Typing tool

Complete norovirus genomes

MK762564  GII.4 Sydney
 GII.P16

Length: 7,529 | 3 CDS

ORF1: 1..5100
ORF2: 5081..6703
ORF3: 6703..7509
LOCUS       MK762564                7529 bp    RNA     linear   VRL 13-APR-2019
DEFINITION  Norovirus GII isolate Hu/US/2016/GII.P16-GII.4 Sydney/CS0195
            nonstructural polyprotein (ORF1), VP1 (ORF2), and VP2 (ORF3) genes,
            complete cds.
ACCESSION   MK762564
VERSION     MK762564.1
KEYWORDS    .
SOURCE      Norovirus GII
  ORGANISM  Norovirus GII
            Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes;
            Picornavirales; Caliciviridae; Norovirus.
REFERENCE   1  (bases 1 to 7529)
  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  JOURNAL   Unpublished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 7529)
  AUTHORS   Barclay,L., Cannon,J.L., 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..7529
                     /organism="Norovirus GII"
                     /mol_type="genomic RNA"
                     /strain="CS0195"
                     /isolate="Hu/US/2016/GII.P16-GII.4 Sydney/CS0195"
                     /isolation_source="stool"
                     /host="Homo sapiens"
                     /db_xref="taxon:122929"
                     /country="USA"
                     /collection_date="03-Mar-2016"
                     /note="genotype: GII.P16-GII.4 Sydney"
     gene            1..5100
                     /gene="ORF1"
     CDS             1..5100
                     /gene="ORF1"
                     /codon_start=1
                     /product="nonstructural polyprotein"
                     /protein_id="QBX91019.1"
                     /translation="MKMASNDATVAVACNNNNDKEKSSGEGLFTNMSSTLKKALGARP
                     KQPAPRGEPQKPPRPPTPELVKRIPPPPPNGEEEEEPVIRYEVKSGISGLPELTTVPQ
                     PDVANTAFSVPPLSLRENREAKEPLTGAILEMWDGEIYHYGLYVEKGLVLGVHKPPAA
                     ISMARVELTPLSLYWRVVYTPQYLISPETLRRLNGEAFPYTAFDNNCYAFCCWVLDLN
                     DSWLSRRMVQRTTGFFRPYQEWNRKPLPTMDDSKIKKVANIFLCSLSTLFTRPIKDLI
                     GKIKPLNILNILATCDWTFAGIVESLILLAELFGVFWTPPDVSAMIAPLLGDYELQGP
                     EDLAVELVPVVMGGIGLVLGFTKEKIGKMLSSAASTLRACKDLGAYGLEILKLVMKWF
                     FPKKEEANELAMVRAIEDAVLDLEAIENNHMTTLLKDKDSLATYMKTLDMEEEKARRL
                     STKSASPDIVGTINALLARIAAARSLVHRAKEELSSRIRPVVVMISGKPGIGKTHLAR
                     EVARKVASTLTGDQRVGLIPRNGVDHWDAYKGERVVLWDDYGMSNPIHDALRIQELAD
                     TCPLTLNCDRIENKGKVFDSEVIIITTNLANPAPLDYVNFEACSRRIDFLVYAEAPEV
                     EKAKRDFPGQPDMWKDAFKPDFSHIKLQLAPQGGFDKNGNTPHGKGVMKTLTTGSLIA
                     RASGLLHERMDEFELQGPTITTFNFDRNRITAFRQLAAENKYGLVDTMKVGNQLKGVK
                     TMEELKQAIRNVTIKRCQIIYGGSTYDLESDGKGKVLVEKVKNTSVQTNNELAGALHH
                     LKHARIRYYVKCVQEAVYSIIQIAGAAFVTTRIARRMNIQELWSKPQLDQNESETKEE
                     APKSEDDEFIISSKDIKEEGKKGKNKTGRGKKHTAFSSKGLSDEEYDEYKRIREERNG
                     KYSIEEYLQDRDRYYEELAIAKATEEDFCEEEEIKIRQRIFRPTRKQRKEERATLGLV
                     TGSEIRKRNPDDFKPKGKLWADDNRSVDYNEKLDFEAPPSIWSRIVSFGSGWGFWVSP
                     SLFITSTHVIPAGITEAFGVPIKQIQVHKSGEFCRFRFPKPIRPDVTGMILEEGAPEG
                     TVATVLIKRPTGELMPLAARMGTHATMKIQGRMVGGQMGMLLTGSNAKGMDLGTTPGD
                     CGCPYIYKRGNDYIVIGVHTAAARGGNTVICATQGSEGEATLEGGDDKGTYCGAPILG
                     PGGAPKLSTKTKFWRSSNTPLPPGTYEPAYLGGRDPRVKGGPSLQQVMRDQLKPFTEP
                     RGKPPRPSVLEAAKQTIINVLEQTLDPPQKWTYAQACASLDKTTSSGHPHHVRKNEFW
                     NGETFTGKLADQASKANLMFEEGKHMTPVYTAALKDELVKTEKIYGKIKKRLLWGSDL
                     STMIRCARSFGGLMDEMKAHCISLPVRVGMNMNEDGPIIFEKHSRYKYHYDADYSRWD
                     STQQRAVLAAALEIMVRFSAEPQLAQIVAEDLLAPSVVDVGDFKITINEGLPSGVPCT
                     SQWNSIAHWLLTLCALSEVTKLSPDIIQANSMFSFYGDDEIVSTDIKLDPEQLTAKLK
                     EYGLKPTRPDKTEGPLIISEDLNGLTFLRRTVTRDPAGWFGKLDQNSILRQMYWTRGP
                     NHEDPNETMIPHSQRPIQLMALLGEASLHGPSFYSKISKLVITELKEGGMDFYVPRQE
                     PMFRWMRFSDLSTWEGDRNLAPNFVNEDGVE"
     mat_peptide     1..996
                     /gene="ORF1"
                     /product="p48"
     mat_peptide     997..2094
                     /gene="ORF1"
                     /product="NTPase"
     mat_peptide     2095..2625
                     /gene="ORF1"
                     /product="p22"
     mat_peptide     2626..3024
                     /gene="ORF1"
                     /product="VPg"
     mat_peptide     3025..3567
                     /gene="ORF1"
                     /product="Pro"
     mat_peptide     3568..5097
                     /gene="ORF1"
                     /product="RdRp"
     gene            5081..6703
                     /gene="ORF2"
     CDS             5081..6703
                     /gene="ORF2"
                     /note="major capsid protein"
                     /codon_start=1
                     /product="VP1"
                     /protein_id="QBX91020.1"
                     /translation="MKMASSDANPSDGSAANLVPEVNNEVMALEPVVGAAIAAPVAGQ
                     QNVIDPWIRNNFVQAPGGEFTVSPRNAPGEILWSAPLGPDLNPYLSHLARMYNGYAGG
                     FEVQVILAGNAFTAGKIIFAAVPPNFPTEGLSPSQVTMFPHIIVDVRQLEPVLIPLPD
                     VRNNFYHYNQSNDSTIKLIAMLYTPLRANNAGDDVFTVSCRVLTRPSPDFDFIFLVPP
                     TVESRTKPFSVPVLTVEEMTNSRFPIPLEKLFTGPSSAFVVQPQNGRCTTDGVLLGTT
                     QLSPVNICTFRGDVTHITGSRNYTMNLASQNWNNYDPTEEIPAPLGTPDFVGKIQGML
                     TQTTRTDGSTRGHKATVYTGSADFSPKLGRVQFETDTDHDFEANQNTKFTPVGVIQDG
                     STTHRNEPQQWVLPSYSGRNTHNVHLAPAVAPTFPGEQLLFFRSTMPGCSGYPNMDLD
                     CLLPQEWVQYFYQEAAPAQSDVALLRFVNPDTGRVLFECKLHKSGYVTVAHTGQHDLV
                     IPPNGYFRFDSWVNQFYTLAPMGNGTGRRRVV"
     gene            6703..7509
                     /gene="ORF3"
     CDS             6703..7509
                     /gene="ORF3"
                     /note="minor structural protein; small basic protein"
                     /codon_start=1
                     /product="VP2"
                     /protein_id="QBX91021.1"
                     /translation="MAGAFFAGLASDVLGSGLGSLINAGAGAINQKVEFENNRKLQQA
                     SFQFSSNLQQASFQHDKEMLQAQIEATKKLQQEMMKVKQAMLLEGGFSETDAARGAIN
                     APMTKALDWSGTRYWAPDARTTTYNAGRFSTPQPSGALPGRANLRDAVPARGPSNKSS
                     NSSTVTSVYSNQTISTRLGSTAGSGTSVSSLPSTARTRSWVEDQSRNLSPFMRGAHNI
                     SFVTPPSSRSSSQGTVSTVPKEILDSWTGAFNTRRQPLFAHIRKRGESRV"
ORIGIN      
        1 atgaagatgg cgtctaatga cgctaccgtt gccgttgctt gcaacaacaa caacgacaag
       61 gaaaaatctt caggtgaagg cttattcaca aatatgtctt ccaccttaaa gaaagccctc
      121 ggggctaggc ccaaacagcc tgccccgaga ggcgaaccac aaaagccccc aagaccacca
      181 actcccgagt tggtcaagag gataccccct cctccaccta atggcgaaga agaagaagaa
      241 ccagtcatta ggtatgaggt taagagtggg atctctggcc tgcccgagct cacaacagtc
      301 ccccaaccgg acgtggccaa cacagcattc agtgttccac cactgagctt gagagaaaac
      361 agggaggcca aggaaccgtt aacaggggca atattagaga tgtgggatgg agagatatac
      421 cactatggcc tgtacgtgga gaaaggctta gtgttgggtg tgcacaaacc acctgcagcc
      481 ataagcatgg caagagtgga gctgacgccg ctgtcattgt actggcgtgt ggtgtacact
      541 ccccaatacc tcatctcccc tgaaactctc aggaggctca acggagaggc gttcccttac
      601 accgcctttg acaacaactg ctatgccttt tgctgctggg tgttagacct caatgactca
      661 tggcttagca ggaggatggt gcaaagaaca acgggcttct tcagacctta ccaagagtgg
      721 aacagaaaac ccctgcctac catggatgac tccaaaatta agaaggtagc aaatatattc
      781 ctatgttcat tgtccacatt attcaccaga cccataaaag acctcatagg aaaaattaaa
      841 ccattaaaca tattgaacat cctggcaacg tgtgactgga cgtttgccgg aatagtggag
      901 tccctgatat tacttgctga actcttcgga gttttctgga cacccccaga tgtgtctgct
      961 atgatcgctc ccttactcgg ggactacgag ttgcaagggc cagaagacct cgccgttgaa
     1021 ctcgtacctg tggtaatggg agggattggt ttggtgttgg gattcaccaa agagaaaatt
     1081 ggcaaaatgt tgtcctcagc agcatcaaca ctcagggctt gcaaagatct tggtgcctat
     1141 ggcttagaga tactcaaact ggtcatgaag tggttcttcc caaagaaaga ggaggccaat
     1201 gagctagcca tggtgagggc catagaggat gccgtactag atcttgaggc aatagaaaat
     1261 aaccacatga caaccctgtt gaaagacaaa gacagcttag caacatacat gaaaacactg
     1321 gacatggagg aggagaaagc cagaaggttg tccacaaaat ctgcatcccc tgacatagtt
     1381 gggacaatca acgccctgct ggctcgaata gcagcggcca ggtcattagt ccacagggcc
     1441 aaggaagagc tatctagcag gataagacca gtagttgtta tgatatctgg caaaccagga
     1501 ataggcaaaa ctcatctggc cagggaggtg gcaagaaagg tggcatccac tctcacaggg
     1561 gatcaaagag tcggactcat accaagaaac ggtgtggacc attgggatgc atacaaaggt
     1621 gagagagtcg tgctgtggga cgactatggc atgagtaacc ccattcatga tgctcttcgc
     1681 atacaggaat tggctgatac gtgtcccctt accttaaatt gtgacagaat tgagaataag
     1741 ggaaaagttt ttgacagtga agtcataata attacaacaa accttgccaa tccagcccca
     1801 cttgattatg tcaactttga ggcctgttcc aggagaattg atttcctggt gtacgctgag
     1861 gcaccagaag tagaaaaagc aaaacgggac tttcctggtc agccagatat gtggaaggac
     1921 gccttcaagc cggacttttc acacatcaag ctacagcttg cacctcaggg cggttttgac
     1981 aagaatggca acaccccaca tgggaaagga gtgatgaaga ccctcactac cggttctctg
     2041 attgcccgtg catcaggcct actgcacgag aggatggatg aatttgaact ccaaggtccc
     2101 acaatcacca ccttcaattt cgaccggaac agaatcacag cattcagaca attggctgca
     2161 gaaaacaagt atggattggt ggataccatg aaagttggca atcaactaaa aggagtaaaa
     2221 accatggaag aactcaaaca agcaatcagg aatgtgacca tcaagaggtg ccagatcatc
     2281 tacggtggct ccacgtatga ccttgaatct gatggcaagg gcaaagtttt ggtggaaaag
     2341 gtcaagaaca cctctgtaca gaccaacaac gagttggccg gggccctgca ccatctcaaa
     2401 cacgcccgaa tcaggtacta tgtcaaatgt gtgcaagaag cagtctattc catcatacaa
     2461 attgccggcg ctgcgtttgt caccacgcgc attgcacgcc gcatgaacat acaagaactc
     2521 tggtcgaagc cacaattaga tcaaaatgaa tcagagacta aggaagaggc ccccaagtca
     2581 gaagatgacg agttcatcat atcttctaag gacatcaagg aggaaggaaa gaagggcaaa
     2641 aacaaaactg gccgtggcaa gaaacacact gcattctcca gcaagggctt gagcgatgag
     2701 gagtatgacg agtacaagag gataagagaa gagagaaatg ggaagtactc tatagaggag
     2761 tatcttcaag acagagacag gtactatgag gagctcgcca ttgccaaggc cacggaagaa
     2821 gacttctgtg aagaggagga gatcaaaatc cgccagagaa ttttccgtcc caccaggaaa
     2881 caaagaaagg aagagagggc cacattaggg ctagtaacag gttcagaaat cagaaaaaga
     2941 aaccctgatg acttcaaacc caaagggaag ctgtgggccg atgacaacag aagtgttgac
     3001 tacaatgaga aactagactt tgaggccccc ccaagcatat ggtctaggat tgtgagcttt
     3061 ggttctggct ggggcttctg ggtatcacca agcctgttca taacatcaac tcatgtaatc
     3121 cccgcaggca taacagaagc atttggagtc cccatcaaac aaattcaggt ccacaaatca
     3181 ggtgaatttt gccgattcag attcccaaaa ccaattagac cagatgtgac aggaatgatc
     3241 ttggaagaag gtgcgcctga aggcaccgtg gcaactgtgc tcatcaaacg ccccaccgga
     3301 gagctcatgc ctcttgcagc cagaatggga acacacgcaa ccatgaaaat tcaaggccgc
     3361 atggttggcg gacaaatggg tatgttgctc actggatcaa atgctaaagg aatggatttg
     3421 ggaacaactc ctggtgactg tggctgtcct tacatctata aaaggggcaa tgactatata
     3481 gtcattgggg tgcacactgc agcagcccgt ggcggaaaca ccgtcatctg tgccacacag
     3541 ggaagtgagg gtgaggcaac tcttgagggt ggagatgaca aaggaacata ctgtggggca
     3601 cccattctag gccctggggg tgcaccaaaa ttgagcacca aaaccaaatt ttggaggtca
     3661 tcgaacacgc ctcttccacc agggacatat gagcctgcct acctcggtgg ccgtgatccg
     3721 cgtgttaagg gtgggccctc cttgcagcag gtaatgagag accagttgaa gccattcact
     3781 gaacccaggg gcaaacctcc aagaccaagt gtattggaag cagccaaaca aaccattatc
     3841 aatgtcctcg aacaaaccct ggatcctcca caaaaatgga catacgcaca ggcgtgtgcc
     3901 tcacttgaca aaaccacctc cagcgggcat ccccatcacg tccgaaagaa tgaattctgg
     3961 aatggtgaga ccttcactgg taaattggca gaccaagcat caaaagcaaa cctaatgttt
     4021 gaggaaggga aacacatgac accagtgtac acagcagcac tcaaggacga gctagtcaag
     4081 actgagaaaa tctatggaaa gatcaagaag agactgctct ggggctctga cttgtccacc
     4141 atgatccggt gcgctaggtc atttggtggg ctcatggatg agatgaaggc acactgcata
     4201 tcactcccag tacgagttgg catgaatatg aatgaagatg gcccaataat atttgagaaa
     4261 cattccagat acaaatacca ctatgatgca gactactctc gttgggattc aacacaacag
     4321 agggcagtac tagcagcagc cttggaaatc atggtcagat tttctgcaga accacaattg
     4381 gcacaaatag tcgctgagga tctgctggcc cctagtgtag tagatgtagg agactttaaa
     4441 atcacaataa atgaagggct cccatctggt gtgccatgca cttctcaatg gaactccatc
     4501 gcacactggc tgctaactct ctgtgccttg tctgaagtca ccaaactgtc ccctgacatt
     4561 atacaagcaa attccatgtt ctcattttac ggtgatgacg agattgttag caccgacata
     4621 aaattggacc ctgaacagtt aaccgccaaa ttgaaggagt acggcctgaa accaacccgc
     4681 ccagacaaga ccgagggacc cctgatcatc agtgaagatt tgaacggact cactttcctc
     4741 cgaaggacgg tgactcgtga cccagctggc tggtttggaa aactggacca aaactcaata
     4801 ttgaggcaga tgtactggac tagaggacca aatcatgaag accccaatga gacaatgata
     4861 ccccattctc aaagacccat acagctcatg gcactgcttg gtgaagcctc tcttcacgga
     4921 ccctctttct acagtaaaat cagtaagttg gtcataactg aactcaaaga aggtgggatg
     4981 gacttttacg tgccaaggca ggaacccatg ttcaggtgga tgaggttttc tgacttgagc
     5041 acgtgggagg gcgatcgcaa tctggctccc aattttgtga atgaagatgg cgtcgagtga
     5101 cgccaaccca tctgatgggt ccgcagccaa cctcgtacca gaggtcaaca atgaggttat
     5161 ggctttggag cccgttgttg gtgccgctat tgcggcacct gtagcgggcc aacaaaatgt
     5221 aattgacccc tggattagaa ataattttgt acaagcccct ggtggggagt ttacagtatc
     5281 ccctagaaac gctccaggtg aaatactatg gagcgcgccc ctaggccctg acctaaatcc
     5341 ctacctatcc catttggcca gaatgtacaa tggttatgca ggtggttttg aagtgcaggt
     5401 aattctcgcg gggaacgcgt tcaccgccgg gaagatcata tttgcagcag tcccaccaaa
     5461 ttttccaact gaaggcttaa gtcctagcca ggtcactatg ttcccccata taatagtaga
     5521 tgttagacaa ttagaacctg tgctgattcc cttacccgat gtcaggaata atttctatca
     5581 ttacaatcag tcaaatgact ccactattaa gttgatagca atgttgtaca caccacttag
     5641 ggctaataat gctggggatg atgttttcac agtttcgtgc cgagttctca cgagaccatc
     5701 ccccgatttt gatttcatat ttttagtgcc acccacagtt gagtcaagaa ctaaaccatt
     5761 ctctgtccca gttttaactg ttgaggagat gaccaattca agattcccca ttcctttgga
     5821 aaagttgttc acgggcccca gcagtgcctt tgttgttcaa ccacaaaacg gcaggtgcac
     5881 aactgatggc gtgctcctag gcaccaccca actgtctcct gtcaacatct gcaccttcag
     5941 aggggatgtc acccacatca caggtagtcg caactacaca atgaatttgg cttctcaaaa
     6001 ttggaacaac tatgacccaa cagaagaaat cccagcccct ctaggaactc cagattttgt
     6061 ggggaagatt caaggcatgc tcacccaaac cacaaggaca gatggttcaa cacgcggcca
     6121 caaagctaca gtgtacactg ggagcgccga cttttctcca aaactaggta gagttcaatt
     6181 tgaaactgac acagaccatg attttgaagc taaccaaaac acaaagttca ccccagtcgg
     6241 tgtcatccaa gatggtagca ccacccaccg aaacgaaccc caacagtggg tgctcccaag
     6301 ttactcaggc agaaatactc acaatgtaca cctggccccc gctgtagccc ccacctttcc
     6361 gggtgagcaa cttctcttct tcagatccac catgcccgga tgcagcgggt accccaacat
     6421 ggatttggac tgtctgctcc cccaggaatg ggtgcagtac ttctaccaag aggcagcccc
     6481 agcacaatct gatgtggctc tgctaagatt tgtgaatcca gacacaggta gggttttgtt
     6541 tgagtgcaag cttcacaaat caggctatgt tacagtggct cacactggcc aacatgattt
     6601 ggttatcccc cccaatggtt actttaggtt tgattcctgg gtcaaccagt tctacacgct
     6661 tgcccccatg ggaaatggaa cggggcgtag acgtgtagta taatggctgg agctttcttt
     6721 gctggattgg catctgatgt ccttggctct ggacttggtt cccttatcaa tgctggggct
     6781 ggggccatca accaaaaagt tgagtttgaa aataacagaa aattgcaaca agcatccttc
     6841 caatttagca gcaatctgca acaggcttcc tttcaacatg ataaagagat gctccaagca
     6901 caaattgagg ccaccaaaaa gctacaacag gaaatgatga aagttaagca ggcaatgctc
     6961 ctagagggtg ggttctctga gacagatgca gcccgcgggg caattaacgc ccccatgaca
     7021 aaagctttgg actggagcgg gacaaggtac tgggctcccg atgctaggac tacaacatat
     7081 aatgcaggcc gcttttccac ccctcaacca tcgggggcac tgccaggaag agctaatctt
     7141 agggatgctg tccctgctcg gggaccctcc aacaaatctt ccaactcttc tactgtcacc
     7201 tctgtgtact caaatcaaac tatttcaacg aggcttggtt ctacagctgg ttctggaacc
     7261 agtgtctcga gcctcccgtc aactgcaagg actaggagct gggttgagga tcaaagtagg
     7321 aatttgtcac ctttcatgag gggggcccac aacatatcat ttgtcacccc accatctagc
     7381 agatcctcta gccaaggcac agtctcaacc gtgcctaaag agattttgga ctcctggact
     7441 ggcgctttca acacgcgcag gcagcctctc ttcgctcaca ttcgtaagcg aggggagtca
     7501 cgggtgtaat gtgaaaagac aaaactgac
//