Typing tool

Complete norovirus genomes

KY947547  GII.4 Sydney
 GII.P4 New Orleans

Length: 7,554 | 3 CDS

ORF1: 4..5103
ORF2: 5084..6706
ORF3: 6706..7512
LOCUS       KY947547                7554 bp ss-RNA     linear   VRL 18-MAY-2017
DEFINITION  Norovirus GII strain Hu/USA/2014/GII.P4 New Orleans-GII.4
            Sydney/Ellsworth 7118 polyprotein, VP1, and VP2 genes, complete
            cds.
ACCESSION   KY947547
VERSION     KY947547.1
KEYWORDS    .
SOURCE      Norovirus GII
  ORGANISM  Norovirus GII
            Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes;
            Picornavirales; Caliciviridae; Norovirus.
REFERENCE   1  (bases 1 to 7554)
  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 7554)
  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..7554
                     /organism="Norovirus GII"
                     /mol_type="genomic RNA"
                     /strain="Hu/USA/2014/GII.P4 New Orleans-GII.4
                     Sydney/Ellsworth 7118"
                     /isolation_source="stool"
                     /host="Homo sapiens"
                     /db_xref="taxon:122929"
                     /country="USA"
                     /collection_date="20-Nov-2014"
                     /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="ARR95957.1"
                     /translation="MKMASNDASAAAVANSNNDTAKSSSDGVLSSMAVTFKRALGARP
                     KQPPPREKPQRPPRPPTPELVKNIPPPPPNGEDEIVVSYSVKDGVSGLPDLSTVRQPE
                     ESNTAFSVPPLNQRENRDAKEPLTGTILEMWDGEIYHYGLYVERGLVLGVHKPPAAIS
                     LAKVELAPLSLYWRPVYTPQYLISPDTLKKLSGETFPYTAFDNNCYAFCCWVLDLNDS
                     WLSRRMIQRTTGFFRPYQDWNRKPLPTMDDSKIKKVANIFLCALSSLFTRPIKDIIGK
                     IRPLNILNILASCDWTFAGIVESLILLAELFGVFWTPPDVSAMIAPLLGDYELQGPED
                     LAVELVPVVMGGIGLVLGFTKEKIGKMLSSAASTLRACKDLGAYGLEILKLVMKWFFP
                     KKEEANELAIVRSIEDAVLDLEAIENNHMTTLLKDKDSLATYMRTLDLEEEKARKLST
                     KSASPDIVGTINALLARIAAARSLVHRAKEELSSRPRPVVLMISGRPGIGKTHLAREV
                     AKRIAASLTGDQRVGLIPRNGVDHWDAYKGERVVLWDDYGMSNPIHDALRLQELADTC
                     PLTLNCDRIENKGKVFDSDVIIITTNLANPAPLDYVNFEACSRRIDFLVYAEAPEVEK
                     AKRDFPGQPDMWKNAFSSDFSHIKLALAPQGGFDKNGNTPHGKGVMKTLTTGSLIARA
                     SGLLHERLDEFELQGPALTVFNFDRNKVLAFRQLAAENKYGLMDTMRVGKQLKDVRTM
                     PELRQALKNVSIKKCQIVYSGCTYTLESDGKGNVRVDRVQNAAVQTNNELAGALHHLR
                     CARIRYYVKCVQEALYSIIQIAGAAFVTTRIAKRMNIQDLWSKPQVENTEETTSKDGC
                     PKPKDDEEFIISSDDIKTEGKKGKNKTGRGKKHTAFSSKGLSDEEYDEYKRIREERNG
                     KYSIEEYLQDRDKYYEEVAIARATEEDFCEEEEAKIRQRIFRPTRKQRKEERASLGLV
                     TGSEIRKRNPDDFKPKGKLWADDDRSVDYSEKLNFEAPPSIWSRIVNFGSGWGFWVSP
                     SLFITSTHVIPQGAKEFFGVPIKQIQVHKSGEFCRLRFPKPIRTDVTGMILEEGAPEG
                     TVVTLLIKRSTGELMPLAARMGTHATMKIQGRTVGGQMGMLLTGSNAKSMDLGTTPGD
                     CGCPYIYKRGNDYVVIGVHTAAARGGNTVICATQGSEGEATLEGGDNKGTYCGAPILG
                     PGSAPTLSTKTKFWRSSTTSLPPGTYEPAYLGGKDPRVKGGPSLQQVMREQLKPFTEP
                     RGKPPKPSVLEAAKKTIINVLEQTIDPPEKWSFAQACASLDKTTSSGHPHHMRKNDCW
                     NGESFTGKLADQASKANLMFEEGKNMTPVYTAALKDELVKTDKIYGKIKKRLLWGSDL
                     ATMIRCARAFGGLMDELKAHCVTLPIRVGMNMNEDGPIIFERHSRYTYHYDADYSRWD
                     STQQRAVLAAALEIMVKFSPEPHLAQVVAEDLLSPSVVDVGDFTISINEGLPSGVPCT
                     SQWNSIAHWLLTLCALSEVTNLSPDTIQANSLFSFYGDDEIVSTDIKLDPEKLTAKLR
                     EYGLKPTRPDKTEGPLVISEDLNGLTFLRRTVTRDPAGWFGKLEQSSILRQMYWTRGP
                     NHGDPSETMIPHSQRPIQLMSLLGEAALHGPAFYSKISKLVIAELKEGGMDFYVPRQE
                     PMFRWMRFSDLSTWEGDRNLAPSFVNEDGVE"
     CDS             5084..6706
                     /note="major capsid protein; ORF2"
                     /codon_start=1
                     /product="VP1"
                     /protein_id="ARR95958.1"
                     /translation="MKMASSDANPSDGSAANLVPEVNNEVMALEPVVGAAIAAPVAGQ
                     QNVIDPWIRNNFVQAPGGEFTVSPRNAPGEILWSAPLGPDLNPYLSHLARMYNGYAGG
                     FEVQVILAGNAFTAGKIIFAAVPPNFPTEGLSPSQVTMFPHIIVDVRQLEPVLIPLPD
                     VRNNFYHYNQLNDSTIKLIAMLYTPLRANNAGDDVFTVSCRVLTRPSPDFDFIFLVPP
                     TVESRTKPFSVPILTVEEMTNSRFPIPLEKLFTGPSSAFVVQPQNGRCTTDGVLLGTT
                     QLSPVNICTFRGDITHTTGSHNYTMNLASQNWNSYDPTEEIPAPLGTPDFVGKIQGVL
                     TQTTRADGSTRGHKATVYTGSADFAPKLGRVQFETDTNHDFEANQNTKFTPVGVIQDG
                     GTTHRNEPQQWVLPSYSGRNTHNVHLAPAVAPTFPGEQLLFFRSTMPGCSGYPNMDLD
                     CLLPQEWVQFFYQEAAPAQSDVALLRFVNPDTGRVLFECKLHKSGYVTVAHTGQHDLV
                     IPPNGYFRFDSWVNQFYTLAPMGNGTGRRRVV"
     CDS             6706..7512
                     /note="minor structural protein; ORF3"
                     /codon_start=1
                     /product="VP2"
                     /protein_id="ARR95959.1"
                     /translation="MAGAFFAGLASDVLGSGLGSLINAGAGAINQKVEFENNRKLQQA
                     SFQFSSNLQQASFQHDKEMLQAQIEATKRLQQEMMKVKQAMLLEGGFSETDAARGAIN
                     APMTKVLDWSGTRYWAPDARTTTYNAGRFSTPQPSGALPGRANLRDVVPARGSSSKAS
                     NSSTATSVYSNQTTSTRLGSTAGSGTSVSSLPSTARTRSWVEDQNRNLSPFMRGAHNI
                     SFVTPPSSRSSSQGTVSTVPKEILDSWTGAFNTRRQPLFAHIRKRGESRA"
     3'UTR           7513..7554
ORIGIN      
        1 tgaatgaaga tggcgtctaa cgacgcttcc gctgccgctg ttgctaacag caacaacgac
       61 accgcaaaat cttcaagcga cggagtgctt tctagcatgg ctgtcacttt taaacgagcc
      121 ctcggggcgc ggcctaaaca gccccccccg agggaaaaac cacaaagacc cccacgacca
      181 cctactccag aactggttaa aaatattccc cctcccccac ctaacggaga ggatgaaata
      241 gtggtttctt atagtgtcaa agatggtgtc tccggcttgc ctgacctatc caccgtcagg
      301 caaccggaag aatctaacac ggccttcagt gtccctccac tcaatcagag ggagaataga
      361 gatgctaagg agccacttac tggaacaatc ctggaaatgt gggacggtga aatctaccac
      421 tatggcctgt atgtggagcg aggtcttgtg ctaggtgtgc acaaaccacc agctgccatc
      481 agcctcgcta aggttgagct agcaccactc tccttgtact ggagacctgt gtacactcct
      541 cagtacctca tctccccaga cactcttaag aaactatccg gagaaacgtt cccctacaca
      601 gcctttgaca acaactgtta tgccttttgt tgctgggtcc tggacctaaa cgactcgtgg
      661 ctaagcagga gaatgatcca gagaacaact ggtttcttca ggccctacca agactggaat
      721 aggaaacccc ttcccactat ggatgactcc aaaataaaga aggtggccaa cattttcctg
      781 tgtgctctgt cctcgctgtt caccagaccc ataaaagata taatagggaa gataaggcct
      841 cttaacatcc tcaacatctt agcctcatgt gattggactt ttgcaggcat agtggagtcc
      901 ctgatactct tggcagaact ctttggagtt ttctggacac ccccagatgt gtctgcgatg
      961 attgccccct tacttggtga ctacgagcta caagggcctg aggaccttgc agtggagctc
     1021 gttcccgtgg tgatgggggg aattggtttg gtgctaggat tcaccaagga gaagattggg
     1081 aagatgttgt catctgccgc gtccaccttg agagcttgta aagaccttgg tgcatatggg
     1141 ctagagatcc taaagttggt catgaagtgg ttctttccga aaaaggagga ggcaaatgag
     1201 ctggccatag tgaggtctat cgaggatgca gtcctagatc tcgaggcaat cgaaaacaat
     1261 cacatgacca ccttactcaa agacaaagac agtctggcaa cctatatgag aacacttgac
     1321 cttgaggagg agaaagccag gaaactctca accaagtctg cctcacccga catcgtgggc
     1381 acaatcaacg ccctcctggc gagaatcgct gccgcacgtt ctctggtgca tcgagcaaag
     1441 gaggagcttt ccagcagacc aagacctgtg gttctgatga tatcaggcag gccaggaata
     1501 gggaagaccc acctcgctag ggaagtggct aagagaatcg cagcctccct tacaggagat
     1561 cagcgtgtgg gcctcatccc acgcaatggc gtcgaccatt gggatgcgta caagggggag
     1621 agggtcgtcc tatgggacga ctatggaatg agcaacccta ttcacgatgc cctcaggctg
     1681 caagaactcg ctgacacttg ccccctcact ctaaactgtg acagaattga aaacaaagga
     1741 aaggtctttg acagcgatgt catcattatc accactaatt tggccaaccc agcaccactg
     1801 gactatgtca actttgaagc gtgttcgagg cgcatcgact tcctcgtgta tgcagaagcc
     1861 cctgaagtcg aaaaggcgaa gcgtgacttc ccaggtcagc ctgacatgtg gaagaacgct
     1921 ttcagttctg atttctcaca cataaaacta gcactggccc cgcagggtgg tttcgacaag
     1981 aacgggaaca ccccacacgg aaagggcgtc atgaagactc tcaccactgg ctcccttatt
     2041 gcccgggcat cagggctact ccatgagagg ttagatgagt ttgaactaca gggcccagct
     2101 ctcaccgtct tcaatttcga tcgcaataaa gtgcttgcct ttagacaact tgctgctgaa
     2161 aacaaatatg ggttgatgga caccatgaga gttgggaaac agctcaagga tgtcaggacc
     2221 atgccagaac ttagacaagc actcaagaat gtctcaatca agaagtgcca aatagtgtac
     2281 agtggttgca cctacacact tgaatctgat ggcaagggca atgtgagggt tgacagggtc
     2341 caaaacgccg ccgtgcagac caataatgag ctggctggtg ctctgcacca tttgaggtgc
     2401 gccaggatta gatactatgt caagtgtgtc caagaggccc tgtactccat cattcaaatt
     2461 gctggggctg catttgtcac cacgcgcatc gccaagcgca tgaacataca agacctatgg
     2521 tccaagccac aagtggaaaa cacagaggag actaccagca aggacgggtg cccaaaacct
     2581 aaagatgatg aggagtttat catttcatcc gacgacatca aaactgaggg caagaaaggg
     2641 aagaacaaaa ctggccgcgg caagaagcac acagcgtttt caagcaaagg cctcagtgat
     2701 gaagagtacg atgagtacaa gaggatcagg gaggaaagga atggcaagta ctccatagaa
     2761 gagtaccttc aggacaggga caagtactat gaggaggtag ccattgccag ggcgactgag
     2821 gaagacttct gtgaagagga agaggccaag atccggcaaa ggatttttag gccaacaagg
     2881 aaacaacgca aggaggaaag agcttctctc ggtctggtca caggctctga aattaggaaa
     2941 agaaacccag atgacttcaa acccaagggg aaattgtggg ctgacgatga caggagtgtg
     3001 gactatagtg agaaactcaa ttttgaggcc ccaccaagca tctggtcgag aatagtcaat
     3061 tttggttcag gctgggggtt ctgggtctct cccagtctgt tcataacatc aacccatgtc
     3121 ataccccagg gtgcaaagga gttctttgga gtccctatca aacaaataca ggtacacaag
     3181 tcaggcgagt tctgtcgctt gagattccca aaaccaatca ggactgatgt gacaggcatg
     3241 atcttagaag aaggcgcgcc tgagggcacc gtggtcacac tactcatcaa gaggtccact
     3301 ggggaactca tgcccctagc agctaggatg gggacccacg cgaccatgaa gattcaaggg
     3361 cgcactgttg gaggccagat gggcatgctt ctgacaggat ccaacgccaa gagcatggac
     3421 ctgggcacta caccaggtga ttgtggctgc ccctatatct acaagagagg taatgactat
     3481 gtggtcattg gagtccacac ggctgccgca cgtgggggaa acactgtcat atgtgccacc
     3541 caggggagtg aaggagaagc tacacttgaa ggtggtgaca acaaggggac gtactgtggt
     3601 gcaccaatcc taggcccagg gagtgcccca acacttagca ccaagactaa attctggaga
     3661 tcgtccacaa catcactccc acctggcacc tatgaaccag cctaccttgg tggcaaggac
     3721 cctagagtca agggtggccc ttcgctgcag caagttatga gggaacagtt gaagccattc
     3781 acagagccca ggggtaagcc accaaaacca agcgtattag aagctgccaa gaagaccatc
     3841 atcaatgttc ttgagcaaac aattgaccca cctgagaaat ggtcgttcgc acaagcttgc
     3901 gcgtcccttg acaagaccac ttccagtggt catccgcacc acatgcggaa aaacgactgc
     3961 tggaatgggg agtccttcac aggcaagctg gcagaccagg cttccaaggc caacctgatg
     4021 tttgaagaag ggaagaacat gaccccagtc tacacagctg cgctcaagga tgagttagtc
     4081 aaaactgaca aaatttatgg taagatcaag aagaggcttc tctggggttc ggacttggcg
     4141 accatgatcc ggtgtgctcg agcattcgga ggcctaatgg atgaactcaa agcacactgt
     4201 gtcacactcc ccattagagt tggcatgaat atgaatgagg atggccccat catcttcgag
     4261 aggcattcca ggtacacata tcattatgat gctgattact ctcgatggga ctcaacacaa
     4321 cagagagccg tgttggcagc agctctagaa atcatggtta aattctcccc agaaccacac
     4381 ctggctcagg tagtcgcgga agaccttctt tctcctagcg tggtggacgt gggcgacttc
     4441 acaatatcaa tcaacgaggg tcttccctct ggagtgccct gcacctccca atggaattcc
     4501 atcgcccact ggcttctcac tctctgcgcg ctctctgaag tcacaaattt gtccccagac
     4561 accatacagg ctaattccct cttctctttt tatggtgatg atgaaattgt tagtacagat
     4621 ataaaattgg acccagagaa attaacagca aagctcaggg aatatgggtt gaaaccaacc
     4681 cgccctgata aaaccgaagg accccttgtt atctctgaag atttaaatgg cctaactttc
     4741 ctgcggagga ctgtgacccg cgacccagct ggttggtttg gaaaattgga gcagagttca
     4801 atactcaggc aaatgtactg gactaggggc cccaaccatg gagacccttc tgagacaatg
     4861 attccacact cccaaagacc tatacaattg atgtccctac tgggggaggc cgctctccac
     4921 ggcccagcat tctacagcaa aatcagcaag ctggtcattg cagagctaaa agagggcggc
     4981 atggattttt acgtgcccag acaagagcca atgttcaggt ggatgagatt ctcagatctg
     5041 agcacgtggg agggcgatcg caatctggct cccagttttg tgaatgaaga tggcgtcgag
     5101 tgacgccaac ccatctgatg ggtccgcagc caacctcgtc ccagaggtca acaatgaggt
     5161 tatggctctg gagcccgttg ttggtgccgc cattgcggca cctgtagcgg gccaacaaaa
     5221 tgtcattgac ccctggatta gaaacaactt tgtacaagcc cctggtgggg agtttacagt
     5281 atcccctaga aacgctccag gtgaaatact atggagcgcg cccttaggcc ctgacctaaa
     5341 tccctaccta tcccacttgg ccaggatgta caatggttat gcaggtggtt ttgaagtgca
     5401 ggtaattctt gcggggaacg cgttcaccgc cgggaagatc atatttgcag cagtcccacc
     5461 aaatttccca actgaaggct tgagccctag ccaggtcact atgttccccc atataatagt
     5521 agatgttagg caactagaac ctgtgttgat ccctttaccc gatgttagga ataatttcta
     5581 tcactacaat caattaaatg attccaccat taagttgata gcaatgttgt acacaccact
     5641 tagggctaat aatgctgggg acgatgtctt cacagtttcc tgtcgagtcc tcacgagacc
     5701 gtcccccgat tttgatttca tatttctagt gccacccaca gttgagtcaa gaactaaacc
     5761 attctctgtc ccgattttaa ctgttgagga gatgaccaat tcaagattcc ccattccctt
     5821 ggaaaagttg ttcacgggcc ccagcagtgc ctttgttgtt caaccacaaa acggcagatg
     5881 cacgactgat ggcgtgctcc taggcaccac ccaactgtct cctgtcaaca tctgcacctt
     5941 cagaggggat atcacccata ccacaggtag ccataactac acaatgaact tggcttccca
     6001 aaactggaac agttacgatc caacagaaga aatcccagct cctctaggga ctccagattt
     6061 tgtggggaag attcaaggtg tgctcaccca aaccacaagg gcagatggct cgacacgcgg
     6121 ccacaaggct acagtgtaca ctgggagcgc cgactttgct ccaaaactgg gtagggttca
     6181 atttgaaact gacacaaacc atgattttga agccaaccaa aacacaaagt tcaccccagt
     6241 cggcgtcatc caagatggtg gcaccaccca ccgaaatgaa ccccaacagt gggtgctccc
     6301 aagttactcg ggcagaaata ctcacaatgt gcacctggcc cccgctgtag cccccacttt
     6361 cccgggcgag caacttctct tcttcaggtc cactatgccc ggatgcagcg ggtaccccaa
     6421 catggatttg gactgtctgc tcccccagga atgggtgcag ttcttctacc aagaggcagc
     6481 cccagcacaa tctgatgtgg ctctgttaag atttgtaaat ccagacacag gcagggtttt
     6541 atttgagtgt aagcttcata aatcaggcta tgttacagtg gctcacactg gccaacatga
     6601 tttggttatc ccccccaatg gttactttag gtttgactcc tgggttaatc agttctacac
     6661 gcttgccccc atgggaaatg gaacggggcg tagacgtgtg gtataatggc tggagctttc
     6721 tttgctggat tggcatctga tgtccttggc tctggacttg gttctcttat caatgctggg
     6781 gctggggcca tcaaccaaaa agttgaattt gaaaataaca gaaaattgca acaagcttcc
     6841 ttccaattta gcagcaatct gcaacaggct tcttttcaac atgacaaaga gatgctccaa
     6901 gcacaaattg aggccacaaa aagattacaa caggagatga tgaaagttaa gcaggcaatg
     6961 ctcctagagg gtgggttctc tgagacagat gcagcccgcg gggcaatcaa cgcccccatg
     7021 acaaaagttt tggactggag cgggacaagg tactgggcac ccgatgccag gactacaaca
     7081 tataatgcag gccgcttttc caccccccaa ccatcggggg cactgccagg aagggctaat
     7141 cttagggatg ttgttcccgc tcggggttcc tctagcaaag cttctaactc ttctactgcc
     7201 acttctgtgt actcaaatca aactacttca acgagacttg gttctacagc tggttctggc
     7261 accagtgtct cgagcctccc gtcaactgca agaactagga gttgggttga ggaccaaaat
     7321 aggaatttgt cacctttcat gaggggggcc cacaacatat cgtttgtcac cccaccatct
     7381 agcagatcct ctagccaagg cacagtctca accgtgccta aagagatttt ggactcctgg
     7441 actggcgctt tcaacacgcg caggcagccc ctcttcgctc acattcgtaa gcgaggggag
     7501 tcacgggcgt aatgtgaaaa gacaaaattg attatctttc tttttcttta gtgt
//