Typing tool

Complete norovirus genomes

MH218721  GI.3
 GI.P13

Length: 7,704 | 3 CDS

ORF1: 5..5404
ORF2: 5388..7025
ORF3: 7025..7672
LOCUS       MH218721                7704 bp    RNA     linear   VRL 11-JUN-2018
DEFINITION  Norovirus GI isolate NORO_80_24_09_2014, complete genome.
ACCESSION   MH218721
VERSION     MH218721.1
KEYWORDS    .
SOURCE      Norovirus GI
  ORGANISM  Norovirus GI
            Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes;
            Picornavirales; Caliciviridae; Norovirus.
REFERENCE   1  (bases 1 to 7704)
  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 7704)
  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..7704
                     /organism="Norovirus GI"
                     /mol_type="genomic RNA"
                     /isolate="NORO_80_24_09_2014"
                     /host="Homo sapiens"
                     /db_xref="taxon:122928"
                     /country="United Kingdom"
                     /collection_date="24-Sep-2014"
                     /note="genotype: GI.Pd_GI.3"
     gene            5..5404
                     /gene="ORF1"
     CDS             5..5404
                     /gene="ORF1"
                     /codon_start=1
                     /product="nonstructural polyprotein"
                     /protein_id="AWR17821.1"
                     /translation="MMMASNDAIAVADVSNNNANTNNENIGSRLMAKIRGRIGPQRGE
                     TTTKIKDADMALDLLRRSQTPSPCRQDSAPKAQRDRPPRTASEVKRALGWDAEPEHQE
                     STARAWCDLSKEEKEEIIRNNERLFDAGGVTPSTLPSTFERTDSSSVTDEQQPVTWSS
                     NGGVDLGINELTTVRGPFWNMCPLPPLEARNSGPAKEPLIGDMVEFYEGHIFHYAIYI
                     GQGKTIGVHSPQAAFSIPRITIHPLVAWWRVCYIPTSQQRLTYEQLKELENEPWPYAS
                     ITNNCYEFCCKVMALDDTWLQRRLVTSGKFNHPTQDWSQDTPDFHQDSKLEMVRDAVL
                     SAINGLVSQPFKNILSKIKPLNVLNLLSNCDWTFMGVVELVVLLAELFDVFWTPPDIS
                     SFIASLLPDFHLQGPEDLARDLVPLILGGIGLAIGFTRDKITKVMKSAVDGLRSATQL
                     GQYGLEIFSIIKKYFFGGDQTEKTLRGIEDAVIDMEVLSSTNVTQLVKDKKLAKAYMN
                     VLDNEEEKARKLSVRSADPHIVTSVNNLISRISMARSALAKAQAELTSRPRPVVIMMC
                     GPPGIGKTKAAEHLAGRLAAEIRPGGKVGLVPRESIDHWDGYHGEDVLLWDDYGMSKI
                     TEDCNKLQAIADTAPLSLNCDRIENKGMQFSSDAIIITTNAPGPAPVDFVNLGPVCRR
                     VDFLVYCSAPEIEQTRRAHPGDTNAIKDLFKKDFSHLKMELAPQGGFDSQGNTPFGKG
                     VMKTTTLNRLLIQATALAMERQDEFQLQGAVYNFDEDRVAAFTNLARANGLGLISMAT
                     LGKKLRSVKSMEGLRNALLGYKIGECNIIWNTRVYSVKSDGSNVTIKEKQAPSSPQHQ
                     AISTATLALSRLRAARALAYASCLQSAVLSILQVAGSALVVSRAVKRMFGTRTEQPIL
                     EGKHKEHNCRVHRAEAAGHGPIGHDGIIERYGLCESEQEGEDDQTVELPTAGKEGKNK
                     GKTKKGRGRKSNFNAFSRRGLSDEEYEEYKKVREEKGGNYSIQEYLEDRQRYEEELAE
                     VQAGGDGGIGETEAEIRHRVFYKSKSGLRKQRQEERRQLGLVSGTEIRKRKPIDWTPP
                     KNDWSEDTRTVNYDEHISFEAPPSIWSRVVKFGSGWGFWVSSTVFITTTHVIPPGAKE
                     IFGENISNIAIHRVGEFTQFRFSKKMRPDLSGMVLEEGCPEGTVCTIMIKRDSGELLP
                     LAVRMGAVASMKIQGKLMHGQSGMLLTGANAKGMDLGTIPGDCGAPYIHKRGNDWVVC
                     GVHAAATKSGNTVVCAIQGGEGEATLEGGDQNKGHYAGHPILRYGSGPSLSTKTKFWK
                     SNPQPLPPGTYEPAYLGGKDPRVEGGPSLQQVLRDQLKPFAEPRGRLPEAGLLEAAVE
                     TVTNAIEQVMDTPVAWSYSDACMSLDKTTSSGYPHHKRKNDDWNGSSFVRELGDQAAH
                     ANSMYELGKSMKPVYTAALKDELVKPDKVYNKIKKRLLWGADLGTVIRAARAFGPFCE
                     AIKPHVIKLPIKVGMNAIEDGPLIYAEHSKYKYHFDADYTAWDSTQNREIMMESFNIM
                     CKLTANPSLAAVVAQDLLSPSEMDVGDYVISVKDGLPSGFPCTSQVNSINHWIYTLCA
                     LSEVTGLAPDVIQSQSYFSFYGDDEIVSTDIEFDSNRLTQVLKEYGLKPTRPDKTDGP
                     IIVRQQVDGLVFLRRTISKDAIGYQGRLDRNSIERQLWWTRGPNHDDPFETLVPHTQR
                     KVQLISLLGEAALHGEKFYRKIASRVIQEVKEGGLEIYIPGWQAMFRWMRFHDLSLWT
                     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="AWR17822.1"
                     /translation="MMMASKDAPTNMDGTSGAGQLVPEANTAEPISMEPVAGAATAAA
                     TAGQVNMIDPWIMNNYVQAPQGEFTISPNNTPGDILFDLQLGPHLNPFLSHLAQMYNG
                     WVGNMKVKVLLAGNAFTAGKIIISCIPPGFVSQNISIAQATMFPHVIADVRVLEPIEV
                     PLEDVRNVLFHNNDNTPTMRLVCMLYTPLRASGSSSGTDPFVIAGRVLTCPSPDFSFL
                     FLVPPNVEQKTKPFSVPDLPLNVLSNSRVPSLIKFMMVSQDHGQMVQFQNGRVTLDGQ
                     LQGTTPTSASQLCKMRGTVYHASGGQGLNLTEIDGTPYHAFESPAPIGFPDIGDSDWH
                     INASPATAFGSGESVKRLDMEQGSSFAPHLGTVQLYYMPAMRANTDLICSLEWLSPPS
                     GGTPNKVNPWAIPRYGSTLTEAAQLAPPIYPPGFGEAIVFFMSDFPIANGQDGLRVPC
                     TIPQEFVTHFVNEQAPTRGEAALLHYVDPDTHRNLGEFKLYPEGFMTCVPNSSGSGPQ
                     TLPINGVFTFVSWVSRFYQLKPVGTTGPVRRLGIRRS"
     gene            7025..7672
                     /gene="ORF3"
     CDS             7025..7672
                     /gene="ORF3"
                     /codon_start=1
                     /product="VP2"
                     /protein_id="AWR17823.1"
                     /translation="MAQAIFGAIAATAAGSAVGAGIQAGTEAALQHQRFQQDLTLQSN
                     TFKHDKEMLGLQVGASTALLQNSLNTRYNMLTNAGLSSSDAARVVVGAPATRVVDWNG
                     TRVSAPQSTATTLRSGGFMTIPTLYKGKQQQKPTEIGLSNPNYGSSVSSSRVADWVSS
                     QNSSRSSLGPYHPSALQTTWVTPPGSSSTSTISSVSTAPRYFNTDRLPLFANMRK"
ORIGIN      
        1 gtgaatgatg atggcgtcta acgacgctat tgccgttgct gatgtcagca ataacaatgc
       61 taacaccaac aatgaaaaca taggatctcg ccttatggca aagatccgtg ggcgtatagg
      121 cccacaacgt ggtgaaacaa ccacaaagat caaagatgcc gacatggcgc tcgacctttt
      181 gcgccggtca caaacaccat ctccatgtcg gcaagacagc gcccccaagg ctcaaaggga
      241 ccgtcccccg cggaccgctt cagaggtaaa aagggcgctg gggtgggatg ctgaaccaga
      301 acaccaagaa agcacggcta gggcatggtg tgacctctca aaagaggaga aggaagagat
      361 aatacgtaac aatgagaggc tttttgacgc tggaggtgtc actccatcga ccctgcccag
      421 cacatttgag aggactgatt caagcagtgt cactgacgaa caacaacctg tgacatggtc
      481 ttctaatgga ggggttgacc ttggcatcaa tgaattgacc acagttcgtg gcccgttttg
      541 gaacatgtgc cccctcccac cactagaagc ccgtaatagt ggccctgcta aggaacccct
      601 tataggtgac atggtcgagt tctatgaagg acacatattc cattatgcca tttacatcgg
      661 acagggcaag actattggag tccactcacc acaggccgct ttttccatac ccagaataac
      721 catccaccca ctggtggcct ggtggcgtgt gtgttacatc cccactagcc aacaacgcct
      781 tacctacgaa cagcttaagg agttggagaa tgaaccatgg ccctatgcct caatcaccaa
      841 caactgttat gagttttgct gtaaagtgat ggcacttgat gatacctggc tccaaagaag
      901 actggttact agtggaaaat ttaaccaccc tacacaggac tggtcacagg acaccccaga
      961 tttccatcag gattcgaagc ttgaaatggt aagggacgct gtcttgtcgg ccatcaacgg
     1021 tcttgtatca caacccttta agaacatcct gtctaaaatt aaaccattaa atgtgcttaa
     1081 tcttttatca aactgtgatt ggaccttcat gggcgtcgtg gaactggtag tgctcctggc
     1141 agaactgttt gatgtgttct ggaccccacc agatatttca agcttcattg catctttact
     1201 acctgatttt catctacaag gcccagaaga cctagccagg gacttagttc ccctcatatt
     1261 gggtggcata ggcttagcaa ttggttttac aagagacaaa ataacaaaag tgatgaagag
     1321 cgccgttgat gggctgcggt cagcaacgca gctcggacaa tatggactgg agatattctc
     1381 aattatcaag aaatacttct ttggagggga ccaaacagaa aagaccctgc gaggcattga
     1441 agatgcggtg atagacatgg aagtgttgtc cagcaccaat gtgacacaac tagtcaaaga
     1501 taagaagtta gccaaagctt acatgaatgt actggacaat gaggaggaaa aagcaagaaa
     1561 gctctcagtc cgtagtgctg acccacatat agtgacctct gtcaacaact tgatatcacg
     1621 catctctatg gcaagatcag ctctggctaa agcccaagct gagttgacgt cccgcccacg
     1681 accagtggtt ataatgatgt gtggtcctcc tggtatcgga aagactaagg ccgctgagca
     1741 cctagccggc cgactagctg ctgaaatcag acctggaggt aaagttggcc ttgtgccccg
     1801 ggagtccata gaccattggg atggatatca tggcgaggac gtcttgctct gggatgacta
     1861 tggcatgtca aagataacag aggattgtaa taagttacag gctatagctg atactgcacc
     1921 actgtcactt aattgtgaca gaatagaaaa caaaggcatg caattctctt ctgatgcaat
     1981 aattataacc accaatgccc ctggcccagc cccagtcgac tttgtcaact taggccccgt
     2041 gtgcagacga gtggactttt tagtttactg ttctgcaccc gagattgaac aaacgcggag
     2101 ggctcatcca ggtgacacca atgccatcaa ggatctgttt aaaaaggact tctcacactt
     2161 gaaaatggaa ctggctccac agggcggctt tgatagtcag ggcaatacac cttttgggaa
     2221 gggtgtcatg aaaaccacaa ccctcaatag gctactgata caggccacag cattagccat
     2281 ggagcgacaa gatgaattcc aactccaggg ggctgtctac aactttgacg aggatagagt
     2341 ggccgccttc accaatctag ctcgagctaa tggcctgggg cttataagta tggcaacatt
     2401 aggcaagaag ttgagaagtg ttaagtccat ggaaggcttg cgcaatgcac tactgggata
     2461 caagattgga gagtgcaata taatctggaa caccagggtg tattcagtta agagtgacgg
     2521 gagcaatgtc acaattaaag aaaagcaggc accgtcctca ccccaacatc aagctatttc
     2581 cacagccacc ctggcgctct ctagactgcg ggctgccaga gcccttgcgt acgcttcctg
     2641 cttacaaagt gcagtgttgt caatacttca ggttgccggc tctgccttag tggtgagcag
     2701 ggctgtaaaa cgcatgtttg gcacacgcac cgaacagccc attctggagg gtaagcataa
     2761 agaacacaac tgcagagtac accgtgcaga ggccgccggt catggcccca ttggccatga
     2821 tggaatcatt gaacgttatg gtctgtgtga gagtgagcag gaaggagaag atgaccaaac
     2881 tgtggagttg cccactgctg gcaaagaagg caagaacaaa ggcaaaacca aaaagggccg
     2941 cggacggaaa tccaacttca atgcattctc taggcgtgga cttagtgatg aggaatacga
     3001 ggagtacaag aaagtaagag aagagaaggg tggcaactac agcatacaag agtaccttga
     3061 ggaccgccag cgctatgaag aagaactcgc tgaggtgcaa gctggtggag atggtggaat
     3121 cggcgaaact gaagctgaga tccgccaccg tgttttctat aaatcaaagt ctggcttgag
     3181 aaaacagcgg caagaggaac gccgccagtt aggcctcgtg agcggtactg aaatccgcaa
     3241 acgcaaaccc atagactgga ccccccccaa aaatgattgg tcagaggaca ctagaactgt
     3301 taattatgat gaacacatca gctttgaagc ccccccttca atctggagta gagtagttaa
     3361 atttggcagt ggctggggtt tttgggtgag ttcaacagtg ttcatcacca caacacatgt
     3421 tataccacct ggtgctaaag agatctttgg tgagaacatt agcaatattg ccatccatag
     3481 agttggcgaa ttcactcaat tccgtttttc caagaaaatg aggcctgacc tctctggcat
     3541 ggtcctggaa gagggatgcc ctgagggcac agtgtgcacc ataatgataa aaagagactc
     3601 tggagaactg ttgccgctgg ctgttcgtat gggagcagtg gcctcaatga agatccaagg
     3661 gaagctcatg catggacagt cagggatgtt gctcaccggt gccaacgcca agggcatgga
     3721 ccttggcacc atacctgggg attgtggagc gccctatatc cataagagag ggaatgactg
     3781 ggtggtttgt ggggtgcatg cagcagccac gaaatcaggc aataccgtgg tgtgcgccat
     3841 acaaggtggt gaaggtgaag ccacgctaga gggtggcgat caaaataagg gtcattatgc
     3901 aggacaccca atactaagat atggtagtgg cccttcattg tcaactaaaa caaagttttg
     3961 gaaatcaaac ccccaacctc taccccctgg tacatatgaa ccagcctacc tcggtggcaa
     4021 agaccccagg gttgaaggtg gtccatcttt gcagcaagtg ttgcgagacc agctaaaacc
     4081 atttgctgaa ccccgtggca ggttgcctga agcaggattg ctagaagccg cggttgaaac
     4141 tgtcaccaat gcaattgaac aggtcatgga cacacctgtg gcatggagtt acagcgacgc
     4201 ctgcatgtcc ttggacaaaa caaccagttc tggctaccct catcacaaaa ggaagaatga
     4261 tgactggaac gggagttcat ttgtgagaga attgggagac caggcagcgc atgctaatag
     4321 catgtatgag cttggtaaat ctatgaaacc agtgtacaca gcagcactca aggatgagct
     4381 tgttaagcca gacaaggtgt acaataaaat taagaaaagg ctactctggg gggcggacct
     4441 cggcaccgtc atacgtgctg ctagggcttt tgggccattt tgtgaagcaa taaagcccca
     4501 tgtgattaag ttgcccatta aagtgggcat gaatgccata gaagatggac ccttaattta
     4561 tgcagaacac tccaaatata agtatcactt tgatgctgat tacacagcat gggactcaac
     4621 acaaaacagg gagattatga tggagtcctt taacatcatg tgtaaactca ccgctaatcc
     4681 ctccctggcc gcagtggtgg cacaggacct gctctctcct tctgagatgg atgtcggtga
     4741 ttatgtgatc agtgtcaaag atggtctacc atctggcttt ccatgcacct cacaagtgaa
     4801 cagtatcaac cattggatct acactttgtg cgccttatca gaggttactg gtttggctcc
     4861 tgatgtaata cagtcacagt cttacttttc attttatggt gatgatgaaa tagtttcaac
     4921 agatattgaa tttgactcaa acagactaac acaggtgcta aaagagtatg gcctaaaacc
     4981 cacaagacct gataaaactg atggtccgat cattgtaagg caacaggttg atggcttggt
     5041 tttccttcgg cgcaccatct cgaaggatgc catcgggtac cagggtcggc ttgatcgcaa
     5101 ttccattgaa agacagctct ggtggacccg agggcccaat catgatgatc catttgaaac
     5161 cttggtccca cacacacaga ggaaggtcca attaatatcc ctattaggtg aggccgcact
     5221 ccatggtgag aaattttata gaaagatagc cagtagggtg atccaggagg ttaaagaagg
     5281 aggattggaa atttacatcc ctgggtggca ggccatgttc cgctggatgc gattccatga
     5341 tttgagtttg tggacaggag accgcgatct cctgcccgat tatgtaaatg atgatggcgt
     5401 ctaaggacgc cccaacaaac atggatggca ccagtggtgc cggccagctg gtaccagagg
     5461 caaatacagc tgagcctata tcaatggagc cagtggctgg ggcagcgaca gctgccgcaa
     5521 ccgctggcca agttaacatg attgacccct ggattatgaa taattatgtg caagccccac
     5581 aaggtgaatt caccatatca ccaaacaaca caccaggtga tattctattt gatttacaat
     5641 taggccctca cctcaacccc tttctatccc atttggctca aatgtacaat gggtgggtag
     5701 gtaacatgaa agtgaaagtt ctattggcag gtaatgcttt cacggcagga aaaattatta
     5761 ttagttgtat accccctggt tttgtctcac agaatatatc tatagctcaa gctacaatgt
     5821 tcccccacgt tatagctgat gtcagggtcc tggagcccat tgaggtccca ttggaggatg
     5881 tgaggaatgt gttgttccac aataatgata acacaccaac catgagactg gtatgcatgc
     5941 tctacacccc cttgcgtgcc agcggaagct catctgggac agaccccttt gtgattgctg
     6001 ggcgtgtgtt gacctgccct agccctgatt ttagcttctt attcttggtg ccccccaatg
     6061 tagaacaaaa gactaaacct tttagtgttc cagatctccc actcaatgtt ctatcaaatt
     6121 caagggtgcc gtcactgata aaattcatga tggtgtcaca ggaccatgga cagatggtac
     6181 aatttcagaa tggcagggtc acactggatg gacagctcca gggcaccaca ccaacatcgg
     6241 ccagccagct ctgcaagatg cgggggacgg tttaccatgc ctccggtggt caagggctca
     6301 atttaactga gattgatggc accccctatc atgcatttga aagcccagct cccattggtt
     6361 tccctgacat aggagacagc gattggcata tcaacgcttc acccgccacc gctttcggca
     6421 gtggcgaaag cgtcaaaaga ctagatatgg aacagggctc ttcatttgcc ccacatttgg
     6481 gtactgtaca gctatactac atgccagcta tgagagctaa cactgacctg atctgctcat
     6541 tggagtggct atccccgcct agcggaggca ctccaaacaa agtcaaccct tgggccattc
     6601 cacggtatgg ttcaacttta actgaagctg ctcagctagc cccaccaatt tacccccctg
     6661 gctttggaga agctatagtt ttctttatgt ctgattttcc tatagcaaat ggtcaagatg
     6721 ggttaagagt gccctgcact ataccccaag aatttgtaac ccattttgtc aatgaacaag
     6781 caccaacccg tggggaagct gcccttcttc attatgttga ccccgacaca catcgcaatt
     6841 tgggtgagtt taagttatac cctgaaggat ttatgacttg tgtaccaaat tctagtggta
     6901 gtggtcccca aacgctgcct atcaatggag tcttcacttt tgtctcttgg gtttcccgtt
     6961 tctatcaatt aaagcctgtg ggaacgaccg gaccggttcg taggctagga atcaggagat
     7021 cataatggcc caggcaatat ttggagcaat agctgcgacg gctgctggta gcgctgtggg
     7081 tgcaggcatt caggctggta ctgaggccgc actccaacat cagcggttcc agcaggattt
     7141 aacgttgcag agcaacactt tcaaacatga caaagaaatg ctagggctac aggttggtgc
     7201 ctccactgct cttttgcaaa acagcctcaa cacccgctac aacatgctca caaatgctgg
     7261 tctctcgtcc tcagatgcag cacgcgtggt ggttggcgcg ccagctacac gtgttgttga
     7321 ctggaacggc accagggtgt cagcaccaca atctacagct accacgttga ggtctggtgg
     7381 gttcatgaca atcccaactc tgtacaaggg caaacaacag cagaaaccaa ctgaaattgg
     7441 cttatctaac ccaaattatg gttcatctgt ctcgtcttct agggttgctg attgggtttc
     7501 ctctcaaaat tcttctcgct catccttggg cccgtatcac cccagtgctt tgcagacaac
     7561 atgggtgacc ccacccggtt ctagttctac ttctactatt tcttctgtgt ctactgcacc
     7621 tagatatttc aatactgata ggttgcctct attcgcaaat atgaggaaat aatttttgta
     7681 atatgaaaga tcggaaggcg tcgt
//