Typing tool

Complete norovirus genomes

MK753032  GII.4 Sydney
 GII.P16

Length: 7,572 | 3 CDS

ORF1: 5..5104
ORF2: 5085..6707
ORF3: 6707..7513
LOCUS       MK753032                7572 bp    RNA     linear   VRL 11-APR-2019
DEFINITION  Norovirus GII isolate Hu/US/2016/GII.P16-GII.4
            Sydney/SanJoaquin0116, complete genome.
ACCESSION   MK753032
VERSION     MK753032.1
KEYWORDS    .
SOURCE      Norovirus GII
  ORGANISM  Norovirus GII
            Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes;
            Picornavirales; Caliciviridae; Norovirus.
REFERENCE   1  (bases 1 to 7572)
  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  JOURNAL   Unpublished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 7572)
  AUTHORS   Barclay,L., Cannon,J.L., Pan,C.-Y., 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..7572
                     /organism="Norovirus GII"
                     /mol_type="genomic RNA"
                     /strain="SanJoaquin0116"
                     /isolate="Hu/US/2016/GII.P16-GII.4 Sydney/SanJoaquin0116"
                     /isolation_source="stool"
                     /host="Homo sapiens"
                     /db_xref="taxon:122929"
                     /country="USA"
                     /collection_date="08-Sep-2016"
                     /note="genotype: GII.P16-GII.4 Sydney"
     gene            5..5104
                     /gene="ORF1"
     CDS             5..5104
                     /gene="ORF1"
                     /codon_start=1
                     /product="nonstructural polyprotein"
                     /protein_id="QBS54666.1"
                     /translation="MKMASNDATVAVACNNNNDKEKSSGEGLFTNMSSTLKKALGARP
                     KQPAPRDEPQKPPRPPTPELVKRIPPPPPNGEEEEEPVIRYDVKSGISGLPELTTVPQ
                     SDVANTAFSVPPLSLRENREAKEPLTGAILEMWDGEIYHYGLYVEKGLVLGVHKPPAA
                     ISMARVELTPLSLYWRVVYTPQYLISPETLRRLNGEAFPYTAFDNNCYAFCCWVLDLN
                     DSWLSRRMVQRTTGFFRPYQEWNRKPLPTMDDSKIKKVANIFLCSLSTLFTRPIKDLI
                     GKIKPLNILNILATCDWTFAGIVESLILLAELFGVFWTPPDVSAMIAPLLGDYELQGP
                     EDLAVELVPVVMGGIGLVLGFTKEKIGKMLSSAASTLRACKDLGAYGLEILKLVMKWF
                     FPKKEEANELAMVRAIEDAVLDLEAIENNHMTTLLKDKDSLATYMKTLDMEEEKARRL
                     STKSASPDIVGTINALLARIAAARSLVHRAKEELSSRIRPVVVMISGKPGIGKTHLAR
                     EVARKVASTLTGDQRVGLIPRNGVDHWDAYKGERVVLWDDYGMSNPIHDALRIQELAD
                     TCPLTLNCDRIENKGKVFDSEVIIITTNLANPAPLDYVNFEACSRRIDFLVYAEAPEV
                     EKAKRDFPGQPDMWKDAFKPDFSHIKLQLAPQGGFDKNGNTPHGKGVMKTLTTGSLIA
                     RASGLLHERMDEFELQGHTITTFNFDRNRITAFRQLAAENKYGLVDTMKVGNQLKGVK
                     TMEELKQAIRNVTIKRCRIIYGGSVYDLESDGKGKVLVEKVKNTSVQTNNELAGALHH
                     LKHARIRYYVKCVQEAVYSIIQIAGAAFVTTRIARRMNIQELWSKPQLDQNESETKEE
                     ALKSEDDEFIISSKDIKEEGKKGKNKTGRGKKHTAFSSKGLSDEEYDEYKRIREERNG
                     KYSIEEYLQDRDRYYEELAIAKATEEDFCEEEEIKIRQRIFRPTRKQRKEERATLGLV
                     TGSEIRKRNPDDFKPKGKLWADDNRSVDYNEKLDFEAPPSIWSRIVSFGSGWGFWVSP
                     SLFITSTHVIPAGITEAFGVPIKQIQIHKSGEFCRFRFPKPIRPDVTGMILEEGAPEG
                     TVATVLIKRPTGELMPLAARMGTHATMKIQGRMVGGQMGMLLTGSNAKGMDLGTTPGD
                     CGCPYIYKRGNDYIVIGVHTAAARGGNTVICATQGSEGEATLEGGDDKGTYCGAPILG
                     PGGAPKLSTKTKFWRSSNTPLPPGTYEPAYLGGRDPRVKGGPSLQQVMRDQLKPFTEP
                     RGKPPRPSVLEAAKQTIINVLEQTLDPPQKWTYSQACASLDKTTSSGHPHHVRKNEFW
                     NGETFTGKLADQASKANLMYEEGKHMTPVYTAALKDELVKTEKIYGKIKKRLLWGSDL
                     STMIRCARSFGGLMDEMKAHCISLPVRVGMNMNEDGPIIFEKHSRYKYHYDADYSRWD
                     STQQRAVLASALEIMVRFSAEPQLAQIVAEDLLAPSVVDVGDFKITINEGLPSGVPCT
                     SQWNSIAHWLLTLCALSEVTKLSPDIIQANSMFSFYGDDEIVSTDIKLDPEQLTAKLK
                     EYGLKPTRPDKTEGPLIISEDLNGLTFLRRTVTRDPAGWFGKLDQSSILRQMYWTRGP
                     NHEDPNETMIPHSQRPIQLMALLGEASLHGPSFYSRISKLVITELKEGGMDFYVPRQE
                     PMFRWMRFSDLSTWEGDRNLAPNFVNEDGVE"
     mat_peptide     5..1000
                     /gene="ORF1"
                     /product="p48"
     mat_peptide     1001..2098
                     /gene="ORF1"
                     /product="NTPase"
     mat_peptide     2099..2629
                     /gene="ORF1"
                     /product="p22"
     mat_peptide     2630..3028
                     /gene="ORF1"
                     /product="VPg"
     mat_peptide     3029..3571
                     /gene="ORF1"
                     /product="Pro"
     mat_peptide     3572..5101
                     /gene="ORF1"
                     /product="RdRp"
     gene            5085..6707
                     /gene="ORF2"
     CDS             5085..6707
                     /gene="ORF2"
                     /note="major capsid protein"
                     /codon_start=1
                     /product="VP1"
                     /protein_id="QBS54667.1"
                     /translation="MKMASSDANPSDGSAANLVPEVNNEVMALEPVVGAAIAAPVAGQ
                     QNVIDPWIRNNFVQAPGGEFTVSPRNAPGEILWSAPLGPDLNPYLSHLARMYNGYAGG
                     FEVQVILAGNAFTAGKIIFAAVPPNFPTEGLSPSQVTMFPHIIVDVRQLEPVLIPLPD
                     VRNNFYHYNQSNDSTIKLIAMLYTPLRANNAGDDVFTVSCRVLTRPSPDFDFIFLVPP
                     TVESRTKPFSVPVLTVEEMTNSRFPIPLEKLFTGPSSAFVVQPQNGRCTTDGVLLGTT
                     QLSPVNICTFRGDVTHITGSRNYTMNLASQNWNNYDPTEEIPAPLGTPDFVGKIQGML
                     TQTTRTDGSTRGHKATVYTGSADFAPKLGRVQFETDTDHDFEANQNTKFTPVGVIQDG
                     STTHRNEPQQWVLPSYSGRNTHNVHLAPAVAPTFPGEQLLFFRSTMPGCSGYPNMDLD
                     CLLPQEWVQYFYQEAAPAQSDVALLRFVNPDTGRVLFECKLHKSGYVTVAHTGQHDLV
                     IPPNGYFRFDSWVNQFYTLAPMGNGTGRRRVV"
     gene            6707..7513
                     /gene="ORF3"
     CDS             6707..7513
                     /gene="ORF3"
                     /note="minor structural protein; small basic protein"
                     /codon_start=1
                     /product="VP2"
                     /protein_id="QBS54668.1"
                     /translation="MAGAFFAGLASDVLGSGLGSLINAGAGAINQKVEFENNRKLQQA
                     SFQFSSNLQQASFQHDKEMLQAQIEATKKLQQEMMKVKQAMLLEGGFSETDAARGAIN
                     APMTKTLDWSGTRYWAPDARITTYNAGHFSTPQPSRALPGRANLRDAVPARGPSNKSS
                     NPSTATSVYSNQTISTRLGSTAGSGTSVSSLPSTARTRSWVEDQNRNLSPFMRGAHNI
                     SFVTPPSSRSSSQGTVSTVSKEILDSWTGAFNTRRQPLFAHIRKRGESRV"
ORIGIN      
        1 gtgaatgaag atggcgtcta acgacgctac cgttgccgtt gcttgcaaca acaacaacga
       61 caaggaaaaa tcttcaggtg aaggcttatt cacaaatatg tcttccacct taaagaaagc
      121 cctcggggct aggcccaaac agcctgcccc gagagacgaa ccacaaaaac ccccaagacc
      181 accaactccc gagttggtca agaggatacc ccctcctcca cctaatggcg aagaagaaga
      241 agaaccagtc attaggtatg atgttaagag tgggatctct ggcctgcccg agctcacaac
      301 agtcccccaa tcggacgtgg ccaacacagc attcagtgtt ccaccactga gcctgagaga
      361 aaacagggag gccaaggaac cgctaacagg ggcaatatta gagatgtggg acggagagat
      421 ataccactat ggcctgtacg tggagaaagg cttagtgttg ggtgtgcaca aaccacctgc
      481 agccataagc atggcaagag tggagctgac gccgctgtca ttgtactggc gtgtggtgta
      541 cactccccaa tacctcatct cccctgaaac tctcaggagg ctcaacggag aggcgttccc
      601 ttacaccgcc ttcgacaaca actgttatgc cttttgctgc tgggtgttag acctcaatga
      661 ctcatggctt agcaggagga tggtgcaaag aacaacgggc ttcttcagac cttaccaaga
      721 gtggaacaga aaacccctgc ctaccatgga tgactccaaa ataaagaagg tagcaaatat
      781 attcctatgt tcattgtcca cattgtttac cagacccata aaagacctca taggaaaaat
      841 caaaccatta aacatattga acatcctggc aacgtgtgac tggacgtttg ccggaatagt
      901 ggagtctctg atattacttg ctgaactctt cggagttttc tggacacccc cagatgtgtc
      961 tgctatgatc gctcccttac tcggggacta cgagttgcaa gggccagaag acctcgccgt
     1021 tgaactcgta cctgtggtaa tgggagggat tggtttggtg ttgggattca ccaaagagaa
     1081 aattggcaaa atgttgtcct cagcagcatc aacactcagg gcttgcaaag atcttggtgc
     1141 ctatggctta gagatactca aattggtcat gaagtggttc ttcccaaaga aagaggaggc
     1201 caatgaacta gccatggtga gggccataga ggatgccgta ctagatcttg aggcaataga
     1261 aaataaccac atgacaaccc tgttgaaaga caaagacagc ttagcaacat acatgaaaac
     1321 actggacatg gaggaggaga aagccagaag gttgtccaca aaatctgcat cccctgacat
     1381 agttggaaca atcaacgccc tgctggctcg aatagcagcg gccaggtcat tagtccacag
     1441 ggccaaggaa gagctatcta gcaggataag accagtagtt gttatgatat ctggcaaacc
     1501 aggaataggt aaaactcatc tggccaggga ggtggcaaga aaagtggcat ccactctcac
     1561 aggggatcaa agagtcggac tcataccaag aaacggtgtg gaccattggg atgcatacaa
     1621 aggtgagaga gtcgtgctgt gggacgacta tggcatgagt aaccccattc atgatgctct
     1681 tcgcatacag gaattggctg atacgtgtcc cctcacctta aattgtgaca gaattgaaaa
     1741 taagggaaaa gtttttgaca gtgaagtcat aataatcaca acaaaccttg ccaacccagc
     1801 cccacttgat tatgtcaact ttgaggcctg ttccaggaga attgatttcc tggtgtacgc
     1861 tgaggcacca gaagtagaaa aggcaaaacg ggactttcct ggtcagccag atatgtggaa
     1921 ggacgccttc aagccggact tttcacacat caagctacag cttgcacctc agggcggctt
     1981 tgacaagaat ggcaacaccc cacatgggaa aggagtgatg aagaccctca ctaccggttc
     2041 tctgattgcc cgtgcatcag gcctactgca tgagaggatg gatgaatttg aactccaagg
     2101 tcacacaatc accaccttca atttcgaccg gaacagaatc acagcattca gacaattggc
     2161 tgcagaaaac aagtatggat tggtggacac catgaaagtt ggcaatcaac taaaaggagt
     2221 gaaaaccatg gaagaactca aacaagcaat caggaatgtg accatcaaga ggtgccggat
     2281 catctatggt ggctccgtgt atgaccttga atctgatggc aagggcaaag ttttggtgga
     2341 aaaggtcaag aacacctctg tacagaccaa caacgagttg gccggggccc tgcaccacct
     2401 caaacacgcc cgaatcaggt actatgtcaa atgtgtgcaa gaagcagtct attccatcat
     2461 acaaattgcc ggcgctgcgt ttgtcaccac gcgcattgca cgccgcatga acatacaaga
     2521 actctggtcg aagccacaat tagatcaaaa tgaatcagag actaaggaag aggccctcaa
     2581 gtcagaagat gacgagttca tcatatcttc taaggacatc aaggaggaag gaaagaaggg
     2641 caaaaacaaa actggtcgtg gtaagaaaca cactgcattc tccagcaagg gcttgagcga
     2701 tgaggagtat gacgagtaca agaggataag agaagagaga aatgggaagt actctataga
     2761 ggagtatctt caagacagag acaggtacta tgaggagcta gccattgcca aggccacgga
     2821 agaagacttc tgtgaagagg aggagatcaa aatccgtcag agaattttcc gtcccaccag
     2881 gaaacaaaga aaggaagaga gggccacatt agggctggta acaggttcag aaatcagaaa
     2941 aagaaaccct gatgacttca aacccaaagg gaagctgtgg gccgatgaca acagaagtgt
     3001 tgactacaat gagaaactgg actttgaggc ccccccaagc atatggtcta ggattgtgag
     3061 ctttggttct ggctggggct tctgggtatc accaagcctg ttcataacat caactcatgt
     3121 aatccccgca ggcataacag aagcatttgg agtccccatc aaacaaattc agatccacaa
     3181 atcaggtgaa ttttgccgat tcagattccc aaaaccaatt agaccagatg tgacaggaat
     3241 gatcttggaa gaaggtgcgc ctgaaggcac cgtggcaact gtgctcatca aacgccccac
     3301 cggggagctc atgcctcttg cagccagaat gggaacacac gcaaccatga aaattcaagg
     3361 ccgcatggtt ggcggacaga tgggtatgtt gctcactgga tcaaatgcta aaggaatgga
     3421 tttgggaaca actcctggtg actgtggctg tccttacatc tataaaaggg gcaatgacta
     3481 tatagtcatt ggggtgcaca ctgcagcagc ccgtggtgga aacaccgtca tctgtgccac
     3541 acagggaagt gagggtgagg caactcttga gggtggagat gacaaaggaa catactgtgg
     3601 ggcacccatt ctaggccctg ggggtgcacc aaaattgagc accaaaacca aattttggag
     3661 gtcatcgaac acgccccttc caccagggac atatgagcct gcctacctcg gtggccgtga
     3721 tccgcgtgtt aagggtgggc cctccttgca gcaggtgatg agagaccagt tgaagccatt
     3781 cactgaaccc aggggcaaac ctccaagacc aagtgtattg gaggcagcca aacaaaccat
     3841 tatcaatgtt ctcgaacaaa ccctggaccc tccacaaaaa tggacatact cacaggcgtg
     3901 tgcctcactt gacaaaacca cctccagcgg gcatccccat cacgtccgaa agaatgaatt
     3961 ctggaatggt gagaccttca ctggtaaatt ggcagaccaa gcatcaaaag caaacctaat
     4021 gtatgaggaa gggaaacaca tgacaccagt gtatacagca gcactcaagg acgagctagt
     4081 caagactgag aaaatctatg gaaagatcaa gaagagactg ctctggggct ctgacttgtc
     4141 cactatgatc cggtgcgcta ggtcatttgg tgggctcatg gacgagatga aggcacactg
     4201 catatcactc ccagtacgag ttggcatgaa tatgaatgaa gatggcccaa taatatttga
     4261 gaaacattcc agatacaaat accactatga tgcagactac tctcgttggg attcaacaca
     4321 acagagggca gtactagcat cagccttgga aatcatggtc agattctctg cagaaccaca
     4381 attggcacaa atagtcgctg aggatctact ggcccctagt gtagtagatg taggagactt
     4441 taaaatcaca ataaatgaag ggctcccatc tggtgtgcca tgcacttctc aatggaactc
     4501 catcgcacac tggctgctaa ctctctgtgc cttgtctgaa gtcaccaaac tgtcccctga
     4561 cattatacaa gcaaattcca tgttctcatt ttacggtgat gacgagattg tcagcaccga
     4621 cataaaattg gaccctgaac agttaaccgc caagctgaag gagtacggcc tgaaaccaac
     4681 ccgcccagac aagaccgagg gacccctgat catcagtgaa gatttgaacg gactcacctt
     4741 cctccgaagg acggtgactc gtgacccagc tggctggttt ggaaaactgg accaaagttc
     4801 aattttgagg cagatgtact ggactagagg accaaatcat gaagacccca atgagacaat
     4861 gataccccac tctcaaagac ccatacagct catggcactg cttggtgaag cctctcttca
     4921 cggaccctct ttctacagta gaattagtaa attggtcata actgaactca aagaaggtgg
     4981 gatggacttt tacgtgccaa ggcaggaacc catgttcagg tggatgaggt tttctgactt
     5041 gagcacgtgg gagggcgatc gcaatctggc tcccaatttt gtgaatgaag atggcgtcga
     5101 gtgacgccaa cccatctgat gggtccgcag ccaacctcgt accagaggtc aacaatgagg
     5161 ttatggcttt ggagcccgtt gttggtgccg ctattgcggc acctgtagcg ggccaacaaa
     5221 atgtaattga cccctggatt agaaataatt ttgtacaagc ccctggtggg gagtttacag
     5281 tatcccctag aaacgctcca ggtgaaatac tatggagcgc gcccctaggc cctgacctaa
     5341 atccctacct atcccatttg gccagaatgt acaatggtta tgcaggtggt tttgaagtgc
     5401 aggtaattct cgcggggaac gcgttcaccg ccgggaagat tatatttgca gctgtcccac
     5461 caaattttcc aactgaaggc ttaagtccta gccaggtcac tatgttcccc catataatag
     5521 tagatgttag acagttagaa cctgtgctga ttcccttacc cgatgttagg aataatttct
     5581 atcattacaa tcagtcaaat gattccacta ttaagttgat agcaatgttg tatacaccac
     5641 ttagggctaa taatgctggg gatgatgttt tcacagtttc gtgccgagtt ctcacgagac
     5701 catcccccga ttttgatttc atatttttag tgccacccac ggttgagtca agaactaaac
     5761 cattctctgt cccagtttta actgttgagg agatgaccaa ttcaagattc cccatccctt
     5821 tggaaaagtt gttcacaggc cccagcagtg cctttgttgt tcaaccacaa aacggcaggt
     5881 gcacaactga tggcgtgctc ctaggcacca cccaactttc tcctgtcaac atctgcacct
     5941 tcagagggga tgtcacccac atcacaggta gtcgcaacta cacaatgaat ttggcttctc
     6001 aaaattggaa caactatgac ccaacagaag aaatcccagc ccctctagga actccagatt
     6061 ttgtggggaa gattcaaggc atgctcaccc aaactacaag gacagatggt tcaacacgcg
     6121 gccacaaagc tacagtgtac actgggagcg ccgactttgc tccaaaactg ggtagagttc
     6181 aatttgaaac tgacacagac catgattttg aagctaatca aaacacaaag ttcaccccag
     6241 tcggtgtcat ccaagatggt agcaccaccc accgaaacga accccaacag tgggtgctcc
     6301 caagttactc aggcagaaat actcacaatg tacatttggc ccccgctgta gcccccactt
     6361 ttccgggtga gcaacttctc ttcttcagat ccaccatgcc cggatgcagc gggtacccca
     6421 acatggattt ggactgtctg ctcccccagg aatgggtgca gtacttctac caagaggcag
     6481 ccccagcaca atctgatgtg gctctgctaa gatttgtgaa tccagacaca ggtagggttt
     6541 tgtttgagtg caagcttcac aaatcaggct acgttacagt ggctcacact ggccaacatg
     6601 atttggtcat tccccccaat ggttacttta ggtttgattc ctgggtcaac cagttctaca
     6661 cgcttgcccc catgggaaat ggaacggggc gtagacgtgt agtataatgg ctggagcttt
     6721 ctttgctgga ttggcatctg atgtccttgg ctctggactt ggttccctta tcaatgctgg
     6781 ggctggggcc atcaaccaaa aagttgagtt tgaaaataac agaaaattgc aacaagcatc
     6841 cttccaattt agcagcaatc tgcaacaggc ttcctttcag catgataaag agatgctcca
     6901 agcacaaatt gaggccacca aaaagctaca acaggaaatg atgaaagtta agcaggcaat
     6961 gctcctagag ggtgggttct ctgagacaga tgcagcccgc ggggcaatta acgcccccat
     7021 gacaaaaact ttggactgga gcgggacaag gtactgggct ccagatgcta ggattacaac
     7081 atacaatgca ggccactttt ccacccctca accatcgagg gcactgccag gaagagctaa
     7141 tcttagggat gctgtccctg ctcggggacc ctccaacaaa tcttctaacc cttctactgc
     7201 cacctctgtg tactcaaatc aaactatttc aacgagactt ggttctacag ctggttctgg
     7261 aaccagtgtc tcgagcctcc cgtcaactgc aaggactagg agctgggttg aggatcaaaa
     7321 taggaatttg tcacctttca tgaggggggc ccacaacata tcatttgtca ccccaccatc
     7381 tagcagatcc tctagccaag gcacagtctc aaccgtgtct aaagagattt tggactcctg
     7441 gactggcgct ttcaacacgc gcaggcagcc tctcttcgct cacattcgta agcgagggga
     7501 gtcacgggtg taatgtgaaa agacaaaact gattatttta ctttttcttt tctttagtgt
     7561 cttttaaaaa aa
//