Typing tool

Complete norovirus genomes

MH218606  GII.4 Sydney
 GII.P4 New Orleans

Length: 7,513 | 3 CDS

ORF1: 5..5104
ORF2: 5085..6707
ORF3: 6707..7513
LOCUS       MH218606                7513 bp    RNA     linear   VRL 11-JUN-2018
DEFINITION  Norovirus GII isolate NORO_135_30_01_2015, complete genome.
ACCESSION   MH218606
VERSION     MH218606.1
KEYWORDS    .
SOURCE      Norovirus GII
  ORGANISM  Norovirus GII
            Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes;
            Picornavirales; Caliciviridae; Norovirus.
REFERENCE   1  (bases 1 to 7513)
  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 7513)
  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..7513
                     /organism="Norovirus GII"
                     /mol_type="genomic RNA"
                     /isolate="NORO_135_30_01_2015"
                     /host="Homo sapiens"
                     /db_xref="taxon:122929"
                     /country="United Kingdom"
                     /collection_date="30-Jan-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="AWR17476.1"
                     /translation="MKMASNDASAAAVANSNNDTAKTSSDGVLSSMAVTFKRALGARP
                     KQPPPREIPQRPPRPPTPELVKNIPPPPPNGEDEIVVSYSVKNGVSGLPDLSTVRQPE
                     ETNTAFSVPPLNQRENKDAKEPLTGTILEMWDGEIYHYGLYVERGLVLGVHKPPAAIS
                     LAKIELTPLSLYWRPVYTPQYLISPDSLKKLAGETFPYTAFDNNCYAFCCWVLDLNDS
                     WLSRRMIQRTTGFFRPYQDWNRKPLPTMDSSKIKKVADIFLCTLSSLFTRPIKDIIGK
                     IRPLNILNILASCDWTFAGIVESLILLAELFGVFWTPPDVSAMIAPLLGDYELQGPED
                     LAVELVPVVMGGIGLVLGFTKEKIGKMLSSAASTLRACKDLGAYGLEILKLVMKWFFP
                     KKEEANELAMVRSIEDAVLDLEAIENNHMTTLLKDKDSLATYMRTLDLEEEKARKLST
                     KSASPDIVGTVNALLARIAAARSLVHRAKEELSSRPRPVVLMISGRPGIGKTHLAREV
                     AKRIATSLTGDQRVGLVPRNGVDHWDAYKGERVVLWDDYGMSNPIHDALRLQELADTC
                     PLTLNCDRIENKGKVFDSDVIIITTNLANPAPLDYVNFEACSRRIDFLVYAEAPEVEK
                     AKRDFPGQPDMWKNAFSSDFSHIKLTLAPQGGFDKNGNTPHGKGVMKTLTTGSLIARA
                     SGLLHERLDEFELQGPALTTFNFDRNKVLAFRQLAAENKYGLMDTMRVGKQLKDVKTM
                     PELKQALKNVSIKKCQIVYSGCTYMLESDGKGNVKVDKIQSAAVQTNNELTGALHHLR
                     CARIRYYVKCVQEALYSIIQIAGAAFVTTRIAKRMNIQDLWSKPQVENTEETTSKDGC
                     PKPKDDEEFVITSDDIKAEGKKGKNKTGRGKKHTAFSSKGLSDEEYDEYKRIREERNG
                     KYSIEEYLQDRDKYYEEVAIARATEEDFCEEEEAKIRQRIFRPTRKQRKEERVSLGLV
                     TGSEIRKRNPDDFKPKGKLWADDDRNVDYNEKLSFEAPPSIWSRIVNFGSGWGFWVSP
                     SLFITSTHVIPQGAKEFFGVPIKQIQVHKSGEFCRLRFPKPIRTDVTGMILEEGAPEG
                     TVVTLLIKRPTGELMPLAARMGTHATMKIQGRTVGGQMGMLLTGSNAKSMDLGTTPGD
                     CGCPYIYKRGNDYVVIGVHTAAARGGNTVICATQGSEGEATLEGGDNKGTYCGAPILG
                     PGSAPTLSTKTKFWRSSTASLPPGTYEPAYLGGKDPRVKGGPSLQQVMREQLKPFTEP
                     RGKPPKPSVLEAAKKTIINVLEQTIDPPEKWSFAQACASLDKTTSSGHPHHMRKNDCW
                     NGESFTGKLADQASKANLMYEEGKNMTPVYTAALKDELVKTDKIYGKIKKRLLWGSDL
                     ATMIRCARAFGGLMDELKAHCVTLPIRVGMNMNEDGPIIFERHSRYTYHYDADYSRWD
                     STQQRAVLAAALEIMVKFSPEPHLAQVVAEDLLSPSVVDVGDFTISINEGLPSGVPCT
                     SQWNSIAHWLLTLCALSEVTNLSPDTIQANSLFSFYGDDEIVSTDIKLDPEKLTAKLR
                     EYGLKPTRPDKTEGPLAISEDLDGLTFLRRTVTRDPAGWFGKLEQSSILRQMYWTRGP
                     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="AWR17477.1"
                     /translation="MKMASSDANPSDGSAANLVPEVNNEVMALEPVVGAAIAAPVAGQ
                     QNVIDPWIRNNFVQAPGGEFTVSPRNAPGEILWSAPLGPDLNPYLSHLARMYNGYAGG
                     FEVQVILAGNAFTAGKVIFAAVPPNFPTEGLSPSQVTMFPHIVVDVRQLEPVLIPLPD
                     VRNNFYHYNQSNDSTIKLIAMLYTPLRANNAGDDVFTVSCRVLTRPSPDFDFIFLVPP
                     TVESRTKPFSVPVLTVEEMTNSRFPIPLEKLFTGPSSAFVVQPQNGRCTTDGVLLGTT
                     QLSPVNICTFRGDVTHTTGSHNYTMNLASLNWNNYDPTEEIPAPLGTPDFVGKIQGVL
                     TQTTRTDGSTRGHKATVYTGSADFAPKLGRVQFATDTDHDFEANQNTKFTPVGVIQDG
                     STTHRNEPQQWVLPSYSGRNIHNVHLAPAVAPTFPGEQLLFFRSTMPGCSGYPNMDLD
                     CLLPQEWVQHFYQEAAPAQSDVALLRFVNPDTGRVLFECKLHKSGYVTVAHTGQHDLV
                     IPPNGYFRFDSWVNQFYTLAPMGNGTGRRRAV"
     gene            6707..7513
                     /gene="ORF3"
     CDS             6707..7513
                     /gene="ORF3"
                     /codon_start=1
                     /product="VP2"
                     /protein_id="AWR17478.1"
                     /translation="MAGAVFAGLASDVLSSGLGSLINAGAGAINQTIEFENNRKLQQA
                     SFQFSSNLQQASFQHDKEMLQAQIESTKKLQQEMMKVKQAVLLEGGFSETDAARGAIN
                     APMTKALDWSGTRYWAPDARTTTYNAGRFSTPQPSGALPGRANLRDAVPARGSSSKSS
                     NSSTVTSVYSNQTTSTRLGSTAGSGASVSSLPSTARTRSWVEDQNRNLSPFMRGAHNI
                     SFVTPPSSRSSSQGTVSTVPKEVLDSWTGAFNTRRQPLFAHIRKRGESRV"
ORIGIN      
        1 gtgaatgaag atggcgtcta acgacgcttc cgctgccgct gttgctaaca gcaacaacga
       61 caccgcaaaa acttcaagtg acggagtgct ttctagcatg gctgtcactt ttaaacgagc
      121 cctcggggcg cggcctaaac agcctccccc gagggaaata ccacaaagac ccccacgacc
      181 acctactcca gaactggtta agaacatccc ccctcccccg cccaacgggg aagatgaaat
      241 agtggtctct tatagtgtca aaaatggtgt ctccggcttg cctgaccttt ctaccgtcag
      301 gcaaccggaa gaaaccaaca cagccttcag tgtccctccg ctcaatcaga gggagaataa
      361 agatgctaag gagccactca ctggaacaat tctggaaatg tgggacgggg aaatctatca
      421 ttatggcctg tatgtggagc gaggccttgt actaggtgtg cacaaaccgc cagctgccat
      481 cagccttgct aagattgagc tgacaccact ctccttgtac tggagacctg tgtacactcc
      541 tcagtacctc atctctccag acagtctcaa gaaattggcc ggagagacgt tcccctacac
      601 agcctttgat aacaactgtt atgccttttg ctgctgggtt ctggacctga atgactcgtg
      661 gctgagcaga agaatgatcc agagaacaac tggtttcttc aggccctacc aggactggaa
      721 caggaaaccc ctccccacta tggatagctc caaaataaag aaggtggctg acatatttct
      781 gtgtaccctg tcctcgctat tcaccagacc cataaaagat ataataggga agataaggcc
      841 tcttaacatc ctcaacatct tggcctcatg tgattggacc tttgcgggca tagtggagtc
      901 cctgatactc ttggcagaac tctttggagt tttctggaca cccccagatg tgtctgcgat
      961 gattgccccc ttactcggtg actacgagct acaaggacct gaggaccttg cagtggagct
     1021 tgtccccgtg gtgatggggg gaattggttt ggtgctagga ttcaccaaag agaagattgg
     1081 gaaaatgttg tcatctgctg cgtccacttt gagagcttgc aaagaccttg gtgcatatgg
     1141 gctagagatc ctaaagttag tcatgaaatg gttcttccca aagaaggagg aggcaaatga
     1201 gctggctatg gtgaggtcca tcgaggatgc agtcctggat ctcgaggcaa ttgaaaacaa
     1261 tcacatgacc accttgctta aagataaaga cagtctggca acctacatga gaacacttga
     1321 ccttgaagag gagaaagcca ggaaactctc aaccaagtct gcctcacccg acatcgtggg
     1381 tacagtcaac gccctcctgg cgagaatcgc cgccgcacgt tctctggtgc atcgagcgaa
     1441 ggaggagctt tccagcagac caagacctgt ggtgctgatg atatcaggca ggccaggaat
     1501 agggaagacc cacctcgcta gggaagtggc taagagaatc gcaacctccc ttacagggga
     1561 tcagcgcgtg ggcctcgtcc cacgcaatgg tgtcgaccat tgggatgcgt acaaggggga
     1621 gagggtcgtc ctgtgggacg attatggaat gagcaaccct attcacgatg ccctcaggct
     1681 gcaagaactc gctgacactt gtcccctcac tctgaactgt gacaggattg aaaacaaagg
     1741 aaaggtcttt gacagcgatg tcatcattat caccactaat ctggccaacc cagcaccact
     1801 ggactatgtc aactttgaag catgctcgag gcgcattgac tttctcgtgt atgcagaggc
     1861 ccctgaagtc gaaaaggcga agcgtgactt cccaggccag cctgacatgt ggaagaacgc
     1921 tttcagttct gatttctcac acataaaact aacactggcc ccacaaggtg gtttcgataa
     1981 gaacgggaac accccacacg gaaagggcgt catgaagacc ctcaccactg gctcccttat
     2041 tgcccgggca tcagggctac tccatgagag gttggatgaa tttgaactgc agggcccagc
     2101 tctcaccacc ttcaacttcg atcgcaataa agtgcttgcc tttagacagc ttgctgctga
     2161 aaacaaatat ggattgatgg acacaatgag ggttgggaaa cagctcaagg atgtcaaaac
     2221 catgccagaa ctcaagcaag cactcaagaa tgtctcaatc aagaagtgcc aaatagtgta
     2281 tagtggctgc acttacatgc ttgagtctga tggcaagggc aatgtgaaag ttgacaaaat
     2341 ccaaagcgcc gccgtgcaga ccaacaatga gctgactggc gccctgcacc acttgaggtg
     2401 cgccagaatc agatactatg tcaagtgtgt tcaggaggcc ctgtattcca tcatccaaat
     2461 cgctggggct gcatttgtca ccacgcgcat tgccaagcga atgaacatac aagacctgtg
     2521 gtccaagcca caagtggaaa acacagagga gactaccagc aaggatgggt gcccaaaacc
     2581 caaggatgat gaggagttcg tcattacatc cgacgacatc aaagctgagg gcaagaaagg
     2641 gaagaacaag actggccgtg gcaagaagca cacagcattc tcaagcaaag gtctcagtga
     2701 tgaagagtat gatgaataca agaggattag agaagaaagg aatggcaagt actctataga
     2761 agagtacctt caggacagag acaaatacta tgaggaggtg gccattgcca gggcgactga
     2821 ggaagacttc tgtgaagagg aggaggccaa gatccggcaa aggatcttta ggccaacgag
     2881 gaaacaacgc aaggaggaaa gagtctctct tggtctggtc acaggctctg aaattaggaa
     2941 aagaaaccca gatgacttca aacccaaggg gaaattgtgg gctgacgatg acaggaatgt
     3001 ggactacaat gagaaactca gctttgaggc cccaccaagc atttggtcga gaatagtcaa
     3061 ctttggctca ggctggggat tctgggtctc ccccagtctg ttcataacat caacccatgt
     3121 cataccccag ggcgcaaagg agttctttgg agtccccatc aaacaaatac aggtacacaa
     3181 gtcaggcgag ttctgtcgct tgagattccc taaaccaatc aggactgatg tgacgggtat
     3241 gatcttggaa gaaggcgctc ctgagggcac cgtggtcaca ctgctcatca agaggcccac
     3301 tggggaactc atgcccctag cagctaggat ggggacccat gcgaccatga agatccaagg
     3361 acgcactgtt ggaggccaga tgggcatgct tctgacagga tccaacgcca agagcatgga
     3421 cctgggtaca acaccaggtg attgtggctg cccctacatc tacaagagag gtaatgacta
     3481 tgtggtcatt ggagtccaca cggctgccgc acgtggggga aacactgtca tatgtgccac
     3541 ccaagggagt gaaggggagg ctacacttga gggtggtgac aacaagggga catactgtgg
     3601 tgcaccaatc ctaggcccag ggagtgcccc gacacttagc accaaaacca aattctggag
     3661 gtcgtccaca gcatcacttc cacctggcac ctatgaacca gcctatcttg gtggcaagga
     3721 ccctagagtc aagggtggcc cttcactgca gcaagtcatg agagaacagt tgaagccatt
     3781 cacagagccc aggggcaagc caccaaaacc aagtgtacta gaagctgcca agaagaccat
     3841 cattaatgtc cttgagcaaa caattgatcc accagagaaa tggtcgttcg cacaagcttg
     3901 cgcgtccctc gacaagacca cttccagtgg ccatccgcac cacatgcgga aaaacgactg
     3961 ctggaacggg gagtccttca cgggcaagct ggcagaccag gcttccaagg ccaacctgat
     4021 gtatgaagaa gggaagaaca tgaccccagt ctacacagct gcgctcaagg atgagttggt
     4081 taaaactgac aaaatctatg gtaagatcaa gaagaggctt ctctggggct cggatctggc
     4141 aaccatgatt cggtgtgctc gagcattcgg aggcctaatg gatgaactca aagcgcactg
     4201 tgtcacactc cccattagag ttggcatgaa tatgaatgag gatggcccca tcatcttcga
     4261 gaggcattcc aggtacacgt accactatga tgctgactac tctcggtggg attcaacaca
     4321 acagagagcc gtgctggcag cagctctgga aatcatggtt aaattctccc cagaaccaca
     4381 tttggctcag gtagtcgcgg aagaccttct ctcccccagc gtggtggacg tgggcgactt
     4441 cacaatatca atcaatgagg gtcttccctc tggggtgccc tgcacctccc aatggaactc
     4501 catcgcccac tggcttctca ctctctgtgc gctctctgaa gtcacaaacc tgtctcctga
     4561 caccatacag gctaattccc tcttctcttt ttatggtgat gatgaaattg ttagcacaga
     4621 cataaaattg gacccagaga aattgacagc aaaactcaga gaatatgggt taaaaccaac
     4681 ccgccctgac aaaactgaag gaccccttgc catctctgaa gacctggatg gcctaacttt
     4741 cctgcggaga actgtgaccc gcgacccagc tggttggttt ggaaaactgg agcagagttc
     4801 aatactcagg caaatgtact ggactagggg tcccaaccat ggagacccat ctgaaacaat
     4861 gattccacac tcccaaaggc ccatacaatt gatgtcccta ctaggggagg ccgctctcca
     4921 cggcccagca ttttacagca 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 ctattgcggc acctgtagcg ggccaacaaa
     5221 atgtaattga cccctggatt agaaacaatt ttgtacaagc ccctggtgga gagtttacag
     5281 tatcccctag aaacgctcca ggtgaaatac tatggagcgc gcccttaggc cctgatctaa
     5341 acccctacct atcccattta gccagaatgt acaatggtta tgcaggtggc tttgaagtgc
     5401 aggtaattct cgcggggaac gcgttcaccg ccgggaaggt catatttgca gcagtcccac
     5461 caaattttcc aactgaaggc ttaagcccca gccaggtcac catgttcccc catatagtgg
     5521 tagatgttag gcaactagaa cctgtgttga ttcccttacc cgatgttagg aataatttct
     5581 atcattataa ccaatcaaat gactccacca ttaagctgat agcaatgttg tatacaccac
     5641 ttagggctaa taatgctggg gacgatgttt tcacagtttc ttgccgagtt ctcacaaggc
     5701 catcccccga ttttgatttc atatttttgg tgccccccac agttgagtca agaactaaac
     5761 cattctctgt cccagtttta actgttgagg agatgaccaa ttcaagattc cccattcctt
     5821 tggaaaagct gttcacgggt cccagcagtg cctttgttgt tcaaccacaa aacggcaggt
     5881 gcacgactga tggcgtgctt ctaggcacca cccaactgtc tcctgtcaac atctgcacct
     5941 tcagagggga tgtcacccat accacaggca gtcacaacta cacaatgaat ttggcttctc
     6001 taaattggaa caattatgac ccaacagaag aaatcccagc ccctctagga actccagact
     6061 ttgtggggaa gattcaaggc gtgctcaccc aaaccacaag gacagatggc tcaacacgcg
     6121 gccacaaagc cacagtgtac actgggagtg ccgattttgc tccaaaactg ggtagagttc
     6181 aatttgcaac tgacacagac catgattttg aagctaacca aaacacaaag ttcaccccag
     6241 tcggtgtcat tcaagatggt agcaccaccc accgaaatga acctcaacag tgggtgcttc
     6301 ctagttactc aggcagaaat attcataatg tgcatctggc ccccgctgta gcccccactt
     6361 ttccaggtga gcaacttctc tttttcagat ccaccatgcc cggatgcagc gggtacccca
     6421 acatggattt ggactgcttg ctcccccagg aatgggtgca gcacttctac caagaggcag
     6481 ccccagcaca atctgatgtg gccctgctga gatttgtgaa tccagacaca ggtagggttt
     6541 tgtttgagtg caagcttcat aaatcaggct atgttacagt ggctcacact ggccaacacg
     6601 atctggttat cccccccaat ggttatttta ggtttgattc ttgggtcaac cagttctaca
     6661 cgcttgcccc catgggaaat ggaacggggc gtagacgtgc agtataatgg ctggagctgt
     6721 ctttgctgga ttggcatctg atgtcctcag ctctggactt ggttccctta tcaatgctgg
     6781 ggccggggcc atcaaccaaa caattgagtt tgaaaataac agaaaattgc aacaagcatc
     6841 attccaattt agcagcaatc tgcaacaggc ttccttccaa catgacaaag agatgctcca
     6901 agcacaaatt gagtctacca aaaagctaca acaggaaatg atgaaagtta agcaggcagt
     6961 gctcctagag ggtgggttct ctgagacaga tgcagcccgc ggggcaatca acgcccccat
     7021 gacaaaagct ttggactgga gcgggacaag gtactgggct cccgatgcca ggaccacaac
     7081 atacaatgca ggccgctttt ccacccctca accatcgggg gcactgccag gaagagctaa
     7141 tcttagggat gctgtccctg ctcggggttc ctccagcaaa tcttctaact cttctactgt
     7201 tacttctgtg tattcaaatc aaaccacttc aacgagactt ggttctacag ctggttctgg
     7261 tgccagtgtc tcgagcctcc cgtcaactgc aaggactagg agctgggttg aggatcaaaa
     7321 taggaatttg tcacctttca tgaggggggc ccacaatata tcgtttgtca ccccaccatc
     7381 tagcagatcc tctagccaag gcacagtctc aaccgtgcct aaagaggttt tggactcctg
     7441 gactggcgct ttcaacacgc gcaggcagcc tctcttcgct cacattcgta agcgagggga
     7501 gtcacgggtg taa
//