Typing tool

Complete norovirus genomes

MH218729  GI.3
 GI.P3

Length: 7,745 | 3 CDS

ORF1: 5..5404
ORF2: 5388..7025
ORF3: 7025..7672
LOCUS       MH218729                7745 bp    RNA     linear   VRL 11-JUN-2018
DEFINITION  Norovirus GI isolate NORO_90_22_06_2015, complete genome.
ACCESSION   MH218729
VERSION     MH218729.1
KEYWORDS    .
SOURCE      Norovirus GI
  ORGANISM  Norovirus GI
            Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes;
            Picornavirales; Caliciviridae; Norovirus.
REFERENCE   1  (bases 1 to 7745)
  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 7745)
  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..7745
                     /organism="Norovirus GI"
                     /mol_type="genomic RNA"
                     /isolate="NORO_90_22_06_2015"
                     /host="Homo sapiens"
                     /db_xref="taxon:122928"
                     /country="United Kingdom"
                     /collection_date="22-Jun-2015"
                     /note="genotype: GI.P3_GI.3"
     gene            5..5404
                     /gene="ORF1"
     CDS             5..5404
                     /gene="ORF1"
                     /codon_start=1
                     /product="nonstructural polyprotein"
                     /protein_id="AWR17845.1"
                     /translation="MMMASNDAIAVADVSNNNANTNNDNIGSRLMARIRGRMGPQRGE
                     TTTKITDANMALNLLRRSQTPSPSRQESPPKSQRDRPPRTASEVKKVLGWDVEPEHQE
                     STAKAWCDLTQEEKEEIMRNNEKLFDAGGITPSTLPSTFERADPVDSPIEQQPVTWSA
                     SSGVDIGVNDLTTVSGPFWNMCPLPPLDARNNGPAKEPLIGDMIEFYEGHIFHYAIYI
                     GQGKTIGVHSPQAAFSIPRITIHPLVAWWRVCYVPTNQQRLTYDQLKELENEPWPYAS
                     ITNNCYEFCCRVMALDDTWLERRLVSTGKFNHPTQDWSQDTPDFHQDSKLEMVRDAVL
                     SAINGLVSQPFKNILSKIKPLNVLNLLSNCDWTFMGIVELIVLLAELFDVFWTPPDIS
                     SFIASLLPEFHLQGPEDLARDLVPLILGGIGLAIGFTRDKVTKVMKSAVDGLRSATQL
                     GQYGLEIFSIIKKYFFGGDQTEKTLRGIEDAVIDMEVLSSTNVTQLVKDKKLARTYMN
                     VLDNEEEKARKLSVRSADPHIVTSVNNLISRISMARSALAKAQAEMTSRPRPVVIMMC
                     GPPGIGKTKAAEHLAGRLASEIRPGGKVGLVPRESIDHWDGYHGEDVLLWDDYGMSKI
                     TEDCNKLQAIADTAPLSLNCDRIENKGMQFSSDAIIITTNAPGPAPVDFVNLGPVCRR
                     VDFLVYCSAPEIEQMRRTHPGDANAIKDLYKRDYSHLKMELAPQGGFDSQGNTPFGKG
                     IMKPTTLNRLLIQATALAMERQDEFQLQGAVYNFDEDRVSAFTSLARANGLGLLSMAT
                     LGKRLRSVKSMEGLRNALVGYKIGECDIIWNTRVYSIKSDGSTVTIKEKQTPTSPQYQ
                     AISIATLALSRLRAARALAYASCLQSAVLSILQVAGSALVVSRAVKRMFGTRTEQPML
                     EGKHKEHNCRVHRAEAAGHGPIGHDGVIERYGLCESEQEEEGEQTVELPTANKEGKNK
                     GKTKKGRGRKSNFNAFSRRGLSDEEYEEYKKIREEKSGNYSIQEYLEDRQRYEEELAE
                     VQAGGDGGIGETEAEIRHRVFYKSKSGMRKQRQEERRQLGLVSGSEIRKRKPIDWTPP
                     KNDWSEDTRTVNYDEHISFEAPPSIWSRVVKFGSGWGFWVSSTVFITTTHVIPPGAKE
                     VFGEDLSNVAIHRVGEFTQFRFSKKMRPDLTGMVLEEGCPEGTVCTIMIKRDSGELLP
                     LAVRMGAVASMKIQGKLMHGQSGMLLTGANAKGMDLGTIPGDCGAPYVHKRGNDWVVC
                     GVHAAATKSGNTVVCAIQGGDGEATLEGGGQNKGHYAGHPILRYGNGPSLSTKTKFWK
                     STPQPLPPGTYEPAYLGGRDPRVEGGPSLQQVLRDQLKPFAEPRGRLPEAGLLEAAVE
                     TVTNAIEQVMDTPVAWSYSDACMSLDKTTSSGHPHHKKKNDDWNGNSFVRELGDQAAH
                     ANSMYELGKPMKPVYTAALKDELVKPDKVYTKIKKRLLWGADLGTVIRAARAFGPFCE
                     AIKPHVIKLPIKVGMNAIEDGPLIYAEHSKYKFHYDADYTAWDSTQNREIMMESFNIM
                     CKLTANPSLAAVVAQDLLSPSEMDVGDYVISVKDGLPSGFPCTSQVNSINHWILTLCA
                     LSEVTGLSPDVIQSQSYFSFYGDDEIVSTDIEFDPIRLTQILKEYGLKPTRPDKTDGP
                     IIIRQQVDGLVFLRRTISKDAIGYQGRLDRNSIERQLWWTRGPNHEDPFETLVPHSQR
                     KVQLISLLGEAALHGEKFYRKIAGRVIQEVKEGGLEIYIPGWQAMFRWMRFHDLSLWT
                     GDRDLLPDYVNDDGV"
     mat_peptide     5..1219
                     /gene="ORF1"
                     /product="p48"
     mat_peptide     1220..2308
                     /gene="ORF1"
                     /product="NTPase"
     mat_peptide     2309..2908
                     /gene="ORF1"
                     /product="p22"
     mat_peptide     2909..3328
                     /gene="ORF1"
                     /product="VPg"
     mat_peptide     3329..3871
                     /gene="ORF1"
                     /product="Pro"
     mat_peptide     3872..5401
                     /gene="ORF1"
                     /product="RdRp"
     gene            5388..7025
                     /gene="ORF2"
     CDS             5388..7025
                     /gene="ORF2"
                     /codon_start=1
                     /product="VP1"
                     /protein_id="AWR17846.1"
                     /translation="MMMASKDAPTNMDGTSGAGQLVPEANTAEPISMEPVAGAATAAA
                     TAGQVNMIDPWIMNNYVQAPQGEFTISPNNTPGDILFDLQLGPHLNPFLSHLAQMYNG
                     WVGNMKVKVLLAGNAFTAGKIIISCIPPGFAAQNISIAQATMFPHVIADVRVLEPIEV
                     PLEDVRNVLFHNNDNTPTMRLVCMLYTPLRASGSSSGTDPFVIAGRVLTCPSPDFSFL
                     FLVPPNVEQKTKPFSVPNLPLNTLSNSRVPSLIKSMMVSRDHGQMVQFQNGRVTLDGQ
                     LQGTTPTSASQLCKIRGSVFHANGGNGYNLTELDGSPYHAFESPAPIGFPDLGECDWH
                     MEASPTTQFNTGDVIKQINVKQESAFAPHLGTVQVDGLSDVSVNTNMIAKLGWVSPVS
                     DGHKGDVDPWVIPRYGSTLTEAAQLAPPIYPPGFGEAIVFFMSDFPIAHGTNGLSVPC
                     TIPQEFVTHFVNEQAPTRGEAALLHYLDPDTNRNLGEFKLYPDGFMTCVPNSSGTGPQ
                     TLPINGVFVFVSWVSRFYQLKPVGTAGPARRLGIRRS"
     gene            7025..7672
                     /gene="ORF3"
     CDS             7025..7672
                     /gene="ORF3"
                     /codon_start=1
                     /product="VP2"
                     /protein_id="AWR17847.1"
                     /translation="MAQAILGAIAATAAGSAVGAGIQAGTEAALQHQRFQQDLTLQKN
                     SFIHDKEMMGLQVEASTVLLQNSLGTRYNMLTKAGMTSADAARMVVGAPATRVVDWNG
                     TRIAAPMSTATTLRSGGFMTVPTVYRGSKNKQSIGGGFSNVNYDPSVSSSRTSQWVSS
                     QNSMRSTLEPFHPGALRTTWVTPPGSTSTSTISTVSTVPKFFNTERLPLFANRGK"
ORIGIN      
        1 gtgaatgatg atggcgtcta acgacgctat tgccgttgct gatgtcagca ataacaatgc
       61 taacaccaac aatgataaca ttggatcccg cctcatggca aggatccgtg ggcgcatggg
      121 cccacaacgt ggtgaaacaa ccacaaaaat aacagacgcc aatatggcgc ttaatctgct
      181 acgccggtca caaacacctt ccccatcccg gcaagagagc cctcctaaga gccagagaga
      241 ccgcccccct cgtactgctt ctgaggtgaa gaaagtgttg gggtgggatg ttgaaccaga
      301 acaccaggaa agcacggcta aggcatggtg cgacctcacg caagaagaga aggaggagat
      361 aatgcgcaat aatgaaaaac tcttcgatgc tgggggaatc accccatcaa ctttgcctag
      421 cacgtttgaa agggccgacc cagttgatag ccccattgaa cagcaacctg tgacatggtc
      481 tgctagtagt ggggtcgata ttggtgtcaa tgatttgacc accgtcagtg gcccattttg
      541 gaatatgtgc cccctcccgc cactggatgc tcggaataat ggccccgcta aggaacccct
      601 cataggagat atgatagagt tctatgaggg tcatatattc cattatgcca tctatattgg
      661 acaaggtaag accattgggg tccactcacc acaagcagct ttctccatac caaggataac
      721 catccatcct ctggtagcct ggtggcgcgt gtgctacgtc ccaactaacc agcagcgcct
      781 cacttatgac cagctcaaag agttggagaa tgagccatgg ccctacgctt ccattacaaa
      841 caattgctat gagttttgct gcagagtgat ggcacttgac gatacatggc ttgagaggag
      901 gttagtcagc actggaaaat tcaatcaccc cacacaagat tggtcacagg ataccccgga
      961 ttttcaccag gactcgaaac ttgagatggt aagagatgcc gtgctatcag ctattaatgg
     1021 ccttgtgtca cagcccttta aaaacatttt gtcaaagatc aaaccattaa acgttctcaa
     1081 tctcttgtca aattgcgatt ggaccttcat ggggattgtg gaactgattg tgctcctagc
     1141 ggagttgttt gatgtgttct ggaccccacc agacatctca agtttcattg cctcactact
     1201 acctgaattt cacctgcagg gcccagaaga cctagctagg gacttggtcc ctctcatcct
     1261 aggtggcata ggcctggcca ttggctttac aagagacaaa gtgacgaaag tgatgaagag
     1321 tgccgtcgat gggttgagat cggcgacaca gctcgggcag tacggactgg aaatattctc
     1381 aatcatcaag aaatatttct ttggtgggga ccaaacggaa aagaccttgc ggggtattga
     1441 ggatgcagtg atagacatgg aggtgttatc tagcaccaat gtgacacaat tggttaaaga
     1501 taagaaattg gccagaacct acatgaatgt gctagacaat gaagaggaaa aagcaaggaa
     1561 actctcagtc cgtagtgctg atccgcacat agtgacctca gtcaacaatc tgatatcacg
     1621 aatatccatg gcaagatcag ccttggccaa agcccaggct gagatgacat ctcgcccacg
     1681 ccctgtggtc ataatgatgt gtggcccccc cggcatcgga aaaaccaagg ccgccgaaca
     1741 cctggctggc cgattggcaa gcgagattag accagggggt aaggttggac ttgtgccccg
     1801 ggaatccata gatcactggg acggatacca tggcgaggat gtcctactat gggatgacta
     1861 tggcatgtca aagataacag aggactgtaa taagctacaa gccatagctg acactgcacc
     1921 cctatcactt aattgtgaca ggatagagaa caaaggtatg caattctcct cagatgcaat
     1981 aatcataacc accaatgccc ctggcccggc cccggtggac tttgtcaacc taggccctgt
     2041 gtgcaggcga gtggactttt tagtttactg ttctgcccct gaaattgagc aaatgagaag
     2101 gacccatcct ggtgatgcca atgccatcaa ggacttatac aaaagggact actcacactt
     2161 aaaaatggaa ttggccccac aaggtggttt tgatagtcag ggtaacacac catttgggaa
     2221 gggcatcatg aaacctacga ccctcaatag gctactcatt caggcaacag cattagctat
     2281 ggagcggcaa gacgagttcc agctccaagg ggctgtctac aacttcgatg aagacagggt
     2341 gtccgccttc acaagcctgg cccgagctaa cggcttgggg cttttaagta tggcaacatt
     2401 gggtaaaagg ctcagaagtg tcaaatctat ggagggcctg cgcaacgcat tggtaggcta
     2461 caaaatagga gagtgtgata taatctggaa cactagagtg tattcaatta aaagtgatgg
     2521 tagtactgtc acaatcaagg aaaaacaaac cccaacttca ccccaatacc aagccattag
     2581 catagccact cttgcactct ctaggttgcg ggccgctaga gctctcgcgt acgcctcctg
     2641 cctacagagt gcagtgctgt caatacttca agtagctggc tctgccctgg tggtgagcag
     2701 agccgttaag cgcatgtttg gcacgcgcac tgaacaacct atgttggaag gcaagcacaa
     2761 agaacacaac tgtagagtgc accgcgcaga ggcagctggc catggtccta ttgggcacga
     2821 tggagtcatc gaacgctatg gcctctgtga gagtgaacaa gaagaagaag gcgagcaaac
     2881 agttgagcta cccactgcca ataaagaagg caaaaacaag ggcaagacca aaaagggccg
     2941 tggacgaaaa tccaatttta atgctttctc aagacgaggc ctcagtgatg aagagtatga
     3001 agaatacaag aagatcagag aagaaaagag tggcaattac agcatccagg agtacctcga
     3061 ggaccgccaa cgatatgagg aagaacttgc tgaagtgcag gctggtgggg atggtggaat
     3121 tggtgagact gaagcagaga ttcgccatcg ggttttctat aaatcaaaat ccggcatgag
     3181 aaagcagcgc caagaagaac ggcgtcagtt gggtctcgtt agcggttctg agatccgcaa
     3241 acgcaagccc atagactgga ccccccctaa gaatgattgg tcagaagaca ccaggactgt
     3301 caactatgat gaacacatta gctttgaagc ccctccctca atttggagta gggtggtgaa
     3361 gtttggcagt ggttggggtt tttgggtgag ctcaacagtg ttcataacca cgacccatgt
     3421 cataccacct ggggccaaag aagtctttgg tgaagacctc agtaatgtgg caatccatag
     3481 agttggtgaa ttcacccagt tccgtttctc caaaaagatg aggcctgacc tcaccggtat
     3541 ggttttagaa gaaggttgcc cagagggaac agtgtgcacc ataatgatca agagagattc
     3601 tggtgagttg ctgccgctcg ccgttcggat gggggcagtg gcatcaatga agatccaagg
     3661 caaacttatg catgggcaat cagggatgtt gctcaccggt gctaatgcca aaggcatgga
     3721 ccttgggact atacccggtg attgtggggc accctatgtc cacaagaggg gaaatgactg
     3781 ggtggtctgt ggggtacatg cagccgccac aaaatcaggc aacactgtgg tgtgcgccat
     3841 acaaggtggc gatggtgaag ccactctaga aggcggcggt caaaacaagg gccactatgc
     3901 agggcatccg atactaaggt atgggaatgg cccttcacta tcaaccaaaa caaaattttg
     3961 gaaatcaacc ccccagcctt tgcctcctgg tacatatgag ccagcttacc ttggaggcag
     4021 agaccccaga gttgaggggg gcccatcctt acagcaggta ttaagggacc agttaaaacc
     4081 atttgccgag ccccgtggca gattacccga agcgggcttg ttggaagctg cagttgaaac
     4141 agtcaccaat gctattgaac aggtcatgga cacaccggtg gcatggagct atagtgatgc
     4201 ttgcatgtca ctagataaga caaccagttc cggccacccc catcacaaga agaaaaatga
     4261 tgattggaat gggaattcat ttgtgagaga attgggtgac caggcggcac acgctaacag
     4321 catgtatgag cttggtaagc ccatgaaacc tgtgtataca gcagccctaa aggatgagct
     4381 agtcaaacca gataaagtgt acacaaaaat caaaaagaga ctgctttggg gcgcggacct
     4441 cggtaccgtc attcgcgctg ccagagcatt tggaccattt tgtgaggcca taaaacccca
     4501 tgtaattaag ttgcctatta aggtgggcat gaatgccata gaggatggcc ccttgattta
     4561 tgctgagcac tccaagtata aatttcatta tgatgctgac tatacagctt gggactcaac
     4621 acaaaacaga gaaatcatga tggaatcttt caacattatg tgcaagctta cagccaatcc
     4681 ctccttggcc gcagtggtgg cacaggatct actctcccca tctgaaatgg atgttggtga
     4741 ctatgtgatc agtgtcaaag atggtttgcc atctggcttt ccatgcactt cacaggtgaa
     4801 cagtatcaac cactggatac tgaccctgtg tgcactgtca gaagtcactg gcttgtcccc
     4861 agatgtgata cagtcacagt cctacttctc attttatggt gatgatgaaa tagtctcaac
     4921 agatatagaa tttgacccaa ttagattgac acaaatattg aaggaatatg gtttgaagcc
     4981 tacaagacct gacaaaactg atggcccaat tattattaga caacaggttg atggcctggt
     5041 cttcctccgg cgcaccattt ctaaggatgc cattggatac cagggacgac ttgaccgtaa
     5101 ctctattgaa aggcagcttt ggtggactcg tggaccaaac catgaggacc catttgagac
     5161 actggtccca cattcacaga gaaaggtcca attaatatcc ttgctaggtg aagcagcact
     5221 ccacggtgaa aagttctaca ggaagatagc tggtagggtc attcaagaag tcaaagaggg
     5281 agggcttgaa atctacattc ctggttggca ggccatgttc cgctggatgc gattccatga
     5341 tctaagtttg tggacaggag accgcgatct cttgcccgat tatgtaaatg atgatggcgt
     5401 ctaaggacgc cccaacaaac atggatggca ccagtggtgc cggccagctg gtaccagagg
     5461 caaacacagc tgagcctata tcaatggagc ccgtggctgg ggcagcaaca gctgccgcaa
     5521 ctgctggcca agttaatatg attgacccct ggataatgaa caattatgta caagcccccc
     5581 aaggtgaatt taccatatcg cctaataaca caccaggtga cattttgttt gatttacaat
     5641 taggccccca ccttaaccct ttcttatctc atttggccca aatgtataat ggctgggttg
     5701 gcaatatgaa agtgaaggtt ctattggctg gtaatgcttt cacggctggt aaaataatca
     5761 ttagttgcat accccctggc tttgccgcac aaaatatttc tattgcccag gccaccatgt
     5821 tcccccatgt tatagctgat gttagggttt tggagcccat tgaggtgcca ttggaagatg
     5881 tgaggaatgt gctcttccac aacaatgata acacgccaac tatgcggttg gtgtgcatgc
     5941 tatacacccc cttgcgggcc agtggtagtt cgtctggaac tgaccccttt gtgattgctg
     6001 ggcgtgtttt gacatgccca agtcctgatt ttagcttttt gtttttggtc ccccccaatg
     6061 tagagcaaaa gactaaacct tttagtgtcc caaaccttcc attgaatacc ctttcaaatt
     6121 cgagagtccc ttctctaatc aaatcaatga tggtgtctag ggaccatggg cagatggttc
     6181 agtttcaaaa tggtagggtc accctagatg ggcagctgca aggcaccaca cccacatcag
     6241 ctagtcagct gtgcaaaatc agaggcagtg tctttcatgc caatggtggg aatgggtaca
     6301 acttaacaga actggatggg agcccatacc acgcatttga gagccccgcg ccaatagggt
     6361 ttccagatct aggtgaatgt gattggcaca tggaggcttc tcctaccacc caatttaata
     6421 ctggagatgt tataaaacaa attaatgtta aacaagagtc agcatttgcc ccccaccttg
     6481 gcaccgtaca ggtagacggc ctgagtgatg tgagtgtcaa caccaacatg atagctaaat
     6541 taggatgggt gtctcccgtc agtgatggac acaaagggga tgtcgacccg tgggtcattc
     6601 cacgctatgg ttcaaccctg actgaggccg cccaattagc ccccccaata tatcccccag
     6661 gctttggtga ggccattgtg tttttcatgt cagattttcc cattgcccat ggcaccaatg
     6721 gcttgagtgt gccctgcact ataccccaag aatttgtcac ccattttgtc aatgaacagg
     6781 cccccactag aggggaagca gccttgctac actatctgga ccctgatact aatagaaatc
     6841 ttggtgagtt taaattatat cctgatggct tcatgacttg tgtgcctaat tccagtggca
     6901 ctggcccaca aactcttcca atcaatggtg tctttgtctt tgtgtcctgg gtttctagat
     6961 tttatcaatt aaagcctgtg ggaacagccg gcccggctcg taggcttggg attaggagat
     7021 cataatggct caagctatac ttggagccat agcagcaaca gcagccggta gtgctgttgg
     7081 tgctggtata caggctggaa ccgaagctgc cctacagcat caaagatttc agcaagattt
     7141 gaccttacaa aagaattcct ttattcatga taaagagatg atgggcctac aggtagaggc
     7201 ttcaactgta ctcctccaaa acagcttggg tacgaggtac aatatgttga ccaaagcagg
     7261 gatgacatcc gcagacgcgg cacgtatggt agtgggggca cccgcgactc gtgtcgttga
     7321 ctggaacggg actaggatcg ccgcacccat gtcaactgcg acgacactta ggtctggtgg
     7381 tttcatgacc gtaccaactg tttatagggg tagtaaaaat aaacaatcaa ttggtggtgg
     7441 tttttctaat gtaaattatg atccctcagt ctcctcttcc cgcacttctc aatgggtctc
     7501 ttctcaaaat tcaatgcgtt ccactctgga accatttcat ccaggtgctc tgagaaccac
     7561 gtgggtcacc ccacctgggt caacttctac ttctacaatt tctacagttt ctactgtgcc
     7621 aaaattcttt aatacagaaa ggttaccctt attcgcaaac aggggtaagt gattttgtaa
     7681 tatgaattag tgggcatcat attcaatttg gaatcaatta gatatttaga ttggcagatg
     7741 atgtt
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