Typing tool

Complete norovirus genomes

MH218659  GI.3
 GI.P3

Length: 7,745 | 3 CDS

ORF1: 5..5404
ORF2: 5388..7025
ORF3: 7025..7672
LOCUS       MH218659                7745 bp    RNA     linear   VRL 11-JUN-2018
DEFINITION  Norovirus GI isolate NORO_198_10_11_2015, complete genome.
ACCESSION   MH218659
VERSION     MH218659.1
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_198_10_11_2015"
                     /host="Homo sapiens"
                     /db_xref="taxon:122928"
                     /country="United Kingdom"
                     /collection_date="10-Nov-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="AWR17635.1"
                     /translation="MKMASNDAIAVADVSNNNANTNNDNIGSRLMARIRGRLGPQRGE
                     TTTKITDANMALSLLRRSQTPSPSRQESPPKSQRDRPPRTASEVKKVLGWDVEPEHQE
                     STAKAWCDLTQEEKEEIMRNNEKLFDAGGVTPSTLPSTFERADPVDSPIEQQPVTWSA
                     NGGVDIGVNDLTTVSGPFWNMCPLPPLDARNNGPAKEPLIGDMIEFYEGHIFHYAIYI
                     GQGKTIGVHSPQAAFSIPRITIHPLVAWWRVCYVPTNQQRLTYDQLKELENEPWPYAS
                     ITNNCYEFCCRVMALDDTWLERRLVITGKFNHPTQDWSQDTPDFHQDSKLEMVRDAVL
                     SAINGLVSQPFKNILSKIKPLNVLNLLSNCDWTFMGVVELIVLLAELFDVFWTPPDIS
                     SFIASLLPEFHLQGPEDLARDLVPLILGGIGLAIGFTRDKVTKVMKSAVDGLRSATQL
                     GQYGLEIFSIIKKYFFGGDQTEKTLRGIEDAVIDMEVLSSTNVTQLVKDKKLARTYMN
                     VLDNEEEKARKLSVRSADPHIVTSVNNLISRISMARSALAKAQAEMTSRPRPVVIMMC
                     GPPGIGKTKAAEHLAGRLANEIRPGGKVGLVPRESIDHWDGYHGEDVLLWDDYGMSKI
                     TEDCNKLQAIADTAPLSLNCDRIENKGMQFSSDAIIITTNAPGPAPVDFVNLGPVCRR
                     VDFLVYCSAPEIEQMRRTHPGDANAIKDLYKRDYSHLKMELAPQGGFDSQGNTPFGKG
                     IMKPTTLNRLLIQATALAMERQDEFQLQGAVYNFDEDRVSAFTSLARANGLGLLSMAT
                     LGKRLRSVKSMEGLRNALVGYKIVECDIIWNTRVYSIKSDGSTVTIKEKQTPTSPQYQ
                     AISTATLALSRLRAARALAYASCLQSAVLSILQVAGSALVVSRAVKRMFGTRTEQPML
                     EGKHKEHNCRVHRAEAAGHGPIGHDGVIERYGLCESEQEEEGEQTVELPTANKEGKNK
                     GKTKKGRGRKSNFNAFSRRGLSDEEYEEYKKIREEKSGNYSIQEYLEDRQRYEEELAE
                     VQAGGDGGIGETEAEIRHRVFYKSKSGMRKQRQEERRQLGLVSGSEIRKRKPIDWTPP
                     KNDWSEDTRTVNYDEHISFEAPPSIWSRVVKFGSGWGFWVSSTVFITTTHVIPPGAKE
                     VFGEDLSNVAIHRVGEFTQFRFSKKMRPDLTGMVLEEGCPEGTVCTIMIKRDSGELLP
                     LAVRMGAVASMKIQGKLMHGQSGMLLTGANAKGMDLGTIPGDCGAPYVHKRGNDWVVC
                     GVHAAATKSGNTVVCAIQGGDGEATLEGGGQNKGHYAGHPILRYGNGPSLSTKTKFWK
                     STPQPLPPGTYEPAYLGGRDPRVEGGPSLQQVLRDQLKPFAEPRGRLPEAGLLEAAVE
                     TVTNTIEQVMDTPVAWSYSDACMSLDKTTSSGHPHHKKKNDDWNGNSFVRELGDQAAH
                     ANSMYELGKSMKPVYTAALKDELVKPDKVYTKIKKRLLWGADLGTVIRAARAFGPFCE
                     AIKPHVIRLPIKVGMNAIEDGPLIYAEHSKYKFHYDADYTAWDSTQNREIMMESFNIM
                     SKLTANPSLAAVVAQDLLSPSEMDVGDYVISVKDGLPSGFPCTSQVNSINHWILTLCA
                     LSEVTGLSPDVIQSQSYFSFYGDDEIVSTDIEFDPIRLTQVLKEYGLKPTRPDKTDGP
                     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="AWR17636.1"
                     /translation="MMMASKDAPTNMDGTSGAGQLVPEANTAEPISMEPVAGAATAAA
                     TAGQVNMIDPWIMNNYVQAPQGEFTISPNNTPGDILFDLQLGPHLNPFLSHLAQMYNG
                     WVGNMKVKVLLAGNAFTAGKIIISCIPPGFAAQNISIAQATMFPHVIADVRVLEPIEV
                     PLEDVRNVLFHNNDNTPTMRLVCMLYTPLRASGSSSGTDPFVIAGRVLTCPSPDFSFL
                     FLVPPNVEQKTKPFSVPNLPLNTLSNSRVPSLIKSMMVSRDHGQMVQFQNGRVTLDGQ
                     LQGTTPTSASQLCKIRGSVFHANGGDGYNLTELDGSPYHAFESPAPIGFPDLGECDWH
                     MEASPTTQFNTGELIKQINVKQESAFAPHLGTVQVDGLDGVNVNTNMIAKLGWVSPVT
                     DGHKKEVDPWVIPRYGSTLTEAAQLAPPIYPPGFGEAIVFFMSDFPITHGTNGLSVPC
                     TIPQEFVTHFVNEQAPTRGEAALLHYLDPDTNRNLGEFKLYPDGFMTCVPNSSGTGPQ
                     TLPINGVFVFVSWVSRFYQLKPVGTAGPARRLGIRRS"
     gene            7025..7672
                     /gene="ORF3"
     CDS             7025..7672
                     /gene="ORF3"
                     /codon_start=1
                     /product="VP2"
                     /protein_id="AWR17637.1"
                     /translation="MAQAILGAIAATAAGSAVGAGIQAGTEAALQHQRFQQDLTLQKN
                     SFIHDKEMMGLQVEASTALLQNSLGTRYNMLTKAGMTSADAARMVVGAPATRVVDWNG
                     TRIAAPMSTATTLRSGGFMTVPTVYRGSKNKQSIGGGFSNVNYDPSVSSSRTSQWVSS
                     QNSMRSTLEPFHPGALRTTWVTPPGSTSTSTISTVSTVPKFFNTERLPLFANRGK"
ORIGIN      
        1 gtgaatgaag atggcgtcca acgacgctat tgccgttgct gatgtcagca ataacaatgc
       61 taacaccaac aatgataaca ttggatcccg cctcatggcg aggatccgtg ggcgcttggg
      121 cccacaacgt ggtgaaacaa ccacaaaaat aacagacgcc aatatggcgc ttagtctgct
      181 acgccggtca caaacacctt ccccatcccg gcaagagagc cctcctaaaa gccagagaga
      241 tcgcccccct cggactgctt ctgaggtgaa gaaagtgttg gggtgggatg ttgaaccaga
      301 acaccaggaa agcacggcca aggcatggtg cgacctcacg caagaagaga aggaggagat
      361 aatgcgcaat aatgaaaagc tcttcgatgc tgggggagtc accccatcaa ctttgcctag
      421 cacgtttgaa agggccgacc cagtcgatag ccccattgaa cagcaacctg tgacatggtc
      481 tgctaatggt ggggtcgata ttggtgtcaa tgatttgacc accgtcagtg gcccattttg
      541 gaatatgtgc cccctcccgc cactggatgc tcggaataat ggccccgcta aggagcccct
      601 cataggagac atgatagagt tctatgaggg tcatatattc cattatgcca tctatattgg
      661 acaaggtaag accattgggg tccactcacc gcaagcagct ttctccatac caaggataac
      721 catccatcct ctggtagcct ggtggcgcgt gtgctacgtt ccaactaacc agcagcgcct
      781 cacttatgac cagctcaaag agttggagaa tgagccatgg ccctacgctt ccattacaaa
      841 caattgctat gagttttgct gcagagtgat ggcacttgac gatacatggc ttgagaggag
      901 gttagtcatc actggaaaat tcaatcaccc cacacaagat tggtcacagg ataccccgga
      961 ttttcaccag gactcgaaac ttgagatggt aagagatgcc gtgctatcag ctattaatgg
     1021 ccttgtgtca cagcccttta aaaacatttt gtcaaagatc aaaccattaa acgttctcaa
     1081 tctcttgtca aattgtgatt ggaccttcat gggggttgtg gaactgattg tgctcctagc
     1141 ggagttgttt gatgtgttct ggaccccacc agacatctca agtttcattg cctcactact
     1201 acctgaattt cacctgcagg gcccagaaga cctagctagg gacttggtcc ctctcatcct
     1261 aggtggtata ggcctggcta ttggctttac aagagacaaa gtgacgaaag tgatgaagag
     1321 tgccgtcgat gggttgagat cggcgacaca gctcgggcag tacgggctgg aaatattctc
     1381 aatcatcaag aaatatttct ttggtgggga tcaaacggaa aagaccttac ggggtattga
     1441 ggatgcagtg atagacatgg aggtgttatc tagcaccaat gtgacacaat tggttaaaga
     1501 taagaaattg gccagaacct acatgaatgt gctagacaat gaagaggaaa aagcaaggaa
     1561 actctcagtc cgtagtgctg atccgcacat agtgacctca gttaacaatc tgatatcacg
     1621 aatatctatg gcaagatcag ccttggccaa agcccaggct gagatgacat ctcgcccacg
     1681 ccctgtggtc ataatgatgt gtggcccccc cggcatcgga aaaaccaagg ccgccgaaca
     1741 cctggctggc cgattggcaa acgagattag accaggaggt aaggttggac ttgtgccccg
     1801 ggaatccata gatcactggg acggatacca tggcgaggat gtcctactat gggatgacta
     1861 tggcatgtca aagataacag aggactgtaa caagctacaa gccatagctg acactgcacc
     1921 cctatcactt aattgtgaca ggatagagaa caaaggcatg caattctcct cagatgcaat
     1981 aatcataacc accaatgccc ctggcccggc cccggtggac tttgtcaacc taggccctgt
     2041 gtgcaggcga gtggactttt tagtttactg ttctgcccct gaaattgagc aaatgagaag
     2101 gacccaccct ggtgatgcca atgccatcaa agacctatac aaaagggact actcacactt
     2161 aaagatggaa ttggccccac aaggtggttt tgatagtcag ggtaacacac catttgggaa
     2221 gggcatcatg aaacccacga ccctcaatag gctactcatt caggcaacag cattagctat
     2281 ggagcggcaa gacgagttcc agctccaagg tgctgtctac aactttgatg aagacagagt
     2341 gtccgccttc acaagcctgg cccgagctaa cggcttgggg cttttaagca tggcaacatt
     2401 gggtaaaagg ctcagaagtg tcaaatctat ggagggcctg cgtaacgcat tggtgggcta
     2461 caaaatagta gagtgtgata taatctggaa cactagagtg tattcaatta aaagtgatgg
     2521 tagtactgtc acaatcaagg aaaaacaaac cccaacttca ccccaatacc aagccattag
     2581 cacagccact cttgcactct ctaggttgcg ggccgctaga gctctcgcgt acgcctcctg
     2641 cctgcagagt gcagtgctgt caatacttca agtagctggc tctgccctgg tggtgagtag
     2701 agccgttaag cgcatgtttg gcacgcgcac tgaacaacct atgttggaag gcaaacacaa
     2761 agaacacaac tgtagagtgc accgcgcaga ggcagctggc catggtccta ttgggcacga
     2821 tggagtcatc gaacgctatg gcctctgtga gagtgagcaa gaagaagaag gcgagcaaac
     2881 agttgagcta cccactgcca ataaagaagg caaaaacaag ggcaagacca aaaagggccg
     2941 tggacgaaaa tccaatttta atgctttctc aagacgaggc ctcagtgatg aagaatatga
     3001 agaatacaag aagatcagag aagaaaagag tggcaattac agcatccagg agtacctcga
     3061 ggaccgccag cgatatgagg aagaacttgc tgaagtgcaa gctggtgggg atggtggaat
     3121 tggtgagact gaagcagaga ttcgccatcg ggttttctat aaatcaaaat ccggcatgag
     3181 aaagcaacgc caagaagaac ggcgtcagtt gggtctcgtt agcggttctg agatccgcaa
     3241 acgcaagccc atagactgga ccccccctaa gaacgattgg tcagaagaca ccaggactgt
     3301 caactatgat gaacatatta gctttgaagc tcctccctca atttggagta gggtggtgaa
     3361 gtttggcagt ggttggggtt tttgggtgag ctcaacagtg ttcataacca cgacccatgt
     3421 cataccacct ggggccaaag aagtctttgg tgaagacctc agtaacgtgg ccatccatag
     3481 ggttggtgag ttcacccagt tccgtttctc caaaaagatg agacctgacc tcaccggtat
     3541 ggttttagaa gaaggttgcc cagagggaac agtgtgcacc ataatgatca aaagagattc
     3601 tggtgagttg ctgccgctcg ccgttcggat gggggcagtg gcatcaatga agatccaagg
     3661 caaacttatg catgggcaat caggaatgtt actcaccggt gctaatgcca aaggcatgga
     3721 ccttgggact atacccggtg attgtggggc accctatgtc cacaagaggg gaaatgactg
     3781 ggtggtctgt ggagtacatg cagccgccac aaaatcaggt aacactgtgg tgtgcgccat
     3841 acaaggtggc gatggtgaag ccactctaga aggcggcggt caaaacaagg gccactatgc
     3901 agggcatccg atactaaggt atgggaatgg cccttcacta tcaaccaaaa caaaattttg
     3961 gaagtcaacc ccccagcctt tgcctcctgg tacatatgag ccagcttacc ttggaggcag
     4021 agaccccaga gttgaggggg gcccatcctt acagcaggtg ttaagagacc agttaaagcc
     4081 atttgccgag ccccgtggca gattacccga agcgggtttg ttggaagctg cagttgaaac
     4141 ggtcaccaat actattgaac aggtcatgga cacaccggtg gcatggagct atagtgatgc
     4201 ttgcatgtca ctagataaga caaccagctc cggccacccc caccacaaga agaaaaatga
     4261 tgattggaat gggaattcat ttgtgagaga attgggtgac caggcggcac acgctaacag
     4321 catgtatgag cttggtaagt ccatgaagcc tgtgtataca gcagccctaa aggatgagct
     4381 agtcaaacca gataaggtgt atacaaaaat caaaaagaga ctgctttggg gcgcggacct
     4441 cggtactgtc attcgcgctg ccagagcatt tggaccattt tgtgaggcca taaaacccca
     4501 tgtaattagg ttgcctatca aggtgggtat gaatgccata gaggatggcc ccttgattta
     4561 tgctgagcac tccaaatata aatttcatta tgatgctgac tatacagctt gggactcaac
     4621 acaaaacaga gaaatcatga tggaatcttt caacattatg agcaagctta cagccaatcc
     4681 ctccttggcc gcagtggtgg cacaggatct actctcccca tctgaaatgg atgttggtga
     4741 ctatgtaatc agtgtcaaag atggtttacc atctggcttt ccatgcactt cacaggtgaa
     4801 cagtatcaac cactggatac taaccctgtg tgcactatca gaagtcactg gcttgtcccc
     4861 agatgtgata cagtcacaat cctacttctc attttatggt gatgatgaaa tagtctcaac
     4921 agatatagaa tttgacccaa tcagattgac acaagttctg aaggaatatg gtttgaagcc
     4981 tacaagacct gacaaaactg atggcccaat tattattaga caacaggttg atggcctggt
     5041 cttcctccgg cgcaccattt ctaaggatgc cattggatac cagggacgac tcgaccgtaa
     5101 ctctattgaa aggcagcttt ggtggactcg tggaccaaac catgaggacc catttgagac
     5161 actggttcca cattcacaga gaaaggtcca attaatatcc ttgctaggtg aagcagcact
     5221 ccacggtgaa aagttctaca ggaagatagc tggtagggtc attcaagaag tcaaagaggg
     5281 agggcttgaa atctacattc ctggttggca ggccatgttc cgctggatgc gattccatga
     5341 tctaagtttg tggacaggag accgcgatct cctgcccgat 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 tattttgttt gatttacaat
     5641 taggccccca ccttaaccct ttcttatctc atttggccca aatgtataat ggctgggttg
     5701 gcaatatgaa agtaaaggtt ctattggctg gtaatgcttt tacggctggt aaaataatta
     5761 ttagttgcat accccctggc tttgccgcac aaaatatttc tattgcccag gccaccatgt
     5821 tcccccatgt catagctgat gttagggttt tggaacccat tgaggtgcca ttggaagatg
     5881 tgaggaatgt gctcttccac aacaatgaca acacgccaac tatgcggttg gtgtgcatgc
     5941 tatacacccc cttgcgggcc agcggtagct cgtctggaac tgaccccttt gtgattgctg
     6001 ggcgtgtttt gacatgccca agtcctgatt ttagcttttt gtttttggtc ccccccaatg
     6061 tagagcaaaa gactaaacct ttcagtgtcc caaaccttcc attgaatacc ctttcaaatt
     6121 cgagagtccc ttctctaatc aaatcaatga tggtgtccag ggaccatggg cagatggttc
     6181 agttccaaaa tggtagggtc accctagatg ggcagctgca aggcaccaca cccacatcag
     6241 ctagtcagct gtgcaaaatc aggggcagtg tcttccatgc caatggtggg gatgggtata
     6301 acttaacaga attggatggg agcccatacc acgcatttga gagccccgca ccaatagggt
     6361 ttccagatct aggtgaatgt gattggcaca tggaggcttc tcctaccacc caatttaata
     6421 ctggagaact tataaaacaa atcaatgtta aacaagagtc agcatttgcc ccccaccttg
     6481 gcaccgtaca ggtagacggc ctggatggtg tgaatgtcaa caccaacatg atagctaaat
     6541 taggatgggt gtctcctgtc actgatggac acaaaaagga agtcgacccg tgggtcattc
     6601 cacgctatgg ttcaaccctg actgaggccg cccaattagc ccccccaata tatcccccag
     6661 gctttggtga ggccattgtg tttttcatgt cagattttcc cattacccat ggcaccaatg
     6721 gtttgagtgt gccttgcact ataccccaag aatttgtcac ccattttgtc aatgaacagg
     6781 cccctactag aggggaagca gccctactac actatctgga ccctgatact aatagaaatc
     6841 ttggtgagtt taaattatat cctgatggct tcatgacatg tgtgcctaac tccagtggca
     6901 ctggtccaca aactcttcca atcaatggcg tctttgtctt tgtgtcctgg gtttctagat
     6961 tttatcaatt aaagcctgtg ggaacagccg gcccggctcg taggcttggg attaggagat
     7021 cataatggct caagccatac ttggagccat agcagcaaca gcagccggta gtgctgttgg
     7081 tgctggtata caagctggaa ccgaagctgc cctacagcat caaagatttc agcaagattt
     7141 gaccttacaa aagaattcct ttatccatga taaagagatg atgggcctac aggtagaggc
     7201 ttcaactgca ctccttcaaa acagcttggg tacgaggtac aatatgttga ccaaagcagg
     7261 gatgacatcc gcagatgcgg 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 accgtttcat ccaggtgctc tgagaaccac
     7561 atgggtcacc ccacctgggt caacttctac ttctacaatt tctacagttt ctactgtgcc
     7621 aaaattcttt aatacagaaa ggttaccctt attcgcaaat aggggtaagt gattttgtaa
     7681 tatgaattag tgggcatcat attcaatttg gaatcaatta gatatttaga ttggcagatg
     7741 atgtt
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