Typing tool

Complete norovirus genomes

MK762629  GII.4 Sydney
 GII.P16

Length: 7,535 | 3 CDS

ORF1: 4..5103
ORF2: 5084..6706
ORF3: 6706..7512
LOCUS       MK762629                7535 bp    RNA     linear   VRL 13-APR-2019
DEFINITION  Norovirus GII isolate Hu/US/2017/GII.P16-GII.4 Sydney/Lee0113
            nonstructural polyprotein (ORF1), VP1 (ORF2), and VP2 (ORF3) genes,
            complete cds.
ACCESSION   MK762629
VERSION     MK762629.1
KEYWORDS    .
SOURCE      Norovirus GII
  ORGANISM  Norovirus GII
            Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes;
            Picornavirales; Caliciviridae; Norovirus.
REFERENCE   1  (bases 1 to 7535)
  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  JOURNAL   Unpublished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 7535)
  AUTHORS   Barclay,L., Cannon,J.L., Chesnutt,C., 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..7535
                     /organism="Norovirus GII"
                     /mol_type="genomic RNA"
                     /strain="Lee0113"
                     /isolate="Hu/US/2017/GII.P16-GII.4 Sydney/Lee0113"
                     /isolation_source="stool"
                     /host="Homo sapiens"
                     /db_xref="taxon:122929"
                     /country="USA"
                     /collection_date="24-Oct-2017"
                     /note="genotype: GII.P16-GII.4 Sydney"
     gene            4..5103
                     /gene="ORF1"
     CDS             4..5103
                     /gene="ORF1"
                     /codon_start=1
                     /product="nonstructural polyprotein"
                     /protein_id="QBX91114.1"
                     /translation="MKMASNDATVAVACNNNNDKEKSSGEGLFTNMSSTLKKALGARP
                     KQPAPRNEPQKPPRPPTPELVKRIPPPPPNGEEEEEPVIRYEVKSGISGLPELTTVPQ
                     PDVANTAFSVPPLSLRENREAKEPLTGAILEMWDGEIYHYGLYVEKGLVLGVHKPPAA
                     ISMARVELIPLSLYWRVVYTPQYLISPETLRRLNGEAFPYTAFDNNCYAFCCWVLDLN
                     DSWLSRRMVQRTTGFFRPYQEWNRKPLPTMDDSKIKKVANIFLCSLSTLFTRPIKDLI
                     GKIKPLNILNILATCDWTFAGIVESLILLAELFGVFWTPPDVSAMIAPLLGDYELQGP
                     EDLAVELVPVVMGGIGLVLGFTKEKIGKMLSSAASTLRACKDLGAYGLEILKLVMKWF
                     FPKKEEANELAMVRAIEDAVLDLEAIENNHMTTLLKDKDSLATYMKTLDMEEEKARRL
                     STKSASPDIVGTINALLARIAAARSLVHRAKEELSSRMRPVVVMISGKPGIGKTHLAR
                     EVARKVASTLTGDQRVGLIPRNGVDHWDAYKGERVVLWDDYGMSNPIHDALRIQELAD
                     TCPLTLNCDRIENKGKVFDSEVIIITTNLANPAPLDYVNFEACSRRIDFLVYAEAPEV
                     EKAKRDFPGQPDMWKDAFKPDFSHIKLQLAPQGGFDKNGNTPHGKGVMKTLTTGSLIA
                     RASGLLHERMDEFELQGPTTTTFNFDRNRITAFRQLAAENKYGLVDTMKVGNQLKGVK
                     TMEELKQAIRNVTIKRCRIIYGGSTYDLESDGKGKVLVEKVKNTSVQTNNELAGALHH
                     LKHARIRYYVKCVQEAVYSIIQIAGAAFVTTRIARRMNIQELWSKPQLDQNESETKEE
                     TPKSEDDEFIISSKDIKEEGKKGKNKTGRGKKHTAFSSKGLSDEEYDEYKRIREERNG
                     KYSIEEYLQDRDRYYEELAIAKATEEDFCEEEEIKIRQRIFRPTRKQRKEERVTLGLV
                     TGSEIRKRNPDDFKPKGKLWADDNRSVDYNEKLDFEAPPSIWSRIVSFGSGWGFWVSP
                     SLFITSTHVIPAGITEAFGVPIKQIQIHKSGEFCRFRFPKPIRPDVTGMILEEGAPEG
                     TVATVLIKRPSGELMPLAARMGTHATMKIQGRMVGGQMGMLLTGSNAKGMDLGTTPGD
                     CGCPYIYKRGNDYIVIGVHTAAARGGNTVICATQGSEGEATLEGGDDKGTYCGAPILG
                     PGGAPKLSTKTKFWRSSNTPLPPGTYEPAYLGGRDPRVKGGPSLQQVMRDQLKPFTEP
                     RGKPPRPSVLEAAKQTIINVLEQTLDPPQKWSYAQACASLDKTTSSGHPHHVRKNEFW
                     NGETFTGKLADQASKANLMFEEGKHMTPVYTAALKDELVKTEKIYGNIKKRLLWGSDL
                     STMIRCARSFGGLMDEMKAHCITLPVRVGMNMNEDGPIIFEKHSRYKYHYDADYSRWD
                     STQQRAVLAAALEIMVRFSAEPQLAQIVAEDLLAPSVVDVGDFKITINEGLPSGVPCT
                     SQWNSIAHWLLTLCALSEVTKLSPDIIQANSMFSFYGDDEIVSTDIKLDPEQLTAKLK
                     EYGLKPTRPDKTEGPLIISEDLNGLTFLRRTVTRDPAGWFGKLDQSSILRQMYWTRGP
                     NHEDPNETMIPHSQRPIQLMALLGEASLHGPSFYSKISKLVITELKEGGMDFYVPRQE
                     PMFRWMRFSDLSTWEGDRNLAPNFVNEDGVE"
     mat_peptide     4..999
                     /gene="ORF1"
                     /product="p48"
     mat_peptide     1000..2097
                     /gene="ORF1"
                     /product="NTPase"
     mat_peptide     2098..2628
                     /gene="ORF1"
                     /product="p22"
     mat_peptide     2629..3027
                     /gene="ORF1"
                     /product="VPg"
     mat_peptide     3028..3570
                     /gene="ORF1"
                     /product="Pro"
     mat_peptide     3571..5100
                     /gene="ORF1"
                     /product="RdRp"
     gene            5084..6706
                     /gene="ORF2"
     CDS             5084..6706
                     /gene="ORF2"
                     /note="major capsid protein"
                     /codon_start=1
                     /product="VP1"
                     /protein_id="QBX91115.1"
                     /translation="MKMASSDANPSDGSAANLVPEVNNEVMALEPVVGAAIAAPVAGQ
                     QNVIDPWIRNNFVQAPGGEFTVSPRNAPGEILWSAPLGPDLNPYLSHLARMYNGYAGG
                     FEVQVILAGNAFTAGKIIFAAVPPNFPTEGLSPSQVTMFPHIIVDVRQLEPVLIPLPD
                     VRNNFYHYNQSNDSTIKLIAMLYTPLRANNAGDDVFTVSCRVLTRPSPDFDFIFLVPP
                     TVESRTKPFSIPVLTVEEMTNSRFPIPLEKLFTGPSSAFVVQPQNGRCTTDGVLLGTT
                     QLSPVNICTFRGDVTHITGSRNYTMNLASQNWNNYDPTEEIPAPLGTPDFVGKIQGML
                     TQTTRTDGSTRGHKATVYTGSADFAPKLGRVQFETDTDHDFEANQNTKFTPVGVIQDG
                     STTHRNEPQQWVLPSYSGRNTHNVHLAPAVAPTFPGEQLLFFRSTMPGCSGYPNMDLD
                     CLLPQEWVQYFYQEAAPAQSDVALLRFVNPDTGRVLFECKLHKSGYVTVAHTGQHDLV
                     IPPNGYFRFDSWVNQFYTLAPMGNGTGRRRVV"
     gene            6706..7512
                     /gene="ORF3"
     CDS             6706..7512
                     /gene="ORF3"
                     /note="minor structural protein; small basic protein"
                     /codon_start=1
                     /product="VP2"
                     /protein_id="QBX91116.1"
                     /translation="MAGAFFAGLASDVLGSGLGSLINAGAGAINQKVEFENNRKLQQA
                     SFQFSSNLQQASFQHDKEMLQAQIEATKKLQQEMMKVKQAMLLEGGFSETDAARGAIN
                     APMTKALDWSGTRYWAPDARTTTYNAGRFSTPQPSGALPGRANLRDAVPARGPSNKSS
                     NSSTATSVYSNQTISTRLGSTAGSGTSASSLPSTARTRSWVEDQSRNLSPFMRGAHNI
                     SFVTPPSSRSSSQGTVSTVPKEILDSWTGAFNTRRQPLFAHIRKRGESRV"
ORIGIN      
        1 tgaatgaaga tggcgtctaa cgacgctacc gttgccgttg cttgcaacaa caacaacgac
       61 aaggaaaaat cttcaggtga aggcttattc acaaatatgt cttccacctt aaagaaagcc
      121 ctcggggcta ggcccaaaca gcctgccccg agaaacgaac cacaaaagcc cccaagacca
      181 ccaactcccg agttggtcaa gaggataccc cctcctccac ctaatggcga agaagaagaa
      241 gaaccagtca ttaggtatga ggttaagagt gggatctctg gcctgcccga gctcacaaca
      301 gtcccccaac cggacgtggc caacacagca ttcagtgttc caccactgag cttgagagaa
      361 aacagggagg ccaaggaacc gctaacaggg gcaatattag agatgtggga tggagagata
      421 taccactacg gcctgtacgt ggagaaaggc ttagtgttgg gtgtgcacaa accacctgca
      481 gccataagca tggcaagagt ggagctaata ccgctgtcat tgtactggcg tgtggtgtac
      541 actccccaat acctcatctc ccctgaaact ctcaggaggc tcaacggaga ggcattccct
      601 tacaccgcct tcgacaacaa ctgctatgcc ttttgctgct gggtgttgga cctcaatgac
      661 tcatggctta gcaggaggat ggtgcaaaga acaacgggct tcttcagacc ttaccaagag
      721 tggaacagaa aacccctgcc taccatggat gactccaaaa ttaagaaggt agcaaatata
      781 ttcctatgtt cattgtccac attattcacc agacccataa aagacctcat aggaaaaatt
      841 aaaccattaa acatattgaa catcctggca acgtgcgact ggacgtttgc cggaatagtg
      901 gagtctctga tattacttgc tgaactcttc ggagttttct ggacaccccc agatgtgtct
      961 gctatgatcg ctcccttact cggggactac gagttgcaag ggccagaaga cctcgccgtt
     1021 gaactcgtac ctgtggtaat gggagggatt ggtttggtgt tgggattcac caaagagaaa
     1081 attggcaaaa tgttgtcctc agcagcatca acactcaggg cttgcaaaga tcttggtgcc
     1141 tatggcttag agatactcaa attggtcatg aaatggttct tcccaaagaa agaggaggcc
     1201 aatgagctag ccatggtgag ggccatagag gacgccgtac tagatcttga ggcaatagaa
     1261 aataaccaca tgacaaccct gttgaaagac aaagacagct tagcaacata catgaaaaca
     1321 ctggacatgg aggaggaaaa agccagaagg ttgtccacaa aatctgcatc ccctgacata
     1381 gttgggacaa tcaacgctct gctggctcga atagcagcgg ccaggtcatt agtccacagg
     1441 gccaaggaag agttatctag caggatgaga ccagtagttg ttatgatatc tggtaaacca
     1501 ggaataggca aaactcatct ggccagggag gtggcaagaa aggtggcatc cactctcaca
     1561 ggggatcaaa gagtcggact cataccaaga aacggtgtgg accattggga tgcatacaaa
     1621 ggtgagagag tcgtgctgtg ggacgactat ggcatgagta accccattca tgatgctctt
     1681 cgcatacaag aattggctga tacgtgtccc cttaccttaa attgtgacag aattgaaaat
     1741 aagggaaaag tttttgatag tgaagtcata ataattacaa caaaccttgc caacccagcc
     1801 ccacttgatt atgtcaactt tgaggcctgt tccaggagaa ttgatttcct ggtgtacgct
     1861 gaggcaccag aagtggaaaa ggcgaaacga gacttccctg gtcagccaga tatgtggaag
     1921 gacgccttca agccggactt ttcacacatc aagctacagc ttgcacctca gggcggcttt
     1981 gacaagaatg gcaacacccc acatgggaaa ggagtgatga agaccctcac taccggttct
     2041 ctgattgccc gtgcatcagg cctactgcat gagaggatgg atgaatttga actccaaggt
     2101 cccacaacca ccaccttcaa tttcgaccgg aatagaatca cagcatttag acaattggct
     2161 gcagaaaaca agtatggatt ggtggatacc atgaaggttg gcaatcaact aaaaggagtg
     2221 aaaaccatgg aagaactcaa acaagcaatc aggaatgtga ccatcaagag gtgccggatc
     2281 atctacggtg gctccacgta tgaccttgaa tctgatggca agggcaaagt tttggtggaa
     2341 aaggtcaaga acacctctgt acagaccaac aacgagttgg ccggggccct acaccatctc
     2401 aaacacgccc gaatcaggta ctatgtcaaa tgtgtgcaag aagcagtcta ttccatcata
     2461 caaattgccg gcgctgcgtt tgtcaccacg cgcattgcac gccgcatgaa catacaagaa
     2521 ctctggtcga agccacaatt agatcaaaat gaatcagaga ctaaggaaga gacccccaag
     2581 tcagaagatg acgagttcat catatcttct aaggacatca aggaggaagg aaagaagggc
     2641 aaaaacaaaa ctggccgtgg caagaaacac actgcattct ccagcaaggg cttgagcgat
     2701 gaggagtacg acgagtacaa gaggataaga gaagagagaa atgggaagta ctctatagag
     2761 gagtatcttc aagacagaga caggtactat gaggagctcg ccattgccaa ggccacggag
     2821 gaagacttct gtgaagagga ggagatcaaa atccgtcaga gaattttccg tcccaccagg
     2881 aagcaaagga aggaagagag ggtcacatta gggctagtga caggttcaga aatcagaaaa
     2941 agaaaccctg atgacttcaa acccaaaggg aagctgtggg ccgatgacaa cagaagtgtt
     3001 gattacaatg agaaactgga ctttgaggcc cccccaagca tatggtctag gattgtgagc
     3061 tttggttctg gctggggctt ctgggtgtca ccaagcctgt tcataacatc aactcatgta
     3121 atccccgctg gcataacaga agcatttgga gtccccatca aacaaattca gatccacaaa
     3181 tcaggtgaat tttgccgatt cagattccca aaaccaatta gaccagatgt gacaggaatg
     3241 atcttggaag aaggtgcgcc tgaaggcacc gtggcaactg tgctcatcaa acgcccctcc
     3301 ggagagctca tgcctcttgc agccagaatg ggaacacacg caaccatgaa aattcaaggc
     3361 cgcatggttg gcggacagat gggtatgttg ctcactggat caaatgctaa aggaatggat
     3421 ttgggaacaa ctcctggtga ctgtggctgt ccttacatct ataaaagggg caatgactat
     3481 atagtcattg gggtgcacac tgcagcagcc cgtggtggaa acaccgttat ctgtgccaca
     3541 cagggaagtg agggtgaggc aacccttgag ggtggggatg acaaaggaac atactgtggg
     3601 gcacccattc taggccctgg gggtgcacca aaattgagca ccaaaaccaa attttggagg
     3661 tcgtcgaaca cgccccttcc accagggaca tatgagcctg cctacctcgg tggccgtgat
     3721 ccgcgtgtta agggtgggcc ctccttgcag caggtaatga gagaccagtt gaagccattc
     3781 actgaaccca ggggcaaacc tccaagacca agtgtattgg aagcagccaa acaaaccatt
     3841 atcaatgtcc tcgaacaaac cctggaccct ccacaaaaat ggtcatacgc gcaggcgtgt
     3901 gcctcacttg acaaaaccac ctccagcggg catccccatc acgtccgaaa gaatgaattc
     3961 tggaatggtg agaccttcac tggtaaattg gcagaccaag catcaaaagc aaacctgatg
     4021 tttgaggaag ggaaacatat gacaccagtg tatacagcag cactcaagga cgagctagtc
     4081 aagactgaga aaatctatgg aaatatcaag aagagactgc tctggggctc tgacttgtcc
     4141 accatgatcc ggtgcgctag gtcatttggt gggctcatgg acgagatgaa ggcacactgc
     4201 ataacactcc cagtacgagt tggcatgaat atgaatgaag atggcccaat aatatttgag
     4261 aaacattcca gatacaaata tcactatgat gcagactact ctcgttggga ttcaacacaa
     4321 cagagggcag tactagcagc agccttggaa atcatggtca gattctctgc agaaccacaa
     4381 ttggcacaaa tagtcgctga ggatctgctg gcccctagtg tagtagatgt aggagacttt
     4441 aaaatcacaa taaatgaagg gctcccatct ggtgtgccat gcacttccca atggaactcc
     4501 atcgcacact ggctgctaac tctctgtgcc ttgtctgaag tcaccaaact gtcccctgac
     4561 attatacaag caaattccat gttctcattt tacggtgatg acgagattgt cagcaccgac
     4621 ataaaattgg accctgaaca gttaaccgcc aaattgaagg agtacggcct gaaaccaacc
     4681 cgcccagaca agaccgaggg acccctgatc atcagtgaag atttgaacgg actcactttc
     4741 ctccgaagga cggtgactcg tgacccagct ggctggtttg gaaaactgga ccaaagctca
     4801 attttgaggc agatgtactg gactagagga ccaaatcatg aagaccccaa tgagacaatg
     4861 ataccccatt ctcaaagacc catacagctc atggcactgc ttggtgaagc ctctctccac
     4921 ggaccctctt tctacagtaa aatcagtaaa ttggtcataa ctgaactcaa agaaggtggg
     4981 atggactttt acgtgccaag gcaggaaccc atgttcaggt ggatgaggtt ttctgacttg
     5041 agcacgtggg agggcgatcg caatctggct cccaattttg tgaatgaaga tggcgtcgag
     5101 tgacgccaac ccatctgatg ggtccgcagc caacctcgta ccagaggtca acaatgaggt
     5161 tatggctttg gagcccgttg ttggtgccgc tattgcggca cctgtagcgg gccaacaaaa
     5221 tgtaattgac ccctggatta gaaataattt tgtacaagcc cctggtgggg agtttacagt
     5281 atcccctaga aacgctccag gtgaaatact atggagcgcg cccctaggcc ctgacctaaa
     5341 tccctaccta tcccatttgg ccagaatgta caatggttat gcaggtggtt ttgaagtgca
     5401 ggtaattctc gcggggaacg cgttcaccgc cgggaagatc atatttgcag cagtcccacc
     5461 aaatttccca actgaaggct taagtcctag ccaggtcact atgttccccc atataatagt
     5521 agatgttaga caattagaac ctgtgctgat tcccttaccc gatgtcagga ataatttcta
     5581 tcattacaac cagtcaaatg attccactat taagttgata gcaatgttgt atacaccact
     5641 tagggctaat aatgctgggg atgatgtttt cacagtttcg tgccgagttc tcacgagacc
     5701 atcccccgat tttgatttca tatttttagt gccacccaca gttgaatcaa gaactaaacc
     5761 attctctatc ccagttttga ctgttgagga gatgaccaat tcaagattcc ccattccttt
     5821 ggaaaagttg ttcacgggcc ccagcagtgc ctttgttgtt caaccacaaa acggcaggtg
     5881 cacaactgat ggcgtgctcc taggcaccac ccaactgtct cctgtcaaca tctgcacctt
     5941 cagaggggat gtcacccaca tcacaggtag tcgcaactac acaatgaact tggcttctca
     6001 aaattggaat aactatgatc caacagaaga aatcccagcc cctctaggaa ctccagattt
     6061 cgtggggaag attcaaggca tgctcaccca aaccacaagg acagatggtt caacacgcgg
     6121 ccacaaagct acagtgtaca ctgggagcgc tgattttgct ccaaaactgg gtagagttca
     6181 atttgaaact gatacagacc atgattttga agctaatcaa aacacaaagt tcaccccagt
     6241 cggtgtcatc caagatggta gcaccaccca ccgaaacgaa ccccaacagt gggtgctccc
     6301 aagttactca ggcagaaata ctcacaatgt acatctggcc cccgctgtag cccccacctt
     6361 tccaggtgag caacttctct tcttcagatc caccatgccc ggatgcagcg ggtaccccaa
     6421 catggatttg gactgtctgc tcccccagga atgggtgcag tacttctatc aagaggcagc
     6481 cccagcacaa tctgatgtgg ctctgctaag atttgtgaat ccagacacag gtagggtttt
     6541 gtttgagtgc aagcttcaca aatcaggcta cgttacagtg gctcacactg gccaacatga
     6601 tttggttatc ccccccaatg gttactttag gtttgattcc tgggtcaatc agttctacac
     6661 gcttgccccc atgggaaatg gaacggggcg tagacgtgta gtataatggc tggagctttc
     6721 tttgctggat tggcatctga tgtccttggc tctggacttg gttcccttat caatgctggg
     6781 gctggggcca tcaaccaaaa agttgagttt gaaaataaca gaaaattgca acaagcatcc
     6841 ttccaattta gcagcaatct gcaacaggct tcctttcaac atgataaaga gatgctccaa
     6901 gcacaaattg aggccaccaa aaagttacaa caggaaatga tgaaagttaa gcaggcaatg
     6961 ctcctagagg gtggattctc tgagacggat gcagcccgcg gggcaattaa cgctcccatg
     7021 acaaaagctt tggactggag cgggacaagg tactgggctc ccgatgctag gactacaaca
     7081 tacaatgcag gccgcttttc cacccctcaa ccatcggggg cactgccagg aagagctaac
     7141 cttagggatg ctgtccctgc tcggggaccc tccaacaaat cttctaactc ttctactgcc
     7201 acctctgtgt actcaaatca aaccatttca acgaggcttg gttctacagc tggttctgga
     7261 accagtgcct cgagcctccc gtcaactgca aggactagga gctgggttga ggatcaaagt
     7321 aggaatttgt cacctttcat gaggggggcc cacaatatat catttgtcac cccaccatct
     7381 agcagatcct ctagccaagg cacagtctca accgtgccta aagagatttt ggactcctgg
     7441 actggcgctt tcaacacgcg caggcagcct ctcttcgctc acattcgtaa gcgaggggag
     7501 tcacgggtgt aatgtgaaaa gacaaaactg attat
//