Typing tool

Complete norovirus genomes

KY947548  GII.13
 GII.P16

Length: 7,457 | 3 CDS

ORF1: 4..5100
ORF2: 5081..6709
ORF3: 6709..7440
LOCUS       KY947548                7457 bp ss-RNA     linear   VRL 18-MAY-2017
DEFINITION  Norovirus GII strain Hu/USA/2015/GII.P16-GII.13/Carlsbad 4246
            polyprotein, VP1, and VP2 genes, complete cds.
ACCESSION   KY947548
VERSION     KY947548.1
KEYWORDS    .
SOURCE      Norovirus GII
  ORGANISM  Norovirus GII
            Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes;
            Picornavirales; Caliciviridae; Norovirus.
REFERENCE   1  (bases 1 to 7457)
  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 7457)
  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..7457
                     /organism="Norovirus GII"
                     /mol_type="genomic RNA"
                     /strain="Hu/USA/2015/GII.P16-GII.13/Carlsbad 4246"
                     /isolation_source="stool"
                     /host="Homo sapiens"
                     /db_xref="taxon:122929"
                     /country="USA"
                     /collection_date="03-Jan-2016"
                     /note="genotype: GII.P16-GII.13"
     5'UTR           1..3
     CDS             4..5100
                     /note="nonstructural protein; ORF1"
                     /codon_start=1
                     /product="polyprotein"
                     /protein_id="ARR95960.1"
                     /translation="MKMASNDATVAVACNNNNDKEKSSGEGLFTNMSSTLKKALGARP
                     KQPAPRDNSQKPPRPPTPELVKRMPPPPPNGEEEEPVIRYEVKSGISGLPELTTVPQP
                     DVANTAFSVPPLSLRENREAKEPLTGAILEMWDGEIYHYGLYVEKGLVLGVHKPPAAI
                     SMAKVELTPLSLYWRVVYTPQYLISPETLRRLNGEAFPYTAFDNNCYAFCCWVLDLND
                     SWLSRRMVQRTTGFFRPYQEWNRKPLPTMDDSKIKKVANIFLCSLSTLFTRPIKDLMG
                     KIKPLNILNILATCDWTFAGIVESLILLAELFGVFWTPPDVSAMIAPLLGDYELQGPE
                     DLAVELVPVVMGGIGLVLGFTKEKIGKMLSSAASTLRACKDLGAYGLEILKLVMKWFF
                     PKKEEANELAMVRAIEDAVLDLEAIENNHMTTLLKDKDSLATYMKTLDMEEEKARRLS
                     TKSASPDIVGTINALLARIAAARSLVHRAKEELSSRIRPVVVMISGKPGIGKTHLARE
                     VARKVASTLTGDQRVGLIPRNGVDHWDAYKGERVVLWDDYGMSNPIHDALRIQELADT
                     CPLTLNCDRIENKGKVFDSEVIIITTNLANPAPLDYVNFEACSRRIDFLVYAEAPEVE
                     KAKRDFPGQPDMWKDAFKSDFSHIKLQLAPQGGFDKNGNTPHGKGVMKTLTTGSLIAR
                     ASGLLHERMDEFELQGPTVTTFNFDRNRIAAFRQLAAENKYGLVDTMRVGNQLKGVKT
                     MEELKQAIKNVTIKRCRIIYGGSTYDLESDGKGRVLVEKVKNTSVQTNNELAGALHHL
                     KHARIRYYVKCVQETVYSIIQIAGAAFVTTRIVRRMNIQELWSKPPLDQIESETKEEA
                     PKLEDDEFIISSKDIKEEGKKGKNKTGRGKKHTAFSSKGLSDEEYDEYKRIREERNGK
                     YSIEEYLQDRDRYYEELAIAKATEEDFCEEEEIKIRQRIFRPTRKQRKEERATLGLVT
                     GSEIRKRNPDDFKPKGKLWADDNRSVDYNEKLDFEAPPSIWSRIVSFGSGWGFWVSPS
                     LFITSTHVIPAGITEAFGVPIKQIQVHKSGEFCRFRFPKPIRSDVTGMILEEGAPEGT
                     VATVLIKRPTGELMPLAARMGTHATMKIQGRMVGGQMGMLLTGSNAKGMDLGTTPGDC
                     GCPYIYKRGNDYIVIGVHTAAARGGNTVICATQGSEGEATLEGGDDKGTYCGAPILGP
                     GGAPKLSTKTKFWRSSNTPLPPGTYEPAYLGGRDPRVKGGPSLQQVMRDQLKPFTEPR
                     GKPPRPSVLEAAKQTIINVLEQTLDPPQKWTYAQACASLDKTTSSGHPHHVRKNEFWN
                     GETFTGKLADQASKANLMFEEGKHMTPVYTAALKDELVKTDKVYGKIKKRLLWGSDLS
                     TMIRCARSFGGLMDEMKAHCISLPVRVGMNMNEDGPIIFEKHSRYKYHYDADYSRWDS
                     TQQRAVLAAALEIMVRFSAEPQLAQIVAEDLLAPSVVDVGDFKISINEGLPSGVPCTS
                     QWNSIAHWLLTLCALSEVTKLSPDIVQANSMFSFYGDDEIVSTDIKLDPEKLTTKLKE
                     YGLKPTRPDKTEGPLIISEDLNGLTFLRRTVTRDPAGWFGKLDQSSILRQMYWTRGPN
                     HEDPNETMIPHSQRPIQLMALLGEASLHGPSFYSKISKLVITELKEGGMDFYVPRQEP
                     MFRWMRFSDLSTWEGDRNLAPNFVNEDGVE"
     CDS             5081..6709
                     /note="major capsid protein; ORF2"
                     /codon_start=1
                     /product="VP1"
                     /protein_id="ARR95961.1"
                     /translation="MKMASNDAAPSNDGAASLVPEAINETMPLEPVAGASIAAPVAGQ
                     TNIIDPWIRTNFVQAPNGEFTVSPRNSPGEILLNLELGPDLNPYLAHLSRMYNGYAGG
                     VEVQVLLAGNAFTAGKILFAAIPPNFPVDMISPAQITMLPHLIVDVRTLEPIMIPLPD
                     VRNVFYHFNNQPQPRMRLVAMLYTPLRSNGSGDDVFTVSCRVLTRPTPDFEFIYLVPP
                     SVESKTKPFTLPILTISELTNSRFPIPIEQLYTAPNENNVVQCQNGRCTLDGELQGTT
                     QLLSSAVCSYRGRTVANSGDNWDQNLLQLTYPSGASYDPTDEVPAPLGTQDFSGILYG
                     VLTQDNVSEGTGEAKNAKGVYISTTSGRFTPKIGTIGLHSITENVHPNQQSRFTPVGV
                     AQNENTPFQQWVLPHYAGALALNTNLAPAVAPTFPGEQLLFFRSRVPCVQGLRGQDAF
                     IDCLLPQEWVNHFYQEAAPSQADVALIRYVNPDTGRTLFEAKLHRSGFITVSHTGTYP
                     LVVPPNGHFRFDSWVNQFYSLAPMGTGNGRRRVQ"
     CDS             6709..7440
                     /note="minor structural protein; ORF3"
                     /codon_start=1
                     /product="VP2"
                     /protein_id="ARR95962.1"
                     /translation="MAGAFIAGLAGDMLTSAVGSLTSAGANAINQKLNFDYNKQLQNA
                     SFQHDKEMLQAQIDATKKLQSEMIAIKHGVLTAGGFSPADAARGAVNAPMTRVLDWSG
                     TRYYAPNSVQTTSYSGQFTPSPVHRAQVKSPSNSSQRTAAPSSIRSLSTQSTSLGSTS
                     SGGSSTISSSSRTADWVQQQRALSPYMQGALQTAYVTPPSSRASSVSSVSTVPKGVLD
                     SWTPVFNTRRQPLFAHLRKRGESQA"
     3'UTR           7441..7457
ORIGIN      
        1 tgaatgaaga tggcgtctaa cgacgctacc gttgccgttg cttgcaacaa caacaacgac
       61 aaggaaaaat cttcaggtga aggcttattc acaaacatgt cttccacctt aaagaaagcc
      121 ctcggggccc ggcccaaaca gcctgccccg agggacaact cacaaaagcc cccgagacca
      181 ccaactcccg agttggttaa gaggatgccc cctcccccac ctaacggaga agaagaagaa
      241 ccagtcatta ggtatgaggt taagagtgga atctctggcc tgcccgagct cacaacagtc
      301 cctcaaccgg atgtggccaa cacggcattc agtgtcccac cgctgagctt gagagaaaac
      361 agggaggcca aggaaccgct gacaggggca atattagaga tgtgggatgg agagatatac
      421 cactatggcc tgtacgtgga gaaaggctta gtgttgggtg tgcacaaacc acctgcagct
      481 ataagcatgg caaaagtgga gctgacgccg ttgtcattgt actggcgtgt ggtctacacc
      541 ccccaatacc tcatctcccc tgaaactctc aggaggctca acggagaggc attcccttac
      601 actgcctttg acaacaactg ctatgccttt tgctgttggg tattagacct caatgactca
      661 tggcttagca ggaggatggt gcaaagaaca acaggcttct tcagacctta ccaagagtgg
      721 aacagaaaac ccctgcccac tatggatgac tccaaaatca agaaggtggc aaacatattc
      781 ctgtgctcat tgtccacgtt gttcaccaga cctataaaag acctcatggg aaaaattaag
      841 ccattaaaca tcttgaacat cctggcaacg tgtgactgga cattcgccgg aatagtggag
      901 tctcttatat tacttgctga actctttgga gttttctgga cacccccaga tgtgtctgct
      961 atgatcgctc ctttacttgg agactacgag ttgcaggggc cagaagacct tgccgttgag
     1021 ctcgtacctg tagtaatggg agggattggt ttggtgttgg gattcaccaa agagaaaatt
     1081 ggaaaaatgt tgtcctcagc agcatcaacg ctcagggctt gtaaagatct tggtgcctat
     1141 ggcttagaga tactcaaact ggtcatgaag tggttcttcc caaagaaaga agaggccaat
     1201 gagctagcca tggtgagagc tatagaggat gctgtactgg atcttgaggc aatagaaaat
     1261 aatcacatga caactttgtt gaaagacaaa gacagcctag caacctacat gaaaacacta
     1321 gacatggagg aggaaaaggc cagaagattg tccacaaaat ctgcatcccc tgacatagtt
     1381 gggacgatca acgccctgct ggctcgaata gcagcggcta ggtcactagt ccacagggcc
     1441 aaggaggagt tgtctagcag gataagacca gtggttgtta tgatatctgg taagccaggg
     1501 ataggcaaaa ctcatttggc cagggaagtg gcaagaaagg tggcatccac tctcacaggg
     1561 gatcaaagag tcgggctcat accgagaaac ggtgtggacc attgggatgc atacaaaggt
     1621 gagagagtcg tgctgtggga cgactatggc atgagcaacc ccattcatga tgctctgcgc
     1681 atacaagaat tggctgacac gtgtcccctt accttaaatt gtgacagaat tgaaaataag
     1741 ggaaaagttt ttgacagtga agtcataata atcacaacaa acctcgccaa tccagctcca
     1801 cttgattatg ttaactttga ggcctgttcc aggagaattg acttcctggt gtacgccgag
     1861 gcaccagaag tagaaaaggc aaaacgagat tttcctggtc aaccagatat gtggaaggac
     1921 gccttcaagt cggacttttc acacatcaag ctgcaacttg cacctcaggg cggctttgac
     1981 aagaatggca acaccccaca tggaaaagga gtgatgaaga ccctcaccac cggctccctg
     2041 atcgcccgtg catcaggctt actgcatgag aggatggatg aatttgaact ccaaggcccc
     2101 acagtcacca ccttcaattt tgaccggaac agaatcgctg cattcagaca attggctgca
     2161 gaaaacaagt atggattggt ggacaccatg agagttggca atcaattaaa aggggtgaaa
     2221 accatggaag aactcaaaca agcaatcaag aatgtgacca tcaagaggtg ccggatcatc
     2281 tacggcggct ccacgtatga ccttgaatct gacggtaagg gcagagttct ggtggaaaag
     2341 gtcaagaaca cctccgtaca gaccaacaac gaattggccg gagccctgca tcacctcaaa
     2401 catgcccgaa tcaggtacta tgtcaaatgt gtgcaagaaa cagtctactc tattatacaa
     2461 atcgccggcg ctgcgtttgt caccacacgc atagtacgcc gcatgaacat acaagagctt
     2521 tggtcgaagc caccattaga tcaaattgaa tcagagacca aggaagaggc ccccaagtta
     2581 gaagatgacg agttcatcat atcttctaag gacatcaagg aggaaggaaa gaagggcaaa
     2641 aacaaaactg gccgtggcaa gaaacatact gcattctcta gcaagggctt gagcgatgag
     2701 gagtacgacg agtacaagag gataagagaa gagagaaatg ggaagtactc tatagaggag
     2761 tatcttcaag acagagacag gtactatgag gaactcgcca tcgccaaggc cacggaagaa
     2821 gacttctgtg aggaggagga gatcaaaatc cgtcagagga tcttccgtcc caccaggaag
     2881 caaaggaagg aagagagggc cacactaggg ctagtaactg gttcagaaat cagaaaaaga
     2941 aaccctgatg actttaaacc taaagggaaa ctgtgggctg atgacaacag aagtgttgac
     3001 tacaatgaga aactggactt tgaggccccc ccaagcatat ggtctaggat tgtgagtttt
     3061 ggttctggtt ggggcttctg ggtgtcacca agcctgttca taacatcaac tcacgtaatc
     3121 cctgcaggca taacagaggc atttggagtc cccatcaagc aaatccaggt ccacaaatca
     3181 ggtgaatttt gccggttcag attcccaaaa ccaattagat cagatgtgac aggaatgatc
     3241 ttggaagaag gtgcgcctga gggcaccgtg gcaaccgtgc ttatcaaacg ccctaccgga
     3301 gagctcatgc cccttgcggc cagaatggga acacacgcaa ccatgaaaat tcagggccgc
     3361 atggttggcg gacagatggg tatgttgctc actggttcaa atgctaaagg aatggatttg
     3421 ggaacaactc ctggtgattg tggctgtccc tacatctaca aaaggggcaa tgactatata
     3481 gtcattgggg tgcacacagc agcagcccgt ggtggaaaca ccgtcatctg tgccacacag
     3541 ggaagtgagg gtgaggcaac ccttgagggt ggagatgaca aaggaacata ttgtggggca
     3601 cccattctag gccccggggg ggcaccaaaa ttgagcacca aaaccaaatt ttggaggtca
     3661 tcgaacacgc ctcttccacc agggacgtat gagcctgcct acctcggtgg ccgtgacccg
     3721 cgtgttaagg gtgggccctc cttgcagcag gtaatgagag accagttgaa gccattcacc
     3781 gagcccaggg gtaaacctcc aagaccaagt gtgttggaag cagccaaaca aaccatcatc
     3841 aatgtcctcg aacaaaccct ggaccctcca caaaaatgga catacgcaca ggcgtgtgct
     3901 tcacttgaca aaaccacctc cagcgggcac ccccaccacg tccgaaagaa tgaattctgg
     3961 aatggtgaga ccttcactgg taaattggca gaccaagcat caaaagcaaa tctaatgttt
     4021 gaggaaggga aacatatgac accagtgtat acagcagccc tcaaggatga gctggtcaag
     4081 actgacaaag tctatggaaa gatcaagaag agactgctct ggggctctga cttgtccacc
     4141 atgatccggt gcgccaggtc ctttggtggg ctcatggatg agatgaaagc acactgcata
     4201 tcactcccag tccgagttgg catgaacatg aatgaagatg gtccaataat atttgagaag
     4261 cactccagat acaagtatca ctatgatgca gactactccc gctgggattc aacacaacag
     4321 agggcagtac tagcagcagc cttggagatc atggtcaggt tctctgcaga gccacaattg
     4381 gcacaaatag tcgctgagga tctgctggcc cccagtgtgg tagatgtagg agactttaaa
     4441 atttcaataa atgaagggct cccctctggt gtaccatgca cttctcaatg gaattccatc
     4501 gcacactggc tgctaaccct ctgcgccttg tctgaagtca ccaaactgtc ccccgacatt
     4561 gtacaggcaa actccatgtt ctcattttac ggtgatgacg agattgtcag caccgatata
     4621 aaattggacc ctgaaaagtt aaccaccaaa ttgaaggagt acggcctgaa accaactcgc
     4681 ccagacaaaa ccgagggacc cctgatcatc agtgaggatt tgaacggact cactttcctc
     4741 cggagaacgg tgactcgtga cccagctggc tggtttggaa aattggacca aagctcaata
     4801 ttgaggcaga tgtactggac tagaggacca aatcatgaag accccaacga gacaatgata
     4861 ccccactctc aaagacccat acagctcatg gcactgcttg gtgaggcctc ccttcacgga
     4921 ccctctttct acagcaaaat tagtaagttg gtcataactg aactcaaaga aggtgggatg
     4981 gatttttacg tgccaaggca ggaacccatg ttcaggtgga tgaggttttc tgacttgagc
     5041 acgtgggagg gcgatcgcaa tctggctccc aattttgtga atgaagatgg cgtcgaatga
     5101 cgccgctcca tcgaatgatg gtgcagctag tctcgtacca gaggccatta atgagactat
     5161 gccattggaa cccgttgctg gcgcatctat tgctgcccca gtggcgggac aaactaacat
     5221 aattgacccc tggataagaa caaattttgt gcaagcccct aatggagagt tcacagtatc
     5281 accgagaaat tcccctggag agattctatt aaatttagag ttaggaccag atttgaatcc
     5341 ttatttggcc catctgtcaa ggatgtacaa tggatatgcc ggaggtgttg aggtgcaagt
     5401 gcttcttgct gggaacgcgt tcacagcagg aaagatatta tttgcagcaa tcccacccaa
     5461 ctttcctgta gatatgatta gcccagctca aattactatg cttccccatt tgattgtaga
     5521 tgttaggaca ttggaaccta ttatgatacc cttaccagat gtcaggaatg tgttctatca
     5581 ttttaataat caaccccaac ctaggatgag attagtggct atgctctata ccccattgag
     5641 atctaatggt tcaggagatg atgtctttac tgtgtcttgt agagtgttga ctaggccaac
     5701 ccctgacttt gaatttattt acctagtgcc tccctctgta gagtccaaaa ctaaaccatt
     5761 cacacttcca atattgacca tttctgaact aaccaactcc cggtttccca tcccaattga
     5821 gcaactgtat acggccccaa atgagaataa tgttgtacag tgtcaaaatg gaaggtgcac
     5881 cttggatgga gagcttcagg gcaccaccca gctgctatca agtgcagttt gctcttacag
     5941 gggtaggact gtggctaaca gtggggacaa ttgggaccag aatctgctcc agctgaccta
     6001 cccaagcggt gcaagctatg accccactga tgaagtacca gcacccttgg gcacccagga
     6061 tttcagtggg atattgtatg gggtgttaac ccaagacaat gtaagtgagg gtacagggga
     6121 ggccaaaaat gctaagggag tatacatatc caccaccagt ggaagattca ccccaaaaat
     6181 tgggacaatt ggattgcatt caataactga aaatgtgcac cccaatcagc aatcacggtt
     6241 cacccccgtt ggagtcgctc agaatgaaaa cacccccttc cagcaatggg ttctaccaca
     6301 ctacgcaggt gctctcgctc taaacaccaa tttggcacct gctgttgccc cgactttccc
     6361 tggcgagcaa ttactgttct tcaggtcccg tgtcccatgt gttcaaggtc tgcgggggca
     6421 ggatgctttc atagattgtc tcctacctca agagtgggtg aaccattttt atcaagaggc
     6481 tgctccctcc caagcagacg ttgctctcat caggtatgtc aaccctgaca ctggtcgcac
     6541 gctgtttgag gccaaattgc acaggtcagg tttcattact gtgtcacaca ctggtaccta
     6601 cccccttgtg gtccccccaa atggtcattt caggtttgat tcttgggtta accaattcta
     6661 ctcactcgcc cccatgggaa ctggcaatgg gcgcagaaga gttcaataat ggcaggagca
     6721 tttatagctg gtctagccgg tgacatgctg acttctgctg ttggttcgct gacctctgca
     6781 ggagccaatg ccatcaatca gaaattgaat tttgattaca ataaacaact ccaaaacgca
     6841 tcctttcaac atgacaagga aatgttgcag gcccaaattg atgctacgaa gaagctccaa
     6901 tcagaaatga ttgcaattaa gcatggggtt ttgaccgcgg gcggcttttc cccagctgat
     6961 gcagccagag gggcagtcaa cgccccaatg actcgagtgt tggattggtc agggacacgc
     7021 tattacgctc caaattctgt gcaaaccacc agttattctg ggcaattcac cccctcgcca
     7081 gtccatcggg cgcaggtgaa gtccccttcc aattcatctc agcggactgc agctccaagc
     7141 agtatccgca gcctgtcaac ccaatcaact tctttaggct ccacctcctc aggggggtcc
     7201 tctacaatct cctctagttc gaggacagca gactgggtgc aacaacaaag ggctcttagc
     7261 ccgtacatgc agggagccct gcagacggca tacgtcacac cgccgtctag tagggcttcc
     7321 agtgtgagct ctgtctcaac agtgcccaaa ggggttttgg actcctggac acctgtgttt
     7381 aacacacgca ggcagccgct gtttgcacac ctcaggaaga ggggggagtc acaggcttag
     7441 tgaaaaggat aatcaac
//