Typing tool

Complete norovirus genomes

MH218624  GII.4 Sydney
 GII.P31

Length: 7,560 | 3 CDS

ORF1: 5..5104
ORF2: 5085..6707
ORF3: 6707..7513
LOCUS       MH218624                7560 bp    RNA     linear   VRL 11-JUN-2018
DEFINITION  Norovirus GII isolate NORO_153_19_02_2015, complete genome.
ACCESSION   MH218624
VERSION     MH218624.1
KEYWORDS    .
SOURCE      Norovirus GII
  ORGANISM  Norovirus GII
            Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes;
            Picornavirales; Caliciviridae; Norovirus.
REFERENCE   1  (bases 1 to 7560)
  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 7560)
  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..7560
                     /organism="Norovirus GII"
                     /mol_type="genomic RNA"
                     /isolate="NORO_153_19_02_2015"
                     /host="Homo sapiens"
                     /db_xref="taxon:122929"
                     /country="United Kingdom"
                     /collection_date="19-Feb-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="AWR17530.1"
                     /translation="MKMASNDASAAAVANSNNDIAKSSSDGVFSNMAVTFKRALGARP
                     KQPPPKEIPPRPPRPPTPELVKKIPPPPPNGEDELVVSYSARDGVSGLPELTTVRQPE
                     ETNTAFSVPPLNQRESRDAKEPLTGTIIEMWDGEIYHYGLYVERGLVLGVHKPPAAIS
                     LAKVELTPLSLFWRPVYTPQYLISPDTLRRLHGESFPYTAFDNNCYAFCCWVLDLNDS
                     WLSRRMIQRTTGFFRPYQDWNKKPLPTMDDSKLKKVANIFLCTLSSLFTRPIKDIIGK
                     LKPLNILNILATCDWTFAGIVESLILLAELFGVFWTPPDVSAMIAPLLGDYELQGPED
                     LAVELVPIVMGGIGLVLGFTKEKIGKMLSSAASTLRACKDLGAYGLEILKLVMKWFFP
                     KKEEANELAMVRSIEDAVLDLEAIENNHMTTLLKDKDSLATYMRTLDLEEEKARKLST
                     KSASPDIVGTINALLARIAAARSLVHRAKEELSSRLRPVVVMISGRPGIGKTHLAREL
                     AKKIAASLTGDQRVGLIPRNGVDHWDAYKGERVVLWDDYGMSNPIHDALRLQELADTC
                     PLTLNCDRIENKGKVFDSDAIIITTNLANPAPLDYVNFEACSRRIDFLVYAEAPEVEK
                     AKRDFPGQPDMWKNAFSPDFSHIKLSLAPQGGFDKNGNTPHGKGVMKTLTTGSLIARA
                     SGLLHERLDEYELQGPALTTFNFDRNKILAFRQLAAENKYGLMDTMRVGKQLKDVKTM
                     SDLKQALKNIAIKKCQIVYNGGTYTLEADGKGSVKVDKVQSATVQTNNELAGALHHLR
                     CARIRYYVKCVQEALYSIIQIAGAAFVTTRIAKRMNIQNLWSKPQVEDTEEMTNKDGC
                     LKPKDDEEFVVSSDDIKTEGKKGKNKSGRGKKHTAFSSKGLSDEEYDEYKRIREERNG
                     KYSIEEYLQDRDRYYEEVAIARATEEDFCEEEEAKIRQRIFRPTRKQRKEERASLGLV
                     TGSEIRKRNPEDFKPKGKLWADDDRSVDYNEKLNFEAPPSIWSRIVNFGSGWGFWVSP
                     SLFITSTHVIPQGAKEFFGVPIKQIQIHKSGEFCRLRFPKPIRTDVTGMILEEGAPEG
                     TVVTLLIKRPTGELMPLAARMGTHATMKIQGRTVGGQMGMLLTGSNAKSMDLGTTPGD
                     CGCPYIYKRGNDYVVIGVHTAAARGGNTVICATQGSEGEATLEGGDSKGTYCGAPILG
                     PGSAPKLSTKTKFWRSSTTPLPPGTYEPAYLGGKDPRVKGGPSLQQVMRDQLKPFTEP
                     RGKPPRPNVLEAAKKTIINVLEQTIDPPQKWSFAQACASLDKTTSSGHPHHMRKNDCW
                     NGESFTGKLADQASKANLMFEEGKNMTPVYTGALKDELVKTDKVYGKIKKRLLWGSDL
                     ATMIRCARAFGGLMDELKAHCVTLPVRVGMNMNEDGPIIFEKHSRYRYHYDADYSRWD
                     STQQRDVLAAALEIMVKFSPEPHLAQVVAEDLLSPSVMDVGDFQISISEGLPSGVPCT
                     SQWNSIAHWLLTLCALSEVTDLSPDIIQANSLFSFYGDDEIVSTDIKLDPEKLTAKLK
                     EYGLRPTRPDKTEGPLVISENLDGLTFLRRTVTRDPAGWFGKLEQSSILRQMYWTRGP
                     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"
                     /note="predicted CDS stop by homology is invalid; there
                     may be a valid stop in a different location due to
                     truncation (trc) or extension (ext) (TAG|TAA|TGA) [TAT
                     ending at position 6705 on + strand];first in-frame stop
                     codon exists 3' of stop position predicted by homology to
                     reference [homology search predicted 5085..6705 revised to
                     5085..6707 (stop shifted 2 nt)]"
                     /codon_start=1
                     /product="VP1"
                     /protein_id="AWR17531.1"
                     /translation="MKMASSDANPSDGSAANLVPEVTNEVMALEPVVGAAIAAPVAGQ
                     QNVIDPWIRNNFVQAPGGEFTVSPRNAPGEILWSAPLGPDLNPYLSHLARMYNGYAGG
                     FEVQVILAGNAFTAGKVIFAAVPPNFPTEGLSPSQVTMFPHIVVDVRQLEPVLIPLPD
                     VRNNFYHYNQSNDPTIKLIAMLYTPLRANNAGDDVFTVSCRVLTRPSPDFDFIFLVPP
                     TVESRTKPFSVPVLTVEEMTNSRFPIPLEKLFTGPSSAFVVQPQNGRCTTDGVLLGTT
                     QLSPVNICTFRGDVTHITGSRNYTMNLASQNWNNYDPTEEIPAPLGTPDFVGKIQGVL
                     TQTTRTDGSTRGHKATVYTGSADFAPKLGRVQFETDTDHDFEANQNTKFTPVGVIQDG
                     STTHRNEPQQWVLPSYSGRNTHNVHLAPAVAPTFPGEQLLFFRSTMPGCSGYPNMDLD
                     CLLPQEWVQYFYQEAAPAQSDVALLRFVNPDTGRVLFECKLHKSGYVTVAHTGQHDLV
                     IPPNGYFRFDSWVNQFYTLAPMGNGTGRRRAV"
     gene            6707..7513
                     /gene="ORF3"
     CDS             6707..7513
                     /gene="ORF3"
                     /codon_start=1
                     /product="VP2"
                     /protein_id="AWR17532.1"
                     /translation="MAGAFFAGLASDVLGSGLGSLINAGAGAINQKVEFENNRKLQQA
                     SFQFSSNLQQASFQHDKEMLQAQIEATKKLQQEMMRVKQAMLLEGGFSETDAARGAIN
                     APMTKALDWSGTRYWAPDARTTTYNAGRFSTPQPSGALPERAILRDAVPARGSSSKSS
                     NSSVATSVYSNQTTSTRLGSTAGSGASVSSLPSTARTRSWVEDQNRSLSPFMRGAHNI
                     SFVTPPSSRSSSQGTVSTVPKEILDSWTGAFNTRRQPLFAHIRKRGESRA"
ORIGIN      
        1 gtgaatgaag atggcgtcta acgacgcttc cgctgccgct gttgccaaca gcaacaacga
       61 catcgcaaaa tcttcaagtg acggtgtgtt ttctaacatg gctgtcactt ttaagcgggc
      121 cctcggggcg cggcctaaac agccgccccc gaaggagata ccacccagac ccccgcgacc
      181 acccacacca gaactggtca aaaagatccc tcctccccca cccaacgggg aggatgaact
      241 agtggtctct tacagcgcca gagatggcgt ttccggactg cctgagctca ccactgtcag
      301 gcaaccggaa gaaaccaaca cggcgttcag tgtcccccca ctcaaccaaa gggagagcag
      361 ggacgccaag gagccactaa ctggaacaat tattgaaatg tgggatggag aaatctacca
      421 ttacggcctg tacgtggaac gaggtcttgt acttggtgtg cataagccac cggcagctat
      481 cagccttgcc aaggtcgagc taacaccgct ctctttgttc tggagacctg tatacacccc
      541 ccagtacctc atctctccag acactcttag gaggttgcat ggagagtcat tcccctacac
      601 tgcatttgac aacaattgct acgccttttg ttgttgggta ttagacctaa acgactcatg
      661 gttaagcagg agaatgattc agagaacaac aggtttcttc aggccgtacc aggattggaa
      721 caagaaaccc ctccccacta tggatgactc caaattaaag aaggtagcca acatattctt
      781 gtgcactttg tcttcactat tcaccagacc cattaaggac ataataggga agttgaaacc
      841 tcttaacatc ctcaacattc tggctacatg tgattggact ttcgcaggca tagtggaatc
      901 tttaatactc ttagcagaac tctttggagt tttctggaca cccccagatg tgtctgcgat
      961 gatcgccccc ttgctaggtg attatgaact gcaaggacct gaggaccttg cagtggaact
     1021 ggtccctata gtgatggggg ggataggttt ggtgttagga tttaccaaag agaaaattgg
     1081 aaagatgcta tcatccgctg catccacttt aagagcttgt aaagaccttg gtgcatacgg
     1141 actggaaatc ttaaaattgg tcatgaagtg gttcttccca aagaaagagg aagcaaatga
     1201 actggctatg gtgagatcca tcgaggatgc agtgctagac ctcgaggcaa ttgaaaacaa
     1261 ccacatgacc accctactca aagacaaaga cagcttggca acctacatga gaacccttga
     1321 ccttgaggag gagaaagcca gaaaactctc aaccaaatct gcttcacccg atattgtggg
     1381 cacaatcaac gctcttctgg caagaatcgc tgccgcacgc tccctagtgc accgggcgaa
     1441 agaagagctc tccagcaggc tgagacctgt cgttgtgatg atatcgggaa gaccagggat
     1501 agggaaaact caccttgcca gggagctggc caagaaaatc gcggcctccc tcacagggga
     1561 ccagcgtgtg ggtcttatcc cacgcaatgg tgtcgatcac tgggacgcat acaagggcga
     1621 aagagttgtc ctatgggacg actatggaat gagcaacccc atccatgatg ccctcaggtt
     1681 gcaggaactt gctgacactt gccccctcac gttaaattgt gacagaattg agaacaaagg
     1741 gaaagtcttt gacagtgatg ccataattat caccaccaat ctggccaacc cagcaccact
     1801 ggattatgtc aattttgaag catgttcgag acgtattgac ttcctcgtgt acgcagaagc
     1861 ccctgaggtg gagaaggcaa agcgtgactt cccaggtcaa cctgacatgt ggaagaacgc
     1921 tttcagtcct gacttctcac acataaaact gtcattggct ccacagggtg gttttgacaa
     1981 gaacggcaac 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 ttgaggccga tggcaagggt agtgtgaaag ttgacaaagt
     2341 gcaaagtgcc actgtgcaga ccaacaatga gctagccggc gccctacacc acctaaggtg
     2401 cgctagaatc agatactatg ttaagtgcgt ccaggaggcg ctgtattcca tcatccaaat
     2461 cgctggggct gcattcgtca ccacgcgcat cgctaagcgc atgaatatac agaatctctg
     2521 gtccaagcca caggtggaag acacagaaga aatgaccaac aaagatggtt gcctaaaacc
     2581 caaagatgat gaagagtttg tcgtctcatc cgacgacatc aaaactgagg gcaagaaagg
     2641 gaagaacaag tccggccgtg gcaagaagca cacagccttt tcaagcaaag ggctcagtga
     2701 tgaggagtac gatgagtaca agagaatcag agaagaaagg aatggtaagt actccataga
     2761 agaatacctt caggacagag acaggtacta cgaggaggtg gccattgcca gggcaaccga
     2821 agaggacttt tgtgaagaag aagaggccaa aatccggcag agaattttca gaccaacaag
     2881 gaaacaacgc aaagaagaga gggcctctct cggcctggtc acaggttctg aaatcaggaa
     2941 gagaaaccca gaagacttca aacccaaggg gaagctgtgg gctgatgatg acagaagtgt
     3001 tgactacaat gagaaactca actttgaggc cccaccaagc atttggtcgc ggatagtcaa
     3061 ctttggttca ggctggggct tctgggtctc ccccagtctg tttataacat caacccatgt
     3121 cataccccaa ggtgcaaaag agttcttcgg agtccctatc aagcaaatcc aaatacacaa
     3181 atcaggtgaa ttctgccggt tgagattccc aaagccaatc agaactgatg tgacgggcat
     3241 gattctagaa gaaggtgcgc ccgaggggac cgtggtcaca 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 ccgtggagga aacaccgtca tatgtgccac
     3541 ccaggggagt gagggagaag ccacacttga aggaggtgac agtaaaggga catactgtgg
     3601 cgcaccaatc ttgggcccag ggagcgcccc gaagctcagt accaagacta agttttggag
     3661 atcatccaca acaccactcc cacctggcac ctacgaacca gcctacctcg gtggcaaaga
     3721 ccccagagtc aaaggtggcc cctcattgca acaagttatg agggaccagc taaaaccatt
     3781 cacagaaccc agaggcaaac caccaagacc aaatgtgttg gaagctgcca agaaaaccat
     3841 catcaatgtc cttgagcaaa caattgatcc accccaaaaa tggtcatttg cgcaagcttg
     3901 cgcatccctt gacaaaacca cttccagcgg ccacccgcac cacatgcgga aaaacgattg
     3961 ttggaatggg gagtccttta caggaaaatt ggctgatcaa gcctccaagg ccaacctaat
     4021 gtttgaagag ggaaagaaca tgactccagt ctacacaggt gcacttaaag atgagttggt
     4081 aaagaccgat aaagtttatg gtaagatcaa gaagaggctt ctgtggggtt cagatctggc
     4141 gaccatgata cggtgcgccc gagcttttgg aggccttatg gatgaactca aggcgcactg
     4201 tgtcacactt cctgtcagag ttggcatgaa catgaatgag gatggcccca tcatctttga
     4261 gaagcactcc agatatagat atcactatga tgctgattat tcccggtggg actcaacaca
     4321 acaaagggat gtgctagcag cagcactaga aatcatggtt aagttctccc cagaaccaca
     4381 cctggcccag gtagttgcag aagacctcct ttcccctagc gtaatggatg taggtgactt
     4441 tcaaatatca ataagtgagg gtcttccctc tggggtgcct tgtacctccc agtggaattc
     4501 catcgcccac tggctcctca ctctttgtgc actctctgaa gtcacggacc tgtcccctga
     4561 catcatacag gccaactccc tcttctcctt ctatggtgat gatgagattg tgagcacaga
     4621 tataaagttg gacccagaga agctgacagc aaaactcaag gagtacgggc tgagaccaac
     4681 ccgccccgac aaaactgaag gaccccttgt tatctctgaa aacctggatg gcctaacatt
     4741 cctccggaga actgtgaccc gtgacccagc tggctggttt ggaaaattgg aacaaagttc
     4801 aattcttaga caaatgtact ggaccagggg tcccaaccat gaagatccat tcgaaacaat
     4861 gataccacac tcccaaagac ccatacaatt gatgtccttg ctgggcgagg ctgcactcca
     4921 tggcccggca ttttatagca aaattagcaa attagtcatt gcagagttga aggaaggtgg
     4981 catggatttt tacgtgccca gacaagagcc aatgttcaga tggatgagat tctcagatct
     5041 gagcacgtgg gagggcgatc gcaatctggc tcccagtttt gtgaatgaag atggcgtcga
     5101 gtgacgccaa cccatctgat gggtccgcag ccaacctcgt cccagaggtc accaatgagg
     5161 ttatggctct ggagcccgtt gttggtgccg ccattgcggc acctgtagcg ggccaacaaa
     5221 atgtaattga cccctggatt agaaacaatt ttgtacaagc ccctggtgga gagtttacag
     5281 tatcccctag aaacgctcca ggtgaaatac tatggagcgc gcccctgggc cctgatctaa
     5341 atccctacct atcccatttg gccagaatgt acaatggtta tgcaggtggt tttgaagtgc
     5401 aggtaattct cgcggggaac gcgttcaccg ccgggaaggt tatatttgca gcagtcccac
     5461 caaattttcc aactgaaggc ttgagcccta gccaggtcac tatgttcccc catatagtag
     5521 tagatgttag gcaactagaa cctgtactga ttcccttacc cgatgttagg aataattttt
     5581 atcattacaa tcaatcaaat gaccccacca ttaagttgat agcaatgttg tatacaccac
     5641 ttagggctaa taatgctggt gatgatgtct tcacagtttc ttgccgagtt ctcacgagac
     5701 catcccccga ttttgatttc atatttctag tgccacccac agttgagtca agaactaaac
     5761 cattctctgt cccagtttta actgttgagg agatgaccaa ttcaagattc cccattcctt
     5821 tggaaaagct gttcacgggc cccagcagtg cctttgttgt ccaaccacaa aacggcaggt
     5881 gcacgactga tggcgtgctc ctaggcacta cccaactgtc tcctgtcaac atctgcacct
     5941 tcagaggaga tgtcacccac atcacaggca gtcgcaacta tacaatgaat ttggcttctc
     6001 aaaattggaa taattatgac ccaacagaag aaatcccagc ccctctagga actccagact
     6061 ttgtggggaa gattcaaggt gtgctcaccc aaaccacaag gacagatggc tcaacacgcg
     6121 gccacaaagc cacagtgtac actgggagcg ccgactttgc tccaaaactg ggtagagttc
     6181 aatttgaaac tgacacagac catgattttg aagctaacca aaacacaaag ttcaccccag
     6241 tcggtgtcat ccaagatggt agtaccaccc accgaaatga accccaacag tgggtgctcc
     6301 caagttactc aggcagaaat actcataatg tgcatctggc ccccgctgta gcccccactt
     6361 ttccgggtga gcaacttctc ttcttcagat ccaccatgcc cggatgcagc gggtacccca
     6421 acatggattt ggattgtctg ctcccccagg aatgggtgca gtacttctac caagaggcag
     6481 ccccagcaca atctgatgtg gctctgctaa gatttgtgaa tccagacact ggtagggttt
     6541 tgtttgagtg taagctccat aaatcaggct atgttacagt ggctcacact ggccaacatg
     6601 atttggttat tccccccaat ggttatttta gatttgattc ctgggtcaac cagttctaca
     6661 cgcttgcccc catgggaaat ggaacggggc gtagacgtgc agtataatgg ctggagcttt
     6721 ctttgctgga ttggcatctg atgtccttgg ctctggactt ggttccctta tcaatgctgg
     6781 ggctggggcc atcaaccaaa aagttgagtt tgaaaacaac agaaaattgc aacaagcatc
     6841 cttccaattt agcagcaatc tacaacaggc ttccttccaa catgacaaag agatgctcca
     6901 agcacaaatt gaggccacca aaaagttaca acaggaaatg atgagagtta agcaggcaat
     6961 gctcctagag ggtgggttct ctgagacgga tgcagcccgt ggggcaatca acgcccccat
     7021 gacaaaagct ctggattgga gcgggacaag gtactgggct cccgatgcta ggactacaac
     7081 atacaatgca ggccgctttt ccacccctca accatcgggg gcactgccag aaagagctat
     7141 tcttagggat gctgtccctg ctcggggttc ctccagtaaa tcttctaact cttctgtcgc
     7201 tacttctgtg tattcaaatc aaactacttc aacgagactt ggttctacag ctggttctgg
     7261 cgccagtgtc tcgagcctcc cgtcaactgc aaggactagg agctgggttg aggatcaaaa
     7321 taggagtttg tcacctttca tgaggggggc ccacaatata tcgtttgtca ccccaccatc
     7381 tagcagatcc tctagccaag gcacagtctc aaccgtgccc aaagagattt tggactcctg
     7441 gactggcgct ttcaacacgc gcaggcagcc actcttcgct cacattcgta agcgagggga
     7501 gtcacgggcg taatgtgaaa agacaaaatt gattaccttt ctctttcttt agtgtctttt
//