Typing tool

Complete norovirus genomes

MH218614  GII.4 Sydney
 GII.P31

Length: 7,560 | 3 CDS

ORF1: 5..5104
ORF2: 5085..6707
ORF3: 6707..7513
LOCUS       MH218614                7560 bp    RNA     linear   VRL 11-JUN-2018
DEFINITION  Norovirus GII isolate NORO_143_12_11_2014, complete genome.
ACCESSION   MH218614
VERSION     MH218614.1
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_143_12_11_2014"
                     /host="Homo sapiens"
                     /db_xref="taxon:122929"
                     /country="United Kingdom"
                     /collection_date="12-Nov-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="AWR17500.1"
                     /translation="MKMASNDASAAAVANSNNDIAKSSSDGVLSNMAVTFKRALGARP
                     KQPPPREIPPRPPRPPTPELVKKIPPPPPNGEDELVVSYSAKDGVSGLPELTTVRQPE
                     ETNTAFSVPPLNQRESRDAKEPLTGTIIEMWDGEIYHYGLYVERGLILGVHKPPAAIS
                     LAKVELAPLSLFWRPVYTPQYLISPDTLRRLHGESFPYTAFDNNCYAFCCWVLDLNDS
                     WLSRRMIQRTTGFFRPYQDWNRKPLPTMDDSKLKKVANIFLCTLSSLFTRPIKDIIGK
                     LKPLNILNILATCDWTFAGIVESLILLAELFGVFWTPPDVSAMIAPLLGDYELQGPED
                     LAVELVPIVMGGIGLVLGFTKEKIGKMLSSAASTLRACKDLGAYGLEILKLVMKWFFP
                     KKEEANELAMVRSIEDAVLDLEAIENNHMTTLLKDKDSLATYMRTLDLEEEKARKLST
                     KSASPDIVGTINSLLARIAAARSLVHRAKEELSSRPRPVVVMISGRPGIGKTHLAREL
                     AKKIAASLTGDQRVGLIPRNGVDHWDAYKGERVVLWDDYGMSNPIHDALRLQELADTC
                     PLTLNCDRIENKGKVFDSDAIIITTNLANPAPLDYVNFEACSRRIDFLVYAEAPEVEK
                     AKRDFPGQPDMWKNAFSPDFSHIKLSLAPQGGFDKNGNTPHGKGVMKTLTTGSLIARA
                     SGLLHERLDEYELQGPALTTFNFDRNKILAFRQLAAENKYGLMDTMRVGKQLKDVKTM
                     SDLKQALKNIAIKKCQIVYNGGTYTLEADGKGSVKVDKVQSATVQTNNELAGALHHLR
                     CARIRYYVKCVQEALYSIIQIAGAAFVTTRIAKRMNIQNLWSKPQVEDTEEMANKDGC
                     LKPKDDEEFVVSSDDIKTEGKKGKNKSGRGKKHTAFSSKGLSDEEYDEYKRIREERNG
                     KYSIEEYLQDRDRYYEEVAIARATEEDFCEEEEAKIRQRIFRPTRKQRKEERASLGLV
                     TGSEIRKRNPEDFKPKGKLWADDDRSVDYNEKLNFEAPPSIWSRIVNFGSGWGFWVSP
                     SLFITSTHVIPQGAKEFFGVPIKQIQIHKSGEFCRLRFPKPIRTDVTGMILEEGAPEG
                     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"
                     /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="AWR17501.1"
                     /translation="MKMASSDANPSDGSAANLVPEVNNEVMALEPVVGAAIAAPVAGQ
                     QNVIDPWIRNNFVQAPGGEFTVSPRNAPGEILWSAPLGPDLNPYLSHLARMYNGYAGG
                     FEVQVILAGNAFTAGKVIFAAVPPNFPTEGLSPSQVTMFPHIVVDVRQLEPVLIPLPD
                     VRNNFYHYNQSNDPTIKLIAMLYTPLRANNAGDDVFTVSCRVLTRPSPDFDFIFLVPP
                     TVESRTKPFSVPVLTVEEMTNSRFPIPLEKLFTGPSSAFVVQPQNGRCTTDGVLLGTT
                     QLSPVNICTFRGDVTHITGSHNYTMNLASQNWNNYDPTEEIPAPLGTPDFVGKIQGVL
                     TQTTRTDGSTRGHKATVYTGSADFAPKLGRVQFETDTNNDFEANQNTKFTPVGVIQDG
                     GTTHRNEPQQWVLPSYSGRNTHNVHLAPAVAPTFPGEQLLFFRSTMPGCSGYPNMDLD
                     CLLPQEWVQYFYQEAAPAQSDVALLRFVNPDTGRVLFECKLHKSGYVTVAHTGQHDLV
                     IPPNGYFRFDSWVNQFYTLAPMGNGTGRRRAV"
     gene            6707..7513
                     /gene="ORF3"
     CDS             6707..7513
                     /gene="ORF3"
                     /codon_start=1
                     /product="VP2"
                     /protein_id="AWR17502.1"
                     /translation="MAGAFFAGLASDVLGSGLGSLINAGAGAINQKVEFENNRKLQQA
                     SFQFSSNLQQASFQHDKEMLQAQIEATKKLQQEMMKVKQAMLLEGGFSETDAARGAIN
                     APMTKALDWSGTRYWAPDARTTTYNAGRFPTPQPSGALPGRANLRDTVPARGSSSKSS
                     NSSTATSVYSNQTTSTRLGSTAGSGTSVSSFPSTARTRSWVEDQSRNLSPFMRGAHNI
                     SFVTPPSSRSSSQGTVSTVPKEILDSWTGAFNTRRQPLFAHIRKRGESRA"
ORIGIN      
        1 gtgtatgaag atggcgtcta acgacgcttc cgctgccgct gttgccaaca gcaacaacga
       61 catcgcaaaa tcttcaagtg acggtgtgct ttctaacatg gctgtcactt ttaagcgggc
      121 cctcggggcg cggcctaaac agccgccccc gagggaaata ccacccagac ccccgcgacc
      181 acccacacca gaattggtca aaaagatccc tcccccccca cccaacgggg aggatgaact
      241 agtggtctct tacagcgcca aagatggcgt ttccggactg cctgagctca ccactgtcag
      301 gcaaccggaa gaaaccaaca cggcgttcag tgtcccccca ctcaaccaaa gggagagcag
      361 ggacgccaag gagccactaa ctggaacgat tattgaaatg tgggatggag aaatctacca
      421 ttacggcctg tacgtggaac gaggtcttat acttggtgtg cacaagccac cggcagctat
      481 cagccttgcc aaggtcgagc tagcaccgct ctctttgttc tggagacctg tatacacccc
      541 ccagtatctc atctctccag acactcttag gagattacat ggagagtcat tcccctacac
      601 tgcatttgac aacaattgct acgccttttg ttgttgggtg ttagacctaa acgactcatg
      661 gctaagcagg agaatgattc agagaacaac aggtttcttc aggccgtacc aggattggaa
      721 caggaaaccc ctccccacta tggatgattc caaattaaag aaggtggcca acatattctt
      781 gtgcactttg tcttcactat tcaccagacc cattaaggac ataataggga agttgaaacc
      841 ccttaacatc cttaacattc tggcaacatg tgattggacc ttcgcaggca tagtggaatc
      901 cttaatactc ttggcagaac tctttggagt tttctggaca cccccagatg tgtctgcgat
      961 gatcgccccc ttgctaggtg attatgaact gcaaggacct gaggaccttg cagtggaact
     1021 ggtcccaata gtgatggggg ggataggttt ggtgctagga 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 acattgtggg
     1381 cacaatcaac tctcttctgg caagaattgc tgccgcacgc tccctagtgc atcgggcgaa
     1441 ggaagagctc tccagcaggc cgagacctgt cgttgtgatg atatcgggaa gaccagggat
     1501 agggaaaact caccttgcca gggagctggc caagaagatc gcggcctccc tcacagggga
     1561 ccagcgtgtg ggtcttatcc cacgcaatgg tgtcgaccac tgggacgcat acaagggcga
     1621 aagagttgtc ctgtgggacg actatggaat gagcaacccc atccatgatg ccctcaggtt
     1681 gcaggagctt gctgacactt gccccctcac gctaaattgt gacagaattg agaacaaagg
     1741 gaaagtcttt gacagtgatg ccataattat caccaccaat ctggccaacc cagcaccact
     1801 ggattatgtc aactttgaag cgtgctcgag acgcattgac tttctcgtgt acgcagaagc
     1861 ccctgaggtg gagaaagcaa agcgcgactt cccaggtcaa cctgacatgt ggaagaacgc
     1921 tttcagtcct gacttctcac acataaaact gtcattggct ccacagggtg gttttgacaa
     1981 gaacggcaac accccgcatg gaaaaggggt catgaagacc ctcaccactg gctccctcat
     2041 cgcccgagca tcagggttgc tccatgagag gctagatgaa tatgaactgc aaggcccagc
     2101 cctcaccact ttcaatttcg accgcaacaa gatacttgct tttagacagc ttgctgctga
     2161 aaacaagtat gggctgatgg acacaatgag ggttggaaaa cagctcaagg atgtcaaaac
     2221 catgtcagac ctcaagcaag cactcaagaa catcgcgatc aagaagtgcc agatagtgta
     2281 caatggtggc acctatacac ttgaggccga tggcaagggt agtgtgaaag ttgacaaagt
     2341 gcaaagtgcc actgtgcaga ccaacaatga actagccggt gccctacacc acctaaggtg
     2401 cgccagaatc agatactacg ttaagtgcgt ccaggaggca ctgtattcca tcatccaaat
     2461 cgctggggct gcattcgtca ccacgcgcat cgctaagcgc atgaatatac agaacctctg
     2521 gtccaagcca caggtggaag acacagaaga gatggccaac aaagatggtt gcctaaaacc
     2581 caaagatgat gaagagtttg tcgtctcatc cgacgacatc aaaactgagg gcaagaaagg
     2641 gaagaacaag tccggccgtg gcaagaagca cacagccttt tcaagcaaag ggctcagtga
     2701 tgaggagtac gatgagtaca agagaatcag agaagaaagg aatggtaagt actccataga
     2761 agagtacctt caggacagag acaggtatta cgaggaggtg gccattgcca gggcaaccga
     2821 agaggacttc tgtgaagaag aagaagccaa aatccggcag agaattttta gaccaacaag
     2881 gaaacaacgt aaagaagaga gggcctctct cggcttggtc acaggctctg aaatcaggaa
     2941 gagaaaccca gaagacttca aacccaaggg aaagctatgg gctgatgatg acagaagtgt
     3001 tgactacaat gagaaactca actttgaggc cccaccaagc atctggtcgc gaatagtcaa
     3061 ctttggttca ggctggggct tctgggtctc ccccagtctg tttataacat caacccatgt
     3121 cataccccaa ggtgcaaaag agttcttcgg agtccctatc aagcaaatcc agatacacaa
     3181 atcaggtgaa ttctgccggt tgagattccc aaagccaatc agaactgatg tgacgggcat
     3241 gattctagaa gaaggtgcgc ccgaggggac cgtggccaca ctgctcatta agagaccaac
     3301 tggggagctc atgcctctgg cagccagaat gggaacccat gcaaccatga aaatccaggg
     3361 acgcacagtt ggagggcaaa tgggtatgct cctgacagga tccaacgcca agagtatgga
     3421 cctaggcaca acaccaggcg actgcggctg cccctatatc tacaagaggg ggaatgacta
     3481 cgtggtcata ggagtccata cggccgctgc ccgcggagga aacactgtta tatgtgccac
     3541 ccaggggagt gagggagaag ccacacttga aggaggtgac agtaaaggga catactgtgg
     3601 cgcaccaatc ttgggcccag ggagcgctcc gaagctcagc accaagacta agttctggag
     3661 atcatccaca acgccactcc cacccggcac ctacgaacca gcctacctcg gtggcaaaga
     3721 ccccagggtc 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 aaaacgattg
     3961 ttggaatggg gagtccttca caggaaaatt ggctgatcaa gcctccaagg ccaacctaat
     4021 gtttgaagag ggaaagaaca tgactccagt ctacacaggt gcacttaaag atgagttagt
     4081 aaagaccgat aaagtttatg gtaaggtcaa gaagaggctt ctgtggggtt cagatctggc
     4141 gaccatgata cggtgcgccc gagcttttgg aggccttatg gatgaactca aggcacactg
     4201 tgtcacactt cctgtcagag ttggtatgaa catgaatgag gatggcccca ttatatttga
     4261 gaagcactcc agatatagat atcactatga tgctgattat tcccggtggg actcaacaca
     4321 acaaagggat gtgctagcag cagcactaga aatcatggtt aagttctctc cagaaccaca
     4381 cctggcccag atagttgcag aagacctcct ttcccctagc gtaatggatg taggtgactt
     4441 tcaaatatca ataagtgagg gtctcccctc tggggtacct tgcacctccc agtggaattc
     4501 catcgcccac tggcttctca ctctttgtgc actctctgaa gtcacggacc tgtcccctga
     4561 catcattcag gccaactccc ttttctcttt ctatggtgat gatgagattg taagcacaga
     4621 cataaagttg gacccagaga agctgacagc aaaactcaag gagtacgggc tgaaaccaac
     4681 ccgccccgac aaaactgaag gaccccttgt tatctctgaa gacctggatg gcctgacatt
     4741 cctccggaga actgtgaccc gtgatccagc tggctggttt ggaaagttgg aacaaagttc
     4801 aattctcagg caaatgtact ggaccagggg tcccaaccat gaagatccat ttgaaacaat
     4861 gataccacac tcccaaagac ccatacaatt gatgtccctg ctgggcgagg ctgcactcca
     4921 cggcccggca ttctatagca aaattagcaa attagtcatt gcagagttga aggaaggtgg
     4981 catggatttt tacgtgccca gacaagagcc aatgttcaga tggatgagat tctcagacct
     5041 gagcacgtgg gagggcgatc gcaatctggc tcccagtttt gtgaatgaag atggcgtcga
     5101 gtgacgccaa cccatctgat gggtccgcag ccaacctcgt cccagaggtc aacaatgagg
     5161 ttatggctct ggagcccgtt gttggtgccg ccattgcggc acctgtagcg ggccaacaaa
     5221 atgtaattga cccctggatt agaaataatt ttgtacaagc ccctggtgga gagttcacag
     5281 tatcccctag aaacgctcca ggtgaaatac tatggagcgc gcccttgggc cctgatctaa
     5341 atccctacct atcccatttg gccagaatgt acaatggtta tgcaggtggt tttgaagtgc
     5401 aggtaattct cgcggggaat gcgttcaccg ccgggaaggt catatttgca gcagtcccac
     5461 caaattttcc aactgaaggc ttgagcccca gccaggtcac tatgttcccc catatagtag
     5521 tagatgttag gcaattagaa cctgtgttga ttcccttacc cgatgttagg aataatttct
     5581 atcattacaa tcaatcaaat gaccccacca ttaagttgat agcaatgttg tatacaccac
     5641 ttagggctaa taacgctggg gacgatgtct tcacagtttc ttgccgagtt ctcacgagac
     5701 catcccccga ttttgatttc atatttctag tgccacccac agttgagtca aggactaaac
     5761 cattctctgt cccagtttta actgttgagg agatgaccaa ttcaagattc cccattcctt
     5821 tggaaaagtt gttcacgggt cccagtagtg ccttcgttgt ccaaccacaa aacggcaggt
     5881 gcacgactga tggcgtgctc ctaggcacca cccaactgtc tcctgtcaac atctgcacct
     5941 tcaggggaga tgtcacccat attacaggta gtcataacta cacaatgaat ctggcttctc
     6001 aaaattggaa caattatgac ccaacagaag aaatcccagc ccctctggga actccagatt
     6061 ttgtggggaa gattcaaggc gtgctcaccc aaaccacaag gacagatggc tcaacacgcg
     6121 gccacaaagc tacagtgtac actgggagcg ccgactttgc tccaaaactg ggtagagttc
     6181 aatttgaaac tgacacaaac aatgattttg aagctaacca aaacacaaag ttcaccccag
     6241 tcggtgtcat ccaagatggt ggcaccaccc accgaaatga accccaacag tgggtgctcc
     6301 caagttactc aggcagaaat actcataatg tgcatctggc ccccgctgta gcccccactt
     6361 ttccgggtga gcaacttctc ttcttcagat ccaccatgcc cggatgcagc gggtacccca
     6421 acatggattt ggactgtctg ctcccccagg aatgggtgca gtacttctac caagaggcag
     6481 ccccagcaca atctgatgtg gctctgctaa gatttgtgaa tccagacaca ggtagggttt
     6541 tgtttgagtg caagcttcac aaatcaggct atgttacagt ggctcacact ggccaacatg
     6601 atttggttat ccccccaaat ggttatttta ggtttgattc ctgggtcaac cagttttaca
     6661 cgcttgcccc catgggaaat ggaacggggc gtagacgtgc agtataatgg ctggagcttt
     6721 ctttgctgga ttggcatctg acgtccttgg ctctggactt ggttccctta tcaatgctgg
     6781 ggctggggcc atcaaccaaa aagttgagtt tgaaaataac agaaaattgc aacaagcatc
     6841 cttccaattt agcagcaatc tacaacaggc ttcctttcaa catgataaag agatgctcca
     6901 agcgcaaatt gaggctacca aaaagctaca acaggaaatg atgaaagtta agcaggcaat
     6961 gctcctagag ggtgggttct ctgagacaga tgcagcccgc ggggcaatca acgcccccat
     7021 gacaaaagct ttggactgga gcgggacaag gtactgggct cctgatgcta ggactacaac
     7081 atacaatgca ggccgctttc ccacccctca accatcgggg gcactgccag gaagagctaa
     7141 tcttagggat actgtccctg cccggggttc ctccagtaaa tcttctaact cttctactgc
     7201 cacttctgtg tactcaaatc aaactacttc aacgagactt ggttctacag ctggttctgg
     7261 caccagtgtc tcgagcttcc cgtcaactgc aaggactagg agctgggttg aggatcaaag
     7321 taggaatttg tcacctttca tgaggggggc ccacaacata tcgtttgtca ccccaccatc
     7381 tagtagatcc tctagccaag gcacagtctc aaccgtgcct aaagagattt tggactcctg
     7441 gactggcgct ttcaacacgc gcaggcagcc actcttcgct cacattcgta agcgagggga
     7501 gtcacgggcg taatgtgaaa agacaaaatt gattattctt ctttttcttt agtgtctttt
//