Typing tool

Complete norovirus genomes

MH218710  GII.4 Sydney
 GII.P4 New Orleans

Length: 7,517 | 3 CDS

ORF1: 5..5104
ORF2: 5085..6707
ORF3: 6707..7513
LOCUS       MH218710                7517 bp    RNA     linear   VRL 11-JUN-2018
DEFINITION  Norovirus GII isolate NORO_53_19_07_2014, complete genome.
ACCESSION   MH218710
VERSION     MH218710.1
KEYWORDS    .
SOURCE      Norovirus GII
  ORGANISM  Norovirus GII
            Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes;
            Picornavirales; Caliciviridae; Norovirus.
REFERENCE   1  (bases 1 to 7517)
  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 7517)
  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..7517
                     /organism="Norovirus GII"
                     /mol_type="genomic RNA"
                     /isolate="NORO_53_19_07_2014"
                     /host="Homo sapiens"
                     /db_xref="taxon:122929"
                     /country="United Kingdom"
                     /collection_date="19-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="AWR17788.1"
                     /translation="MKMASNDASAAAVANSNNDTEKSSSDGVLSSMAVTFKRALGARP
                     KQPPPREKPQRPPRPPTPELVKNIPPPPPNGEDEIVVSYSVKNGVSGLPDLSTVRQPE
                     ESNTAFSVPPLNQRENRDAKEPLTGTILEMWDGEIYHYGLYVERGLVLGVHKPPAAIS
                     LAKVELAPLSLYWRPVYTPQYLISPDTLKKLSGETFPYTAFDNNCYAFCCWVLDLNDS
                     WLSRRMIQRTTGFFRPYQDWNRKPLPTMDDSKIKKVANIFLCALSSLFTRPIKDIIGK
                     IRPLNILNILASCDWTFAGIVESLILLAELFGVFWTPPDVSAMIAPLLGDYELQGPED
                     LAVELVPVVMGGIGLVLGFTKEKIGKMLSSAASTLRACKDLGAYGLEILKLVMKWFFP
                     KKEEANELAMVRSIEDAVLDLEAIENNHMTTLLKDKDSLATYMRTLDLEEEKARKLST
                     KSASPDIVGTINALLARIAAARSLVHRAKEELSSRPRPVVLMISGKPGIGKTHLAREV
                     AKRIAASLTGDQRVGLIPRNGVDHWDAYKGERVVLWDDYGMSNPIHDALRLQELADTC
                     PLTLNCDRIENKGKVFDSDVIIITTNLANPAPLDYVNFEACSRRIDFLVYAEAPEVEK
                     AKRDFPGQPDMWKNAFSSDFSHIKLALAPQGGFDKNGNTPHGKGVMKTLTTGSLIARA
                     SGLLHERLDEFELQGPALTTFNFDRNKVLAFRQLAAENKYGLMDTMRVGKQLKDVRTM
                     PELKQALKNVSIKKCQIVYSGCTYMLESDGKGNVKVDRIQSTAVQTNNELAGALHHLR
                     CARIRYYVKCVQEALYSIIQIAGAAFVTTRIAKRMNIQDLWSKPQVENTEEATSKDGC
                     PKPKDDEEFVISSDDIKTEGKKGKNKTGRGKKHTAFSSKGLSDEEYDEYKRIREERNG
                     KYSIEEYLQDRDKYYEEVAIARATEEDFCEEEEAKIRQRIFRPTRKQRKEERVSLGLV
                     TGSEIRKRNPDDFKPKGKLWADDDRSVDYNEKLSFEAPPSIWSRIVNFGSGWGFWVSP
                     SLFITSTHVIPQGAKEFFGVPIKQIQVHKSGEFCRLRFPKPIRTDVTGMILEEGAPEG
                     TVVTLLIKRSTGELMPLAVRMGTHATMKIQGRTVGGQMGMLLTGSNAKSMDLGTTPGD
                     CGCPYIYKRGNDYVVIGVHTAAARGGNTVICATQGSEGEATLEGGDNKGTYCGAPILG
                     PGSAPTLSTKTKFWRSSTAPLPPGTYEPAYLGGKDPRVKGGPSLQQVMREQLKPFTEP
                     RGKPPKPSVLEAAKKTIINVLEQTIDPPEKWTFAQACASLDKTTSSGHPHHIRKNDCW
                     NGESFTGKLADQASKANLMFEEGKNMTPVYTAALKDELVKTDKIYGKIKKRLLWGSDL
                     ATMIRCARAFGGLMDELKAHCVTLPIRVGMNMNEDGPIIFERHSRYTYHYDADYSRWD
                     STQQRAVLAAALEIMVKFSPEPHLAQVVAEDLLSPSVVDVGDFTISINEGLPSGVPCT
                     SQWNSIAHWLLTLCALSEVTNLSPDTIQANSLFSFYGDDEIVSTDIKLDPEKLTAKLR
                     EYGLKPTRPDKTEGPLAISEDLNGLTFLRRTVTRDPAGWFGKLEQSSILRQMYWTRGP
                     NHGDPSETMIPHSQRPIQLMSLLGEAALHGPTFYSKISKLVIAELKEGGMDFYVPRQE
                     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="AWR17789.1"
                     /translation="MKMASSDANPSDGSAANLVPEVNNEVMALEPVVGAAIAAPVAGQ
                     QNVIDPWIRNNFVQAPGGEFTVSPRNAPGEILWSAPLGPDLNPYLSHLARMYNGYAGG
                     FEVQVILAGNAFTAGKVIFAAVPPNFPTEGLSPSQVTMFPHIVVDVRQLEPVLIPLPD
                     VRNNFYHYNQSNDPTIKLIAMLYTPLRANNAGDDVFTVSCRVLTRPSPDFDFIFLVPP
                     TVESRTKPFSVPVLTVEEMTNSRFPIPLEKLFTGPSSAFVVQPQNGRCTTDGVLLGTT
                     QLSPVNICTFRGNVAHTTGSHNYIMNLASQNWNNYDPTEEIPAPLGTPDFVGKIQGVL
                     TQTTRADGSTRGHKAIVLTGSADFTPKLGRVQFQTDTDNDFETNQNTKFTPVGVIQNG
                     GTTHQNEPQQWELPSYSGRDTHNVHLAPAVAPTFPGEQLLFFRSTVPGCSGYPNMDLD
                     CLLPQEWVQYFYQEAAPAQSDVALLRFVNPDTGRVLFECKLHKSGYVTVAHTGRHDLV
                     IPPNGYFRFDSWVNQFYTLAPMGNGTGRRRVV"
     gene            6707..7513
                     /gene="ORF3"
     CDS             6707..7513
                     /gene="ORF3"
                     /codon_start=1
                     /product="VP2"
                     /protein_id="AWR17790.1"
                     /translation="MAGAFFAGLASDVLGSGLGSLINAGAGAINQKVEFENNRKLQQA
                     SFQFGSNLQQASFQHDKEMLQAQIEATKKLQQEMMKIKQAMLLEGGFSETDAARGAIN
                     APMTKALDWSGTRYWAPDARTTTYNAGRFSTPQPSGALPGRVNLRDAVPARGSSSKSS
                     NPSIATSVYSNQTTSTRLGSTAGSGTSVSSLPSTARTRSWVEDQSRNLSPFMRGAHNI
                     SFVTPPSSRSSSQGTVSTVPKEVLDSWTGAFNTRRQPLFAHLRKRGESRV"
ORIGIN      
        1 gtgaatgaag atggcgtcta acgacgcttc cgctgccgct gttgccaata gcaacaacga
       61 caccgaaaaa tcttcaagtg acggagtgct ttctagcatg gctgtcactt tcaaacgagc
      121 cctcggggcg cggcctaaac agcctccccc gagggaaaaa ccacaaagac ccccacgacc
      181 acctactcca gaactggtta agaatatccc ccctccccca cccaacggag aggatgaaat
      241 agtggtctct tatagtgtca aaaatggtgt ttccggcttg cctgaccttt ctaccgtcag
      301 gcaaccggaa gaatccaaca cagctttcag tgtccctcca ctcaatcaga gggagaatag
      361 agatgctaag gagccactca ctggaacaat cctggaaatg tgggacgggg aaatctacca
      421 ttatggcttg tatgtggagc gaggtcttgt actaggtgtg cacaaaccgc cagctgccat
      481 cagccttgct aaggttgagc tggcaccact ctccttgtac tggagacctg tgtacacccc
      541 tcagtacctc atctctccag acactctcaa gaaattgtcc ggagagacgt tcccctacac
      601 agcctttgac aacaactgtt atgccttttg ttgctgggtt ctggacctaa atgactcgtg
      661 gcttagtaga agaatgatcc agagaacaac tggtttcttc aggccctatc aggactggaa
      721 taggaaaccc cttcccacta tggatgactc caaaataaag aaggtagcta acatatttct
      781 gtgtgcccta tcctcgctat tcaccagacc cataaaagat ataataggga agataaggcc
      841 tctcaatatc ctcaacatct tagcctcatg tgattggacc tttgcgggta tagtggagtc
      901 cctgatactc ttggcagaac tctttggagt tttctggaca cccccagatg tgtctgcgat
      961 gattgccccc ttacttggtg actacgagct acaaggacct gaggaccttg cagtggagct
     1021 cgtccccgtg gtgatggggg gaattggtct ggtgctagga ttcaccaaag agaagattgg
     1081 gaagatgttg tcatctgccg cgtccacttt gagagcttgc aaagaccttg gtgcatatgg
     1141 gctagagatc ctaaagttag tcatgaagtg gttctttcca aagaaggagg aggcaaatga
     1201 gctggctatg gtgaggtcca tcgaggatgc agtcctggat ctcgaggcaa ttgaaaacaa
     1261 tcatatgacc accttgctta aggataaaga cagtctggcg acctacatga gaacacttga
     1321 ccttgaagag gagaaagcca ggaaactctc aaccaagtct gcctcacccg acatcgtggg
     1381 tacaatcaac gccctcctgg cgagaatcgc tgccgcacgt tctctggtgc atcgagcgaa
     1441 ggaggagctt tccagcagac caagacctgt ggtgttgatg atatcaggca agccaggaat
     1501 agggaagacc cacctcgcta gggaagtggc taagagaatc gcagcctccc ttacaggaga
     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 caccactaat ctggccaacc cagcaccact
     1801 ggactatgtc aactttgaag catgctcgag gcgcattgac tttctcgtgt 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 agggcccagc
     2101 tctcaccacc ttcaacttcg atcgcaataa 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 ccaaagcacc gccgtgcaga ccaacaatga gctggctggt gccctgcacc acttgaggtg
     2401 cgccagaatc agatactatg tcaagtgtgt tcaggaagcc ctgtattcca tcatccaaat
     2461 cgctggggct gcatttgtca ccacacgcat tgccaagcgc atgaacatac aagacctatg
     2521 gtccaagcca caagtggaaa acacagagga ggctaccagc aaggacgggt 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 gccatcgcca gggcgactga
     2821 ggaagacttc tgtgaagagg aggaggccaa gatccggcaa aggatcttta ggccaacaag
     2881 gaaacaacgc aaggaggaaa gagtctctct tggtctggtc acaggctctg aaattaggaa
     2941 aagaaaccca gatgacttca aacccaaggg gaaattgtgg gctgacgatg acaggagtgt
     3001 ggactacaat gagaaactca gctttgaggc cccaccaagc atttggtcga gaatagtcaa
     3061 ctttggctca ggctgggggt tctgggtctc ccccagtctg ttcataacat caacccatgt
     3121 cataccccag ggcgcaaagg agttctttgg agtccccatc aaacaaatac aggtacacaa
     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 tctgacagga tccaacgcca agagcatgga
     3421 tctgggcact acaccaggtg attgtggctg cccctacatc tacaagagag gtaatgacta
     3481 tgtggttatt ggagtccaca cggctgccgc acgcggggga aacactgtca tatgtgccac
     3541 ccaagggagt gaaggggagg ctacacttga gggtggcgac aacaagggga catactgtgg
     3601 tgcaccaatc ctaggcccag ggagtgcccc aacacttagc accaagacca aattctggag
     3661 atcgtccaca gcaccacttc cacctggcac ctatgaacca gcctatcttg gtggcaagga
     3721 ccctagagtc aagggtggcc cttcattgca gcaagtcatg agggaacagt tgaagccatt
     3781 tacagagccc aggggcaagc caccaaaacc aagtgtatta gaagctgcca agaagaccat
     3841 cattaatgtc cttgagcaaa caattgaccc acctgagaaa tggacgtttg cacaagcttg
     3901 cgcgtccctt gacaagacca cttccagtgg ccatccgcac cacatacgga aaaacgactg
     3961 ctggaacggg gagtccttca cgggcaagct ggcagaccag gcttccaagg ccaacttgat
     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 gagacattcc aggtacacgt accactatga tgctgactac tctcggtggg attcaacaca
     4321 acagagagcc gtgctggcag cagctctaga 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 gacctgaatg gcctaacttt
     4741 cctgcggaga actgtgactc gcgacccagc tggttggttt ggaaaactgg agcagagttc
     4801 aatactcagg caaatgtact ggactagggg tcccaaccat ggagacccat ctgaaacaat
     4861 gattccacac tcccaaagac ccatacaatt gatgtcccta ctgggggagg ccgctctcca
     4921 cggcccaaca 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 ccattgcggc acctgtagcg ggccaacaaa
     5221 atgtaattga cccctggatt agaaacaatt ttgtacaagc ccctggtgga gagtttacag
     5281 tatcccctag aaacgctcca ggtgaaatac tatggagcgc gcccttaggc cctgatctaa
     5341 atccctacct atcccatttg gccagaatgt acaatggtta tgcaggtggt tttgaagtgc
     5401 aggtaattct cgcggggaac gcgttcaccg ccgggaaggt catatttgca gcagtcccac
     5461 caaattttcc aactgaaggc ttaagcccca gccaggtcac tatgttcccc catatagtag
     5521 tagatgttag gcaactagaa cctgtgttga ttcccttacc cgatgttagg aataatttct
     5581 atcactataa tcaatcaaat gaccccacca ttaaattgat agcaatgttg tatacaccac
     5641 ttagggctaa taatgctggg gacgatgtct tcacagtttc ttgccgagtt ctcacaagac
     5701 catcccccga ttttgatttc atatttttgg 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 tcagagggaa tgtcgcccat actacaggca gtcacaacta cataatgaat ttggcttctc
     6001 aaaattggaa caattatgac ccaacagaag aaatcccagc ccctctagga actccagact
     6061 ttgtggggaa gattcaaggc gtgctcaccc aaaccacaag ggcagatggc tcaacacgcg
     6121 gccacaaagc tatagtgctc actgggagcg ccgattttac tccaaaactg ggtagagttc
     6181 aatttcaaac tgacacagac aatgattttg aaactaacca aaacacgaag ttcaccccag
     6241 tcggtgtcat ccaaaatggt ggcaccaccc accaaaatga acctcaacag tgggagctcc
     6301 ctagttattc aggcagagat actcataatg tgcatctggc ccccgctgta gcccccactt
     6361 ttccgggtga gcaacttctc ttcttcagat ccaccgtacc cggatgcagc gggtacccca
     6421 acatggattt ggactgtctg ctcccccagg aatgggtgca gtacttctac caagaggcag
     6481 ccccagcaca atctgatgtg gctctgctga gatttgtgaa tccagacaca ggtagggttt
     6541 tgtttgagtg taagcttcat aaatcaggct atgttacagt ggctcacact ggccgacatg
     6601 atttggttat cccccccaat ggttatttta ggtttgattc ttgggtcaac cagttctaca
     6661 cgcttgcccc catgggaaat ggaacggggc gtagacgtgt agtgtaatgg ctggagcttt
     6721 ctttgctgga ttagcatctg atgtccttgg ctctggactt ggttccctta tcaatgctgg
     6781 ggctggggcc atcaaccaaa aagttgagtt tgaaaataac agaaaattgc aacaagcatc
     6841 attccaattt ggcagcaatc tgcaacaggc ttcctttcaa catgacaaag agatgctcca
     6901 agcacaaatt gaggccacca aaaagctaca acaggaaatg atgaaaatta aacaggcaat
     6961 gctcctagag ggtgggttct ctgagacgga tgcagcccgc ggggcaatta acgcccccat
     7021 gacaaaagct ttggactgga gcgggacaag gtactgggct cccgatgcta ggactacaac
     7081 atacaatgca ggccgctttt ccacccctca accatcaggg gcactgccag gaagagttaa
     7141 tcttagggat gctgtccctg ctcggggttc ctccagcaaa tcctctaacc cttctattgc
     7201 tacttctgtg tattcaaatc aaactacttc aacgagactt ggttctacag ctggttctgg
     7261 taccagtgtc tcgagcctcc cgtcaactgc aaggactagg agctgggttg aggatcaaag
     7321 taggaatttg tcacctttca tgaggggggc ccacaacata tcgtttgtca ccccaccatc
     7381 tagcagatcc tccagccaag gcacagtctc aaccgtgcct aaagaggttt tggactcctg
     7441 gactggcgct ttcaacacgc gcaggcagcc tctcttcgct caccttcgta agcgagggga
     7501 gtcacgggtg taatgtg
//