Typing tool

Complete norovirus genomes

MK762566  GII.4 Sydney
 GII.P16

Length: 7,551 | 3 CDS

ORF1: 1..5100
ORF2: 5081..6703
ORF3: 6703..7509
LOCUS       MK762566                7551 bp    RNA     linear   VRL 13-APR-2019
DEFINITION  Norovirus GII isolate Hu/US/2016/GII.P16-GII.4 Sydney/CS0275
            nonstructural polyprotein (ORF1), VP1 (ORF2), and VP2 (ORF3) genes,
            complete cds.
ACCESSION   MK762566
VERSION     MK762566.1
KEYWORDS    .
SOURCE      Norovirus GII
  ORGANISM  Norovirus GII
            Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes;
            Picornavirales; Caliciviridae; Norovirus.
REFERENCE   1  (bases 1 to 7551)
  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  JOURNAL   Unpublished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 7551)
  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..7551
                     /organism="Norovirus GII"
                     /mol_type="genomic RNA"
                     /strain="CS0275"
                     /isolate="Hu/US/2016/GII.P16-GII.4 Sydney/CS0275"
                     /isolation_source="stool"
                     /host="Homo sapiens"
                     /db_xref="taxon:122929"
                     /country="USA"
                     /collection_date="22-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="QBX91025.1"
                     /translation="MKMASNDATVAVACNNNNDKEKSSGEGLFTNMSSTLKKALGARP
                     KQPAPRDEPQKPPRPPTPELVKRIPPPPPNGEEEEEPAIRYEVKSGISGLPELTTVPQ
                     PDVANTAFSVPPLSLRENREAKEPLTGAILEMWDGEIYHYGLYVEKGLVLGVHKPPAA
                     ISMARVELTPLSLYWRVVYTPQYLISPETLRRLNGEAFPYTAFDNNCYAFCCWVLDLN
                     DSWLSRRMVQRTTGFFRPYQEWNRKPLPTMDDSKIKKVANIFLCSLSTLFTRPIKDLI
                     GKIKPLNILNILATCDWTFAGIVESLILLAELFGVFWTPPDVSAMIAPLLGEYELQGP
                     EDLAVELVPVVMGGIGLVLGFTKEKIGKMLSSAASTLRACKDLGAYGLEILKLVMKWF
                     FPKKEEANELAMVRAIEDAVLDLEAIENNHVTTLLKDKDSLATYMKTLDMEEEKARRL
                     STKSASPDIVGTINALLARIAAARSLVHRAKEELSSRIRPVVVMISGKPGIGKTHLAR
                     EVARKVASTLTGDQRVGLIPRNGVDHWDAYKGERVVLWDDYGMSNPIHDALRIQELAD
                     TCPLTLNCDRIENKGKVFDSEVIIITTNLANPAPLDYVNFEACSRRIDFLVYAEAPEV
                     EKAKRDFPGQPDMWKDAFKPDFSHIKLQLAPQGGFDKNGNTPHGKGVMKTLTTGSLIA
                     RASGLLHERMDEFELQGPTITTFNFDRNRITAFRQLAAENKYGLVDTMKVGNQLKGVK
                     TMEELKQAIRNVTIKRCRIIYGGSTYDLESDGKGKVLVEKVKNTSVQTNNELAGALHH
                     LKHARIRYYVKCVQEAIYSIIQIAGAAFVTTRIARRMNIQELWSKPQLDQNESETKEE
                     APKSEDDEFIISSKDIKEEGKKGKNKTGRGKKHTAFSSKGLSDEEYDEYKRIREERNG
                     KYSIEEYLQDRDRYYEELAIAKATEEDFCEEEEIKIRQRIFRPTRKQRKEERATLGLV
                     TGSEIRKRNPDDFKPKGKLWADDNRIVDYNEKLDFEAPPSIWSRIVSFGSGWGFWVSP
                     SLFITSTHVIPAGITEAFGVPIKQIQIHKSGEFCRFRFPKPIRPDVTGMILEEGAPEG
                     TVATVLIKRPTGELMPLAARMGTHATMKIQGRMVGGQMGMLLTGSNAKGMDLGTTPGD
                     CGCPYIYKRGNDYIVIGVHTAAARGGNTVICATQGSEGEATLEGGDDKGTYCGAPILG
                     PGGAPKLSTKTKFWRSSNTPLPPGTYEPAYLGGRDPRVKGGPSLQQVMRDQLKPFTEP
                     RGKPPRPSVLEAAKQTIINVLEQTLDPPQKWTYAQACASLDKTTSSGHPHHVRKNEFW
                     NGETFTGKLADQASKANLMFEEGKHMTPVYTAALKDELVKTEKIYGKIKKRLLWGSDL
                     STMIRCARSFGGLMDEMKAHCISLPVRVGMNMNEDGPIIFEKHSRYKYHYDADYSRWD
                     STQQRAVLAAALEIMVRFSAEPQLAQIVAEDLLAPSVVDVGDFKITINEGLPSGVPCT
                     SQWNSIAHWLLTLCALSEVTKLSPDIIQANSMFSFYGDDEIVSTDIKLDPEQLTAKLK
                     EYGLKPTRPDKTEGPLIISEDLNGLTFLRRTVTRDPAGWFGKLDQSSILRQMYWTRGP
                     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="QBX91026.1"
                     /translation="MKMASSDANPSDGSAANLVPEVNNEVMALEPVVGAAIAAPVAGQ
                     QNVIDPWIRNNFVQAPGGEFTVSPRNAPGEILWSAPLGPDLNPYLSHLARMYNGYAGG
                     FEVQVILAGNAFTAGKIIFAAVPPNFPTEGLSPSQVTMFPHIIVDVRQLEPVLIPLPD
                     VRNNFYHYNQSNDSTIKLIAMLYTPLRANNAGDDVFTVSCRVLTRPSPDFDFIFLVPP
                     TVESRTKPFSVPVLTVEEMTNSRFPIPLEKLFTGPSSAFVVQPQNGRCTTDGVLLGTT
                     QLSPVNICTFRGDVTHITGSRNYTMNLASQNWNNYDPTEEIPAPLGTPDFVGKIQGML
                     TQTTRTDGSTRGHKATVYTGSADFAPKLGRVQFETDTDHDFEANQNTKFTPVGVIQDG
                     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="QBX91027.1"
                     /translation="MAGAFFAGLASDVLGSGLGSLINAGAGAINQKVEFENNRKLQQA
                     SFQFSSNLQQASFQHDKEMLQAQIEATKKLQQEMMKVKQAVLLEGGFSETDAARGAIN
                     APMTKALDWSGTRYWAPDARTTTYNAGRFSTPQPSGALPGRANLRDAVPARGPSNKSS
                     NSSTVTSVYSNQTISTRLGSTAGSGTSVSSLPSTARTRSWVEDQSRNLSPFMRGVHNI
                     SFVTPPSSRSSSQGTVSTVPKEILDSWTGAFNTRRQPLFAHIRKRGESRV"
ORIGIN      
        1 atgaagatgg cgtctaacga cgctaccgtt gccgttgctt gcaacaacaa caacgacaag
       61 gaaaaatctt caggtgaagg cttattcaca aatatgtctt ccaccttaaa gaaagccctc
      121 ggggctaggc ccaaacagcc cgccccgaga gacgaaccac aaaagccccc aagaccacca
      181 actcccgagt tggtcaagag gataccccct cctccaccta atggcgaaga agaagaagaa
      241 ccagccatta ggtatgaggt taagagtggg atctctggcc tgcccgagct cacaacagtc
      301 ccccaaccgg acgtggccaa cacagcattc agtgttccac cactgagctt gagagaaaac
      361 agggaggcca aggaaccgct 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 accgccttcg acaacaactg ctatgccttt tgctgctggg tgttagacct caatgactca
      661 tggcttagca ggaggatggt gcaaagaaca acgggcttct tcagacctta ccaagagtgg
      721 aacagaaaac ccctgcctac catggatgac tccaaaatta agaaggtagc aaatatattc
      781 ctatgttcat tgtccacgtt attcaccaga cccataaaag acctcatagg aaaaattaaa
      841 ccattaaaca tattgaacat cctggcaacg tgtgactgga cgtttgccgg aatagtggaa
      901 tctctgatat tacttgctga actcttcgga gttttctgga cacccccaga tgtgtctgct
      961 atgatcgctc ccttactcgg ggaatacgag ttgcaagggc cagaagacct cgccgttgaa
     1021 ctcgtacctg tggtaatggg agggattggt ttggtgttgg gattcaccaa agagaaaatt
     1081 ggcaaaatgt tgtcctcagc agcatcaaca ctcagggctt gcaaagatct tggtgcctat
     1141 ggcttagaga tactcaaatt ggtcatgaag tggttcttcc caaagaaaga ggaggccaat
     1201 gagctagcca tggtgagggc catagaggat gccgtactag atcttgaggc aatagaaaat
     1261 aaccacgtga 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 atacaagaat tggctgatac gtgtcccctt accttaaatt gtgacagaat tgaaaataag
     1741 ggaaaagttt ttgacagtga agtcataata attacaacaa accttgccaa tccagcccca
     1801 cttgattatg tcaactttga ggcctgttcc aggagaattg atttcctggt gtacgctgag
     1861 gcaccagaag tagaaaaggc aaaacgggac tttcctggtc agccagatat gtggaaggac
     1921 gccttcaagc cggacttttc acacatcaag ctacagcttg cacctcaggg cggctttgac
     1981 aagaatggca acaccccaca tgggaaagga gtgatgaaga ccctcactac cggctctctg
     2041 attgcccgtg catcaggcct actgcatgag aggatggatg aatttgaact tcaaggtccc
     2101 acaatcacca ccttcaattt cgaccggaac agaatcacag cattcagaca attggctgca
     2161 gaaaacaagt atggattggt ggataccatg aaagttggca atcaactaaa aggagtgaaa
     2221 accatggaag aactcaaaca agcaatcagg aatgtgacca tcaagaggtg ccggatcatc
     2281 tacggtggct ccacgtacga cctcgaatct gatggcaagg gcaaagtttt ggtggaaaag
     2341 gtcaagaaca cctctgtaca gaccaacaac gagttggccg gggccctgca ccatctcaaa
     2401 cacgcccgaa tcaggtacta tgtcaaatgt gtgcaagaag caatctactc catcatacaa
     2461 attgccggcg ctgcgtttgt caccacgcgc attgcacgcc gcatgaacat acaagaactc
     2521 tggtcgaagc cacaattaga tcaaaatgaa tcagagacta aggaagaggc ccccaagtca
     2581 gaagacgacg agttcatcat atcttctaag gacatcaagg aggaaggaaa gaagggtaaa
     2641 aacaaaactg gccgtggcaa gaaacacact gcattctcca gcaagggttt gagcgatgag
     2701 gagtatgacg agtataagag gataagagag gagagaaatg ggaagtactc tatagaggag
     2761 tatcttcaag atagagacag gtactatgag gagctcgcca ttgccaaggc cacagaagaa
     2821 gacttctgtg aagaggagga gatcaaaatc cgtcagagaa ttttccgtcc caccaggaaa
     2881 caaagaaagg aagagagggc cacattaggg ctagtaacag gttcagaaat cagaaaaaga
     2941 aaccctgatg acttcaaacc caaagggaag ctgtgggccg atgacaacag aattgttgac
     3001 tacaatgaga aactggactt tgaggccccc ccaagcatat ggtctaggat tgtgagcttt
     3061 ggttctggct ggggcttctg ggtatcacca agcctgttca taacatcaac tcatgtaatc
     3121 cccgcaggca taacagaagc gtttggagtc cccatcaaac aaattcagat ccacaaatca
     3181 ggtgaatttt gccgattcag attcccaaaa ccaattagac cagatgtgac aggaatgatc
     3241 ttggaagaag gtgcgcctga aggcaccgtg gcaactgtgc tcatcaaacg ccccaccgga
     3301 gagctcatgc ctcttgcagc cagaatggga acacacgcaa ccatgaaaat tcaaggccgc
     3361 atggttggcg gacagatggg tatgttgctc actggatcaa atgctaaagg aatggatttg
     3421 ggaacaactc ctggtgactg tggctgtcct tacatctata aaaggggcaa tgactacata
     3481 gtcattgggg tgcacactgc agcagcccgt ggtggaaaca ccgtcatctg tgctacacag
     3541 ggaagtgagg gtgaggcaac tcttgagggt ggagatgaca aaggaacata ctgtggggca
     3601 cccattctag gccctggggg tgcaccaaaa ttgagcacca aaaccaaatt ttggaggtca
     3661 tcgaacacgc cccttccacc agggacatat gagcctgcct acctcggtgg ccgtgatccg
     3721 cgtgttaagg gtgggccctc cttgcagcag gtaatgagag accagttgaa gccattcact
     3781 gagcccaggg gcaaacctcc aagaccaagt gtattggaag cagccaaaca aaccattatc
     3841 aatgtcctcg aacaaaccct ggaccctcca caaaaatgga catacgcaca ggcgtgtgcc
     3901 tcacttgaca aaaccacctc cagcgggcat ccccatcacg tccgaaagaa tgaattctgg
     3961 aatggtgaga ccttcactgg taaattggca gaccaagcat caaaagcaaa cctaatgttt
     4021 gaggaaggga aacacatgac accagtgtat acagcagcac tcaaggatga gctagtcaag
     4081 actgagaaaa tctatggaaa gatcaagaag agactgctct ggggctctga cttgtccacc
     4141 atgatccggt gcgctaggtc atttggtggg ctcatggacg agatgaaggc acactgcata
     4201 tcactcccag tacgagttgg catgaatatg aatgaagatg gcccaataat atttgagaaa
     4261 cattccagat ataaatacca ctatgatgca gactactctc gttgggattc aacacaacag
     4321 agggcagtac tagcagcagc tttggaaatc atggtcagat tctctgcaga 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 agattgtcag caccgacata
     4621 aaattggacc ctgaacagtt aaccgccaag ttgaaggagt acggcctgaa accaacccgc
     4681 ccagacaaga ccgagggacc cctgatcatc agtgaagatt tgaacggact cactttcctc
     4741 cgaaggacgg tgactcgtga cccagctggc tggtttggaa aactggacca aagctcaatt
     4801 ttgaggcaga tgtactggac tagaggacca aatcatgaag accccaatga gacaatgata
     4861 ccccattctc aaagacccat acagctcatg gcactgcttg gtgaagcctc tcttcacgga
     4921 ccctctttct acagtaaaat cagtaaattg 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 agtcactatg ttcccccata taatagtaga
     5521 tgttagacaa ttagaacctg tgctgattcc cttacccgat gttaggaata atttctatca
     5581 ttataatcag tcaaatgact ccactattaa gttgatagca atgttgtata caccacttag
     5641 ggctaataat gctggggatg atgttttcac tgtttcgtgc 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 ttggaacaat tatgacccaa cagaagaaat cccagcccct ctaggaactc cagattttgt
     6061 ggggaagatt caaggcatgc tcacccaaac cacaaggaca gatggttcaa cacgcggcca
     6121 caaagctaca gtgtacactg ggagcgccga ctttgctcca aaactgggta gagttcaatt
     6181 tgaaactgac acagaccatg attttgaagc taatcaaaac acaaagttca ccccagtcgg
     6241 tgtcatccaa gatggtagca ccacccaccg aaacgaaccc caacagtggg tgctcccaag
     6301 ttactcaggc agaaatactc ataatgtaca tctggccccc 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 ggttatccct cccaatggtt actttaggtt tgattcctgg gtcaaccagt tctacacgct
     6661 tgcccccatg ggaaatggaa cggggcgtag acgtgtagta taatggctgg agctttcttt
     6721 gctggattgg catctgatgt ccttggctct ggacttggtt ccctcatcaa tgctggggct
     6781 ggggccatca accaaaaagt tgagtttgaa aataacagaa aattgcaaca agcatccttc
     6841 caatttagca gcaatctgca acaggcttcc tttcaacatg ataaagagat gctccaagca
     6901 caaattgagg ccaccaaaaa gctacaacag gaaatgatga aagttaagca ggcagtgctc
     6961 ctagagggtg ggttctctga gacagatgca gcccgcgggg caattaacgc ccccatgaca
     7021 aaagctttgg attggagcgg gacaaggtac tgggctcccg atgctaggac tacaacatac
     7081 aatgcaggcc gcttttccac ccctcaacca tcgggggcac tgccaggaag agctaatctt
     7141 agggatgctg tccctgctcg gggaccctcc aacaaatctt ctaactcttc tactgtcacc
     7201 tctgtgtact caaatcaaac tatttcaacg agacttggtt ctacagctgg ttctggaacc
     7261 agtgtctcga gcctcccgtc aactgcaagg actaggagct gggttgagga tcaaagtagg
     7321 aatttgtcac ctttcatgag gggggtccac aacatatcat ttgtcacccc accatctagc
     7381 agatcctcta gccaaggcac agtctcaacc gtgcctaaag agattttgga ctcctggact
     7441 ggcgctttca acacgcgcag gcagcctctc ttcgctcaca ttcgtaagcg aggggagtca
     7501 cgggtgtaat gtgaaaagac aaaactgatt atctttcttt ttctttagtg t
//