Typing tool

Complete norovirus genomes

MH218612  GII.4 Sydney
 GII.P4 New Orleans

Length: 7,564 | 3 CDS

ORF1: 5..5104
ORF2: 5085..6707
ORF3: 6707..7513
LOCUS       MH218612                7564 bp    RNA     linear   VRL 11-JUN-2018
DEFINITION  Norovirus GII isolate NORO_141_02_11_2014, complete genome.
ACCESSION   MH218612
VERSION     MH218612.1
KEYWORDS    .
SOURCE      Norovirus GII
  ORGANISM  Norovirus GII
            Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes;
            Picornavirales; Caliciviridae; Norovirus.
REFERENCE   1  (bases 1 to 7564)
  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 7564)
  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..7564
                     /organism="Norovirus GII"
                     /mol_type="genomic RNA"
                     /isolate="NORO_141_02_11_2014"
                     /host="Homo sapiens"
                     /db_xref="taxon:122929"
                     /country="United Kingdom"
                     /collection_date="02-Nov-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="AWR17494.1"
                     /translation="MKMASNDASAAAVANSNNDTAKSSSDGVLSSMAVTFKRALGARP
                     KQPPPREKPQRPPRPPTPELVKNIPPPPPNGEDEIVVSYSVKGGVSGLPDLSTVRQPE
                     ESNTAFSVPPLNQRENRDAKEPLTGTILEMWDGEIYHYGLYVERGLVLGVHKPPAAIS
                     LAKVELAPLSLYWRPVYTPQYLISPDTLKKLSGETFPYTAFDNNCYAFCCWVLDLNDS
                     WLSRRMIQRTTGFFRPYQDWNRKPLPTMDDSKIKKVANIFLCAMSSLFTRPIKDIIGK
                     IRPLNILNILASCDWTFAGIVESLILLAELFGVFWTPPDVSAMIAPLLGDYELQGPED
                     LAVELVPVVMGGIGLVLGFTKEKIGKMLSSAASTLRACKDLGAYGLEILKLIMKWFFP
                     KKEEANELAIVRSIEDAVLDLEAIENNHMTTLLKDKDSLATYMRTLDLEEEKARKLST
                     KSASPDIVGTINALLARIAAARSLVHRAKEELSSRPRPVVLMISGRPGIGKTYLAREV
                     AKRIAASLTGDQRVGLIPRNGVDHWDAYKGERVVLWDDYGMSNPIHDALRLQELADTC
                     PLTLNCDRIENKGKVFDSDVIIITTNLANPAPLDYVNFEACSRRIDFLVYAEAPDVEK
                     AKRDFPGQPDMWKNAFSSDFSHIKLALAPQGGFDKNGNTPHGKGVMKTLTTGSLIARA
                     SGLLHERLDEFELQGPALTTFNFDRNKVLAFRQLAAENKYGLMDTMRVGKQLKDVKTM
                     PELKQALKNVSIKKCQIVYSGCTYMLESDGKGNVKVDRIQSAAVQTNNELAGALHHLR
                     CARIRYYVKCVQEALYSIIQIAGAAFVTTRIAKRMNIQDLWSKPQVENTEETTSKDGC
                     PKPKDDEEFVISSDDIKTEGKKGKNKTGRGKKHTAFSSKGLSDEEYDEYKRIREERNG
                     KYSIEEYLQDRDKYYEEVAIARATEEDFCEEEEAKIRQRIFRPTRKQRKEERVSLGLV
                     TGSEIRKRNPDDFKPKGKLWADDDRSVDYNEKLSFEAPPSIWSRIVNFGSGWGFWVSP
                     SLFITSTHVIPQGAKEFFGVPIKQIQVHKSGEFCRLRFPKPIRTDVTGMILEEGAPEG
                     TVVTLLIKRSTGELMPLAARMGTHATMKIQGRTVGGQMGMLLTGSNAKSMDLGTTPGD
                     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="AWR17495.1"
                     /translation="MKMASSDANPSDGSAANLVPEVNNEVMALEPVVGAAIAAPVAGQ
                     QNVIDPWIRNNFVQAPGGEFTVSPRNAPGEILWSAHLGPDLNPYLSHLARMYNGYAGG
                     FEVQVILAGNAFTAGKVIFAAVPPNFPTEGLSPSQVTMFPHIVVDVRQLEPVLIPLPD
                     VRNNFYHYNQSNDPTIKLIAMLYTPLRANNAGDDVFTVSCRVLTRPSPDFDFIFLVPP
                     TVESRTKPFSVPVLTVEEMTNSRFPIPLEKLFTGPSSAFVVQPQNGRCTTDGVLLGTT
                     QLSPVNICTFRGDVIHITGSRNYTMNLASQNWNNYDPTEEIPAPLGAPDFVGKIQGML
                     TQTTRADGSTRGHKATVYTGSADFAPKLGRVQFETDTDHDFEANQNTKFTPVGVIQDG
                     STTHRNEPQQWVLPSYSGRNTHNVHLAPAVAPTFPGEQLLFFRSTMPGCSGYPNMDLD
                     CLLPQEWVQYFYQEAAPAQSDVALLRFVNPDTGRVLFECKLHKSGYVTVAHTGQHDLV
                     IPPNGYFRFDSWVNQFYTLAPMGNGAGRRRVV"
     gene            6707..7513
                     /gene="ORF3"
     CDS             6707..7513
                     /gene="ORF3"
                     /codon_start=1
                     /product="VP2"
                     /protein_id="AWR17496.1"
                     /translation="MAGAFFAGLASDVLGSGLGSLINAGAGAINQKVEFENNRKLQQA
                     SFQFSSNLQQASFQHDKEMLQAQIEATKKLQQEMMKVKQAMLLEGGFSETDAARGAIN
                     APMTKALDWSGTRYWAPDARTTTYNAGRFSTPQPSGALPGRANLRDAVPARGSSSKSS
                     NSSTATSVYSNQTTSTRLGSTAGSGTSVSSLPSTARTRSWVEDQSRNLSPFMRGAHNI
                     SFVTPPSSRSSSQGTVSTVPKEVLDSWTGAFNTRRQPLFAHIRKRGESRV"
ORIGIN      
        1 gtgaatgaag atggcgtcta acgacgcttc cgctgccgct gttgctaaca gcaacaacga
       61 caccgcaaaa tcttcaagtg acggagtgct ttctagcatg gctgtcactt ttaaacgagc
      121 cctcggggcg cggcctaaac agcccccccc gagggaaaaa ccacaaagac ccccacgacc
      181 acctacacca gaactggtta aaaatattcc ccccccccca cccaacggag aggatgaaat
      241 agtggtttct tatagtgtca aaggtggtgt ttccggcttg cctgaccttt ccaccgtcag
      301 gcagccggaa gaatccaaca cggccttcag tgtccctcca ctcaatcaga gggagaatag
      361 agatgctaag gaaccactca ctggaacaat tctggaaatg tgggacgggg aaatctacca
      421 ttatggcctg tatgtggagc gaggtcttgt actaggcgtg cacaaaccgc cagctgccat
      481 cagcctcgct aaggttgagt tagcaccact ctccttgtac tggagacctg tgtacactcc
      541 tcagtacctc atctctccag acactctcaa gaaattgtcc ggagaaacat tcccctacac
      601 agcctttgac aacaactgct atgccttttg ttgctgggtc ctggacctaa atgactcgtg
      661 gctgagcagg agaatgatcc agagaacaac tggtttcttc aggccctacc aagactggaa
      721 taggaaaccc cttcccacta tggatgactc caaaataaag aaggtggcta acatatttct
      781 gtgtgctatg tcctcgctat tcaccaggcc cataaaagat ataataggga agataaggcc
      841 tcttaacatc ctcaacatct tagcctcatg tgattggacc tttgcgggca tagtggagtc
      901 cctgatactc ttggcagaac tctttggagt tttctggaca cccccagatg tgtctgcgat
      961 gattgccccc ttacttggtg actacgagct acaaggacct gaggaccttg cagtggagct
     1021 cgtccccgtg gtgatggggg gaattggttt ggtgctagga ttcaccaaag agaagattgg
     1081 gaaaatgttg tcatcagctg cgtccacctt aagagcttgc aaagaccttg gtgcatatgg
     1141 gctagagatc ctaaagttaa tcatgaagtg gttcttcccg aagaaggagg aggcaaatga
     1201 gctggctata gtgaggtcca tcgaggatgc agtcctggat ctcgaagcaa ttgaaaacaa
     1261 tcatatgacc accttgctta aagataaaga cagtctggca acctacatga gaacacttga
     1321 ccttgaagag gagaaagcca ggaaactctc aaccaagtct gcctcacccg acatcgtggg
     1381 cacaatcaac gccctcctgg cgagaatcgc tgccgcacgt tctctggtgc atcgagcgaa
     1441 ggaggagctt tccagcagac caagacctgt ggtgttgatg atatcaggca ggccaggaat
     1501 agggaagacc tacctcgcta gggaagtggc taagagaatc gcagcctccc ttacaggaga
     1561 ccagcgtgtt ggtctcatcc cacgcaatgg cgtcgaccat tgggatgcgt ataaggggga
     1621 gagggtcgtc ctatgggacg attatggaat gagcaaccct attcacgatg ccctcaggct
     1681 gcaagaactc gctgacactt gccccctcac tctgaactgt gacaggattg aaaataaagg
     1741 aaaggtcttt gacagcgatg tcatcattat caccactaat ctggccaacc cagccccact
     1801 ggactatgtc aactttgaag catgctcgag gcgcattgac ttcctcgtat atgcagaagc
     1861 ccctgatgtc gaaaaggcga agcgtgactt cccaggccag cctgacatgt ggaagaacgc
     1921 tttcagttct gatttctcac acataaaact agcactggcc ccacagggtg gtttcgacaa
     1981 gaacgggaac accccacacg gaaagggcgt catgaagact ctcaccactg gctcccttat
     2041 tgcccgggca tcagggttac tccatgagag gctagatgaa tttgaactgc agggcccagc
     2101 tctcaccacc ttcaatttcg atcgcaataa agtgcttgcc tttagacagc ttgctgctga
     2161 aaataaatat ggattgatgg acacaatgag ggttgggaaa cagctcaagg atgtcaaaac
     2221 catgccagaa ctcaaacaag cactcaagaa tgtctcaatc aagaagtgtc aaatagtgta
     2281 tagtggttgc acctacatgc ttgagtctga tggcaagggc aatgtgaaag ttgacaggat
     2341 ccaaagcgcc gccgtgcaga ccaacaatga gctggctggt gccctgcacc acttgaggtg
     2401 cgccagaatc agatactatg tcaagtgtgt ccaggaagcc ctgtattcca tcatccaaat
     2461 tgctggggct gcatttgtca ccacgcgcat tgccaagcgc atgaacatac aagacctatg
     2521 gtccaagcca caagtggaaa acacagagga gactaccagc aaggacgggt gcccaaaacc
     2581 taaggatgat gaggagtttg tcatttcatc cgacgacatc aaaactgagg gcaagaaagg
     2641 gaagaacaag actggccgtg gcaagaagca cacagcattt tcaagcaaag gcctcagtga
     2701 tgaagagtac gatgaataca agaggatcag agaagaaagg aatggcaagt actctataga
     2761 agagtacctt caggacaggg acaaatatta tgaggaggtg gccattgcca gggcgactga
     2821 ggaagacttc tgtgaagagg aggaagccaa gatccgacaa aggatcttta ggccaacaag
     2881 gaaacaacgc aaggaggaaa gagtctctct cggtttagtc acaggttctg aaattaggaa
     2941 aagaaaccca gatgatttta aacccaaggg gaaattgtgg gctgacgatg acaggagtgt
     3001 ggactacaat gagaaactca gttttgaggc cccgccaagc atttggtcaa gaatagtcaa
     3061 ctttggttca ggctggggat tctgggtctc ccccagcttg ttcataacat caacccatgt
     3121 tataccccag ggcgcaaagg agttctttgg agtccccatc aaacaaatac aggtacacaa
     3181 gtcaggcgag ttctgtcgct tgagattccc taaaccaatc aggactgatg tgacgggcat
     3241 gatcttagaa gaaggcgcac ctgagggcac cgtggttaca ctactcatca aaaggtccac
     3301 tggggaactt atgcccctag cagctaggat ggggacccat gcgaccatga agatccaagg
     3361 gcgcactgtt gggggccaga tgggcatgct tctgacagga tccaacgcca agagtatgga
     3421 cctgggtact acaccaggtg attgtggctg cccctacatc tacaagagag gtaatgacta
     3481 tgtggtcatt ggagtccaca cggctgccgc acgtgggggg aacactgtca tatgtgccac
     3541 ccaggggagt gaaggagagg ctacacttga gggtggtgac aacaagggga catactgtgg
     3601 tgcaccaatc ctaggcccag ggagtgcccc aacacttagc accaagacca aattctggag
     3661 atcgtccaca gcatcactcc cacctggcac ctatgaacca gcctatcttg gtggcaagga
     3721 ccctagagtc aagggtggcc cttcactgca gcaagtcatg agggaacagt tgaagccatt
     3781 cacagagccc aggggtaagc caccaaaacc aagtgtgtta gaagctgcca agaaaaccat
     3841 cattaatgtc cttgagcaaa caattgatcc acctgagaaa tggtcgttcg cacaagcttg
     3901 cgcgtctctt gacaagacca cttccagtgg tcatccgcac cacatgcgga aaaacgactg
     3961 ctggaacggg gagtccttca caggcaagct ggcagaccag gcttccaagg ccaacctgat
     4021 gtttgaagag gggaagaaca tgaccccagt ctacacagct gcgctcaagg atgagttagt
     4081 taaaactgac aaaatttatg gtaagatcaa gaagaggctt ctttggggct cggacttggc
     4141 gaccatgatc cggtgtgctc gagcattcgg aggcctaatg gatgaactca aagcgcactg
     4201 tgtcacactt cccattagag ttggcatgaa tatgaatgag gatggcccca tcatcttcga
     4261 gaggcattcc aggtacacgt accactatga tgctgattac tctcgatggg attcaacaca
     4321 acagagagcc gtgttggcag cagctctaga aatcatggta aaattctccc cagaaccaca
     4381 tttggctcag gtagtcgctg aagaccttct ttctcctagc gtggtggacg tgggcgactt
     4441 cacaatatca atcaacgagg gtcttccctc tggggtgccc tgcacctccc aatggaactc
     4501 catcgcccac tggcttctca ctctctgtgc gctctccgaa gtcacaaacc tgtctcctga
     4561 taccatacag gctaattctc tcttctcttt ttatggtgat gatgaaattg ttagcacaga
     4621 cataaaattg gacccagaga aattgacagc aaagctcaga gaatatgggt taaaaccaac
     4681 ccgccctgac aaaactgaag gaccccttgt catctctgaa gacctgaatg gcctaacttt
     4741 cctgcggaga actgtgaccc gcgacccagc tggttggttt ggaaaactgg agcagagttc
     4801 aatactcagg caaatgtact ggactagggg tcccaaccat ggagacccat ctgagacaat
     4861 gattccacac tcccaaagac ccatacaatt gatgtcccta ctgggggagg ccgctctcca
     4921 cggcccagca ttttacagta aaattagcaa attggtcatt gcagagctaa aagaaggtgg
     4981 tatggatttt tacgtgccca gacaagagcc aatgttcaga tggatgagat tctcagatct
     5041 gagcacgtgg gagggcgatc gcaatctggc tcccagtttt gtgaatgaag atggcgtcga
     5101 gtgacgccaa cccatctgat gggtccgcag ccaacctcgt cccagaggtc aacaacgagg
     5161 ttatggctct ggagcccgtt gttggtgccg ccattgcggc acctgtagcg ggccaacaaa
     5221 atgtaattga cccctggatt agaaacaatt ttgtacaagc ccctggtgga gagtttacag
     5281 tgtcccccag aaacgctcca ggtgaaatac tatggagcgc gcacttaggc cctgatttaa
     5341 atccctacct atcccatttg gccagaatgt ataatggtta tgcaggtggt tttgaagtgc
     5401 aggtaattct cgcggggaac gcgttcaccg ccgggaaggt catatttgca gcagtcccac
     5461 caaattttcc aactgaaggc ttgagcccca gccaggtcac tatgttcccc catatagtag
     5521 tagatgttag gcaactagaa cctgtgttga ttcccttacc cgatgttagg aataatttct
     5581 atcattacaa tcaatcaaat gaccccacca ttaagttgat agcaatgttg tatacaccac
     5641 ttagggctaa taatgctggg gacgatgtct tcacagtttc ttgccgagtt ctcacgagac
     5701 catcccccga ttttgatttc atatttctag tgccacccac agttgagtct agaactaaac
     5761 cattctctgt cccagtttta actgttgagg agatgaccaa ttcaagattc cccattcctt
     5821 tggaaaagtt gttcacgggt cccagcagtg cctttgttgt tcaaccacaa aacggtaggt
     5881 gcacgactga tggcgtgctc ctaggcacca cccaattgtc tcctgtcaac atctgcacct
     5941 tcagagggga tgtcatccac attacaggta gtcgtaacta cacaatgaat ttggcttctc
     6001 aaaattggaa caattatgac ccaacagaag aaatcccagc ccctctagga gctccagatt
     6061 ttgtggggaa gattcaaggc atgctcaccc aaaccacaag ggcagatggc tcaacacgcg
     6121 gccacaaggc tacggtgtac actgggagcg ccgactttgc tccaaaactg ggcagagttc
     6181 aatttgaaac tgacacagac catgattttg aagctaacca aaacacaaag ttcaccccag
     6241 tcggtgtcat ccaagatggt agcaccaccc accgaaatga accccaacag tgggtgctcc
     6301 caagttactc aggcagaaat actcataatg ttcatctggc ccccgctgta gcccccactt
     6361 ttccgggtga gcaacttctc ttctttagat ccaccatgcc cggatgtagc gggtacccca
     6421 acatggattt ggactgtctg ctcccccagg aatgggtgca gtacttctac caagaggcag
     6481 ccccagcaca atctgatgtg gctctgctaa gatttgtgaa tccagacaca ggtagggttt
     6541 tgtttgagtg taaacttcat aaatcaggct atgttacagt ggctcacact ggccaacatg
     6601 atttggttat cccccccaat ggttatttta ggtttgattc ctgggtcaac cagttctaca
     6661 cgcttgcccc catgggaaat ggagcggggc gtagacgtgt agtataatgg ctggagcttt
     6721 ctttgctgga ttagcatctg atgtccttgg ctctggactt ggttccctta tcaatgctgg
     6781 ggctggggcc atcaaccaaa aagttgagtt tgaaaataac agaaaattgc aacaagcatc
     6841 cttccaattt agcagcaatc tacaacaggc ttcctttcaa catgacaaag aaatgctcca
     6901 agcacaaatt gaggccacca aaaagctaca acaggaaatg atgaaagtta agcaggcaat
     6961 gctcctagag ggtgggttct ctgaaacaga tgcagcccgc ggggcaatca acgcccccat
     7021 gacaaaagct ttggactgga gcgggacaag gtactgggct cctgatgcta ggactacaac
     7081 atacaatgca ggccgctttt ccacccctca accatcgggg gcactgccag gaagagctaa
     7141 tcttagggat gctgtccctg ctcggggttc ctctagtaaa tcttctaact cttctactgc
     7201 tacttcagtg tactcaaatc aaaccacttc aacgagactt ggttctacag ctggttctgg
     7261 taccagtgtc tcgagtctcc cgtcaactgc aaggactagg agctgggttg aggatcaaag
     7321 taggaatttg tctcctttca tgaggggggc ccacaacata tcgtttgtca ccccaccatc
     7381 tagcagatcc tctagccaag gcacagtctc aaccgtgcct aaagaggttt tggactcctg
     7441 gactggcgct ttcaacacgc gcaggcagcc tctcttcgct cacattcgta aacgagggga
     7501 gtcacgggtg taatgtgaaa agacaaaatt gattatcttt ctttttcttt ttttagtgtc
     7561 tttt
//