Typing tool

Complete norovirus genomes

MH218733  GII.2
 GII.P31

Length: 7,550 | 3 CDS

ORF1: 5..5104
ORF2: 5085..6713
ORF3: 6713..7492
LOCUS       MH218733                7550 bp    RNA     linear   VRL 11-JUN-2018
DEFINITION  Norovirus GII isolate NORO_94_23_10_2014, complete genome.
ACCESSION   MH218733
VERSION     MH218733.1
KEYWORDS    .
SOURCE      Norovirus GII
  ORGANISM  Norovirus GII
            Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes;
            Picornavirales; Caliciviridae; Norovirus.
REFERENCE   1  (bases 1 to 7550)
  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 7550)
  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..7550
                     /organism="Norovirus GII"
                     /mol_type="genomic RNA"
                     /isolate="NORO_94_23_10_2014"
                     /host="Homo sapiens"
                     /db_xref="taxon:122929"
                     /country="United Kingdom"
                     /collection_date="23-Oct-2014"
                     /note="genotype: GII.Pe_GII.2"
     gene            5..5104
                     /gene="ORF1"
     CDS             5..5104
                     /gene="ORF1"
                     /codon_start=1
                     /product="nonstructural polyprotein"
                     /protein_id="AWR17857.1"
                     /translation="MKMASNDASAAAAANSNNDIAKSSSDGMFSNMAVTFKRALGARP
                     KQPPPKEIPPRPPRPPTPELVKKIPPPPPNGEDELVVSYSARDGVSGLPELTTVRQPE
                     ETNTAFSVPPLNQRENRDAKEPLTGTIIEMWDGEIYHYGLYVERGLILGVHKPPAAIS
                     LAKVELTPLSLFWRPVYTPQYLISPDTLRRLHGESFPYTAFDNNCYAFCCWVLDLNDS
                     WLNRRMIQRTTGFFRPYQDWNRKPLPTMDDSKLKKVANIFLCTLSSLFTRPIKDIIGK
                     LKPLNILNILATCDWTFAGIVESLILLAELFGVFWTPPDVSAMIAPLLGDYELQGPED
                     LAVELVPIVMGGIGLVLGFTKEKIGKMLSSAASTLRACKDLGAYGLEILKLVMKWFFP
                     KKEEANELAMVRSIEDAVLDLEAIENNHMTTLLKDKDSLATYLRTLDLEEEKARKLST
                     KSASPDIVGTINSLLARIAAARSLVHRAKEELSSRPRPVVVMISGKPGIGKTHLAREL
                     AKKIAASLTGDQRVGLIPRNGVDHWDAYKGERVVLWDDYGMSNPIHDALRLQELADTC
                     PLTLNCDRIENKGKVFDSDAIIITTNLANPAPLDYVNFEACSRRIDFLVYADAPGVEK
                     AKRDFPGQPDMWKDAFNPDFSHIKLSLAPQGGFDKNGNTPHGKGVMKTLTTGSLIARA
                     SGLLHERLDEYELQGPALTTFNFDRNKILAFRQLAAENKYGMMDTMRVGRQLKDVKTM
                     SDLKQALKNIAIKKCQIVYGGSTYTLEADGKGSVRVDKVQSATVQTNNELAGALHHLR
                     CARIRYYVKCVQEALYSIIQIAGAAFVTTRIAKRMNIQNLWSKPQVEDTEEMVNADGC
                     PKLKDDEEFVVSSDDIKTEGKKGKNKSGRGKKHTAFSSKGLSDEEYDEYKRIREERNG
                     KYSIEEYLQDRDKYYEEVAIARATEEDFCEEEEAKIRQRIFRPTRKQRKEERASLGLV
                     TGSEIRKRNPEDFKPKGKLWADDDRSVDYNEKLNFEAPPSIWSRIVNFGSGWGFWVSP
                     SLFITSTHVIPQGAKEFFGVSIKQIQIHKSGEFCRLRFPKPIRTDVTGMILEEGAPEG
                     TVATLLIKRPTGELMPLAARMGTHATMKIQGRTVGGQMGMLLTGSNAKSMDLGTTPGD
                     CGCPYIYKRGNDYVVIGVHTAAARGGNTVICATQGSEGEATLEGGDNKGTYCGAPILG
                     PGSAPKLSTKTKFWRSSTTPLPPGTYEPAYLGGKDPRVKGGPSLQQVMRDQLKPFTEP
                     RGKPPRPNVLEAAKKTIINVLEQTIDPPQKWSFAQACASLDKTTSSGYPHHMRKNDCW
                     NGDSFTGKLADQASKANLMFEEGKNMTPVYTGALKDELVKTDKIYGKIKKRLLWGSDL
                     ATMIRCARAFGGLMDEFKAHCVTLPVRVGMNMNEDGPIIFEKHSRYKYHYDADYSRWD
                     STQQRDVLAAALEIMVKFSPEPHLAQVVAEDLLSPSVMDVGDFQISISEGLPSGVPCT
                     SQWNSIAHWLLTLCALSEVTDLSPDIIQANSLFSFYGDDEIVSTDIKLDPEKLTAKLK
                     EYGLKPTRPDKTEGPLVISEDLDGLTFLRRTVTRDPAGWFGKLEQSSILRQMYWTRGP
                     NHEDPSETMIPHSQRPIQLMSLLGEAALHGPTFYSKISKLVIAELKEGGMDFYVPRQE
                     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..6713
                     /gene="ORF2"
     CDS             5085..6713
                     /gene="ORF2"
                     /codon_start=1
                     /product="VP1"
                     /protein_id="AWR17858.1"
                     /translation="MKMASNDAAPSTDGAAGLVPESNNEVMALEPVAGAALAAPVTGQ
                     TNIIDPWIRANFVQAPNGEFTVSPRNAPGEVLLNLELGPELNPYLAHLARMYNGYAGG
                     MEVQVMLAGNAFTAGKLVFAAVPPHFPVENLSPQQITMFPHMIIDVRTLEPVLLPLPD
                     VRNNFFHYNQKDDPKMRIVAMLYTPLRSNGSGDDVFTVSCRVLTRPSPDFDFTYLVPP
                     TVESKTKPFTLPILTLGELSNSRFPVSIDQMYTSPNEVISVQCQNGRCTLDGELQGTT
                     QLQVSGICAFKGEVTAHLHDNDHLYNVTITNLNGSPFDPSEDIPAPLGVPDFQGRVFG
                     IISQRDKHNSPGHNEPANRGHDAVVPTYTAQYTPKLGQIQIGTWQTDDLTVNQPVKFT
                     PVGLNDTEHFNQWVVPRYAGALNLNTNLAPSVAPVFPGERLLFFRSYIPLKGGYGNPA
                     IDCLLPQEWVQHFYQEAAPSMSEVALVRYINPDTGRALFEAKLHRAGFMTVSSNTSAP
                     VVVPANGYFRFDSWVNQFYSLAPMGTGNGRRRVQ"
     gene            6713..7492
                     /gene="ORF3"
     CDS             6713..7492
                     /gene="ORF3"
                     /codon_start=1
                     /product="VP2"
                     /protein_id="AWR17859.1"
                     /translation="MAGAFVAGLAGDVLSNGLSSLINAGANAINQRAEFDFNQRLQQN
                     SFNHDKEMLQAQIQATKQLQADMMAIKQGVLTAGGFSPADAARGAVNAPMTQALDWNG
                     TRYWAPGSMRTTSYSGRFTSTAPVRQADFQHTQSRPSSGSSVSSFTTQSSRPTLTTTT
                     GSSHSTVSSNSTRSTNLSQSTVSRATSRTGEWVRDQNKNLEPYMHGALQTAFVTPPSS
                     RASDGTVSTVPKGVLDSWTPAFNTRRQPLFAHLRKRGESQA"
ORIGIN      
        1 gtgaatgaag atggcgtcta acgacgcttc cgctgccgct gctgccaaca gcaacaacga
       61 catcgcaaaa tcttcaagtg acggtatgtt ctctaacatg gctgtcactt ttaaacgggc
      121 cctcggggcg cggcctaaac agccgccccc gaaggaaata ccacccagac ccccacgacc
      181 gcccacccca gaattggtca aaaagatccc tcctccccca cccaacgggg aggatgaact
      241 agtggtctcc tacagcgcca gagatggcgt ttccggactg cctgagctca ccactgtcag
      301 acaaccggaa gaaaccaaca cggcgttcag tgttccccca ctcaaccaaa gggagaacag
      361 ggacgccaag gaaccactaa ctggaacaat tattgaaatg tgggatggag aaatctacca
      421 ttatggcctg tacgtggaac gaggccttat actcggtgtg cacaagccac cggcagctat
      481 cagccttgcc aaggtcgagc taacaccact ctctttgttc tggagacctg tatacacccc
      541 ccagtatctc atctctccag acactctcag gagattacat ggagagtcat tcccctacac
      601 tgcttttgac aacaattgct acgccttttg ttgttgggta ttagacctaa acgactcatg
      661 gctaaacagg agaatgattc agagaacaac aggtttcttc aggccgtacc aggattggaa
      721 caggaaaccc ctccccacta tggatgattc taaattaaag aaggtagcca acatattctt
      781 gtgcacctta tcttcactat tcaccagacc cattaaggac ataataggaa aattgaaacc
      841 tctcaacatc cttaacattc tggctacatg tgattggacc ttcgcaggca tagtggaatc
      901 cttaatactc ttggcagaac tctttggagt tttctggaca cccccagatg tgtctgcgat
      961 gatcgccccc ttactaggtg attatgaact gcaagggcct gaggaccttg cagtggaact
     1021 ggtcccaata gtgatggggg ggataggttt ggtgctagga tttaccaaag agaaaattgg
     1081 aaagatgcta tcatccgccg catccacttt aagagcttgt aaagaccttg gtgcatacgg
     1141 actggaaatt ttgaaattgg tcatgaagtg gttcttccca aagaaagagg aagcgaatga
     1201 actggctatg gtgagatcca tcgaggatgc agtgctggac ctcgaggcaa ttgaaaacaa
     1261 ccacatgacc actctgctca aagacaaaga cagcttggca acctacttga gaacccttga
     1321 ccttgaggag gagaaagcca ggaaactctc aaccaaatct gcttcacccg acatcgtggg
     1381 cacaatcaac tctctactgg caagaatcgc tgctgcacgc tctctagtgc atcgggcgaa
     1441 agaagagctc tccagcaggc caagacccgt tgttgtgatg atatcgggaa aaccagggat
     1501 agggaaaact caccttgcca gggagctggc caaaaagatc gcggcctccc tcacggggga
     1561 ccagcgtgtg ggtcttatcc cgcgcaatgg tgtcgaccac tgggacgcat acaaaggtga
     1621 aagagttgtc ctatgggacg actatggaat gagcaacccc atccatgatg ccctcaggct
     1681 gcaggaactt gctgacactt gccccctcac gctaaattgt gatagaattg agaacaaagg
     1741 gaaagtcttt gacagtgatg ccataattat caccaccaat ctggccaacc cagcaccact
     1801 ggattatgtc aactttgaag cgtgctcgag acgcattgac ttcctcgtgt acgcagatgc
     1861 tcctggggtg gagaaggcga agcgcgactt cccaggccaa cctgacatgt ggaaggacgc
     1921 tttcaatcct gacttctcac acataaaact gtcgttggct ccacagggtg gttttgacaa
     1981 gaacggcaac accccgcatg ggaaaggtgt catgaagacc ctcaccaccg gctccctcat
     2041 cgcccgggct tcagggttac tccatgagag gctagatgaa tatgaactgc aaggcccagc
     2101 cctcaccact ttcaactttg accgcaacaa gatacttgct tttaggcagc ttgctgctga
     2161 aaacaagtat gggatgatgg acacaatgag agttggaaga cagctcaagg atgtcaagac
     2221 catgtcggac ctcaaacaag cactcaagaa catcgcgatc aagaagtgcc agatagtgta
     2281 tggtggtagc acctacacac ttgaggccga tggcaagggt agtgtgagag ttgacaaagt
     2341 acaaagtgcc actgtgcaaa ccaataatga attagccggt gccctacacc acctaaggtg
     2401 cgccagaatt agatactatg ttaagtgtgt ccaggaggca ctgtattcca tcatccaaat
     2461 cgctggggct gcattcgtca ccacgcgcat cgctaagcgc atgaatatac agaacctctg
     2521 gtccaagcca caagtggaag acacagaaga gatggttaac gcagatggtt gcccaaaact
     2581 caaagatgat gaagagtttg tcgtctcatc cgacgacatc aaaactgagg gtaagaaagg
     2641 gaagaacaag tccggccgtg gcaagaagca cacagccttc tcaagcaaag gactcagtga
     2701 tgaggagtac gacgagtaca agagaatcag agaggaaagg aatggtaagt attccataga
     2761 agagtacctt caggacagag acaagtacta cgaggaggtg gccattgcta gggcaaccga
     2821 agaggacttc tgtgaagaag aagaggccaa aatccgacag agaattttta gaccaacaag
     2881 aaaacaacgc aaagaagaga gggcctctct cggcttggtc acaggttctg aaatcaggaa
     2941 aagaaaccca gaagatttca aacccaaggg aaagctgtgg gccgatgatg acagaagtgt
     3001 tgattacaat gagaaactta actttgaggc cccaccaagc atctggtcgc ggatagtcaa
     3061 ctttggttct ggttggggct tctgggtgtc ccccagcctg tttataactt caacccatgt
     3121 catacctcaa ggtgcaaaag agttcttcgg agtctctatc aagcaaatcc agatacacaa
     3181 atcaggtgaa ttctgccgac tgagattccc aaaaccaatc agaactgatg tgacgggcat
     3241 gattctagaa gaaggcgcgc ccgaagggac cgtggccaca ctgctcatca agagaccgac
     3301 tggagagctc atgcctctgg cagccagaat ggggacccac gcaaccatga agattcaggg
     3361 gcgcacagtt ggagggcaaa tgggtatgct cctgacagga tccaacgcca agagcatgga
     3421 cctaggcaca acaccaggtg actgcggctg tccctacatc tacaagagag ggaatgacta
     3481 cgtggtcata ggagtccata cggccgctgc ccgtggagga aacactgtca tatgtgccac
     3541 ccaggggagt gagggagaag ccacacttga aggaggtgac aataaaggaa catactgtgg
     3601 tgcaccaatc ttgggcccag ggagcgctcc gaagctcagt accaagacta agttttggag
     3661 gtcatccaca acaccactcc cgcctggcac ctacgaacca gcatacctcg gtggcaaaga
     3721 tcccagagtt aaaggtggcc cttcattgca acaagttatg agggaccagt tgaagccatt
     3781 cacagaaccc agaggcaaac caccaagacc aaatgttcta gaagctgcca agaaaaccat
     3841 catcaatgtt cttgagcaaa caattgaccc accccaaaaa tggtcattcg cgcaggcctg
     3901 cgcatccctt gacaaaacca cctccagtgg ctacccgcac catatgcgga agaacgactg
     3961 ttggaatggg gattccttca caggaaaatt ggcagaccag gcctccaagg ctaatctaat
     4021 gtttgaagag ggaaagaaca tgaccccagt ctacacaggt gcacttaaag atgagttggt
     4081 gaagactgat aaaatttatg gtaagatcaa gaagagactt ctgtggggct cagatctggc
     4141 gaccatgata cggtgtgccc gggctttcgg aggccttatg gatgaattca aggcacactg
     4201 tgtcacactt cctgtcagag ttggtatgaa catgaatgag gatggcccca tcatctttga
     4261 gaagcactcc agatataaat accactatga tgctgattat tcccggtggg actcaacaca
     4321 acaaagggat gtgctggcag cagcactaga aatcatggta aaattctctc cagaaccaca
     4381 cctggcccag gtagttgcag aagatctcct ttcccctagc gttatggatg taggtgactt
     4441 tcaaatatca ataagtgagg ggctcccctc cggggtacct tgtacctccc agtggaattc
     4501 catcgcccac tggctcctca ctctttgtgc actctctgaa gtcacggacc tgtcccctga
     4561 catcattcag gccaattccc ttttctcctt ctatggtgat gatgagattg tgagcacaga
     4621 cataaagttg gatccggaga agctgacagc aaaactcaag gagtacgggc tgaaaccaac
     4681 ccgccccgac aaaactgaag gacctcttgt tatctctgaa gatctggatg gtctaacatt
     4741 ccttcggagg actgtgaccc gtgacccagc tggctggttt ggaaaactgg aacaaagctc
     4801 aattctcagg caaatgtact ggaccagggg tcccaaccat gaagacccat ctgaaacaat
     4861 gataccacac tcccaaagac ccatacaatt gatgtccttg ctgggcgagg ctgcactcca
     4921 cggcccgaca ttttatagca aaattagcaa attagtcatt gcagagctga aggaaggtgg
     4981 catggatttt tacgtgccca gacaagagcc aatgttcaga tggatgagat tctcagatct
     5041 gagcacgtgg gagggcgatc gcaatctggc tcccagtttt gtgaatgaag atggcgtcga
     5101 atgacgccgc tccatctact gatggtgcag ccggcctcgt gccagaaagt aataatgagg
     5161 tcatggctct tgaacccgtg gctggtgccg ccttggcagc cccagtcacc ggacaaacaa
     5221 atattataga cccttggatt agagcaaatt ttgtccaggc ccctaatggt gaatttacag
     5281 tttctccccg taatgcccct ggtgaagtgt tattgaatct agagttgggt ccagagttaa
     5341 atccttatct ggcacattta gcaagaatgt acaacgggta tgctggtggg atggaggtgc
     5401 aggtcatgtt ggctgggaac gcgttcacag ccggcaagtt ggtctttgcc gccgtaccac
     5461 ctcacttccc ggttgaaaac cttagtccac agcaaattac catgtttccc catatgatta
     5521 tagatgtgag aactttggaa cctgttttat taccactccc tgatgttaga aataatttct
     5581 tccattacaa tcagaaggat gatcctaaga tgagaattgt ggctatgctt tatactcccc
     5641 ttagatctaa tggctcaggt gatgacgtgt ttacagtctc atgcagggtg ttgactagac
     5701 cctcccctga ttttgacttc acatatttgg tgccaccaac agtggaatct aagactaaac
     5761 cattcaccct cccaatcctc acgcttgggg agctctccaa ttctagattt ccagtgtcca
     5821 tagatcagat gtataccagc cccaatgaag ttatatcagt gcaatgtcaa aatggtaggt
     5881 gcacactgga tggggaactc caaggaacaa cacaactcca agtcagtggc atttgtgcct
     5941 tcaagggaga ggtgaccgcc catttgcatg acaatgacca tctatataat gtcaccatca
     6001 caaacttgaa cgggtcccct tttgacccct ccgaggacat ccctgcccct ttgggcgtac
     6061 ctgattttca gggaagggtc tttggtatca tctcccaaag agacaaacac aacagccctg
     6121 ggcataatga accagcaaac aggggacacg acgctgtggt ccctacttac acagcacagt
     6181 acaccccaaa attgggtcaa attcaaattg gcacatggca gaccgatgat cttacagtca
     6241 accaaccagt caaattcacc ccagttggac ttaatgacac tgaacatttt aaccaatggg
     6301 tggtccccag atatgctggt gctctaaacc tcaacacaaa tcttgcccct tctgttgctc
     6361 cagtttttcc aggggagcgc ctgctctttt tcagatcata tatccccctc aagggtggtt
     6421 atggaaatcc agctattgat tgtctgctac cacaagagtg ggtgcaacat ttctatcagg
     6481 aagcagcccc ttcaatgagt gaggtggccc ttgtcagata catcaacccg gacactggtc
     6541 gagcactgtt tgaggccaag ctccacagag ctggtttcat gacggtctcg agcaacacca
     6601 gtgccccggt ggttgtgcct gccaacggat acttcagatt tgattcttgg gtgaaccaat
     6661 tctattctct cgcccccatg ggaactggaa atgggcgtag aagggttcaa taatggctgg
     6721 agcttttgta gctggtcttg caggggacgt gctcagcaat gggctcagtt cactaattaa
     6781 tgcaggtgct aatgcaataa atcagagggc agaatttgat tttaatcaga gattacaaca
     6841 aaattctttc aatcatgata aggagatgtt acaggctcag attcaggcaa ccaagcagct
     6901 gcaggcagac atgatggcta taaagcaggg agtcttgacc gctggcggct tctcccccgc
     6961 tgacgcagcc agaggtgctg tgaatgcacc catgacacag gcgctggatt ggaacggcac
     7021 aaggtattgg gcaccaggct ccatgaggac cacatcttac tctggaagat tcacatcaac
     7081 cgccccagtg aggcaggccg acttccaaca cacccagagc cggccttcga gtggctcttc
     7141 tgtgtcctcc ttcactactc agtcttcaag gccaactctg actacaacca ctgggtcctc
     7201 acatagtaca gtttcatcaa attcaactcg cagcacaaac ctctcccaat caacggtttc
     7261 cagggctaca tctaggacag gtgagtgggt tagagatcaa aataaaaatt tggaacctta
     7321 catgcatggt gccttacaga cagcctttgt caccccacct tccagcaggg cttctgatgg
     7381 gacagtctca accgtcccaa aaggtgtttt ggactcctgg acacctgcgt tcaacacccg
     7441 caggcagccg ctttttgcac acctccgtaa gaggggggag tcacaagcct agtgaaaagg
     7501 taaatttatt tagaatgaaa tgattttatc ttttaaaaaa aaaaaaaaaa
//