Typing tool

Complete norovirus genomes

MH218669  GII.4 Sydney
 GII.P4 Yerseke

Length: 7,564 | 3 CDS

ORF1: 5..5104
ORF2: 5085..6707
ORF3: 6707..7513
LOCUS       MH218669                7564 bp    RNA     linear   VRL 11-JUN-2018
DEFINITION  Norovirus GII isolate NORO_211_16_12_2015, complete genome.
ACCESSION   MH218669
VERSION     MH218669.1
KEYWORDS    .
SOURCE      Norovirus GII
  ORGANISM  Norovirus GII
            Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes;
            Picornavirales; Caliciviridae; Norovirus.
REFERENCE   1  (bases 1 to 7564)
  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 7564)
  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..7564
                     /organism="Norovirus GII"
                     /mol_type="genomic RNA"
                     /isolate="NORO_211_16_12_2015"
                     /host="Homo sapiens"
                     /db_xref="taxon:122929"
                     /country="United Kingdom"
                     /collection_date="16-Dec-2015"
                     /note="genotype: GII.P4_GII.4"
     gene            5..5104
                     /gene="ORF1"
     CDS             5..5104
                     /gene="ORF1"
                     /codon_start=1
                     /product="nonstructural polyprotein"
                     /protein_id="AWR17665.1"
                     /translation="MKMASNDASAAAVANSNNDTAKSSSDGVLSSMAVTFKRALGARP
                     KQPPPREIPQRPPRPPTPELVKKIPPPPPNGEDEIVVSYSVKDGVSGLPDLSTVKQPE
                     ESNTAFSVPPLSQRENRDAKEPLTGSILEMWDGEIYHYGLYVERGLVLGVHKPPAAIS
                     LARIELAPLSLYWRTVYTPQYLISPDTLKKLHGETFPYTAFDNNCYAFCCWVLDLNDS
                     WLSRRMIQRTTGFFRPYQDWNRKPLPTMDDSKLKKVANIFLCTLSSLFTRPIKDIIGK
                     LKPLNILNILASCDWTFAGIVESLILLAELFGVFWTPPDVSAMIAPLLGDYELQGPED
                     LAVELVPVVMGGIGLVLGFTKEKVGKMLSSAASTLRACKDLGAYGLEILKLVMKWFFP
                     KKEEANELAIVRSIEDAVLDLEAIENNHLTTLLKDKDSLATYMRTLDLEEEKARKLST
                     KSASPDIVGTINALLARIAAARSLVHRAKEELSSRPRPVVMMISGKPGIGKTHLAREV
                     AKRIATSLTGDQRVGLIPRNGVDHWDAYKGERVVLWDDYGMSNPVHDALRLQELADTC
                     PLTLNCDRIENKGKVFDSDVIIITTNLANPAPLDYVNFEACSRRIDFLVYAEAPEVEK
                     AKRDFPGQPDMWKNAFSSDFSHIKLTLAPQGGFDKNGNTPHGKGVMKTLTTGSLIARA
                     SGLLHERLDEFELQGPTLTTFNFDRNKVLAFRQLAAENKYGLMDTMRIGKQLKGVKTM
                     PELKQALKNVSIRKCQIVYSGCTYMLESDGKGNVKVDKTQSASVQTNNELTGALHHLR
                     CARIRYYVKCVQEALYSIIQIAGAAFVTTRIVKRMNIQDLWSKPQVENTEETTNKDGC
                     PKPKDDEEFVISSDDIKTEGKKGKNKTGRGKKHTAFSSKGLSDEEYDEYKRIREERNG
                     KYSIEEYLQDRDKYYEEVAIARATEEDFCEEEEAKIRQRIFRPTRKQRKEERASLGLV
                     TGSEIRKRNPDDFKPKGKLWADDDRSVDYNEKLSFEAPPSIWSRIVNFGSGWGFWVSP
                     SLFITSTHVIPQGAKEFFGVPIKQIQVHKSGEFCRLRFPKPIRTDVTGMILEEGAPEG
                     TVVTLLIKRSTGELMPLAARMGTHATMKIQGRTVGGQMGMLLTGSNAKSMDLGTTPGD
                     CGCPYIYKRGNDYVVIGVHTAAARGGNTVICATQGSEGEATLEGGNDKGTYCGAPILG
                     PGSAPTLSTKTKFWRSSTAPLPPGTYEPAYLGGKDPRVKGGPSLQQVMREQLKPFTEP
                     RGKPPKPSVLEAAKKTIINVLEQTIDPPEKWSFAQACASLDKTTSSGHPHHMRKNDCW
                     NGESFTGKLADQASKANLMYEEGKSMTPVYTAALKDELVKTDKIYGKIKKRLLWGSDL
                     ATMIRCARAFGGLMDELKAHCVTLPIRVGMNMNEDGPIIFERHSRYTYHYDADYSRWD
                     STQQRAVLAAALEILVKFSPEPHLAQVVAEDLLSPSVVDVGDFTISINEGLPSGVPCT
                     SQWNSVAHWLLTLCALSEVTNLSPDTIQANSLFSFYGDDEIVSTDIKLDPEKLTAKLR
                     EYGLKPTRPDKTEGPLVISEDLNGLTFLRRTVTRDPAGWFGKLEQSSILRQMYWTRGP
                     NHGDPSETMIPHSQRPIQLMSLLGEAALHGPAFYSKISKLVIAELKEGGMDFYVPRQE
                     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..6707
                     /gene="ORF2"
     CDS             5085..6707
                     /gene="ORF2"
                     /codon_start=1
                     /product="VP1"
                     /protein_id="AWR17666.1"
                     /translation="MKMASSDANPSDGSAANLVPEVNNEVMALEPVVGAAIAAPVAGQ
                     QNVIDPWIRNNFVQAPGGEFTVSPRNAPGEILWSAPLGPDLNPYLSHLARMYNGYAGG
                     FEVQVILAGNAFTAGKIIFAAVPPNFPTEGLSPSQVTMFPHIIVDVRQLEPVLIPLPD
                     VRNNFYHYNQSNDPTIKLIAMLYTPLRANNAGDDVFTVSCRVLTRPSPDFDFIFLVPP
                     TVESRTKPFSVPILTVEEMTNSRFPIPLEKLFTGPSSAFVVQPQNGRCTTDGVLLGTT
                     QLSPVNICTFRGDVTHIKDSRNYTMNLASQNWNNYDPTEEIPAPLGTPDFVGKIQGVL
                     TQTTKSNGSTRGHKATVLTGSTDFTPKLGRIQFATDTDHDFEANQNTKFTPVGVIQDG
                     DTAHQNEPQQWMLPSYSGRDIHNVHLAPAVAPTFPGEQLLFFRSTMPGCSGYPNMDLD
                     CLLPQEWVQYFYQEAAPAQSDVALLRFVNPDTGRVLFECKLHKSGYVTVAHTGRHDLV
                     IPPNGYFRFDSWVNQFYTLAPMGNGTGRRRAV"
     gene            6707..7513
                     /gene="ORF3"
     CDS             6707..7513
                     /gene="ORF3"
                     /codon_start=1
                     /product="VP2"
                     /protein_id="AWR17667.1"
                     /translation="MAGAFFAGLASDVLGSGLGSLINAGAGAINQKVEFENNRKLQQA
                     SFQFSSNLQQASFQHDKEMLQAQIEATKKLQQEMMKVKQAVLLEGGFSETDAARGAIN
                     APMTKTLDWSGTRYWAPDARTTTYNAGRFSTPQPPGALPGRANLRDAVPARGSSSKSS
                     NSSTVTSVYSNQTVSTRLGSTAGSGTSVSSLPSTARTRSWVEDQNRSLSPFMRGAHNI
                     SFVTPPSSRSSSQGTVSTVPKEILDSWTGAFNTHRQPLFAHIRKRGESRA"
ORIGIN      
        1 gtgaatgaag atggcgtcta acgacgcttc cgctgccgct gttgccaaca gcaacaacga
       61 caccgcaaaa tcttcaagtg acggagtgct ttccagcatg gctgtcactt ttaaacgagc
      121 cctcggggcg cggcctaaac agcccccccc gagggaaata ccacaaagac ccccacgacc
      181 acccacccca gaattggtta aaaagatccc ccctcccccg cccaacggag aggatgaaat
      241 agtggtctct tatagtgtca aagatggcgt ttccggtttg cctgaccttt ccaccgtcaa
      301 gcaaccggaa gaatctaaca cggctttcag tgtcccccca ctcagtcaga gggagaatag
      361 agacgccaag gagccactta ctgggtcaat tctggaaatg tgggatggag aaatctacca
      421 ttatggcctg tatgtggagc gaggtctcgt gctaggcgtg cacaaaccac cagctgccat
      481 cagcctcgct aggattgagc tagcaccact ctccctgtac tggagaactg tgtacactcc
      541 tcagtacctc atctctccag acactctcaa gaaattacac ggagagacgt tcccctacac
      601 agcctttgac aacaattgtt atgccttctg ttgctgggtc ctggacctaa acgactcgtg
      661 gctgagcagg agaatgatcc aaagaacaac tggtttcttt agaccctacc aagactggaa
      721 taggaaaccc cttcccacta tggatgactc caaattaaag aaggtagcta acatatttct
      781 gtgtactctg tcctcgttat tcaccaggcc cataaaagac ataataggga agttaaagcc
      841 cctcaatatc ctcaacatct tagcctcatg tgattggacc ttcgcaggta tcgtggagtc
      901 cctgatactc ttggcagagc tctttggggt tttctggaca cccccagatg tgtctgcgat
      961 gattgccccc ttactcggtg actacgagct gcaaggacct gaggaccttg cggtggagct
     1021 cgtccccgta gtgatgggtg gaattggttt ggtactagga ttcaccaaag agaaggttgg
     1081 gaaaatgttg tcatctgctg catccacctt gagagcttgc aaagacctcg gtgcatatgg
     1141 gctagaaatc ctaaagttgg tcatgaagtg gttcttcccg aaaaaggagg aagcaaatga
     1201 actggctata gtgagatcta tcgaggatgc agtcttggat ctcgaggcaa ttgaaaacaa
     1261 ccacttgacc accctgctca aagacaaaga cagtctggca acctacatga gaactcttga
     1321 ccttgaggag gagaaagcca ggaaactttc aaccaagtct gcctcgcctg acattgtggg
     1381 cacaatcaac gcccttctgg cgagaatcgc cgctgcacgc tctctagtgc atcgggcgaa
     1441 ggaggaactt tccagcagac caagacctgt agtgatgatg atatcaggca agccaggaat
     1501 agggaagacc caccttgcta gggaagtggc taagagaatc gcaacctccc ttacaggaga
     1561 ccagcgcgta ggcctcatcc cacgtaacgg cgtcgaccat tgggatgctt acaaggggga
     1621 gagggttgtc ctttgggatg attatggaat gagcaacccc gttcatgatg ccctcagatt
     1681 gcaggaactc gctgacacct gccccctcac tctaaactgt gacaggattg agaacaaagg
     1741 aaaggtcttt gacagcgatg tcatcattat caccactaac ctggccaacc cagcaccact
     1801 agactatgtc aactttgaag catgctcgag gcgcatcgac ttcctcgtgt acgcagaagc
     1861 ccctgaagtc gaaaaggcga agcgtgactt cccaggtcag cctgacatgt ggaagaacgc
     1921 cttcagttct gatttctcac acataaaact gacactggcc ccacaaggtg gcttcgacaa
     1981 gaacgggaac accccacacg gaaagggtgt catgaagacc ctcaccactg gctccctcat
     2041 tgcccgggca tctgggttac tccatgagag gttagatgag tttgagctac aaggcccaac
     2101 cctcaccacc ttcaatttcg accgcaataa agtgcttgcc tttagacaac ttgctgctga
     2161 gaacaaatat gggttgatgg acacaatgag aattgggaaa cagctcaagg gtgtcaaaac
     2221 catgccagaa ctcaaacaag cacttaagaa tgtctcaatc aggaaatgcc aaatagtgta
     2281 tagtggttgc acttacatgc ttgaatctga tggcaagggc aatgtgaaag ttgacaaaac
     2341 tcagagcgcc tccgtgcaga ccaacaatga gctgactggt gccctgcacc atttgaggtg
     2401 cgccaggatc agatactatg tcaagtgtgt ccaggaggcc ctgtactcca tcatccaaat
     2461 tgccggagct gcatttgtca ccacgcgcat cgtcaagcgc atgaacatac aagacttgtg
     2521 gtccaaacca caagtggaaa acacagagga aaccaccaac aaagacggat gcccaaaacc
     2581 caaagatgat gaggagtttg tcatctcatc cgacgacatc aagactgagg gtaagaaagg
     2641 gaagaacaaa actggccgcg gcaagaaaca tacagccttc tcaagtaaag gtctcagtga
     2701 cgaagagtac gatgagtaca agaggattag ggaagaaagg aatggcaagt actccataga
     2761 ggagtacctt caggacaggg acaaatacta tgaggaggta gccattgcca gggcgactga
     2821 ggaagacttc tgtgaagagg aggaagccaa gatccggcaa aggattttca ggccaacaag
     2881 gaaacaacga aaggaggaga gagcttctct cggtctagtc acaggttctg aaattaggaa
     2941 aagaaaccca gatgatttca aacccaaggg gaaactgtgg gctgacgatg acaggagtgt
     3001 ggattataac gagaaactca gttttgaggc cccaccaagc atctggtcga ggatagtcaa
     3061 ctttggttca ggttggggat tttgggtctc ccctagcctg ttcataacat caacccatgt
     3121 cataccccag ggtgcaaaag agttctttgg agtccccatc aaacaaattc aggtacacaa
     3181 gtcaggcgaa ttctgtcgct tgagattccc aaaaccaatc aggactgatg tgacaggcat
     3241 gatcttagaa gaaggcgcac ctgagggcac cgtagttaca ctacttatca agaggtccac
     3301 tggggaactt atgcccctag cagctaggat ggggacccat gcaactatga agatccaagg
     3361 gcgcactgtt gggggccaaa tgggcatgct tctgacaggg tccaacgcca aaagcatgga
     3421 tctgggtact acaccaggtg attgtggctg tccctacatc tacaagagag gtaatgacta
     3481 tgtggtcatt ggagtccaca cggctgccgc tcgcggagga aacactgtca tatgtgccac
     3541 ccaggggagt gaaggagagg ccacacttga aggtggtaac gacaagggga catactgtgg
     3601 tgcacccatc ctaggcccag ggagtgcccc aacacttagc accaagacca aattctggag
     3661 atcatccaca gcaccactcc cacccggcac ctatgaacca gcctatcttg gtggcaagga
     3721 ccccagagtc aagggtggcc cttcactgca gcaagtcatg agggaacagt taaagccatt
     3781 cacagagccc aggggcaaac caccaaagcc aagtgtgttg gaagctgcca agaagaccat
     3841 catcaatgtc cttgagcaaa caattgatcc acctgagaaa tggtcattcg cacaagcttg
     3901 cgcgtccctt gacaagacta cttccagcgg tcatccccac cacatgcgga aaaacgattg
     3961 ctggaacggg gaatccttca cgggcaagct ggctgaccag gcttccaaag ccaacctgat
     4021 gtatgaagaa gggaagagca tgaccccagt ctacacagct gcactcaagg atgaattggt
     4081 taaaactgac aaaatttatg gtaagatcaa gaagaggctt ctctggggct cggacttggc
     4141 gaccatgatc cgttgcgctc gagcgttcgg aggcctaatg gatgaactca aagcacactg
     4201 tgtcacactc cccattagag ttggtatgaa tatgaatgag gatggcccca tcatcttcga
     4261 gaggcattcc aggtacacat atcactatga cgctgattac tctcgatggg attcaacaca
     4321 acagagagcc gtgttggcag cagctctaga aatcctggtt aaattctccc cagaaccaca
     4381 tttggctcag gtagttgcgg aagacctcct ttctcctagc gtggtggacg tgggcgactt
     4441 cacaatatca atcaacgagg gtcttccctc tggggtgccc tgcacctctc agtggaattc
     4501 tgtcgcccat tggcttctca cactctgcgc gctctctgaa gtcacaaact tgtcccccga
     4561 caccatacag gctaactccc tcttctcttt ttatggtgat gatgaaattg ttagcacaga
     4621 cataaaattg gacccagaga aattaacagc aaagctcagg gagtatgggt tgaaaccaac
     4681 ccgccctgat aaaaccgaag gaccccttgt catctctgaa gacttgaatg gcctaacttt
     4741 cctgcggagg actgtgaccc gcgacccagc tggttggttt ggaaaactgg agcagagttc
     4801 aatactcagg caaatgtact ggactagggg ccccaaccat ggagacccat ctgaaacaat
     4861 gattccacac tcccaaaggc ctatacaatt gatgtcccta ttgggggagg ccgctcttca
     4921 cggcccagca ttctacagca aaatcagtaa attggtcatt gcagagctaa aagaaggtgg
     4981 catggatttt tacgtgccca gacaagagcc aatgttcagg tggatgagat tctcagacct
     5041 gagcacgtgg gagggcgatc gcaatctggc tcccagtttt gtgaatgaag atggcgtcga
     5101 gtgacgccaa cccatctgat gggtccgcag ccaacctcgt cccagaggtc aacaatgagg
     5161 ttatggcttt ggagcccgtt gttggtgccg ccattgcggc gcccgtagcg ggccaacaaa
     5221 atgtaattga cccctggatt agaaataatt ttgtgcaagc ccctggtgga gagtttacag
     5281 tgtcccctag aaacgctcca ggtgagatac tatggagcgc gcccttaggc cctgatttaa
     5341 atccctacct atcccatttg gctagaatgt acaatggtta tgcaggtggc tttgaagtgc
     5401 aggtaattct cgcggggaac gcgtttaccg ccgggaagat catatttgca gcagtcccac
     5461 caaattttcc aactgaaggc ttgagcccca gccaggtcac tatgttcccc catataatag
     5521 tagatgttag gcaattagaa cctgtgttga ttcccttacc cgatgttagg aataatttct
     5581 atcattataa tcaatcaaat gaccccacta ttaagttgat agcaatgttg tacacaccac
     5641 ttagggctaa taatgctggg gatgatgtct tcacggtttc ttgccgagtt ctcacgagac
     5701 catcccccga ttttgatttc atattcctag tgccacccac agttgagtca agaactaaac
     5761 cattctctgt cccaatctta actgtcgagg agatgaccaa ttcaagattt cccattcctt
     5821 tggaaaagtt gttcacgggt cccagcagtg cctttgttgt ccaaccacaa aatggcaggt
     5881 gcacgactga tggcgtgctt ctaggtacca cccaactgtc tcctgtcaac atttgcacct
     5941 tcagagggga tgtcacccat atcaaagata gtcgtaacta cacaatgaat ttggcttctc
     6001 aaaattggaa caattatgac ccaacagaag aaatcccagc ccctctagga actccagatt
     6061 ttgtggggaa gattcaaggt gtgctcactc aaaccacgaa atcgaatggc tcgacacgcg
     6121 gccacaaagc cacagtgctc actgggagca ccgactttac tccaaaactg ggtagaattc
     6181 aatttgcaac tgacacagac catgattttg aagctaacca aaatacaaaa ttcaccccag
     6241 tcggtgtcat ccaagatggt gacactgccc accaaaatga acctcaacag tggatgctcc
     6301 caagttattc aggcagggac attcataatg tgcatctggc ccccgctgta gcccccactt
     6361 ttccgggtga gcagctgctc ttcttcaggt ccactatgcc cggatgcagc gggtatccca
     6421 acatggattt ggactgtctg cttccccagg aatgggtgca gtacttctac caagaggcag
     6481 ccccagcaca atctgatgtg gctctgttaa gatttgtgaa cccagacaca ggtagggttt
     6541 tgtttgagtg caaactccat aaatcaggct atgtcacagt ggctcacact ggtcgacatg
     6601 atttggttat tccccctaat ggttacttta gatttgattc ctgggttaat cagttctaca
     6661 cgcttgcccc catgggaaat ggaacggggc gtagacgtgc ggtataatgg ctggagcttt
     6721 ctttgctgga ttggcatctg atgtccttgg ctctggactt ggttccctca tcaatgctgg
     6781 ggctggggcc atcaaccaaa aagttgaatt tgaaaataac agaaaattgc aacaagcttc
     6841 cttccaattt agcagcaatc tacaacaagc ttcctttcaa catgacaagg agatgctcca
     6901 agcacaaatt gaggccacca aaaagctaca acaggaaatg atgaaagtta agcaggcagt
     6961 gctcctagag ggtgggttct ctgagacaga tgcagcccgc ggggcaatca acgcccccat
     7021 gacaaaaact ttggactgga gtgggacaag gtactgggct cccgacgcta ggactacaac
     7081 atacaatgca ggtcgctttt ccacccccca accaccgggg gcactgccag gaagagctaa
     7141 tcttagggat gctgtccccg ctcggggttc ctctagtaaa tcttctaact cttctactgt
     7201 cacttctgtg tattcaaatc aaactgtttc aacgagactt ggttctacag ctggttctgg
     7261 taccagtgtc tcgagtctcc cgtcgactgc aaggactagg agctgggttg aggatcaaaa
     7321 taggagtttg tcacctttca tgaggggggc ccacaacata tcgtttgtca ccccaccatc
     7381 tagcagatcc tctagccaag gcacagtctc aaccgtgcct aaagaaattt tggactcctg
     7441 gactggtgct ttcaacacgc acaggcagcc tctcttcgct cacattcgta agcgagggga
     7501 gtcacgggct taatgtgaaa agacaaaatt gattattttt ctttttcttt ctttagtgtc
     7561 tttt
//