Typing tool

Complete norovirus genomes

MH218707  GII.4 Sydney
 GII.P31

Length: 7,517 | 3 CDS

ORF1: 5..5104
ORF2: 5085..6707
ORF3: 6707..7513
LOCUS       MH218707                7517 bp    RNA     linear   VRL 11-JUN-2018
DEFINITION  Norovirus GII isolate NORO_49_15_10_2014, complete genome.
ACCESSION   MH218707
VERSION     MH218707.1
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_49_15_10_2014"
                     /host="Homo sapiens"
                     /db_xref="taxon:122929"
                     /country="United Kingdom"
                     /collection_date="15-Oct-2014"
                     /note="genotype: GII.Pe_GII.4"
     gene            5..5104
                     /gene="ORF1"
     CDS             5..5104
                     /gene="ORF1"
                     /codon_start=1
                     /product="nonstructural polyprotein"
                     /protein_id="AWR17779.1"
                     /translation="MKMASNDASAAAVANSNNDIAKSSSDGVFSNMAVTFKRALGARP
                     KQPPPKEIPPRPPRPPTPELVKKIPPPPPNGEDELVVSYSAKDGVSGLPELTTVRQPE
                     ETNTAFSVPPLNQRESRDAKEPLTGTIIEMWDGEIYHYGLYVERGLILGVHKPPAAIS
                     LAKVELAPLSLFWRPVYTPQYLISPDTLRRLHGESFPYTAFDNNCYAFCCWVLDLNDS
                     WLSRRMIQRTTGFFRPYQDWNRKPLPTMDDSKLKKVANIFLCTLSSLFTRPIKDIIGK
                     LKPLNILNILATCDWTFAGIVESLILLAELFGVFWTPPDVSAMIAPLLGDYELQGPED
                     LAVELVPIVMGGIGLVLGFTKEKIGKMLSSAASTLRACKDLGAYGLEILKLVMKWFFP
                     KKEEANELAMVRSIEDAVLDLEAIENNHMTTLLKDKDSLATYMRTLDLEEEKARKLST
                     KSASPDIVGTINSLLARIAAARSLVHRAKEELSSRPRPVVVMISGRPGIGKTHLAREL
                     AKKIAASLTGDQRVGLIPRNGVDHWDAYKGERVVLWDDYGMSNPIHDALRLQELADTC
                     PLTLNCDRIENKGKVFDSDAIIITTNLANPAPLDYVNFEACSRRIDFLVYAEAPEVEK
                     AKRDFPGQPDMWKNAFSPDFSHIKLSLAPQGGFDKNGNTPHGKGVMKTLTTGSLIARA
                     SGLLHERLDEYELQGPALTTFNFDRNKILAFRQLAAENKYGLMDTMRVGKQLKDVKTM
                     SDLKQALKNIAIKKCQIVYNGGTYTLEADGEGSVKVDKVQSATVQTNNELAGALHHLR
                     CARIRYYVKCVQEALYSIIQIAGAAFVTTRIAKRMNIQNLWSKPQVEDTEETANKDGC
                     LKPKDDEEFVVSSDDIKTEGKKGKNKSGRGKKHTAFSSKGLSDEEYDEYKRIREERNG
                     KYSIEEYLQDRDRYYEEVAIARATEEDFCEEEEAKIRQRIFRPTRKQRKEERASLGLV
                     TGSEIRKRNPEDFKPKGKLWADDDRSVDYNEKLNFEAPPSIWSRIVNFGSGWGFWVSP
                     SLFITSTHVIPQGAKEFFGVPIKQIQIHKSGEFCRLRFPKPIRTDVTGMILEEGAPEG
                     TVATLLIKRPTGELMPLAARMGTHATMKIQGRTVGGQMGMLLTGSNAKSMDLGTTPGD
                     CGCPYIYKRGNDYVVIGVHTAAARGGNTVICATQGSEGEATLEGGDSRGTYCGAPILG
                     PGSAPKLSTKTKFWRSSTTPLPPGTYEPAYLGGKDPRVKGGPSLQQVMRDQLKPFTEP
                     RGKPPRPNVLEAAKKTIINVLEQTIDPPQKWSFAQACASLDKTTSSGHPHHMRKNDCW
                     NGESFTGKLADQASKANLMFEEGKNMTPVYTGALKDELVKTDKVYGKVKKRLLWGSDL
                     ATMIRCARAFGGLMDELKAHCVTLPVRVGMNMNEDGPIIFEKHSRYRYHYDADYSRWD
                     STQQRDVLAAALEIMVKFSPEPHLAQIVAEDLLSPSVMDVGDFQISISEGLPSGVPCT
                     SQWNSIAHWLLTLCALSEVTDLSPDIIQANSLFSFYGDDEIVSTDIKLDPEKLTAKLK
                     EYGLKPTRPDKTEGPLVISEDLDGLTFLRRTVTRDPAGWFGKLEQSSILRQMYWTRGP
                     NHGDPFETMIPHSQRPIQLMSLLGEAALHGPAFYSKISKLVIAELKEGGMDFYVPRQE
                     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="AWR17780.1"
                     /translation="MKMASSDANPSDGSAANLVPEVNNEVMALEPVVGAAIAAPVAGQ
                     QNVIDPWIRNNFVQAPGGEFTVSPRNAPGEILWSAPLGPDLNPYLSHLARMYNGYAGG
                     FEVQVILAGNAFTAGKVIFAAVPPNFPTEGLSPSQVTMFPHIVVDVRQLEPVLIPLPD
                     VRNNFYHYNQSNDPTIKLIAMLYTPLRANNAGDDVFTVSCRVLTRPSPDFDFIFLVPP
                     TVESRTKPFSVPVLTVEEMTNSRFPIPLEKLFTGPSSAFVVQPQNGRCMTDGVLLGTT
                     QLSPVNICTFRGDVTHITGSRNYTMNLASQNWSNYDPTEEIPAPLGTPDFVGKIQGVL
                     TQTTRTDGSTRGHKATVYTGSADFAPKLGRVQFETDTDHDFEANQNTKFTPVGVIQDG
                     STTHRNEPQQWVLPSYSGRNTPNVHLAPAVAPTFPGEQLLFFRSTMPGCSGYPNMDLD
                     CLLPQEWVQYFYQEAAPAQSDVALLRFVNPDTGRVLFECKLHKSGYVTVAHTGQHDLV
                     IPPNGYFRFDSWVNQFYTLAPMGNGTGRRRAL"
     gene            6707..7513
                     /gene="ORF3"
     CDS             6707..7513
                     /gene="ORF3"
                     /codon_start=1
                     /product="VP2"
                     /protein_id="AWR17781.1"
                     /translation="MAGAFFAGLASDVLGSGLGSLINAGAGAINQKVEFENNRKLQQA
                     SFQFSSNLQQASFQHDKEMLQAQIEATKRLQQEMMKVKQAMLLEGGFSEADAARGAIN
                     APMTKALDWSGTRYWAPDARTTTYNAGRFSTPQPSGALPGRANLRDAVPARGSSSKSS
                     NSSTATSVYSNQTTSTRLGSTAGSGTSVSSFPSTARTRSWVEDQSRNLSPFMRGAHNI
                     SFVTPPSSRSSSQGTVSTVPKEILDSWTGAFNTRRQPLFAHIRKRGESRA"
ORIGIN      
        1 gtgaatgaag atggcgtcta acgacgcttc cgctgccgct gttgccaaca gcaacaacga
       61 catcgcaaaa tcttcaagtg acggtgtgtt ttctaacatg gctgtcactt ttaagcgggc
      121 cctcggggcg cggcctaaac agccgccccc gaaggaaata ccacccagac ccccgcgacc
      181 acccacacca gaattggtca aaaagatccc tcctccccca cccaacgggg aagatgaact
      241 agtggtctct tacagcgcca aagatggcgt ttccggactg cctgagctca ccactgtcag
      301 acaaccggaa gaaaccaaca cggcgtttag tgtcccccca ctcaaccaaa gggagagtag
      361 ggacgccaag gagccactaa ctggaacaat cattgaaatg tgggatggag aaatctacca
      421 ttacggcctg tacgtggaac gaggtcttat acttggtgtg cataagccac cggcagccat
      481 tagccttgcc aaggtcgagc tagcaccgct ctctttattc tggagacctg tatacacccc
      541 ccagtatctc atctccccag acactcttag gagattacat ggagagtcat tcccctacac
      601 tgcatttgat aacaattgct acgccttttg ttgttgggta ttagacctga acgactcatg
      661 gctaagcagg agaatgattc agagaacaac aggcttcttt aggccgtacc aggattggaa
      721 caggaaaccc ctccccacta tggatgattc caaattaaag aaggtagcca acatattctt
      781 gtgcactttg tcttcactat tcaccaggcc cattaaggac ataataggga agttgaaacc
      841 tcttaacatc cttaacattc tggctacatg tgattggacc ttcgcaggca tagtggaatc
      901 cttaatactc ttggcagaac tctttggagt tttctggaca cccccagatg tgtctgcgat
      961 gatcgccccc ttgctaggtg attatgaact gcaaggacct gaggaccttg cagtggaact
     1021 ggtcccaata gtgatggggg ggataggttt ggtgctagga tttaccaaag agaaaatcgg
     1081 aaagatgcta tcatccgctg catccacttt aagagcttgt aaagaccttg gtgcatacgg
     1141 actggaaatc ttaaaattgg tcatgaagtg gttcttccca aagaaagagg aagcaaatga
     1201 actggctatg gtgagatcca tcgaggatgc agtgctagat ctcgaggcaa ttgaaaacaa
     1261 ccacatgacc accctactca aagacaaaga cagcttggca acctacatga gaacccttga
     1321 ccttgaggag gagaaagcca gaaaactctc aaccaaatct gcttcacccg atattgtggg
     1381 cacaatcaac tctcttctgg caagaatcgc tgctgcacgt tccctagtgc atcgggcgaa
     1441 agaagagctc tccagcaggc cgagacctgt cgttgtgatg atatcgggaa gaccagggat
     1501 agggaaaact caccttgcca gggagctggc caagaagatc gcggcctccc tcacagggga
     1561 ccagcgtgtg ggtcttatcc cacgcaatgg tgtcgaccac tgggacgcat acaagggcga
     1621 aagagttgtc ctttgggacg actatggaat gagcaacccc atccatgatg ccctcaggtt
     1681 gcaggagctt gctgacactt gccccctcac gctaaattgt gacagaattg agaacaaagg
     1741 gaaagtcttt gacagtgatg ccataattat caccaccaat ctggccaacc cagcaccact
     1801 ggattatgtc aactttgaag cgtgctcgag acgcattgat ttcctcgtgt acgcagaagc
     1861 ccctgaggtg gagaaggcaa agcgcgactt cccaggtcaa cctgacatgt ggaagaacgc
     1921 tttcagtcct gacttctcac acataaaact gtcattggct ccacagggtg gttttgacaa
     1981 aaacggcaac accccgcatg gaaaaggggt catgaagacc ctcaccactg gctccctcat
     2041 cgcccgagca tcagggttac tccatgagag gctagatgaa tatgaactgc aaggcccagc
     2101 cctcaccact ttcaactttg accgcaacaa gatacttgct tttagacagc ttgctgctga
     2161 aaacaagtat gggctgatgg acacaatgag agttggaaaa cagctcaagg atgtcaagac
     2221 catgtcagac ctcaaacaag cactcaagaa catcgcgatc aagaagtgcc agatagtgta
     2281 caatggtggc acctacacac ttgaggctga tggcgagggt agtgtgaaag ttgacaaagt
     2341 gcaaagtgcc actgtgcaga ccaacaatga actagccggt gccctacacc acctaaggtg
     2401 cgctagaatc agatactatg ttaagtgcgt ccaggaggca ctgtattcca tcatccaaat
     2461 cgctggggcc gcattcgtca ccacgcgcat cgctaagcgc atgaatatac agaatctctg
     2521 gtccaagcca caggtggaag acacagaaga gacggccaac aaagatggtt gcctaaagcc
     2581 caaagatgat gaagagtttg tcgtctcatc cgacgacatc aaaactgagg gcaagaaagg
     2641 gaagaacaag tccggccgtg gcaagaagca cacagccttt tcaagtaaag ggctcagtga
     2701 tgaggagtac gatgagtaca agagaatcag agaagaaagg aatggtaagt actccataga
     2761 agagtacctt caggacagag acaggtacta cgaggaggtg gccattgcca gggcaaccga
     2821 agaggacttc tgtgaagaag aagaggccaa aatccggcag agaattttca gaccaacacg
     2881 gaaacaacgc aaagaagaga gggcctctct cggcttggtc acaggctctg aaatcaggaa
     2941 gagaaaccca gaagacttca aacccaaggg aaagctgtgg gctgatgatg acagaagtgt
     3001 tgactacaat gagaaactca actttgaggc cccaccaagc atctggtcgc ggatagtcaa
     3061 ctttggttca ggctggggct tctgggtctc ccccagtctg tttataacat caacccatgt
     3121 cataccccaa ggtgcaaaag agttcttcgg agtccctatc aagcaaatcc agatacacaa
     3181 gtcaggtgaa ttctgccggt tgagattccc gaagccaatc agaactgatg tgacgggcat
     3241 gattctagaa gaaggtgcgc ccgaggggac cgtggccaca ctgctcatca agagaccaac
     3301 tggagagctc atgcctctgg cagccagaat ggggacccat gcaaccatga aaattcaggg
     3361 gcgcacagtt ggagggcaaa tgggtatgct cctgacagga tccaacgcca agagtatgga
     3421 cctaggcaca acaccaggcg actgcggctg cccctacatc tacaagaggg ggaatgacta
     3481 cgtggtcata ggggtccata cggccgctgc ccgtggagga aacactgtca tatgtgccac
     3541 ccaggggagt gagggagaag ccacacttga aggaggtgac agcagaggga catactgtgg
     3601 cgcaccaatc ttgggcccag ggagcgctcc gaagctcagt accaagacta agttttggag
     3661 atcatccaca acaccactcc cacctggcac ctacgaacca gcctacctcg gtggcaaaga
     3721 ccctagagtc aaaggtggcc cttcattgca acaagttatg agggaccagc tgaagccatt
     3781 cacagaaccc agaggcaaac caccaagacc aaatgtgttg gaagctgcca agaaaaccat
     3841 catcaatgtc cttgagcaaa caattgatcc accccaaaaa tggtcatttg cgcaagcttg
     3901 tgcatccctt gacaaaacca cctccagcgg ccacccgcac cacatgcgga aaaacgactg
     3961 ttggaatggg gagtccttca caggaaaatt ggctgatcaa gcctccaagg ccaacctaat
     4021 gtttgaagag ggaaagaaca tgactccagt ctacacaggt gcacttaaag atgagttggt
     4081 aaagaccgat aaagtttatg gtaaggtcaa gaagaggctt ctgtggggtt cagacctggc
     4141 gaccatgata cggtgcgccc gagcttttgg aggccttatg gatgaactca aggcacactg
     4201 tgtcacactt cctgtcagag ttggtatgaa catgaatgag gatggcccca tcatctttga
     4261 gaagcactcc agatatagat accactatga tgctgattat tcccggtggg actcaacaca
     4321 acaaagggat gtgctagcag cagcactaga aatcatggtt aagttctctc cagaaccaca
     4381 cctggcccag atagttgcag aagacctcct ttcccctagc gtgatggatg taggtgactt
     4441 tcaaatatca ataagtgagg gtctcccctc tggggtgcct tgtacctccc agtggaattc
     4501 catcgcccac tggctcctca ctctgtgcgc actctctgaa gtcacggacc tgtcccctga
     4561 tatcattcag gccaactccc ttttctcctt ctatggtgat gatgagattg taagcacaga
     4621 cataaagttg gacccagaga agctgacagc aaaactcaag gagtacgggc tgaaaccaac
     4681 ccgccccgac aaaactgaag gaccccttgt tatctctgaa gacctggatg gcctgacatt
     4741 cctccggaga actgtgaccc gtgatccagc tggctggttt ggaaaattgg aacaaagttc
     4801 aattctcagg caaatgtact ggaccagggg tcccaaccat ggagacccat ttgaaacaat
     4861 gataccacac tcccaaagac ccatacaatt gatgtccttg ctgggcgagg ctgcactcca
     4921 cggcccggca ttctatagca aaattagcaa attagtcatt gcagagttga aggaaggtgg
     4981 catggacttt tacgtaccca gacaagaacc aatgttcaga tggatgagat tctcagatct
     5041 gagcacgtgg gagggcgatc gcaatctggc tcccagtttt gtgaatgaag atggcgtcga
     5101 gtgacgccaa cccatctgat gggtccgcag ccaacctcgt cccagaggtc aacaatgagg
     5161 ttatggctct ggagcccgtt gttggcgccg ccattgcggc acctgtagcg ggccaacaaa
     5221 atgtaattga cccctggatt agaaataatt ttgtacaagc ccctggtgga gagtttacag
     5281 tatcccctag aaacgctcca ggtgaaatac tatggagcgc gcccttgggc cctgatctaa
     5341 atccctacct atcccatttg gccagaatgt ataatggtta tgcaggtggt tttgaagtgc
     5401 aagtaattct cgcggggaac gcgttcaccg ccgggaaggt catatttgca gcagtcccac
     5461 caaattttcc aactgaaggc ttgagtccca gccaggttac tatgtttccc catatagtag
     5521 tagatgttag gcaattagaa cctgtgttga ttcccttacc cgatgttagg aataatttct
     5581 atcattataa tcaatcaaat gaccccacca ttaagttgat agcaatgttg tatacaccac
     5641 ttagggctaa taatgctggg gatgatgtct tcacagtttc ttgccgagtt ctcacgagac
     5701 catcccccga ttttgatttc atatttctag tgccacccac agttgagtca agaactaaac
     5761 cattctctgt cccagtttta actgttgagg agatgaccaa ttcaagattc cccattcctt
     5821 tggagaagtt gttcacgggt cccagcagtg cctttgttgt ccaaccacaa aacggtaggt
     5881 gcatgactga tggcgtgctc ctaggcacca cccaactgtc tcctgtcaac atctgcacct
     5941 tcagaggaga tgtcacccat atcacaggta gtcgtaacta cacaatgaat ttggcttctc
     6001 aaaattggag caattatgac ccaacagaag aaatcccagc tcctctagga actccagatt
     6061 ttgtggggaa gattcaaggc gtgctcaccc aaaccacaag gacagatggc tcaacacgcg
     6121 gccacaaagc cacagtgtac actgggagcg ccgactttgc tccaaaactg ggtagagtcc
     6181 aatttgaaac tgacacagac catgattttg aagctaacca aaacacaaag ttcaccccag
     6241 ttggtgtcat ccaagatggt agcaccaccc accgaaatga accccaacag tgggtgctcc
     6301 caagttactc aggcagaaat actcctaatg tgcatttggc ccccgctgta gctcccactt
     6361 ttccgggtga gcaacttctc ttcttcagat ccaccatgcc cggatgcagc gggtacccca
     6421 acatggattt ggactgcctg ctcccccagg aatgggtgca gtacttctac caagaggcag
     6481 ccccagcaca atctgatgtg gctctgttaa gatttgtgaa tccagacaca ggtagggttt
     6541 tgtttgagtg taagcttcat aaatcaggct atgttacagt ggctcacact ggccaacatg
     6601 atttggttat cccccccaat ggttatttta ggtttgattc ctgggtcaac cagttttaca
     6661 cgcttgcccc catgggaaat ggaacggggc gtagacgtgc actataatgg ctggagcttt
     6721 ctttgctgga ttggcatctg atgtccttgg ctctggactt ggttccctta tcaatgctgg
     6781 ggctggggcc atcaaccaaa aagttgagtt tgaaaataac agaaaattgc aacaagcatc
     6841 cttccaattt agcagcaatc tacaacaggc ttccttccaa catgacaaag agatgctcca
     6901 agcacaaatt gaggccacca aaaggctaca acaggaaatg atgaaagtta agcaggcaat
     6961 gctcctagag ggtgggttct ctgaggcaga tgcggcccgc ggggcaatca acgcccccat
     7021 gacaaaagct ttggactgga gcgggacaag gtactgggct cccgatgcta ggactacaac
     7081 atacaatgca ggccgctttt ccacccctca accatcgggg gcactgccag gaagagctaa
     7141 tcttagggat gctgtccctg ctcggggttc ctccagtaag tcttctaatt cttccactgc
     7201 tacttctgtg tactcaaatc aaaccacttc aacgagactt ggttctacag ctggttctgg
     7261 taccagtgtc tcgagcttcc cgtcaactgc aaggactagg agctgggttg aggatcaaag
     7321 taggaatttg tcacctttca tgaggggggc ccacaacata tcgtttgtca ccccaccatc
     7381 tagcagatcc tctagccaag gcacagtctc aaccgtgcct aaagagattt tggactcctg
     7441 gactggcgct ttcaacacgc gcaggcagcc actcttcgct cacattcgta agcgagggga
     7501 gtcacgggcg taatgtg
//