Typing tool

Complete norovirus genomes

MH218703  GII.4 Sydney
 GII.P4 New Orleans

Length: 7,552 | 3 CDS

ORF1: 5..5104
ORF2: 5085..6707
ORF3: 6707..7513
LOCUS       MH218703                7552 bp    RNA     linear   VRL 11-JUN-2018
DEFINITION  Norovirus GII isolate NORO_45_31_07_2014, complete genome.
ACCESSION   MH218703
VERSION     MH218703.1
KEYWORDS    .
SOURCE      Norovirus GII
  ORGANISM  Norovirus GII
            Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes;
            Picornavirales; Caliciviridae; Norovirus.
REFERENCE   1  (bases 1 to 7552)
  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 7552)
  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..7552
                     /organism="Norovirus GII"
                     /mol_type="genomic RNA"
                     /isolate="NORO_45_31_07_2014"
                     /host="Homo sapiens"
                     /db_xref="taxon:122929"
                     /country="United Kingdom"
                     /collection_date="31-Jul-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="AWR17767.1"
                     /translation="MKMASNDASAAAVASSNNDTAKSSSDGVLSSMAVTFKRALGARP
                     KQPPPREIPQRPPRPPTPELVKNIPPPPPNGEDEIVVSYSVKNGVSGLPDLSTVRQPE
                     ETNTAFSVPPLNQRENRDAKEPLTGTILEMWDGEIYHYGLYVERGLVLGVHKPPAAIS
                     LAKIELAPLSLYWRPVYTPQYLISPDTLKKLSGETFPYTAFDNNCYAFCCWVLDLNDS
                     WLSRRMIQRTTGFFRPYQDWNRKPLPTMDNSKIKKVADIFLCALSSLFTRPIKDIIGK
                     IRPLNILNILASCDWTFAGIVESLILLAELFGVFWTPPDVSAMIAPLLGDYELQGPED
                     LAVELVPVVMGGIGLVLGFTKEKIGKMLSSAASTLRACKDLGAYGLEILKLVMKWFFP
                     KKEEANELAMVRSIEDAVLDLEAIENNHMTTLLKDKDSLATYMRTLDLEEEKARKLST
                     KSASPDIVGTVNALLARIAAARSLVHRAKEELSSRPRPVVLMISGRPGIGKTHLAREV
                     AKRIAASLTGDQRVGLVPRNGVDHWDAYKGERVVLWDDYGMSNPIHDALRLQELADTC
                     PLTLNCDRIENKGKVFDSDVIIITTNLANPAPLDYVNFEACSRRIDFLVYAEAPEVEK
                     AKRDFPGQPDMWKNAFSSDFSHIKLALAPQGGFDKNGNTPHGKGVMKTLTTGSLIARA
                     SGLLHERLDEFELQGPALTTFNFDRNKVLAFRQLAAENKYGLMDTMRVGKQLKDVKTM
                     PELKQALKNVSIKKCQIVYSGCTYMLESDGKGNVKVDRIQSAAVQTNNELAGALHHLR
                     CARIRYYVKCVQEALYSIIQIAGAAFVTTRIAKRMNIQDLWSKPQVENTEETTSKDGC
                     PKPKDDEEFVISSDDIKTEGKKGKNKTGRGKKHTAFSSKGLSDEEYDEYKRIREERNG
                     KYSIEEYLQDRDKYYEEVAIARATEEDFCEEEEAKIRQRIFRPTRKQRKEERVSLGLV
                     TGSEIRKRNPDDFKPKGKLWADDDRNVDYNEKLSFEAPPSIWSRIVNFGSGWGFWVSP
                     SLFITSTHVIPQGAKEFFGVPIKQIQVHKSGEFCRLRFPKPIRTDVTGMILEEGAPEG
                     TVVTLLIKRSTGELMPLAARMGTHATMKIQGRTVGGQMGMLLTGSNAKSMDLGTTPGD
                     CGCPYIYKRGNDYVVIGVHTAAARGGNTVICATQGSEGEATLEGGDNKGTYCGAPILG
                     PGSAPTLSTKTKFWRSSTAPLPPGTYEPAYLGGKDPRVKGGPSLQQVMREQLKPFTEP
                     RGKPPKPSVLEAAKKTIINVLEQTIDPPEKWSFAQACASLDKTTSSGHPHHMRKNDCW
                     NGESFTGKLADQASKANLMYEEGKNMTPVYTAALKDELVKTDKIYGKIKKRLLWGSDL
                     ATMIRCARAFGGLMDELKAHCVTLPIRVGMNMNEDGPIIFERHSRYTYHYDADYSRWD
                     STQQRAVLAAALEIMVKFSPEPHLAQVVAEDLLSPSVVDVGDFTISINEGLPSGVPCT
                     SQWNSIAHWLLTLCALSEVTNLSPDTIQANSLFSFYGDDEIVSTDIKLDPEKLTAKLR
                     EYGLKPTRPDKTEGPLAISEDLDGLTFLRRTVTRDPAGWFGKLEQSSILRQMYWTRGP
                     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="AWR17768.1"
                     /translation="MKMASSDANPSDGSAANLVPEVNNEVMALEPVVGAAIAAPVAGQ
                     QNVIDPWIRNNFVQAPGGEFTVSPRNAPGEILWSAPLGPDLNPYLSHLARMYNGYAGG
                     FEVQVILAGNAFTAGKVIFAAVPPNFPTEGLSPSQVTMFPHIVVDVRQLEPVLIPLPD
                     VRNNFYHYNQSNDSTIKLIAMLYTPLRANNAGDDVFTVSCRVLTRPSPDFDFIFLVPP
                     TVESRTKPFSVPVLTVEEMTNSRFPIPLEKLFTGPSSAFVVQPQNGRCTTDGVLLGTT
                     QLSPVNICSFRGDVTHITGSHNYTMNLASQNWNNYDPTEEIPAPLGTPDFVGKIQGVL
                     TQTTRTDGSTRGHKATVYTGSADFAPKLGRVQFATDTDHDFEANQNTKFTPVGVIQDG
                     STTHRNEPQQWVLPSYSGRNTHNVHLAPAVAPTFPGEQLLFFRSTMPGCSGYPNMDLD
                     CLLPQEWVQYFYQEAAPAQSDVALLRFVNPDTGRVLFECKLHKSGYITVAYTGQHDLV
                     IPPNGYFRFDSWVNQFYTLAPMGNGTGRRRVV"
     gene            6707..7513
                     /gene="ORF3"
     CDS             6707..7513
                     /gene="ORF3"
                     /codon_start=1
                     /product="VP2"
                     /protein_id="AWR17769.1"
                     /translation="MAGAVFAGLASDVLSSGLGSLINAGAGAINQTIEFENNRKLQQA
                     SFQFSSNLQQASFQHDKEMLQAQIETTKKLQQEMMKVKQAVLLEGGFSETDAARGAIN
                     APMTKALDWSGTRYWAPDARTTTYNAGRFSTPQPSGALPGRANLRDAVPARGSSSKSS
                     NSSTVTSVYSNQTTSTRLGSTAGSGASVSSLPSTARTRSWVEDQNRNLSPFMRGAHNI
                     SFVTPPSSRSSSQGTVSTVPKEVLDSWTGAFNTRRQPLFAHIRKRGESRV"
ORIGIN      
        1 gtgaatgaag atggcgtcta acgacgcttc cgctgccgct gttgctagca gcaacaacga
       61 caccgcaaaa tcttcaagtg acggagtgct ttctagcatg gctgtcactt ttaaacgagc
      121 cctcggggcg cggcctaaac agcctccccc gagggaaata ccacaaagac ccccacgacc
      181 acctactcca gaactggtta agaatatccc ccctcccccg cccaacgggg aagatgaaat
      241 agtggtctct tatagtgtca aaaatggtgt ttccggcttg cctgaccttt ctaccgtcag
      301 gcaaccggaa gaaaccaaca cagccttcag tgtccctcca ctcaatcaga gggagaatag
      361 agatgctaag gagccactca ctggaacaat tctggaaatg tgggacgggg aaatctacca
      421 ttatggcctg tatgtggagc gaggtcttgt actaggtgtg cacaaaccgc cagccgccat
      481 cagccttgct aagattgagc tggcaccact ctccttgtac tggagacctg tgtacactcc
      541 tcagtacctc atctctccag acactctcaa gaaattgtcc ggagagacgt tcccctacac
      601 agcctttgat aacaactgtt atgccttttg ttgctgggtt ctggacctga atgactcgtg
      661 gctgagcaga agaatgatcc agagaacaac tggtttcttc agaccctatc aggactggaa
      721 taggaaaccc cttcccacta tggacaactc caagataaag aaggtagctg acatatttct
      781 gtgtgccctg tcctcgctat tcaccagacc cataaaagat ataataggga agataaggcc
      841 tcttaatatc ctcaacatct tggcctcatg tgattggacc tttgcaggta tagtggagtc
      901 cctgatactc ttggcagaac tctttggagt tttctggaca cccccagatg tgtctgcgat
      961 gattgccccc ttactcggtg actacgagct acaaggacct gaggaccttg cagtggagct
     1021 tgtccccgtg gtgatggggg gaattggttt ggtgctagga ttcaccaaag agaagattgg
     1081 gaaaatgttg tcatctgctg cgtccacttt gagggcttgc aaagaccttg gtgcatatgg
     1141 gctagagatc ctaaagttag tcatgaaatg gttcttccca aagaaggagg aggcaaatga
     1201 gctggctatg gtgagatcca tcgaggatgc agtcctggat ctcgaggcaa ttgaaaacaa
     1261 tcatatgacc accttgctta aagataaaga cagtctggca acctacatga gaacacttga
     1321 ccttgaagag gagaaagcca ggaaactctc aaccaagtct gcctcacccg acatcgtggg
     1381 tacagtcaac gccctcctgg cgagaatcgc tgccgcacgt tctctggtgc atcgagcgaa
     1441 ggaggagctt tccagcagac caagacctgt ggtgttgatg atatcaggca ggccaggaat
     1501 agggaagacc cacctcgcta gggaagtggc taagagaatc gcagcctccc ttacaggaga
     1561 tcagcgtgtg ggcctcgtcc cacgcaatgg tgtcgaccat tgggacgcgt acaaggggga
     1621 gagggtcgtc ctgtgggacg attatggaat gagcaaccct attcacgatg ccctcaggct
     1681 gcaagaactc gctgacactt gtcccctcac tctgaactgt gacaggattg aaaataaagg
     1741 aaaggtcttt gacagcgatg tcatcattat caccactaat ctggccaacc cagcaccact
     1801 ggactatgtc aactttgaag catgctcgag gcgcattgac tttctcgtgt atgcagaggc
     1861 ccctgaagtc gaaaaggcga agcgtgactt cccaggccag cctgacatgt ggaagaacgc
     1921 tttcagttct gatttctcac acataaaact agcactggcc ccacagggtg gtttcgataa
     1981 gaacgggaac accccacacg gaaagggcgt catgaagacc ctcaccactg gctctctcat
     2041 tgcccgggca tcagggctac tccatgagag gttggatgaa tttgaactgc agggcccagc
     2101 tctcaccacc ttcaacttcg atcgcaataa agtgcttgcc tttagacagc ttgctgctga
     2161 aaacaaatat ggattgatgg acacaatgag ggttgggaaa cagctcaagg atgtcaaaac
     2221 catgccagaa ctcaaacaag cactcaagaa tgtctcaatc aagaagtgcc aaatagtgta
     2281 tagtggctgc acttacatgc ttgagtctga tggcaagggc aatgtgaaag ttgacagaat
     2341 ccaaagcgcc gccgtgcaga ccaacaatga gctggctggt gccctgcacc acttgaggtg
     2401 cgccagaatc agatactatg tcaagtgtgt tcaggaagcc ctgtattcca tcatccaaat
     2461 cgctggggct gcatttgtca ccacgcgcat tgccaagcgc atgaacatac aagacctgtg
     2521 gtccaagcca caagtggaaa acacagagga gactaccagt aaggacgggt gcccaaaacc
     2581 caaggatgat gaggagttcg tcatttcatc cgacgacatc aaaaccgagg gcaagaaagg
     2641 gaagaacaag actggccgtg gcaagaagca cacagcattc tcaagcaaag gtctcagtga
     2701 tgaagagtat gatgaataca agaggattag agaagaaagg aatggcaagt actctataga
     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 aaaattgtgg gctgacgatg acaggaatgt
     3001 ggactacaat gagaaactca 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 tggggaactc atgcccctag cagctaggat ggggacccat gcgaccatga agatccaagg
     3361 gcgcactgtt 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 ggagtgcccc aacacttagc accaaaacca aattctggag
     3661 atcgtccaca gcaccacttc cacctggtac ctatgaacca gcctatcttg gtggcaagga
     3721 ccctagagtc aagggtggcc cttcactgca gcaagtcatg agggaacagt tgaagccatt
     3781 cacagagccc aggggcaagc caccaaaacc aagtgtacta gaagctgcca agaagaccat
     3841 cattaatgtc cttgagcaaa caattgatcc accagagaaa tggtcgttcg cacaagcttg
     3901 cgcgtccctt gacaagacca cttccagtgg ccatccgcac cacatgcgga aaaacgactg
     3961 ctggaacggg gagtccttca cgggcaagct ggcagaccag gcttccaagg ccaacctgat
     4021 gtatgaagaa gggaagaaca tgaccccagt ctacacagct gcgctcaagg atgagttggt
     4081 taaaactgac aaaatttatg gtaagatcaa gaagaggctt ctctggggct cggatctggc
     4141 aaccatgatt cggtgcgctc gagcattcgg aggcctaatg gatgaactca aagcgcactg
     4201 tgtcacactc cccattagag ttggcatgaa tatgaatgag gatggcccca tcatcttcga
     4261 gaggcattcc aggtacacgt accactatga tgctgactac tctcggtggg attcaacaca
     4321 acagagagcc gtgctggcag cagctctgga aatcatggtt aaattctccc cagaaccaca
     4381 tttggctcag gtagtcgcgg aagaccttct ttcccccagc gtggtggacg tgggcgactt
     4441 cacaatatca atcaatgagg gtcttccctc tggggtgccc tgcacctccc 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 gacctggatg 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 agaaacaatt ttgtacaagc ccctggtgga gagtttacag
     5281 tatcccctag aaacgctcca ggtgaaatac tatggagcgc gcccttaggc cctgatctaa
     5341 acccctacct atcccattta gccagaatgt acaatggtta tgcaggtggc tttgaagtgc
     5401 aggtaattct cgcggggaat gcgttcaccg ccgggaaggt catatttgca 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 gacgatgttt tcacagtttc ttgccgagtt ctcacaagac
     5701 catcccccga ttttgatttc atatttttgg tgccccccac agttgagtca agaactaaac
     5761 cattctctgt cccagtttta actgttgagg agatgaccaa ttcaagattc cccattcctt
     5821 tggaaaagct gttcacgggt cccagcagtg cctttgttgt tcaaccacaa aacggcaggt
     5881 gcacgactga tggcgtgctc ctaggcacca cccaactgtc tcctgtcaac atctgctcct
     5941 tcagagggga tgtcacccat atcacaggca gtcacaacta cacaatgaat ttggcttctc
     6001 aaaattggaa caattatgac ccaacagaag aaatcccagc ccctctaggg actccagact
     6061 ttgtggggaa gattcaaggc gtgctcaccc aaaccacaag gacagatggc tcaacacgcg
     6121 gccacaaagc cacagtgtac actgggagcg ccgactttgc tccaaaactg ggtagagttc
     6181 aatttgcaac tgacacagac catgattttg aagctaacca aaacacaaag ttcaccccag
     6241 tcggtgtcat ccaagatggt agcaccaccc accgaaatga acctcaacag tgggtgctcc
     6301 ctagttactc aggcagaaat actcataatg tgcatctggc ccccgctgta gcccccactt
     6361 ttccgggtga gcaacttctc tttttcagat ccaccatgcc cggatgcagc gggtacccca
     6421 acatggattt ggactgcctg ctcccccagg aatgggtgca gtacttctac caagaggcag
     6481 ccccagcaca atctgatgtg gctctgctga gatttgtgaa tccagacaca ggtagggttt
     6541 tgtttgagtg caagcttcat aaatcaggct atattacagt ggcttacact ggccaacacg
     6601 atttggttat cccccccaat ggttatttta gatttgattc ttgggtcaac cagttctaca
     6661 cgcttgcccc catgggaaat ggaacggggc gtagacgtgt agtataatgg ctggagctgt
     6721 ctttgctgga ttggcatctg atgtccttag ctctggactt ggttccctta tcaatgctgg
     6781 ggctggggcc atcaaccaaa caattgagtt tgaaaataac agaaaattgc aacaagcatc
     6841 attccaattt agcagcaatc tgcaacaggc ttcctttcaa catgacaaag agatgctcca
     6901 agcacaaatt gagactacca aaaagctaca acaggaaatg atgaaagtta agcaggcagt
     6961 gctcctagag ggtgggttct ctgagacaga tgcagcccgc ggggcaatca acgcccccat
     7021 gacaaaagct ttggactgga gcgggacaag gtactgggct cccgatgcca ggaccacaac
     7081 atacaatgca ggccgctttt ccacccctca accatcgggg gcactgccag gaagagctaa
     7141 tcttagggat gctgtccctg ctcggggttc ctccagcaaa tcttctaact cttctactgt
     7201 tacttctgtg tattcaaatc aaaccacttc aacgagactt ggttctacag ctggttctgg
     7261 tgccagtgtc tcgagcctcc cgtcaactgc aaggactagg agctgggttg aggatcaaaa
     7321 taggaatttg tcacctttca tgaggggggc ccacaatata tcgtttgtca ccccaccatc
     7381 tagcagatcc tctagccaag gcacagtctc aaccgtgcct aaagaagttt tggactcctg
     7441 gactggcgct ttcaacacgc gcaggcagcc tctcttcgct cacattcgta agcgagggga
     7501 gtcacgggtg taatgtgaaa agacaaaatt gattattctt cctttttctt ta
//