Typing tool

Complete norovirus genomes

MH218714  GII.4 Sydney
 GII.P4 New Orleans

Length: 7,513 | 3 CDS

ORF1: 5..5104
ORF2: 5085..6707
ORF3: 6707..7513
LOCUS       MH218714                7513 bp    RNA     linear   VRL 11-JUN-2018
DEFINITION  Norovirus GII isolate NORO_58-1_13_10_2015, complete genome.
ACCESSION   MH218714
VERSION     MH218714.1
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_58-1_13_10_2015"
                     /host="Homo sapiens"
                     /db_xref="taxon:122929"
                     /country="United Kingdom"
                     /collection_date="13-Oct-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="AWR17800.1"
                     /translation="MKMASNDASAAAVANSNNDTAKTSSDGVLSSMAVTFKRALGTRP
                     KQPPPREIPQRPPRPPTPELVKNIPPPPPNGEDEIVVSYSAKNGVSGLPDLSTVRQPE
                     ETNTAFSVPPLNQRENRDAKEPLTGTILEMWDGEIYHYGLYVERGLVLGVHKPPAAIS
                     LAKVELAPLSLYWRPVYTPQYLISPDTLKRLSGETFPYTAFDNNCYIFCCWVLDLNDS
                     WLSRRMIQRTTGFFRPYQDWNRKPLPTMDSSKIKKVADIFLCALSSLFTRPIKDLIGK
                     IRPLNILNILASCDWTFAGIVESLILLAELFGIFWTPPDVSAMIAPLLGDYELQGPED
                     LAVELVPVVMGGIGLVLGFTKEKIGKMLSSAASTLRACKDLGAYGLEILKLVMKWFFP
                     KKEEANELAMVRSIEDAILDLEAIENNHMTTLLKDKDSLATYMRTLDLEEEKARKLST
                     KSASPDIVGTINALLARIAAARSLVHRAKEELSSRPRPVVLMISGRPGIGKTHLAREV
                     AKRIAASLTGDQRVGLIPRNGVDHWDAYKGERVVLWDDYGMSNPIHDALRLQELADTC
                     PLTLNCDRIENKGKVFDSDVIIITTNLANPAPLDYVNFEACSRRIDFLVYAEAPEVEK
                     AKRDFPGQPDMWKNAFSSDFSHIKLSLAPQGGFDKNGNTPHGKGVMKTLTTGSLIARA
                     SGLLHERLDEFELQGPALTTFNFDRNKVLAFRQLAAENKYGLMDTMRVGKQLKDVKTM
                     PELKQALKNVSIKKCQIVYSGSTYMLESDGKGNVKVDKVQSAAVQTNNELAGALHHLR
                     SARIRYYVKCVQEALYSIIQIAGAAFVTTRIAKRMNIQDLWSKPQVENTEETTSKDGC
                     PKPRDDEEFVISSDDIKTEGKKGKNKTGRGKKHTAFSSKGLSDEEYDEFKRIREERNG
                     KYSIEEYLQDRDKYYEEVAIARATEEDFCEEEEAKIRQRIFRPTRKQRKEERVSLGLV
                     TGSEIRKRNPDDFKPKGKLWADDDRNVDYNERLSFEAPPSIWSRIVNFGSGWGFWVSP
                     SLFITSTHVIPQGAKEFFGVPIKQIQVHKSGEFCRLRFPKPIRTDVTGMILEEGAPEG
                     TVVTLLIKRSTGELMPLAARMGTHATMKIQGRAVGGQMGMLLTGSNAKSMDLGTTPGD
                     CGCPYIYKRGNDYVVIGVHTAAARGGNTVICATQGSEGEATLEGGDNKGTYCGAPILG
                     PGSAPTLSTKTKFWRSSTAPLPPGTYEPAYLGGKDPRVKGGPSLQQVMREQLKPFTEP
                     RGKPPKPSVLEAAKKTIINVLEQTIDPPEKWSFAQACASLDKTTSSGHPHHMRKNDCW
                     NGESFTGKLADQASKANLMYEEGKNMTPVYTAALKDELVKTDKIYGKIKKRLLWGSDL
                     ATMIRCARAFGGLMDELKAHCVSLPIRVGMNMNEDGPIIFERHSRYTYHYDADYSRWD
                     STQQRAVLAAALEIMVKFSPEPQLAQVVAEDLLSPSVVDVGDFTISINEGLPSGVPCT
                     SQWNSIAHWLLTLCALSEVTNLSPDTIQANSLFSFYGDDEIVSTDIKLDPEKLTAKLR
                     EYGLKPTRPDKTEGPLAISEDLNGLTFLRRTVTRDPAGWFGKLEQSSILRQMYWTRGP
                     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="AWR17801.1"
                     /translation="MKMASSDANPSDGSAANLVPEVNNEVMALEPVVGAAIAAPVAGQ
                     QNVIDPWIRNNFVQAPGGEFTVSPRNAPGEILWSAPLGPDLNPYLSHLARMYNGYAGG
                     FEVQVILAGNAFTAGKVIFAAVPPNFPTEGLSPSQVTMFPHIVVDVRQLEPVLIPLPD
                     VRNNFYHYNQSNDSTIKLIAMLYTPLRANNAGDDVFTVSCRVLTRPSPDFDFIFLVPP
                     TVESRTKPFSVPVLTVEEMTNSRFPIPLEKLFTGPSSAFVVQPQNGRCTTDGVLLGTT
                     QLSPVNICTFRGDVTHITGSHNYTLNLASQNWNDYDPTEEIPAPLGTPDFVGKIQGVL
                     TQTTRTDGSTRGHKATVYTGSADFAPKLGRVQFATDTDHDFEANQNTKFTPVGVIQDG
                     STTHRNEPLQWVLPSYSGRSTHNVHLAPAVAPTFPGEQLLFFRSTMPGCSGYPNTDLD
                     CLLPQEWVQHFYQEAAPAQSDVALLRFVNPDTGRVLFECKLHKSGYVTVAHTGQHDLV
                     IPPNGYFRFDSWVNQFYTLAPMGNGTGRRRVV"
     gene            6707..7513
                     /gene="ORF3"
     CDS             6707..7513
                     /gene="ORF3"
                     /codon_start=1
                     /product="VP2"
                     /protein_id="AWR17802.1"
                     /translation="MAGAVLAGLASDVLSSGLGSLINAGAGAINQTIDFENNRKLQQA
                     SFQFSSNLQQASFQHDKEMLQAQVETTKKLQQEMMKIKQAMLLEGGFSETDAARGAIN
                     APMTKALDWSGTRHWAPDARTTTYNAGRFSTPQPSGALPGRANLRDAAPARGSSSKSS
                     NSSTVSSVYSNQTTSTRLGSTAGSGASVSSLPSTARTRSWVEDQSRNLSPFMRGAHNI
                     SFVTPPSSRSSSQGTVSTVPKEVLDSWTGAFNTRRQPLFAHIRRRGESRV"
ORIGIN      
        1 gtgaatgaag atggcgtcta acgacgcttc cgctgccgct gttgccaaca gcaacaacga
       61 caccgcaaaa acttcaagtg acggagtgct ttctagcatg gctgtcactt ttaaacgagc
      121 cctcgggacg cggcctaaac agcctccccc gagggaaata ccacaaaggc ccccacgacc
      181 acccactcca gaactggtta agaacatccc ccctccccca cccaacgggg aagatgaaat
      241 agtggtctct tatagtgcca aaaatggtgt ttccggcttg cctgaccttt ctaccgtcag
      301 gcaaccggaa gaaaccaaca cagccttcag tgtccctcca ctcaatcaga gggagaatag
      361 agatgctaag gagccactca ctgggacaat tctggaaatg tgggacgggg aaatctacca
      421 ttatggcctg tatgtggagc gaggtcttgt actaggtgtg cacaaaccgc cagctgccat
      481 cagccttgct aaggttgagt tggcaccact ctccttgtac tggagacctg tgtacacccc
      541 tcagtacctc atctctccag acaccctcaa gagattgtcc ggagagacgt tcccctacac
      601 agcctttgat aacaactgtt atatcttttg ctgctgggtt ctggacctaa atgactcgtg
      661 gttgagcaga aggatgatcc agagaacaac tggtttcttc aggccctatc aggactggaa
      721 taggaaaccc cttcctacta tggatagctc caaaataaag aaggtggctg acatatttct
      781 gtgtgccctg tcctcgctat tcaccagacc cataaaagat ttaataggga agataaggcc
      841 tcttaatatc ctcaacatct tggcctcatg tgattggacc tttgcgggca tagtggagtc
      901 cctgatactc ttggcagaac tctttggaat tttctggaca cccccagatg tgtctgcgat
      961 gattgccccc ttactcggtg actacgagct gcaaggacct gaggaccttg cagtggagct
     1021 agtccccgtg gtgatggggg gaattggttt ggtgctagga ttcaccaaag agaagattgg
     1081 gaaaatgttg tcatctgctg cgtccacttt gagagcttgt aaagaccttg gtgcatatgg
     1141 gctagagatc ctaaagttag tcatgaaatg gttcttccca aagaaggagg aggcaaatga
     1201 gctggctatg gtgaggtcca tcgaggatgc aatcctggat ctcgaggcaa ttgaaaacaa
     1261 tcacatgacc accttgctta aagataaaga cagtctggca acctacatga gaacacttga
     1321 tcttgaagag gagaaagcca ggaaactctc aaccaagtct gcctcacccg acatcgtggg
     1381 tacaatcaac gccctcctgg cgagaatcgc cgccgcacgt tctctggtgc atcgagcgaa
     1441 ggaggagctt tccagcagac caagacctgt ggtgctgatg atatcaggca ggccaggaat
     1501 agggaagacc cacctcgcca gggaagtggc caagagaatc gcagcctccc ttacaggaga
     1561 tcagcgtgtg ggcctcatcc cacgcaacgg tgtcgaccat tgggatgcgt acaaggggga
     1621 gagggtcgtc ctctgggacg attatggaat gagtaaccct attcacgatg ccctcaggct
     1681 gcaagaactc gctgacactt gtcccctcac tctgaactgt gacaggattg aaaataaagg
     1741 aaaggtcttt gatagcgatg tcatcattat caccactaat ctggccaacc cagcaccact
     1801 ggactatgtc aactttgaag catgctcgag gcgcattgac tttctcgtgt atgcagaggc
     1861 ccctgaagtc gaaaaggcga agcgtgactt cccaggccag cctgacatgt ggaagaacgc
     1921 tttcagttct gatttctcac acataaaact atcactggcc ccacagggtg gtttcgacaa
     1981 gaacgggaac accccacacg gaaagggcgt catgaagacc ctcaccactg gctcccttat
     2041 tgcccgggca tcagggcttc tccatgagag gttggatgaa tttgaattgc agggcccagc
     2101 tctcaccacc ttcaacttcg atcgcaataa agtgcttgcc tttagacagc ttgctgctga
     2161 aaacaaatat ggattgatgg acacaatgag ggttgggaaa cagctcaagg atgtcaaaac
     2221 catgccagaa ctcaaacaag cactcaagaa tgtctcaatc aagaagtgcc aaatagtgta
     2281 tagtggcagc acttacatgc ttgagtccga tggcaagggc aatgtgaaag ttgacaaagt
     2341 ccaaagcgcc gctgtgcaga ccaacaatga gctggctggt gccctgcacc acttgaggtc
     2401 cgccagaatc agatactatg tcaagtgtgt tcaggaagcc ctgtattcca tcatccaaat
     2461 cgctggggct gcatttgtca ccacgcgcat tgccaagcgc atgaacatac aagacctgtg
     2521 gtccaagcca caagtggaaa acacagagga gaccaccagt aaggacgggt gcccaaaacc
     2581 cagggatgat gaggagttcg tcatttcatc cgacgacatc aagactgagg gcaagaaagg
     2641 gaagaacaag actggccgtg gcaagaagca cacagcattc tcaagcaaag gtctcagtga
     2701 tgaagagtat gatgaattca agaggattag agaagaaagg aatggcaagt actccataga
     2761 agagtacctt caggacagag acaaatacta tgaggaggtg gccattgcca gggcgactga
     2821 ggaagacttc tgtgaagagg aggaggccaa gatccggcaa aggatcttta ggccaacaag
     2881 gaaacaacgc aaggaggaaa gagtctctct tggtctggtc acaggctctg aaattaggaa
     2941 aagaaaccca gatgacttca aacccaaggg gaaattgtgg gctgacgatg acaggaatgt
     3001 ggactacaat gagagactca gctttgaggc cccaccaagc atttggtcga gaatagtcaa
     3061 ctttggttca ggctggggat tctgggtctc ccccagtctg ttcataacat caacccatgt
     3121 cataccccag ggcgcaaagg agttctttgg agtccccatc aaacaaatac aggtacacaa
     3181 gtcaggcgag ttctgtcgct tgagattccc taaaccaatc aggactgatg tgacgggcat
     3241 gatcttggaa gaaggcgcac ctgagggcac cgtggtcaca ctactcatca agaggtccac
     3301 cggggagctc atgcccctag cagctaggat ggggacccat gcgaccatga agatccaagg
     3361 gcgcgctgtt ggaggccaga tgggcatgct tctgacagga tccaacgcca agagcatgga
     3421 cctgggtaca acaccaggtg attgtggctg cccctacatc tacaagagag gtaatgacta
     3481 tgtggtcatt ggagtccaca cggctgccgc acgtggggga aacactgtca tatgtgccac
     3541 ccaagggagt gaaggggagg ctacacttga gggtggtgac aacaagggga catactgtgg
     3601 tgcaccaatc ctaggcccag ggagtgctcc aacacttagc accaaaacca aattctggag
     3661 atcgtccaca gcaccacttc cacctggtac ctatgaacca gcctatcttg gtggcaagga
     3721 ccctagagtc aagggtggcc cttcactgca gcaagtcatg agggaacagt tgaagccatt
     3781 cacagagccc aggggcaagc caccaaaacc aagtgtacta gaagctgcca agaaaaccat
     3841 catcaatgtc cttgagcaaa caattgatcc accagagaaa tggtcgttcg cacaagcttg
     3901 cgcgtccctt gacaagacca cttccagtgg ccatccgcac cacatgcgga aaaacgactg
     3961 ctggaacggg gagtccttca cgggcaagct ggcagaccag gcttccaagg ccaacctgat
     4021 gtatgaagaa gggaagaaca tgactccagt ctacacagct gcgctcaagg atgagttggt
     4081 taaaactgac aaaatttatg gtaagatcaa gaagaggctt ctctggggct cggatctggc
     4141 aaccatgatt cggtgtgctc gagcattcgg aggcctaatg gatgagctca aagcgcactg
     4201 tgtctctctc cccatcagag ttggcatgaa catgaacgag gatggcccca tcatcttcga
     4261 gaggcattcc aggtacacgt accactatga tgctgactac tctcggtggg attcaacaca
     4321 acagagagcc gtgctggcag cagctctgga aatcatggtt aaattctccc cagaaccaca
     4381 attggctcag gtagtcgcgg aagacctcct ttcccccagc gtggtggacg tgggcgactt
     4441 cacaatatca attaatgagg gtcttccctc tggggtgccc tgcacctctc aatggaactc
     4501 catcgcccac tggcttctca ctctctgtgc gctctctgaa gtcacaaacc tgtctcctga
     4561 taccatacag gctaattccc tcttctcttt ttatggtgat gatgaaattg ttagcacaga
     4621 cataaaattg gacccagaga aattgacagc aaaactcaga gaatatgggt taaaaccaac
     4681 ccgccctgac aaaactgaag gaccccttgc catctctgaa gacctgaatg gcctaacttt
     4741 cctgcggaga actgtgaccc gcgacccagc tggttggttt ggaaaactgg agcagagttc
     4801 aatactcagg caaatgtact ggactagggg tcccaaccat ggagacccat ctgaaacaat
     4861 gattccacac tcccaaagac ccatacaatt gatgtcccta ctaggggagg ccgctctcca
     4921 cggcccagca ttttacagca aaatcagcaa attggtcatt gcagagctaa aagaaggtgg
     4981 tatggatttt tacgtgccca gacaagagcc aatgttcaga tggatgagat tctcagatct
     5041 gagcacgtgg gagggcgatc gcaatctggc tcccagtttt gtgaatgaag atggcgtcga
     5101 gtgacgccaa cccatctgat gggtccgcag ccaacctcgt cccagaggtc aacaatgagg
     5161 ttatggctct ggagcccgtt gttggtgccg ctattgcggc acctgtagcg ggccaacaaa
     5221 atgtaattga cccctggatt agaaataatt ttgtacaagc ccctggtgga gagtttacag
     5281 tatcccctag aaacgctcca ggtgaaatac tatggagcgc gcccttaggc cctgatctaa
     5341 acccctacct atcccattta gccagaatgt acaatggtta tgcaggtggc tttgaagtgc
     5401 aggtaattct cgcggggaac gcgttcaccg ccgggaaggt tatatttgca gcagtcccac
     5461 caaattttcc aactgaaggc ttaagcccca gccaggtcac catgttcccc catatagtgg
     5521 tagatgttag gcaactagaa cctgtgttga ttcccttacc cgatgttagg aataatttct
     5581 atcattataa ccaatcaaat gactccacca ttaagctgat agcaatgttg tatacaccac
     5641 ttagggctaa taatgctggg gacgatgtct tcacagtttc ttgccgagtc cttacaagac
     5701 catcccccga ttttgatttc atatttttgg tgccccccac agttgagtca agaactaaac
     5761 cattctctgt cccagtttta actgttgagg agatgaccaa ttcaagattc cccattcctc
     5821 tggaaaagct gttcacgggt cccagcagtg cctttgttgt tcaaccacaa aacggcaggt
     5881 gcacgactga tggcgtgctc ctaggcacca cccaactgtc tcctgtcaac atctgcacct
     5941 tcagagggga tgtcactcat atcacaggca gtcacaacta cacattgaat ttggcttctc
     6001 aaaattggaa cgattatgac ccaacagaag aaattccagc ccctctagga actccagact
     6061 ttgtggggaa gattcaaggc gtgctcaccc aaaccacaag gacagatggc tcaacacgcg
     6121 gccacaaagc cacagtgtac actgggagtg ccgactttgc tccaaaactg ggtagagttc
     6181 aatttgcaac tgacacagac catgattttg aagctaacca aaacacaaag ttcaccccag
     6241 tcggtgtcat ccaagatggc agcaccaccc accgaaatga acctctacag tgggtgctcc
     6301 ctagttactc aggcagaagt actcataatg tgcatctggc ccccgctgtg gcccccactt
     6361 ttccgggtga gcaacttctc tttttcagat ccaccatgcc cggatgcagc gggtacccca
     6421 acacggattt ggactgcctg ctcccccagg aatgggtgca gcacttctac caagaggcag
     6481 ccccagcaca atctgatgtg gctttgctga gatttgtgaa tccagacaca ggtagggttt
     6541 tgtttgagtg caagctccat aaatcaggct atgttacagt ggctcacact ggccaacacg
     6601 atttggttat cccccccaat ggttacttta ggtttgattc ttgggtcaac cagttctaca
     6661 cgcttgcccc catgggaaat ggaacggggc gtagacgtgt agtataatgg ctggagctgt
     6721 ccttgctgga ttggcatctg atgtccttag ctctggactt ggttccctca tcaatgctgg
     6781 ggctggggcc atcaaccaaa caattgattt tgaaaataac agaaaattgc aacaagcatc
     6841 attccaattt agcagcaatc tgcaacaggc ttcctttcaa catgacaaag agatgctcca
     6901 agcacaagtt gagaccacca aaaagctaca acaggaaatg atgaaaatta agcaggcaat
     6961 gctcctagag ggtgggttct ctgagacaga tgcagcccgc ggggcaatca acgcccccat
     7021 gacaaaagct ttggactgga gcgggacaag gcactgggct cccgatgcca ggaccacaac
     7081 atacaatgca ggccgctttt ccacccctca accatcgggg gcactgccag ggagagctaa
     7141 tcttagggat gctgcccccg ctcggggttc ctccagcaaa tcttctaact cttctactgt
     7201 ctcttctgtg tattcaaatc aaaccacttc aacgagactt ggttctacag ctggttctgg
     7261 tgccagtgtc tcgagcctcc cgtcaactgc aaggactagg agctgggttg aggatcaaag
     7321 taggaatttg tcacctttca tgaggggggc tcacaatata tcgtttgtca ccccaccatc
     7381 tagcagatcc tccagccaag gcacagtctc aaccgtgcct aaagaggttt tggactcctg
     7441 gactggcgct ttcaacacgc gcaggcagcc tctcttcgct cacattcgta ggcgagggga
     7501 gtcacgggtg taa
//