Typing tool

Complete norovirus genomes

MH218657  GII.2
 GII.P31

Length: 7,497 | 3 CDS

ORF1: 5..5104
ORF2: 5085..6713
ORF3: 6713..7492
LOCUS       MH218657                7497 bp    RNA     linear   VRL 11-JUN-2018
DEFINITION  Norovirus GII isolate NORO_196_18_10_2015, complete genome.
ACCESSION   MH218657
VERSION     MH218657.1
KEYWORDS    .
SOURCE      Norovirus GII
  ORGANISM  Norovirus GII
            Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes;
            Picornavirales; Caliciviridae; Norovirus.
REFERENCE   1  (bases 1 to 7497)
  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 7497)
  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..7497
                     /organism="Norovirus GII"
                     /mol_type="genomic RNA"
                     /isolate="NORO_196_18_10_2015"
                     /host="Homo sapiens"
                     /db_xref="taxon:122929"
                     /country="United Kingdom"
                     /collection_date="18-Oct-2015"
                     /note="genotype: GII.Pe_GII.2"
     gene            5..5104
                     /gene="ORF1"
     CDS             5..5104
                     /gene="ORF1"
                     /codon_start=1
                     /product="nonstructural polyprotein"
                     /protein_id="AWR17629.1"
                     /translation="MKMASNDASAAAAANSNNDIAKSSSDGMFSNMAVTFKRALGARP
                     KQPPPKEIPPRPPRPPTPELVKKIPPPPPNGEDELVVSYSAKDGVSGLPELTTVRQPE
                     ETNTAFSVPPLNQRENRDAKEPLTGTIIEMWDGEIYHYGLYVDRGLILGVHKPPAAIS
                     LAKVELTPLSLFWRPVYTPQYLISPDTLRRLHGELFPYTAFDNNCYAFCCWVLDLNDS
                     WLSRRMIQRTTGFFRPYQDWNRKPLPTMDDSKLKKVANIFLCTLSSLFTRPIKDIIGK
                     LKPLNILNILATCDWTFAGIVESLILLAELFGIFWTPPDVSAMIAPLLGDYELQGPED
                     LAVELVPIVMGGIGLVLGFTKEKIGKMLSSAASTLRACKDLGAYGLEILKLVMKWFFP
                     KKEEANELAMVRSIEDAVLDLEAIENNHMTTLLKDKDSLATYMRTLDLEEEKARKLST
                     KSASPDIVGTINSLLARIAAARSLVHRAKEELSSRPRPVVVMISGKPGIGKTHLAREL
                     AKKIASSLTGDQRVGLIPRNGVDHWDAYKGERVVLWDDYGMSNPIHDALRLQELADTC
                     PLTLNCDRIENKGKVFDSDAIIITTNLANPAPLDYVNFEACSRRIDFLVYADAPGVEK
                     AKRDFPGQPDMWKDAFNPDFSHIKLSLAPQGGFDKNGNTPHGKGVMKTLTTGSLIARA
                     SGLLHERLDEYELQGPALTTFNFDRNKILAFRQLAAENKYGMMDTMRVGRQLKDVKTM
                     SDLKQALKNIAIKKCQIVYGGSTYTLEADGKGSVRVDKVQSATVQTNNELAGALHHLR
                     CARIRYYVKCVQEALYSIIQIAGAAFVTTRIAKRMNIQNLWSKPQVEDTEEMVNEDGC
                     PKLKDDEEFVVSSDDIKTEGKKGKNKSGRGKKHTAFSSKGLSDEEYEEYKRIREERNG
                     KYSIEEYLQDRDKYYEEVAIARATEEDFCEEEEAKIRQRIFRPTRKQRKEERASLGLV
                     TGSEIRKRNPEDFKPKRKLWADDDRSVDYNEKLNFEAPPSIWSRIVNFGSGWGFWVSP
                     SLFITSTHVIPQGAKEFFGVSIKQIQIHKSGEFCRLRFPKPIRTDVAGMILEEGAPEG
                     TVATLLIKRPTGELMPLAARMGTHATMKIQGRTVGGQMGMLLTGSNAKSMDLGTTPGD
                     CGCPYIYKRGNDYVVIGVHTAAARGGNTVICATQGSEGEATLEGGDNKGTYCGAPILG
                     PGSAPKLSTKTKFWRSSTTPLPPGTYEPAYLGGKDPRVKGGPSLQQVMRDQLKPFTEP
                     RGKPPRPNVLEAAKKTIINVLEQTIDPPQKWSFAQACASLDKTTSSGHPHHMRKNDCW
                     NGDSFTGKLADQASKANLMFEEGKNMTPVYTGALKDELVKTDKIYGKIKKRLLWGSDL
                     ATMIRCARAFGGLMDELKAHCVTLPVRVGMNMNEDGPIIFEKHSRYKYHYDADYSRWD
                     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="AWR17630.1"
                     /translation="MKMASNDAAPSTDGAAGLVPESNNEVMALEPVAGAALAAPVTGQ
                     TNIIDPWIRANFVQAPNGEFTVSPRNAPGEVLLNLELGPELNPYLAHLARMYNGYAGG
                     MEVQVMLAGNAFTAGKLVFAAVPPHFPVENLSPQQITMFPHVIIDVRTLEPVLLPLPD
                     VRNNFFHYNQKDDPKMRIVAMLYTPLRSNGSGDDVFTVSCRVLTRPSPDFDFTYLVPP
                     TVESKTKPFTLPILTLGELSNSRFPVSIDQMYTSPNEVISVQCQNGRCTLDGELQGTT
                     QLQVSGICAFKGEVTAHLHDNDHLYNVTITNLNGSPFDPSEDIPAPLGVPDFQGRVFG
                     IISQRDKHNSPGHNEPANRGHDAVVPTYTAQYTPKLGQIQIGTWQTDDLTVNQPVKFT
                     PVGLNDTEHFNQWVVPRYAGALNLNTNLAPSVAPVFPGERLLFFRSYIPLKGGYGNPA
                     IDCLLPQEWVQHFYQEAAPSMSEVALVRYINPDTGRALFEAKLHRAGFMTVSSNTSAP
                     VVVPANGYFRFDSWVNQFYSLAPMGTGNGRRRVQ"
     gene            6713..7492
                     /gene="ORF3"
     CDS             6713..7492
                     /gene="ORF3"
                     /codon_start=1
                     /product="VP2"
                     /protein_id="AWR17631.1"
                     /translation="MAGAFVAGLAGDVLSNGLSSLINAGANAINQRAEFDFNQRLQQN
                     SFNHDKEMLQAQIQATKQLQADMMAIKQGVLTAGGFSPADAARGAVNAPMTQALDWNG
                     TRYWAPGSMRTTSYSGRFTSTAPVRQADFQHTQSRPSSGSSVSSFTTQSSRPTLTTTT
                     GSSHNTVSSNSTRSTNLSQSTVSRATSRTGEWVRDQNKNLEPYMHGALQTAFVTPPSS
                     RASDGTVSTAPKGVLDSWTPAFNTRRQPLFAHLRKRGESQA"
ORIGIN      
        1 gtgaatgaag atggcgtcta acgacgcttc cgctgccgct gctgccaaca gcaacaacga
       61 catcgcaaaa tcttcaagtg acggtatgtt ctctaacatg gctgtcactt ttaaacgggc
      121 cctcggggcg cggcctaaac agccgccccc gaaggaaata ccacccagac ctccacgacc
      181 gcccacccca gaattggtca aaaagatccc tcctccccca cccaacgggg aggatgaact
      241 agtggtctcc tacagcgcca aagatggcgt ttccgggctg cctgagctca ccactgtcag
      301 acaaccggaa gaaaccaaca cggcgttcag tgttccccca ctcaatcaaa gggagaacag
      361 ggacgccaag gaaccactaa ctggaacaat tattgaaatg tgggatggag aaatctacca
      421 ttatggcctg tacgtggatc gaggccttat actcggtgtg cacaagccac cggcagccat
      481 cagccttgcc aaggtcgagc taacaccact ctctttattc tggaggcctg tatacacccc
      541 ccagtatctc atctctccag acactctcag gagattacat ggagagttat tcccctacac
      601 tgcttttgac aacaattgct acgccttttg ttgttgggta ctagacctaa acgactcatg
      661 gctaagcagg agaatgattc agagaacaac aggtttcttc aggccgtacc aggattggaa
      721 caggaaaccc ctccccacta tggatgattc taaattaaag aaggtagcca acatattttt
      781 gtgcacctta tcttcactat tcaccagacc cattaaggac ataataggaa aattgaaacc
      841 tctcaacatc cttaacattc tggctacatg tgattggacc ttcgcaggca tagtggaatc
      901 cttaatactc ttggcagaac tctttggaat tttctggaca cccccagatg tgtctgcgat
      961 gatcgccccc ttactaggtg attatgaact gcaagggcct gaggaccttg cagtggaact
     1021 ggtcccaata gtgatggggg ggataggttt ggtgctagga tttaccaaag agaaaattgg
     1081 aaagatgcta tcatccgccg catccacttt aagagcttgc aaagaccttg gtgcatacgg
     1141 actggaaatt ttgaaattgg tcatgaagtg gttcttccca aagaaagagg aagcgaatga
     1201 actggctatg gtgagatcca tcgaggatgc agtgctggac ctcgaggcaa ttgaaaacaa
     1261 ccacatgacc accctgctca aagacaaaga cagcttggca acctacatga gaacccttga
     1321 ccttgaggag gagaaagcca ggaaactctc aaccaaatct gcttcacccg atatcgtggg
     1381 cacaatcaac tctctactgg caagaatcgc tgctgcacgc tctctagtgc atcgggcgaa
     1441 agaagagctc tccagcaggc cgagacccgt tgttgtgatg atatcgggaa aaccagggat
     1501 agggaaaact caccttgcca gggagctggc caaaaagatc gcgtcctccc tcacggggga
     1561 ccagcgcgtg ggtcttatcc cgcgcaatgg tgtcgaccac tgggacgcat acaaaggtga
     1621 aagagttgtc ctatgggacg actatggaat gagcaacccc atccatgatg ccctcaggct
     1681 acaggaactt gctgacactt gccccctcac gctaaattgt gatagaattg agaacaaagg
     1741 gaaagtcttt gacagtgatg ccataattat caccaccaat ctggccaacc cagcaccact
     1801 ggattatgtc aactttgaag cgtgctcgag acgcattgac ttcctcgtgt acgcagatgc
     1861 tcctggggtg gagaaggcaa agcgcgactt cccaggccaa cctgacatgt ggaaggacgc
     1921 tttcaatcct gacttctcac acataaaact gtcactggct ccacagggtg gttttgacaa
     1981 gaacggcaac accccgcatg gaaaaggtgt catgaagacc ctcaccaccg gctccctcat
     2041 cgcccgggca tcagggttac tccatgagag gctagatgaa tatgaactgc aaggcccagc
     2101 cctcaccact ttcaactttg accgcaacaa gatacttgct tttaggcagc ttgctgctga
     2161 aaacaagtat gggatgatgg acacaatgag agttggaaga cagctcaagg atgtcaagac
     2221 catgtcagac ctcaagcaag cactcaagaa catcgcgatc aaaaagtgtc agatagtgta
     2281 cggtggtagc acctacacac ttgaggccga tggcaagggt agtgtgaggg ttgacaaagt
     2341 acaaagtgcc actgtgcaaa ccaataatga attagccggt gccctacacc acctgaggtg
     2401 cgccagaatt agatactatg ttaagtgtgt ccaggaggca ctgtattcca tcatccaaat
     2461 cgctggggct gcattcgtca ccacgcgcat cgctaagcgc atgaatatac agaacctctg
     2521 gtccaagcca caagtggaag acacagaaga gatggttaac gaagatggtt gcccaaaact
     2581 taaagatgat gaagagtttg tcgtctcatc cgacgacatc aaaactgagg gtaagaaagg
     2641 gaagaacaag tccggccgtg gcaagaagca cacagccttc tcaagcaaag gacttagtga
     2701 tgaggagtac gaagagtaca agagaatcag agaagaaagg aacggtaagt attccataga
     2761 agagtatctt caggacagag acaagtacta cgaggaggtg gccattgcta gggcaaccga
     2821 agaggacttc tgtgaagaag aagaggccaa aatccgacag agaattttta gaccaacaag
     2881 aaaacaacgc aaagaagaga gggcctctct cggcttggtc acaggttctg aaatcaggaa
     2941 aagaaaccca gaagatttca aacccaagag aaagctgtgg gctgatgatg acagaagtgt
     3001 tgactacaat gagaaactta actttgaggc cccaccaagc atctggtcgc ggatagtcaa
     3061 ctttggttca ggttggggct tctgggtgtc ccccagcctg tttataactt caacccatgt
     3121 catacctcaa ggtgcaaaag agtttttcgg agtctctatc aagcaaatcc agatacacaa
     3181 atcaggtgaa ttctgccgat tgagattccc aaaaccaatc agaactgatg tggcgggcat
     3241 gattctagaa gaaggcgcgc ccgaaggaac cgtggcaaca ctgcttatca agagaccaac
     3301 tggagagctc atgcctctgg cagccagaat ggggacccac gcaaccatga agattcaggg
     3361 gcgcacagtt ggagggcaaa tgggtatgct cctgacagga tccaacgcca agagcatgga
     3421 cctaggcaca acaccaggtg actgcggctg tccctacatc tacaagagag ggaatgatta
     3481 cgtggtcata ggagtccata cggccgctgc ccgtggagga aacactgtca tatgtgccac
     3541 ccaggggagt gagggagaag ccacacttga aggaggtgac aataaaggaa catattgtgg
     3601 tgcaccaatc ttgggcccag ggagcgctcc gaagctcagt accaagacta agttttggag
     3661 gtcatccaca acaccactcc caccaggcac ctacgaacca gcctacctcg gtggcaaaga
     3721 tcccagagtt aaaggtggcc cttcattgca acaagttatg agggaccagt tgaagccatt
     3781 cacagaaccc agaggcaaac caccaagacc aaatgttcta gaagctgcca agaaaaccat
     3841 catcaatgtt cttgaacaaa caattgaccc accccaaaaa tggtcatttg cgcaggcctg
     3901 cgcatccctt gacaaaacca cctccagtgg ccacccgcac catatgcgga agaacgactg
     3961 ttggaatggg gattccttca caggaaaatt ggcagaccag gcctccaagg ctaatctaat
     4021 gtttgaagag ggaaagaaca tgaccccagt ctacacaggt gcactaaaag atgaattggt
     4081 gaagactgat aaaatttatg gtaagatcaa gaagagactt ctgtggggct cagatctggc
     4141 gaccatgata cggtgtgccc gggctttcgg aggccttatg gatgaactca aggcacactg
     4201 tgtcacactt cctgtcagag ttggtatgaa catgaatgag gatggcccca tcatctttga
     4261 gaagcactcc aggtataaat atcactatga tgctgattat tcccggtggg actcaacaca
     4321 acaaagggat gtgctggcag cagcactaga aattatggtc 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 gatccagaga agctgacagc aaaactcaag gagtacgggc tgaaaccaac
     4681 ccgccccgat aaaactgaag gaccccttgt tatctctgaa gatctggatg gcctaacatt
     4741 ccttcggagg actgtgaccc gtgacccagc tggctggttt ggaaaactgg aacaaagctc
     4801 aattctcagg caaatgtact ggaccagggg gcccaaccat gaagacccat ctgaaacaat
     4861 gataccacac tcccaaagac ccatacaatt gatgtccttg ctgggcgagg ctgcactcca
     4921 cggcccgaca ttttatagca aaattagcaa attagtcatt gcagagctga aggaaggtgg
     4981 catggatttt tacgtgccca gacaagagcc aatgttcaga tggatgagat tttcagatct
     5041 gagcacgtgg gagggcgatc gcaatctggc tcccagtttt gtgaatgaag atggcgtcga
     5101 atgacgccgc tccatctact gatggtgcag ccggcctcgt gccagaaagt aataatgagg
     5161 tcatggctct tgaacccgtg gctggtgccg ccctggcagc cccagtcacc ggacaaacaa
     5221 atattataga cccttggatt agagcaaatt ttgtccaggc ccctaatggt gaatttacag
     5281 tttctccccg taatgcccct ggtgaagtgt tattgaatct agagttgggt ccagagttaa
     5341 atccttatct ggcacattta gcaagaatgt acaacgggta tgccggtggg atggaggtgc
     5401 aggtcatgtt ggctgggaac gcgttcacag ccggcaagtt ggtctttgcc gccgtaccac
     5461 ctcacttccc ggttgaaaac cttagtccac agcaaattac catgtttccc catgtgatta
     5521 tagatgtgag aactttggaa cctgttttat taccactccc tgatgttaga aataatttct
     5581 tccattacaa tcagaaggat gatcctaaga tgagaattgt ggctatgctt tatactcccc
     5641 ttaggtctaa tggctcaggt gatgacgtgt ttacagtctc atgcagggtg ttgactagac
     5701 cctcccctga ttttgatttc acatatttgg tgccaccaac agtggagtct aagactaaac
     5761 cattcaccct cccaatcctc acgcttgggg agctctccaa ttctagattt ccagtgtcca
     5821 tagaccagat 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 ctgggcgtac
     6061 ctgattttca gggaagggtc tttggtatca tctcccaaag agacaaacac aacagccctg
     6121 gacataatga accagcaaac aggggacacg atgctgtggt ccctacttac acagcacagt
     6181 acaccccaaa attgggtcaa attcaaattg gcacatggca gaccgatgat cttacagtca
     6241 accaaccagt caaattcacc ccagttggac ttaacgacac tgaacatttt aaccaatggg
     6301 tggtccccag atatgctggt gctctaaacc tcaacacaaa tcttgcccct tctgttgctc
     6361 cagtttttcc aggggagcgc ctgctctttt tcagatcata tatccccctc aagggtggtt
     6421 atggaaatcc agctattgat tgtctgctac cacaagagtg ggtgcaacat ttctatcagg
     6481 aagcagctcc 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 ctaagcagct
     6901 gcaggcagac atgatggcta taaagcaggg agtcttgacc gctggcggct tctcccccgc
     6961 tgatgcagcc agaggtgctg ttaatgcacc catgacacag gcgctggatt ggaacggcac
     7021 aaggtattgg gcaccaggct ccatgaggac cacatcttac tctggaagat tcacatcaac
     7081 cgccccagtg aggcaggccg acttccaaca cacccagagc cggccttcga gtggctcttc
     7141 tgtgtcctcc tttactactc agtcttcaag gccaactctg actacaacca ctgggtcctc
     7201 acataacaca gtttcatcaa attcaactcg cagtacaaac ctctcccaat caacggtttc
     7261 tagggctaca tctaggacag gtgagtgggt tagagatcaa aataaaaatt tggaacctta
     7321 catgcatggt gccttgcaga cagcctttgt caccccacct tctagcaggg cgtctgatgg
     7381 gacagtctca accgccccaa aaggtgtttt ggactcctgg acacctgcgt tcaacacccg
     7441 caggcagccg ctttttgcac acctccgtaa gaggggggag tcacaagcct agtgaaa
//