Typing tool

Complete norovirus genomes

MK762632  GII.4 Sydney
 GII.P16

Length: 7,547 | 3 CDS

ORF1: 5..5101
ORF2: 5082..6704
ORF3: 6704..7510
LOCUS       MK762632                7547 bp    RNA     linear   VRL 13-APR-2019
DEFINITION  Norovirus GII isolate Hu/US/2017/GII.P16-GII.4 Sydney/Natrona0468
            nonstructural polyprotein (ORF1), VP1 (ORF2), and VP2 (ORF3) genes,
            complete cds.
ACCESSION   MK762632
VERSION     MK762632.1
KEYWORDS    .
SOURCE      Norovirus GII
  ORGANISM  Norovirus GII
            Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes;
            Picornavirales; Caliciviridae; Norovirus.
REFERENCE   1  (bases 1 to 7547)
  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  JOURNAL   Unpublished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 7547)
  AUTHORS   Barclay,L., Cannon,J.L., Christensen,R., 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..7547
                     /organism="Norovirus GII"
                     /mol_type="genomic RNA"
                     /strain="Natrona0468"
                     /isolate="Hu/US/2017/GII.P16-GII.4 Sydney/Natrona0468"
                     /isolation_source="stool"
                     /host="Homo sapiens"
                     /db_xref="taxon:122929"
                     /country="USA"
                     /collection_date="28-Dec-2017"
                     /note="genotype: GII.P16-GII.4 Sydney"
     gene            5..5101
                     /gene="ORF1"
     CDS             5..5101
                     /gene="ORF1"
                     /codon_start=1
                     /product="nonstructural polyprotein"
                     /protein_id="QBX91123.1"
                     /translation="MKMASNDATVAVACNNNNDKEKSSGEGLFTNMSSTLKKALGARP
                     KQPAPRDGPQKPPRPPTPELVKRIPPPPPNGEEEEPVIRYEVKSGISGLPELTTVPQP
                     DVANTAFSVPPLSLRENREAKEPLTGAILEMWDGEIYHYGLYVEKGLVLGVHKPPAAI
                     SMARVELMPLSLYWRVVYTPQYLISPETLRRLNGEAFPYTAFDNNCYAFCCWVLDLND
                     SWLSRRMVQRTTGFFRPYQEWNRKPLPTMDDSKIKKVANIFLCSLSTLFTRPIKDLIG
                     KIKPLNILNILATCDWTFAGIVESLILLAELFGVFWTPPDVSAMIAPLLGDYELQGPE
                     DLAVELVPVVMGGIGLVLGFTKEKIGKMLSSAASTLRACKDLGAYGLEILKLVMKWFF
                     PKKEEANELAMVRAIEDAVLDLEAIENNHMTTLLKDKDSLATYMKTLDMEEEKARRLS
                     TKSASPDIVGTINALLARIAAARSLVHRAKEELSSRIRPVVVMISGKPGIGKTHLARE
                     VARKVASTLTGDQRVGLVPRNGVDHWDAYKGERVVLWDDYGMSNPIHDALRIQELADT
                     CPLTLNCDRIENKGKVFDSEVIIITTNLANPAPLDYVNFEACSRRIDFLVYAEAPEVE
                     KAKRDFPGQPDMWKDAFKPDFSHIKLQLAPQGGFDKNGNTPHGKGVMKTLTTGSLIAR
                     ASGLLHERMDEFELQGPTITTFNFDRNRITAFRQLAAENKYGLVDTMKVGNQLKGVKT
                     MEELKQAIRNVTIKRCRIIYGGSTYDLESDGKGKVLVEKVKNTSVQTNNELAGALHHL
                     KHARIRYYVKCVQEAVYSIIQIAGAAFVTTRIARRMNIQELWSKPQLDQNESEAKEEA
                     PKSEDDEFIISSKDIKEEGKKGKNKTGRGKKHTAFSSKGLSDEEYDEYKRIREERNGK
                     YSIEEYLQDRDRYYEELAIAKATEEDFCEEEEIKIRQRIFRPTRKQRKEERATLGLVT
                     GSEIRKRNPDDFKPKGKLWADDNRSVDYNEKLDFEAPPSIWSRIVSFGSGWGFWVSPS
                     LFITSTHVIPAGITEAFGVPIKQIQIHKSGEFCRFRFPKPIRPDVTGMILEEGAPEGT
                     VATVLIKRPTGELMPLAARMGTHATMKIQGRMVGGQMGMLLTGSNAKGMDLGTTPGDC
                     GCPYIYKRGNDYIAIGVHTAAARGGNTVICATQGSEGEATLEGGDDKGTYCGAPILGP
                     GGAPKLSTKTKFWRSSNTPLPPGTYEPAYLGGRDPRVKGGPSLQQVMRDQLKPFTEPR
                     GKPPRPSVLEAAKQTIINVLEQTLDPPQKWTYAQACASLDKTTSSGHPHHVRKNEFWN
                     GETFIGKLADQASKANLMFEEGKHMTPVYTAALKDELVKTEKIYGKIKKRLLWGSDLS
                     TMIRCARSFGGLMDEMKAHCISLPVRVGMNMNEDGPIIFEKHSRYKYHYDADYSRWDS
                     TQQRAVLAAALEIMVRFSAEPQLAQIVAEDLLAPSVVDVGDFKITINEGLPSGVPCTS
                     QWNSIAHWLLTLCALSEVTKLSPDIIQANSMFSFYGDDEIVSTDIKLDPEQLTAKLKE
                     YGLKPTRPDKTEGPLIISEDLNGLTFLRRTVTRDPAGWFGKLDQSSILRQMYWTRGPN
                     HEDPNETMIPHSQRPIQLMALLGEASLHGPSFYSRISKLVITELKEGGMDFYVPRQEP
                     MFRWMRFSDLSTWEGDRNLAPNFVNEDGVE"
     mat_peptide     5..997
                     /gene="ORF1"
                     /product="p48"
     mat_peptide     998..2095
                     /gene="ORF1"
                     /product="NTPase"
     mat_peptide     2096..2626
                     /gene="ORF1"
                     /product="p22"
     mat_peptide     2627..3025
                     /gene="ORF1"
                     /product="VPg"
     mat_peptide     3026..3568
                     /gene="ORF1"
                     /product="Pro"
     mat_peptide     3569..5098
                     /gene="ORF1"
                     /product="RdRp"
     gene            5082..6704
                     /gene="ORF2"
     CDS             5082..6704
                     /gene="ORF2"
                     /note="major capsid protein"
                     /codon_start=1
                     /product="VP1"
                     /protein_id="QBX91124.1"
                     /translation="MKMASSDANPSDGSAANLVPEVNNEVMALEPVVGAAIAAPVAGQ
                     QNVIDPWIRNNFVQAPGGEFTVSPRNAPGEILWSAPLGPDLNPYLSHLARMYNGYAGG
                     FEVQVILAGNAFTAGKIIFAAVPPNFPTEGLSPSQVTMFPHIIVDVRQLEPVLIPLPD
                     VRNNFYHYNQSNDSTIKLIAMLYTPLRANNAGDDVFTVSCRVLTRPSPDFDFIFLVPP
                     TVESRTKPFSVPVLTVEEMTNSRFPIPLEKLFTGPSSAFVVQPQNGRCTTDGVLLGTT
                     QLSPVNICTFRGDVTHITGSRNYTMNLASQNWNNYDPTEEIPAPLGTPDFVGKIQGML
                     TQTTRTDGSTRGHKATVYTGSADFAPKLGRVQFETDTDHDFEANQNTKFTPVGVIQDG
                     STTHRNEPQQWVLPSYSGRNTHNVHLAPAVAPTFPGEQLLFFRSTMPGCSGYPNMDLD
                     CLLPQEWVQYFYQEAAPAQSDVALLRFVNPDTGRVLFECKLHKSGYVTVAHTGQHDLV
                     IPPNGYFRFDSWVNQFYTLAPMGNGTGRRRVV"
     gene            6704..7510
                     /gene="ORF3"
     CDS             6704..7510
                     /gene="ORF3"
                     /note="minor structural protein; small basic protein"
                     /codon_start=1
                     /product="VP2"
                     /protein_id="QBX91125.1"
                     /translation="MAGAFFAGLASDVLGSGLGSLINAGAGAINQKVEFENNRKLQQA
                     SFQFSSNLQQASFQHDKEMLQAQIEATKKLQQEMMKVKQAMLLEGGFSETDAARGAIN
                     APMTKALDWNGTRYWAPDARITTYNAGHFTTPQPSRAPPGRANLRDAVPARGPPNQSS
                     NSSTATSVHSNQTISTRLGSTAGSGTSVSSLPSTARTRSWVEDQNRNLSPFMRGAHNI
                     SFVTPPSSRSSSQGTVSTVPKEILDSWTGAFNTRRQPLFAHIRKRGESRV"
ORIGIN      
        1 gtgaatgaag atggcgtcta acgacgctac cgttgccgtt gcttgcaaca acaacaacga
       61 caaggaaaaa tcttcaggtg aaggcttatt cacaaatatg tcttccacct taaagaaagc
      121 cctcggggct aggcccaaac agcctgcccc gagagacgga ccacaaaagc ccccaagacc
      181 accaactccc gagttggtca agaggatacc ccctcctcca cctaatggcg aagaagaaga
      241 accagtcatt aggtatgagg ttaagagtgg gatctctggc ctgcccgagc tcacaacagt
      301 cccccaaccg gacgtggcca atacagcatt cagcgttcca ccactgagct tgagagaaaa
      361 cagggaggcc aaggaaccgc taacaggggc aatattagag atgtgggacg gagagatata
      421 ccactatggc ctgtacgtgg agaaaggctt agtgttgggt gtgcacaaac cacctgcagc
      481 cataagcatg gcaagagtgg agctgatgcc gttgtcattg tactggcgtg tggtgtacac
      541 tccccaatac ctcatctccc ctgaaactct caggaggctc aacggagagg cgttccctta
      601 cactgccttc gacaacaact gctatgcctt ttgctgctgg gtgttagacc tcaatgactc
      661 atggcttagc aggaggatgg tgcaaagaac aacgggcttc ttcagacctt accaagagtg
      721 gaacagaaaa cccctgccca ccatggatga ctccaaaata aagaaggtag caaatatatt
      781 cctatgttca ttatccacat tattcaccag acccataaaa gacctcatag gaaaaattaa
      841 accattaaac atattgaaca tcctggcaac gtgtgactgg acgtttgccg gaatagtgga
      901 gtctctgata ttacttgctg aactcttcgg agttttctgg acacccccag atgtgtctgc
      961 tatgatcgct cccttactcg gggactacga gttgcaaggg ccagaagacc tcgccgttga
     1021 gctcgtacct gtggtaatgg gagggattgg tttggtgttg ggattcacca aagagaaaat
     1081 tggcaaaatg ttgtcctcag cagcatcaac actcagggct tgtaaagatc ttggtgccta
     1141 tggcttagag atactcaaat tggtcatgaa gtggttcttc ccaaagaaag aggaggccaa
     1201 tgagctagcc atggtgaggg ccatagagga tgccgtacta gatcttgagg caatagaaaa
     1261 taaccacatg acaaccctgt tgaaagacaa agacagctta gcaacataca tgaaaacact
     1321 ggacatggag gaggagaaag ccagaaggtt gtccacaaaa tctgcgtccc ctgacatagt
     1381 tgggacaatc aacgccctgc tggctcgaat agcagcagcc aggtcattag tccacagggc
     1441 caaggaagag ctatctagca ggataagacc agtagttgtt atgatatctg gcaaaccagg
     1501 aataggcaaa acccatctgg ccagggaggt ggcaagaaag gtggcatcca ctcttacagg
     1561 ggatcaaaga gtcggactcg taccaagaaa cggtgtggac cattgggatg catataaagg
     1621 tgagagagtc gtgctgtggg acgactatgg catgagtaac cccattcatg atgctcttcg
     1681 catacaagaa ttggctgata cgtgtcccct taccttaaat tgtgacagaa ttgaaaataa
     1741 gggaaaagtt tttgacagtg aagtcataat aattacaaca aaccttgcca acccagcccc
     1801 acttgattat gtcaattttg aggcctgttc caggagaatt gatttcctgg tgtacgctga
     1861 ggcaccagaa gtagaaaagg caaaacggga ttttcctggt cagccagata tgtggaagga
     1921 cgccttcaag ccggactttt cacacatcaa gctacagctt gcacctcagg gcggctttga
     1981 caagaatggc aacaccccac atgggaaagg ggtgatgaag accctcacta ccggttctct
     2041 gattgcccgt gcatcaggcc tgctgcatga gaggatggat gaatttgaac tccaaggtcc
     2101 cacaatcacc acctttaatt tcgaccggaa cagaatcaca gcattcagac aattggctgc
     2161 agaaaacaag tatggattgg tggacaccat gaaagttggc aatcaactaa aaggagtgaa
     2221 aaccatggaa gaactcaaac aagcaatcag gaatgtgacc atcaagaggt gccggatcat
     2281 ctacggtggc tccacgtatg accttgaatc tgatggcaag ggcaaagttt tggtggaaaa
     2341 ggtcaagaac acctctgtac agaccaacaa cgagttggcc ggggccctgc accatctcaa
     2401 acatgcccga atcaggtact atgtcaaatg tgtgcaagaa gcagtctatt ccatcataca
     2461 aattgccggc gctgcttttg tcaccacgcg cattgcacgc cgcatgaaca tacaagaact
     2521 ctggtcgaag ccacaattag atcaaaatga atcagaggct aaggaagagg cccccaagtc
     2581 agaagatgac gagttcatca tatcttctaa ggacatcaag gaggaaggaa agaagggcaa
     2641 aaacaaaact ggccgtggca agaaacacac tgcattctcc agcaagggct tgagcgatga
     2701 ggagtatgac gagtacaaga gaataagaga agagagaaat gggaagtact ctatagagga
     2761 gtatcttcaa gacagagaca ggtactacga ggagcttgcc attgccaagg ccacggaaga
     2821 agacttctgt gaagaggagg agatcaaaat ccgtcaaaga attttccgtc ccaccaggaa
     2881 acaaagaaag gaagagaggg ccacattagg gctggtaaca ggttcagaaa tcagaaaaag
     2941 aaaccctgat gacttcaaac ccaaagggaa gctgtgggcc gatgacaaca gaagtgttga
     3001 ctacaatgag aaactggact ttgaggcccc cccaagcata tggtctagga ttgtaagctt
     3061 tggttctggc tggggcttct gggtgtcacc aagcctgttc ataacatcaa ctcatgtaat
     3121 ccccgcaggc ataacagaag catttggagt ccccatcaaa caaattcaga tccacaaatc
     3181 aggtgaattt tgccggttca gattcccaaa gccgattaga ccagatgtga caggaatgat
     3241 cttggaagag ggtgcgcctg agggcaccgt ggcaactgtg ctcatcaaac gccccaccgg
     3301 agagctcatg cctcttgcag ccagaatggg aacacatgca accatgaaaa ttcaaggccg
     3361 catggttggc gggcagatgg gtatgttgct cactggatca aatgctaaag gaatggattt
     3421 gggaacaact cctggtgact gtggctgccc ttacatctat aaaaggggca atgactatat
     3481 agccattggg gtgcacactg cagcggcccg tggtggaaac accgtcatct gtgccacaca
     3541 gggaagtgag ggtgaggcaa ctcttgaggg tggagatgac aaaggaacat actgtggggc
     3601 acccatttta ggccctgggg gtgcaccaaa attgagcacc aaaaccaaat tttggaggtc
     3661 atcgaacacg ccccttccac cagggacata tgaacctgcc tacctcggtg gccgtgatcc
     3721 gcgtgttaaa ggtgggccct ccttgcagca ggtaatgaga gaccagttga agccattcac
     3781 tgaacccagg ggcaaacctc caagaccaag tgtattggaa gcagccaaac aaaccattat
     3841 caatgttctc gaacaaaccc tggaccctcc acaaaaatgg acatacgcac aggcgtgtgc
     3901 ctcacttgac aaaaccacct ccagcgggca tccccatcac gtccgaaaga atgaattctg
     3961 gaatggtgag accttcattg gtaaattggc agaccaagca tcaaaagcaa acctaatgtt
     4021 tgaggaaggg aaacacatga caccagtgta tacagcagca ctcaaggacg agctagtcaa
     4081 aactgagaaa atctatggaa agatcaagaa aagactgctc tggggctctg acttgtccac
     4141 catgatccgg tgcgctaggt catttggtgg gctcatggac gagatgaagg cacactgtat
     4201 atcactccca gtacgagttg gcatgaatat gaatgaagat ggcccaataa tatttgagaa
     4261 acattccagg tacaaatacc actatgatgc agactactct cgttgggatt caacacaaca
     4321 gagggcagta ttagcagcag ccttggaaat catggtcaga ttctctgcag aaccacaatt
     4381 ggcacaaata gtcgctgagg atctactggc ccctagtgta gtagatgtag gagactttaa
     4441 aatcacaata aatgaagggc tcccatctgg tgtgccatgc acttctcaat ggaactccat
     4501 cgcacactgg ctgctaactc tctgtgcctt gtctgaagtc accaaactgt cccctgacat
     4561 tatacaagca aattccatgt tctcatttta cggtgatgac gagattgtca gcaccgacat
     4621 aaaattggat cctgaacagt taaccgccaa gttgaaggag tacggcctga aaccaacccg
     4681 cccagacaag accgagggac ctctaatcat cagtgaagat ttgaacggac tcactttcct
     4741 ccgaaggacg gtaactcgtg acccagctgg ctggtttgga aaactggacc aaagttcaat
     4801 tttgaggcag atgtactgga ctagaggacc aaatcatgaa gatcccaatg agacgatgat
     4861 accccactct caaagaccca tacagctcat ggcattactt ggtgaagcct ctcttcacgg
     4921 accctctttc tacagtagaa tcagtaaatt ggtcataact gaactcaaag aaggtgggat
     4981 ggacttttac gtgccaaggc aggaacccat gttcaggtgg atgaggtttt ctgacttgag
     5041 cacgtgggag ggcgatcgca atctggctcc caattttgtg aatgaagatg gcgtcgagtg
     5101 acgccaaccc atctgatggg tccgcagcca acctcgtacc agaggtcaac aatgaggtta
     5161 tggctttgga gcccgttgtt ggtgccgcta ttgcggcacc tgtagcgggc caacaaaatg
     5221 tgattgaccc ctggattaga aataattttg tacaagcccc tggtggggag tttacagtgt
     5281 cccctagaaa cgctccaggt gaaatactat ggagcgcgcc cctaggccct gacctaaacc
     5341 cctacctatc ccatttggcc agaatgtaca atggttatgc aggtggtttt gaagtgcagg
     5401 taattctcgc ggggaacgcg ttcaccgccg gaaagattat atttgcagca gtcccaccaa
     5461 attttccaac tgaaggctta agtcctagcc aggtcactat gttcccccat ataatagtag
     5521 atgttagaca attagaacct gtgctgattc ccttacccga tgttaggaat aatttctatc
     5581 attataatca gtcaaatgat tccactatta agttgatagc aatgttgtat acaccactta
     5641 gggctaataa tgctggagat gatgttttca cggtttcgtg ccgagttctc acgagaccat
     5701 cccccgattt tgatttcata tttttagtgc cacccacagt tgagtcaaga actaaaccat
     5761 tctctgtccc agttttaact gttgaggaga tgaccaattc aagattcccc atccctttgg
     5821 aaaagttgtt cacaggcccc agcagtgcct ttgttgttca accacaaaac ggcaggtgca
     5881 caactgatgg cgtgctctta ggcaccaccc aactttctcc tgtcaacatc tgcaccttca
     5941 gaggggatgt cacccacatc acaggtagtc gcaactacac aatgaatttg gcttctcaaa
     6001 attggaataa ctatgaccca acagaagaaa tcccagcccc tctaggaacc ccagattttg
     6061 tggggaagat tcaaggcatg ctcacccaaa ccacaaggac agatggttca acacgcggcc
     6121 acaaagctac agtgtacact gggagcgccg actttgctcc aaaactgggt agagttcaat
     6181 ttgaaactga cacagaccat gattttgagg ctaatcaaaa cacaaagttc accccagtcg
     6241 gtgtcatcca agatggtagc accacccacc gaaacgaacc tcaacagtgg gtgctcccaa
     6301 gttactcagg cagaaacact cacaatgtac atttggcccc cgctgtagcc cccacctttc
     6361 cgggtgagca acttctcttc ttcaggtcca ccatgcccgg atgcagcggg taccccaaca
     6421 tggatttgga ctgtctgctc ccccaggaat gggtgcagta cttctaccaa gaggcagccc
     6481 cagcacaatc tgatgtggct ctgctaagat ttgtgaaccc agacacaggt agggttttgt
     6541 ttgagtgcaa gcttcacaaa tcaggctatg ttacagtggc tcacactggc caacatgatt
     6601 tggttatccc ccccaatggt tactttagat ttgattcctg ggtcaaccag ttctacacgc
     6661 ttgcccccat gggaaatgga acggggcgta gacgtgtagt ataatggctg gagctttctt
     6721 tgcaggattg gcatctgacg tccttggctc tggacttggt tcccttatca atgctggggc
     6781 tggggccatc aaccaaaaag ttgaatttga aaataacaga aaattacaac aagcatcctt
     6841 ccaatttagc agcaatctgc aacaggcttc ctttcaacat gataaagaga tgctccaagc
     6901 acaaattgag gccaccaaaa agctacaaca ggaaatgatg aaagttaagc aggcaatgct
     6961 cctagagggt gggttctctg agacagatgc agcccgcggg gcaattaacg cccccatgac
     7021 aaaagctttg gactggaacg ggacaaggta ctgggctcca gatgctagga ttacaacata
     7081 caatgcaggc cactttacca cccctcaacc atcgagggca ccgccaggaa gagctaatct
     7141 tagggatgct gtcccagctc ggggaccccc caaccaatct tctaactctt ctactgccac
     7201 ctctgtgcac tcaaatcaaa ctatttcaac gagacttggt tctacagctg gttctgggac
     7261 cagtgtctcg agcctcccgt caactgcaag gactaggagc tgggttgagg atcaaaatag
     7321 gaatttgtca cctttcatga ggggggccca caacatatca tttgtcaccc caccatctag
     7381 cagatcctct agccaaggca cagtctcaac cgtgcctaaa gagattttgg actcctggac
     7441 tggcgctttc aacacgcgca ggcagcctct cttcgctcac attcgtaagc gaggggagtc
     7501 acgggtgtaa tgtgaaaaga caaaactgat tatttttctt tttcttt
//