Typing tool

Complete norovirus genomes

MK762558  GII.4 Sydney
 GII.P31

Length: 7,509 | 3 CDS

ORF1: 1..5100
ORF2: 5081..6703
ORF3: 6703..7509
LOCUS       MK762558                7509 bp    RNA     linear   VRL 13-APR-2019
DEFINITION  Norovirus GII isolate Hu/US/2014/GII.Pe-GII.4 Sydney/CS0031
            nonstructural polyprotein (ORF1), VP1 (ORF2), and VP2 (ORF3) genes,
            complete cds.
ACCESSION   MK762558
VERSION     MK762558.1
KEYWORDS    .
SOURCE      Norovirus GII
  ORGANISM  Norovirus GII
            Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes;
            Picornavirales; Caliciviridae; Norovirus.
REFERENCE   1  (bases 1 to 7509)
  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  JOURNAL   Unpublished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 7509)
  AUTHORS   Barclay,L., Cannon,J.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..7509
                     /organism="Norovirus GII"
                     /mol_type="genomic RNA"
                     /strain="CS0031"
                     /isolate="Hu/US/2014/GII.Pe-GII.4 Sydney/CS0031"
                     /isolation_source="stool"
                     /host="Homo sapiens"
                     /db_xref="taxon:122929"
                     /country="USA"
                     /collection_date="28-Jan-2014"
                     /note="genotype: GII.Pe-GII.4 sydney"
     gene            1..5100
                     /gene="ORF1"
     CDS             1..5100
                     /gene="ORF1"
                     /codon_start=1
                     /product="nonstructural polyprotein"
                     /protein_id="QBX91001.1"
                     /translation="MKMASNDASAAAVANSNNDIAKSSSDGVFSNMAVTFKRALGARP
                     KQPPPKEIPPRPPRPPTPELVKKIPPPPPNGEDELVVSYSAKDGVSGLPELTTVRQPE
                     ETNTAFSVPPLNQRESRDAKEPLTGTIIEMWDGEIYHYGLYVERGLILGVHKPPAAIS
                     LAKVELTPLSLFWRPVYTPQYLISPDTLRRLHGESFPYTAFDNNCYAFCCWVLDLNDS
                     WLSRRMIQRTTGFFRPYQDWNRKPLPTMDDSKLKKVANIFLCTLSSLFTRPIKDIIGK
                     LKPLNILNILATCDWTFAGIVESLILLAELFGVFWTPPDVSAMIAPLLGDYELQGPED
                     LAVELVPIVMGGIGLVLGFTKEKIGKMLSSAASTLRACKDLGAYGLEILKLVMKWFFP
                     KKEEANELAMVRSIEDAVLDLEAIENNHMTTLLKDKDSLATYMRTLDLEEEKARKLST
                     KSASPDIVGTINSLLARIAAARSLVHRAKEELSSRPRPVVVMISGRPGIGKTHLAREL
                     AKKIATSLTGDQRVGLIPRNGVDHWDAYKGERVVLWDDYGMSNPIHDALRLQELADTC
                     PLTLNCDRIENKGKVFDSDAIIITTNLANPAPLDYVNFEACSRRIDFLVYAEAPEVEK
                     AKRDFPGQPDMWKNAFSPDFSHIKLSLAPQGGFDKNGNTPHGKGVMKTLTTGSLIARA
                     SGLLHERLDEYELQGPALTTFNFDRNKILAFRQLAAENKYGLMDTMRVGKQLKDVKTM
                     PDLKQALKNIAIKKCQIVYNGGTYTLEADGKGSVKVDKVQSATVQTNNELAGALHHLR
                     CARIRYYVKCVQEALYSIIQIAGAAFVTTRIAKRMNIQNLWSKPQVEDTEEMTNKDGC
                     LKPKDDEEFVVSSDDIRTEGKKGKNKSGRGKKHTAFSSKGLSDEEYDEYKRIREERNG
                     KYSIEEYLQDRDRYYEEVAIARATEEDFCEEEEAKIRQRIFRPTRKQRKEERTSLGLV
                     TGSEIRKRNPEDFKPKGKLWADDDRSVDYNEKLNFEAPPSIWSRIVNFGSGWGFWVSP
                     SLFITSTHVIPQGAKEFFGVPIKQIQIHKSGEFCRLRFPKPIRTDVTGMILEEGAPEG
                     TVATLLIKRPTGELMPLAARMGTHATMKIQGRTVGGQMGMLLTGSNAKSMDLGTTPGD
                     CGCPYIYKRGNDYVVIGVHTAAARGGNTVICATQGSEGEATLEGGDSKGTYCGAPILG
                     PGSAPKLSTKTKFWRSSTTPLPPGTYEPAYLGGKDPRVKGGPSLQQVMRDQLKPFTEP
                     RGKPPRPNVLEAAKKTIINVLEQTIDPPQKWSFAQACASLDKTTSSGHPHHMRKNDCW
                     NGESFTGKLADQASKANLMFEEGKNMTPVYTGALKDELVKTDKVYGKIKKRLLWGSDL
                     ATMIRCARAFGGLMDELKAHCVTLPVRVGMNMNEDGPIIFEKHSRYRYHYDADYSRWD
                     STQQRDVLAAALEIMVKFSPEPHLAQVVAEDLLSPSVMDVGDFQISISEGLPSGVPCT
                     SQWNSIAHWLLTLCALSEVTDLSPDIIQANSLFSFYGDDEIVSTDIKLDPEKLTTKLK
                     EYGLKPTRPDKTEGPLVISEDLDGLTFLRRTVTRDPAGWFGKLEQSSILRQMYWTRGP
                     NHEDPFETMIPHSQRPIQLMSLLGEAALHGPAFYSKISKLVIAELKEGGMDFYVPRQE
                     PMFRWMRFSDLSTWEGDRNLAPSFVNEDGVE"
     mat_peptide     1..990
                     /gene="ORF1"
                     /product="p48"
     mat_peptide     991..2088
                     /gene="ORF1"
                     /product="NTPase"
     mat_peptide     2089..2625
                     /gene="ORF1"
                     /product="p22"
     mat_peptide     2626..3024
                     /gene="ORF1"
                     /product="VPg"
     mat_peptide     3025..3567
                     /gene="ORF1"
                     /product="Pro"
     mat_peptide     3568..5097
                     /gene="ORF1"
                     /product="RdRp"
     gene            5081..6703
                     /gene="ORF2"
     CDS             5081..6703
                     /gene="ORF2"
                     /note="major capsid protein"
                     /codon_start=1
                     /product="VP1"
                     /protein_id="QBX91002.1"
                     /translation="MKMASSDANPSDGSAANLVPEVNNEVMALEPVVGAAIAAPVAGQ
                     QNVIDPWIRNNFVQAPGGEFTVSPRNAPGEILWSAPLGPDLNPYLSHLARMYNGYAGG
                     FEVQVILAGNAFTAGKVIFAAVPPNFPTEGLSPSQVTMFPHIVVDVRQLEPVLIPLPD
                     VRNNFYHYNQSNDPTIKLIAMLYTPLRANNAGDDVFTVSCRVLTRPSPDFDFIFLVPP
                     TVESRTKPFSVPVLTVEEMTNSRFPIPLEKLFTGPSSAFVVQPQNGRCTTDGVLLGTT
                     QLSPVNICTFRGDVTHITGSHNYTMNLASQNWNNYDPTEEIPAPLGTPDFVGKIQGVL
                     TQTTRTDGSTRGHKATVYTGSADFAPKLGRVQFETDTNHDFEANQNTKFTPVGVIQDG
                     STTHRNEPQQWVLPSYSGRNTHNVHLAPAVAPTFPGEQLLFFRSTMPGCSGYPNMDLD
                     CLLPQEWVQYFYQEAAPAQSDVALLRFVNPDTGRVLFECKLHKSGYVTVAHTGQHDLV
                     IPPNGYFRFDSWVNQFYTLAPMGNGTGRRRAV"
     gene            6703..7509
                     /gene="ORF3"
     CDS             6703..7509
                     /gene="ORF3"
                     /note="minor structural protein; small basic protein"
                     /codon_start=1
                     /product="VP2"
                     /protein_id="QBX91003.1"
                     /translation="MAGAFFAGLASDVLGSGLGSLINAGAGAINQKVEFENNRKLQQA
                     SFQFSSNLQQASFQHDKEMLQSQIEATKKLQQEMMKVKQAMLLEGGFSETDAARGAIN
                     APMTKALDWSGTRYWAPDARTTTYNAGRFSTPQPSGALPGRANLRDVVPARGSSSKSS
                     NSSTATSVYSNQTTSTRLGSTAGSGTSVSSLPSTARTRSWVEDQSRNLSPFMRGAHNI
                     SFVTPPSSRSSSQGTVSTVPKEVLDSWTGAFNTRRQPLFAHIRKRGESRA"
ORIGIN      
        1 atgaagatgg cgtctaacga cgcttccgct gccgctgttg ccaacagcaa caacgacatc
       61 gcaaaatctt caagtgacgg tgtgttttct aacatggctg tcacttttaa gcgggccctc
      121 ggggcgcggc ctaaacagcc gcccccgaag gagataccac ccagaccccc gcgaccaccc
      181 acaccagaat tggtcaaaaa gatccctcct cccccaccca acggggagga tgaactagtg
      241 gtctcttaca gcgccaaaga tggcgtttcc ggactgcctg agctcaccac tgtcagacag
      301 ccggaagaaa ccaacacggc gttcagtgtc cccccactca accaaaggga gagcagggac
      361 gccaaggagc cactaactgg aacaattatt gaaatgtggg atggagaaat ctaccattac
      421 ggcctgtacg tggaacgagg tcttatactt ggtgtgcaca agccaccggc agccatcagc
      481 cttgccaagg tcgagctaac accgctctct ttgttctgga gacctgtata caccccccag
      541 tatctcatct ctccagacac tcttaggaga ttacatggag agtcattccc ctacactgca
      601 tttgacaaca attgctacgc cttttgttgt tgggtattag acctaaacga ctcatggcta
      661 agcaggagaa tgattcagag aacaacaggt ttcttcaggc cgtaccagga ttggaacagg
      721 aaacccctcc ccactatgga tgattccaaa ttaaagaagg tagccaacat attcttgtgc
      781 actttgtctt cactattcac cagacccatt aaggacataa tagggaagtt gaaacctctt
      841 aacatcctta acattctggc tacatgtgat tggaccttcg caggcatagt ggaatcttta
      901 atactcttag cagaactctt tggagttttc tggacacccc cagatgtgtc tgcgatgatc
      961 gcccccttgc taggtgacta tgaactgcaa ggacctgagg accttgcagt ggaactggtc
     1021 ccaatagtga tgggggggat aggtttggtg ctaggattta ccaaagagaa aattggaaag
     1081 atgctatcat ccgctgcatc cactttaaga gcttgtaaag accttggtgc atacggactg
     1141 gaaatcttaa aattggtcat gaagtggttc ttcccaaaga aagaggaagc aaatgaactg
     1201 gctatggtga gatccatcga ggatgcagta ctagacctcg aggcaattga aaacaaccac
     1261 atgaccaccc tactcaaaga caaagacagc ttggcaacct acatgagaac ccttgacctt
     1321 gaggaggaga aagccagaaa actctcaacc aaatctgcct cacccgatat tgtgggcaca
     1381 atcaactctc ttctggcaag aatcgctgct gcacgctccc tagtgcatcg ggcgaaagaa
     1441 gagctctcca gcaggccgag acctgtcgtt gtgatgatat cgggaagacc agggataggg
     1501 aaaactcacc ttgccaggga gctggccaag aagatcgcga cctccctcac aggggaccag
     1561 cgtgtgggtc ttatcccacg caatggtgtc gatcactggg acgcatacaa gggcgaaaga
     1621 gttgtcctat gggacgacta tggaatgagt aaccccatcc atgatgccct caggttgcag
     1681 gagcttgctg acacttgccc cctcacgcta aattgtgaca gaattgagaa caaagggaaa
     1741 gtctttgaca gtgatgccat aatcatcacc accaatctgg ccaacccagc accactggat
     1801 tatgtcaact ttgaagcgtg ctcgagacgt attgacttcc tcgtgtacgc agaagcccct
     1861 gaggtggaga aggcaaagcg cgacttccca ggtcaacctg acatgtggaa gaacgctttc
     1921 agtcctgact tctcacacat aaaactgtca ttggctccac agggtggttt tgacaagaac
     1981 ggcaacaccc cgcatggaaa aggggtcatg aagaccctca ccactggctc cctcatcgcc
     2041 cgagcatcag ggttactcca tgagaggcta gatgaatatg aactgcaagg cccagccctt
     2101 accactttca actttgaccg aaacaagata cttgctttta gacagcttgc tgctgaaaac
     2161 aagtatgggc tgatggacac aatgagagtg ggaaaacagc tcaaggatgt caagaccatg
     2221 ccagacctca aacaagcact caagaacatc gcgatcaaga agtgccagat agtgtacaat
     2281 ggtggcacct acacacttga ggccgatggc aagggtagtg tgaaagttga caaagtgcaa
     2341 agtgccactg tgcagaccaa caatgaacta gccggtgccc tacaccacct aaggtgcgct
     2401 agaatcagat actatgttaa gtgcgtccag gaggcactgt attccatcat ccaaatcgct
     2461 ggggctgcat tcgtcaccac gcgcatcgct aagcgcatga atatacagaa tctctggtcc
     2521 aagccacagg tggaagacac agaagagatg accaacaaag atggttgcct aaaacccaaa
     2581 gatgatgaag agtttgtcgt ctcatccgac gacatcagaa ctgagggcaa gaaagggaag
     2641 aacaagtccg gccgtggcaa gaagcacaca gccttttcaa gcaaagggct cagtgatgag
     2701 gagtacgatg agtacaagag aatcagagaa gaaaggaatg gtaagtactc catagaagag
     2761 taccttcagg acagagacag gtactacgag gaggtggcca ttgccagggc gaccgaagag
     2821 gacttctgtg aagaagaaga ggccaaaatc cggcagagaa tttttagacc aacaaggaaa
     2881 caacgcaaag aagagaggac ctctctcggc ttggtcacag gctctgaaat caggaagaga
     2941 aacccagaag actttaaacc caagggaaag ctgtgggctg atgatgacag aagtgttgac
     3001 tacaacgaga aactcaactt tgaggcccca ccaagcattt ggtcgcggat agtcaacttt
     3061 ggttcaggct ggggtttctg ggtctccccc agtctgttta taacatcaac ccatgtcata
     3121 ccccaaggtg caaaagagtt cttcggagtc cctatcaagc aaatccagat acacaaatca
     3181 ggtgaattct gccggttgag attcccaaag ccaatcagaa ctgatgtgac gggcatgatt
     3241 ctagaagaag gtgcgcccga ggggaccgtg gccacactgc tcatcaagag accaactgga
     3301 gaactcatgc ctctggcagc cagaatgggg acccatgcaa ccatgaaaat tcaggggcgc
     3361 acagttggag ggcaaatggg tatgctcctg acaggatcca acgccaagag tatggaccta
     3421 ggcacaacac caggcgactg cggctgcccc tacatctaca agagggggaa tgactacgtg
     3481 gtcataggag tccatacggc cgctgcccgt ggaggaaaca ctgtcatatg tgccacccag
     3541 gggagtgagg gagaagccac acttgaagga ggtgacagta aagggacata ctgtggcgca
     3601 ccaatcttgg gcccagggag cgctccgaaa ctcagtacca agactaagtt ttggagatca
     3661 tccacaacac cactcccacc tggcacctac gaaccagcct atctcggtgg caaagacccc
     3721 agagtcaaag gtggcccttc attgcaacaa gttatgaggg accagctaaa gccattcaca
     3781 gaacccagag gcaaaccacc aagaccaaat gtgttggaag ctgccaagaa aaccatcatc
     3841 aatgttcttg agcaaacaat tgatccaccc caaaaatggt catttgcgca agcttgcgcg
     3901 tcccttgaca aaaccacctc cagcggccac ccgcaccaca tgcggaaaaa cgattgttgg
     3961 aatggagagt ccttcacagg aaaactggct gatcaagcct ccaaggccaa cctaatgttt
     4021 gaagagggaa agaacatgac tccagtctac acaggtgcac ttaaagatga gttggtaaag
     4081 accgataaag tttatggtaa gatcaagaag aggcttctgt ggggttcaga tctggcgacc
     4141 atgatacggt gcgcccgagc ttttggaggc cttatggatg aactcaaggc gcactgtgtc
     4201 acacttcctg tcagagttgg tatgaacatg aatgaggatg gccccatcat ctttgagaag
     4261 cactccagat atagatatca ctatgatgct gattattccc ggtgggactc aacacaacaa
     4321 agggatgtgc tagcagcagc actagaaatc atggttaagt tctctccaga accacacctg
     4381 gcccaggtag ttgcagaaga ccttctttcc cctagcgtga tggatgtagg tgactttcaa
     4441 atatcaataa gtgagggtct tccctctggg gtaccttgta cctcccagtg gaattccatc
     4501 gcccactggc tcctcactct ttgtgcactc tctgaagtca cggacctgtc ccctgacatc
     4561 attcaggcca actccctttt ctccttctat ggtgatgatg agattgtgag cacagacata
     4621 aagttggacc cagagaagct gacgacaaaa ctcaaggagt acgggctgaa accaacccgc
     4681 cccgacaaaa ctgaaggacc ccttgtcatc tctgaagacc tggatggcct gacattcctc
     4741 cggagaactg tgacccgtga tccagctggc tggtttggaa aattggaaca aagttcaatt
     4801 ctcagacaaa tgtactggac caggggtcct aaccatgaag atccatttga aacaatgata
     4861 ccacactccc aaagacccat acaattgatg tccttgctgg gcgaggctgc actccacggc
     4921 ccggcatttt atagcaaaat tagcaaatta gtcattgcag agttgaagga aggtggcatg
     4981 gatttttacg tgcccaggca agagccaatg ttcagatgga tgagattctc agatctgagc
     5041 acgtgggagg gcgatcgcaa tctggctccc agttttgtga atgaagatgg cgtcgagtga
     5101 cgccaaccca tctgatgggt ccgcagccaa cctcgtccca gaggtcaaca atgaggttat
     5161 ggctctggag cccgttgttg gtgccgccat tgcggcacct gtagcgggcc aacaaaatgt
     5221 aattgacccc tggattagaa acaattttgt acaagcccct ggtggagaat ttacagtgtc
     5281 ccctagaaac gctccaggtg aaatactatg gagcgcgccc ttgggccctg atctaaatcc
     5341 ctacctatcc catttggcca gaatgtacaa tggttatgca ggtggttttg aagtgcaggt
     5401 aattctcgcg gggaacgcgt tcaccgccgg gaaggtcata tttgcagcag tcccaccaaa
     5461 ttttccaact gaaggcttga gccccagcca ggtcactatg ttcccccata tagtagtaga
     5521 tgttaggcaa ctagaacctg tgttgattcc cttacccgat gttaggaata atttctatca
     5581 ttataatcaa tcaaatgacc ccaccattaa gttgatagca atgttgtata caccacttag
     5641 ggctaataat gctggggatg atgtcttcac agtttcttgc cgagttctca ccagaccatc
     5701 ccccgatttt gatttcatat ttctagtgcc acccacagtt gagtcaagaa ctaaaccatt
     5761 ctctgtccca gttttaactg ttgaggagat gaccaattca agattcccca ttcctttgga
     5821 aaagctgttc acgggtccca gcagtgcctt tgttgtccaa ccacaaaacg gcaggtgcac
     5881 gactgatggc gtgctcctag gcaccaccca attgtctcct gtcaacatct gcaccttcag
     5941 aggagatgtc acccacatca caggtagtca taactacaca atgaatttgg cttctcaaaa
     6001 ttggaacaat tacgacccaa cagaagaaat cccagcccct ctaggaactc cagactttgt
     6061 ggggaagatt caaggcgtgc tcacccagac cacaaggaca gatggctcaa cacgcggcca
     6121 caaagccaca gtgtacactg ggagcgccga ctttgctcca aaactgggta gagttcaatt
     6181 tgaaactgac acaaaccatg attttgaagc caaccaaaac acaaagttca ccccagtcgg
     6241 tgtcatccaa gatggtagca ccacccaccg aaatgaaccc caacagtggg tgctcccaag
     6301 ttactcaggc agaaatactc ataatgtgca tctggccccc gctgtagccc ccacttttcc
     6361 gggtgagcaa cttctcttct tcagatccac catgcccgga tgcagcgggt accccaacat
     6421 ggatttggac tgtctactcc cccaggaatg ggtgcagtac ttctaccaag aggcagcccc
     6481 agcacaatct gatgtggctc tgctaagatt tgtgaatcca gatacaggta gggttttgtt
     6541 tgagtgtaag cttcataaat caggctatgt tacagtggct cacactggcc aacatgattt
     6601 ggttattccc cccaatggtt actttagatt tgattcctgg gtcaaccagt tctacacgct
     6661 tgcccccatg ggaaatggaa cggggcgtag acgtgcagta taatggctgg agctttcttt
     6721 gctggattgg catctgatgt ccttggctct ggacttggtt cacttatcaa tgctggggct
     6781 ggggccatca accaaaaagt cgagtttgaa aataacagaa aactgcaaca agcatccttc
     6841 caatttagca gcaatctaca acaggcttcc tttcaacatg acaaagagat gctccaatca
     6901 caaattgagg ccaccaaaaa gttacaacag gaaatgatga aagttaagca ggcaatgctc
     6961 ctagagggtg ggttctctga gacggatgca gcccgcgggg caatcaacgc ccccatgaca
     7021 aaagctttgg actggagcgg gacaaggtac tgggctcctg atgctaggac tacaacatac
     7081 aatgcaggcc gcttttccac ccctcaacca tcgggggcac tgccaggaag agctaatctt
     7141 agggatgttg tccctgctcg gggttcctcc agtaaatctt ctaactcttc tactgctact
     7201 tctgtgtact caaatcaaac tacttcaacg agacttggtt ctacagctgg ttctggcacc
     7261 agtgtctcga gcctcccgtc aactgcaagg actaggagct gggttgagga tcaaagtagg
     7321 aatttgtcac ctttcatgag gggggcccac aacatatcgt ttgtcacccc accatctagc
     7381 agatcctcta gccaaggcac agtctcaacc gtgcctaaag aggttttgga ctcctggact
     7441 ggcgctttca acacgcgcag gcagccactc ttcgctcaca ttcgtaagcg aggggagtca
     7501 cgggcgtaa
//