Typing tool

Complete norovirus genomes

KY947546  GII.4 Sydney
 GII.P4 New Orleans

Length: 7,546 | 3 CDS

ORF1: 4..5103
ORF2: 5084..6706
ORF3: 6706..7512
LOCUS       KY947546                7546 bp ss-RNA     linear   VRL 18-MAY-2017
DEFINITION  Norovirus GII strain Hu/USA/2015/GII.P4 New Orleans-GII.4
            Sydney/Titusville 7426 polyprotein, VP1, and VP2 genes, complete
            cds.
ACCESSION   KY947546
VERSION     KY947546.1
KEYWORDS    .
SOURCE      Norovirus GII
  ORGANISM  Norovirus GII
            Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes;
            Picornavirales; Caliciviridae; Norovirus.
REFERENCE   1  (bases 1 to 7546)
  AUTHORS   Cannon,J.L., Barclay,L., Collins,N.R., Wikswo,M.E., Castro,C.J.,
            Magana,L.C., Gregoricus,N., Marine,R.L., Chhabra,P. and Vinje,J.
  TITLE     Genetic and Epidemiologic Trends of Norovirus Outbreaks in the US
            Demonstrated Emergence of Novel GII.4 Recombinant Viruses,
            2013-2016
  JOURNAL   J. Clin. Microbiol. (2017) In press
   PUBMED   28490488
  REMARK    Publication Status: Available-Online prior to print
REFERENCE   2  (bases 1 to 7546)
  AUTHORS   Cannon,J.L., Barclay,L., Collins,N.R., Chhabra,P., Wikswo,M.E.,
            Castro,C.J., Magana,L.C., Gregoricus,N. and Vinje,J.
  TITLE     Direct Submission
  JOURNAL   Submitted (14-APR-2017) Viral Gastroenteritis Branch/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. 8
            Sequencing Technology :: Illumina
            ##Assembly-Data-END##
FEATURES             Location/Qualifiers
     source          1..7546
                     /organism="Norovirus GII"
                     /mol_type="genomic RNA"
                     /strain="Hu/USA/2015/GII.P4 New Orleans-GII.4
                     Sydney/Titusville 7426"
                     /isolation_source="stool"
                     /host="Homo sapiens"
                     /db_xref="taxon:122929"
                     /country="USA"
                     /collection_date="12-Jan-2015"
                     /note="genotype: GII.P4 New Orleans-GII.4 Sydney"
     5'UTR           1..3
     CDS             4..5103
                     /note="nonstructural protein; ORF1"
                     /codon_start=1
                     /product="polyprotein"
                     /protein_id="ARR95954.1"
                     /translation="MKMASNDASAAAVANSNNDTAKSSSDGVLSSMAVTFKRALGARP
                     KQPPPREIPQRPPRPPTPELVKKIPPPPPNGEDEMVVSYSVKDGVSGLPDLSTVKQPE
                     ESNTAFSVPPLSQRENRDAKEPLTGSILEMWDGEIYHYGLYVERGLVLGVHKPPAAIS
                     LARIELAPLSLYWRAVYTPQYLISPDTLKKLHGETFPYTAFDNNCYAFCCWVLDLNDS
                     WLSRRMIQRTTGFFRPYQDWNRKPLPTMDDSKLKKVANIFLCALSSLFTRPIKDIIGK
                     LKPLNILNILASCDWTFAGIVESLILLAELFGVFWTPPDVSAMIAPLLGDYELQGPED
                     LAVELVPVVMGGIGLVLGFTKEKIGKMLSSAASTLRACKDLGAYGLEILKLVMKWFFP
                     KKEEANELAIVRSIEDAVLDLEAIENNHLTTLLKDKDSLATYMKTLDLEEEKARKLST
                     KSASPDIVGTINALLARIAAARSLVHRAKEELSSRPRPVVMMISGRPGIGKTHLAREV
                     AKRIATSLTGDQRVGLIPRNGVDHWDAYKGERVVLWDDYGMSNPVHDALRLQELADTC
                     PLTLNCDRIENKGKVFDSDVIIITTNLANPAPLDYVNFEACSRRIDFLVYAEAPEVEK
                     AKRDFPGQPDMWKNAFSPDFSHIKLTLAPQGGFDKNGNTPHGKGVMKTLTTGSLIARA
                     SGLLHERLDEFELQGPTLTTFNFDRNKVLAFRQLAAENKYGLMDTMRVGKQLKDVRTM
                     PELKQALKNVSIKKCQIVYSGCTYILESDGKGNVKVDKTQSASVQTNNELTGALHHLR
                     CARIRYYVKCVQEALYSIIQIAGAAFVTTRIVKRMNIQDLWSKPQVENTEETTNKDGC
                     PKPKDDEEFVISSDDIKAEGKKGKNKTGRGKKHTAFSSKGLSDEEYDEYKRIREERNG
                     KYSIEEYLQDRDKYYEEVAIARATEEDFCEEEEAKIRQRIFRPTRKQRKEERASLGLV
                     TGSEIRKRNPDDFKPKGKLWADDDRSVDYNEKLSFEAPPSIWSRIVNFGSGWGFWVSP
                     SLFITSTHVIPQGAKEFFGVPIKQIQVHKSGEFCRLRFPKPIRTDVTGMILEEGAPEG
                     TVVTLLIKRSTGELMPLAARMGTHATMKIQGRTVGGQMGMLLTGSNAKSMDLGTTPGD
                     CGCPYIYKRGNDYVVIGVHTAAARGGNTVICATQGSEGEATLEGGDDKGTYCGAPILG
                     PGSAPTLSTKTKFWRSSTAPLPPGTYEPAYLGGKDPRVKGGPSLQQVMREQLKPFTEP
                     RGKPPKPSVLEAAKKTIINVLEQTIDPPEKWSFAQACASLDKTTSSGHPHHMRKNDCW
                     NGESFTGKLADQASKANLMYEEGKNMTPVYTAALKDELVKTDKIYGKIKKRLLWGSDL
                     ATMIRCARAFGGLMDELKAHCVTLPIRVGMNMNEDGPIIFERHSRYTYHYDADYSRWD
                     STQQRAVLAAALEILVKFSPEPHLAQVVAEDLLSPSVVDVGDFTISINEGLPSGVPCT
                     SQWNSVAHWLLTLCALSEVTNLSPDTIQANSLFSFYGDDEIVSTDIKLDPEKLTAKLR
                     EYGLKPTRPDKTEGPLVISEDLNGLTFLRRTVTRDPAGWFGKLEQSSILRQMYWTRGP
                     NHGDPSETMIPHSQRPIQLMSLLGEAALHGPAFYSKISKLVIAELKEGGMDFYVPRQE
                     PMFRWMRFSDLSTWEGDRNLAPSFVNEDGVE"
     CDS             5084..6706
                     /note="major capsid protein; ORF2"
                     /codon_start=1
                     /product="VP1"
                     /protein_id="ARR95955.1"
                     /translation="MKMASSDANPSDGSAANLVPEVSNEVMALEPVVGAAIAAPVAGQ
                     QNIIDPWIRNNFVQAPGGEFTVSPRNAPGEILWSAPLGPDLNPYLSHLARMYNGYAGG
                     FEVQVILAGNAFTAGKIIFAAVPPNFPTEGLSPSQVTMFPHIIVDVRQLEPVLIPLPD
                     VRNNFYHYNQSNDPTIKLIAMLYTPLRANNAGDDVFTVSCRVLTRPSPDFDFIFLVPP
                     TVESRTKPFSVPILTVEEMTNSRFPIPLEKLFTGPSSAFVVQPQNGRCTTDGVLLGTT
                     QLSPVNICTFRGDVTHITGSHNYTMNLASQNWNNYDPTEEIPAPLGTPDFVGKIQGVL
                     TQTTRSDGSTRGHKATVYTGSADFAPKLGRVQFETDTDRDFETNQNTKFTPVGVIQDG
                     TTAHRNEPQQWVLPSYSGRNIHNVHLAPAVAPTFPGEQLLFFRSTMPGCSGYPNMDLD
                     CLLPQEWVQYFYQEAAPAQSDVALLRFVNPDTGRVLFECKLHKSGYVTVAHTGQHDLV
                     IPPNGYFRFDSWVNQFYTLAPMGNGTGRRRAV"
     CDS             6706..7512
                     /note="minor structural protein; ORF3"
                     /codon_start=1
                     /product="VP2"
                     /protein_id="ARR95956.1"
                     /translation="MAGAFFAGLASDVLGSGLGSLINAGAGAINQKVEFENNRKLQQA
                     SFQFSSNLQQASFQHDKEMLQAQIEATKKLQQEMMKVKQAVLLEGGFSETDAARGAIN
                     APMTKALDWSGTRYWAPDARTTTYNAGRFSTPQPPGALPGRANFRDVVPARGSSSKSS
                     NSSTVASVYSNQTASTRLGSTAGSGSSVSSLPSTARTRSWVEDQNRSLSPFMRGAHNI
                     SFVTPPSSRSSSQGTVSTVPKEVLDSWTGAFNTHRQPLFAHIRKRGESRA"
     3'UTR           7513..7546
ORIGIN      
        1 tgaatgaaga tggcgtctaa cgacgcttcc gctgccgctg ttgccaacag caacaacgac
       61 accgcaaaat cttcaagtga cggagtgctt tccagcatgg ctgtcacttt taaacgagcc
      121 ctcggggcgc ggcctaaaca gccccccccg agggagatac cacaaagacc cccacgacca
      181 cctaccccag aattggttaa aaagatcccc ccccctccgc ccaacggaga ggatgaaatg
      241 gtggtttctt atagtgtcaa agatggtgtt tccggtttgc ctgacctttc caccgtcaag
      301 caaccggaag aatctaacac ggccttcagt gtccccccac tcagtcagag ggagaatagg
      361 gacgccaagg agccacttac tggatcaatt ttggaaatgt gggatggaga aatctaccat
      421 tatggcctgt atgtggagcg aggtctcgtg ctaggtgtac acaaaccacc agctgccatc
      481 agcctcgcta ggattgagct agcaccactc tccttgtact ggagagctgt gtacactcct
      541 cagtacctca tctctccaga cactctcaag aaattgcacg gagagacgtt cccctacaca
      601 gcctttgaca acaattgtta tgccttctgt tgctgggtcc tggacctaaa cgactcgtgg
      661 ctgagcagga gaatgatcca aagaacaact ggtttcttta ggccctacca agactggaat
      721 aggaaacccc ttcccactat ggatgactcc aaattaaaga aggtagctaa catattcctg
      781 tgtgctctgt cctcgctatt caccaggccc ataaaggata taatagggaa gttaaagcct
      841 ctcaatatcc tcaacatctt agcctcatgt gattggacct ttgcaggtat cgtggagtcc
      901 ctgatactct tggcagagct ctttggggtt ttctggacac ccccagatgt gtctgcgatg
      961 attgccccct tactcggtga ctacgagctg caaggacctg aggaccttgc agtggagctc
     1021 gtccccgtag tgatgggtgg aattggtttg gtactaggat tcaccaaaga gaagattggg
     1081 aaaatgttgt catctgctgc atccaccttg agagcttgca aagaccttgg tgcatatggg
     1141 ctagaaatcc taaagttggt catgaagtgg ttcttcccga aaaaggagga agcaaatgaa
     1201 ctggccatag tgagatctat cgaggatgca gtcttggatc tcgaggcaat tgaaaacaac
     1261 cacttgacca ccctgctcaa agacaaagac agtctggcaa cctacatgaa aactcttgac
     1321 cttgaggagg agaaagccag gaaactttca accaagtctg cctcgcctga cattgtgggc
     1381 acaatcaacg cccttctggc gagaatcgcc gccgcacgct ctctggtgca tcgagcgaag
     1441 gaggaacttt ccagcagacc aagacctgta gtgatgatga tatcaggcag gccaggaata
     1501 gggaagactc accttgctag ggaagtggct aagagaatcg caacctccct tacaggagat
     1561 cagcgtgtag gcctcatccc acgcaacggc gtcgaccatt gggatgcata caagggggag
     1621 agggtcgtcc tttgggatga ttatggaatg agcaaccccg ttcatgatgc cctcagattg
     1681 caggaactcg ctgacacctg ccccctcact ctaaactgtg acaggattga gaacaaagga
     1741 aaggtctttg acagcgatgt cattattatc accactaacc tggccaaccc agcaccactg
     1801 gactatgtca attttgaagc atgctcgagg cgcatcgact tcctcgtgta cgcagaagcc
     1861 cctgaagtcg aaaaggcgaa gcgtgacttc ccaggccagc ctgacatgtg gaagaacgcc
     1921 ttcagtcctg atttctcaca tataaaactg acactggccc cacaaggtgg cttcgacaag
     1981 aacgggaaca ccccacacgg aaagggtgtc atgaagaccc tcaccactgg ctccctcatt
     2041 gcccgggcat ctgggttact ccatgagagg ttagatgagt ttgaactaca aggcccaacc
     2101 ctcaccacct tcaatttcga ccgcaataaa gtacttgcct ttagacaact tgctgctgag
     2161 aataaatatg ggttgatgga cacaatgagg gttgggaaac agctcaagga tgtcagaacc
     2221 atgccagaac tcaaacaagc acttaagaat gtctcaatca agaagtgcca aatagtgtat
     2281 agtggttgca cttacatact tgaatctgat ggcaagggta atgtgaaagt tgacaaaacc
     2341 cagagcgcct ccgtgcagac caacaatgag ctgactggtg ccctgcatca tttgaggtgc
     2401 gccaggatca gatactatgt caagtgtgtc caggaggccc tgtactccat catccaaatt
     2461 gctggagccg catttgtcac cacgcgcatc gtcaagcgca tgaacataca agacctgtgg
     2521 tccaagccac aagtggaaaa cacagaggag accaccaaca aagacgggtg cccaaaaccc
     2581 aaagacgatg aggagttcgt catctcatcc gacgacatca aggctgaggg taagaaaggg
     2641 aagaacaaga ctggccgcgg caagaaacac acagccttct caagtaaagg tctcagtgat
     2701 gaagagtatg atgagtacaa gaggattagg gaagaaagga atggcaagta ctccatagag
     2761 gagtaccttc aggacaggga caaatactat gaggaggtgg ccattgccag ggcgactgag
     2821 gaagacttct gtgaagagga ggaagccaag atccggcaaa ggattttcag gccaacaagg
     2881 aaacaacgaa aggaggaaag agcttctctc ggcctagtca caggttctga aattaggaaa
     2941 agaaacccag atgatttcaa acccaagggg aaactgtggg ctgacgatga cagaagtgtg
     3001 gattataacg agaaactcag ttttgaggcc ccaccaagca tctggtcgag gatagtcaat
     3061 tttggttcag gttggggatt ttgggtctcc cctagtctgt tcataacatc aacccatgtc
     3121 ataccccagg gtgcaaaaga gttctttgga gtccccatca aacaaattca ggtacacaag
     3181 tcaggcgagt tctgtcgctt gagattccca aaaccaatca ggactgatgt gacgggcatg
     3241 atcttagaag aaggcgcacc tgagggcacc gtagttacat tactcatcaa gaggtccact
     3301 ggggaactta tgcccctagc agctaggatg gggacccatg caactatgaa gatccaaggg
     3361 cgcactgttg ggggccaaat gggcatgctt ctgacagggt ccaacgccaa aagcatggat
     3421 ctgggtacta caccaggtga ttgtggctgt ccctacatct acaagagagg taatgactat
     3481 gtggtcattg gagtccacac ggctgccgct cgcggaggaa acactgtcat atgtgctacc
     3541 caggggagtg aaggagaggc tacacttgaa ggtggtgacg acaaggggac atactgtggt
     3601 gcacccatcc taggcccagg gagtgcccca acacttagca ccaagaccaa attctggaga
     3661 tcatccacag caccactccc acccggcacc tatgaacctg cctatcttgg tggcaaggac
     3721 cccagagtca agggtggccc ttcactgcag caagttatga gggaacagtt aaagccattc
     3781 acagagccca ggggcaaacc accaaaacca agtgtgttgg aagctgccaa gaagaccatc
     3841 atcaatgtcc ttgagcaaac aattgatcca cctgagaaat ggtcattcgc acaagcttgt
     3901 gcgtcccttg acaagaccac ttccagcggc catccccacc acatgcggaa aaacgactgc
     3961 tggaacgggg agtccttcac gggcaagctg gctgaccagg cttccaaggc caacctgatg
     4021 tatgaagaag ggaagaatat gaccccagtc tacacagctg cactcaagga tgaattggtt
     4081 aaaactgaca aaatttatgg taagatcaag aagaggcttc tctggggctc ggacttggcg
     4141 accatgatcc gctgcgctcg agcgttcgga ggcttaatgg atgaactcaa agcacactgt
     4201 gtcacactcc ccattagagt tggtatgaat atgaatgagg atggccccat catcttcgag
     4261 aggcattcca ggtacacata tcactatgat gctgattact ctcgatggga ttcaacacaa
     4321 cagagagccg tgttggcagc agctctagaa atcttagtca aattctcccc agaaccacat
     4381 ttggctcagg tagtcgcgga agacctcctt tctcctagcg tggtggacgt gggcgacttc
     4441 acaatatcaa tcaacgaggg ccttccctct ggggtgccct gtacctctca atggaattct
     4501 gtcgcccact ggcttctcac actctgcgcg ctctctgaag tcacaaactt gtcccctgac
     4561 accatacaag ctaattccct cttctctttt tatggtgatg atgaaattgt tagcacagat
     4621 ataaagttgg acccagagaa attgacagca aagctcaggg aatatgggtt gaaaccaacc
     4681 cgccctgata aaactgaagg accccttgtc atctctgaag acttgaatgg cctaactttc
     4741 ctgcggagaa ctgtgacccg cgacccagct ggttggtttg gaaaactgga gcagagttca
     4801 atactcaggc aaatgtactg gactaggggc cccaaccatg gagacccatc tgaaacaatg
     4861 attccacact cccaaagacc tatacaactg atgtccctat tgggggaggc cgctctccac
     4921 ggcccagcat tctacagcaa aatcagtaaa ttggtcattg cagagctaaa agaaggcggc
     4981 atggattttt acgtgcccag acaagagcca atgttcaggt ggatgagatt ctcagacctg
     5041 agcacgtggg agggcgatcg caatctggct cccagttttg tgaatgaaga tggcgtcgag
     5101 tgacgccaac ccatctgatg ggtccgcagc caacctcgtc ccagaggtca gcaatgaggt
     5161 tatggctctg gagcccgttg ttggtgccgc cattgcggca cctgtagcgg gccaacaaaa
     5221 tataattgac ccctggatta gaaacaattt tgtacaagcc cctggtggag agtttacagt
     5281 gtcccctaga aacgctccag gtgagatact atggagcgcg cccttaggcc ctgatttaaa
     5341 tccctaccta tcccatttgg ctagaatgta caatggttat gcaggtggct ttgaagtgca
     5401 ggtaatcctc gcggggaacg cgttcaccgc cgggaagatc atatttgcag cagtcccacc
     5461 aaattttcca actgaaggct tgagccccag ccaggtcact atgttccccc acataatagt
     5521 ggatgttagg caattagaac ctgtgttgat tcccttacct gatgttagga ataattttta
     5581 ccattataat caatcaaatg accccactat taagttgata gcaatgttgt atacaccact
     5641 tagggctaat aatgctgggg acgatgtctt cacggtttct tgccgagttc tcacgagacc
     5701 atcccccgat tttgatttca tatttctagt gccacccaca gttgagtcaa gaactaaacc
     5761 attctctgtc ccaatcttaa ctgttgagga gatgaccaat tcaagatttc ccattccttt
     5821 ggaaaagttg ttcacgggtc ccagcagtgc ctttgttgtc caaccacaaa atggcagatg
     5881 cacgactgat ggcgtgctcc taggtaccac ccagttatct cctgtcaaca tttgcacctt
     5941 cagaggggat gtcacccata tcacaggtag ccataactac acaatgaatt tggcttctca
     6001 aaattggaac aattatgacc caacagaaga aatcccagcc cctctaggaa ctccagactt
     6061 tgtggggaag attcaaggtg tgctcaccca aaccacaagg tcggatggct cgacacgcgg
     6121 ccacaaagcc acagtgtaca ctgggagcgc cgactttgct ccaaaactgg gtagagttca
     6181 atttgaaact gacacagacc gtgattttga aactaaccaa aatacaaaat tcaccccagt
     6241 cggtgtcatc caagatggta ccactgccca ccgaaatgaa cctcaacagt gggtgctccc
     6301 aagttattca ggcagaaaca ttcataatgt gcacctggcc cccgctgtag cccccacttt
     6361 tccgggtgag caactgctct tcttcaggtc cactatgccc ggatgcagcg ggtatcccaa
     6421 catggatttg gactgtctgc ttccccagga atgggtgcag tacttctacc aagaggcagc
     6481 cccagcacaa tctgatgtgg ctctgttaag atttgtgaat ccagacacag gtagggtttt
     6541 gtttgagtgt aaacttcata aatcaggcta tgttacagtg gctcatactg gccaacatga
     6601 tttggttatt ccccccaatg gttactttag atttgattcc tgggttaatc agttctacac
     6661 gcttgccccc atgggaaatg gaacggggcg tagacgtgca gtataatggc tggagctttc
     6721 tttgctggat tggcatctga tgtccttggc tctggacttg gttcccttat caatgctggg
     6781 gctggggcca tcaaccaaaa agttgaattt gaaaataaca gaaaattgca acaagcttcc
     6841 ttccaattta gcagcaatct acaacaagct tcctttcaac atgacaaaga gatgctccaa
     6901 gcacaaattg aggccaccaa gaagctacaa caggaaatga tgaaagtcaa gcaggcagtg
     6961 ctcctagagg gtgggttctc tgagacagat gcagcccgcg gggcaatcaa cgcccccatg
     7021 acaaaagctt tggactggag cgggacaagg tactgggctc ccgatgctag gactacaaca
     7081 tacaatgcag gccgcttttc caccccccaa ccaccggggg cactgccagg aagagctaat
     7141 tttagggatg ttgtccccgc tcggggttcc tctagtaaat cttctaattc ttctactgtc
     7201 gcttctgtgt attcaaatca aactgcttca acgagacttg gttctacagc tggttctggt
     7261 tccagtgtct cgagtctccc gtcaactgcg aggactagga gctgggttga ggatcaaaat
     7321 aggagtttgt cacctttcat gaggggggcc cacaacatat cgtttgtcac cccaccatct
     7381 agcagatcct ctagccaagg cacagtctca accgtgccta aagaagtttt ggactcctgg
     7441 actggtgctt tcaacacgca caggcagcct ctcttcgctc acattcgtaa gcgaggggag
     7501 tcacgggctt aatgtgaaaa gacaaaattg attatcttta catcac
//