc agcttgtgta
     2281 cggtgggggc acatacacac ttgaatctga tggcaaaggc aatgtgcatg tcgaaaaggt
     2341 gaacaacacc agtgtgcaaa ctaacaacga gctctccggg gttttgcacc atctcaggtg
     2401 tgctagaatc aggtactatg ttaagtgtgt tcaggaagct ctctactcca tcttacaaat
     2461 tgccggggct gcattcatca ccacgcgcat tgcaaagcgc acaaacatac aaagcctctg
     2521 gtccaaacca caagtagaag atctagagga aactaacaac gaggagggtt gtccaaaacc
     2581 taaaaatgat gaagaatttg tcgtctcctc tgatgacatc aaaactgagg gtaagaaagg
     2641 aaagaacaag actggccgtg gtaagaagca cacagccttt tccagcaaag gactcagtga
     2701 tgaggagtac gatgagtata agagaatcag ggaagaaaga aatggtaagt actccataga
     2761 ggaataccta caggacagag acaaatacta tgaagaggtg gccatagcca gggcgactga
     2821 ggaagatttc tgtgaagaag aggaggccaa aatccggcag aggatattca gaccaacaag
     2881 gaaacaacgc aaagaggaaa gagcttctct tggtttggtt acaggctctg agatcaggaa
     2941 gagaaaccca gatgacttca agcccaaagg gaaactatgg gctgatgatg acaggagtgt
     3001 tgactacaat gagaaactta gcttcgaggc tccaccaagc atttggtcac gaatagtcaa
     3061 ctttggctca gggtggggct tttgggtctc gcccagcctc ttcataacat caacccatgt
     3121 cattccccaa ggcgcgcagg agttctttgg agtgcccatc aaacaaatac aaattcacaa
     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 gagggtgaag ccatgctaga aggtggtgac aataagggaa cttactgtgg
     3601 agcaccaata ttaggccctg gaaatgcccc caaactcagc accaaaacca agttctggag
     3661 gtcttccacc acccccctgc cacccggaac ctatgagcca gcttatctgg gtggtaagga
     3721 ccctagagtg aaaggtggcc cctcactgca acaggttatg agagaccaac taaaaccatt
     3781 cactgagccc agaggcaaac cacccaaacc aagtgtgcta gaagctgcta agaaaactat
     3841 aatcaatgtg cttgagcaaa caatagaccc acctcaaaaa tggacatacg cacaagcgtg
     3901 tgcatcatta gataagacca cttccagcgg tcaccctcac cacatgcgga agaacgattg
     3961 ctggaatggg gactctttca caggaaaact ggcagaccaa gcatcaaggg ccaacctaat
     4021 gtttgaggaa ggaaagaaca tgactccagt atacacaggg gctctgaaag atgagctagt
     4081 caagactgac aagatttatg 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 cagcactgga aataatggtc aaattctcac cagaacccca
     4381 cctggcccag gtggttgcag aagacctttt gtcccccagt gtgatggatg tgggtgattt
     4441 taggatatca atcaacgagg gattaccctc tggtgttcct tgcacttcac aatggaactc
     4501 cattgctcac tggctcctca cactatgtgc actgtctgaa gtcacagacc tgtcccctga
     4561 catcatccag gcgaattccc tgttctcctt ttatggtgat gatgaaatag tgagcacaga
     4621 catcaaatta gacccagaga aattgacagc aaagctgagg gaatacgggc ttaaaccaac
     4681 ccgccctgac aaaacagagg gacccttaat tatctctgaa gatttgaatg gcctgacctt
     4741 cttgcggaga acagtgaccc gcgacccggc cggatggttt ggcaaactag accaaagttc
     4801 aatactcaga cagatgtact ggaccaaggg gccaaaccat gaagacccct ttgaaacaat
     4861 gataccacac tcccaaagac ccatacaatt gatgtcatta cttggtgaag ctgcattgca
     4921 tggtccatca ttctacagta aaatcagcaa attggtcatc tcagaactga 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 ggccagcaga
     5221 atataattga tccctggatt atgaataatt ttgtgcaagc acctggtggt gagttcacag
     5281 tgtcccccag aaattcccct ggtgaagtcc ttcttaattt ggaactgggc ccagaaataa
     5341 atccctattt ggcccatctc gctagaatgt ataatggtta tgcaggtgga tttgaggtgc
     5401 aggtggtcct agctggaaat gcgtttacag caggaaagat aatctttgca gctattcccc
     5461 ccaattttcc aattgacaat ctaagtgcag cacagatcac aatgtgccca catgtgattg
     5521 tggatgtcag acagttggaa ccagtcaacc tcccgatgcc tgacgttcgc aataacttct
     5581 ttcattataa tcaagggtct gattcaagat tacgcttaat tgcaatgcta tacacacctc
     5641 ttagggcaaa caattctggg gatgacgttt ttactgtgtc ttgtagagtg ctaactagac
     5701 ctagtcctga tttctcattc aatttccttg tgccacctac tgtggagtca aagacaaaac
     5761 ccttttccct ccctatcctg actatctctg aaatgtccaa ttctaggttc ccagtaccaa
     5821 ttgattctct gcacaccagt cctactgaga atattgttgt tcagtgccaa aatgggcgcg
     5881 tcacccttga tggtgagttg atgggcacca cccaaatctt gcctagccaa atctgtgctt
     5941 tcaggggcgt tctcaccaga tcaacaagca gggccagtga ccaggccgat acagcaaccc
     6001 ctagattgtt taattattat tggcatatac aattggataa tctaaatgga accccttatg
     6061 atcctgcaga agatatacca ggccccctag ggacaccaga tttccgtggc aaagtctttg
     6121 gcgtggccag ccaaagaaat cctgatgcca cgactagggc acatgaagca aagatagaca
     6181 ccacatctgg ccgcttcacc ccaaagctag gctcattaga gatgtctact gaatctagtg
     6241 actttgacca aaaccaacca acgagattca ccccagttgg cattggagtt gaccatgagg
     6301 cagactttca acaatggacc ctacccgact acgctggtca gttcacacac aacatgaact
     6361 tagccccagc tgttgctccc aacttccctg gtgagcagct ccttttcttc cgctcacatt
     6421 tgccatcttc tggtgggcga tccaacggga ttctagactg cctggtcccc caagaatggg
     6481 tacagcactt ctaccaagag tcagccccct ctcagtctca agtggctctg gttagatacg
     6541 ttaaccctga cactggtaga gtgttgtttg aggccaagtt acacaaatta ggtttcatga
     6601 ctatagccaa aaatggtgat tctccaataa ctgttcctcc aaatgggtat tttaggtttg
     6661 agtcttgggt gaaccccttt tacacacttg cccccatggg aactgggaat gggcgtagaa
     6721 ggattcaata atggctggag cttttatagc aggattggct ggtgacatgc tcacaaatac
     6781 tgtaggatct ttagttaatg caggagctaa tgttattaat cagacaattg attttgaaaa
     6841 taataaatat ttgcaaaatg cttcttttaa tcatgataag gagatgttaa atgcacaaat
     6901 tgaggcaaca aagaagttac aggctgacat gattgctatc aagcaagggg tcttgaccgc
     6961 tggcggcttc tcccctactg atgcagcccg tggggcaatt aacgccccca tgacaaaagt
     7021 cctagattgg aatggaacga gatactgggc accaggtgcc acctccacaa cctcgatgtc
     7081 gggtggcttt acacatcaaa ctgtgcacag atccacacca aattttaaaa cgaaccaggc
     7141 tcccaaaccc acacccagca gtgggtcttc ggtgaggtca aactcaaccc aaatcactag
     7201 cctgagctca cactcgtccg ggtcgtctcg atccagcggg tctacagttg tcagctcaat
     7261 accatcctct aacaggacta gggactgggt caaccaacaa aattttaatt tggaaccaca
     7321 catgcctgga tctcttagga cagcttttgt cactccacca tctagcacag cctctagctc
     7381 aggcacagtc tcaactgtgc ccaaaaatgt tttggactcc tggacatctg cgtttaacac
     7441 gcgcagacag ccgctattcg cacaccttcg cagaaggggg gagtcaaatg tttagtgaaa
     7501 agattatttt aaatttgatt taaaattagg tttaatttgg aatctttt
//