Typing tool

Complete norovirus genomes

MK764016  GII.4 Sydney
 GII.P16

Length: 7,555 | 3 CDS

ORF1: 5..5104
ORF2: 5085..6707
ORF3: 6707..7513
LOCUS       MK764016                7555 bp    RNA     linear   VRL 13-APR-2019
DEFINITION  Norovirus GII isolate Hu/US/2018/GII.P16-GII.4 Sydney/Bay0244,
            complete genome.
ACCESSION   MK764016
VERSION     MK764016.1
KEYWORDS    .
SOURCE      Norovirus GII
  ORGANISM  Norovirus GII
            Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes;
            Picornavirales; Caliciviridae; Norovirus.
REFERENCE   1  (bases 1 to 7555)
  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  JOURNAL   Unpublished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 7555)
  AUTHORS   Barclay,L., Cannon,J.L., Mosher,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..7555
                     /organism="Norovirus GII"
                     /mol_type="genomic RNA"
                     /strain="Bay0244"
                     /isolate="Hu/US/2018/GII.P16-GII.4 Sydney/Bay0244"
                     /isolation_source="stool"
                     /host="Homo sapiens"
                     /db_xref="taxon:122929"
                     /country="USA"
                     /collection_date="06-Feb-2018"
                     /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="QBX92727.1"
                     /translation="MKMASNDATVVVACNNNNDKEKSSGEGLFTNMSSTLKKALGARP
                     KQPAPRDKSQKPPRPPTPELVKRIPPPPPNGEEEEEPVIRYEVKSGISGLPELTTVPQ
                     PDVANTAFSVPPLSLRENREAKEPLTGAILEMWDGEIYHYGLYVEKGLVLGVHKPPAA
                     ISMARVELTPLSLYWRVVYTPQYLISPETLRRLNGEAFPYTAFDNNCYAFCCWVLDLN
                     DSWLSRRMVQRTTGFFRPYQEWNRKPLPTMDDSKIKKVANIFLCSLSTLFTRPIKDLI
                     GKIKPLNILNILATCDWTFAGIVESLILLAELFGVFWTPPDVSAMIAPLLGDYELQGP
                     EDLAVELVPVVMGGIGLVLGFTKEKIGKMLSSAASTLRACKDLGAYGLEILKLVMKWF
                     FPKKEEANELAMVRAIEDAVLDLEAIENNHMTTLLKDKDSLATYMKTLDMEEEKARRL
                     STKSASPDIVGTINALLARIAAARSLVHRAKEELSSRIRPVVVMISGKPGIGKTHLAR
                     EVARKVASTLTGDQRVGLIPRNGVDHWDAYKGERVVLWDDYGMSNPIHDALRIQELAD
                     TCPLTLNCDRIENKGKVFDSEVIIITTNLANPAPLDYVNFEACSRRIDFLVYAEAPEV
                     EKAKRDFPGQPDMWKDAFKSDFSHIKLQLAPQGGFDKNGNTPHGKGVMKTLTTGSLIA
                     RASGLLHERMDEFELQGPTITTFNFDRNKITAFRQLAAENKYGLVDTMKVGNQLKGVK
                     TMEELKQAIRNVTIKRCRIIYGGSTYDLESDGKGKVLVEKVKNTSVQTNNELAGALHH
                     LKHARIRYYVKCVQEAVYSIIQIAGAAFVTTRIARRMNIQELWSKPQLDQNESETKEE
                     APKSEDDEFIISSKDIKEEGKKGKNKTGRGKKHTAFSSKGLSDEEYDEYKRIREERNG
                     KYSIEEYLQDRDRYYEELAIAKATEEDFCEEEEIKIRQRIFRPTRKQRKEERATLGLV
                     TGSEIRKRNPDDFKPKGKLWADDNRSVDYNEKLDFEAPPSIWSRIVSFGSGWGFWVSP
                     SLFITSTHVIPAGITEAFGVPIKQIQIHKSGEFCRFRFPKPIRPDVTGMILEEGAPEG
                     TVATVLIKRPTGELMPLAARMGTHATMKIQGRMVGGQMGMLLTGSNAKGMDLGTTPGD
                     CGCPYIYKRGNDYIVIGVHTAAARGGNTVICATQGSEGEATLEGGDDKGTYCGAPILG
                     PGGAPKLSTKTKFWRSSNTPLPPGTYEPAYLGGRDPRVKGGPSLQQVMRDQLKPFTEP
                     RGKPPRPSVLEAAKQTIINVLEQTLDPPQKWTYAQACASLDKTTSSGHPYHVRKNEFW
                     NGETFTSKLADQASKANLMFEEGKHMTPVYTAALKDELVKTEKIYGKIKKRLLWGSDL
                     STMIRCARSFGGLMDEMKAHCISLPVRVGMNMNEDGPIIFEKHSRYKYHYDADYSRWD
                     STQQRAVLAAALEIMVRFSAEPQLAQIVAEDLLAPSVVDVGDFKITINEGLPSGVPCT
                     SQWNSIAHWLLTLCALSEVTKLSPDIIQANSMFSFYGDDEIVSTDIKLDPEQLTAKLK
                     EYGLKPTRPDKTEGPLIISEDLNGLTFLRRTVTRDPAGWFGKLDQSSILRQMYWTRGP
                     NHEDPNETMIPHSQRPIQLMALLGEASLHGPSFYSKISKLVIAELKEGGMDFYVPRQE
                     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="QBX92728.1"
                     /translation="MKMASSDANPSDGSAANLVPEVNNEVMALEPVVGAAIAAPVAGQ
                     QNVIDPWIRNNFVQAPGGEFTVSPRNAPGEILWSAPLGPDLNPYLSHLARMYNGYAGG
                     FEVQVILAGNAFTAGKIIFAAVPPNFPTEGLSPSQVTMFPHIIVDVRQLEPVLIPLPD
                     VRNNFYHYNQSNDSTIKLIAMLYTPLRANNAGDDVFTVSCRVLTRPSPDFDFIFLVPP
                     TVESRTKPFSVPVLTVEEMTNSRFPIPLEKLFTGPSSAFVVQPQNGRCTTDGVLLGTT
                     QLSPVNICTFRGDVTHITGSHNYTMNLASQNWNNYDPTEEIPAPLGAPDFVGKIQGML
                     TQTTRTDGSTRGHKATVYTGSADFAPKLGRVQFETDTNHDFEANQNTKFTPVGVIQDG
                     STTHRNEPQQWVLPSYSGRSTHNVHLAPAVAPTFPGEQLLFFRSTMPGCSGYPNMDLD
                     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="QBX92729.1"
                     /translation="MAGAFFAGLASDVLGSGLGSLINAGAGAINQKVEFENNRKLQQA
                     SFQFSSNLQQASFQHDKEMLQAQIEATKKLQQEMMKVKQAMLLEGGFSETDAARGAIN
                     APMTKALDWSGTRYWAPDARTTTYNAGRFSTPQSSGALPGRTNLRDAVPARGPPSKSS
                     NSSTATSVYSNQTASTRLGSTAGSGTSVSSLPSTARTRSWVEDQSRNLSPFVRGAHNI
                     SFVTPPSSRSSSQGTVSTVPKEILDSWTGAFNTRRQPLFAHIRRRGESRV"
ORIGIN      
        1 gtgaatgaag atggcgtcta acgacgctac cgttgtcgtt gcttgcaaca acaacaacga
       61 caaggaaaaa tcttcaggtg aaggcttatt cacaaatatg tcttccacct taaagaaagc
      121 cctcggggct aggcccaaac agcctgcccc gagagacaaa tcacaaaagc ccccaagacc
      181 accaactccc gagttggtca agaggatacc ccctcctcca cctaatggcg aagaagaaga
      241 agaaccagtc attaggtatg aggttaagag tgggatctct ggcctgcccg agctcacaac
      301 agtcccccaa ccggacgtgg ccaacacagc attcagcgtt ccaccactga gcttgagaga
      361 aaacagggag gccaaggaac cgctaacagg ggcaatatta gagatgtggg atggagagat
      421 ataccactac ggcctgtacg tggagaaagg cttagtgttg ggtgtgcaca aaccacctgc
      481 agccataagc atggcaagag tagagctgac gccgctgtca ttgtactggc gtgtagtgta
      541 cactccccaa tacctcatct cccctgaaac tctcaggagg ctcaacggag aggcattccc
      601 ttacaccgcc tttgacaaca actgctatgc cttttgctgc tgggtgttag acctcaatga
      661 ctcatggctt agcaggagga tggtgcaaag aacaacgggc ttcttcagac cttaccaaga
      721 gtggaacaga aaacccctgc ccaccatgga tgactccaaa atcaagaagg tagcaaatat
      781 attcctatgt tcattgtcca cattattcac cagacccata aaagacctca taggaaaaat
      841 caaaccatta aacatattga atatcctggc aacgtgtgac tggacgtttg ccggaatagt
      901 ggagtctctg atattgcttg ctgaactctt cggagttttc tggacacccc cagatgtgtc
      961 tgctatgatc gctcccttac tcggggacta cgagttgcaa gggccagaag acctcgccgt
     1021 tgaactcgtg cctgtggtaa tgggagggat tggtttggtg ttgggattca ccaaagagaa
     1081 aattggcaaa atgttgtcct cagcagcatc aacactcagg gcttgcaaag atcttggtgc
     1141 ctatggctta gagatactca aattggtcat gaagtggttc ttcccgaaga aagaggaggc
     1201 caatgagcta gccatggtga gggccataga ggatgctgta ctagatcttg aggcaataga
     1261 aaataaccac atgacaaccc tgttgaaaga caaagacagc ttagcaacat acatgaaaac
     1321 actggacatg gaggaggaga aagccagaag gttgtccaca aaatctgcat cccctgacat
     1381 agttgggaca atcaacgccc tgttggctcg aatagcagcg gccaggtcac tagtccacag
     1441 ggccaaggaa gagctatcta gcaggataag accagtagtt gttatgatat ctggcaaacc
     1501 aggaatagga aaaactcatc tggccaggga ggtggcaaga aaggtggcat ccactctcac
     1561 aggggatcaa agagtcggac tcataccaag aaacggtgtc gaccattggg atgcatacaa
     1621 aggtgagaga gtcgtgctgt gggacgacta tggcatgagt aaccccattc atgatgctct
     1681 tcgcatacaa gagttggctg atacgtgtcc ccttacctta aattgtgaca gaattgaaaa
     1741 taagggaaaa gtttttgaca gtgaagtcat aataattaca acaaaccttg ccaatccagc
     1801 cccacttgat tatgtcaact ttgaggcctg ttccaggaga attgatttcc tggtgtacgc
     1861 tgaggcacca gaagtagaaa aggcaaaacg ggactttcct ggtcagccag atatgtggaa
     1921 ggacgccttc aagtcggact tttcacacat caagctacag cttgcaccac agggcggctt
     1981 tgataagaat ggcaacaccc cacatgggaa aggagtgatg aagaccctca ccaccggttc
     2041 tctgattgcc cgcgcatcag gcctactgca cgagaggatg gatgaatttg agctccaagg
     2101 tcccacaatc accaccttca acttcgaccg gaacaaaatc acagcattca gacaattggc
     2161 tgcagaaaac aagtatggat tggtggatac catgaaagtt ggcaatcaac taaaaggagt
     2221 gaaaaccatg gaagaactca aacaagcaat caggaatgtg accattaaga ggtgccggat
     2281 catctacggt ggttccacgt atgaccttga atctgatggc aagggcaaag ttctggtgga
     2341 aaaggtcaag aacacctctg tacagaccaa caacgagttg gccggggccc tgcaccatct
     2401 caaacacgcc cgaatcaggt actatgtcaa atgtgtgcaa gaagcagtct attccatcat
     2461 acagattgcc ggcgctgcgt ttgtcaccac gcgcattgca cgccgcatga acatacaaga
     2521 actctggtcg aagccacaat tagatcaaaa tgaatcagag actaaggaag aggcccccaa
     2581 gtcagaagat gacgagttca tcatatcttc taaggacatc aaggaagaag gaaagaaggg
     2641 caaaaacaaa actggccgtg gcaagaaaca cactgcattc tccagcaagg gcttgagcga
     2701 tgaggagtat gacgagtaca agagaataag agaagagaga aatgggaagt actctataga
     2761 ggagtatctt caagacagag acaggtacta tgaggagctc gccattgcca aagccacgga
     2821 agaagacttc tgtgaagagg aggagatcaa aatccgtcag agaattttcc gtcccaccag
     2881 gaaacaacga aaggaagaga gggccacatt agggctagta acaggttcag aaatcagaaa
     2941 aagaaaccct gatgacttca aacccaaagg aaagctgtgg gccgatgaca acagaagtgt
     3001 tgactataat gagaaactgg actttgaggc ccctccaagc atatggtcta ggattgtgag
     3061 ctttggttct ggctggggct tctgggtatc accaagcctg ttcataacat caactcatgt
     3121 aatccccgca ggcataacag aagcatttgg ggttcccatt aaacaaattc agatccacaa
     3181 atcaggtgaa ttttgccgat tcagattccc aaaaccaatt agaccagatg tgacaggaat
     3241 gatcttggaa gaaggtgcgc ctgagggcac cgtggcaact gtgctcatca aacgccccac
     3301 cggagagctc atgcctcttg cagctagaat gggaactcac gcaaccatga aaattcaagg
     3361 ccgcatggtt ggcggacaga tgggtatgtt gctcactgga tcaaatgcta aaggaatgga
     3421 tttaggaaca actcctggtg actgtggctg tccttacatc tataaaaggg gcaatgacta
     3481 catagtcatt ggggtgcaca ctgcagcagc ccgtggtgga aacaccgtca tctgcgccac
     3541 acagggaagt gagggtgagg caactcttga aggtggagat 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 aagtgtatta gaagcagcca aacaaaccat
     3841 catcaatgtc ctcgaacaaa ccctggaccc tccacaaaaa tggacatatg cacaggcgtg
     3901 tgcctcactt gacaaaacca cctccagcgg gcatccctat cacgtccgaa agaacgaatt
     3961 ctggaatggt gagaccttca ctagtaaatt ggcagaccaa gcatcaaaag caaacctaat
     4021 gtttgaggaa gggaaacaca tgacaccagt gtatacagca gcactcaagg acgagctagt
     4081 caagactgag aaaatctatg gaaagatcaa gaagagactg ctctggggct ctgacttgtc
     4141 caccatgatc cgatgcgcta ggtcatttgg tgggctcatg gacgagatga aggcacactg
     4201 catatcactc ccagtccgag tcggcatgaa tatgaatgaa gatggtccaa taatatttga
     4261 gaaacattcc agatacaaat atcactatga tgcagactac tctcgttggg attcaacaca
     4321 acagagggca gtactagcag cagccttgga aatcatggtc agattctctg cagaaccaca
     4381 attggcacaa atagtcgctg aggatctgct agcccccagt gtagtagatg tgggagactt
     4441 taaaataaca ataaatgaag ggctcccctc tggtgtgcca tgtacttctc aatggaactc
     4501 catcgcacat tggctgctaa ctctatgtgc cttgtctgaa gtcaccaaac tgtcccctga
     4561 cattatacag gcaaattcca tgttctcatt ttacggtgat gacgagattg tcagcaccga
     4621 cataaaactg gaccctgaac agctaaccgc taaattaaag gagtacggcc tgaaaccaac
     4681 ccgcccagac aaaaccgagg gacccctgat catcagtgaa gatttaaacg gactcacttt
     4741 cctccggagg acggtgactc gtgacccagc tggctggttt ggaaaactgg accaaagctc
     4801 aattttgagg cagatgtact ggactagagg accaaatcat gaagacccca atgagacaat
     4861 gataccccat tctcaaagac ccatacagct catggcactg cttggtgaag cctctcttca
     4921 cggaccctct ttttacagta aaattagcaa attggtcata gctgaactca 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 ccctggtgga gagtttacag
     5281 tgtcccctag aaacgctcca ggtgaaatac tatggagcgc gcccctaggc cctgacctaa
     5341 atccctacct atcccatctg gccagaatgt acaatggtta tgcaggtggt tttgaagtgc
     5401 aggtaatcct cgcggggaac gcgttcaccg ccgggaagat catatttgca gcagtcccac
     5461 caaattttcc aactgaaggc ttaagtccta gccaggtcac tatgttcccc catataatag
     5521 tagatgttag acaattagaa cctgtgctga ttcccttacc cgatgtcagg aataatttct
     5581 atcattataa tcaatcaaat gactccacta ttaagttgat agcaatgttg tatacaccac
     5641 ttagggctaa caatgctggg gacgatgtct tcacagtttc gtgccgagtt ctcacgagac
     5701 catcccccga ctttgatttc atattcttag tgccacccac agttgagtca agaactaaac
     5761 cattctctgt cccagtcttg accgttgagg agatgaccaa ttcaagattt cccattcctt
     5821 tggaaaagtt gttcacgggc cccagcagtg cctttgttgt tcaaccacaa aacggcaggt
     5881 gcacaactga tggcgtgctc ctaggcacca cacaactgtc tcctgtcaac atctgcacct
     5941 tcagagggga tgtcacccac atcacaggta gtcacaacta cacgatgaat ttggcttctc
     6001 aaaattggaa caactatgac ccaacagaag aaatcccagc ccctctagga gctccagatt
     6061 ttgtggggaa gattcaaggc atgctcaccc aaaccacaag gacagatggt tcaacgcgcg
     6121 gccacaaagc tacagtgtac actgggagcg ccgactttgc tccaaaattg ggtagagttc
     6181 aatttgaaac tgacacaaac catgattttg aagccaacca aaacacaaag ttcaccccag
     6241 tcggtgtcat ccaagatggt agcaccaccc accgaaatga accccaacag tgggtgctcc
     6301 caagttactc aggcagaagc actcacaatg tacatctggc ccccgctgta gctcccacct
     6361 ttccgggtga acaacttctc ttctttagat ccaccatgcc cggatgcagc gggtacccca
     6421 acatggattt ggactgtctg ctcccccagg aatgggtgca gtacttctac caagaggcag
     6481 ccccagcaca atctgatgtg gctttgctaa gatttgtgaa tccagacaca ggtagggttt
     6541 tgtttgaatg caagcttcac aaatcaggct atgttacagt ggctcacact ggccaacatg
     6601 atttggttat cccccccaat ggttacttta ggtttgattc ctgggtcaac cagttctaca
     6661 cacttgcccc catgggaaat ggaacggggc gtagacgtgt agtataatgg ctggagcttt
     6721 ctttgctgga ttggcgtctg atgtcctcgg ctctggactt ggttccctta tcaatgctgg
     6781 ggctggggcc atcaaccaaa aagttgagtt cgaaaacaac agaaaattgc aacaagcatc
     6841 cttccaattt agcagcaatc tgcaacaggc ttcctttcaa catgacaaag agatgctcca
     6901 agcacaaatt gaggccacca aaaagctaca acaggaaatg atgaaggtta agcaggcaat
     6961 gctcctagag ggtgggttct ctgagacaga tgcagcccgc ggggcaatta acgcccccat
     7021 gacaaaagct ctagactgga gcgggacaag gtactgggct cccgatgcta ggactacaac
     7081 atacaacgca ggccgctttt ccacccctca atcatcgggg gcactgccag gaagaactaa
     7141 tcttagggac gctgttcctg ctcggggacc ccccagtaaa tcttctaact cttctactgc
     7201 cacctctgtg tactcaaatc aaactgcttc aacgagactt ggttctacag ctggttctgg
     7261 aaccagtgtt tcgagcctcc cgtcgactgc aaggactagg agctgggttg aggaccaaag
     7321 taggaatttg tcacctttcg tgaggggggc ccacaacata tcatttgtca ccccaccatc
     7381 tagtaggtcc tctagccaag gcacagtctc aaccgtgcct aaagagattt tggactcctg
     7441 gactggcgct ttcaacacgc gcaggcagcc tctcttcgct cacattcgta ggcgagggga
     7501 gtcacgggtg taatgtgaaa agacaaaatt gattatcttt ctttttcttt tgtgt
//