Typing tool

Complete norovirus genomes

KY947549  GII.4 Sydney
 GII.P16

Length: 7,530 | 3 CDS

ORF1: 4..5103
ORF2: 5084..6706
ORF3: 6706..7512
LOCUS       KY947549                7530 bp ss-RNA     linear   VRL 18-MAY-2017
DEFINITION  Norovirus GII strain Hu/USA/2016/GII.P16-GII.4 Sydney/CS4243
            polyprotein, VP1, and VP2 genes, complete cds.
ACCESSION   KY947549
VERSION     KY947549.1
KEYWORDS    .
SOURCE      Norovirus GII
  ORGANISM  Norovirus GII
            Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes;
            Picornavirales; Caliciviridae; Norovirus.
REFERENCE   1  (bases 1 to 7530)
  AUTHORS   Cannon,J.L., Barclay,L., Collins,N.R., Wikswo,M.E., Castro,C.J.,
            Magana,L.C., Gregoricus,N., Marine,R.L., Chhabra,P. and Vinje,J.
  TITLE     Genetic and Epidemiologic Trends of Norovirus Outbreaks in the US
            Demonstrated Emergence of Novel GII.4 Recombinant Viruses,
            2013-2016
  JOURNAL   J. Clin. Microbiol. (2017) In press
   PUBMED   28490488
  REMARK    Publication Status: Available-Online prior to print
REFERENCE   2  (bases 1 to 7530)
  AUTHORS   Cannon,J.L., Barclay,L., Collins,N.R., Chhabra,P., Wikswo,M.E.,
            Castro,C.J., Magana,L.C., Gregoricus,N. and Vinje,J.
  TITLE     Direct Submission
  JOURNAL   Submitted (14-APR-2017) Viral Gastroenteritis Branch/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. 8
            Sequencing Technology :: Illumina
            ##Assembly-Data-END##
FEATURES             Location/Qualifiers
     source          1..7530
                     /organism="Norovirus GII"
                     /mol_type="genomic RNA"
                     /strain="Hu/USA/2016/GII.P16-GII.4 Sydney/CS4243"
                     /isolation_source="stool"
                     /host="Homo sapiens"
                     /db_xref="taxon:122929"
                     /country="USA"
                     /collection_date="24-Mar-2016"
                     /note="genotype: GII.P16-GII.4 Sydney"
     5'UTR           1..3
     CDS             4..5103
                     /note="nonstructural protein; ORF1"
                     /codon_start=1
                     /product="polyprotein"
                     /protein_id="ARR95963.1"
                     /translation="MKMASNDATVAVACNNNNDKEKSSGEGLFTNMSSTLKKALGARP
                     KQPAPRDEPQKPPRPPTPELVKRIPPPPPNGEEEEEPVIRYEVKSGISGLPELTTVPQ
                     PDVANTAFSVPPLSLRENREAKEPLTGAILEMWDGEIYHYGLYVEKGLVLGVHKPPAA
                     ISMARVELTPLSLYWRVVYTPQYLISPETLRRLNGEAFPYTAFDNNCYAFCCWVLDLN
                     DSWLSRRMVQRTTGFFRPYQEWNRKPLPTMDDSKIKKVANIFLCSLSTLFTRPIKDLI
                     GKIKPLNILNILATCDWTFAGIVESLILLAELFGVFWTPPDVSAMIAPLLGDYELQGP
                     EDLAVELVPVVMGGIGLVLGFTKEKIGKMLSSAASTLRACKDLGAYGLEILKLVMKWF
                     FPKKEEANELAMVRAIEDAVLDLEAIENNHMTTLLKDKDSLATYMKTLDMEEEKARRL
                     STKSASPDIVGTINALLARIAAARSLVHRAKEELSSRIRPVVVMISGKPGIGKTHLAR
                     EVARKVASTLTGDQRVGLIPRNGVDHWDAYKGERVVLWDDYGMSNPIHDALRIQELAD
                     TCPLTLNCDRIENKGKVFDSEVIIITTNLANPAPLDYVNFEACSRRIDFLVYAEAPEV
                     EKAKRDFPGQPDMWKDAFKPDFSHIKLQLAPQGGFDKNGNTPHGKGVMKTLTTGSLIA
                     RASGLLHERMDEFELQGPTITTFNFDRNRITAFRQLAAENKYGLVDTMKVGNQLKGVK
                     TMEELKQAIRNVTIKRCRIIYGGSTYDLESDGKGKVLVEKVKNTSVQTNNELAGALHH
                     LKHARIRYYVKCVQEAVYSIIQIAGAAFVTTRIARRMNIQELWSKPQLDQNESETKEE
                     APKSEDDEFIISSKDIKEEGKKGKNKTGRGKKHTAFSSKGLSDEEYDEYKRIREERNG
                     KYSIEEYLQDRDRYYEELAIAKATEEDFCEEEEIKIRQRIFRPTRKQRKEERATLGLV
                     TGSEIRKRNPDDFKPKGKLWADDNRSVDYNEKLDFEAPPSIWSRIVSFGSGWGFWVSP
                     SLFITSTHVIPAGITEAFGVPIKQIQIHKSGEFCRFRFPKPIRPDVTGMILEEGAPEG
                     TVATVLIKRPTGELMPLAARMGTHATMKIQGRMVGGQMGMLLTGSNAKGMDLGTTPGD
                     CGCPYIYKRGNDYIAIGVHTAAARGGNTVICATQGSEGEATLEGGDDKGTYCGAPILG
                     PGGAPKLSTKTKFWRSSNTPLPPGTYEPAYLGGRDPRVKGGPSLQQVMRDQLKPFTEP
                     RGKPPRPSVLEAAKQTIINVLEQTLDPPQKWTYAQACASLDKTTSSGHPHHVRKNEFW
                     NGETFTGKLADQASKANLMFEEGKHMTPVYTAALKDELVKTEKIYGKIKKRLLWGSDL
                     STMIRCARSFGGLMDEMKAHCISLPVRVGMNMNEDGPIIFEKHSRYKYHYDADYSRWD
                     STQQRAVLAAALEIMVRFSAEPQLAQIVAEDLLAPSVVDVGDFKITINEGLPSGVPCT
                     SQWNSIAHWLLTLCALSEVTKLSPDIIQANSMFSFYGDDEIVSTDIKLDPEQLTAKLK
                     EYGLKPTRPDKTEGPLIISEDLNGLTFLRRTVTRDPAGWFGKLDQSSILRQMYWTRGP
                     NHEDPNETMIPHSQRPIQLMALLGEASLHGPSFYSKISKLVITELKEGGMDFYVPRQE
                     PMFRWMRFSDLSTWEGDRNLAPNFVNEDGVE"
     CDS             5084..6706
                     /note="major capsid protein; ORF2"
                     /codon_start=1
                     /product="VP1"
                     /protein_id="ARR95964.1"
                     /translation="MKMASNDANPSDGSAANLVPEVNNEVMALEPVVGAAIAAPVAGQ
                     QNVIDPWIRNNFVQAPGGEFTVSPRNAPGEILWSAPLGPDLNPYLSHLARMYNGYAGG
                     FEVQVILAGNAFTAGKIIFAAVPPNFPTEGLSPSQVTMFPHIIVDVRQLEPVLIPLPD
                     VRNNFYHYNQSNDSTIKLIAMLYTPLRANNAGDDVFTVSCRVLTRPSPDFDFIFLVPP
                     TVESRTKPFSVPVLTVEEMTNSRFPIPLEKLFTGPSSAFVVQPQNGRCTTDGVLLGTT
                     QLSPVNICTFRGDVTHITGSRNYTMNLASQNWNNYDPTEEIPAPLGTPDFVGKIQGML
                     TQTTRTDGSTRGHKATVYTGSADFAPKLGRVQFETDTDHDFEANQNTKFTPVGVIQDG
                     STTHRNEPQQWVLPSYSGRNAHNVHLAPAVAPTFPGEQLLFFRSTMPGCSGYPNMDLD
                     CLLPQEWVQYFYQEAAPAQSDVALLRFVNPDTGRVLFECKLHKSGYVTVAHTGQHDLV
                     IPPNGYFRFDSWVNQFYTLAPMGNGTGRRRAV"
     CDS             6706..7512
                     /note="minor structural protein; ORF3"
                     /codon_start=1
                     /product="VP2"
                     /protein_id="ARR95965.1"
                     /translation="MAGAFFAGLASDVLGSGLGSLINAGAGAINQKVEFENNRKLQQA
                     SFQFSSNLQQASFQHDKEMLQAQIEATKKLQQEMMKVKQAMLLEGGFSETDAARGAIN
                     APMTKVLDWSGTRYWAPDARTTTYNAGRFSTPQPSGTLPGRANLRDAVPARGPSNKSS
                     NSSTATSVYSNQTISTRLGSTAGSGTSVSSLPSTARTRSWVEDQSRNLSPFMRGAHNI
                     SFVTPPSSRSSSQGTVSTVPKEILDSWTGAFNTRRQPLFAHIRRRGESRV"
     3'UTR           7513..7530
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 caacacagca ttcagtgttc caccactgag cttgagagaa
      361 aacagggagg ccaaagaacc gctaacaggg gcaatattag agatgtggga tggagagata
      421 taccactatg gcctgtacgt ggagaaaggc ttagtgttgg gtgtgcacaa accacctgca
      481 gccataagca tggcaagagt ggagttgacg ccgctgtcat tgtactggcg tgtggtgtac
      541 actccccaat acctcatctc ccctgaaact ctcaggaggc tcaacggaga ggcgttccct
      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 aggaaagatt
      841 aaaccattaa acatattgaa catcctggca acgtgtgact ggacgtttgc cggaatagtg
      901 gagtctctga tattacttgc tgaactcttc ggagttttct ggacaccccc agatgtgtct
      961 gctatgatcg ctcccttact cggggactac gaattgcaag ggccagaaga cctcgccgtt
     1021 gaactcgtac ctgtggtaat gggagggatt ggtttggtgt tgggattcac caaagagaaa
     1081 attggcaaaa tgttgtcctc agcagcatca acactcaggg cttgcaaaga tcttggtgcc
     1141 tatggcttag agatactcaa attggtcatg aagtggttct tcccaaagaa agaggaggcc
     1201 aatgagctag ccatggtgag ggccatagag gatgccgtac tagatcttga ggcaatagaa
     1261 aataaccaca tgacaaccct gttgaaagac aaagacagct tagcaacata catgaaaaca
     1321 ctggacatgg aagaggagaa agccagaagg ttgtccacaa aatctgcatc ccctgacata
     1381 gttgggacaa tcaacgccct gctggctcga atagcagcgg ccaggtcatt agtccacagg
     1441 gccaaggaag agctgtctag caggataaga ccagtagttg ttatgatatc tggcaaacca
     1501 ggaataggca aaactcatct ggccagggag gtggcaagaa aggtggcatc cactctcaca
     1561 ggggatcaaa gagtcggact cataccaaga aacggtgtgg accattggga tgcatacaaa
     1621 ggtgagagag tcgtgctgtg ggacgactat ggcatgagta accccattca tgatgctctt
     1681 cgcatacaag aattggctga cacgtgtccc cttaccttaa attgtgacag aattgaaaat
     1741 aagggaaaag tttttgacag tgaggtcata ataatcacaa caaaccttgc caatccagcc
     1801 ccacttgatt atgtcaactt tgaggcctgt tccaggagaa ttgattttct ggtgtacgct
     1861 gaggcaccag aagtagaaaa ggcaaaacgg gactttcctg gtcagccaga tatgtggaag
     1921 gacgccttca agccggactt ctcacacatc aagctacagc ttgcacctca gggcggcttt
     1981 gacaagaatg gcaacactcc acatgggaag ggagtgatga agaccctcac taccggttct
     2041 ctgattgccc gcgcgtcagg cctactgcat gagaggatgg atgaatttga actccaaggt
     2101 cccacaatca ccaccttcaa tttcgaccgg aacagaatca cagcattcag gcaattggct
     2161 gcggaaaaca agtatggatt ggtggatacc atgaaagttg gcaatcaact aaaaggagtg
     2221 aaaaccatgg aagaactcaa acaagcaatc aggaatgtga ccatcaagag gtgccggatc
     2281 atctacggtg gctccacgta tgaccttgaa tctgatggca agggcaaagt tttggtggaa
     2341 aaggtcaaga acacctctgt acagaccaac aacgagctgg ctggggccct gcaccatctc
     2401 aaacacgccc gaatcaggta ctatgtcaaa tgtgtgcaag aagcagtcta ttccatcata
     2461 caaattgccg gcgctgcgtt tgtcaccacg cgcattgcgc gccgcatgaa catacaggaa
     2521 ctctggtcga agccacaatt agatcaaaat gaatcagaga ctaaggaaga ggcccccaag
     2581 tcagaagatg acgagttcat catatcttct aaggacatca aggaggaagg aaagaagggc
     2641 aaaaacaaga ctggccgtgg caagaaacac actgcattct ccagcaaggg cttgagcgat
     2701 gaggagtacg acgagtacaa gaggataaga gaagagagaa atgggaagta ctctatagag
     2761 gagtatcttc aagacagaga caggtactat gaggagctcg ccattgccaa ggccacggaa
     2821 gaagacttct gtgaagagga ggagatcaaa atccgtcaga gaattttccg tcccaccagg
     2881 aaacaaagaa aggaagagag ggccacatta 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 gattcacaaa
     3181 tcaggtgaat tttgccgatt cagattccca aaaccaatta gaccagatgt gacaggaatg
     3241 atcttagaag aaggtgcgcc tgaaggcacc gtagcaactg tgcttatcaa acgccccacc
     3301 ggagagctca tgcctcttgc agccagaatg ggaacacacg caaccatgaa aattcaaggc
     3361 cgcatggttg gcggacagat gggtatgttg ctcactggat caaatgctaa aggaatggat
     3421 ttgggaacaa ctcctggtga ctgtggctgt ccttacatct ataaaagggg caatgactat
     3481 atagccattg gggtgcacac tgcagcagcc cgtggtggaa acaccgtcat ctgtgccaca
     3541 cagggaagtg agggtgaggc aactcttgag ggtggagatg acaaaggaac atactgtggg
     3601 gcacctattc taggccctgg gggtgcacca aaattgagca ccaaaaccaa attttggagg
     3661 tcatcgaaca cgccccttcc accagggaca tatgagcctg cctacctcgg tggccgtgat
     3721 ccgcgtgtta agggtgggcc ctccttgcag caggtaatga gagaccagtt aaagccattc
     3781 actgaaccca ggggcaaacc tccaagacca agtgtattgg aagcagccaa acaaaccatt
     3841 atcaacgtcc tcgaacaaac cctggaccct ccacaaaaat ggacatacgc acaggcgtgt
     3901 gcatcacttg acaaaaccac ctccagcggg catccccatc acgtccgaaa gaatgaattc
     3961 tggaatggtg agaccttcac tggcaaattg gcagaccaag catcaaaagc aaacctaatg
     4021 tttgaggaag ggaaacacat gacaccagtg tatacagcag cactcaagga cgagctagtc
     4081 aagactgaga aaatctatgg aaagatcaag aagagactgc tctggggctc tgacttgtcc
     4141 accatgatcc ggtgcgctag gtcatttggt gggctcatgg acgagatgaa ggcgcactgc
     4201 atatcactcc cagtacgagt tggcatgaat atgaatgaag atggcccaat aatatttgag
     4261 aaacattcca gatacaaata ccactatgat gcagactact ctcgttggga ttcaacacaa
     4321 cagagggcag tgctagcagc agccttggaa atcatggtca gattctctgc agaaccacaa
     4381 ttggcacaaa 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 gaaaccaacc
     4681 cgcccagaca agaccgaggg acccctgatt atcagtgaag atttgaacgg actcactttc
     4741 ctccgaagga cggtgactcg tgacccagct ggctggtttg gaaaactgga ccaaagctca
     4801 attttgaggc agatgtactg gactagagga ccaaatcatg aagaccccaa tgagacaatg
     4861 ataccccatt ctcaaagacc catacagctc atggcactgc ttggtgaagc ctctcttcac
     4921 ggaccctctt tctacagtaa aatcagtaaa ttggtcataa ctgaactcaa agaaggtggg
     4981 atggactttt acgtgccaag gcaggaaccc atgttcagat ggatgaggtt ttctgacttg
     5041 agcacgtggg agggcgatcg caatctggct cccaattttg tgaatgaaga tggcgtcgaa
     5101 tgacgccaac ccatctgatg ggtccgcagc caacctcgta ccagaggtca acaatgaggt
     5161 tatggctttg gagcccgttg ttggtgccgc tattgcggca cctgtagcgg gccaacaaaa
     5221 tgtaattgac ccctggatta gaaataattt tgtacaagcc cctggtgggg agtttacagt
     5281 atcccccaga aacgctccag gtgaaatact atggagcgcg cccctaggcc ctgacctaaa
     5341 tccctaccta tcccatttgg ccagaatgta caatggttat gcaggtggtt ttgaagtgca
     5401 ggtaattctc gcggggaacg cgttcactgc cgggaagatc atatttgcag cagtcccacc
     5461 aaattttcca actgaaggct taagtcctag ccaggtcact atgttccccc atataatagt
     5521 ggatgttaga caattagaac ctgtgctgat tcccttaccc gatgtcagga ataatttcta
     5581 tcattataac cagtcaaatg attccactat taagttgata gcaatgttgt atacaccact
     5641 tagggctaat aatgctgggg atgatgtttt cacagtttcg tgccgagttc tcacgagacc
     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 ccaattgtct cctgtcaata 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 agctaatcaa aacacaaagt tcaccccagt
     6241 cggtgtcatc caagatggta gcaccaccca tcgaaacgaa ccccaacagt gggtgctccc
     6301 aagttactca ggcagaaatg ctcacaatgt acatctggcc cctgctgtag cccccacctt
     6361 cccgggtgag caacttctct tcttcagatc caccatgccc ggatgcagcg ggtaccccaa
     6421 catggatttg gactgtctgc ttccccagga atgggtgcag tacttctacc aagaggcagc
     6481 cccagcacaa tctgatgtgg ctctgctaag atttgtgaac ccagacacag gtagggtttt
     6541 gtttgagtgc aagcttcaca aatcaggcta tgttacagtg gctcacactg gccaacatga
     6601 tttggttatc ccccccaatg gttactttag gtttgattcc tgggtcaacc agttctacac
     6661 gcttgccccc atgggaaatg gaacggggcg tagacgtgca gtataatggc tggtgctttc
     6721 tttgctggat tggcatccga tgtccttggc tctggacttg gttcccttat caatgctggg
     6781 gctggggcca tcaaccaaaa agttgagttt gaaaataaca gaaaattgca acaagcatcc
     6841 ttccaattta gcagcaatct gcaacaggct tcctttcaac atgataaaga gatgctccaa
     6901 gcacaaattg aggccaccaa aaagctacaa caggaaatga tgaaagttaa gcaggcaatg
     6961 ctcctagagg gtgggttctc tgagacagat gcagcccgcg gggcaattaa cgcccccatg
     7021 acaaaagttt tggactggag cgggacaagg tactgggctc ccgatgctag gactacaaca
     7081 tacaatgcag gtcgcttttc cacccctcaa ccatcgggga cactgccagg aagagctaat
     7141 cttagggatg ctgtccctgc tcggggaccc tccaacaaat cttctaactc ttctactgcc
     7201 acctctgtgt actcaaatca aactatctca acgagacttg gttctacagc tggttctgga
     7261 accagtgtct cgagcctccc gtcaactgca aggactagga gctgggttga ggatcaaagt
     7321 aggaatttgt cacctttcat gaggggggcc cacaacatat catttgtcac cccaccatct
     7381 agcagatcct ctagccaagg cacagtctca accgtgccta aagagatttt ggactcctgg
     7441 actggcgctt tcaacacgcg caggcagcct ctcttcgctc acattcgtag gcgaggggag
     7501 tcacgggtgt aatgtgaaaa gacaaaactg
//