Typing tool

Complete norovirus genomes

MH218646  GII.3
 GII.P21

Length: 7,548 | 3 CDS

ORF1: 5..5104
ORF2: 5085..6731
ORF3: 6731..7495
LOCUS       MH218646                7548 bp    RNA     linear   VRL 11-JUN-2018
DEFINITION  Norovirus GII isolate NORO_177-2_26_01_2016, complete genome.
ACCESSION   MH218646
VERSION     MH218646.1
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_177-2_26_01_2016"
                     /host="Homo sapiens"
                     /db_xref="taxon:122929"
                     /country="United Kingdom"
                     /collection_date="26-Jan-2016"
                     /note="genotype: GII.P21_GII.3"
     gene            5..5104
                     /gene="ORF1"
     CDS             5..5104
                     /gene="ORF1"
                     /codon_start=1
                     /product="nonstructural polyprotein"
                     /protein_id="AWR17596.1"
                     /translation="MKMASNDASAAAAAKSNNDNAKSSSDGVLSNMAVTFKRALGARS
                     KQPPPSDKPPKPPRPPTPELVKAIPPPPPNGEDEPIISYNVKGGVSGLPELTTVTQPE
                     ENSTAFSVPPLSQRENKDAKEPLTGTILEMWDGEIYHYGLYVERGLVLGVHKPPAAVS
                     LAKVELTPLSLYWRPVYTPQYLISPDTLRKLHGETFPYTAFDNNCYAFCCWVLDLNDS
                     WLNRRMIQRTTGFFRPYQDWNRKPLPTTDDSKVKKVANIVLCALSSLFTRPIKDIIGK
                     LKPLNILNILATCDWTFAGIVESLILLAELFGVFWTPPDVSAMIAPLLGDYELQGPED
                     LAVELVPVVMGGIGLVLGFTKEKIGKMLSSAASTLRACKDLGAYGLEILKLVMKWFFP
                     KKEEKNELAMVRSIEDAVLDLEAIENNHMTSLLKDKDSLATYMRTLDMEEEKARKLST
                     KSASPDIVGTINALLSRIAAARSLVHRAKEELSSRPRPVVVMISGKPGIGKTHLAREL
                     AKKIASTLTGDQRVGLIPRNGVDHWDAYKGERVVLWDDYGMSSPVHDALRLQELADTC
                     PLTLNCDRIENKGKVFDSDVMIITTNLANPAPLDYVNFEACSRRIDFLVYADAPEVEK
                     AKRDFPGQPDMWKDTFKPDFSHIKLALAPQGGFDKNGNTPHGKGVMKTLTASSLVARA
                     SGLLHERLDEYELQGPTPTTFNFDRNKVLAFRQLAAENKYGLVDTMRVGSQLKNVKTM
                     TELKQALKNISVKKCQLVYGGGTYTLESDGKGNVHVEKVNNTSVQTNNELSGVLHHLM
                     CARIRYYVKCVQEALYSILQIAGAAFITTRIAKRTNIQNLWSKPQAEDLEETNNEEGC
                     PKPKNDEEFVVSSDDIKTEGKKGKNKTGRGKKHTAFSSKGLSDEEYDEYKRIREERNG
                     KYSIEEYLQDRDKYYEEVAIARATEEDFCEEEEAKIRQRIFRPTRKQRKEERASLGLV
                     TGSEIRKRNPDDFRPKGKLWADDDRSVDYNEKLSFEAPPSIWSRIVNFGSGWGFWVSP
                     SLFITSTHVIPQGAQEFFGVPIKQIQIHKSGEFCRLRFPKPIRTDVTGMILEEGAPEG
                     TVATLLIKRPTGELMPLAARMGTHATMKIQGRTVGGQMGMLLTGSNAKSMDLGTTPGD
                     CGCPYIYKRGNDYVVIGVHTAAARGGNTVICATQGNEGEAMLEGGDNKGTYCGAPILG
                     PGNAPKLSTKTKFWRSSTTPLPPGTYEPAYLGGKDPRVKGGPSLQQVMRDQLKPFTEP
                     RGKPPKPSVLEAAKKTIINVLEQTIDPPQKWTYAQACASLDKTTSSGHPHHVRKNDCW
                     NGESFTGKLADQASKANLMFEEGKNMTPVYTGALKDELVKTDKIYGVVKKRLLWGSDL
                     STMIRCARAFGGLMDELKAHCVTLPVRVGMNMNEDGPIIFEKHSRYKYHYDADYSRWD
                     STQQRAVLAAALEIMVKFSPEPHLAQVVAEDLLSPSVMDVGDFKISINEGLPSGVPCT
                     SQWNSIAHWLLTLCALSEVTDLSPDIIQANSLFSFYGDDEIVSTDIKLDPEKLTAKLR
                     EYGLKPTRPDKTEGPLIISEDLNGLTFLRRTVTRDPAGWFGKLDQSSILRQMYWTRGP
                     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="AWR17597.1"
                     /translation="MKMASNDAAPSNDGAAGLVPEINNEAMALEPVAGAAIASPLTGQ
                     QNMIDPWIMNNFVQAPGGEFTVSPRNSPGEVLLNLELGPEINPYLAHLARMYNGYAGG
                     FEVQVVLAGNAFTAGKIIFAAIPPNFPVDNLSAAQITMCPHVIVDVRQLEPVNLPMPD
                     VRNNFFHYNQGSDSRLRLIAMLYTPLRANNSGDDVFTVSCRVLTRPSPDFSFNFLVPP
                     TVESKTKPFSLPILTISEMSNSRFPVPIDSLHTSPTENIVVQCQNGRVTLDGELMGTT
                     QLLPSQICAFRGVLTRSTSRANDQADTATPRHFGLSWHIQLDNLNGTPYDPAEDIPGP
                     LGIPDFRGKVFGVASQRNPDTTTRAHEAKIDTSSPRFTPKLGSLEISTESDDFELNQP
                     TRFTPVGIGVDHEEDFRQWALPDYAGQLTHNMNLAPAVAPNYPGEQVLFFRSQLPSSG
                     GRSNGILDCLVPQEWVQHFYQESAPSQSQVALVRYVNPDTGRVLFEAKLHKLGFMTIA
                     KNGDSPITVPPNGYFRFESWVNPFYTLAPMGTGNGRRRIQ"
     gene            6731..7495
                     /gene="ORF3"
     CDS             6731..7495
                     /gene="ORF3"
                     /codon_start=1
                     /product="VP2"
                     /protein_id="AWR17598.1"
                     /translation="MAGAFVAGLAGDMLTNTVGSLVNAGANAINQTIDFENNRYLQNA
                     SFNHDKEMLNAQVEATKKLQADMIAIKQGVLTAGGFSPTDAARGAINAPMTKVLDWNG
                     TRYWAPGATSTTSMSGGFTHQTVHRSTPNFKTNQAPKSTPSSGSSVRSNSTQITSLSS
                     HSSGSSRSSGSTVISSIPSSNRTRDWVNQQNFNLEPHMPGSLRTAFVTPPSSTASSSG
                     TVSTVPKDVLDSWTSAFNTRRQPLFAHLRRRGESNV"
ORIGIN      
        1 gtgaatgaag atggcgtcta acgacgcttc cgctgccgct gctgccaaaa gcaacaacga
       61 caacgcaaaa tcttcaagtg acggagtatt atctaatatg gctgtcactt ttaaacgagc
      121 cctcggggcg cggtctaaac agccgccccc gagtgacaaa ccaccaaaac ccccaagacc
      181 acccacacca gagttggtta aggcaattcc ccctccccca cccaacgggg aagacgaacc
      241 aattatttct tacaacgtca aagggggtgt ttctggtttg cctgagctca caactgtcac
      301 ccaaccggaa gagaactcta cagcattcag cgttccccct cttagtcaga gggagaacaa
      361 agatgcaaag gaaccattga ctggaaccat cctggagatg tgggacgggg agatctacca
      421 ttatggctta tacgtagaac gagggttagt gctcggtgtg cacaaaccac cagcagcagt
      481 cagccttgct aaggttgagc tgaccccctt gtctttgtat tggagaccag tgtacacccc
      541 acagtacctc atttcccctg acactctcag aaagctgcat ggggagacat tcccttacac
      601 agcctttgac aacaactgtt atgccttctg ctgttgggtg cttgacttga atgattcatg
      661 gttgaacaga aggatgatac agaggacaac aggcttcttc cgaccctacc aggattggaa
      721 caggaaaccc ctccccacga cggatgactc caaagtgaaa aaggtggcca atattgtcct
      781 atgtgctctc tcatcattgt tcacaagacc aattaaggac attattggga agttaaaacc
      841 cctaaacatc ctcaacatct tagccacatg tgattggact tttgcaggca tagtagaatc
      901 cctgatcctt ttggctgaac tttttggagt tttctggaca cccccagatg tgtctgcgat
      961 gatcgctccc ttactgggtg attatgaact acagggaccc gaggatctcg ctgtggaact
     1021 cgtacccgta gtaatgggag ggataggttt ggtgctggga ttcaccaaag agaaaatcgg
     1081 caagatgctt tcttctgctg cttcaaccct gagggcatgt aaagaccttg gtgcatatgg
     1141 gctggagatc ctaaaattgg ttatgaaatg gtttttccca aagaaagaag agaaaaacga
     1201 attggcaatg gtgagatcca tcgaggatgc tgtgctagac cttgaagcca ttgagaacaa
     1261 ccatatgaca tctctactta aggataaaga cagccttgca acctacatga ggactcttga
     1321 catggaggag gagaaggcga gaaaactttc caccaagtct gcctctccgg atattgtggg
     1381 tacgataaat gccctactgt caagaattgc agctgcccgg tctctagtgc acagggctaa
     1441 ggaagagctg tcaagcaggc cccgaccggt cgttgtaatg atttcaggga 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 tcatgataat aaccaccaat ttggccaacc cagcgccact
     1801 ggattatgtc aactttgaag cttgctcgag acgcatagac ttccttgtct atgctgatgc
     1861 tcctgaagtt gagaaggcta agcgggactt cccaggccaa ccagacatgt ggaaagacac
     1921 cttcaaaccc gacttctcac acataaaatt ggcattagcc ccgcaaggag gttttgacaa
     1981 gaatggtaac actcctcatg ggaagggagt catgaagacc ctcactgcca gttccctcgt
     2041 tgcccgagca tcagggctcc tccacgagag gttagacgag tatgagctgc agggcccaac
     2101 tcctacaaca ttcaacttcg accgcaacaa ggtgcttgct tttaggcagc ttgctgctga
     2161 aaacaagtac ggtctagttg acacaatgag ggtcgggtca caactcaaga atgtcaaaac
     2221 tatgacagaa ctcaaacagg cacttaagaa catctcagtc aagaaatgtc agcttgtgta
     2281 cggtgggggc acatacacac tcgaatctga tggcaaaggc aatgtgcatg tcgagaaggt
     2341 gaacaacacc agtgtgcaaa ctaacaacga gctctccggg gttttgcacc atctcatgtg
     2401 tgctagaatc aggtactatg ttaagtgtgt tcaggaagct ctctactcca tcttacaaat
     2461 tgccggggct gcattcatca ccacgcgcat tgctaagcgc acaaacatac agaacctctg
     2521 gtccaagcca caagcagaag atctagagga gaccaacaac gaggagggtt gtccaaaacc
     2581 caaaaatgat gaagaatttg tcgtctcctc tgatgacatc aaaactgagg gtaagaaagg
     2641 aaagaacaaa actggccgtg gtaagaagca cacagccttt tccagcaaag gactcagtga
     2701 tgaggagtac gatgagtata agagaatcag ggaagaaaga aatggcaagt actccataga
     2761 ggaataccta caggacagag acaaatacta tgaggaggtg gccatagcca gagcaactga
     2821 ggaagatttc tgtgaagaag aggaggccaa aatccggcag aggatattca gaccaacaag
     2881 gaaacaacgc aaagaggaaa gagcttctct tggtttggtt acaggttctg agattaggaa
     2941 gagaaaccca gatgacttca ggcccaaagg gaaactatgg gctgatgatg acaggagtgt
     3001 tgactacaat gagaaactta gtttcgaggc tccaccaagc atttggtcgc gaatagtcaa
     3061 cttcggctca gggtggggct tctgggtctc gcccagcctc ttcataacat caacccatgt
     3121 cattccccaa ggcgcgcagg agttctttgg agtgcccatc aaacaaatac aaattcacaa
     3181 atcaggtgag ttctgccggc tcagattccc aaaaccaatc aggacagatg ttacgggcat
     3241 gattttggag gaaggtgccc cagaaggcac tgttgccaca cttctcatca agagaccaac
     3301 tggggaactc atgcccttgg cagccaggat gggcacccac gccaccatga aaattcaggg
     3361 tcgcactgtt ggtggacaga tgggcatgct actcacaggg tctaacgcta agagcatgga
     3421 tttgggcaca actcctggcg attgtggttg tccctacatc tacaagagag ggaacgacta
     3481 cgtggtcatt ggagtccaca ctgccgccgc tcgtggagga aacactgtca tctgtgcaac
     3541 ccaaggaaac gagggtgagg ccatgctaga gggtggtgat aataagggaa cttattgtgg
     3601 agcaccaata ttaggccctg gaaatgcccc caaactcagc accaaaacca aattctggag
     3661 gtcttccacc acccccctgc cacccggaac ctatgagcca gcctatctgg gtggcaagga
     3721 ccctagagtg aaaggtggcc cctcactgca acaggtaatg agagaccaac tgaaaccatt
     3781 cactgagccc agaggcaaac cacccaaacc aagtgtgcta gaagctgcca agaagactat
     3841 aatcaatgtg cttgaacaaa caatagaccc acctcaaaaa tggacatatg cacaagcgtg
     3901 tgcatcacta gacaagacca cttccagcgg tcaccctcac catgtgcgga aaaacgattg
     3961 ctggaatggg gaatctttca caggaaaact ggcagaccaa gcatcaaagg ccaacctaat
     4021 gtttgaggaa ggaaagaaca tgactccagt atacacagga gctctgaaag atgaactagt
     4081 caagactgac aagatctatg gggtggtcaa gaagaggctc ctgtggggtt cagacctatc
     4141 aaccatgata cggtgtgcac gagccttcgg tgggctaatg gacgagctca aggcccattg
     4201 cgtcacacta ccagtcaggg ttggtatgaa catgaatgag gatggaccca taatatttga
     4261 gaagcactcc 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 cattgctcac tggctcctca cactatgtgc actgtctgaa gtcacagacc tgtcccctga
     4561 catcatccag gcaaattccc tgttctcctt ttatggtgat gatgaaatag tgagcacaga
     4621 catcaaatta gacccagaga aattgacagc aaaactgagg gaatatgggc ttaaaccaac
     4681 ccgccctgac aaaacagagg gacccttaat tatctctgaa gatctgaatg gcctgacctt
     4741 cctgcggaga acagtgaccc gcgacccggc cggatggttt ggcaaactgg accaaagctc
     4801 aatacttagg cagatgtact ggaccagggg gccaaaccat 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 caatagcatc acccctcact ggtcagcaaa
     5221 atatgattga tccctggatt atgaataatt ttgtgcaagc acctggtggt gagtttacag
     5281 tgtcccccag aaattcccct ggtgaagtcc ttcttaattt ggaactgggc ccagaaataa
     5341 atccctattt ggcccatctt gctagaatgt acaatggtta tgcaggtgga tttgaagtgc
     5401 aggtggtcct agctggaaat gcgtttacag caggaaagat aatctttgca gctatccccc
     5461 ccaattttcc agttgacaat ttaagtgcag cacagatcac aatgtgccca catgtgattg
     5521 tggatgtcag acagttggaa ccagtcaacc tcccgatgcc tgacgttcgc aacaacttct
     5581 ttcattataa tcaagggtct gactcgaggt tacgcctaat tgcaatgcta tatacacctc
     5641 ttagagcaaa caattctggg gatgatgttt ttactgtgtc ttgtagagtg ctaactagac
     5701 ctagtcctga tttctcattc aatttccttg tgccacccac tgtggagtca aagacaaaac
     5761 ctttttccct ccctatcctg actatctctg aaatgtccaa ttctaggttc ccagtgccaa
     5821 ttgattccct acacaccagt cccactgaga atattgttgt tcagtgccaa aatgggcgcg
     5881 tcacccttga tggtgagctg atgggcacca cccaactctt gccaagccaa atctgtgctt
     5941 tcaggggcgt cctcaccaga tcaacaagca gagccaatga ccaggccgat acagcaaccc
     6001 ctagacactt tggtctttct tggcacatac aattggataa tctaaatgga accccttatg
     6061 atcctgcaga agacatacca ggccccctag ggataccaga tttccgtggc aaagtctttg
     6121 gcgtggccag ccagaggaat cctgatacca cgactagggc gcatgaagca aagatagata
     6181 cctcttctcc ccgcttcacc ccaaagctag gctcattaga gatatccact gaatctgatg
     6241 attttgaact caaccaacca acaagattca ccccagttgg cattggagtt gaccatgagg
     6301 aagactttag acagtgggcc ctacccgact acgctggtca gctcacacat aacatgaact
     6361 tagccccagc tgttgctccc aactaccctg gtgagcaggt ccttttcttc cgctcacaat
     6421 tgccatcttc tggtgggcga tccaacggga ttctagactg cctagttccc caagaatggg
     6481 tacagcactt ctaccaagag tcagccccct ctcagtccca agtggccctg gtcaggtatg
     6541 ttaatcctga cactggtaga gtgttatttg aggccaaatt acataaatta ggtttcatga
     6601 ctatagccaa gaatggtgat tctccaataa ctgtcccccc aaatggatac tttaggtttg
     6661 aatcttgggt gaaccccttt tacacacttg cccccatggg aactgggaat gggcgtagaa
     6721 ggattcaata atggctggag cttttgtagc aggattggct ggtgacatgc tcacaaatac
     6781 tgtaggatct ttagttaatg caggggctaa tgctattaat caaacaattg attttgaaaa
     6841 taatagatat ttgcaaaatg cttcttttaa tcatgataag gagatgttga 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 cctccagctc
     7381 aggcacagtc tcaactgtgc ccaaagatgt tttggactcc tggacatctg cgtttaacac
     7441 gcgcagacag ccgctattcg cacaccttcg cagaaggggg gagtcaaatg tttagtgaaa
     7501 agattatttt aaatttggtt taaaattagg tttaatttgg aatctttt
//