Typing tool

Complete norovirus genomes

MH218663  GII.4 Sydney
 GII.P31

Length: 7,559 | 3 CDS

ORF1: 5..5104
ORF2: 5085..6707
ORF3: 6707..7513
LOCUS       MH218663                7559 bp    RNA     linear   VRL 11-JUN-2018
DEFINITION  Norovirus GII isolate NORO_205_02_12_2015, complete genome.
ACCESSION   MH218663
VERSION     MH218663.1
KEYWORDS    .
SOURCE      Norovirus GII
  ORGANISM  Norovirus GII
            Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes;
            Picornavirales; Caliciviridae; Norovirus.
REFERENCE   1  (bases 1 to 7559)
  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 7559)
  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..7559
                     /organism="Norovirus GII"
                     /mol_type="genomic RNA"
                     /isolate="NORO_205_02_12_2015"
                     /host="Homo sapiens"
                     /db_xref="taxon:122929"
                     /country="United Kingdom"
                     /collection_date="02-Dec-2015"
                     /note="genotype: GII.Pe_GII.4"
     gene            5..5104
                     /gene="ORF1"
     CDS             5..5104
                     /gene="ORF1"
                     /codon_start=1
                     /product="nonstructural polyprotein"
                     /protein_id="AWR17647.1"
                     /translation="MKMASNDASAAAVANSNNDIAKSSSDGVFSNMAVTFKRALGARP
                     KQPPPKEIPPRPPRPPTPELVKKIPPPPPNGEDELVVSYSAKDGVSGLPELTTVRQPE
                     ETNTAFSIPPLNQRESRDAREPLAGTIIEMWDGEIYHYGLYVERGLILGVHKPPAAIS
                     LARVELAPLSLFWRPVYTPQYLISPDTLRRLHGESFPYTAFDNNCYAFCCWVLDLNDS
                     WLSRRMIQRTTGFFRPYQDWNRKPLPTMDDSKLKKVANIFLCTLSSLFTRPIKDIIGK
                     LKPLNILNILATCDWTFAGIVESLILLAELFGVFWTPPDVSALIAPLLGDYELQGPED
                     LAVELVPIVMGGIGLVLGFTKEKIGKMLSSAASTLRACKDLGAYGLEILKLVMKWFFP
                     KKEEANELAMVRSIEDAVLDLEAIENNHMTTLLKDKDSLATYMRTLDLEEEKARKLST
                     KSASPDIVGTINSLLARIAAARSLVHRAKEELSSRPRPVVVMISGRPGIGKTHLAREL
                     ARKIAASLTGDQRVGLIPRNGVDHWDAYKGERVVLWDDYGMSNPIHDALRLQELADTC
                     PLTLNCDRIENKGKVFDSDAIIITTNLANPAPLDYVNFEACSRRIDFLVYAEAPEVEK
                     AKRDFPGQPDMWKNAFSPDFSHIKLSLAPQGGFDKNGNTPHGKGVMKTLTTGSLIARA
                     SGLLHERLDEYELQGPALTTFNFDRNKVLAFRQLAAENKYGLMDTMRVGKQLKDVKTM
                     SDLKQALKNIAIKKCQIVYNGGTYTLEADGKGSVKVDKVQSATVQTNNELAGALHHLK
                     CARIRYYVKCVQEALYSIIQIAGAAFVTTRIAKRMNIQNLWSKPQVEDTEEMANKDGC
                     LKPKDDEEFVVSSDDIKTEGKKGKNKSGRGKKHTAFSSKGLSDEEYDEYKRIREERNG
                     KYSIEEYLQDRDKYYEEVAIARATEEDFCEEEEAKIRQRIFRPTRKQRKEERASLGLV
                     TGSEIRKRNPEDFKPKGKLWADDDRSVDYNEKLNFEAPPSIWSRIVNFGSGWGFWVSP
                     SLFVTSTHVIPQGAKEFFGVPIKQIQIHKSGEFCRLRFPKPIRTDVTGMILEEGAPEG
                     TVATLLIKRPTGELMPLAARMGTHATMKIQGRTVGGQMGMLLTGSNAKSMDLGTTPGD
                     CGCPYIYKRGNDYVVIGVHTAAARGGNTVICATQGSEGEATLEGGDSKGTYCGAPILG
                     PGSAPKLSTKTKFWRSSTTPLPPGTYEPAYLGGKDPRVKGGPSLQQVMRDQLKPFTEP
                     RGKPPRPNVLEAAKKTIINVLEQTIDPPQKWSFAQACASLDKTTSSGHPHHMRKNDCW
                     NGESFTGKLADQASKANLMFEEGKNMTPVYTGALKDELVKTDKVYGKVKKRLLWGSDL
                     ATMIRCARAFGGLMDELKAHCVTLPVRVGMNMNEDGPIIFEKHSRYRYHYDADYSRWD
                     STQQRDVLAAALEIMVKFSPEPHLAQIVAEDLLSPSVMDVGDFQISISEGLPSGVPCT
                     SQWNSIAHWLLTLCALSEVTDLSPDIIQANSLFSFYGDDEIVSTDIKLDPEKLTAKLK
                     EYGLKPTRPDKTEGPLVISEDLDGLTFLRRTVTRDPAGWFGKLEQSSILRQMYWTRGP
                     NHEDPFETMIPHSQRPIQLMSLLGEAALHGPAFYSKISKLVIAELKEGGMDFYVPRQE
                     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="AWR17648.1"
                     /translation="MKMASSDANPSDGSTANLVPEVNNEVMALEPVVGAAIAAPVAGQ
                     QNVIDPWIRNNFVQAPGGEFTVSPRNAPGEILWSAPLGPDLNPYLSHLARMYNGYAGG
                     FEVQVILAGNAFTAGKVIFAAVPPNFPTEGLSPSQVTMFPHIVVDVRQLEPVLIPLPD
                     VRNNFYHYNQSNDPTIKLIAMLYTPLRANNAGDDVFTVSCRVLTRPSPDFDFIFLVPP
                     TVESRTKPFSVPVLTVEEMTNSRFPIPLEKLFTGPSSAFVVQPQNGRCTTDGVLLGTT
                     QLSSVNICTFRGDVTHITGSHNYTMNLASQNWNNYDPTEEVPAPLGTPDFVGKIQGVL
                     TQTTRTDGSTRGHKATVYTGSADFAPKLGRVQFETDTNHDFEANQNTKFTPVGVIQDA
                     STTHRNEPQQWVLPSYSGRNTPNVHLAPAVAPTFPGEQLLFFRSTMPGCSGYPNMDLD
                     CLLPQEWVQHFYQEAAPAQSDVALLRFVNPDTGRVLFECKLHKSGFVTVAHTGQHDLV
                     IPPNGYFRFDSWVNQFYTLAPMGNGTGRRRAL"
     gene            6707..7513
                     /gene="ORF3"
     CDS             6707..7513
                     /gene="ORF3"
                     /codon_start=1
                     /product="VP2"
                     /protein_id="AWR17649.1"
                     /translation="MAGAFFAGLASDVLGSGLGSLINAGAGAINQKVEFENNRKLQQA
                     SFQFSSNLQQASFQHDKEMLQAQIEATKRLQQEMMKVKQAVLLEGGFSETDAARGAIN
                     APMTKALDWSGTRYWAPDARTTTYNAGRFSTPQPSGALPGRANLRDAVPARGSSSKSS
                     NSSTATSVYSNQTISTRLGSAAGSGTSVSSFPSAARTRSWVEDQSRNLSPFMRGAHNI
                     SFVTPPSSRSSSQGTVSTVPKEVLDSWTGAFNTRRQPLFAHIRKRGESRV"
ORIGIN      
        1 gtgaatgaag atggcgtcta acgacgcttc cgctgccgct gttgccaaca gcaacaacga
       61 catcgcaaaa tcttcaagtg acggtgtgtt ttccaacatg gctgtcactt ttaagcgggc
      121 cctcggggcg cggcctaaac agccgccccc gaaggaaata ccacccagac ccccgcgacc
      181 acccacacca gaattggtca aaaagatccc ccctccccca cccaacgggg aggatgaact
      241 agtggtctct tacagcgcca aagatggcgt ttccggactg cctgagctca ccactgtcag
      301 acaaccggaa gaaaccaaca cggcgttcag tatcccccca ctcaaccaaa gggagagcag
      361 ggacgccagg gagccactag ctggaacaat cattgaaatg tgggatggag aaatctacca
      421 ttacggcctg tacgtggaac gaggtcttat acttggtgtg cacaagccac cagcagccat
      481 tagccttgcc agggtcgagc tggcaccgct ctctttgttc tggagacctg tatacacccc
      541 ccagtacctc atctctccag acactcttag gagattacat ggagagtcat tcccctacac
      601 tgcattcgac aacaattgct acgccttttg ttgttgggtg ttagacctaa acgactcgtg
      661 gctaagcagg agaatgattc agagaacaac aggcttcttc aggccgtacc aggattggaa
      721 caggaagcct ctccccacta tggatgactc caaattaaag aaggtagcca acatattctt
      781 gtgcactttg tcttcactat ttaccagacc cattaaggac ataataggga agttaaaacc
      841 tcttaacatc cttaatattc tggctacatg tgattggacc ttcgcaggca tagtggaatc
      901 cttaatactc ttggcagaac tctttggagt tttctggaca cccccagatg tgtctgcgtt
      961 gatcgccccc ttgctaggtg attatgaact gcaaggacct gaggaccttg cagtggaact
     1021 ggtcccaata gtgatggggg ggataggttt ggtgctagga tttaccaaag agaagatcgg
     1081 aaagatgctg tcatccgctg catccacttt aagagcttgt aaagaccttg gtgcatacgg
     1141 actggaaatc ttaaaattgg tcatgaagtg gttcttccca aagaaagagg aagcaaatga
     1201 actggctatg gtgagatcca tcgaggatgc agtactagac ctcgaagcaa ttgaaaacaa
     1261 ccacatgacc accctgctca aagacaaaga cagcttggca acctacatga gaacccttga
     1321 ccttgaggag gagaaagcca gaaaactctc aaccaaatct gcttcacccg atattgtggg
     1381 cacaatcaac tctcttctgg caagaatcgc tgctgcacgc tccctagtgc atcgggcgaa
     1441 agaagagctc tccagcaggc cgagacctgt cgttgtaatg atatcgggaa ggccagggat
     1501 agggaaaact caccttgcca gggagctggc caggaagatc gcggcctccc tcacagggga
     1561 ccagcgtgtg ggtcttatcc cacgcaatgg tgtcgaccac tgggacgcat acaagggcga
     1621 aagagttgtc ctatgggacg actatggaat gagcaacccc atccatgatg ccctcaggtt
     1681 gcaggagctt gctgacactt gccccctcac gctaaattgt gacagaattg agaacaaagg
     1741 gaaagtcttt gacagtgatg ccataattat caccaccaat ctggccaacc cagcaccact
     1801 ggattatgtc aactttgagg cgtgctcgag acgcattgat ttcctcgtgt acgcagaagc
     1861 ccctgaggtg gagaaggcaa agcgcgactt cccaggtcaa cctgacatgt ggaagaacgc
     1921 tttcagtcct gacttctcac acataaaact gtcactggct ccacagggtg gttttgacaa
     1981 gaacggcaac accccgcatg gaaaaggggt catgaagacc ctcaccactg gctccctcat
     2041 cgcccgagca tcagggttac tccatgagag gctagatgaa tatgaactgc aaggcccagc
     2101 cctcaccact ttcaactttg accgcaacaa ggtacttgct tttagacagc ttgctgctga
     2161 aaacaagtat gggctgatgg acacaatgag agttggaaaa cagctcaagg atgtcaagac
     2221 catgtcagac ctcaaacaag cactcaagaa catcgcgatc aagaagtgcc agatagtgta
     2281 caatggtggc acctacacac ttgaggctga tggcaagggt agcgtgaaag ttgacaaagt
     2341 gcaaagtgcc actgtgcaga ccaacaatga actagccggt gccctacacc acctaaagtg
     2401 cgctagaatc agatactatg ttaagtgcgt ccaggaggca ctgtattcca tcatccaaat
     2461 cgctggggct gcattcgtca ccacgcgcat cgctaagcgc atgaacatac agaatctctg
     2521 gtccaagcca caggtggaag acacagaaga gatggccaac aaagatggtt gcctaaaacc
     2581 caaagatgat gaagagtttg tcgtctcatc cgacgacatc aaaactgagg gcaagaaagg
     2641 gaagaacaag tccggccgtg gcaagaagca cacagccttt tcaagtaaag ggctcagtga
     2701 tgaggagtac gatgagtaca agagaatcag agaagaaagg aatggtaagt actccataga
     2761 agagtacctt caggacagag acaagtacta cgaggaggtg gccattgcca gggcaaccga
     2821 agaggacttc tgtgaagaag aagaggccaa aatccggcag agaattttca gaccaacaag
     2881 gaaacaacgc aaagaagaga gggcctctct cggcttggtc acaggctctg agatcaggaa
     2941 gagaaaccca gaagacttca aacccaaggg aaagctgtgg gctgatgatg acagaagtgt
     3001 cgactacaat gagaaactca actttgaggc cccaccaagc atctggtcgc ggatagtcaa
     3061 ctttggttca ggctggggct tctgggtctc ccccagtctg tttgtaacat caacccatgt
     3121 cataccccaa ggtgcaaaag agttcttcgg agtccctatc aagcaaatcc agatacacaa
     3181 gtcaggtgaa ttctgccggt tgagattccc aaaaccaatc agaaccgatg 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 ggagtccata cggccgctgc ccgcggagga aacactgtca tatgtgccac
     3541 ccagggaagt gagggagagg ccacacttga aggaggtgac agtaaaggga catactgtgg
     3601 tgcaccaatc ttgggcccag ggagcgctcc gaagctcagc 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 cgcatccctt gacaaaacca cctccagcgg ccacccgcac cacatgcgga aaaacgactg
     3961 ttggaatggg gagtccttca caggaaaatt ggctgatcaa gcctccaagg ccaacctaat
     4021 gtttgaagag ggaaagaaca tgactccagt ctacacaggt gcacttaaag atgagttggt
     4081 aaagactgat aaagtttatg gtaaggtcaa gaagaggctt ctgtggggtt cagatctggc
     4141 gaccatgata cggtgcgccc gagcttttgg aggccttatg gatgaactca aggcacactg
     4201 tgtcacactc cctgtcagag ttggtatgaa catgaatgag gatggcccca tcatcttcga
     4261 aaagcactcc agatatagat atcactatga tgctgactac tcccggtggg actcaacaca
     4321 acaaagggat gtgctagcag cagcactaga aatcatggtt aagttctccc cagaaccaca
     4381 cctggcccag atagttgcag aagacctcct ctcccctagc gtgatggatg taggtgactt
     4441 tcagatatca ataagtgagg gtctcccctc tggggtacct tgtacctccc agtggaattc
     4501 catcgcccac tggctcctca ctctgtgtgc actctctgaa gtcacggacc tgtcccctga
     4561 tatcattcag gccaactccc ttttctcctt ctatggtgat gatgagattg taagcacaga
     4621 cataaagttg gacccagaga agttgacagc aaaactcaag gagtacgggc tgaaaccaac
     4681 ccgccccgac aaaactgaag gaccccttgt tatctctgaa gacctggatg gtctgacatt
     4741 cctccggaga actgtgaccc gtgatccagc tggctggttt ggaaaattgg aacaaagttc
     4801 aattcttagg caaatgtact ggaccagggg tcccaaccat gaagatccat ttgaaacaat
     4861 gataccacac tcccaaagac ccatacaatt gatgtccttg ctgggcgagg ctgcactcca
     4921 cggcccggca ttctacagca aaattagcaa attagtcatt gcagagttga aggaaggtgg
     4981 catggatttt tacgtaccca gacaagagcc aatgttcaga tggatgagat tctcagatct
     5041 gagcacgtgg gagggcgatc gcaatctggc tcccagtttt gtgaatgaag atggcgtcga
     5101 gtgacgccaa cccatctgat gggtccacag ccaacctcgt cccagaggtc aacaatgagg
     5161 ttatggctct ggagcccgtt gttggtgccg ccattgcggc acctgtagcg ggccaacaaa
     5221 atgtaattga cccctggatt agaaataatt ttgtacaagc ccctggtgga gagtttacag
     5281 tatcccctag aaacgctcca ggtgaaatac tatggagcgc gcccttgggc cctgatctaa
     5341 atccctacct atcccatttg gccagaatgt acaatggtta tgcaggtggt tttgaagtgc
     5401 aggtaattct cgcggggaac gcgttcaccg ccgggaaggt catatttgca gcagtcccac
     5461 caaattttcc aactgaaggc ttgagcccca gccaggttac tatgttcccc catatagtag
     5521 tagatgttag gcaactagaa cctgtgttga ttcccttacc cgatgttagg aataatttct
     5581 atcattacaa 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 tggaaaagtt gtttacgggt cccagcagtg cctttgttgt ccaaccacaa aacggtaggt
     5881 gcacgactga tggcgtgctc ctaggtacca cccagctgtc ttctgtcaac atctgcacct
     5941 tcagaggaga tgtcacccat atcacaggta gtcataacta cacaatgaat ttggcttctc
     6001 aaaattggaa caattacgac ccaacagaag aagtcccagc ccctctagga actccagact
     6061 ttgtggggaa gattcaaggc gtgcttaccc aaaccacaag gacagatggt tcaacacgcg
     6121 gccacaaagc cacagtgtac actgggagcg ccgactttgc tccaaaactg ggtagagttc
     6181 aatttgaaac tgacacaaac catgattttg aagctaacca aaacacaaag ttcaccccag
     6241 ttggtgtcat ccaagatgct agcaccaccc accgaaatga accccaacag tgggtgctcc
     6301 caagttactc aggcagaaat actcctaatg tgcatctggc ccccgctgta gcccccactt
     6361 ttccgggtga gcaacttctc ttcttcagat ccaccatgcc cggatgcagc gggtacccca
     6421 acatggattt ggactgtctg ctcccccagg aatgggtgca gcacttctac caagaggcag
     6481 ccccagcaca atctgatgtg gctctgctaa gatttgtgaa tccagacaca ggtagggttt
     6541 tgtttgaatg taagcttcat aaatcaggct ttgttacagt ggctcacact ggccaacatg
     6601 atttggttat cccccccaat ggttatttta ggtttgattc ctgggtcaac cagttttaca
     6661 cgcttgcccc catgggaaat ggaacggggc gtagacgtgc actataatgg ctggagcttt
     6721 ctttgctgga ttggcatctg atgtccttgg ctctggactt ggttccctca tcaatgctgg
     6781 ggctggggcc atcaaccaaa aagttgagtt tgaaaataac agaaaattgc aacaagcatc
     6841 cttccaattt agcagcaatc tacaacaggc ttcctttcaa catgacaaag agatgctcca
     6901 agcacaaatt gaggccacca aaaggttaca acaggaaatg atgaaagtta agcaggcagt
     6961 gctcctagag ggtgggttct ctgagacaga tgcagcccgc ggggcaatta acgcccccat
     7021 gacaaaagct ttggactgga gcgggacaag atactgggct cctgatgcta ggactacaac
     7081 atataatgca ggccgctttt ccacccctca accatcaggg gcactgccag gaagagctaa
     7141 tcttagggat gctgtccctg ctcggggttc ctccagtaag tcttctaatt cttctactgc
     7201 tacttctgtg tactcaaatc aaactatttc aacgagactt ggttctgcag ctggttctgg
     7261 taccagtgtc tcgagcttcc cgtcagctgc aaggactagg agctgggttg aggatcaaag
     7321 taggaatttg tcacccttca tgaggggggc ccacaacata tcgtttgtca ccccaccatc
     7381 tagcagatcc tctagccaag gcacagtctc aaccgtgcct aaagaggttt tggactcctg
     7441 gactggcgct ttcaacacgc gcaggcagcc actcttcgct cacattcgta agcgagggga
     7501 gtcacgggtg taatgtgaaa agacaagact gattaccttt cttttcttta gtgtctttt
//