Typing tool

Complete norovirus genomes

MK762624  GII.4 Sydney
 GII.P16

Length: 7,558 | 3 CDS

ORF1: 5..5104
ORF2: 5085..6707
ORF3: 6707..7513
LOCUS       MK762624                7558 bp    RNA     linear   VRL 13-APR-2019
DEFINITION  Norovirus GII isolate Hu/US/2017/GII.P16-GII.4 Sydney/Jackson4273,
            complete genome.
ACCESSION   MK762624
VERSION     MK762624.1
KEYWORDS    .
SOURCE      Norovirus GII
  ORGANISM  Norovirus GII
            Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes;
            Picornavirales; Caliciviridae; Norovirus.
REFERENCE   1  (bases 1 to 7558)
  AUTHORS   Barclay,L., Cannon,J.L., Wikswo,M.E., Phillips,A., Browne,H.,
            Montmayeur,A.M., Tatusov,R.L., Burke,R.M., Hall,A.J. and Vinje,J.
  TITLE     Emergence and characterization of multiple viruses associated with
            a novel GII.P16 polymerase in the United States, 2015-2018
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 7558)
  AUTHORS   Barclay,L., Cannon,J.L., Selvarangan,R., Montmayeur,A.M.,
            Tatusov,R.L., Chhabra,P. and Vinje,J.
  TITLE     Direct Submission
  JOURNAL   Submitted (05-APR-2019) Division of Viral Diseases, Centers for
            Disease Control and Prevention, 1600 Clifton Road NE, Atlanta, GA
            30329, USA
COMMENT     ##Assembly-Data-START##
            Assembly Method       :: Geneious v. R10; SPAdes v. 3.6
            Sequencing Technology :: Illumina
            ##Assembly-Data-END##
FEATURES             Location/Qualifiers
     source          1..7558
                     /organism="Norovirus GII"
                     /mol_type="genomic RNA"
                     /strain="Jackson4273"
                     /isolate="Hu/US/2017/GII.P16-GII.4 Sydney/Jackson4273"
                     /isolation_source="stool"
                     /host="Homo sapiens"
                     /db_xref="taxon:122929"
                     /country="USA"
                     /collection_date="05-Jul-2017"
                     /note="genotype: GII.P16-GII.4 Sydney"
     gene            5..5104
                     /gene="ORF1"
     CDS             5..5104
                     /gene="ORF1"
                     /codon_start=1
                     /product="nonstructural polyprotein"
                     /protein_id="QBX91099.1"
                     /translation="MKMASNDATVAVACNNNNDKEKSSGEGLFTNMSSTLKKALGARP
                     KQPAPRGEPQKPPRPPTPELVKRIPPPPPNGEEEEEPVIRYEVKSGISGLPELTTVPQ
                     PDVANTAFSVPPLSLRENREAKEPLTGAILEMWDGEIYHYGLYVEKGLVLGVHKPPAA
                     ISMAKVELTPLSLYWRVVYTPQYLISPETLRRLNGEAFPYTAFDNNCYAFCCWVLDLN
                     DSWLSRRMVQRTTGFFRPYQEWNRKPLPTMDDSKIKKVANIFLCSLSTLFTRPIKDLI
                     GKIKPLNILNILATCDWTFAGIVESLILLAELFGVFWTPPDVSAMIAPLLGDYELQGP
                     EDLAVELVPVVMGGIGLVLGFTKEKIGKMLSSAASTLRACKDLGAYGLEILKLVMKWF
                     FPKKEEANELAMVRAIEDAVLDLEAIENNHMTTLLKDKDSLATYMKTLDMEEEKARRL
                     STKSASPDIVGTINALLARIAAARSLVHRAKEELSSRIRPVVVMISGKPGIGKTHLAR
                     EVARKVASTLTGDQRVGLIPRNGVDHWDAYKGERVVLWDDYGMSNPIHDALRIQELAD
                     TCPLTLNCDRIENKGKVFDSEVIIITTNLANPAPLDYVNFEACSRRIDFLVYAEAPEV
                     EKAKRDFPGQPDMWKDAFKPDFSHIKLQLAPQGGFDKNGNTPHGKGVMKTLTTGSLIA
                     RASGLLHERMDEFELQGPTITTFNFDRNRITAFRQLAAENKYGLVDTMKVGNQLKGVK
                     TMEELKQAIRNVTIKRCQIIYGGSTYDLESDGKGKVLVEKVKNTSVQTNNELAGALHH
                     LKHARIRYYVKCVQEAVYSIIQIAGAAFVTTRIARRMNIQELWSKPQLEQNVSETKEE
                     APKSEDDEFIISSKDIKEEGKKGKNKTGRGKKHTAFSSKGLSDEEYDEYKRIREERNG
                     KYSIEEYLQDRDRYYEELAIAKATEEDFCEEEEIKIRQRIFRPTRKQRKEERATLGLV
                     TGSEIRKRNPDDFKPKGKLWADDNRSVDYNEKLDFEAPPSIWSRIVSFGSGWGFWVSP
                     SLFITSTHVIPAGITEAFGVPIKQIQVHKSGEFCRFRFPKPIRPDVTGMILEEGAPEG
                     TVATVLIKRPTGELMPLAARMGTHATMKIQGRMVGGQMGMLLTGSNAKGMDLGTTPGD
                     CGCPYIYKRGNDYIVIGVHTAAARGGNTVICATQGSEGEATLEGGNDKGTYCGAPILG
                     PGGAPKLSTKTKFWRSSNTPLPPGTYEPAYLGGRDPRVKGGPSLQQVMRDQLKPFTEP
                     RGKPPRPSVLEAAKQTIINVLEQTLDPPQKWTYAQACASLDKTTSSGHPHHARKNEFW
                     NGEAFTGKLADQASKANLMFEEGKHMTPVYTAALKDELVKTEKIYGKIKKRLLWGSDL
                     STMIRCARSFGGLMDEMKAHCISLPVRVGMNMNEDGPIIFEKHSRYKYHYDADYSRWD
                     STQQRAVLAAALEIMVRFSAEPQLAQIVAEDLLAPSVVDVGDFKITINEGLPSGVPCT
                     SQWNSIAHWLLTLCALSEVTKLSPDIIQANSMFSFYGDDEIVSTDIKLDPEQLTAKLK
                     EYGLKPTRPDKTEGPLIISEDLNGLTFLRRTVTRDPAGWFGKLDQNSILRQMYWTRGP
                     NHEDPNETMIPHSQRPIQLMALLGEASLHGPSFYSKISKLVITELKEGGMDFYVPRQE
                     PMFRWMRFSDLSTWEGDRNLAPNFVNEDGVE"
     mat_peptide     5..1000
                     /gene="ORF1"
                     /product="p48"
     mat_peptide     1001..2098
                     /gene="ORF1"
                     /product="NTPase"
     mat_peptide     2099..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="major capsid protein"
                     /codon_start=1
                     /product="VP1"
                     /protein_id="QBX91100.1"
                     /translation="MKMASSDANPSDGSAANLVPEVNNEVMALEPVVGAAIAAPVAGQ
                     QNVIDPWIRNNFVQAPGGEFTVSPRNAPGEILWSAPLGPDLNPYLSHLARMYNGYAGG
                     FEVQVILAGNAFTAGKIIFAAVPPNFPTEGLSPSQVTMFPHIIVDVRQLEPVLIPLPD
                     VRNNFYHYNQSNDSTIKLIAMLYTPLRANNAGDDVFTVSCRVLTRPSPDFDFIFLVPP
                     TVESRTKPFSVPVLTVEEMTNSRFPIPLEKLFTGPSSAFVVQPQNGRCTTDGVLLGTT
                     QLSPVNICTFRGDVTHITGSRNYTMNLASQNWNNYDPTEEIPAPLGTPDFVGKIQGML
                     TQTTRTDGSTRGHKATVYTGSADFSPKLGRVQFETDTDHDFEANQNTKFTPVGVIQDG
                     STTHRNEPQQWVLPSYSGRNTHNVHLAPAVAPTFPGEQLLFFRSTIPGCSGYPNMDLD
                     CLLPQEWVQYFYQEAAPAQSDVALLRFVNPDTGRVLFECKLHKSGYVTVAHTGQHDLV
                     IPPNGYFRFDSWVNQFYTLAPMGNGTGRRRVV"
     gene            6707..7513
                     /gene="ORF3"
     CDS             6707..7513
                     /gene="ORF3"
                     /note="minor structural protein; small basic protein"
                     /codon_start=1
                     /product="VP2"
                     /protein_id="QBX91101.1"
                     /translation="MAGAFFAGLASDVLGSGLGSLINAGAGAINQKVEFENNRKLQQA
                     SFQFSSNLQQASFQHDKEMLQAQIEATKKLQQEMMKVKQAMLLEGGFSETDAARGAIN
                     APMTKALDWSGTRYWAPDARTTTYNAGRFSTSQPSGALLGRANLRDAVPARGPSNKPS
                     NSSTATSVYSNQTISTRLGSTAGSGTNVSSLPSTARTRSWVEDQSRNLSPFMRGAHNI
                     SFVTPPSSRSSSQGTVSTVPKEILDSWTGAFNTRRQPLFAHIRKRGESRV"
ORIGIN      
        1 gtgaatgaag atggcgtcta atgacgctac cgttgccgtt gcttgcaaca acaacaacga
       61 caaggaaaaa tcttcaggtg aaggcttatt cacaaatatg tcttccacct taaagaaagc
      121 cctcggggct aggcccaaac agcctgcccc gagaggcgaa ccacaaaagc ccccaaggcc
      181 accaactccc gagttggtca agaggatacc ccctcctcca cctaatggcg aagaagaaga
      241 agaaccagtc attaggtatg aggttaagag tgggatctct ggcctgcccg agctcacaac
      301 agtcccccaa ccggacgtgg ccaacacagc attcagtgtt ccaccactga gcttgagaga
      361 aaacagggaa gccaaggaac cgttaacagg ggcaatatta gagatgtggg atggagagat
      421 ataccactat ggcctgtacg tggagaaagg cttagtgttg ggtgtgcaca aaccacctgc
      481 agccataagc atggcaaaag tggagctgac gccgctgtca ttgtactggc gtgtggtgta
      541 cactccccaa tacctcatct cccctgaaac tctcaggagg ctcaacggag aggcgttccc
      601 ttacaccgcc tttgacaaca actgctatgc cttttgctgc tgggtgttag acctcaatga
      661 ctcatggctt agcaggagga tggtgcaaag aacaacaggc ttcttcagac cttaccaaga
      721 gtggaacaga aaacccctgc ctaccatgga tgactccaaa attaagaagg tagcaaatat
      781 attcctatgt tcattgtcca cattattcac cagacccata aaagacctca taggaaaaat
      841 taaaccatta aacatattga acatcctggc aacgtgtgac tggacgtttg ccggaatagt
      901 ggagtccctg atattacttg ctgaactctt cggagttttc tggacacccc cagatgtgtc
      961 tgctatgatc gctcccttac tcggggacta cgagttgcaa gggccagaag acctcgccgt
     1021 tgaactcgta cctgtggtaa tgggagggat tggtttggtg ttgggattca ccaaagagaa
     1081 aattggcaaa atgttgtcct cagcagcatc aacactcagg gcttgcaaag atcttggtgc
     1141 ctatggcttg gagatactca aactggtcat gaagtggttc ttcccaaaga aagaggaggc
     1201 caatgagcta gccatggtga gggccataga ggatgccgta ctagatcttg aggcaataga
     1261 aaataaccac atgacaaccc tgttgaaaga caaagacagc ttagcaacat acatgaaaac
     1321 actggacatg gaggaggaga aagctaggag gttgtccaca aaatctgcat cccctgacat
     1381 agttgggaca atcaacgccc tgctggctcg aatagcagcg gccaggtcat tagtccacag
     1441 ggccaaggaa gagctgtcta gcaggataag accagtagtt gttatgatat ccggcaaacc
     1501 aggaataggt aaaactcatc tggccaggga ggtggcaaga aaggtggcat ccactctcac
     1561 aggggatcaa agagtcggac tcataccaag aaacggcgtg gaccattggg atgcatacaa
     1621 aggtgagaga gtcgtgctgt gggacgacta tggcatgagt aaccccattc atgatgctct
     1681 tcgcatacag gaattggccg atacgtgtcc ccttacctta aattgtgaca gaattgagaa
     1741 taagggaaaa gtttttgaca gtgaagtcat aataattaca acaaacctcg ccaacccagc
     1801 cccacttgat tatgtcaact ttgaggcctg ttccaggaga attgatttcc tggtgtacgc
     1861 tgaggcacca gaggtggaaa aggcaaaacg ggactttcct ggtcagccag atatgtggaa
     1921 ggacgccttc aagccggact tttcacacat caagctacag cttgcacctc agggcggttt
     1981 tgacaagaat ggcaacaccc cacatgggaa aggagtgatg aagaccctca ctaccggttc
     2041 tctgattgcc cgtgcatcag gcctactgca tgagaggatg gatgaatttg aactccaagg
     2101 tcccacaatc accaccttca atttcgaccg gaacagaatc acagcattca gacaattggc
     2161 tgcagaaaac aagtatggat tggtggatac catgaaagtt ggcaatcaac taaaaggagt
     2221 aaaaaccatg gaagaactca aacaagcaat caggaatgtg accatcaaga ggtgccagat
     2281 catctacggc ggctccacgt atgaccttga atctgatggc aagggcaaag ttttggtgga
     2341 aaaggtcaag aacacctctg tacagaccaa caacgagttg gccggggccc tgcaccatct
     2401 taaacacgcc cgaatcaggt actatgtcaa atgtgtgcaa gaagcagtct attccatcat
     2461 acaaattgcc ggcgctgcgt ttgtcaccac gcgcattgca cgccgcatga acatacaaga
     2521 actctggtcg aagccacaac tagaacaaaa tgtgtcagag actaaggaag aggcccccaa
     2581 gtcagaagat gacgagttca tcatatcttc taaggacatc aaggaggaag gaaagaaggg
     2641 caaaaacaaa actggtcgtg gcaagaaaca cactgcattc tccagcaagg gcttgagcga
     2701 tgaggagtat gacgagtaca agaggataag agaagagaga aatgggaagt actctataga
     2761 ggagtatctt caagacaggg acaggtacta tgaggagctc gccattgcca aggccacgga
     2821 agaagacttc tgtgaagagg aggagatcaa aatccgtcag agaattttcc gtcccaccag
     2881 gaaacaaaga aaggaagaga gggccacatt agggctagta acaggttcag aaatcagaaa
     2941 gaggaaccct gatgacttca aacccaaagg gaagctgtgg gccgatgaca acagaagtgt
     3001 tgactacaat gagaaactag actttgaggc ccccccaagc atatggtcta ggattgtgag
     3061 ctttggttct ggctggggct tctgggtatc accaagcctg ttcataacat caactcatgt
     3121 aatccccgca ggcataacag aagcatttgg agtccccatc aaacaaattc aggttcacaa
     3181 atcaggtgaa ttttgccgat tcagattccc aaaaccaatt agaccagatg tgacaggaat
     3241 gatcttggaa gaaggtgcgc ctgaaggcac cgtggcaact gtgctcatca aacgccccac
     3301 cggagaactc atgcctcttg cagccagaat gggaacacac gcaaccatga aaattcaagg
     3361 ccgcatggtt ggcggacaaa tgggtatgtt gctcactgga tcaaatgcta aaggaatgga
     3421 tttgggaaca acccctggtg actgtggctg tccttacatc tataaaaggg gcaatgacta
     3481 tatagtcatt ggggtgcaca ctgcagcagc ccgtggcgga aacaccgtca tctgtgccac
     3541 acagggaagt gagggtgagg caactcttga gggtggaaat gacaaaggaa cgtactgtgg
     3601 ggcacccatt ctgggccctg ggggtgcacc aaaattgagc accaaaacca aattttggag
     3661 gtcatcgaac acgcctcttc caccagggac atatgagcct gcctacctcg gtggccgtga
     3721 tccgcgtgtt aagggtgggc cctccttgca gcaggtgatg agagatcagt tgaagccatt
     3781 cactgaaccc aggggcaaac ctccaagacc aagtgtattg gaagcagcca aacaaaccat
     3841 tatcaatgtc ctcgaacaaa ccctggaccc tccacaaaaa tggacatacg cacaggcgtg
     3901 tgcctcactt gacaaaacca cctccagcgg acatccccat cacgcccgaa agaacgaatt
     3961 ctggaatggt gaggccttca ctggtaaatt ggcagaccaa gcatcaaaag cgaacctaat
     4021 gtttgaggaa gggaaacaca tgacaccagt gtatacagca gcactcaagg acgagctagt
     4081 caagactgag aaaatctatg gaaagatcaa gaagagactg ctctggggct ctgacttgtc
     4141 caccatgatc cggtgcgcta ggtcatttgg tgggctcatg gatgagatga aggcacactg
     4201 catatcactc ccagtacgag ttggcatgaa tatgaatgaa gatggcccaa taatatttga
     4261 gaaacattcc agatacaaat atcactatga cgcagactac tctcgttggg attcaacaca
     4321 acagagggca gtactagcag cagccttgga aatcatggtc agattctctg cagaaccaca
     4381 attggcacaa atagtcgctg aggatctgct ggcccctagt gtagtagatg taggagactt
     4441 taaaatcaca ataaatgaag ggctcccatc tggcgtgcca tgcacttctc aatggaactc
     4501 catcgcacac tggctgctaa ctctctgtgc cttgtctgaa gtcaccaaac tgtcccctga
     4561 cattatacaa gcaaattcca tgttctcatt ttacggtgat gacgagattg ttagcaccga
     4621 cataaaattg gaccctgaac agttaaccgc caaattgaag gagtacggcc tgaaaccaac
     4681 ccgcccagac aagaccgagg gacccctgat catcagtgaa gatttgaacg gactcacttt
     4741 cctccgaagg acggtgactc gtgacccagc tggctggttt ggaaaactgg accaaaactc
     4801 aatattgagg cagatgtact ggactagagg accaaatcat gaagacccca atgagacaat
     4861 gataccccat tctcaaagac ccatacagct catggcactg cttggtgaag cctctcttca
     4921 cggaccctct ttctacagta aaatcagcaa gttggtcata actgagctca aagaaggtgg
     4981 gatggacttt tacgtgccaa ggcaggaacc catgttcagg tggatgaggt tttctgactt
     5041 gagcacgtgg gagggcgatc gcaatctggc tcccaatttt gtgaatgaag atggcgtcga
     5101 gtgacgccaa cccatctgat gggtccgcag ccaacctcgt accagaggtc aacaatgagg
     5161 ttatggcttt ggagcccgtt gttggcgccg ctattgcggc acctgtagcg ggccaacaaa
     5221 atgtaattga cccctggatt agaaataatt ttgtacaagc ccctggtggg gagtttacag
     5281 tatcccctag aaacgctcca ggtgaaatac tatggagcgc gcccctaggc cctgacctaa
     5341 atccctacct atcccatttg gccagaatgt acaatggtta tgcaggtggt tttgaagtgc
     5401 aggtaattct cgcggggaac gcgttcaccg ccgggaagat catatttgca gcagtcccac
     5461 caaattttcc aactgaaggc ttaagtccta gccaggtcac tatgttcccc catataatag
     5521 tagatgttag acaattagaa cctgtgctga ttcccttacc cgatgtcagg aataatttct
     5581 atcattacaa tcagtcaaat gactccacta ttaagttgat agcaatgttg tatacaccac
     5641 ttagggctaa taatgctggg gatgatgttt tcacagtttc gtgccgagtt ctcacgagac
     5701 catcccccga ttttgatttc atatttttag tgccacccac agttgagtca agaactaaac
     5761 cattttctgt cccagtttta actgttgagg agatgaccaa ttcaagattc cccattcctt
     5821 tggagaagtt gttcacgggc cccagcagtg cctttgttgt tcaaccacaa aacggcaggt
     5881 gcacaactga tggcgtgctc ctaggcacca cccaactgtc tcctgtcaac atctgcacct
     5941 tcagagggga cgtcacccac atcacaggta gtcgcaacta cacaatgaat ttggcttctc
     6001 aaaattggaa caactatgac ccaacagaag aaatcccagc ccctctagga actccagatt
     6061 ttgtggggaa gattcaaggc atgctcaccc aaaccacaag gacagacggt tcaacacgcg
     6121 gccacaaagc tacagtgtac actgggagcg ccgacttttc tccaaaacta ggtagagttc
     6181 aatttgaaac tgatacagac catgattttg aagctaacca aaacacaaag ttcaccccag
     6241 tcggtgtcat ccaagatggt agcaccaccc accgaaacga accccaacaa tgggtgctcc
     6301 caagttactc aggcagaaat actcacaatg tacatctggc ccccgctgta gcccccacct
     6361 ttccgggtga gcagctcctc tttttcagat ccaccatacc cggatgcagc gggtacccca
     6421 acatggattt ggactgtctg ctcccccagg aatgggtgca gtacttctac caagaggcag
     6481 ccccagcaca atctgatgtg gctctgctaa gatttgtgaa tccagacaca ggtagggttt
     6541 tgtttgagtg caagcttcac aaatcaggct atgttacagt ggctcacact ggccaacatg
     6601 atttggttat cccccccaat ggttacttta ggtttgattc ctgggtcaac cagttctaca
     6661 cgcttgcccc catgggaaat ggaacggggc gtagacgtgt agtataatgg ctggagcttt
     6721 ctttgctgga ttggcatctg atgtccttgg ctccggactt ggttccctta tcaatgctgg
     6781 ggctggggcc atcaaccaaa aagttgagtt tgaaaataac agaaaattgc aacaagcatc
     6841 cttccaattt agcagcaatc tgcaacaggc ttcctttcaa catgataaag agatgctcca
     6901 agcacaaatt gaggccacca aaaagctaca acaggaaatg atgaaagtta agcaggcaat
     6961 gctcctagag ggtgggttct ctgagacaga tgcagcccgc ggggcaatta acgcccccat
     7021 gacaaaagct ttggactgga gcgggacaag gtactgggct cccgatgcta ggactacaac
     7081 atataatgca ggccgctttt ccacctctca accatcggga gcactgctag gaagagctaa
     7141 tcttagggat gctgtccctg ctcggggacc ctccaacaaa ccttctaact cttctactgc
     7201 cacctctgtg tactcaaacc aaactatttc aacgaggctt ggttctacag ctggttctgg
     7261 gaccaatgtc tcgagcctcc cgtcaactgc aaggactagg agctgggttg aggatcaaag
     7321 taggaatttg tcacctttca tgaggggggc ccataacata tcatttgtca ccccaccatc
     7381 tagcagatcc tctagccaag gcacagtctc aaccgtgcct aaagagattt tggactcctg
     7441 gactggcgct ttcaacacgc gcaggcagcc tctcttcgct cacattcgta agcgagggga
     7501 gtcacgggtg tgatgtgaaa agacaaaaaa actgattatc tttctttttc tttagtgt
//