Typing tool

Complete norovirus genomes

MH218687  GII.6
 GII.P7

Length: 7,546 | 3 CDS

ORF1: 5..5098
ORF2: 5079..6722
ORF3: 6722..7498
LOCUS       MH218687                7546 bp    RNA     linear   VRL 11-JUN-2018
DEFINITION  Norovirus GII isolate NORO_229_12_01_2016, complete genome.
ACCESSION   MH218687
VERSION     MH218687.1
KEYWORDS    .
SOURCE      Norovirus GII
  ORGANISM  Norovirus GII
            Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes;
            Picornavirales; Caliciviridae; Norovirus.
REFERENCE   1  (bases 1 to 7546)
  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 7546)
  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..7546
                     /organism="Norovirus GII"
                     /mol_type="genomic RNA"
                     /isolate="NORO_229_12_01_2016"
                     /host="Homo sapiens"
                     /db_xref="taxon:122929"
                     /country="United Kingdom"
                     /collection_date="12-Jan-2016"
                     /note="genotype: GII.P7_GII.6"
     gene            5..5098
                     /gene="ORF1"
     CDS             5..5098
                     /gene="ORF1"
                     /codon_start=1
                     /product="nonstructural polyprotein"
                     /protein_id="AWR17721.1"
                     /translation="MKMASNDATTAFGSQNSVNDSTNTAPSNKEEVGAFSNIKVGFKK
                     MLGAVPKGTKAPSSDQHCPTVKIGTKTLTVPPEPPNGEDIVQFDAKSETVRGLPDLTT
                     VQNEHENTPYTVPPLSEREHRPATEPLPGTILEMWDGEFYHYSVYVSGGKALGVHKPP
                     AAISLATIELTPISLYWRPVYTPNYLVHPDTLKGLAGEKFPYTAFSNNCYNFCCWVLE
                     LNDTWLSRKSISRTTGFFKPYQSWNRKPLPTVDDGKIKKVANAILCALGSLFSKPIKD
                     LLGKLKPLNLLHLLASCDWTFAGIVETVILMAELFNIFWTPPDVSSFIASLIGDFELQ
                     GPEDLAVELVPVVMGGIGMVLGFTAERIGRMLSSAASTLRACKDLGNYALDILKLVMK
                     WFFPKKEEKAEMETLRAIEDAVLDMEAIGNNHLTTLLKDKDSLTAFMKTLDLEEEKAR
                     KLSTKSSSPDIVGTINAILARIAAARSLLHKAKEEMFSRIRPVVVMISGRPGIGKTHM
                     ARHLAKSIANTMSGDQRVGLVPRNGVDHWDAYRGERVVLWDDYGMGNPVKDALTLQEL
                     ADTCPVTLNCDRIENKGKMFDSDVIIITTNLVNPAPLDYVNFEACSRRVDFLVYAESP
                     EIEKVKKDFPGQPDMWKDHFKPDFSHIKLTLAPQGGFDKNGNTPHGKGTMRSLTQGSL
                     TARVAGLVHERRDEFQLQGNDLQTYNFDTNRVSAFRKLAADNKYGIMETMRVGTALKS
                     VKTLEDLKVALRDVKFNECEIIYRNSKYRVSSNGKGSVSVDKVEDQASQTANEVGAAL
                     LRLRQARARYYVSCFQDLIYTLIQVAGASFVVNRISKRFCWERWVKPTETQETSESEK
                     EVAQGRWEVEPKDTEPEGKKGKNKKGRGKKHTAFSSKGLSDEEYDEFKRIREERNGKY
                     SIEEYLQDRDRYYEEVAVARATEEDFCEEEEAKIRQRIFRPTKKQRKEERGVLGLVTG
                     SDIRKRRPDDFQPKGNLWADDTRSVDYNERLDFEAPPSVWSRIVPLGTGWGFWVSSNL
                     LITTTHVLPKGIKELFGVEIKQIQIHKSGEFCRFRFPRPIRPDVTGLVLEEGAPEGTV
                     CSILVKRPTGEMIPLAVRMGTHASMKIQGRTVGGQMGMLLTGANAKNMDLGTGPGDCG
                     CPYIYKRGNDIVVAGVHTAAARGGNTVICATQGQDGEAVLEGNENLGTYCGAPILGPG
                     KAPKLSTKTKFWRSSPDALPPGTYEPAYLGGKDPRVEKGPSLQQVMRDQLKPFTEPRG
                     KPPRPAVLEEAKKTVMNVLEQTIDPAKPWTYSQACASLDKTTSSGSPHHVRKNDHWNG
                     ESFTGPLADQASKANLLYEQAKHVQPVYTAALKDELVKTDKIYKKIKKRLLWGSDLGT
                     MIRCARAFGGLMDSMKASCITLPCRVGMNMNEDGPIIFDKHSKYRYHYDADYSRWDST
                     QQRSILSAAMEVMVRFSAEPELAQVVAEDLLAPSQLDVGDFVISVQEGLPSGVPCTSQ
                     WNSIAHWILTLSAMAEVSGLSPDVVQAHSCFSFYGDDEIVSTDINLDPMKLTQKLREY
                     GLVPTRPDKTEGPLVITEDLTGLTFLRRSIARDPAGWFGKLDQDSILRQLYWTRGPNH
                     ENPYESMVPHSQRATQLMALLGEASLHGPQFYKKVSKMVINEIKSGGLEFYVPRQEAM
                     FRWMRFSDLSTWEGDRNLAPEGVNEDGVE"
     gene            5079..6722
                     /gene="ORF2"
     CDS             5079..6722
                     /gene="ORF2"
                     /codon_start=1
                     /product="VP1"
                     /protein_id="AWR17719.1"
                     /translation="MKMASNDAAPSNDGAANLVPEATNEVMALEPVVGASIAAPVVGQ
                     QNIIDPWIRENFVQAPQGEFTVSPRNSPGEMLLNLELGPELNPYLSHLSRMYNGYAGG
                     MQVQVVLAGNAFTAGKIIFAAVPPHFPVENISAAQITMCPHVIVDVRQLEPVLLPLPD
                     IRNRFFHYNQENTPRMRLVAMLYTPLRANSGEDVFTVSCRVLTRPAPDFQFTFLVPPT
                     VESKTKPFTLPILTLGELSNSRFPAPIDMLYTDPNEAIVVQPQNGRCTLDGTLQGTTQ
                     LVPTQICSFRGTLISQTSRSADSTDSAPRVRNHPLHVQLKNLDGTPYDPTDEVPAVLG
                     AIDFKGTVFGVASQRNTTGGSIGATRAHEVHIDTTNPRYTPKLGSVLMYSESTDFDDG
                     QPTRFTPIGMGADDWHQWELPEYSGHLTLNMNLAPAVAPAFPGERILFFRSVVPSAGG
                     YGSGHIDCLIPQEWVQHFYQEAAPSQSAVALIRYVNPDTGRNIFEAKLHREGFITVAN
                     SGNNPIVVPPNGYFRFEAWVNQFYTLTPMGTGQGRRRVQ"
     gene            6722..7498
                     /gene="ORF3"
     CDS             6722..7498
                     /gene="ORF3"
                     /codon_start=1
                     /product="VP2"
                     /protein_id="AWR17720.1"
                     /translation="MAGAFLAGLAGDAITNGVGSLINAGANAINQKVEYDFNKQLQLA
                     SFKHDKEMLQSQVLATKQLQQEMMNIRQGVLSAGGFSPTDAARGAVNAPMTKILDWNG
                     TRYFAPNSMKTTSYSGQFSSNPVHRQPTLSRSDSPKIKANSDSASVYSSASTVSSQST
                     HSTALTAESKPSRPTSSSTATSTLSRTSDWVRGQNERLSPFMDGALQTTFVTPPSSKA
                     SSYGSVSTVPKAVLDSWTPMFNTHRQPLFAHVRRRGESQI"
ORIGIN      
        1 gtgaatgaag atggcgtcta atgacgctac cactgccttt ggcagccaaa actctgtcaa
       61 tgacagtacc aacaccgccc cttctaataa agaagaggtt ggtgcattct ccaacatcaa
      121 agttggtttt aagaaaatgc tgggtgccgt tcccaagggg accaaagcac ccagtagtga
      181 tcaacactgc cccacagtta agattgggac caaaacatta acagttcccc ctgagccccc
      241 aaatggtgaa gacatcgtac agtttgatgc gaagtcggaa actgtgcgtg ggctaccaga
      301 tttgacaacg gtgcagaatg aacacgaaaa cacaccatac actgtccctc cattgagtga
      361 aagggagcac agaccagcca ctgagccgct tcctggcaca atactggaga tgtgggatgg
      421 tgaattctac cattactccg tgtacgtcag cggtggcaaa gccctagggg ttcacaagcc
      481 ccctgcggca ataagcctcg cgacgataga actcacaccc atatctcttt attggaggcc
      541 cgtttacact cccaactatc tggttcaccc agatacgttg aaaggccttg ctggtgagaa
      601 gttcccctac acggctttca gcaacaactg ttacaacttc tgttgctggg tgcttgagct
      661 caatgataca tggctcagca ggaagagcat ctccaggacc accggtttct tcaaaccata
      721 tcagtcttgg aacaggaagc cccttccaac cgttgatgat ggaaagatca aaaaggtggc
      781 caacgcaatt ctctgcgcac ttggatcact attttcaaaa ccaatcaagg acttattggg
      841 taaacttaaa ccattgaact tgctgcactt gctcgcatca tgtgactgga cgtttgcggg
      901 tatagtagag acagttatcc taatggcgga acttttcaac atcttttgga caccgccaga
      961 tgtttccagc ttcatagcct ccctgatagg tgattttgaa ttgcaggggc ctgaggacct
     1021 ggctgtggag cttgtccctg tggtcatggg tggcatagga atggttctcg gcttcactgc
     1081 tgagaggata ggccgcatgt tgtcgtccgc cgcatcaaca ctacgggcat gtaaagattt
     1141 ggggaattac gcccttgaca tactgaaact ggttatgaag tggttcttcc caaagaaaga
     1201 agagaaagcc gagatggaaa ccttaagggc gatcgaggat gccgtcctgg acatggaagc
     1261 cataggaaac aaccacctca caaccctcct caaggacaag gatagcctca cggccttcat
     1321 gaagactctg gatctagaag aggagaaggc aaggaaactg tccaccaagt catcctcgcc
     1381 agacatcgtc ggcactatta atgccatact ggccagaata gctgctgcca ggtccctctt
     1441 acataaggct aaagaagaga tgtttagcag gatcagaccc gtggtcgtca tgatctcggg
     1501 tagacctggc attggcaaaa cccacatggc aagacacttg gctaagagta tcgccaatac
     1561 catgagcggc gaccagagag tggggctggt cccacgcaat ggggtcgacc actgggacgc
     1621 ctacagggga gagagggtgg ttttatggga cgattatggc atgggaaacc ctgtcaaaga
     1681 tgccctaaca ctgcaagagt tggctgacac ctgcccagta accctaaact gtgacaggat
     1741 tgagaacaag ggaaagatgt tcgacagtga tgtcatcata atcacaacca atctagtcaa
     1801 cccagcgccc ctcgattatg taaacttcga ggcgtgctcc agaagggtcg actttctggt
     1861 atatgcagag tcaccagaaa ttgagaaggt taagaaagac ttccccggcc aacctgacat
     1921 gtggaaggac cattttaagc cagacttctc ccacataaaa ctgaccctag ccccacaggg
     1981 cgggtttgac aagaatggca acaccccgca tggtaagggc accatgcgat ccttaaccca
     2041 ggggtccctg actgcaaggg ttgcaggtct tgttcatgag agaagagacg agtttcagct
     2101 ccaggggaac gaccttcaaa catacaactt tgacaccaac agggtctctg catttaggaa
     2161 gctggccgca gacaacaagt atgggatcat ggagacaatg agagtgggca cggcgcttaa
     2221 gagtgtcaag accttggaag atctgaaagt cgccctgagg gatgtgaagt tcaatgagtg
     2281 tgagataatc tacaggaact ccaaataccg agtctcttcc aatggtaaag gctctgtctc
     2341 tgttgacaaa gttgaggacc aagcatccca gactgcaaac gaagtgggtg cagcactcct
     2401 cagacttagg caggcaagag ctagatacta tgtcagctgc ttccaagatc tcatctacac
     2461 tctaatacag gtcgctggag catcattcgt tgtcaacagg atctctaaaa ggttctgttg
     2521 ggagagatgg gtcaaaccaa ccgagaccca ggaaacgagt gaatccgaaa aggaagtggc
     2581 ccaaggtaga tgggaagttg aacccaagga cacagagcca gaaggtaaga agggtaaaaa
     2641 caagaaggga agaggcaaga aacacacagc tttctccagc aaaggcctga gtgacgagga
     2701 gtatgatgag ttcaagagaa tcagagaaga aaggaacgga aaatactcca ttgaggaata
     2761 cctgcaagac cgggatcgct actatgagga agtggcagtt gcccgggcaa cagaggagga
     2821 cttctgtgaa gaggaggagg ccaagataag acaacgaatc ttccgcccca caaagaaaca
     2881 gaggaaggaa gaaagggggg ttcttggttt ggtcactggc tcagacatca ggaagaggag
     2941 accagacgat tttcaaccga agggcaacct gtgggcagac gacaccagga gtgtagacta
     3001 caacgagaga cttgatttcg aggctccccc gagtgtctgg tcaagaatag tcccattggg
     3061 cactggctgg ggcttttggg tctcatccaa cctcctaatc acaacaacac acgtccttcc
     3121 taaggggatt aaggaacttt ttggagtcga aatcaagcag attcaaattc acaagtctgg
     3181 agagttctgc aggttcaggt tcccgagacc aatcagacca gatgtcacag ggctcgtgtt
     3241 ggaggaaggt gctccagaag gcactgtctg ctccatactc gtaaagagac ctacaggtga
     3301 gatgatcccc ctggcagtga ggatgggcac gcacgcatcc atgaaaatac agggtagaac
     3361 cgtcggtggc cagatgggaa tgctcctcac aggggcaaat gcgaagaaca tggaccttgg
     3421 caccggtcct ggtgactgcg gttgtcctta catctacaaa cgtggcaacg atatagttgt
     3481 cgcgggtgtc cacaccgcgg cagcccgggg tggcaacact gtcatatgtg ccactcaagg
     3541 gcaagatggg gaggcagtcc ttgagggaaa tgagaacctt ggcacttact gcggtgcccc
     3601 aattttgggt ccaggcaaag cgcccaaact tagcacgaag accaagttct ggcgttcatc
     3661 accagacgct ttgccgccag gcacttatga gcctgcctac ttgggaggca aagaccccag
     3721 agtggaaaaa ggaccatccc tgcagcaagt catgagggac cagttaaagc ccttcacaga
     3781 acccaggggc aagccaccta gacctgcagt cttagaagaa gccaaaaaga cagtgatgaa
     3841 tgttctagaa caaaccattg accctgctaa gccatggacc tattcccaag catgtgcctc
     3901 actggacaag accacctcca gcggtagccc ccatcatgtc aggaaaaatg accattggaa
     3961 tggtgaatcc ttcacaggcc cccttgcaga ccaagcatcc aaagccaacc tcttgtacga
     4021 acaggccaaa catgtgcagc ccgtgtacac ggccgcactc aaagatgagt tagttaagac
     4081 tgacaagatc tacaaaaaga taaagaaaag gctcttatgg gggtcggacc ttggtacaat
     4141 gatcagatgt gccagggcct tcggcggcct catggatagc atgaaggcaa gctgcataac
     4201 cctcccatgt agggtaggaa tgaacatgaa tgaagatggt cccatcatat ttgacaaaca
     4261 ttctaaatat aggtaccact atgatgctga ctattcaagg tgggactcaa cccagcaaag
     4321 gagcattctc tcggccgcta tggaagtgat ggtgcggttc tctgccgagc cagagctggc
     4381 acaagtggtt gcagaggacc tcctagcacc cagccaactg gatgttggcg actttgtcat
     4441 ctcagtccag gagggtctgc catcaggggt cccatgtaca tcacaatgga attcaatagc
     4501 acactggatc ctaaccttga gtgcaatggc agaagtgtcg ggtctctcac cggatgttgt
     4561 tcaagcccac tcctgtttct cattctacgg tgatgatgag atcgtcagca ctgacatcaa
     4621 ccttgatccc atgaagttga cacagaaact cagagaatat ggcctggtcc ccacccgacc
     4681 tgacaaaact gagggtcccc tcgtaataac tgaagacctc accggcctaa cgttcctgcg
     4741 taggtcaatt gcacgggacc cagctgggtg gtttggaaaa ttggaccaag actcaatcct
     4801 cagacagttg tactggacaa ggggccccaa ccatgagaac ccatatgaga gcatggtccc
     4861 tcactcccag cgggccacac agctcatggc ccttctcggt gaggcttcac tgcatggccc
     4921 ccagttttac aagaaggtta gcaagatggt catcaatgaa atcaaaagtg gtggtctgga
     4981 gttttatgtg cccagacaag aggccatgtt cagatggatg agattctctg acctcagcac
     5041 atgggagggc gatcgcaatc ttgctcccga gggtgtgaat gaagatggcg tcgaatgacg
     5101 ctgctccatc gaatgatggt gctgccaacc tcgtaccaga ggccaccaat gaggttatgg
     5161 cacttgagcc ggtggtggga gcctcaatag ctgctcctgt tgtcggccaa caaaatataa
     5221 ttgacccctg gattagagaa aattttgttc aggcaccaca gggtgagttt actgtttcac
     5281 caaggaactc acctggtgag atgcttctaa accttgaatt aggccctgag ctcaaccctt
     5341 acctgagtca tttgtcccgc atgtataatg gctatgctgg tggtatgcag gttcaggtgg
     5401 tcctagctgg gaatgcgttc acagctggta aaatcatctt tgccgccgtc ccaccacatt
     5461 tccctgttga gaatattagt gcagcccaaa ttacaatgtg cccccatgta attgttgatg
     5521 ttagacagct tgagccagtg cttttgcccc tccctgacat aaggaataga ttctttcatt
     5581 ataatcagga aaacactccc cgaatgagac ttgtggctat gttgtacaca cctcttagag
     5641 caaattctgg tgaggatgtg ttcacagtgt cttgcagagt cctgacccgc ccagcccctg
     5701 acttccagtt cacatttttg gtaccaccaa ctgtggagtc aaagactaag ccctttacac
     5761 tccctatctt gactcttgga gagctgtcca actccagatt ccccgctccg atagacatgt
     5821 tgtatactga tcccaatgag gcaattgtgg tacaaccaca aaatggcagg tgcactctag
     5881 atggaacact tcaagggacc acccagctgg tgcccaccca aatttgctcc tttaggggca
     5941 cgctgattag ccagacgtcg aggtccgcag attcaacaga ttcagcccca cgggtgagga
     6001 accaccctct ccacgtacag ctgaagaacc tcgatgggac accatatgat ccaacagatg
     6061 aggtgccggc agttctgggc gctatagatt ttaaaggaac tgtgtttggg gtcgctagtc
     6121 aaaggaacac cacagggggc tctataggag cgacccgcgc ccatgaagtg cacatagaca
     6181 ctacaaaccc tagatacacc ccaaagcttg gctctgtact gatgtattct gaatccactg
     6241 attttgatga cggacaaccc acccgcttca cccccattgg tatgggagcc gatgattggc
     6301 accaatggga attgcccgaa tattctggtc accttactct taatatgaac ctggcccccg
     6361 cagttgcccc tgctttcccc ggtgagcgca ttctcttctt cagatcagtg gtgccgtctg
     6421 ctggcggcta tgggtcaggt cacatagatt gcctcatccc acaggaatgg gttcagcatt
     6481 tctaccaaga ggccgctcca tcacagtctg cggtggctct tattagatat gtcaaccctg
     6541 acactgggag gaacatcttt gaggcaaaat tgcatagaga agggttcatc actgtagcaa
     6601 attctggaaa caaccccata gttgtgcccc caaatggtta cttcaggttt gaggcctggg
     6661 tcaatcaatt ctacacactc acccccatgg gaactggaca ggggcgcaga agagttcaat
     6721 aatggcagga gctttcttag ctggattggc aggtgacgcc ataacaaatg gtgtcgggtc
     6781 cctaatcaat gctggggcca atgcaattaa ccaaaaggta gagtatgatt tcaataaaca
     6841 gctccaattg gcatccttca aacatgataa agagatgttg caatcacaag tactggccac
     6901 taaacagctc cagcaggaaa tgatgaatat aaggcaaggg gtcttgtccg ctggcggctt
     6961 ttcccctaca gatgccgcga gaggtgccgt aaacgcgccg atgacaaaaa ttttggattg
     7021 gaatggaaca aggtatttcg ccccaaatag catgaagaca accagttatt cgggccagtt
     7081 ttccagtaat cctgtgcata ggcaacccac tttgtcccgt tctgactccc ccaaaattaa
     7141 ggctaatagt gattctgcta gtgtttatag ttctgcatct actgtttcct cacaatcaac
     7201 tcactcaacg gctttgactg cggagtctaa accatctagg ccaacatcct cttccacagc
     7261 aacttctact ctatctagaa ctagtgactg ggtgagaggg caaaatgaga ggcttagccc
     7321 gtttatggat ggtgctctcc aaacaacttt tgtcacacca ccatcgagca aggcttcatc
     7381 atatgggtcg gtctcaaccg ttcccaaagc tgttttggac tcctggactc ctatgttcaa
     7441 cacccatagg cagcctctct tcgctcatgt gcgcaggcga ggggagtcac agatttagtg
     7501 aaaagattga ttaggttttc tttctctttt cttttccttt tctttc
//