Typing tool

Complete norovirus genomes

MH218611  GII.4 Sydney
 GII.P4 New Orleans

Length: 7,513 | 3 CDS

ORF1: 5..5104
ORF2: 5085..6707
ORF3: 6707..7513
LOCUS       MH218611                7513 bp    RNA     linear   VRL 11-JUN-2018
DEFINITION  Norovirus GII isolate NORO_140_26_10_2014, complete genome.
ACCESSION   MH218611
VERSION     MH218611.1
KEYWORDS    .
SOURCE      Norovirus GII
  ORGANISM  Norovirus GII
            Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes;
            Picornavirales; Caliciviridae; Norovirus.
REFERENCE   1  (bases 1 to 7513)
  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 7513)
  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..7513
                     /organism="Norovirus GII"
                     /mol_type="genomic RNA"
                     /isolate="NORO_140_26_10_2014"
                     /host="Homo sapiens"
                     /db_xref="taxon:122929"
                     /country="United Kingdom"
                     /collection_date="26-Oct-2014"
                     /note="genotype: GII.P4_GII.4"
     gene            5..5104
                     /gene="ORF1"
     CDS             5..5104
                     /gene="ORF1"
                     /codon_start=1
                     /product="nonstructural polyprotein"
                     /protein_id="AWR17491.1"
                     /translation="MKMASNDASAAAVANSNNDTAKSSSDGVLSSMAVTFKRALGARP
                     KQPPPREKPQRPPRPPTPELVKNIPPPPPNGEDEIVVSYSVKNGVSGLPDLSTVRQPE
                     ESNTAFSVPPLNQRENRDAKEPLTGTILEMWDGEIYHYGLYVERGLVLGVHKPPAAIS
                     LAKVELAPLSLYWRPVYTPQYLISPDTLKKLSGETFPYTAFDNNCYAFCCWVLDLNDS
                     WLSRRMIQRTTGFFRPYQDWNRKPLPTMDDSKIKKVANIFLCALSSLFTRPIKDIIGK
                     IRPLNILNILASCDWTFAGIVESLILLAELFGVFWTPPDVSAMIAPLLGDYELQGPED
                     LAVELVPVVMGGIGLVLGFTKEKIGKMLSSAASTLRACKDLGAYGLEILKLVMKWFFP
                     KKEEANELAIVRSIEDAVLDLEAIENNHMTTLLKDKDSLATYMRTLDLEEEKARKLST
                     KSASPDIVGTINALLARIAAARSLVHRAKEELSSRPRPVVLMISGRPGIGKTHLAREV
                     AKRIAASLTGDQRVGLIPRNGVDHWDAYKGERVVLWDDYGMSNPIHDALRLQELADTC
                     PLTLNCDRIENKGKVFDSDVIIITTNLANPAPLDYVNFEACSRRIDFLVYAEAPEVEK
                     AKRDFPGQPDMWKNAFSSDFSHIKLALAPQGGFDKNGNTPHGKGVMKTLTTGSLIARA
                     SGLLHERLDEFELQGPALTTFNFDRNKVLAFRQLAAENKYGLMDTMRVGKQLKDVRTM
                     PELKQALKNVSIKKCQIVYSGCTYMLESDGKGNVKVDRIQSAAVQTNNELAGALHHLR
                     CARIRYYVKCVQEALYSIIQIAGAAFVTTRIAKRMNIQDLWSKPQVESTEETTSRDGC
                     PKPKDDEEFVISSDDIKTEGKKGKNKTGRGKKHTAFSSKGLSDEEYDEYKRIREERNG
                     KYSIEEYLQDRDKYYEEVAIARATEEDFCEEEEAKIRQRIFRPTRKQRKEERVSLGLV
                     TGSEIRKRNPDDFKPKGKLWADDDRSVDYNEKLSFEAPPSIWSRIVNFGSGWGFWVSP
                     SLFITSTHVIPQGAKEFFGVPIKQIQVHKSGEFCRLRFPKPIRTDVTGMILEEGAPEG
                     TVVTLLIKRSTGELMPLAVRMGTHATMKIQGRTVGGQMGMLLTGSNAKSMDLGTTPGD
                     CGCPYIYKRGNDYVVIGVHTAAARGGNTVICATQGSEGEATLEGGDNKGTYCGAPILG
                     PGSAPTLSTKTKFWRSSTASLPPGTYEPAYLGGKDPRVKGGPSLQQVMREQLKPFTEP
                     RGKPPKPSVLEAAKKTIINVLEQTIDPPEKWSFAQACASLDKTTSSGHPHHMRKNDCW
                     NGESFTGKLADQASKANLMFEEGKNMTPVYTAALKDELVKTDKIYGKIKKRLLWGSDL
                     ATMIRCARAFGGLMDELKAHCVTLPIRVGMNMNEDGPIIFERHSRYTYHYDADYSRWD
                     STQQRAVLAAALEIMVKFSPEPHLAQVVAEDLLSPSVVDVGDFTISINEGLPSGVPCT
                     SQWNSIAHWLLTLCALSEVTNLSPDTIQANSLFSFYGDDEIVSTDIKLDPEKLTAKLR
                     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="AWR17492.1"
                     /translation="MKMASSDANPSDGSAANLVPEVNNEVMALEPVVGAAIAAPVAGQ
                     QNVIDPWIRNNFVQAPGGEFTVSPRNAPGEILWSAPLGPDLNPYLSHLARMYNGYAGG
                     FEVQVILAGNAFTAGKVIFAAVPPNFPTEGLSPSQVTMFPHIVVDVRQLEPVLIPLPD
                     VRNNFYHYNQSNDPTIKLIAMLYTPLRANNAGDDVFTVSCRVLTRPSPDFDFIFLVPP
                     TVESRTKPFSVPVLTVEEMTNSRFPIPLEKLFTGPSSAFVVQPQNGRCTTDGVLLGTT
                     QLSPVNICTFRGDVTHITGSRNYTMNLASQNWNNYDPTEEIPAPLGTPDFVGKIQGML
                     TQTTRTDGSTRGHKATVYTGSADFAPKLGRVQFETDTDHDFEANQNTKFTPVGVIQDG
                     STTHRNEPQQWVLPSYSGRNTHNVHLAPAVAPTFPGEQLLFFRSTMPGCSGYPNMDLD
                     CLLPQEWVQYFYQEAAPAQSDVALLRFVNPDTGRVLFECKLHKSGYVTVAHTGQHDLV
                     IPPNGYFRFDSWVNQFYTLAPMGNGTGRRRVV"
     gene            6707..7513
                     /gene="ORF3"
     CDS             6707..7513
                     /gene="ORF3"
                     /codon_start=1
                     /product="VP2"
                     /protein_id="AWR17493.1"
                     /translation="MAGAFFAGLASDVLGSGLGSLINAGAGAINQKVEFENNRKLQQA
                     SFQFSSNLQQASFQHDKEMLQAQIEATKKLQQEMMKVKQAMLLEGGFSETDAARGAIN
                     APMTKALDWSGTRYWAPDARTTTYNAGRFSTPQPSGALPGRANLRDTVPARGSSSKSS
                     NSSTATSVYSNQTTSTRLGSTAGSGTSVSSLPSTARTRSWVEDQSRNLSPFMRGAHNI
                     SFVTPPSSRSSSQGTVSTVPKEVLDSWTGAFNTRRQPLFAHIRKRGESRV"
ORIGIN      
        1 gtgaatgaag atggcgtcta acgacgcttc cgctgccgct gttgctaaca gcaacaacga
       61 caccgcaaaa tcttcaagtg acggagtgct ttctagcatg gctgtcactt ttaaacgagc
      121 cctcggggcg cggcctaaac agccaccccc gagggaaaaa ccacaaagac ccccacgacc
      181 acctactcca gaactggtta agaatatccc ccctccccca cccaacggag aggatgaaat
      241 agtggtctct tatagtgtca aaaatggtgt ttccggcttg cctgaccttt ctaccgtcag
      301 gcaaccggaa gaatccaaca cggccttcag tgtccctcca ctcaatcaga gggagaatag
      361 agatgctaag gagccactca ctggaacaat tctggaaatg tgggacgggg aaatctacca
      421 ttatggcctg tatgtggagc gaggtcttgt actaggtgtg cacaaaccgc cagctgccat
      481 cagccttgct aaggttgagc tggcaccact ctccttgtac tggagacctg tgtacactcc
      541 tcagtacctc atctctccag acactctcaa aaaattgtcc ggagagacgt tcccctacac
      601 agcctttgat aacaactgtt atgccttttg ttgctgggtt ctggacctaa atgactcgtg
      661 gctgagtaga aggatgatcc agagaacgac tggtttcttc aggccctacc aggactggaa
      721 taggaaaccc cttcctacta tggatgactc caaaataaag aaggtagcta acatatttct
      781 gtgtgccctg tcctcgctat tcaccagacc cataaaagat ataataggga agataaggcc
      841 tcttaatatc ctcaacatct tggcctcatg tgactggacc tttgcgggta tagtggagtc
      901 cctgatactc ttggcagaac tctttggagt tttctggaca cccccagatg tgtctgcgat
      961 gattgccccc ttacttggtg actacgagct acaaggacct gaggaccttg cagtggagct
     1021 cgtccccgtg gtgatggggg gaattggttt ggtgctagga ttcaccaaag agaagattgg
     1081 gaaaatgttg tcatctgctg cgtccacttt gagagcttgt aaagaccttg gtgcatatgg
     1141 gctagagatc ctaaagttag tcatgaagtg gttcttccca aagaaggagg aggcaaatga
     1201 gctggctata gtgaggtcca tcgaggacgc agtcctggat ctcgaggcaa ttgaaaacaa
     1261 tcatatgacc accttgctta aagataaaga cagtctggca acctacatga gaacacttga
     1321 ccttgaagaa gagaaagcca ggaaactctc aaccaagtct gcctcacccg acatcgtggg
     1381 tacaatcaac gccctcctgg cgagaatcgc tgccgcacgt tctctggtgc atcgagcgaa
     1441 ggaggagctt tccagcagac caagacctgt ggtgttgatg atatcaggca ggccaggaat
     1501 agggaagacc cacctcgcta gggaagtggc taagagaatc gcagcctccc ttacagggga
     1561 tcagcgtgtg ggcctcatcc cacgcaatgg tgtcgaccat tgggatgcgt acaaggggga
     1621 gagggtcgtc ctgtgggacg attatggaat gagcaaccct attcacgatg ccctcaggct
     1681 gcaagaactc gctgacactt gtcccctcac tctgaactgt gacaggattg aaaataaagg
     1741 aaaggtcttt gacagcgatg tcatcattat caccactaac ctggccaacc cagcaccact
     1801 ggactatgtc aactttgaag catgctcgag gcgcattgac ttcctcgtgt atgcagaagc
     1861 ccctgaagtc gaaaaggcga agcgtgactt cccaggccag cctgacatgt ggaagaacgc
     1921 tttcagttct gatttctcac acataaaact agcactggcc ccacagggtg gtttcgataa
     1981 gaacgggaac accccacacg gaaagggcgt catgaagacc ctcaccactg gctcccttat
     2041 tgcccgggca tcagggctac tccatgagag gttggatgaa tttgaactgc agggcccggc
     2101 tctcaccacc ttcaatttcg accgcaataa agtgcttgcc tttagacagc ttgctgctga
     2161 aaacaaatat ggattgatgg acacaatgag ggttgggaaa cagctcaagg atgtcagaac
     2221 catgccagaa ctcaaacaag cactcaagaa tgtctcaatc aagaagtgcc aaatagtgta
     2281 tagtggttgc acttacatgc ttgagtctga tggcaagggc aatgtgaaag ttgacagaat
     2341 ccaaagtgcc gccgtgcaga ccaacaatga gctggctggt gccctacacc acttgaggtg
     2401 cgccagaatc agatactatg tcaagtgtgt ccaggaagcc ctgtattcca tcatccaaat
     2461 cgctggggct gcatttgtca ccacgcgcat tgccaagcgc atgaacatac aagacctatg
     2521 gtccaagcca caagtggaaa gcacagagga gactaccagc agggacgggt gcccaaaacc
     2581 taaggatgat gaggagttcg tcatttcatc cgacgacatc aaaactgagg gcaagaaagg
     2641 gaagaacaag actggccgtg gcaagaagca cacagcattt tcaagcaaag gcctcagtga
     2701 tgaagagtat gatgaataca agaggattag agaagaaagg aatggcaagt actctataga
     2761 agagtacctt caggacaggg acaaatacta tgaggaggtg gccattgcca gggcgactga
     2821 ggaagacttc tgtgaagagg aggaggccaa gatccggcaa aggatcttta ggccaacgag
     2881 gaaacaacgc aaggaggaaa gagtctctct tggcctggtc acaggctctg aaattaggaa
     2941 aagaaaccca gatgacttca aacccaaggg gaagttgtgg gctgacgatg acaggagtgt
     3001 ggactacaat gagaaactca gctttgaggc cccaccaagc atttggtcga gaatagtcaa
     3061 ctttggttca ggctggggat tctgggtctc ccccagtctg ttcataacat caacccatgt
     3121 cataccccaa ggcgcaaagg agttctttgg agtccccatc aaacaaatac aggtacataa
     3181 gtcaggcgag ttctgtcgct tgagattccc taaaccaatc aggactgatg tgacgggcat
     3241 gatcttggaa gaaggcgcac ctgagggcac cgtggtcaca ctactcatca aaaggtccac
     3301 tggggaactc atgcccctag cagttaggat ggggacccat gcgaccatga agatccaagg
     3361 gcgcactgtt ggaggccaga tgggcatgct tctgacaggg tccaacgcca agagcatgga
     3421 cctgggtact acaccaggtg attgtggctg cccctacatc tacaagagag gtaatgacta
     3481 tgtggtcatt ggagtccaca cggctgccgc acgtggggga aacactgtca tatgtgccac
     3541 ccaagggagt gaaggggagg ctacgcttga gggtggtgac aacaagggga catactgtgg
     3601 tgcaccaatc ctaggcccag ggagtgcccc aactcttagc accaagacca aattctggag
     3661 atcgtccaca gcatcacttc cacctggcac ctatgaacca gcctatcttg gtggcaagga
     3721 ccctagagtc aagggtggcc cttcactaca gcaagtcatg agggaacagt tgaagccatt
     3781 cacagagccc aggggcaagc caccaaaacc aagtgtatta gaagctgcca agaagaccat
     3841 cattaatgtc cttgagcaaa caattgatcc acctgagaaa tggtcgttcg cacaagcttg
     3901 cgcgtccctt gacaagacca cttccagtgg ccatccgcac cacatgcgga aaaacgactg
     3961 ctggaacggg gagtccttca cgggcaagct ggcagaccag gcttccaagg ccaacctgat
     4021 gtttgaagaa gggaagaaca tgaccccagt ctacacagct gcgctcaagg atgagttagt
     4081 taaaactgac aaaatttatg gtaagatcaa gaagaggctt ctctggggct cggatttggc
     4141 aaccatgatt cggtgtgctc gagcattcgg aggcctaatg gatgaactca aagcgcactg
     4201 tgtcacactc cccattagag ttggcatgaa tatgaatgag gatggcccca tcatcttcga
     4261 gaggcattcc aggtacacgt accactatga tgctgactac tctcggtggg attcaacaca
     4321 acagagagcc gtgttggcag cagctctaga aatcatggtt aaattctccc cagaaccaca
     4381 tttggctcag gtagtcgcgg aagaccttct ttcccccagt gtggtggacg tgggcgactt
     4441 cacaatatca atcaatgagg gtcttccctc cggggtgccc tgcacctccc aatggaactc
     4501 catcgcccac tggcttctca ctctctgtgc gctctctgaa gtcacaaacc tgtctcctga
     4561 caccatacag gctaattccc tcttctcttt ttatggtgat gatgaaattg ttagcacaga
     4621 cataaaattg gacccagaga aactgacagc aaaactcaga gaatatgggt taaaaccaac
     4681 ccgccctgac aaaactgaag gaccccttgt catctctgaa gacctgaatg gtctaacttt
     4741 cctgcggaga actgtgaccc gcgacccagc tggttggttt ggaaaactgg agcagagttc
     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 tcccagcttt gtgaatgaag atggcgtcga
     5101 gtgacgccaa cccatctgat gggtccgcag ccaacctcgt cccagaggtc aacaatgagg
     5161 ttatggctct ggagcccgtt gttggtgccg ccattgcggc acctgtagcg ggccaacaaa
     5221 atgtaattga cccctggatt agaaacaatt ttgtacaagc ccctggtgga gagtttacag
     5281 tgtcccctag aaacgctcca ggtgaaatac tatggagcgc gcccttaggc cctgatctaa
     5341 atccctacct atcccatttg gccagaatgt ataatggtta tgcaggtggt tttgaagtgc
     5401 aggtaattct cgcggggaac gcgttcaccg ccgggaaggt catatttgca gcagtcccac
     5461 caaattttcc aactgaaggc ttaagcccca gccaggtcac tatgttcccc catatagtag
     5521 tagatgttag gcaactagaa cctgtgttga ttcccttacc cgatgttagg aataatttct
     5581 accattacaa ccaatcaaat gaccccacca ttaagttgat agcaatgttg tatacaccac
     5641 ttagggctaa taatgccggg gacgatgtct tcacagtttc ttgccgagtt ctcacaagac
     5701 catcccccga ttttgatttc atatttttag tgccacccac agttgagtca agaactaaac
     5761 cattctctgt cccagtttta actgttgagg agatgaccaa ttcaagattc cccattcctt
     5821 tggaaaagtt gttcacgggt cccagcagtg cctttgttgt tcaaccacaa aacggcaggt
     5881 gcacgactga tggcgtgctc ctaggcacca cccaactgtc tcctgtcaac atctgcacct
     5941 tcagagggga tgtcacccat atcacaggca gtcgtaacta cacaatgaat ttggcttctc
     6001 aaaattggaa caattatgac ccaacagaag aaatcccagc ccctctagga actccagact
     6061 ttgtggggaa gattcaaggc atgctcaccc aaaccacgag gactgatggc tcaacacgcg
     6121 gccacaaagc cacagtgtac actgggagcg ccgactttgc tccaaaactg ggtagagtcc
     6181 aatttgaaac tgacacagac catgattttg aagctaacca aaacacaaag ttcaccccag
     6241 tcggtgtcat ccaagatggt agcaccaccc accgaaatga accccaacag tgggtgctcc
     6301 caagttactc aggcagaaat actcataatg tgcatctggc ccccgctgta gcccccactt
     6361 ttccgggtga gcaacttctc ttcttcagat ccaccatgcc cggatgcagc gggtacccca
     6421 acatggattt ggactgtctg ctcccccagg aatgggtgca gtacttctac caagaggcag
     6481 ccccagcaca atctgatgtg gctctactaa gatttgtgaa tccagacaca ggtagggttt
     6541 tgtttgagtg taagcttcat aaatcaggct atgttacagt ggcccacact ggccaacatg
     6601 atttggttat cccccccaat ggttatttta ggtttgattc ttgggtcaac cagttctaca
     6661 cgcttgcccc catgggaaat ggaacggggc gtagacgtgt agtataatgg ctggagcttt
     6721 ctttgctgga ttggcatctg atgtccttgg ctctggactt ggttccctta tcaatgctgg
     6781 ggctggggcc atcaaccaaa aagttgagtt tgaaaataac agaaaattgc aacaagcatc
     6841 cttccaattt agcagcaatc tgcaacaggc ttcctttcaa catgacaaag agatgctcca
     6901 agcacaaatt gaggccacca aaaagctaca acaggaaatg atgaaagtta agcaggcaat
     6961 gctcctagag ggtgggttct ctgagacaga tgcagcccgc ggggcaatta acgctcccat
     7021 gacaaaagct ttggactgga gcgggacaag gtactgggct cccgatgcta ggactacaac
     7081 atataatgca ggccgctttt ccacccctca accatcgggg gcactgccag gaagagctaa
     7141 tcttagggat actgtccctg ctcggggttc ctctagcaaa tcttctaact cttctactgc
     7201 tacttctgtg tactcaaatc aaaccacttc aacgagactt ggttctacag ctggttctgg
     7261 taccagtgtc tcgagcctcc cgtcaactgc aaggactagg agctgggttg aggatcaaag
     7321 taggaatttg tcacctttca tgaggggggc ccacaacata tcgtttgtca ccccaccatc
     7381 tagcagatcc tctagccaag gcacagtctc aaccgtgcct aaagaggttt tggactcctg
     7441 gactggcgct ttcaacacgc gcaggcagcc tctcttcgct cacattcgta aacgagggga
     7501 gtcacgggtg taa
//