Typing tool

Complete norovirus genomes

MH218691  GII.4 Sydney
 GII.P4 New Orleans

Length: 7,550 | 3 CDS

ORF1: 5..5104
ORF2: 5085..6707
ORF3: 6707..7513
LOCUS       MH218691                7550 bp    RNA     linear   VRL 11-JUN-2018
DEFINITION  Norovirus GII isolate NORO_234_25_01_2016, complete genome.
ACCESSION   MH218691
VERSION     MH218691.1
KEYWORDS    .
SOURCE      Norovirus GII
  ORGANISM  Norovirus GII
            Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes;
            Picornavirales; Caliciviridae; Norovirus.
REFERENCE   1  (bases 1 to 7550)
  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 7550)
  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..7550
                     /organism="Norovirus GII"
                     /mol_type="genomic RNA"
                     /isolate="NORO_234_25_01_2016"
                     /host="Homo sapiens"
                     /db_xref="taxon:122929"
                     /country="United Kingdom"
                     /collection_date="25-Jan-2016"
                     /note="genotype: GII.P4_GII.4"
     gene            5..5104
                     /gene="ORF1"
     CDS             5..5104
                     /gene="ORF1"
                     /codon_start=1
                     /product="nonstructural polyprotein"
                     /protein_id="AWR17731.1"
                     /translation="MKMASNDASAAAVANSNNDTAKSSSDGVLSSMAVTFKRALGTRP
                     KQPPPREKPQRPPRPPTPELVKNVPPPPPNGEDEIVVSYSVKDGVSGLPDLSTVRQPE
                     ESNTAFSVPPLNQRENRDAKEPLTGTILEMWDGEIYHYGLYVERGLVLGVHKPPAAIS
                     LAKVELAPLSLYWRPVYTPQYLISPDTLKKLSGETFPYTAFDNNCYAFCCWVLDLNDS
                     WLSRRMIQRTTGFFRPYQDWNRKPLPTMDDSKIKKVANIFLCALSSLFTRPIKDIIGK
                     IRPLNILNILASCDWTFAGIVESLILLAELFGVFWTPPDVSAMIAPLLGDYELQGPED
                     LAVELVPVVMGGIGLVLGFTKEKIGKMLSSAASTLRACKDLGAYGLEILKLVMKWFFP
                     KKEEANELAMVRSIEDAVLDLEAIENNHMTTLLKDKDSLATYMRTLDLEEEKARKLST
                     KSASPDIVGTINALLARIAAARSLVHRAKEELSSRPRPVVLMISGRPGIGKTHLAREV
                     AKRIAASLTGDQRVGLIPRNGVDHWDAYKGERVVLWDDYGMSNPIHDALRLQELADTC
                     PLTLNCDRIENKGKVFDSDVIIITTNLANPAPLDYVNFEACSRRIDFLVYAEAPDVEK
                     AKRDFPGQPDMWKNAFSSDFSHIKLALAPQGGFDKNGNTPHGKGVMKTLTTGSLIARA
                     SGLLHERLDEFELQGPALTTFNFDRNKVLAFRQLAAENKYGLMDTMRVGKQLKDVKTM
                     PELKQALKNVSIKKCQIVYSGCTYILESDGKGNVKVDRIQSAAVQTNNELAGALHHLR
                     CARIRYYVKCVQEALYSIIQIAGAAFVTTRIAKRMNIRDLWSKPQAENTEETTSKDGC
                     PKPKDDEEFVISSDDIKTEGKKGKNKTGRGKKHTAFSSKGLSDEEYDEYKRIREERNG
                     KYSIEEYLQDRDKYYEEVAIARATEEDFCEEEEAKIRQRIFRPTRKQRKEERVSLGLV
                     TGSEIRKRNPDDFKPKGKLWADDDRNVDYNEKLSFEAPPSIWSRIVNFGSGWGFWVSP
                     SLFITSTHVIPQGAKEFFGVPIKQIQVHKSGEFCRLRFPRPIRTDVSGMILEEGAPEG
                     TVVTLLIKRSTGELMPLAARMGTHATMKIQGRTVGGQMGMLLTGSNAKSMDLGTTPGD
                     CGCPYIYKRGNDYVVIGVHTAAARGGNTVICATQGSEGEATLEGGDNKGTYCGAPILG
                     PGSAPTLSTKTKFWRSSTASLPPGTYEPAYLGGKDPRVKGGPSLQQVMREQLKPFTEP
                     RGKPPKPSVLEAAKKTIINVLEQTIDPPEKWSFAQACASLDKTTSSGHPHHMRKNDCW
                     NGESFTGKLADQASKANLMFEEGKNMTPVYTAALKDELVKTDKIYGKIKKRLLWGSDL
                     ATMIRCARAFGGLMDELKAHCVTLPIRVGMNMNEDGPIIFERHSRYTYHYDADYSRWD
                     STQQRAVLAAALEIMVKFSPEPHLAQVVAEDLLSPSVVDVGDFTISINEGLPSGVPCT
                     SQWNSIAHWLLTLCALSEVTNLSPDTIQANSLFSFYGDDEIVSTDIKLDPEKLTAKLR
                     EYGLKPTRPDKTEGPLVISEDLNGLTFLRRTVTRDPAGWFGKLEQSSILRQMYWTRGP
                     NHGDPSETMIPHSQRPIQLMSLLGEAALHGPAFYSKISKLVIAELKEGGMDFYVPRQE
                     PMFRWMRFSDLSTWEGDRNLAPSYVNEDGVE"
     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="AWR17732.1"
                     /translation="MKMASSDANPSDGSAANLVPEVNNEVMALEPVAGAAIAAPVAGQ
                     QNVIDPWIRNNFVQAPGGEFTVSPRNAPGEILWSAPLGPDLNPYLSHLARMYNGYAGG
                     FEVQVILAGNAFTAGKVIFAAVPPNFPTEGLSPSQVTMFPHIVVDVRQLEPVLIPLPD
                     VRNNFYHYNQSNDSTIKLIAMLYTPLRANNAGDDVFTVSCRVLTRPSPDFDFIFLVPP
                     TVESRTKPFSVPVLTVEEMTNSRFPIPLEKLFTGPSSAFVVQPQNGRCTTDGVLLGTT
                     QLSPVNICTFRGDVTHIAGTHNYTMNLASQNWNNYDPTEEIPAPLGTPDFVGKIQGML
                     TQTTRTDGSTRGHKATVLTGSADFAPKLGRVQFGTDTDNDFVTNQNTKFTPVGVIQDG
                     NTAHRNEPQQWVLPSYSGRNTHNVHLAPAVAPTFPGEQLLFFRSTMPGCSGYPNMDLD
                     CLLPQEWVQYFYQEAAPAQSDVALLRFVNPDTGRVLFECKLHKSGYVTVAHTGQHDLV
                     IPPNGYFRFDSWVNQFYTLAPMGNGAGRRRVV"
     gene            6707..7513
                     /gene="ORF3"
     CDS             6707..7513
                     /gene="ORF3"
                     /codon_start=1
                     /product="VP2"
                     /protein_id="AWR17733.1"
                     /translation="MAGAFFAGLASDVLGSGLGSLINAGAGVINQKVDFENNRKLQQA
                     SFQFSSNLQQASFQHDKEMLQAQIEATKKLQQEMMKVKQAVLLEGGFSETDAARGAIN
                     APMTKALDWSGTRYWAPDARTTTYNAGRFSTPQPSGALPGRANLRDAVPARGSSSKSS
                     NSSTATSVYSNQTTSTRLGSTAGSGTSVSSLPSTARTRSWVEDQSRSLSPFMRGAHNI
                     SFVTPPSSRSSSQGTVSTVPKEVLDSWTGAFNTRRQPLFAHIRSRGESRV"
ORIGIN      
        1 gtgaatgaag atggcgtcta acgacgcttc cgctgccgct gttgctaaca gcaacaacga
       61 caccgcaaaa tcttcaagtg acggagtgct ttctagcatg gctgtcactt ttaaacgagc
      121 cctcgggacg cggcctaaac aacctccccc gagggaaaaa ccacaaagac ccccacgacc
      181 acctactcca gaactggtta aaaatgttcc ccctccccca cccaatggag aggatgaaat
      241 agtggtttct tatagtgtca aagatggtgt ctccggcttg cctgaccttt ccaccgtcag
      301 gcaaccggaa gaatccaaca cggccttcag tgtccctcca ctcaatcaga gggagaatag
      361 agatgctaag gaaccactca ctggaacaat tctggaaatg tgggacgggg aaatctacca
      421 ttatggcctg tatgtggagc gaggtcttgt gctaggcgtg cacaaaccgc cagctgctat
      481 cagcctcgct aaggttgagt tagcaccact ctccttgtac tggagacctg tgtacactcc
      541 tcagtacctc atctctccag acactctcaa gaagttgtcc ggagaaacgt tcccctacac
      601 agcctttgac aacaactgct atgccttttg ttgctgggtc ctggacctaa atgactcgtg
      661 gctgagcagg agaatgatcc agagaacaac tggtttcttc aggccctacc aagactggaa
      721 taggaaacct cttcccacta tggatgactc caaaataaag aaggtggcta acatatttct
      781 gtgtgctctg tcctcactgt tcaccaggcc cataaaagat ataataggga agataaggcc
      841 tcttaacatc ctcaacatct tagcttcatg tgattggacc tttgcaggca tagtggagtc
      901 cctgatactc ttggcagaac tctttggagt tttctggaca cccccagatg tgtctgcgat
      961 gattgccccc ttacttggtg actacgagct acaagggcct gaggaccttg cagtggagct
     1021 cgtccccgtg gtgatggggg gaattggttt ggtgctagga ttcaccaaag agaagattgg
     1081 gaaaatgttg tcatcagctg cgtccacctt aagagcttgc aaagaccttg gtgcatatgg
     1141 gctagagatc ctaaagttag tcatgaagtg gttcttcccg aagaaggagg aggcaaatga
     1201 gctggctatg gtgaggtcca tcgaggatgc agtcctggac ctcgaagcaa ttgaaaacaa
     1261 tcatatgacc accttgctta aggataaaga cagtctggca acctacatga gaacacttga
     1321 ccttgaagag gagaaagcca ggaagctctc aaccaagtct gcctcacccg acatcgtggg
     1381 cacaattaac gcccttctgg cgagaatcgc tgccgcacgt tcgctggtgc atcgagcgaa
     1441 ggaggagctt tccagcagac caagacctgt ggtgttgatg atatcaggca ggccaggaat
     1501 agggaagacc cacctcgcta gggaagtggc taagagaatc gcggcctccc ttacaggaga
     1561 ccagcgtgtt ggcctcatcc cacgcaatgg cgtcgaccat tgggatgcgt acaaggggga
     1621 gagggtcgtc ctatgggacg attatggaat gagcaaccct attcacgatg ccctcaggct
     1681 gcaagaactc gctgacactt gccccctcac tctgaactgt gacaggattg aaaataaagg
     1741 aaaggtcttt gacagcgatg tcatcattat caccactaat ctggccaacc cagcaccact
     1801 ggactatgtc aactttgaag catgctcgag gcgcattgac ttcctcgtat atgcagaagc
     1861 ccctgatgtc gaaaaggcga agcgtgactt cccaggccag cctgacatgt ggaagaacgc
     1921 tttcagttct gacttctcac acataaaact agcactggcc ccacagggtg gtttcgacaa
     1981 gaacgggaac accccacacg gaaagggcgt catgaagact ctcaccactg gctcccttat
     2041 tgcccgggca tcagggctac tccacgagag gttagatgaa tttgaactgc agggcccagc
     2101 tctcaccacc ttcaacttcg atcgcaataa agtgcttgcc tttagacagc tcgctgctga
     2161 aaataaatat ggattgatgg acacaatgag ggttgggaaa cagctcaagg atgtcaaaac
     2221 catgccagaa ctcaaacaag cacttaagaa tgtctcaatc aagaagtgtc aaatagtgta
     2281 tagtggttgc acctacatac ttgaatccga tggcaagggc aatgtgaaag ttgataggat
     2341 ccaaagcgcc gccgtgcaga ccaacaatga gctggctggt gccctgcacc acttgaggtg
     2401 cgccagaatc agatactatg tcaagtgtgt ccaggaagcc ctgtattcca tcatccaaat
     2461 tgctggggct gcatttgtca ccacgcgcat tgccaagcgc atgaacatac gagacctatg
     2521 gtccaagcca caagcggaaa acacagagga gactaccagc aaggacgggt gcccaaaacc
     2581 taaggatgat gaggagtttg tcatttcatc cgacgacatc aaaactgagg gcaagaaagg
     2641 gaagaacaag actggccgtg gcaagaaaca cacagcattt tcaagcaaag gtctcagtga
     2701 tgaagagtac gatgaataca agaggatcag agaagaaagg aatggcaagt actctataga
     2761 agagtacctt caggacaggg acaaatatta tgaggaggtg gccattgcca gagcgactga
     2821 ggaagacttc tgtgaggagg aggaagccaa gatccgacaa aggattttta ggccaacaag
     2881 gaaacaacgc aaggaggaaa gagtctccct cggcttggtc acaggttctg aaattaggaa
     2941 aagaaaccca gatgacttca aacccaaggg gaaattgtgg gctgacgatg acaggaatgt
     3001 ggactacaat gagaaactca gttttgaggc cccaccaagc atttggtcaa gaatagtcaa
     3061 ctttggttca ggctggggtt tctgggtctc ccccagcttg ttcataacat caacccatgt
     3121 tataccccag ggcgcaaagg agttctttgg agtccccatc aaacaaatac aggtacacaa
     3181 gtcaggcgag ttctgtcgct tgagattccc tagaccaatc agaactgatg tatcgggcat
     3241 gatcttagaa gaaggcgcac ctgagggcac cgtggttaca ctactcatca aaaggtccac
     3301 tggggaactt atgcctctag cagctaggat ggggacccat gcgaccatga agatccaagg
     3361 gcgcactgtt gggggccaga tgggcatgct tctgacaggg tccaacgcca agagtatgga
     3421 cctgggtact acaccaggtg attgtggttg cccctacatc tacaagagag gtaatgacta
     3481 tgtggtcatt ggagtccaca cggctgccgc acgtgggggg aacactgtca tatgtgccac
     3541 ccaggggagc gaaggggagg ctacacttga gggtggcgac aacaagggga catactgtgg
     3601 tgcaccaatc ctaggcccag ggagtgcccc aacacttagc accaagacca aattctggag
     3661 atcgtccaca gcatcactcc cacctggcac ctatgaacca gcctatcttg gtggcaagga
     3721 ccccagagtc aagggtggcc cttcactgca gcaagtcatg agggaacagt tgaagccatt
     3781 cacagagccc aggggtaagc caccaaaacc aagtgtgtta gaggctgcca agaaaaccat
     3841 cattaatgtc cttgagcaaa caattgatcc acctgagaaa tggtcgttcg cacaagcttg
     3901 cgcgtccctt gacaagacca cttccagtgg tcatccgcac cacatgcgga aaaacgactg
     3961 ctggaacggg gagtccttca caggcaagct ggcagaccag gcctccaagg ccaacctgat
     4021 gtttgaagaa gggaagaaca tgaccccagt ctacacagct gcgctcaagg atgagttggt
     4081 taaaactgac aaaatttatg gtaaaatcaa gaagaggctt ctttggggct cagacttggc
     4141 gaccatgatc cggtgtgctc gagcattcgg aggcctaatg gatgaactca aagcacactg
     4201 tgttacactt cccattagag ttggcatgaa tatgaatgag gatggcccca tcatcttcga
     4261 gaggcattct aggtacacgt accactatga tgctgattac tctcgatggg attcaacaca
     4321 acagagagcc gtgttggcag cagctctaga aatcatggta aaattctccc cagaaccaca
     4381 tttggctcag gtagtcgcgg aagaccttct ttctcctagc gtggtggatg tgggcgactt
     4441 cacgatatca atcaacgagg gtcttccctc tggggtgccc tgcacctccc aatggaactc
     4501 catcgcccac tggcttctca ctctctgtgc gctctccgaa gtcacgaacc tgtctcccga
     4561 taccatacag gctaattctc tcttctcttt ttatggtgat gatgaaattg ttagcacaga
     4621 cataaaattg gacccagaga aattgacagc aaagctcaga gaatatgggt taaaaccaac
     4681 ccgccctgac aaaactgaag gacccctcgt catctctgaa gacctgaatg gcctaacttt
     4741 cctgcggaga actgtgaccc gcgacccagc tggttggttc ggaaaactgg agcaaagttc
     4801 aatactcagg caaatgtact ggactagggg tcccaaccat ggagacccat ctgaaacaat
     4861 gattccacac tcccaaagac ccatacaatt gatgtcccta ctgggggagg ccgctctcca
     4921 cggcccagca ttttacagca aaatcagcaa attggtcatt gcagagctaa aagaaggtgg
     4981 tatggatttt tacgtgccca gacaagagcc aatgttcaga tggatgagat tctcagatct
     5041 gagcacgtgg gagggcgatc gcaatctggc tcccagttat gtgaatgaag atggcgtcga
     5101 gtgacgccaa cccatctgat gggtccgcag ccaacctcgt cccagaggtc aacaatgagg
     5161 ttatggctct ggagcccgtt gctggtgccg ccattgcggc acctgtagcg ggccaacaaa
     5221 atgtaattga cccctggatt agaaacaatt ttgtacaagc ccctggtgga gagtttacag
     5281 tgtcccctag aaacgctcca ggtgaaatac tatggagcgc gcccttaggc cctgatttaa
     5341 atccctacct atcccacttg gccagaatgt ataatggtta tgcaggtggt tttgaagtgc
     5401 aggtaatcct cgcggggaac gcgttcaccg ccgggaaggt catatttgca gcagtcccac
     5461 caaattttcc aactgaaggc ttgagcccta gtcaggtcac tatgtttccc catatagtag
     5521 tagatgttag gcaactagaa cctgtgttga ttcccttacc cgatgttagg aataacttct
     5581 atcattataa tcaatcaaat gactccacca ttaagttgat agcaatgttg tatacaccac
     5641 ttagagctaa taatgctggg gacgatgtct tcacagtttc ttgccgagtt ctcacgaggc
     5701 catcccccga ttttgatttc atatttctag tgccacccac agttgagtct aggactaaac
     5761 cattctctgt tccagtctta actgttgagg agatgaccaa ctcaaggttc cccattcctt
     5821 tggaaaagtt gttcacgggt cccagcagtg cctttgttgt tcaaccacaa aacggtaggt
     5881 gtacgactga tggcgtactc ctaggcacca cccaactgtc tcctgtcaat atctgcacct
     5941 tcagagggga cgtcacccac attgcaggta ctcataacta tacaatgaat ttggcttctc
     6001 aaaattggaa taattatgac ccaacagaag agattccagc ccctctagga actccagact
     6061 ttgtggggaa gattcaaggc atgctcaccc aaaccacaag gacagatggc tcaacacgcg
     6121 gccacaaagc tacggtgctc actgggagcg ccgactttgc tccaaagctg ggcagagttc
     6181 aatttggaac tgacacagac aatgattttg taaccaacca aaacacaaaa ttcaccccag
     6241 tcggtgtcat ccaagatggt aacaccgccc accgaaatga accccaacag tgggtgctcc
     6301 caagttattc aggcagaaat actcataatg ttcacctggc ccccgctgta gcccccactt
     6361 ttccgggtga gcaacttctc ttcttcagat ccaccatgcc cggatgtagc gggtacccca
     6421 acatggattt ggactgtctg ctcccccagg aatgggtgca gtacttctac caagaggcag
     6481 ccccagcaca atctgatgtg gctctgctaa gatttgtgaa tccagacaca ggtagggttt
     6541 tgtttgagtg taaactccat aaatcaggct atgttacagt ggctcacact ggccaacatg
     6601 atttggttat cccccccaat ggctatttta ggtttgattc ctgggtcaac cagttctaca
     6661 cgcttgcccc catgggaaat ggagcggggc gtagacgtgt agtataatgg ctggagcttt
     6721 ctttgctgga ttagcatctg atgtccttgg ctctggactt ggttccctta tcaatgctgg
     6781 ggctggggtc attaatcaaa aagttgattt tgaaaacaac agaaaattgc aacaagcatc
     6841 cttccaattt agcagcaatt tacaacaggc ttcctttcaa catgacaaag aaatgctcca
     6901 agcacaaatt gaggccacca aaaagctaca acaggaaatg atgaaagtta agcaggcagt
     6961 gctcctggag ggtgggttct ctgagacaga tgcagcccgc ggggcaatca acgcccccat
     7021 gacaaaagct ttggactgga gcgggacaag gtactgggct cccgatgcta ggactacaac
     7081 atacaatgca ggccgctttt caacccctca gccatcgggg gcactgccag gaagagctaa
     7141 tcttagggac gctgtccctg ctcggggctc ctccagtaaa tcttctaact cttctactgc
     7201 tacttctgtg tattcaaatc aaaccacttc aacgagactt ggttctacag ctggttctgg
     7261 taccagtgtc tcgagcctcc cgtcaactgc aaggactagg agctgggttg aggatcaaag
     7321 taggagtttg tctcctttca tgaggggggc ccacaacata tcgtttgtca ccccaccatc
     7381 tagcagatcc tctagccaag gcacagtctc aaccgtgcct aaagaggttt tggactcctg
     7441 gactggcgct ttcaacacgc gcaggcagcc tctcttcgct cacattcgta gtcgagggga
     7501 gtcacgggtg taatgtgaaa agacaaaatt gattatcttt ctttttcttt
//