Typing tool

Complete norovirus genomes

MH218584  GII.3
 GII.P21

Length: 7,548 | 3 CDS

ORF1: 5..5104
ORF2: 5085..6731
ORF3: 6731..7495
LOCUS       MH218584                7548 bp    RNA     linear   VRL 11-JUN-2018
DEFINITION  Norovirus GII isolate NORO_114_14_09_2014, complete genome.
ACCESSION   MH218584
VERSION     MH218584.1
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_114_14_09_2014"
                     /host="Homo sapiens"
                     /db_xref="taxon:122929"
                     /country="United Kingdom"
                     /collection_date="14-Sep-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="AWR17410.1"
                     /translation="MKMASNDASAAAAANSNNDNAKSSSDGVFSNMAVSFKRALGARS
                     KQPPPKDKPSRPPRPPTPELVKSIPPPPPNGEDEPIISYNAEKGVSGLPELTTVTQLE
                     ENSTAFSVPPLSQRENRDAKEPLTGTILEMWDGEIYHYGLYVERGLVLGVHKPPAAIS
                     LAKVELTPLSLYWRPVYTPQYLISPDTLRKLHGETFPYTAFDNNCYAFCCWVLDLNDS
                     WLSRRMIQRTTGFFRPYQDWNRKPLPTVDDSKVKKVANIVLCALSALFTRPIKDIIGK
                     LKPLNVLNILATCDWTFAGIVESLILLAELFGVFWTPPDVSAMIAPLLGDYELQGPED
                     LAVELVPVVMGGIGLVLGFTKEKIGKMLSSAASTLRACKDLGAYGLEILKLVMKWFFP
                     KKEEKNELAMVRSIEDAVLDLEAIENNHMTTLLKDKDSLATYMRTLDMEEEKARKLST
                     KSASPDIVGTINALLSRIAAARSLVHRAKEELSSRPRPVVVMISGRPGIGKTHLAREL
                     AKKIASSLTGDQRVGLIPRNGVDHWDAYKGERVVLWDDYGMSNPIHDALRLQELADTC
                     PLTLNCDRIENKGKVFDSDAIIITTNLANPAPLDYVNFEACSRRIDFLVYADAPEVEK
                     AKRDFPGQPDMWKDTFKPDFSHIKLTLAPQGGFDKNGNTPHGKGVMKTLTASSLVARA
                     SGLLHERLDEYELQGPTPTTFNFDRNKVLAFRQLAAENKYGLVDTMRVGSQLKNVKTM
                     TELKQALKNISVKKCQLVYGGGTYTLESDGKGNVYVEKVNNTNVQTNNELSGALHHLK
                     CARIRYYVKCVQEALYSILQIAGAAFITTRIARRTNIQNLWSKPQAENLEETNNEEGC
                     PKPKNDEEFVISSNDITTEGKKGKNKTGRGKKHTAFSSKGLSDEEYDEYKRIREERNG
                     KYSIEEYLQDRDKYYEEVAIARATEEDFCEEEEAKIRQRIFRPTRKQRKEERASLGLV
                     TGSEIRKRNPDDFKPKGKLWADDDRSVDYNEKLSFEAPPSIWSRIVNFGSGWGFWVSP
                     SLFITSTHVIPQGAQEFFGVPIKQIQIHKSGEFCRLRFPKPIRTDVTGMILEEGAPEG
                     TVATLLIKRPTGELMPLAARMGTHATMKIQGRTVGGQMGMLLTGSNAKNMDLGTTPGD
                     CGCPYIYKRGNDYVVIGVHTAAARGGNTVICATQGSEGEAMLEGGDNKGTYCGAPILG
                     PGNAPKLSTKTKFWRSSTTPLPPGTYEPAYLGGKDPRVKGGPSLQQVMRDQLKPFTEP
                     RGKPPKPSVLEAAKRTIINVLEQTIDPPQKWTYAQACASLDKTTSSGHPHHMRKNDCW
                     NGETFTGKLADQASKANLMFEEGKNMTPVYTGALKDELVKTDKIYGKIKKRLLWGSDL
                     STMIRCARAFGGLMDELKAHCVTLPVRVGMNMNEDGPIIFEKHSRYKYHYDADYSRWD
                     STQQRAVLAAALEIMVKFSPEPHLAQVVAEDLLSPSVMDVGDFKISINEGLPSGVPCT
                     SQWNSIAHWLLTLCALSEVTDLSPDIIQANSLFSFYGDDEIVSTDIKLDPEKLTTKLK
                     EYGLKPTRPDKTEGPLIISEDLDGLTFLRRTVTRDPAGWFGKLDQSSILRQMYWTKGP
                     NHGDPSETMIPHSQRPIQLMSLLGEAALHGPSFYSKISKLVISELKEGGMDFYVPRQE
                     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="AWR17411.1"
                     /translation="MKMASNDAAPSNDGAAGLVPEINNEAMALEPVAGAAIAAPLTGQ
                     QNIIDPWIMNNFVQAPGGEFTVSPRNSPGEVLLNLELGPEINPYLAHLARMYNGYAGG
                     FEVQVVLAGNAFTAGKIIFAAIPPNFPIDNLSAAQITMCPHVIVDVRQLEPVNLPMPD
                     VRNNFFHYNQGSDSRLRLIAMLYTPLRANSSGDDVFTVSCRVLTRPSPDFSFNFLVPP
                     TVESKTKPFSLPILTISEMSNSRFPVPIDSLHTSPTENIVVQCQNGRVTLDGELMGST
                     QLLPSQICAFRGVLTRSTSRASDQADTATPRLFNYYWHIQLDNLNGTPYDPAEDIPCP
                     LGTPDFQGKVFGVASQRNPDATTRAHEAKIDTTAGRFTPKLGSLEISTESDDFDQNKP
                     TRFTPVGIGVDREADFQQWALPNYAGQFTHNMNLAPAVAPNFPGEQLLFFRSQLPSSG
                     GRSNGILDCLVPQEWVQHFYQESAPSQSQVALVRYVNPDTGRVLFEAKLHKLGFMTIA
                     KNGDSPITVPPNGYFRFESWVNPFYTLAPMGTGNGRRRIQ"
     gene            6731..7495
                     /gene="ORF3"
     CDS             6731..7495
                     /gene="ORF3"
                     /codon_start=1
                     /product="VP2"
                     /protein_id="AWR17412.1"
                     /translation="MAGAFIAGLAGDMLTNTVGSLVNAGANAINQTIDFENNKYLQNA
                     SFNHDKEMLNAQIEATKRLQADMIAIKQGVLTAGGFSPTDAARGAINAPMTKVLDWNG
                     TRYWAPGATSTTSLSGGFTNQTVHRPTPNFKTGQAPKPAPSSGSSVRSNSTQVTSLSS
                     HSSGSSRSSGSTVVSSIPSSNRTRDWVNQQNFNLEPYMPGSLRTAFVTPPSSTASSSG
                     TVSTVPKNVLDSWTSAFNTRRQPLFAHLRRRGESNA"
ORIGIN      
        1 gtgaatgaag atggcgtcta acgacgcttc cgctgccgct gctgccaaca gcaacaacga
       61 caacgcaaaa tcttcaagtg acggagtatt ttctaatatg gccgtctctt ttaaacgggc
      121 cctcggggcg cggtctaaac agccgccccc gaaggacaaa ccatcaaggc ccccaagacc
      181 acccacacca gaattggtta aatcaatccc ccctccccca cccaacgggg aggacgaacc
      241 aatcatttct tacaacgctg aaaagggtgt ctctggtttg cctgaactca caactgtcac
      301 ccaactggaa gagaactcta cagcattcag cgttccccct cttagtcaga gggagaacag
      361 agatgcaaag gaaccattga ctggaaccat cctggagatg tgggatgggg agatctacca
      421 ttatggctta tacgtggaac gagggttagt gctaggtgta cacaaaccac cagcagccat
      481 cagccttgct aaggttgagc tgaccccttt gtctttgtat tggagaccag tgtacacccc
      541 acaatatctc atttcccctg acactctcag aaagttgcat ggggagacgt tcccttatac
      601 agcctttgac aacaactgtt atgccttctg ctgttgggta cttgacttga acgactcatg
      661 gctgagcaga aggatgatac aaaggacaac aggattcttc cgaccctacc aggactggaa
      721 caggaaaccc ctccccacgg tggatgactc caaagtgaaa aaggtggcca atattgtcct
      781 ctgtgccctc tcagcattgt ttacaagacc aattaaggac attattggga agttgaaacc
      841 cctgaacgtc ctcaacatac tagccacatg tgattggact tttgcaggca tagtagaatc
      901 cctgatcctt ttggctgaac tgtttggagt tttctggaca cccccagatg tgtctgcaat
      961 gatcgctccc ttactgggtg attacgagct gcagggaccc gaggacctcg ctgtggaact
     1021 cgtacccgta gtaatgggag ggataggttt ggtgctggga ttcaccaaag agaaaatcgg
     1081 caaaatgctt tcatcagctg cctcaaccct tagggcatgc aaagatctcg gtgcatatgg
     1141 gttggagatc ctcaagttgg tcatgaaatg gtttttccca aagaaagaag agaaaaacga
     1201 attggcaatg gtgagatcca ttgaggatgc agtgctagat cttgaggcca ttgagaacaa
     1261 ccatatgaca actctactca aggacaaaga cagccttgca acctacatga ggactcttga
     1321 catggaggag gagaaggcga ggaaactttc caccaagtct gcctcgccgg acattgtggg
     1381 cacaataaat gccttactat caaggattgc agctgcccga tctctagtgc acagggccaa
     1441 ggaggagctg tcaagcaggc cccgaccggt cgttgtgatg atttcaggga gaccaggtat
     1501 agggaaaacc catttagcta gagagttggc aaagaagatc gcctcctcac tcacaggtga
     1561 ccagagggtg ggtcttatcc cacgcaacgg agttgaccac tgggatgcat acaaaggtga
     1621 aagagttgtt ctctgggacg actacgggat gagcaaccct atccacgacg ccctcagact
     1681 tcaggagctc gctgatacct gtcctcttac actcaactgt gacaggattg agaacaaagg
     1741 caaagtcttt gacagtgacg ccataataat aaccaccaat ttagccaacc cagcgccact
     1801 ggattatgtc aactttgaag cctgctcaag acgcatagac ttcctcgtct atgctgatgc
     1861 ccctgaggtt gagaaggcta aacgggactt tccaggccaa ccagacatgt ggaaagacac
     1921 cttcaaacct gatttctcac acataaagct gacattagct ccgcaaggag gttttgataa
     1981 gaatggtaac actcctcatg ggaagggtgt catgaagacc ctcactgcca gttccctcgt
     2041 tgcccgagca tcagggctcc tccacgagag attagacgaa tatgagctgc agggcccaac
     2101 ccccacaaca ttcaacttcg accgcaataa ggtgcttgct tttaggcaac ttgctgctga
     2161 aaacaagtac ggtcttgttg acacaatgag agtcggatca cagctcaaga atgtcaagac
     2221 catgacagaa cttaagcagg ctctcaaaaa catctcagtc aagaagtgtc agcttgtgta
     2281 tggtggtggc acgtacacac ttgaatctga tggcaaaggc aatgtgtatg tcgagaaggt
     2341 gaacaacacc aatgtgcaaa ctaacaacga gctctccgga gctttgcacc atctcaagtg
     2401 tgccagaatc aggtactatg ttaagtgtgt ccaggaagct ctctactcca tcttgcaaat
     2461 tgccggggct gcattcatca ctacgcgcat tgcaaggcgc acaaacatac aaaacctctg
     2521 gtctaaacca caagcagaaa atctggagga gactaacaac gaggagggct gtccaaaacc
     2581 taaaaatgat gaagagtttg tcatctcctc taatgacatc acaaccgagg gcaagaaagg
     2641 aaagaacaag actggccgtg gcaagaagca cacagccttt tccagcaaag gactcagtga
     2701 tgaggagtac gatgagtata aaagaatcag agaagagaga aatggcaagt actccataga
     2761 ggaataccta caggacagag acaaatacta tgaggaggtg gccatagcca gggcaactga
     2821 ggaagacttc tgtgaagaag aggaggcaaa aatccggcaa aggatattta gaccaacaag
     2881 gaaacaacgc aaagaggaaa gggcctctct tggtttggtt acaggttctg agatcaggaa
     2941 gagaaaccca gatgacttca agcccaaagg gaaactatgg gccgatgatg acaggagtgt
     3001 tgactacaat gagaaactta gttttgaggc tccaccaagc atttggtcac gaatagtcaa
     3061 ctttggctca gggtggggtt tttgggtctc gcccagcctc ttcataacat caacccatgt
     3121 cattccccaa ggcgcacagg agttctttgg agtgcccatc aaacaaatac aaattcacaa
     3181 gtcaggtgag ttctgccggc tcaggttccc aaaaccaatc aggacagatg ttacaggtat
     3241 gatcttggag gaaggtgctc cagaaggcac cgttgccaca cttctcatca agagaccaac
     3301 tggggaactc atgcccttgg cagccagaat gggcacccac gcgaccatga aaatccaggg
     3361 tcgcactgtt ggtggacaga tgggcatgct actcacaggg tctaacgcta agaacatgga
     3421 cttgggcaca actcctggcg attgtggttg tccctatatc tacaagagag ggaatgacta
     3481 cgtggtcatt ggagtccaca ctgccgccgc tcgtggagga aacactgtca tctgtgcaac
     3541 ccaaggaagc gagggtgagg ccatgttaga aggtggtgac aacaagggaa cttattgtgg
     3601 agcaccaata ttaggtcctg gaaatgcacc caaactcagc accaaaacca aattctggag
     3661 gtcttccacc acccctttgc cacccgggac ctatgagcca gcttatctgg gcggcaagga
     3721 tcctagagta aaaggtggcc cctcactgca acaggttatg agggaccaac taaaaccatt
     3781 cactgagccc agaggtaaac cacccaaacc aagcgtgcta gaagctgcca agaggactat
     3841 aatcaatgtg cttgaacaaa caatagaccc accccaaaaa tggacatacg cacaggcgtg
     3901 tgcatcacta gacaagacca cttctagcgg ccaccctcac cacatgcgga agaacgattg
     3961 ctggaatggg gagaccttca caggaaaact ggcagaccaa gcatcaaagg ctaacctaat
     4021 gtttgaggaa ggaaagaaca tgaccccagt ttacacagga gctctaaaag atgagctagt
     4081 caagactgat aagatctatg gtaaaatcaa gaagagactc ctgtggggtt cagacctatc
     4141 aaccatgata cggtgtgcac gagccttcgg tgggctaatg gacgaactca aggcccattg
     4201 cgtcacgcta ccagtcaggg ttggtatgaa catgaatgag gatggaccca taatatttga
     4261 gaaacattcc agatataaat atcattatga tgcagattac tcccgctggg actcaacaca
     4321 acaaagagcg gtgctggctg cagccctgga aataatggtc aaattctcac cagaacccca
     4381 tctggcccag gtggttgcag aggacctctt gtcccccagt gtgatggatg tgggtgattt
     4441 caagatatca atcaacgagg gattaccctc tggtgttccc tgcacctcac aatggaactc
     4501 cattgcccac tggctcctca cattatgtgc actgtctgaa gtcacagacc tgtcccctga
     4561 catcatccag gcaaattccc tgttctcctt ttatggtgat gatgaaatag tgagcacaga
     4621 catcaaactg gacccagaga aactaacaac aaaattgaag gaatacgggc tgaaaccaac
     4681 ccgccctgac aaaacagaag gacccttaat tatctctgaa gacttggatg gcctgacctt
     4741 cttacgtaga acggtgaccc gtgatccggc cgggtggttt ggcaaactgg accaaagttc
     4801 aatactcagg cagatgtact ggaccaaggg accaaaccat ggggatccct ccgaaacaat
     4861 gataccacac tcccaaagac ccatacaact gatgtcattg ttgggtgaag ctgcgttgca
     4921 tggtccatcg ttctacagca aaatcagcaa attggtcatc tcagaattga aagagggtgg
     4981 aatggatttt tacgtgccca gacaagagcc aatgttcagg tggatgagat tctcagattt
     5041 gagcacgtgg gagggcgatc gcaatctggc tcccagtttt gtgaatgaag atggcgtcga
     5101 atgacgccgc tccatctaat gatggtgccg ccggcctcgt cccagagatc aacaatgagg
     5161 caatggcgct agagccagtg gcgggtgcag cgatagcagc gcccctcact ggtcagcaaa
     5221 atataattga tccctggatt atgaataatt ttgtgcaagc acctggtggt gagtttacag
     5281 tgtcccctag aaattcccct ggtgaagttc ttcttaattt ggaattgggc ccagaaataa
     5341 acccctattt ggcccatctt gccagaatgt ataatggtta tgcaggtgga tttgaagtgc
     5401 aggtggtcct agctggaaat gcgtttacag caggaaagat aatctttgca gctattcccc
     5461 ccaactttcc aattgacaac ctaagtgcgg cacagatcac aatgtgtcca catgtgattg
     5521 tggatgtcag gcagctggaa ccagtcaacc tcccgatgcc tgacgttcgc aacaacttct
     5581 ttcattacaa tcaagggtct gattcgagat tgcgcctaat tgcaatgctg tatacacctc
     5641 ttagggcaaa cagttctgga gatgatgttt ttactgtgtc ttgcagagtg ctaactagac
     5701 ctagccctga tttttcattt aatttccttg tgccacctac tgtggagtca aagacaaaac
     5761 cattttcact ccctattctg actatctctg aaatgtccaa ttctaggttc ccagtaccaa
     5821 ttgattctct gcacactagt cccactgaga atattgttgt ccagtgtcag aatgggcgcg
     5881 ttacccttga tggtgagttg atgggctcca cccaactctt acctagccaa atttgtgctt
     5941 tcaggggcgt gctcaccaga tcaacaagca gggccagtga ccaggccgac acagcaaccc
     6001 ctagattatt taattattat tggcatatac aattggataa tctaaatgga actccttatg
     6061 accctgcaga agatatacca tgccccttag ggacaccaga tttccagggc aaagtctttg
     6121 gcgtggccag ccagagaaat cctgacgcca caactagggc acatgaagca aagatagaca
     6181 caacagctgg ccgtttcacc cctaaactag gctcattaga gatttccact gagtctgatg
     6241 attttgatca aaacaaacca acaagattca ccccagttgg tattggggtt gaccgtgagg
     6301 cagactttca acaatgggct cttcccaact atgctggcca gttcacccat aacatgaact
     6361 tagccccagc tgttgctccc aacttccctg gtgagcagct ccttttcttc cgctcacagt
     6421 tgccatcctc tggtgggcga tccaacggga tcctggactg cctggtcccc caagaatggg
     6481 tacagcattt ctaccaagaa tcagccccct cccaatctca agtggccctg gttaggtatg
     6541 tcaaccctga cactggcaga gtgttatttg aggccaagct gcacaaatta ggtttcatga
     6601 ctatagccaa gaatggtgat tctccaataa ctgtccctcc aaatggatac tttaggtttg
     6661 aatcttgggt gaaccccttt tatacacttg cccccatggg aacagggaat gggcgtagaa
     6721 ggattcaata atggctggag cttttatagc aggattggct ggtgatatgc tcacaaacac
     6781 tgtaggatct ttagttaatg caggggctaa tgctattaat cagacaattg attttgaaaa
     6841 taataaatat ttgcagaatg cttcttttaa tcatgataag gagatgttga atgcacaaat
     6901 tgaggcaaca aagaggttac aggctgacat gattgctatt aaacaagggg ttttgaccgc
     6961 tggcggcttc tcccctactg atgcagcccg cggggcaatt aatgccccca tgacaaaagt
     7021 cctagattgg aacgggacga gatactgggc accaggcgcc acctccacaa cctcgttgtc
     7081 gggtggcttc acaaatcaaa ccgtacacag acccacacca aattttaaaa cgggccaggc
     7141 tcccaaaccc gcacccagca gtgggtcttc agtgaggtca aattcaaccc aagtcactag
     7201 cctgagttca cactcgtccg ggtcgtctcg atccagcggg tccacagttg tcagctcaat
     7261 accatcctcc aacagaacta gggactgggt caaccaacaa aatttcaatt tggaaccata
     7321 tatgcctgga tctcttagga cagcttttgt cactccacca tctagcacag cctctagctc
     7381 aggcacagtc tcaactgtgc ccaaaaatgt tttggactcc tggacatctg cgtttaatac
     7441 gcgcagacag ccgctattcg cacaccttcg cagaaggggg gagtcaaatg cttagtgaaa
     7501 agattatttt aaatttgatt taaaattagg tttaatctgg aatctttt
//