Typing tool

Complete norovirus genomes

MK752942  GII.4 Sydney
 GII.P16

Length: 7,533 | 3 CDS

ORF1: 4..5103
ORF2: 5084..6706
ORF3: 6706..7512
LOCUS       MK752942                7533 bp    RNA     linear   VRL 11-APR-2019
DEFINITION  Norovirus GII isolate Hu/US/2016/GII.P16-GII.4 Sydney/Marathon0626
            nonstructural polyprotein (ORF1), VP1 (ORF2), and VP2 (ORF3) genes,
            complete cds.
ACCESSION   MK752942
VERSION     MK752942.1
KEYWORDS    .
SOURCE      Norovirus GII
  ORGANISM  Norovirus GII
            Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes;
            Picornavirales; Caliciviridae; Norovirus.
REFERENCE   1  (bases 1 to 7533)
  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  JOURNAL   Unpublished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 7533)
  AUTHORS   Barclay,L., Cannon,J.L., Davis,T., Montmayeur,A.M., Tatusov,R.L.
            and Vinje,J.
  TITLE     Direct Submission
  JOURNAL   Submitted (04-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..7533
                     /organism="Norovirus GII"
                     /mol_type="genomic RNA"
                     /strain="Marathon0626"
                     /isolate="Hu/US/2016/GII.P16-GII.4 Sydney/Marathon0626"
                     /isolation_source="stool"
                     /host="Homo sapiens"
                     /db_xref="taxon:122929"
                     /country="USA"
                     /collection_date="06-Mar-2016"
                     /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="QBS47657.1"
                     /translation="MKMASNDATVAVACNNNNDKEKSSGEGLFTNMSSTLKKALGARP
                     KQPAPRDEPQKPPRPPTPELVKRIPPPPPNGEEEEEPVIRYEVKSGISGLPELTTVPQ
                     PDVANTAFSVPPLSLRENREAKEPLTGAILEMWDGEIYHYGLYVEKGLVLGVHKPPAA
                     ISMARVELTPLSLYWRVVYTPQYLISPETLRRLNGEAFPYTAFDNNCYAFCCWVLDLN
                     DSWLSRRMVQRTTGFFRPYQEWNRKPLPTMDDSKIKKVANIFLCSLSTIFTRPIKDLI
                     GKIKPLNILNVLATCDWTFAGIVESLILLAELFGVFWTPPDVSAMIAPLLGDYELQGP
                     EDLAVELVPVVMGGIGLVLGFTKEKIGKMLSSAASTLRACKDLGAYGLEILKLVMKWF
                     FPKKEEANELAMVRAIEDAVLDLEAIENNHMTTLLKDKDSLATYMKTLDMEEEKARRL
                     STKSASPDIVGTINALLARIAAARSLVHRAKEELSSRIRPVVVMISGKPGIGKTHLAR
                     EVARKVASTLTGDQRVGLIPRNGVDHWDAYKGERVVLWDDYGMSNPIHDALRIQELAD
                     TCPLTLNCDRIENKGKVFDSEVIIITTNLANPAPLDYVNFEACSRRIDFLVYAEAPEV
                     EKAKRDFPGQPDMWKDAFKPDFSHIKLQLAPQGGFDKNGNTPHGKGVMKTLTTGSLIA
                     RASGLLHERMDEFELQGPTITTFNFDRNRITAFRQLAAENKYGLVDTMKVGNQLKGVK
                     TMEELKQAIRNVTIKRCRIIYGGSTYDLESDGKGKVLVEKVKNTSVQTNNELAGALHH
                     LKHARIRYYVKCAQEAVYSIIQIAGAAFVTTRIARRMNIQELWSKPQLDQNESETKEE
                     APKSEDDEFIISSKDIREEGKKGKNKTGRGKKHTAFSSKGLSDEEYDEYKRIREERNG
                     KYSIEEYLQDRDRYYEELAIAKATEEDFCEEEEIKIRQRIFRPTRKQRKEERATLGLV
                     TGSEIRKRNPDDFKPKGKLWADDNRSVDYNEKLDFEAPPSIWSRIVSFGSGWGFWVSP
                     SLFITSTHVIPAGITEAFGVPIKQIQIHKSGEFCRFRFPKPIRPDVTGMILEEGAPEG
                     TVATVLIKRPTGELMPLAARMGTHATMKIQGRMVGGQMGMLLTGSNAKGMDLGTTPGD
                     CGCPYIYKRGNDYIVIGVHTAAARGGNTVICATQGSEGEATLEGGDDKGTYCGAPILG
                     PGGAPKLSTKTKFWRSSNTPLPPGTYEPAYLGGRDPRVKGGPSLQQVMRDQLKPFTEP
                     RGKPPRPSVLEAAKQTIINVLEQTLDPPQKWTYAQACASLDKTTSSGHPHHVRKNEFW
                     NGETFTGKLADQASKANLMFEEGKHMTPVYTAALKDELVKTEKIYGKIKKRLLWGSDL
                     STMIRCARSFGGLMDEMKAHCISLPVRVGMNMNEDGPIIFEKHSRYKYHYDADYSRWD
                     STQQRAVLAAALEIMVRFSAEPQLTQIVAEDLLAPSVVDVGDFKITINEGLPSGVPCT
                     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="QBS47658.1"
                     /translation="MKMASSDANPSDGSAANLVPEVNNEVMALEPVVGAAIAAPVAGQ
                     QNVIDPWIRNNFVQAPGGEFTVSPRNAPGEILWSAPLGPDLNPYLSHLARMYNGYAGG
                     FEVQVILAGNAFTAGKIIFAAVPPNFPTEGLSPSQVTMFPHIIVDVRQLEPVLIPLPD
                     VRNNFYHYNQSNDSTIKLIAMLYTPLRANNAGDDVFTVSCRVLTRPSPDFDFIFLVPP
                     TVESRTKPFSVPVLTVEEMTNSRFPIPLEKLFTGPSSAFVVQPQNGRCTTDGVLLGTT
                     QLSPVNICTFRGDVTHITGSRNYTMNLASQNWNNYDPTEEIPAPLGTPDFVGKIQGML
                     TQTTRTDGSTRGHKATVYTGSADFAPKLGRVQFETDTDHDFEVNQNTKFTPVGVIQDG
                     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="QBS47659.1"
                     /translation="MAGAFFAGLASDVLGSGLGSLINAGAGAINQKVEFENNRKLQQA
                     SFQFSSNLQQASFQHDKEMLQAQIETTKKLQQEMMKVKQAMLLEGGFSETDAARGAIN
                     APMTKALDWSGTRYWAPDARTTTYNAGRFSTPQPSGALPGRANLRDAVPARGPSNKSS
                     NSSTATSVYSNQTVSTRLGSTAGSGTSVSSLPSTARTRSWVEDQSRNLSPFMRGAHNI
                     SFVTPPSSRSSSQGTVSTVPKEILDSWTGAFNTRRQPLFAHIRKRGESRV"
ORIGIN      
        1 tgaatgaaga tggcgtctaa cgacgctacc gttgccgttg cttgcaacaa caacaacgac
       61 aaggaaaaat cttcaggtga aggcttattc acaaatatgt cttccacctt aaagaaagcc
      121 ctcggggcta ggcccaaaca gcctgccccg agagacgaac cacaaaagcc cccaagacca
      181 ccaactcccg agttggtcaa gaggataccc cctcctccac ctaatggcga agaagaagaa
      241 gaaccagtca ttaggtatga ggttaagagt gggatctctg gcctgcccga gctcacaaca
      301 gtcccccaac cggacgtggc caacacggca ttcagtgttc caccattgag cttgagagaa
      361 aacagggagg ccaaggaacc gctaacaggg gcaatactag agatgtggga tggagagata
      421 taccactatg gcctgtacgt ggagaaaggc ttagtgttgg gtgtgcacaa accacctgca
      481 gccataagca tggcaagagt ggaactgacg ccgctgtcat tgtactggcg tgtggtgtac
      541 actccccaat acctcatctc ccctgaaact ctcaggaggc tcaacggaga ggcgttccct
      601 tacactgcct ttgacaacaa ttgctatgct ttttgctgct gggtgttgga cctcaatgac
      661 tcatggctta gcaggaggat ggtgcaaaga acaacgggct tcttcagacc ttaccaagag
      721 tggaacagaa aacccctgcc taccatggat gactccaaaa ttaagaaggt agcaaatata
      781 ttcctatgtt cattgtccac aatattcacc agacccataa aagacctcat aggaaaaatt
      841 aaaccattaa acatattgaa tgtcctggca acgtgtgact ggacgtttgc cggaatagtg
      901 gagtctctga tattacttgc tgaactcttc ggagttttct ggacaccccc agatgtgtct
      961 gctatgatcg ctcccttact cggggactac gagttgcaag ggccagaaga cctcgccgtt
     1021 gaactcgtac ctgtggtaat gggagggatt ggtttggtgt tgggattcac caaagagaaa
     1081 attggaaaaa tgttgtcctc agcagcatca acactcaggg cttgcaaaga tcttggtgcc
     1141 tatggcttag agatactcaa attggtcatg aagtggttct tcccaaagaa agaggaggcc
     1201 aatgagctag ccatggtgag ggccatagag gatgccgtac tagatcttga ggcaatagaa
     1261 aataatcaca tgacaacctt gttgaaagac aaagacagct tagcaacata catgaaaaca
     1321 ctggacatgg aggaggagaa agccagaagg ttgtccacaa aatctgcatc ccctgacata
     1381 gttgggacaa tcaacgccct gctggctcga atagcagcgg ccaggtcatt agtccatagg
     1441 gccaaggaag agctatctag caggataaga ccagtagttg ttatgatatc tggcaaacca
     1501 ggaataggca aaacccatct 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 tctttgacag tgaagtcata ataattacaa caaaccttgc caacccagcc
     1801 ccacttgatt atgtcaactt tgaggcctgt tccaggagaa ttgacttcct ggtgtacgct
     1861 gaggcaccag aagtagaaaa ggcaaaacgg gactttcctg gtcagccaga tatgtggaag
     1921 gacgccttca aaccggactt ttcacacatc aagctacagc ttgcacctca gggcggcttt
     1981 gacaagaatg gcaacacccc acatgggaaa ggagtgatga agaccctcac taccggctct
     2041 ctgattgccc gtgcatcagg cctactgcat gagaggatgg atgaatttga actccaaggt
     2101 cccacaatca ccaccttcaa tttcgaccgg aacagaatca cagcattcag acaattggct
     2161 gcagaaaaca agtatggatt ggtggatacc atgaaagttg gcaatcaact aaaaggagtg
     2221 aaaaccatgg aagaactcaa acaagcaatc aggaatgtga ccatcaagag gtgccggatc
     2281 atctacggtg gctccacgta tgaccttgaa tctgatggca agggcaaagt tttggtggaa
     2341 aaggtcaaga acacctctgt acagaccaac aacgagttgg ccggggccct gcaccatctc
     2401 aaacacgccc gaatcaggta ctatgtcaaa tgtgcgcaag aagcagtcta ttccattata
     2461 caaattgccg gcgctgcgtt tgtcaccacg cgcattgcac gccgcatgaa catacaagaa
     2521 ctctggtcga agccacaatt agatcaaaat gagtcagaga ctaaggaaga ggcccccaag
     2581 tcagaagatg acgagttcat catatcttct aaggacatca gggaggaagg aaagaagggc
     2641 aaaaacaaga ctggccgtgg caagaaacac actgcattct ccagcaaggg cttgagcgat
     2701 gaggagtatg acgagtacaa gaggataaga gaagagagaa atgggaagta ctctatagag
     2761 gagtatcttc aagacagaga caggtactat gaggagctcg ccattgccaa ggccacggaa
     2821 gaagacttct gtgaagagga ggagatcaaa atccgtcaga gaattttccg tcctaccagg
     2881 aaacaaagaa aggaagagag ggctacatta gggctagtaa caggttcaga aatcagaaaa
     2941 agaaaccctg atgacttcaa acccaaaggg aagctgtggg ccgatgacaa cagaagtgtt
     3001 gactacaatg agaaactgga ctttgaggcc cccccaagca tatggtctag gattgtgagc
     3061 tttggttctg gctggggctt ctgggtatca ccaagcctgt tcataacatc aactcatgta
     3121 atccccgcag gcataacaga agcatttgga gtccccatca aacaaattca gatccacaaa
     3181 tcaggtgaat tttgccgatt cagattccca aaaccaatta gaccagatgt gacaggaatg
     3241 atcttggaag aaggtgcgcc tgaaggcacc gtggcaactg tgctcatcaa acgccccacc
     3301 ggagagctca tgcctcttgc agccagaatg ggaacacacg caaccatgaa aattcaaggc
     3361 cgcatggttg gcggacagat gggtatgttg ctcactggat caaatgctaa aggaatggat
     3421 ttgggaacaa ctcctggtga ctgtggctgc ccttacatct ataaaagggg caatgactat
     3481 atagtcattg gggtgcacac tgcagcagcc cgtggtggga acaccgtcat ctgtgccaca
     3541 cagggaagtg agggtgaggc aactcttgag ggtggagatg acaaaggaac atactgtggg
     3601 gcacccattc taggccctgg gggtgcacca aaattgagca ccaaaaccaa attttggagg
     3661 tcatcgaaca cgccccttcc accagggaca tatgagcctg cctacctcgg tggccgcgat
     3721 ccgcgtgtta agggtgggcc ctccttgcag caggtaatga gagaccagtt gaagccattc
     3781 actgaaccca ggggcaaacc tccaagacca agtgtattgg aagcagccaa acaaaccatt
     3841 atcaatgtcc tcgaacaaac cctggaccct ccacaaaaat ggacatacgc acaggcgtgt
     3901 gcctcacttg acaaaaccac ctccagcggg catccccatc acgtccgaaa gaatgaattc
     3961 tggaatggtg agaccttcac tggtaaattg gcagaccaag catcaaaagc aaacctaatg
     4021 tttgaggaag ggaaacacat gacaccagtg tatacagcag cactcaagga cgagctagtc
     4081 aagactgaga aaatctatgg aaagatcaag aagagactgc tctggggctc tgacttgtcc
     4141 accatgatcc ggtgcgctag gtcatttggt gggctcatgg acgagatgaa ggcacactgc
     4201 atatcactcc cagtacgagt tggcatgaat atgaatgaag atggcccaat aatatttgaa
     4261 aaacattcca gatacaaata ccactatgat gcagactact ctcgttggga ttcaacacaa
     4321 cagagggcag tactagcagc agccttggaa atcatggtca gattctctgc agaaccacaa
     4381 ttgacacaaa tagtcgctga ggatctgctg gcccctagtg tagtagatgt aggagacttt
     4441 aaaatcacaa taaatgaagg gctcccatct ggtgtgccat gcacttctca atggaactcc
     4501 atcgcacact ggctgctaac tctctgtgcc ttgtctgaag tcaccaaact gtcccctgac
     4561 attatacaag caaattccat gttctcattt tacggtgatg acgagattgt cagcaccgac
     4621 ataaaattgg accctgaaca gttaaccgcc aaattgaagg agtacggcct aaaaccaacc
     4681 cgcccagaca agaccgaggg acccctgatc atcagtgaag acttgaacgg actcactttc
     4741 ctccgaagga cggtgactcg tgacccagct ggctggtttg gaaaactgga ccaaagctca
     4801 attttgaggc agatgtactg gactagagga ccaaatcatg aagaccccaa tgagacaatg
     4861 ataccccatt ctcaaagacc tatacagctc atggcactgc ttggtgaagc ctctcttcac
     4921 ggaccctctt tctatagtaa 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 aaattttcca actgaaggct taagtcctag ccaggtcact atgttccccc atataatagt
     5521 agatgttaga caattagaac ctgtgctgat tcccttaccc gatgtcagga ataatttcta
     5581 tcattacaat cagtcaaatg attccactat taagttgata gcaatgttgt atacaccact
     5641 tagggctaat aatgctgggg atgatgtttt cacagtttcg tgccgagttc tcacgaggcc
     5701 atcccccgat tttgatttca tatttttagt gccacccaca gttgagtcaa gaactaaacc
     5761 attctctgtc ccagttttaa ctgttgagga gatgaccaat tcaagattcc ccattccttt
     5821 ggaaaagttg ttcacgggcc ccagcagtgc ctttgttgtt caaccacaaa acggcaggtg
     5881 cacaactgat ggcgtgctcc taggcaccac ccaactgtct cctgtcaaca tctgcacctt
     5941 cagaggggat gtcacccaca tcacaggtag tcgcaactac acaatgaatt tggcttctca
     6001 aaattggaac aactatgacc caacagaaga aatcccagcc cctctaggaa ctccagattt
     6061 tgtggggaag attcaaggca tgctcaccca aaccacaagg acagatggtt caacacgcgg
     6121 ccacaaagct acagtgtaca ctgggagcgc cgactttgct ccaaaactgg gtagagttca
     6181 atttgaaact gacacagacc atgattttga agttaatcaa aacacaaagt tcaccccagt
     6241 cggtgtcatc caagatggta gcaccaccca ccgaaacgaa ccccaacagt gggtgctccc
     6301 aagttactca ggcagaaata ctcacaatgt acatctggcc cccgctgtag cccccacctt
     6361 cccgggtgag caacttctct tcttcagatc caccatgccc ggatgcagcg ggtaccccaa
     6421 catggatttg gactgtctgc tcccccagga atgggtacag tacttctacc aagaggcagc
     6481 cccagcacaa tctgatgtgg ctttgctaag atttgtgaat ccagacacag gtagggtttt
     6541 gtttgagtgc aagcttcaca aatcaggcta tgttacagtg gctcacactg gccaacatga
     6601 tttggttatc ccccccaatg gttactttag gtttgactcc tgggtcaacc 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 agaccaccaa aaagctacaa caggaaatga tgaaagttaa gcaggcaatg
     6961 ctcctagagg gtgggttctc tgagacagat gcagcccgcg gggcaattaa cgcccccatg
     7021 acaaaagctt tggactggag cgggacaagg tactgggctc ccgatgctag gactacaaca
     7081 tacaatgcag gccgcttttc cacccctcaa ccatcggggg cactgccagg aagagctaat
     7141 cttagggatg ctgtccctgc tcggggaccc tccaacaaat cttctaactc ttctactgcc
     7201 acctctgtgt attcaaatca aactgtttca acgagacttg gttctacagc tggttctgga
     7261 accagtgtct cgagcctccc gtcaactgca aggactagga gttgggttga ggatcaaagt
     7321 aggaatttgt cacctttcat gaggggggcc cacaacatat catttgtcac cccaccatct
     7381 agcagatcct ctagccaagg cacagtctca accgtgccta aagagatttt ggactcctgg
     7441 actggcgctt ttaacacgcg caggcagcct ctcttcgctc acattcgtaa gcgaggggag
     7501 tcacgggtgt aatgtgaaaa gacaaaactg att
//