Typing tool

Complete norovirus genomes

MK762621  GII.4 Sydney
 GII.P16

Length: 7,565 | 3 CDS

ORF1: 5..5104
ORF2: 5085..6707
ORF3: 6707..7513
LOCUS       MK762621                7565 bp    RNA     linear   VRL 13-APR-2019
DEFINITION  Norovirus GII isolate Hu/US/2017/GII.P16-GII.4 Sydney/Jackson1608,
            complete genome.
ACCESSION   MK762621
VERSION     MK762621.1
KEYWORDS    .
SOURCE      Norovirus GII
  ORGANISM  Norovirus GII
            Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes;
            Picornavirales; Caliciviridae; Norovirus.
REFERENCE   1  (bases 1 to 7565)
  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  JOURNAL   Unpublished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 7565)
  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..7565
                     /organism="Norovirus GII"
                     /mol_type="genomic RNA"
                     /strain="Jackson1608"
                     /isolate="Hu/US/2017/GII.P16-GII.4 Sydney/Jackson1608"
                     /isolation_source="stool"
                     /host="Homo sapiens"
                     /db_xref="taxon:122929"
                     /country="USA"
                     /collection_date="05-Jan-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="QBX91090.1"
                     /translation="MKMASNDATVAVACNNNNDKEKSSGEGLFTNMSSTLKKALGARP
                     KQPAPRDEPQKPPRPPTPELVKRIPPPPPNGEEEEEPVIRYEVKSGISGLPELTTVPQ
                     PDVANTAFSVPPLSLRENREAKEPLTGAILEMWDGEIYHYGLYVEKGLVLGVHKPPAA
                     ISMARVELTPLSLYWRVVYTPQYLISPETLRRLNGEAFPYTAFDNNCYAFCCWVLDLN
                     DSWLSRRMVQRTTGFFRPYQEWNRKPLPTMDDSKIKKVANIFLCSLSALFTRPIKDLI
                     GKIKPLNILNILATCDWTFAGIVESLILLAELFGVFWTPPDVSAMIAPLLGDYELQGP
                     EDLAVELVPVVMGGIGLVLGFTKEKIGKMLSSAASTLRACKDLGAYGLEILKLVMKWF
                     FPKKEEANELAMVRAIEDAVLDLEAIENNHMTTLLKDKDSLATYMKTLDMEEEKARRL
                     STKSASPDIVGTINALLARIAAARSLVHRAKEELSSRIRPVVVMISGKPGIGKTHLAR
                     EVARKVASTLTGDQRVGLIPRNGVDHWDAYKGERVVLWDDYGMSNPIHDALRIQELAD
                     TCPLTLNCDRIENKGKVFDSEVIIITTNLANPAPLDYVNFEACSRRIDFLVYAEAPEV
                     EKAKRDFPGQPDMWKDAFKPDFSHIKLQLAPQGGFDKNGNTPHGKGVMKTLTTGSLIA
                     RASGLLHERMDEFELQGPTITTFNFDRNRITAFRQLAAENKYGLVDTMKVGNQLKGVK
                     TMEELKQAIRNVTIKRCRIIYGGSTYDLESDGKGKVLVEKVKNTSVQTNNELAGALHH
                     LKHARIRYYVKCVQEAVYSIIQIAGAAFVTTRIARRMNIQELWSKPQLGQNESETKEE
                     TPKSEDEEFIISSKDIKEEGKKGKNKTGRGKKHTAFSSKGLSDEEYDEYKRIREERNG
                     KYSIEEYLQDRDRYYEELAIAKATEEDFCEEEEIKIRQRIFRPTRKQRKEERATLGLV
                     TGSEIRKRNPDDFKPKGKLWADDNRSVDYNEKLDFEAPPSIWSRIVSFGSGWGFWVSP
                     SLFITSTHVIPAGITEAFGVPIKQIQIHKSGEFCRFRFPKPIRPDVTGMILEEGAPEG
                     TVATVLIKRPTGELMPLAARMGTHATMKIQGRMVGGQMGMLLTGSNAKGMDLGTTPGD
                     CGCPYIYKRGNDYIVIGVHTAAARGGNTVICATQGSEGEATLEGGDDKGTYCGAPILG
                     PGGAPKLSTKTKFWRSSNTPLPPGTYEPAYLGGRDPRVKGGPSLQQVMRDQLKPFTEP
                     RGKPPRPSVLEAAKQTIINVLEQTLDPPQKWTYAQACASLDKTTSSGHPHHVRKNEFW
                     NGETFTGKLADQASKANLMYEEGKHMTPVYTAALKDELVKTEKIYGKIKKRLLWGSDL
                     STMIRCARSFGGLMDEMKAHCISLPVRVGMNMNEDGPIIFEKHSRYKYHYDADYSRWD
                     STQQRAVLAAALEIMVRFSAEPQLAQIVAEDLLAPSVVDVGDFKITINEGLPSGVPCT
                     SQWNSIAHWLLTLCALSEVTKLSPDIIQANSMFSFYGDDEIVSTDIKLDPEQLTAKLK
                     EYGLKPTRPDKTEGPLIISEDLNGLTFLRRTVTRDPAGWFGKLDQSSILRQMYWTRGP
                     NHEDPNETMIPHSQRPIQLMALLGEASLHGPSFYSRISKLVITELKEGGMDFYVPRQE
                     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="QBX91091.1"
                     /translation="MKMASSDANPSDGSAANLVPEVNNEVMALEPVVGAAIAAPVAGQ
                     QNVIDPWIRNNFVQAPGGEFTVSPRNAPGEILWSAPLGPDLNPYLSHLARMYNGYAGG
                     FEVQVILAGNAFTAGKIIFAAVPPNFPTEGLSPSQVTMFPHIIVDVRQLEPVLIPLPD
                     VRNNFYHYNQSNDSTIKLIAMLYTPLRANNAGDDVFTVSCRVLTRPSPDFDFIFLVPP
                     TVESRTKPFSVPVLTVEEMTNSRFPIPLEKLFTGPSSAFVVQPQNGRCTTDGVLLGTT
                     QLSPVNICTFRGDVTHITGSRNYTMNLASQNWNNYDPTEEIPAPLGTPDFVGKIQGML
                     TQTTRTDGSTRGHKATVYTGSADFAPKLGRVQFETDTDHDFEVNQNTKFTPVGVIQDG
                     STTHRNEPQQWVLPSYSGRNTHNVHLAPAVAPTFPGEQLLFFRSTMPGCSGYPNMDLD
                     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="QBX91092.1"
                     /translation="MAGAFFAGLASDVLGSGLGSLINAGAGAINQKVEFENNRKLQQA
                     SFQFSSNLQQASFQHDKEMLQAQIEATKKLQQEMMKVKQAMLLEGGFSETDAARGAIN
                     APMTKALDWSGTRYWAPDARITTYNAGHFSTPQPSRVLPGRANLRDAVPARGPSNKSS
                     NSSTATSVYSNQTISTRLGSTAGSGTSVSSLPSTARTRSWVEDQNRNLSPFMRGAHNI
                     SFVTPPSSRSSSQGTVSTVPKEILDSWTGAFNTRRQPLFAHIRKQGESRV"
ORIGIN      
        1 gtgaatgaag atggcgtcta acgacgctac cgttgccgtt gcttgcaaca acaacaacga
       61 caaggaaaaa tcttcaggtg aaggcttatt tacaaatatg tcttccacct taaagaaagc
      121 cctcggggct aggcccaaac agcctgcccc gagagacgaa ccacaaaagc ccccaagacc
      181 accaactccc gagctagtca agaggatacc ccctcctcca cctaatggcg aagaagaaga
      241 agaaccagtc attaggtatg aggttaagag tgggatctcc ggactgcccg agctcacaac
      301 agtcccccaa ccggacgtgg ccaacacagc attcagtgtt ccaccactga gcttgagaga
      361 aaacagggag gccaaggaac cgctaacagg ggcaatatta gagatgtggg acggagagat
      421 ataccactat ggcctgtacg tggagaaagg cttagtgttg ggtgtgcaca aaccacctgc
      481 agccataagc atggcaagag tggagctgac gccgctgtca ttgtactggc gtgtggtgta
      541 cactccccaa tacctcatct cccctgaaac tctcaggagg ctcaacggag aggcgttccc
      601 ttacaccgcc ttcgacaaca actgctatgc cttttgctgc tgggtgttag acctcaatga
      661 ctcatggctt agcaggagga tggtgcaaag aacaacgggc ttcttcagac cttaccaaga
      721 gtggaacaga aaacccctgc ctaccatgga tgactccaaa ataaagaagg tagcaaatat
      781 attcctatgt tcattgtccg cattgtttac cagacccata aaagacctca taggaaaaat
      841 taaaccatta aacatattga atatcctggc aacgtgtgac tggacgtttg ccggaatagt
      901 ggagtctctg 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 ctatggctta gagatactca aattggtcat gaagtggttc ttcccaaaga aagaggaggc
     1201 caatgaacta gccatggtga gggccataga ggatgccgta ctagatcttg aggcaataga
     1261 aaataaccac atgacaaccc tgttgaaaga caaagacagc ttagcaacat acatgaaaac
     1321 actagacatg gaggaggaga aagccaggag gttgtccaca aaatctgcat cccctgacat
     1381 agttgggaca atcaacgccc tgctggctcg aatagcagcg gccaggtcat tagtccacag
     1441 ggccaaggaa gagctatcta gcaggataag accggtagtt gttatgatat ctggcaaacc
     1501 aggaataggc aaaactcatc tggccaggga ggttgcaaga aaggtggcat ccactctcac
     1561 aggggatcaa agagtcggac tcataccaag aaacggtgtg gaccattggg atgcatacaa
     1621 aggtgagaga gtcgtgctgt gggacgacta tggtatgagt aaccccattc atgatgctct
     1681 tcgcatacag gaattggctg atacgtgtcc ccttacctta aattgtgaca gaattgaaaa
     1741 taagggaaaa gtttttgaca gtgaagtcat aataattaca acaaaccttg ccaacccagc
     1801 cccacttgat tatgtcaact ttgaggcctg ttccaggaga attgatttcc tggtgtacgc
     1861 tgaggcacca gaagtagaaa aggcaaaacg ggactttcct ggtcagccag atatgtggaa
     1921 ggacgccttc aagccggact tttcacacat caagttacag cttgcacctc agggcggctt
     1981 tgacaagaat ggcaacaccc cacatgggaa aggagtgatg aagaccctca ctaccggttc
     2041 tctgatagcc cgtgcatcag gcctactgca tgagaggatg gatgaatttg aactccaagg
     2101 tcccacaatc accaccttca attttgaccg gaacagaatc acagcattca gacaattggc
     2161 tgcagaaaac aagtatggat tggtggatac catgaaagtt ggcaatcaac taaaaggagt
     2221 gaaaaccatg gaagaactca aacaagcaat caggaatgtg accatcaaga ggtgccgaat
     2281 catctatggt ggctccacgt atgaccttga atctgatggc aagggtaaag ttttggtgga
     2341 aaaggtcaag aacacctctg tacagaccaa caacgagttg gccggggccc tgcaccacct
     2401 caaacacgcc cgaatcaggt actatgtcaa atgtgtgcaa gaagcagtct attccatcat
     2461 acaaattgcc ggcgctgcgt ttgtcaccac gcgcattgca cgccgcatga acatacaaga
     2521 actctggtcg aagccacaat taggtcaaaa tgaatcagag actaaggaag agacccccaa
     2581 gtcagaagac gaagagttca tcatatcttc taaggacatc aaggaggaag gaaagaaggg
     2641 caaaaacaaa actggccgtg gcaagaaaca cactgcattc tccagcaagg gcttgagcga
     2701 tgaggagtat gacgagtaca agaggataag agaagagaga aatgggaagt actctataga
     2761 ggagtatctt caagacagag acaggtacta tgaggagctc gccattgcca aggccacgga
     2821 agaagacttc tgtgaagagg aggagatcaa aatccgtcag agaatcttcc gtcccaccag
     2881 gaaacaaaga aaggaagaga gggccacatt agggctggta acaggttcag aaatcagaaa
     2941 aagaaaccct gatgacttca aacccaaagg gaagctgtgg gccgatgaca acagaagtgt
     3001 tgactacaat gagaaactgg actttgaggc ccccccaagc atatggtcta ggattgtgag
     3061 ctttggctct ggctggggct tctgggtatc accaagcctg ttcataacat caactcatgt
     3121 aatccccgca ggcataacag aagcatttgg agtccccatc aaacaaattc agatccacaa
     3181 atcaggtgaa ttttgccgat tcagattccc aaaaccaatt agaccagatg tgacaggaat
     3241 gatcttggaa gaaggtgcgc ctgaaggcac cgtggcaact gtgctcatca aacgccccac
     3301 cggagagctc atgcctcttg cagccagaat gggaacacac gcaaccatga aaattcaagg
     3361 ccgcatggtc ggcggacaga tgggtatgtt gctcactgga tcaaatgcta aaggaatgga
     3421 tttgggaaca actcctggtg actgtggctg tccttacatc tataaaaggg gcaatgacta
     3481 tatagtcata ggggtgcaca ctgcagcagc ccgtggtgga aacaccgtca tctgtgccac
     3541 acagggaagt gagggtgagg caactcttga gggtggagat gacaaaggaa catactgtgg
     3601 ggcacctatt ctaggccctg ggggtgcacc aaaattgagc accaaaacca aattttggag
     3661 gtcatcgaac acgccccttc caccagggac atatgagcct gcctacctcg gtggccgtga
     3721 tccgcgtgtt aagggtgggc cctccttgca gcaggtgatg agagaccagt tgaagccatt
     3781 cactgaaccc aggggcaaac ctccaaggcc aagtgtattg gaagcagcca aacaaaccat
     3841 tatcaatgtt ctcgaacaaa ccctggaccc tccacaaaaa tggacatacg cacaggcgtg
     3901 tgcctcactt gacaaaacca cctccagcgg gcatccccat catgtccgaa agaatgaatt
     3961 ctggaatggt gagaccttca ctggtaaatt ggcagaccaa gcatcaaaag caaacctaat
     4021 gtatgaggaa gggaaacaca tgacaccagt gtatacagca gcactcaagg acgagctagt
     4081 caagactgag aaaatctatg gaaagatcaa gaagaggctg ctctggggct ctgacttgtc
     4141 cactatgatc cggtgcgcta ggtcatttgg tgggctcatg gacgagatga aggcacactg
     4201 catatcactc ccagtacgag ttggcatgaa tatgaatgaa gatggcccaa taatatttga
     4261 gaaacattcc agatataaat atcactatga tgcagattac tctcgttggg attcaacaca
     4321 acagagggca gtactagcag cagccttgga aatcatggtc agattctctg cagaaccaca
     4381 attggcacaa atagtcgctg aggatctact ggcccctagt gtagtagatg taggagactt
     4441 taaaatcaca ataaatgaag ggctcccatc tggtgtgcca tgcacttctc aatggaactc
     4501 catcgcacac tggctgctaa ctctctgtgc cttgtctgaa gtcaccaaac tgtcccctga
     4561 catcatacaa gcaaattcca tgttctcatt ttacggtgat gacgagattg tcagcaccga
     4621 cataaagttg gaccctgaac agttaactgc caagctgaag gagtacggcc tgaaaccaac
     4681 ccgcccagac aagaccgagg gacccctgat catcagtgaa gatttgaacg gactcacctt
     4741 cctccgaagg acggtgactc gtgacccagc tggctggttt ggaaaactgg accaaagttc
     4801 aattttgagg cagatgtact ggactagagg accaaatcat gaagacccca atgagacaat
     4861 gataccccac tctcaaagac ccatacagct catggcactg cttggtgaag cctctcttca
     4921 cggaccctct ttctacagta gaatcagtaa gttggttata actgaactca 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 gttggtgccg ctattgcggc acctgtagcg ggccaacaaa
     5221 atgtaattga cccctggatt agaaacaatt ttgtacaagc ccctggcggg gagtttacag
     5281 tatcccctag aaacgctcca ggtgaaatac tatggagcgc gcccctaggc cctgacctaa
     5341 atccctacct atcccatttg gccagaatgt acaatggtta tgcaggtggt tttgaagtgc
     5401 aggtaattct cgcggggaac gcgttcaccg ccgggaagat tatatttgca gcagtcccac
     5461 caaattttcc aactgaaggc ttaagcccta gccaggtcac tatgttcccc catataatag
     5521 tagatgttag acaattagaa cccgtgctga ttcccttacc cgatgttagg aataatttct
     5581 atcactacaa tcagtcaaat gattccacta ttaagttgat agcaatgttg tatacaccac
     5641 ttagggctaa taatgctggg gatgatgttt tcacagtttc gtgccgagtt ctcacgagac
     5701 catcccccga ttttgatttc atatttttag tgccacccac ggttgagtca agaactaaac
     5761 cattctctgt cccagtttta actgttgagg agatgaccaa ttcaagattc cccatccctt
     5821 tggaaaagtt gtttacaggc cccagcagtg cctttgttgt tcaaccacaa aacggcaggt
     5881 gcacaactga tggcgtgctc ctaggcacca cccaactttc tcctgtcaac atctgcacct
     5941 tcagagggga tgtcacccac atcacaggta gtcgcaacta cacaatgaat ttggcttctc
     6001 aaaattggaa caactatgac ccaacagaag aaatcccagc ccctctagga actccagatt
     6061 ttgtggggaa gattcaaggc atgctcaccc aaaccacaag gacagatggc tcaacacgcg
     6121 gccacaaagc tacagtgtac actgggagcg ccgactttgc tccaaaactg ggtagagttc
     6181 aatttgaaac tgacacagac catgattttg aagttaatca aaacacaaag ttcaccccag
     6241 tcggtgtcat ccaagatggt agcaccaccc accgaaacga accccaacag tgggtgctcc
     6301 caagttactc aggcagaaat actcacaatg tacatttggc ccccgctgta gcccccactt
     6361 ttccgggtga gcaacttctc ttcttcagat ccaccatgcc cggatgcagc gggtacccca
     6421 acatggattt ggactgtctg ctcccccagg aatgggtgca gtacttctac caggaggcag
     6481 ccccagcaca atctgatgtg gctctgctaa gatttgtgaa tccagacaca ggtagggttt
     6541 tgtttgagtg caagcttcac aaatcaggct atgttacagt ggctcacact ggccaacatg
     6601 acttggttat cccccccaat ggttacttta ggtttgattc ctgggtcaac cagttctaca
     6661 cgcttgcccc catgggaaat ggaacggggc gtagacgtgt agtataatgg ctggagcttt
     6721 ctttgctggg ttggcatctg atgtccttgg ctccggactt ggttccctta tcaatgctgg
     6781 ggctggggcc atcaaccaaa aagttgagtt tgaaaataac agaaaattgc aacaagcatc
     6841 cttccaattt agcagcaatc tgcaacaggc ttcttttcaa catgataaag agatgctcca
     6901 agcacaaatt gaggccacca aaaagctaca acaggaaatg atgaaagtca agcaggcaat
     6961 gctcctagag ggtgggttct ctgagacaga tgcagcccgc ggggcaatta acgcccccat
     7021 gacaaaagct ttggactgga gcggaacaag gtactgggct ccagatgcta ggattacaac
     7081 atacaatgca ggccactttt ccaccccaca accatcgagg gtactgccag gaagagctaa
     7141 tctcagggat gctgtccctg ctcggggacc ctccaacaaa tcttctaact cttctactgc
     7201 cacctctgtg tactcaaatc aaactatttc aacgagactt ggttctacag ctggttctgg
     7261 aaccagtgtc tcgagcctcc cgtcaactgc aaggactagg agctgggttg aggatcaaaa
     7321 taggaatttg tcacctttca tgaggggggc ccacaacata tcatttgtca ccccaccatc
     7381 tagcagatcc tctagccaag gcacagtctc aaccgtgcct aaagagattt tggactcctg
     7441 gactggcgct ttcaacacgc gcaggcagcc tctcttcgct cacattcgta agcaagggga
     7501 gtcacgggtg taatgtgaaa agacaaaact gattattttc tttttctttt tcttttcttt
     7561 agtgt
//