Typing tool

Complete norovirus genomes

MH218670  GII.4 Sydney
 GII.P4 New Orleans

Length: 7,550 | 3 CDS

ORF1: 5..5104
ORF2: 5085..6707
ORF3: 6707..7513
LOCUS       MH218670                7550 bp    RNA     linear   VRL 11-JUN-2018
DEFINITION  Norovirus GII isolate NORO_212_17_12_2015, complete genome.
ACCESSION   MH218670
VERSION     MH218670.1
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_212_17_12_2015"
                     /host="Homo sapiens"
                     /db_xref="taxon:122929"
                     /country="United Kingdom"
                     /collection_date="17-Dec-2015"
                     /note="genotype: GII.P4_GII.4"
     gene            5..5104
                     /gene="ORF1"
     CDS             5..5104
                     /gene="ORF1"
                     /codon_start=1
                     /product="nonstructural polyprotein"
                     /protein_id="AWR17668.1"
                     /translation="MKMASNDASAAAVANSNNDTAESSSDGVLSSMAVTFKRALGARP
                     KQPPPREKPQRPPRPPTPELIKNVPPPPPNGEDEIVVSYSVKDGVSGLPDLSTVRQPE
                     ESNTAFSVPPLNQRENRDAKEPLTGTILEMWDGEIYHYGLYVERGLVLGVHKPPAAIS
                     LAKVELTPLSLYWRPVYTPQYLISPDTLKKLSGETFPYTAFDNNCYAFCCWVLDLNDS
                     WLSRRMIQRTTGFFRPYQDWNRKPLPTMDDSKIKKVANIFLCTLSSLFTRPIKDIIGK
                     IRPLNILNILASCDWTFAGIVESLILLAELFGVFWTPPDVSAMIAPLLGDYELQGPED
                     LAVELVPVVMGGIGLVLGFTKEKIGKMLSSAASTLRACKDLGAYGLEILKLVMKWFFP
                     KKEEANELAMVRSIEDAVLDLEAIENNHMTTLLKDKDSLAAYMRTLDLEEEKARKLST
                     KSASPDIVGTINALLARIAAARSLVHRAKEELSSRPRPVVLMISGRPGIGKTHLAREV
                     AKRIAASLTGDQRVGLIPRNGVDHWDAYKGERVVLWDDYGMSNPIHDALRLQELADTC
                     PLTLNCDRIENKGKVFDSDVIIITTNLANPAPLDYVNFEACSRRIDFLVYAEAPDVEK
                     AKRDFPGQPDMWKNAFSPDFSHIKLALAPQGGFDKNGNTPHGKGVMKTLTTGSLIARA
                     SGLLHERLDEFELQGPALTTFNFDRNKVLAFRQLAAENKYGLMDTMRVGKQLKDVKTM
                     PELKQALKNVSIKKCQIVYSGCTYILESDGKGNVKVDRIQSAAVQTNNELAGALHHLR
                     CARIRYYVKCVQEALYSIIQIAGAAFVTTRIAKRMNIQDLWSKPQVENTEETTSKDGC
                     PKPKDDEEFVISSDDIKTEGKKGKNKTGRGKKHTAFSSKGLSDEEYDEYKRIREERNG
                     KYSIEEYLQDRDKYYEEVAIARATEEDFCEEEEAKIRQRIFRPTRKQRKEERASLGLV
                     TGSEIRKRNPDDFKPKGKLWADDDRSVDYNEKLSFEAPPSIWSRIVNFGSGWGFWVSP
                     SLFITSTHVIPQGAKEFFGVPIKQIQVHKSGEFCRLRFPRPIRTDVTGMILEEGAPEG
                     TVVTLLIKRSTGELMPLAARMGTHATMKIQGRTVGGQMGMLLTGSNAKSMDLGTTPGD
                     CGCPYIYKRGNDYVVIGVHTAAARGGNTVICATQGSEGEATLEGGDNKGTYCGAPILG
                     PGNAPTLSTKTKFWRSSTAPLPPGTYEPAYLGGKDPRVKGGPSLQQVMREQLKPFTEP
                     RGKPPKPSVLEAAKKTIINVLEQTIDPPEKWSFAQACASLDKTTSSGHPHHMRKNDCW
                     NGESFTGKLADQASKANLMFEEGKNMTPVYTAALKDELVKTDKIYGKIKKRLLWGSDL
                     ATMIRCARAFGGLMDELKAHCVTLPIRVGMNMNEDGPIIFERHSRYTYHYDADYSRWD
                     STQQRAVLAAALDIMVKFSPEPHLAQVVAEDLLSPSVVDVGDFTISINEGLPSGVPCT
                     SQWNSIAHWLLTLCALSEVTNLSPDTIQANSLFSFYGDDEIVSTDIKLDPEKLTAKLR
                     EYGLKPTRPDKTEGPLVISEDLNGLTFLRRTVTRDPAGWFGKLEQSSILRQMYWTRGP
                     NHGDPSETMIPHSQRPIQLMSLLGEAALHGPAFYSKISKLVIAELKEGGMDFYVPRQE
                     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..6707
                     /gene="ORF2"
     CDS             5085..6707
                     /gene="ORF2"
                     /note="predicted CDS stop by homology is invalid; there
                     may be a valid stop in a different location due to
                     truncation (trc) or extension (ext) (TAG|TAA|TGA) [TAT
                     ending at position 6705 on + strand];first in-frame stop
                     codon exists 3' of stop position predicted by homology to
                     reference [homology search predicted 5085..6705 revised to
                     5085..6707 (stop shifted 2 nt)]"
                     /codon_start=1
                     /product="VP1"
                     /protein_id="AWR17669.1"
                     /translation="MKMASSDANPSDGSAANLVPEVNNEVMALEPVVGAAIAAPVAGQ
                     QNVIDPWIRNNFVQAPGGEFTVSPRNAPGEILWSAPLGPDLNPYLSHLARMYNGYAGG
                     FEVQVILAGNAFTAGKVIFAAVPPNFPTEGLSPSQVTMFPHIVVDVRQLEPVLIPLPD
                     VRNNFYHYNQSNDPTIKLIAMLYTPLRANNAGDDVFTVSCRVLTRPSPDFDFIFLVPP
                     TVESRTKPFSVPVLTVEEMTNSRFPIPLEKLFTGPSSAFVVQPQNGRCTTDGVLLGTT
                     QLSPVNICTFRGDLTHIAGTHNYTMNLASQNWNNYDPTEEIPAPLGTPDFVGKIQGVL
                     TQTTRTDGSTRGHKATVLTGSADFAPKLGRVQFGTDTNNDFDTNQNTKFTPVGVIQDG
                     GTTHQNEPQQWVLPSYSGRNTPNVHLAPAVAPTFPGEQLLFFRSTMPGCSGYPNMDLD
                     CLLPQEWVQYFYQEAAPAQSDVALLRFVNPDTGRVLFECKLHKSGYVTVAHTGQHDLV
                     IPPNGYFRFDSWVNQFYTLAPMGNGAGRRRAV"
     gene            6707..7513
                     /gene="ORF3"
     CDS             6707..7513
                     /gene="ORF3"
                     /codon_start=1
                     /product="VP2"
                     /protein_id="AWR17670.1"
                     /translation="MAGAFFAGLASDVLGSGLGSLINAGAGVINQKVDFENNKNLQQA
                     SFQFSSNLQQASFQHDKEMLQAQIEATKKLQQEMMKIKQAMLLEGGFSETDAARGAIN
                     APMTKTLDWSGTRYWAPDARTTTYNAGRFSTPQPSGALPGRANLRDSVPARGSSSKSS
                     NSSTATSVYSNQTTSTRLGSTAGSGTSVSSLPSTARTRSWVEDQSRSLSPFMRGAHNI
                     SFVTPPSSRSSSQGTVSTVPKEVLDSWTGAFNTRRQPLFAHIRSRGESRV"
ORIGIN      
        1 gtgaatgaag atggcgtcta acgacgcttc cgctgccgct gttgctaaca gcaacaacga
       61 caccgcagaa tcttcaagtg acggagtgct ttctagcatg gccgtcactt ttaaacgagc
      121 cctcggggcg cggcctaaac aacctccccc gagggaaaaa ccacaaagac ccccacgacc
      181 acctactcca gaattgatta aaaatgttcc ccccccccca cccaacggag aggatgaaat
      241 agtggtttct tatagtgtca aagatggtgt ctccggcttg cctgaccttt ccaccgtcag
      301 gcaaccggaa gaatccaaca cggccttcag tgtccctcca ctcaaccaga gggagaatag
      361 agatgctaag gaaccactca ctggaacaat tctggaaatg tgggacgggg aaatctacca
      421 ttatggcttg tatgtggagc gaggtcttgt gctaggcgtg cacaaaccgc cagctgctat
      481 cagcctcgct aaggttgagt taacaccact ctccttgtac tggagacctg tgtacactcc
      541 tcagtacctc atctctccag acactctcaa gaaattgtcc ggagaaacgt tcccctacac
      601 agcctttgac aacaactgct atgccttttg ttgctgggtc ctggacctaa atgactcgtg
      661 gctgagcagg agaatgatcc agagaacaac tggtttcttc aggccctacc aagactggaa
      721 taggaaacct cttcccacta tggatgactc caaaataaag aaggtggcta acatatttct
      781 gtgtactctg tcctcactat tcaccaggcc cataaaagat ataataggga agataaggcc
      841 tcttaacatc ctcaacatct tagcttcatg tgattggacc tttgcaggca tagtggagtc
      901 cctgatactc ttggcagaac tctttggagt tttctggaca cccccagatg tgtctgcgat
      961 gattgccccc ttacttggtg actacgaact acaagggcct gaggaccttg cagtggagct
     1021 cgtccccgtg gtgatggggg gaattggttt ggtgctagga ttcaccaaag agaagattgg
     1081 gaaaatgttg tcatcagctg cgtccacctt aagagcttgc aaagaccttg gtgcatatgg
     1141 gctagagatc ctaaagttag tcatgaagtg gttcttcccg aagaaggagg aggcaaatga
     1201 gctggctatg gtgaggtcca tcgaggatgc agtcctggac ctcgaagcaa ttgaaaacaa
     1261 tcatatgacc accttgctta aagataagga cagtctggca gcctacatga gaacacttga
     1321 ccttgaagag gagaaagcca ggaagctctc aaccaagtct gcctcacccg acatcgtggg
     1381 cacaattaac gccctcctgg cgagaatcgc tgccgcacgt tcgctggtgc atcgagcgaa
     1441 ggaggagctt tccagcagac caagacctgt ggtgttgatg atatcaggca ggccaggaat
     1501 agggaagacc cacctcgcta gggaagtggc taagagaatc gcagcctccc ttacaggaga
     1561 ccagcgtgtt ggcctcattc cacgcaatgg cgtcgaccac tgggatgcgt acaaggggga
     1621 gagggtcgtc ctatgggacg attatggaat gagcaaccct attcacgatg ccctcaggct
     1681 gcaagaactc gctgacactt gccccctcac tctgaactgt gacaggattg aaaataaagg
     1741 aaaggtcttt gacagcgatg tcatcattat caccactaat ctggccaacc cagcaccact
     1801 ggactatgtc aactttgaag catgctcgag gcgcattgac ttcctcgtgt atgcagaagc
     1861 ccctgatgtc gaaaaggcga agcgtgactt cccaggccag cctgacatgt ggaagaacgc
     1921 tttcagtcct gacttctcac acataaaact agcactggcc ccacagggtg gtttcgacaa
     1981 gaacgggaac accccacacg gaaagggcgt catgaagact ctcaccactg gctcccttat
     2041 tgcccgggca tcagggctac tccatgagag gttagatgaa tttgaactgc agggcccagc
     2101 tctcaccacc ttcaacttcg atcgcaataa agtgcttgcc tttagacagc tcgctgctga
     2161 aaataaatat ggattgatgg acacaatgag ggttgggaaa cagctcaagg atgtcaaaac
     2221 catgccagaa ctcaaacaag cacttaagaa tgtctcaatc aagaagtgtc aaatagtgta
     2281 tagtggttgc acctacatac ttgagtctga tggcaagggc aatgtgaaag ttgataggat
     2341 ccaaagcgcc gccgtgcaga ccaacaatga gctggctggt gccctgcacc acttgaggtg
     2401 cgccagaatc agatactatg tcaagtgtgt ccaggaagcc ctgtattcca tcatccaaat
     2461 tgctggggct gcatttgtca ccacgcgcat tgccaagcgc atgaacatac aagacctatg
     2521 gtccaagcca caagtggaaa acacagagga gactaccagc aaggacgggt gcccaaaacc
     2581 taaagatgat gaggagtttg tcatttcatc cgacgacatc aaaactgagg gcaagaaagg
     2641 gaagaacaag actggccgtg gcaagaagca cacagcattt tcaagcaaag gcctcagtga
     2701 tgaagagtat gatgaataca agaggatcag agaagaaagg aatggcaagt actctataga
     2761 agagtacctt caggacaggg acaaatacta tgaggaggtg gccattgcca gagcgactga
     2821 ggaagacttc tgtgaggagg aggaagccaa gatccgacaa aggatcttta ggccaacaag
     2881 gaaacaacgc aaggaggaaa gagcctccct cggcttggtc acaggttctg aaattaggaa
     2941 aagaaaccca gatgacttca aacccaaggg gaaattgtgg gctgacgatg acaggagtgt
     3001 ggactacaat gagaaactca gttttgaggc cccaccaagc atttggtcaa gaatagtcaa
     3061 ctttggttca ggctggggat tttgggtctc ccccagcttg ttcataacat caacccatgt
     3121 cataccccaa ggcgcaaagg agttctttgg agtccccatc aaacaaatac aggtacacaa
     3181 gtcaggcgag ttctgtcgct tgagattccc tagaccaatc agaactgatg tgacgggcat
     3241 gatcttagaa gaaggcgcac ctgagggcac cgtggttaca ctactcatca aaaggtccac
     3301 tggggaactt atgcctctag cagctaggat ggggacccat gcgaccatga agatccaagg
     3361 tcgcactgtt gggggccaga tgggcatgct tctgacagga tccaacgcca agagtatgga
     3421 cctgggtact acaccaggtg attgtggttg cccctacatc tacaagagag gtaatgacta
     3481 tgtggttatt ggggtccaca cggctgccgc acgtgggggg aacactgtca tatgtgccac
     3541 ccaggggagt gaaggggagg ctacacttga gggtggcgac aacaagggga catactgtgg
     3601 tgcaccaatc ctaggcccag ggaatgcccc aacacttagc accaagacca aattctggag
     3661 gtcgtccaca gcaccactcc cacctggcac ctatgaacca gcctatcttg gtggcaagga
     3721 ccctagagtc aagggtggcc cttcactgca gcaagtcatg agggaacagt tgaagccatt
     3781 cacagagccc aggggtaagc caccaaaacc aagtgtgtta gaagctgcca agaaaaccat
     3841 cattaatgtc cttgagcaaa caattgatcc acctgagaaa tggtcgttcg cacaagcttg
     3901 cgcgtccctt gacaagacca cttccagtgg tcatccgcac cacatgcgga aaaacgactg
     3961 ctggaatggg gagtccttca caggcaagct ggcagaccag gcctccaagg ccaacctgat
     4021 gtttgaagaa gggaagaaca tgaccccagt ctacacagct gcgctcaagg atgagttagt
     4081 taaaactgac aaaatttatg gtaagatcaa gaagaggctt ctttggggct cagacctggc
     4141 gaccatgatc cggtgtgctc gagcattcgg aggcctaatg gatgaactca aagcgcactg
     4201 tgttacactt cccattagag ttggcatgaa tatgaatgag gatggcccca tcatcttcga
     4261 gaggcattct aggtacacgt accactatga tgctgattac tcacgatggg attcaacaca
     4321 acagagagcc gtgttggcag cagctctaga tatcatggta aaattctccc cagaaccaca
     4381 tttggctcag gtagtcgcag aagaccttct ttctcctagc gtggtggatg tgggcgactt
     4441 cacaatatca atcaacgagg gtcttccctc tggggtgccc tgcacctccc aatggaactc
     4501 catcgcccac tggcttctca ctctctgtgc gctctccgaa gtcacgaacc tgtctcccga
     4561 taccatacag gctaattctc tcttctcttt ttatggtgat gatgaaattg ttagcacaga
     4621 cataaaattg gacccagaga aattgacagc aaagctcaga gaatatgggt taaaaccaac
     4681 ccgccctgac aaaactgaag gacccctcgt catctctgaa gacctgaatg gcctaacttt
     4741 cctgcggaga actgtgaccc gcgacccagc tggttggttc ggaaaactgg agcagagttc
     4801 aatactcagg caaatgtact ggactagggg tcccaaccat ggagacccat ctgaaacaat
     4861 gattccacac tcccaaagac ccatacaatt gatgtcccta ctgggggagg ccgctctcca
     4921 cggcccagca ttttacagta aaatcagcaa attggtcatt gcagagctaa aagaaggtgg
     4981 tatggatttt tacgtgccca gacaagagcc aatgttcaga tggatgagat tctcagatct
     5041 gagcacgtgg gagggcgatc gcaatctggc tcccagtttt gtgaatgaag atggcgtcga
     5101 gtgacgccaa cccatctgat gggtccgcag ccaacctcgt cccagaggtc aacaatgagg
     5161 ttatggctct ggagcccgtt gttggtgccg ccattgcggc acctgtagcg ggccaacaaa
     5221 atgtaattga cccctggatt agaaacaatt ttgtacaagc ccctggtgga gagtttacag
     5281 tgtcccctag aaacgctcca ggtgaaatac tatggagcgc gcccttaggc cctgatttaa
     5341 atccctacct atcccatttg gccagaatgt ataatggtta tgcaggtggt tttgaagtgc
     5401 aggtaattct cgcggggaac gcgttcaccg ccgggaaggt catatttgca gcagtcccac
     5461 caaattttcc aactgaaggc ttgagcccta gtcaggtcac tatgtttccc catatagtag
     5521 tagatgttag gcaactagaa cctgtgttga ttcccttacc cgatgttagg aataacttct
     5581 atcattataa tcaatcaaat gaccccacca ttaagttgat agcaatgctg tatacaccac
     5641 ttagagctaa taatgctggg gacgatgtct tcacagtttc ttgccgagtt ctcacgaggc
     5701 catcccccga ttttgatttc atattcctag tgccacccac agttgagtct aggactaaac
     5761 cattctctgt tccagtctta actgttgagg agatgaccaa ttcaaggttc cccattcctt
     5821 tggaaaagtt gttcacgggt cccagcagtg cctttgttgt tcaaccacaa aacggtaggt
     5881 gtacgactga tggcgtactc ctaggcacca cccaattgtc tcctgtcaat atctgcacct
     5941 tcagagggga cctcacccac attgcaggta ctcataacta cacaatgaat ttggcttctc
     6001 aaaattggaa taattatgac ccaacagaag agattccagc ccctctagga actccagact
     6061 ttgtggggaa gattcaaggc gtgctcaccc aaaccacaag gacagatggc tcaacacgcg
     6121 gccacaaagc tacggtgctc actgggagcg ccgactttgc tccaaaactg ggcagagttc
     6181 aatttggaac tgacacaaac aatgattttg ataccaacca aaacacaaag ttcaccccag
     6241 tcggtgtcat ccaggatggt ggcaccaccc accaaaatga accccaacag tgggtgctcc
     6301 caagttattc aggcagaaat actcctaatg ttcatctggc ccccgctgta gcccccactt
     6361 ttccgggtga gcaacttctc ttctttagat ccaccatgcc cggatgtagc gggtacccca
     6421 acatggattt ggactgtctg ctcccccagg aatgggtgca gtacttctac caagaggcag
     6481 ccccagcaca atctgatgtg gctctgctaa gatttgtgaa tccagacaca ggtagggttt
     6541 tgtttgagtg taaacttcat aaatcaggct atgtaacagt ggctcacact ggccaacatg
     6601 atttggttat cccccccaat ggctatttta ggtttgattc ctgggtcaac cagttctaca
     6661 cgcttgcccc catgggaaat ggagcggggc gtagacgtgc agtataatgg ctggagcttt
     6721 ctttgctgga ttagcatctg atgtccttgg ctctggactt ggttccctta tcaatgctgg
     6781 ggctggggtc attaatcaaa aagttgactt tgaaaacaac aaaaatttgc aacaagcatc
     6841 cttccaattt agcagcaatt tacaacaggc ttcctttcaa catgacaaag aaatgctcca
     6901 agcacaaatt gaggccacca aaaagctaca acaggaaatg atgaaaatta agcaggcaat
     6961 gctcctggag ggtgggttct ctgagacaga tgcagcccgt ggggcaatca acgcccccat
     7021 gacaaaaact ttggactgga gcgggacaag atactgggct cccgatgcta ggactacaac
     7081 atacaatgca ggccgctttt caacccctca accatcgggg gcactgccag gaagagctaa
     7141 tcttagggat tctgtccctg ctcggggctc ctccagtaaa tcctctaact cttctactgc
     7201 tacttctgtg tactcaaatc aaaccacttc aacgagactt ggttctacag ctggttctgg
     7261 taccagtgtc tcgagtctcc cgtcaactgc aaggactagg agctgggttg aggatcaaag
     7321 taggagtttg tctcctttca tgaggggggc ccacaacata tcgtttgtca ccccaccatc
     7381 tagcagatcc tctagccaag gcacagtctc aaccgtgcct aaagaggttt tggactcctg
     7441 gactggcgct ttcaacacgc gcaggcagcc tctcttcgct cacattcgta gtcgagggga
     7501 gtcacgggtg taatgtgaaa agacaaaatt gattatcttt ctttttcttt
//