Typing tool

Complete norovirus genomes

MK756035  GII.4 Sydney
 GII.P16

Length: 7,511 | 3 CDS

ORF1: 3..5102
ORF2: 5083..6705
ORF3: 6705..7511
LOCUS       MK756035                7511 bp    RNA     linear   VRL 11-APR-2019
DEFINITION  Norovirus GII isolate Hu/US/2016/GII.P16-GII.4 Sydney/Alameda0787
            nonstructural polyprotein (ORF1), VP1 (ORF2), and VP2 (ORF3) genes,
            complete cds.
ACCESSION   MK756035
VERSION     MK756035.1
KEYWORDS    .
SOURCE      Norovirus GII
  ORGANISM  Norovirus GII
            Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes;
            Picornavirales; Caliciviridae; Norovirus.
REFERENCE   1  (bases 1 to 7511)
  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  JOURNAL   Unpublished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 7511)
  AUTHORS   Barclay,L., Cannon,J.L., Johnston,S.H., 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..7511
                     /organism="Norovirus GII"
                     /mol_type="genomic RNA"
                     /strain="Alameda0787"
                     /isolate="Hu/US/2016/GII.P16-GII.4 Sydney/Alameda0787"
                     /isolation_source="stool"
                     /host="Homo sapiens"
                     /db_xref="taxon:122929"
                     /country="USA"
                     /collection_date="02-May-2016"
                     /note="genotype: GII.P16-GII.4 Sydney"
     gene            3..5102
                     /gene="ORF1"
     CDS             3..5102
                     /gene="ORF1"
                     /codon_start=1
                     /product="nonstructural polyprotein"
                     /protein_id="QBW96059.1"
                     /translation="MKMASNDATVAVACNNNNDKEKSSGEGLFTNMSSTLKKALGARP
                     KQPAPRDEPQKPPRPPTPELVKRIPPPPPNGEEEEEPVIRYEVKSGISGLPELTTVPQ
                     PDVANTAFSVPPLSLRENREAKEPLTGAILEMWDGEIYHYGLYVEKGLVLGVHKPPAA
                     ISMARVELTPLSLYWRVVYTPQYLISPETLRRLNGEAFPYTAFDNNCYAFCCWVLDLN
                     DSWLSRRMVQRTTGFFRPYQEWNRKPLPTMDDSKIKKVANIFLCSLSTLFTRPIKDLI
                     GKIKPLNILNILATCDWTFAGIVESLILLAELFGVFWTPPDVSAMIAPLLGDYELQGP
                     EDLAVELVPVVMGGIGLVLGFTKEKIGKMLSSAASTLRACKDLGAYGLEILKLVMKWF
                     FPKKEEANELAMVRAIEDAVLDLEAIENNHMTTLLKDKDSLATYMKTLDMEEEKARRL
                     STKSASPDIVGTINALLARIAAARSLVHRAKEELSSRIRPVVVMISGKPGIGKTHLAR
                     EVARKVASTLTGDQRVGLIPRNGVDHWDAYKGERVVLWDDYGMSNPIHDALRIQELAD
                     TCPLTLNCDRIENKGKVFDSEVIIITTNLANPAPLDYVNFEACSRRIDFLVYAEAPEV
                     EKAKRDFPGQPDMWKDAFKPDFSHIKLQLAPQGGFDKNGNTPHGKGVMKTLTTGSLIA
                     RASGLLHERMDEFELQGPTITTFNFDRNRITAFRQLAAENKYGLVDTMKVGNQLKGVK
                     TMEELKQAIRNVTIKRCRIIYGGSTYDLESDGKGKVLVEKVKNTSVQTNNELAGALHH
                     LKHARIRYYVKCVQEAVYSIIQIAGAAFVTTRIARRMNIQELWSKPQLDQNESETKEE
                     APKSEDDEFIISSKDIKEEGKKGKNKTGRGKKHTAFSSKGLSDEEYDEYKRIREERNG
                     KYSIEEYLQDRDRYYEELAIAKATEEDFCEEEEIKIRQRIFRPTRKQRKEERATLGLV
                     TGSEIRKRNPDDFKPKGRLWADDNRSVDYNEKLDFEAPPSIWSRIVSFGSGWGFWVSP
                     SLFITSTHVIPAGITEAFGVPIKQIQIHKSGEFCRFRFPKPIRPDVTGMILEEGAPEG
                     TVATVLIKRPTGELMPLAARMGTHATMKIQGRMVGGQMGMLLTGSNAKGMDLGTTPGD
                     CGCPYIYKRGNDYIAIGVHTAAARGGNTVICATQGSEGEATLEGGDDKGTYCGAPILG
                     PGGAPKLSTKTKFWRSSNTPLPPGTYEPAYLGGRDPRVKGGPSLQQVMRDQLKPFTEP
                     RGKPPRPSVLEAAKQTIINVLEQTLDPPQKWTYAQACASLDKTTSSGHPHHVRKNEFW
                     NGETFTGKLADQASKANLMFEEGKHMTPVYTAALKDELVKTEKIYRKIKKRLLWGSDL
                     STMIRCARSFGGLMDEMKAHCISLPVRVGMNMNEDGPIIFEKHSRYKYHYDADYSRWD
                     STQQRAVLAAALEIMVRFSAEPQLAQIVAEDLLAPSVVDVGDFKITINEGLPSGVPCT
                     SQWNSIAHWLLTLCALSEVTKLSPDIIQANSMFSFYGDDEIVSTDIKLDPEQLTAKLK
                     EYGLKPTRPDKTEGPLIISEDLNGLTFLRRTVTRDPAGWFGKLDQSSILRQMYWTRGP
                     NHEDPNETMIPHSQRPIQLMALLGEASLHGPSFYSKISKLVITELKEGGMDFYVPRQE
                     PMFRWMRFSDLSTWEGDRNLAPNFVNEDGVE"
     mat_peptide     3..998
                     /gene="ORF1"
                     /product="p48"
     mat_peptide     999..2096
                     /gene="ORF1"
                     /product="NTPase"
     mat_peptide     2097..2627
                     /gene="ORF1"
                     /product="p22"
     mat_peptide     2628..3026
                     /gene="ORF1"
                     /product="VPg"
     mat_peptide     3027..3569
                     /gene="ORF1"
                     /product="Pro"
     mat_peptide     3570..5099
                     /gene="ORF1"
                     /product="RdRp"
     gene            5083..6705
                     /gene="ORF2"
     CDS             5083..6705
                     /gene="ORF2"
                     /note="major capsid protein"
                     /codon_start=1
                     /product="VP1"
                     /protein_id="QBW96060.1"
                     /translation="MKMASNDANPSDGSAANLVPEVNNEVMALEPVVGAAIAAPVAGQ
                     QNVIDPWIRNNFVQAPGGEFTVSPRNAPGEILWSAPLGPDLNPYLSHLARMYNGYAGG
                     FEVQVILAGNAFTAGKIIFAAVPPNFPTEGLSPSQVTMFPHIIVDVRQLEPVLIPLPD
                     VRNNFYHYNQSNDSTIKLIAMLYTPLRANNAGDDVFTVSCRVLTRPSPDFDFIFLVPP
                     TVESRTKPFSVPVLTVEEMTNSRFPIPLEKLFTGPSSAFVVQPQNGRCTTDGVLLGTT
                     QLSPVNICTFRGDVTHITGSRNYTMNLASQNWNNYDPTEEIPAPLGTPDFVGKIQGML
                     TQTTRTDGSTRGHKATVYTGSADFAPKLGRVQFETDTDHDFEANQNTKFTPVGVIQDG
                     STTHRNEPQQWVLPSYSGRNTHNVHLAPAVAPTFPGEQLLFFRSTMPGCSGYPNMDLD
                     CLLPQEWVQYFYQEAAPAQSDVALLRFVNPDTGRVLFECKLHKSGYVTVAHTGQHDLV
                     IPPNGYFRFDSWVNQFYTLAPMGNGTGRRRAV"
     gene            6705..7511
                     /gene="ORF3"
     CDS             6705..7511
                     /gene="ORF3"
                     /note="minor structural protein; small basic protein"
                     /codon_start=1
                     /product="VP2"
                     /protein_id="QBW96061.1"
                     /translation="MAGAFFAGLASDVLGSGLGSLINAGAGAINQKVEFENNRKLQQA
                     SFQFSSNLQQASFQHDKEMLQAQIEATKKLQQEMMKVKQAMLLEGGYSETDAARGAIN
                     APMTKALDWSGTRYWAPDARTTTYNAGRFSTPQPSGTLPGRANLRDAVPARGPSNKSS
                     NSSTATSVYSNQTISTRLGSTAGSGTSVSSLPSTARTRSWVEDQNRNLSPFMRGAHNI
                     SFVTPPSSRPSSQGTVSTVPKEILDSWTGAFNTRRQPLFAHIRRRGESRV"
ORIGIN      
        1 gaatgaagat ggcgtctaac gacgctaccg ttgccgttgc ttgcaacaac aacaacgaca
       61 aggaaaaatc ttcaggtgaa ggcttattca caaatatgtc ttccacctta aagaaagccc
      121 tcggggctag gcccaaacag cctgccccga gagacgaacc acaaaagccc ccaagaccac
      181 caactcccga gttggtcaag aggatacccc ctcctccacc taatggcgaa gaagaagaag
      241 aaccagtcat taggtatgag gtcaagagtg ggatctctgg cctgcccgag ctcacaacag
      301 tcccccaacc ggacgtggcc aacacagcat tcagtgttcc accactgagc ttgagagaaa
      361 acagggaggc caaagaaccg ctaacagggg caatattaga gatgtgggat ggagagatat
      421 accactatgg cctgtacgtg gagaaaggct tagtgttggg tgtgcacaaa ccacctgcag
      481 ccataagcat ggcaagagtg gagttgacgc cgctgtcatt gtactggcgt gtggtgtaca
      541 ctccccagta cctcatctcc cctgaaactc tcaggaggct caacggagag gcgttccctt
      601 acaccgcctt tgacaacaac tgctatgcct tttgctgctg ggtgttagac ctcaatgact
      661 catggcttag caggaggatg gtgcaaagaa caacgggctt cttcagacct taccaagagt
      721 ggaacagaaa acccctgcct accatggatg actccaaaat taagaaggta gcaaatatat
      781 tcctatgttc attgtccaca ttattcacca gacccataaa agacctcata ggaaagatta
      841 aaccattaaa catattgaac atcctggcaa cgtgtgactg gacgtttgcc ggaatagtgg
      901 agtctctgat attacttgct gaactcttcg gagttttctg gacaccccca gatgtgtctg
      961 ctatgatcgc tcccttactc ggggactacg aattgcaagg gccagaagac ctcgccgttg
     1021 aactcgtacc tgtggtaatg ggagggattg gtttggtgtt gggattcacc aaagagaaaa
     1081 ttggcaaaat gttgtcctca gcagcatcaa cactcagggc ttgcaaagat cttggtgcct
     1141 atggcttaga gatactcaaa ttggtcatga agtggttctt cccaaagaaa gaggaggcca
     1201 atgagctagc catggtgagg gccatagagg atgccgtact agatcttgag gcaatagaaa
     1261 ataaccacat gacaaccctg ttgaaagaca aagacagctt ggcaacatac atgaaaacac
     1321 tggacatgga ggaggagaaa gccagaaggt tgtccacaaa atctgcatcc cctgacatag
     1381 ttgggacaat caacgccctg ctggctcgaa tagcagcggc caggtcatta gtccacaggg
     1441 ccaaggaaga gctgtctagc aggataagac cagtagttgt tatgatatct ggcaaaccag
     1501 gaataggcaa aactcatctg gccagggagg tagcaagaaa ggtggcatcc actctcacag
     1561 gggatcaaag agtcggactc ataccaagaa acggtgtgga ccattgggat gcatacaaag
     1621 gtgagagagt cgtgctgtgg gacgactatg gcatgagtaa ccccattcat gatgctcttc
     1681 gcatacaaga attggctgac acgtgtcccc ttaccttaaa ttgtgacaga attgaaaata
     1741 agggaaaagt ttttgacagt gaggtcataa taatcacaac aaaccttgcc aatccagccc
     1801 cacttgatta tgtcaacttt gaggcctgtt ccaggagaat tgattttctg gtgtacgctg
     1861 aagcaccaga agtagaaaag gcaaaacggg actttcctgg tcagccagat atgtggaagg
     1921 acgccttcaa gccggacttc tcacacatca agctacagct tgcacctcag ggcggctttg
     1981 acaagaatgg caacacccca catgggaagg gagtgatgaa gaccctcact accggttctc
     2041 tgattgcccg cgcatcaggc ctactgcatg agaggatgga tgaatttgaa ctccaaggtc
     2101 ccacaatcac caccttcaat ttcgaccgga acagaatcac agcattcaga caattggctg
     2161 cggaaaacaa gtatggattg gtggatacca tgaaagttgg caatcaacta aaaggagtga
     2221 aaaccatgga agaactcaaa caagcaatca ggaatgtgac catcaagagg tgccggatca
     2281 tctacggtgg ctccacgtat gaccttgaat ctgatggcaa gggcaaagtt ttggtggaaa
     2341 aggtcaagaa cacctctgta cagaccaaca acgagctggc tggggccctg caccatctca
     2401 aacacgcccg aatcaggtac tatgtcaaat gtgtgcaaga agcagtctat tccatcatac
     2461 aaattgccgg cgctgcgttt gtcaccacgc gcattgcacg ccgcatgaac atacaagaac
     2521 tctggtcgaa gccacaacta gatcaaaatg aatcagagac taaggaagag gcccccaagt
     2581 cagaagatga cgagttcatc atatcttcta aggacatcaa ggaggaagga aagaagggca
     2641 aaaacaagac tggccgtggc aagaaacaca ctgcattctc cagcaagggc ttgagcgatg
     2701 aggagtatga cgagtacaag aggataagag aagagagaaa tgggaagtac tctatagagg
     2761 agtatcttca agacagagac aggtactatg aggagctcgc cattgccaag gccacggaag
     2821 aagacttctg tgaagaggag gagatcaaaa tccgtcagag aattttccgt cccaccagga
     2881 aacaaagaaa ggaagagagg gccacattag ggctagtaac aggttcagaa atcagaaaaa
     2941 gaaaccctga tgacttcaaa cccaaaggga ggctgtgggc cgatgacaac agaagtgttg
     3001 actacaatga gaaactggac tttgaggctc ccccaagcat atggtctagg attgtgagct
     3061 ttggttctgg ctggggcttc tgggtatcac caagcctgtt cataacatca actcatgtaa
     3121 tccccgcagg cataacagaa gcatttggag tccccatcaa acaaattcag attcacaaat
     3181 caggtgaatt ttgccgattc agattcccaa aaccaattag accagatgtg acaggaatga
     3241 tcttagaaga aggtgcgcct gaaggcaccg tagcaactgt gcttatcaaa cgccccaccg
     3301 gagagctcat gcctcttgca gccagaatgg gaacacacgc aaccatgaaa attcaaggcc
     3361 gcatggttgg cggacagatg ggtatgttgc tcactggatc aaatgctaaa ggaatggatt
     3421 tgggaacaac tcctggtgac tgtggctgtc cttacatcta taaaaggggc aatgactata
     3481 tagccattgg ggtgcacact gcagcagccc gtggtggaaa caccgtcatc tgtgccacac
     3541 agggaagtga gggtgaggca actcttgagg gtggagatga caaaggaaca tactgtgggg
     3601 cacctattct aggccctggg ggtgcaccaa aattgagcac caaaaccaaa ttttggaggt
     3661 catcgaacac gcctcttcca ccagggacat atgagcctgc ctacctcggt ggccgtgatc
     3721 cgcgtgttaa gggtgggccc tccttgcagc aggtaatgag agaccagttg aagccattca
     3781 ctgaacccag gggcaaacct ccaagaccaa gtgtattgga agcagccaaa caaaccatta
     3841 tcaacgtcct cgaacaaacc ctggatcctc cacaaaaatg gacatacgca caggcgtgtg
     3901 catcacttga caaaaccacc tccagcgggc atccccatca cgtccgaaag aatgaattct
     3961 ggaatggtga gaccttcact ggcaaattgg cagaccaagc atcaaaagca aacttaatgt
     4021 ttgaggaagg gaaacacatg acaccagtgt atacagcagc actcaaggac gagctagtca
     4081 agactgagaa aatctataga aagatcaaga agagactgct ctggggctct gacttgtcca
     4141 ccatgatccg gtgcgctagg tcatttggtg ggctcatgga cgagatgaag gcacactgca
     4201 tatcactccc agtacgagtt ggcatgaata tgaatgaaga tggcccaata atatttgaga
     4261 aacattccag atacaaatac cactatgatg cagactactc tcgttgggat tcaacacaac
     4321 agagggcagt gctagcagca gccttggaaa tcatggtcag attctctgca gaaccacaat
     4381 tggcacaaat agtcgctgag gatctgctgg cccctagtgt agtagatgta ggagacttta
     4441 aaatcacaat aaatgaaggg ctcccatctg gtgtgccatg cacttctcaa tggaactcca
     4501 tcgcacactg gctgctaact ctctgtgcct tgtctgaagt caccaaactg tcccctgaca
     4561 ttatacaagc aaattccatg ttctcatttt acggtgatga cgagattgtc agcaccgaca
     4621 taaaattgga ccctgaacag ttaaccgcca aattgaagga gtacggcctg aaaccaaccc
     4681 gcccagacaa gaccgaggga cccctgatta tcagtgaaga tttgaacgga ctcactttcc
     4741 tccgaagaac ggtgactcgt gatccagctg gctggtttgg aaaactggac caaagctcaa
     4801 ttttgaggca gatgtactgg actagaggac caaatcatga agaccccaat gagacaatga
     4861 taccccattc tcaaagaccc atacagctca tggcactgct tggtgaagcc tctcttcacg
     4921 gaccctcttt ctacagtaaa atcagtaaat tggtcataac tgaactcaaa gaaggtggga
     4981 tggactttta cgtgccaagg caggaaccca tgttcagatg gatgaggttt tctgacttga
     5041 gcacgtggga gggcgatcgc aatctggctc ccaattttgt gaatgaagat ggcgtcgaat
     5101 gacgccaacc catctgatgg gtccgcagcc aacctcgtac cagaggtcaa caatgaggtt
     5161 atggctttgg agcccgttgt tggtgccgct attgcggcac ctgtagcggg ccaacaaaat
     5221 gtaattgacc cctggattag aaataatttt gtacaagccc ctggtgggga gtttacagta
     5281 tcccctagaa acgctccagg tgaaatacta tggagcgcgc ccctaggccc tgacctaaat
     5341 ccctacctat ctcacttggc cagaatgtac aatggttatg caggtggttt tgaagtgcag
     5401 gtaattctcg cggggaacgc gttcaccgcc gggaagatca tatttgcagc agtcccacca
     5461 aattttccaa ctgaaggctt aagccctagc caggtcacta tgttccccca tataatagtg
     5521 gatgttagac aattagaacc tgtgctgatt cccttacccg atgtcaggaa taatttctat
     5581 cattacaacc agtcaaatga ttccactatt aagttgatag caatgttgta tacaccactt
     5641 agggctaata atgctgggga tgatgttttc acagtttcgt gtcgagttct cacgagacca
     5701 tcccccgatt ttgatttcat atttttagtg ccacccacag ttgagtcaag aactaaacca
     5761 ttctctgtcc cagttttaac tgttgaggag atgaccaatt caagattccc cattcctttg
     5821 gaaaagttgt tcacgggccc cagcagtgcc tttgttgttc aaccacaaaa cggcaggtgc
     5881 acaactgatg gcgtgctcct aggcaccacc caattgtctc ctgtcaacat ctgcaccttc
     5941 agaggggatg tcacccacat cacaggtagt cgcaactaca caatgaattt ggcttctcaa
     6001 aattggaaca actatgaccc aacagaagaa atcccagccc ctctaggaac tccagatttt
     6061 gtggggaaga ttcaaggcat gctcacccaa accacaagga cagatggttc aacacgcggc
     6121 cacaaagcta cagtgtacac tgggagcgcc gactttgctc caaaactggg tagagttcaa
     6181 tttgaaactg acacagacca tgattttgaa gctaatcaaa acacaaagtt caccccagtc
     6241 ggtgtcatcc aagatggcag caccacccac cgaaacgaac cccaacagtg ggtgctccca
     6301 agttactcag gcagaaatac tcacaatgta catctggccc ccgctgtagc ccccaccttc
     6361 ccgggtgagc aacttctctt cttcagatcc accatgcccg gatgcagcgg gtaccccaac
     6421 atggatttgg actgtctgct cccccaggaa tgggtgcagt acttctacca agaggcagcc
     6481 ccagcacaat ctgatgtggc tctgctaaga tttgtgaatc cagacacagg tagggttttg
     6541 tttgagtgca agcttcacaa atcaggctat gttacagtgg ctcacactgg ccaacatgat
     6601 ttggttatcc cccccaatgg ttactttagg tttgattcct gggtcaacca gttctacacg
     6661 cttgccccca tgggaaatgg aacggggcgt agacgtgcag tataatggct ggtgctttct
     6721 ttgctggatt ggcatccgat gtccttggct ctggacttgg ttcccttatc aatgctgggg
     6781 ctggggccat caaccaaaaa gttgagtttg aaaataacag aaaattgcag caagcatcct
     6841 ttcaatttag cagcaatctg caacaggctt cctttcaaca tgataaagag atgctccaag
     6901 cacaaattga ggccaccaaa aagctacaac aggaaatgat gaaagttaag caggcaatgc
     6961 tcctagaggg tgggtactct gagacagatg cagcccgcgg ggcaattaac gcccccatga
     7021 caaaagcttt ggactggagc gggacaaggt actgggctcc cgatgctagg actacaacat
     7081 acaatgcagg ccgcttttcc acccctcaac catcggggac actaccagga agagctaatc
     7141 ttagggatgc tgtccctgct cggggaccct ccaacaaatc ttctaactct tctactgcca
     7201 cctctgtgta ctcaaatcaa actatctcaa cgagacttgg ttctacagct ggttctggaa
     7261 ccagtgtctc gagcctcccg tcaactgcaa ggactaggag ctgggttgag gatcaaaata
     7321 ggaatttgtc acctttcatg aggggggccc acaacatatc atttgtcacc ccaccatcta
     7381 gcagaccctc tagccaaggc acagtctcaa ccgtgcctaa agagattttg gactcctgga
     7441 ctggcgcttt caatacgcgc aggcagcctc tcttcgctca cattcgtagg cgaggggagt
     7501 cacgggtgta a
//