Typing tool

Complete norovirus genomes

MH218654  GII.3
 GII.P21

Length: 7,548 | 3 CDS

ORF1: 5..5104
ORF2: 5085..6731
ORF3: 6731..7495
LOCUS       MH218654                7548 bp    RNA     linear   VRL 11-JUN-2018
DEFINITION  Norovirus GII isolate NORO_186_28_09_2015, complete genome.
ACCESSION   MH218654
VERSION     MH218654.1
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_186_28_09_2015"
                     /host="Homo sapiens"
                     /db_xref="taxon:122929"
                     /country="United Kingdom"
                     /collection_date="28-Sep-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="AWR17620.1"
                     /translation="MKMASNDASAAAAAKSNNDNAKSSSDGVLSNMAVTFKRALGARS
                     KQPPPSDKPPKPPRPSTPELVKAIPPPPPNGEDEPIISYSVKGGVSGLPELSTVTQLE
                     ENSTAFSVPPLSQRENKDAKEPLTGTILEMWDGEIYHYGLYVERGLVLGVHKPPAAVS
                     LAKIELTPLSLYWRPVYTPQYLISPDTLRKLHGETFPYTAFDNNCYAFCCWVLDLNDS
                     WLNRRMIQRTTGFFRPYQDWNRKPLPTMDDSKVKKVANVVLCALSSLFTRPIKDIIGK
                     LKPLNILNILATCDWTFAGIVESLILLAELFGVFWTPPDVSAMIAPLLGDYELQGPED
                     LAVELVPVVMGGIGLVLGFTKEKVGKMLSSAASTLRACKDLGAYGLEILKLVMKWFFP
                     KKEEKNELAMVRSIEDAVLDLEAIENNHMTALLKDKDSLATYMRTLDMEEEKARKLST
                     KSASPDIVGTINALLSRIAAARSLVHRAKEELSSRPRPVVVMISGKPGIGKTHLAREL
                     AKKIASTLTGDQRVGLIPRNGVDHWDAYKGERVVLWDDYGMSSPVHDALRLQELADTC
                     PLTLNCDRIENKGKVFDSDVIIITTNLANPAPLDYVNFEACSRRIDFLVYADAPEVEK
                     AKRDFPGQPDMWKDTFKPDFSHIKLALAPQGGFDKNGNTPHGKGVMKTLTAGSLVARA
                     SGLLHERLDEYELQGPTPTTFNFDRNKVLAFRQLAAENKYGLVDTMRVGSQLKNVKTM
                     TELKQALKNISVKKCQLVYGGGTYTLESDGKGNVHVEKVNNTSVQTNNELSGVLHHLK
                     CARIRYYVKCVQEALYSILQIAGAAFITTRIAKRTNIQNLWSKPQAEDLEETNNEEGC
                     PKPKNDEEFVVSSDDIKTEGKKGKNKTGRGKKHTAFSSKGLSDEEYDEYKRIREERNG
                     KYSIEEYLQDRDKYYEEVAIARATEEDFCEEEEAKIRQRIFRPTRKQRKEERASLGLV
                     TGSEIRKRNPDDFKPKGKLWADDDRSVDYNEKLSFEAPPSIWSRIVNFGSGWGFWVSP
                     SLFITSTHVIPQGAQEFFGVPIKQIQIHKSGEFCRLRFPKPIRTDVTGMILEEGAPEG
                     TVATLLIKRPTGELMPLAARMGTHATMKIQGRTVGGQMGMLLTGSNAKSMDLGTTPGD
                     CGCPYIYKRGNDYVVIGVHTAAARGGNTVICATQGNEGEAMLEGGDNKGTYCGAPILG
                     PGNAPKLSTKTKFWRSSTTPLPPGTYEPAYLGGKDPRVKGGPSLQQVMRDQLKPFTEP
                     RGKPPKPSVLEAAKKTIINVLEQTIDPPQKWTYAQACASLDKTTSSGHPHHVRKNDCW
                     NGESFTGKLADQASKANLMFEEGKNMTPVYTGALKDELVKTDKIYGVVKKRLLWGSDL
                     STMIRCARAFGGLMDELKAHCVTLPVRVGMNMNEDGPIIFEKHSRYKYHYDADYSRWD
                     STQQRAVLAAALEIMVKFSPEPHLAQVVAEDLLSPSVMDVGDFKISINEGLPSGVPCT
                     SQWNSIAHWLLTLCALSEVTDLSPDIIQANSLFSFYGDDEIVSTDIKLDPEKLTAKLR
                     EYGLKPTRPDKTEGPLIISEDLNGLTFLRRTVTRDPAGWFGRLDQSSILRQMYWTRGP
                     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="AWR17621.1"
                     /translation="MKMASNDAAPSNDGAAGLVPEINNEAMALEPVAGAAIAAPLTGQ
                     QNIIDPWIMNNFVQAPGGEFTVSPRNSPGEVLLNLELGPEINPYLAHLARMYNGYAGG
                     FEVQVVLAGNAFTAGKIIFAAIPPNFPIDNLSAAQITMCPHVIVDVRQLEPVNLPMPD
                     VRNNFFHYNQGSDSRLRLIAMLYTPLRANNSGDDVFTVSCRVLTRPSPDFSFNFLVPP
                     TVESKTKPFSLPILTISEMSNSRFPVPIDSLHTSPTENIVVQCQNGRVTLDGELMGTT
                     QLLPSQICAFRGVLTRSTSRATDQADTATPRHFDHSWHIQLDNLNGTPYDPAEDIPGP
                     LGTPDFRGKVFGVASQRNPDTTTRAHEAKIDTSSPRFTPKLGSLEISTESDDFEHNQP
                     TRFTPVGIGVDHEEDFRQWTLPNYAGQLTHNMNLAPAVAPNFPGEQLLFFRSHLPSSG
                     GRSNGILDCLVPQEWVQHFYQESAPSQSQVALVRYVNPDTGRVLFEAKLHKLGFITIA
                     KNGDSPITVPPNGYFRFESWVNPFYTLAPMGTGNGRRRIQ"
     gene            6731..7495
                     /gene="ORF3"
     CDS             6731..7495
                     /gene="ORF3"
                     /codon_start=1
                     /product="VP2"
                     /protein_id="AWR17622.1"
                     /translation="MAGAFIAGLAGDMLTNTVGSLVNAGANAINQTIDFENNKYLQNA
                     SFNHDKEMLNAQVEATKKLQADMIAIKQGVLTAGGFSPTDAARGAINAPMTKVLDWNG
                     TRYWAPGATSTTSMSGGFTHQTVHRSTPNFKTNQAPKSTPSSGSSVRSNSTQITSLSS
                     HSSGSSRSSGSTVISSIPSSNRTRDWVNQQNFNLEPHMPGSLRTAFVTPPSSTASSSG
                     TVSTVPKNVLDSWTSAFNTRRQPLFAHLRGRGESNV"
ORIGIN      
        1 gtgaatgaag atggcgtcta acgacgcttc tgctgccgct gctgccaaaa gcaacaacga
       61 caacgcaaaa tcttcaagtg acggagtatt atctaatatg gctgtcactt ttaaacgagc
      121 cctcggggcg cggtctaaac agccgccccc gagtgacaaa ccaccaaaac ccccaagacc
      181 atccacacca gagttggtta aggcaattcc ccctccccca cccaacgggg aagacgaacc
      241 aattatttct tacagcgtca aagggggtgt ttctggtttg cctgagctct caactgtcac
      301 ccaactggaa gagaactcta cagcattcag cgttccccct cttagccaga gggagaacaa
      361 agatgcaaag gaaccattga ctggaaccat cctggagatg tgggacgggg agatctacca
      421 ttatggctta tacgtagaac gagggttagt gctcggtgtg cacaaaccac cagcagcagt
      481 cagccttgcc aagattgagc tgaccccctt gtccttgtat tggagaccag tgtacacccc
      541 acagtacctc atttcccctg acactctcag aaagctgcat ggggagacat tcccttatac
      601 agcctttgac aacaactgtt atgccttctg ctgttgggtg cttgacttga atgattcatg
      661 gctgaacaga aggatgatac agaggacaac aggcttcttc cgaccctacc aggattggaa
      721 caggaaaccc ctccccacga tggatgactc caaagtgaaa aaggtggcca atgttgtcct
      781 atgtgctctc tcatcattgt tcacaagacc aattaaggac attattggaa agttaaaacc
      841 cctaaacatc ctcaacatct tagccacatg tgattggact tttgcaggca tagtagaatc
      901 cctgatcctt ttggctgaac tttttggagt tttctggaca cccccagatg tgtctgcgat
      961 gatcgctccc ttactgggtg attacgaact acagggaccc gaggatctcg ctgtggaact
     1021 cgtacccgta gtaatgggag ggataggttt ggtgctggga ttcaccaaag agaaagtcgg
     1081 caagatgctt tcttctgctg cttcaaccct gagggcatgt aaagatcttg gtgcatatgg
     1141 gttggagatc ctcaaattgg ttatgaaatg gtttttccca aagaaagaag agaaaaacga
     1201 attggcaatg gtgagatcca tcgaggatgc agtgctagac cttgaagcca ttgagaacaa
     1261 ccatatgaca gctctactta aggataaaga cagccttgca acctacatga ggactcttga
     1321 catggaggag gagaaggcga gaaaactttc caccaagtct gcctctccgg atattgtggg
     1381 tacgataaat gccctactgt caaggattgc agctgcccgg tctctagtgc acagggctaa
     1441 ggaagagctg tcaagcaggc cccgaccggt cgttgtaatg atctcaggga aaccgggtat
     1501 agggaaaacc catctagcta gagagttggc aaagaagatc gcctccacac tcacaggtga
     1561 ccagagggtg ggtcttatcc cacgtaacgg ggtcgaccac tgggatgcat acaaaggtga
     1621 gagagtcgtt ctctgggacg actatgggat gagcagccct gtccacgacg ccctcagact
     1681 ccaggagctc gctgacacct gtcctctcac actcaactgt gacaggattg agaacaaagg
     1741 taaagtcttt gacagtgacg tcataataat aaccaccaat ttggccaacc cagcgccact
     1801 ggattatgtc aactttgaag cttgctcgag acgcatagac ttcctcgtct atgctgatgc
     1861 tcctgaagtt gagaaggcta agcgggactt cccaggccaa ccagacatgt ggaaagacac
     1921 cttcaaaccc gacttctcac acataaaatt ggcattagcc ccgcaaggag gttttgacaa
     1981 gaatggtaac actcctcatg ggaagggagt catgaagacc ctcactgctg gttccctcgt
     2041 tgcccgagca tcagggctcc tccacgagag attagacgag tatgagctgc agggcccaac
     2101 ccccacaaca ttcaacttcg accgcaacaa ggtgcttgct tttaggcagc ttgctgctga
     2161 aaacaagtac ggtctagttg acacaatgag ggtcgggtca caactcaaga atgtcaaaac
     2221 tatgacagaa ctcaaacagg cactcaagaa catctcagtc aagaaatgtc agcttgtgta
     2281 cggtgggggc acatacacac tcgaatctga tggcaaaggc aatgtgcatg tcgaaaaggt
     2341 gaacaacacc agtgtgcaaa ctaacaacga gctctccggg gttttgcacc atctcaagtg
     2401 tgctagaatc aggtattatg ttaagtgtgt gcaggaagcc ctctactcca tcttacaaat
     2461 tgccggggct gcattcatca ccacgcgcat tgctaagcgc acgaacatac aaaacctctg
     2521 gtccaagcca caagcagaag atctagagga gactaacaat gaggagggtt gtccaaaacc
     2581 caaaaatgat gaagaatttg ttgtctcctc tgatgacatc aaaactgagg gtaagaaagg
     2641 aaagaacaag actggccgtg gtaagaagca cacagccttt tccagcaaag gactcagtga
     2701 tgaggagtac gatgagtata agagaatcag ggaagaaaga aatggtaagt actccataga
     2761 ggaataccta caggacagag acaaatacta tgaggaggtg gccatagcca gggcaactga
     2821 ggaagatttc tgtgaagaag aggaggccaa aatccggcag aggatattca gaccaacaag
     2881 gaaacaacgc aaagaggaaa gagcttccct tggtttggtt acaggttctg agattaggaa
     2941 gagaaaccca gatgacttca agcccaaagg gaaactatgg gctgatgatg acaggagtgt
     3001 tgactacaat gagaaactta gtttcgaggc tccaccaagc atttggtcac gaatagtcaa
     3061 cttcggctca gggtggggct tttgggtctc gcccagcctc ttcataacat caacccatgt
     3121 cattccccaa ggcgcgcagg agttctttgg agtgcccatc aaacaaatac aaattcacaa
     3181 atcaggtgag ttctgccggc tcaggttccc aaaaccaatc aggacagatg ttacgggcat
     3241 gattttggag gaaggtgctc cagaaggcac cgttgccaca cttctcatca agagaccaac
     3301 tggggaactc atgcccttgg cagccaggat gggcacccac gctaccatga aaatccaggg
     3361 tcgcactgtt ggtggacaga tgggcatgct actcacgggg tctaacgcta agagcatgga
     3421 tttgggcaca actcctggcg attgtggttg tccctacatc tacaagagag ggaacgacta
     3481 cgtggtcatt ggagttcaca ctgccgccgc tcgtggagga aacactgtca tctgtgcaac
     3541 ccaaggaaac gagggtgagg ccatgctaga gggtggtgac aacaagggaa cttattgtgg
     3601 agcaccaata ttaggccctg gaaatgcccc caaactcagc accaaaacca aattctggag
     3661 gtcttccacc acccccctgc cacccggaac ctacgagcca gcctatctgg gtggcaagga
     3721 ccctagagtg aaaggtggcc cctcactgca acaggtaatg agagaccaac taaaaccatt
     3781 cactgagccc agaggcaaac cacccaaacc aagtgtgcta gaagcagcca agaagactat
     3841 aatcaatgtg cttgaacaaa caatagaccc acctcaaaaa tggacatatg cacaagcgtg
     3901 tgcatcacta gacaagacca cttccagcgg tcaccctcac catgtgcgga agaacgattg
     3961 ctggaatggg gaatctttca caggaaaact ggcagaccaa gcatcaaagg ccaacctaat
     4021 gtttgaggaa ggaaagaaca tgactccagt atacacagga gctctgaaag atgagctagt
     4081 caagactgac aagatttatg gggtggtcaa gaagaggctc ctgtggggtt cagatctatc
     4141 aaccatgata cggtgtgcac gagccttcgg tgggctaatg gacgagctca aggcccattg
     4201 cgtcacacta ccagtcaggg ttggtatgaa catgaatgag gatggaccca taatatttga
     4261 gaaacactcc agatacaagt accattatga tgcagattac tcccgctggg actcaacaca
     4321 acaaagagca gtgctagccg cagccctgga aataatggtc aaattctcac cagaacctca
     4381 tctggcccaa gtggttgcag aagacctttt gtcccccagt gtgatggatg tgggtgattt
     4441 caagatatca atcaacgagg gactgccctc tggtgtccct tgcacttcac aatggaactc
     4501 cattgcccac tggctcctca cactgtgtgc actgtctgaa gtcacagacc tgtcccctga
     4561 catcatccag gcgaattccc tgttctcctt ttatggtgat gatgaaatag tgagcacaga
     4621 cataaaatta gacccagaga aattgacagc aaaactgagg gaatacgggc ttaaaccaac
     4681 ccgccctgac aaaacagagg gacccttaat tatctctgaa gatctgaatg gcctgacctt
     4741 cctgcggaga acagtgaccc gcgacccggc cggatggttt ggcagactgg accaaagctc
     4801 aatactcagg cagatgtact ggaccagggg accaaaccat gaagacccct ttgaaacaat
     4861 gataccacac tcccagagac ccatacaact gatgtcatta cttggtgaag ctgcattgca
     4921 tggtccgtca ttctacagta aaatcagcaa attggtcatt tcggaactga aagagggtgg
     4981 aatggatttt tacgtgccca gacaagaacc aatgttcagg tggatgaggt tctcagactt
     5041 gagcacgtgg gagggcgatc gcaatctggc tcccagtttt gtgaatgaag atggcgtcga
     5101 atgacgccgc tccatctaac gatggtgccg ccggcctcgt cccagagatc aacaatgagg
     5161 caatggcgct agagccagtg gcgggtgcag caatagcagc acccctcact ggtcagcaaa
     5221 atataattga tccctggatt atgaataatt ttgtgcaagc acctggtggt gagttcacag
     5281 tgtcccccag aaactcccct ggtgaagtcc ttcttaattt ggaactgggc ccagaaataa
     5341 atccctattt ggcccatctt gctagaatgt acaatggtta tgcaggtgga tttgaagtgc
     5401 aggtggtcct agctggaaat gcgtttacag caggaaagat aatctttgca gccatccccc
     5461 caaattttcc aattgacaat ttaagtgcag cacagatcac aatgtgccca catgtgattg
     5521 tggatgtcag acagttggaa ccagtcaacc tcccgatgcc tgacgttcgc aacaacttct
     5581 ttcattataa tcaagggtct gattcgaggt tgcgcctaat tgcaatgcta tacacacctc
     5641 ttagggcaaa caattctggg gatgatgttt ttactgtgtc ttgtagagtg ctaactagac
     5701 ctagtcctga tttctcattc aatttccttg tgccacccac tgtggagtca aagacaaaac
     5761 ctttttccct ccctatcctg accatctctg aaatgtccaa ttctaggttc ccagtaccaa
     5821 ttgattccct acacaccagt cccactgaga atattgttgt tcagtgccaa aatgggcgcg
     5881 tcacccttga tggtgagctg atgggcacca cccaactctt gcctagccaa atctgtgctt
     5941 tcaggggcgt tctcaccaga tcaacaagca gagccactga ccaggccgac acagcaaccc
     6001 ctagacattt tgatcattcc tggcatatac aattggataa tctaaatgga accccttatg
     6061 atcctgcaga agacatacca ggccccctag ggacaccaga tttccgtggc aaagtctttg
     6121 gcgtggccag ccagagaaat cctgatacca cgactagggc gcatgaagca aagatagaca
     6181 cctcatctcc ccgcttcacc ccaaagctag gctcattaga gatatccact gaatctgatg
     6241 attttgaaca caaccaacca acaagattca ccccagttgg cattggagtt gaccatgagg
     6301 aagactttag acagtggacc ctacccaact acgctggtca gctcacacat aacatgaatt
     6361 tagccccagc tgttgctccc aacttccctg gtgagcagct cctcttcttc cgctcacatt
     6421 tgccatcttc tggtgggcga tctaacggga ttctagactg cctagttccc caagaatggg
     6481 tacagcactt ctaccaagag tcagccccct ctcaatccca agtggccctg gttaggtatg
     6541 ttaatcctga cactggtaga gtgttatttg aggccaaact acataaatta ggtttcataa
     6601 ctatagccaa gaatggtgac tctccaataa ctgtcccccc 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 gagatgctga atgcacaagt
     6901 tgaggcaaca aagaagttac aggctgacat gattgctatc aaacaagggg ttttgaccgc
     6961 tggcggcttc tcccctactg atgcagcccg tggggcaatt aatgccccca tgacaaaagt
     7021 cctagattgg aatggaacga gatactgggc accaggtgcc acctccacaa cctcgatgtc
     7081 gggtggcttt acacaccaaa ctgtgcacag atccacacca aattttaaaa cgaaccaggc
     7141 ccccaaatcc acacccagta gtgggtcttc agtgaggtca aactcaaccc aaatcactag
     7201 cctgagctca cactcgtccg ggtcgtctcg atccagcgga 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 cggaaggggg gagtcaaatg tttagtgaaa
     7501 agattatttt aaatttggtt taaaattagg tttaatttgg aatctttt
//