Typing tool

Complete norovirus genomes

KY865306  GII.2
 GII.P16

Length: 7,499 | 3 CDS

ORF1: 5..5104
ORF2: 5085..6713
ORF3: 6713..7492
LOCUS       KY865306                7499 bp ss-RNA     linear   VRL 18-MAY-2017
DEFINITION  Norovirus GII strain Hu/USA/2016/GII.P16-GII.2/Santa Rosa 1764
            polyprotein, VP1, and VP2 genes, complete cds.
ACCESSION   KY865306
VERSION     KY865306.1
KEYWORDS    .
SOURCE      Norovirus GII
  ORGANISM  Norovirus GII
            Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes;
            Picornavirales; Caliciviridae; Norovirus.
REFERENCE   1  (bases 1 to 7499)
  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 7499)
  AUTHORS   Cannon,J.L., Barclay,L., Collins,N.R., Chhabra,P., Wikswo,M.E.,
            Castro,C.J., Magana,L.C., Gregoricus,N., Marine,R.L. and Vinje,J.
  TITLE     Direct Submission
  JOURNAL   Submitted (31-MAR-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..7499
                     /organism="Norovirus GII"
                     /mol_type="genomic RNA"
                     /strain="Hu/USA/2016/GII.P16-GII.2/Santa Rosa 1764"
                     /isolation_source="stool"
                     /host="Homo sapiens"
                     /db_xref="taxon:122929"
                     /country="USA"
                     /collection_date="30-Nov-2016"
                     /note="genotype: GII.P16-GII.2"
     5'UTR           1..4
     CDS             5..5104
                     /note="nonstructural protein; ORF1"
                     /codon_start=1
                     /product="polyprotein"
                     /protein_id="ARR95870.1"
                     /translation="MKMASNDATVAVACNNNNDKEKSSGEGLFTNMSSTLKKALGARP
                     KQPAPRDKPQKPPRPPTPELVKRIPPPPPNGEEEEEPVIRYEVKSGISGLPELTTVPQ
                     PDVANTAFSVPPLSLRENREAKEPLTGAILEMWDGEIYHYGLYVEKGLVLGVHKPPAA
                     ISMARVELTPLSLYWRVVYTPQYLISPETLRRLNGEAFPYTAFDNNCYAFCCWVLDLN
                     DSWLSRRMVQRTTGFFRPYQEWNRKPLPTMDDSKIKKVANIFLCSLSTLFTRPIKDLI
                     GKIKPLNILNILATCDWTFAGIVESLILFAELFGVFWTPPDVSAMIAPLLGDYELQGP
                     EDLAVELVPVVMGGIGLVLGFTKEKIGKMLSSAASTLRACKDLGAYGLEILKLVMKWF
                     FPKKEEANELAMVRAIEDAVLDLEAIENNHMTTLLKDKDSLATYMKTLDMEEEKARRL
                     STKSASPDIVGTINALLARIAAARSLVHRAKEELSSRIRPVVVMISGKPGIGKTHLAR
                     EVARKVASTLTGDQRVGLIPRNGVDHWDAYKGERVVLWDDYGMSNPIHDALRIQELAD
                     TCPLTLNCDRIENKGKVFDSEVIIITTNLANPAPLDYVNFEACSRRIDFLVYAEAPEV
                     EKAKRDFPGQPDMWKDAFKPDFSHIKLQLAPQGGFDKNGNTPHGKGVMKTLTTGSLIA
                     RASGLLHERMDEFELQGPTITTFNFDRNRITAFRQLAAENKYGLVDTMKVGNQLKGVK
                     TMEELKQAIRNVTIKRCQIIYGGSTYDLESDGKGKVLVEKVKNTSVQTNNELAGALHH
                     LKHARIRYYVKCVQEAVYSIIQIAGAAFVTTRIARRMNIQELWSKPQLDQNESETKEE
                     APKSEDDEFIISSKDIKEEGKKGKNKTGRGKKHTAFSSKGLSDEEYDEYKRIREERNG
                     KYSIEEYLQDRDRYYEELAIAKATEEDFCEEEEIKIRQRIFRPTRKQRKEERATLGLV
                     TGSEIRKRNPDDFKPKGKLWADDNRSVDYNEKLDFEAPPSIWSRIVSFGSGWGFWVSP
                     SLFITSTHVIPAGITEAFGVPIKQIQIHKSGEFCRFRFPKPIRPDVTGMILEEGAPEG
                     TVATVLIKRPTGELMPLAARMGTHATMKIQGRMVGGQMGMLLTGSNAKGMDLGTTPGD
                     CGCPYIYKRGNDYIAIGVHTAAARGGNTVICATQGSEGEATLEGGDDKGTYCGAPILG
                     PGGAPKLSTKTKFWRSSNTPLPPGTYEPAYLGGRDPRVKGGPSLQQVMRDQLKPFTEP
                     RGKPPRPSVLEAAKQTIINVLEQTLDPPQKWTYAQACASLDKTTSSGHPHHVRKNEFW
                     NGETFTGKLADQASKANLMFEEGKHMTPVYTAALKDELVKTEKIYGKIKKRLLWGSDL
                     STMIRCARSFGGLMDEMKAHCISLPVRVGMNMNEDGPIIFEKHSRYKYHYDADYSRWD
                     STQQRAVLAAALEIMVRFSAEPQLAQIVAEDLLAPSVVDVGDFKITINEGLPSGVPCT
                     SQWNSIAHWLLTLCALSEVTKLSPDIIQANSMFSFYGDDEIVSTDIKLDPEQLTAKLK
                     EYGLKPTRPDKTEGPLIISEDLNGLTFLRRTVTRDPAGWFGKLDQSSILRQMYWTRGP
                     NHEDPNETMIPHSQRPIQLMALLGEASLHGPSFYSKISKLVITELKEGGMDFYVPRQE
                     PMFRWMRFSDLSTWEGDRNLAPNFVNEDGVE"
     CDS             5085..6713
                     /note="major capsid protein; ORF2"
                     /codon_start=1
                     /product="VP1"
                     /protein_id="ARR95871.1"
                     /translation="MKMASNDAAPSTDGAAGLVPESNNEVMALEPVAGAALAAPVTGQ
                     TNIIDPWIRANFVQAPNGEFTVSPRNAPGEVLLNLELGPELNPYLAHLARMYNGYAGG
                     MEVQVMLAGNAFTAGKLVFAAVPPHFPVENLSPQQITMFPHVIIDVRTLEPVLLPLPD
                     VRNNFFHYNQKDDPKMRIVAMLYTPLRSNGSGDDVFTVSCRVLTRPSPDFDFTYLVPP
                     TVESKTKPFTLPILTLGELSNSRFPVSIDQMYTSPNEIISVQCQNGRCTLDGELQGTT
                     QLQVSGICAFKGEVTAHLHDNDHLYNVTITNLNGSPFDPSEDIPAPLGVPDFQGRVFG
                     IISQRDKHNSPGHNEPANRGHDAVVPTYTAQYTPKLGQIQIGTWQTDDLTVNQPVKFT
                     PVGLNDTEHFNQWVVPRYAGALNLNTNLAPSVAPVFPGERLLFFRSYIPLKGGYGNPA
                     IDCLLPQEWVQHFYQEAAPSMSEVALVRYINPDTGRALFEAKLHRAGFMTVSSNTSAP
                     VVVPANGYFRFDSWVNQFYSLAPMGTGNGRRRVQ"
     CDS             6713..7492
                     /note="minor structural protein; ORF3"
                     /codon_start=1
                     /product="VP2"
                     /protein_id="ARR95872.1"
                     /translation="MAGAFVAGLAGDVLSNGLSSLINAGANAINQRAEFDFNQKLQQN
                     SFNHDKEMLQAQIQATKQLQADMMAIKQGVLTAGGFSPADAARGAVNAPMTQALDWNG
                     TRYWAPNSMRTTSYSGKFTSTAPVRQADFQHTQSRPSSGSSVSSFATQSSRPTLTTTT
                     GSSHGTASSNSTRSTSLSQSTVSRATSRTGEWVRDQNRNLEPYMHGALQTAFVTPPSS
                     RASNGTVSTVPKGVLDSWTPAFNTRRQPLFAHLRKRGESQA"
     3'UTR           7493..7499
ORIGIN      
        1 gtgaatgaag atggcgtcta acgacgctac cgttgccgtt gcttgcaaca acaacaacga
       61 caaagaaaaa tcttcaggtg aaggcttatt cacaaatatg tcttccacct taaagaaagc
      121 cctcggggct aggcccaaac agcctgcccc gagagacaaa ccacaaaagc ccccaagacc
      181 accaactccc gagttggtca agaggatacc ccctcctcca cctaacggcg aagaagaaga
      241 agaaccagtc attaggtatg aggttaagag tgggatctct ggcctgcccg agctcacaac
      301 agtcccccaa ccggacgtgg ccaacacagc attcagtgtt ccaccactga gcttgagaga
      361 aaacagggag gccaaggagc cgctaacagg ggcaatatta gagatgtggg atggagagat
      421 ataccactat ggcctgtacg tggagaaagg cttagtgttg ggtgtgcaca aaccacctgc
      481 agccataagc atggcaagag tggagctgac gccgttgtca ttgtactggc gtgtggtgta
      541 cactccccaa tacctcatct cccctgaaac cctcaggagg ctcaacggag aggcattccc
      601 ttacaccgcc tttgacaaca actgctatgc cttttgctgc tgggtgttag acctcaatga
      661 ctcatggctt agcaggagga tggtacaaag aacaacgggc ttcttcagac cttaccaaga
      721 gtggaataga aaacccctgc ctaccatgga tgactccaaa attaagaagg tagcaaatat
      781 attcctatgt tcattgtcca cattattcac cagacccata aaagacctca taggaaaaat
      841 taaaccattg aacatattga atatcctggc aacgtgtgac tggacttttg ccggaatagt
      901 ggagtctctg atattatttg ctgaactctt cggagttttc tggacacccc cagatgtgtc
      961 tgctatgatc gctcccttac tcggggacta cgagttgcaa gggccagaag acctcgccgt
     1021 tgaactcgta cctgtggtaa tgggggggat tggtttggtg ttgggattca ccaaagagaa
     1081 aattggcaaa atgttgtcct cagcagcatc aacactcagg gcttgcaaag atcttggtgc
     1141 ctatggctta gagatactca aattggtcat gaagtggttc ttcccaaaga aagaggaggc
     1201 caatgagcta gctatggtga gggccataga ggatgctgta ctagaccttg aggcaataga
     1261 aaataaccac atgacaaccc tgttgaaaga caaagacagc ttagcaacat acatgaaaac
     1321 actggacatg gaggaggaga aagccaggag gttgtccaca aaatctgcat cccctgacat
     1381 agttgggaca atcaacgccc tgctggctcg aatagcagcg gccaggtcat tagtccacag
     1441 ggccaaggaa gagctatcta gtaggataag gccagtagtt gttatgatat ctggcaagcc
     1501 aggaataggc aaaactcatc tggccaggga ggtggcaaga aaggtggcat ccactctcac
     1561 aggggatcaa agagtcggac tcataccacg aaacggtgtg gaccattggg atgcatacaa
     1621 aggtgagaga gtcgtgctat gggacgacta tggcatgagt aaccctattc atgatgccct
     1681 tcgcatacaa gaattggctg atacgtgtcc ccttacctta aattgtgaca gaattgaaaa
     1741 taagggaaaa gtttttgaca gtgaagtcat aataattaca acaaaccttg ccaatccagc
     1801 cccacttgat tatgtcaact ttgaggcctg ttccaggaga attgatttcc tggtgtacgc
     1861 tgaggcacca gaagtagaaa aggcaaaacg ggactttcct ggtcagccag atatgtggaa
     1921 ggacgccttc aagccggact tttcacacat caagctacag cttgcacccc agggcggctt
     1981 tgacaagaat ggcaacaccc cacatgggaa aggagtgatg aagaccctca ctaccggttc
     2041 tctgattgcc cgtgcatcag gcctactgca tgagaggatg gatgaatttg aactccaagg
     2101 ccccacaatc accaccttca atttcgaccg aaacagaatc acggcattca gacaattggc
     2161 tgcagaaaac aagtatggat tggtggacac catgaaagtt ggcaaccaat taaaaggagt
     2221 gaaaaccatg gaagaactca aacaagcaat caggaatgtg accatcaaga ggtgccagat
     2281 catctacggt ggttccacgt atgaccttga atctgatggc aagggcaaag ttttggtgga
     2341 aaaggtcaag aacacctctg tacagaccaa taacgagttg gctggggccc tgcaccatct
     2401 caaacatgcc cgaatcaggt actatgtcaa atgtgtgcaa gaagcagtct attccatcat
     2461 acaaattgcc ggcgctgcgt ttgtcaccac gcgcattgca cgccgcatga acatacaaga
     2521 actctggtcg aagccacaac tagatcaaaa tgaatcagag actaaggaag aggcccccaa
     2581 gtcagaagat gacgagttca tcatatcttc taaggacatc aaggaggaag gaaagaaggg
     2641 caaaaacaaa actggccgtg gcaagaaaca cactgcattc tccagcaagg gcttgagcga
     2701 tgaggagtat gacgagtaca agaggataag agaagagaga aatgggaagt actctataga
     2761 ggagtatctt caagacagag acaggtacta tgaggagctc gccattgcca aggccacgga
     2821 agaagacttc tgtgaagagg aggagatcaa aatccgtcag agaattttcc gtcccaccag
     2881 gaaacaaaga aaggaagaga gggccacatt agggctagta acaggttcag aaatcagaaa
     2941 aagaaaccct gatgacttca aacccaaagg gaagctgtgg gccgatgaca acaggagtgt
     3001 tgactacaat gagaaactgg actttgaggc ccccccaagc atatggtcta ggattgtgag
     3061 ctttggctct ggctggggct tctgggtgtc accaagcctt tttataacat caactcatgt
     3121 aatccccgca ggcataacag aagcatttgg agtccccatc aaacaaattc agatccacaa
     3181 atcaggcgaa ttttgccgat tcagattccc aaaaccaatt agaccagatg tgacaggaat
     3241 gatcttggaa gaaggtgcgc ctgagggcac cgtggcaact gtgctcatca aacgccccac
     3301 cggagagctc atgcctcttg cagccagaat gggaacacac gcaaccatga aaattcaagg
     3361 ccgcatggtt ggcggacaga tgggtatgtt gctcactgga tcaaatgcta aaggaatgga
     3421 cttgggaaca actcctggtg actgtggctg tccttacatc tataaaaggg gcaatgacta
     3481 tatagccatt ggggtgcaca ctgcagcagc ccgtggtgga aacactgtca tctgtgccac
     3541 acagggaagt gagggtgagg caactcttga gggtggagat gacaaaggaa catactgtgg
     3601 ggcacccatt ctaggccctg ggggtgcacc aaaattgagc accaaaacca aattttggag
     3661 gtcatcgaac acgccccttc caccagggac atatgagcct gcctacctcg gtggccgtga
     3721 tccgcgtgtt aagggtgggc cttccctgca gcaggtgatg agagaccagt tgaagccatt
     3781 cactgaaccc aggggcaaac ctccaagacc aagtgtattg gaagcagcca aacaaaccat
     3841 catcaatgtc ctcgaacaaa ccctggaccc tccacaaaaa tggacatacg cacaggcttg
     3901 tgcctcactt gacaaaacca cctccagcgg gcacccccat cacgtccgaa agaatgaatt
     3961 ctggaatggt gagaccttca ctggtaaact ggcagaccaa gcatcaaaag caaacctaat
     4021 gtttgaggaa gggaaacaca tgacaccagt gtacacagca gcactcaagg acgagctagt
     4081 caagactgag aaaatctatg gaaagatcaa gaagagactg ctctggggct ctgacttgtc
     4141 caccatgatc cggtgcgcta ggtcatttgg tgggcttatg gacgagatga aggcacactg
     4201 catatcactc ccagtccgag ttggcatgaa tatgaatgaa gatggcccaa taatatttga
     4261 gaaacattcc agatacaaat atcactatga tgcagactac tctcgttggg attcaacaca
     4321 acagagggca gttctagcag cagccttgga aatcatggtc agattctctg cagaaccaca
     4381 attggcacaa atagtcgctg aggatctgct ggcccctagt gtagtagatg taggagactt
     4441 caaaattaca ataaatgaag ggctcccttc tggtgtgcca tgcacttctc aatggaactc
     4501 catcgcacac tggctgctaa ctctctgtgc cttgtctgaa gtcaccaaac tgtcccctga
     4561 cattatacag gcaaattcca tgttctcatt ttacggtgat gacgagattg tcagtaccga
     4621 cataaaattg gaccctgaac agttaaccgc caaattgaag gagtacggcc tgaaaccaac
     4681 ccgcccagac aaaaccgagg gacccctgat tatcagtgaa gatttgaacg gtctcacttt
     4741 cctccgaagg acggtgactc gtgacccagc tggctggttt ggaaaactgg accaaagctc
     4801 aattttgagg cagatgtact ggactagagg accaaatcat gaagacccca atgagacaat
     4861 gataccccat tcccaaagac ccatacagct catggcactg cttggtgaag cctctcttca
     4921 cggaccctct ttctacagta aaatcagtaa attggtcata actgaactca aagaaggtgg
     4981 gatggacttt tacgtgccaa ggcaggaacc catgttcagg tggatgaggt tttctgactt
     5041 gagcacgtgg gagggcgatc gcaatctggc tcccaatttt gtgaatgaag atggcgtcga
     5101 atgacgccgc tccatctact gatggtgcag ccggcctcgt gccagaaagt aacaatgagg
     5161 tcatggctct tgaacccgtg gctggtgccg ccttggcagc cccggtcacc ggtcaaacaa
     5221 atattataga cccttggatt agagcaaatt ttgtccaggc ccccaatggt gaatttacag
     5281 tctctccccg aaatgcccct ggtgaagtgc tactgaatct agagttgggt ccagaattaa
     5341 atccttatct ggcacattta gcaagaatgt acaatgggta tgccggtggg atggaggtgc
     5401 aggtcatgtt ggctgggaac gcgttcacag ccggcaagtt ggtcttcgcc gccgtgccac
     5461 cccacttccc ggttgaaaac cttagcccac agcaaatcac catgttccct catgtgatca
     5521 tagatgtgag aaccttggaa cctgttttat taccactccc tgatgttagg aataacttct
     5581 tccattataa ccagaaagat gatcccaaga tgagaattgt ggctatgctt tatacccccc
     5641 tcaggtctaa tggttcaggt gatgatgtgt ttacagtctc ctgtagagta ttgactagac
     5701 cttcccctga ctttgacttc acatacctgg tgccaccaac agtggagtct aaaacaaagc
     5761 cattcaccct cccaatcctc acacttgggg aactttccaa ttctaggttc ccagtgtcca
     5821 tagaccagat gtacaccagc cctaatgaaa ttatatcagt gcagtgtcaa aatggtaggt
     5881 gcacactgga cggggagctc caagggacaa cacaactcca agtcagtggc atttgtgctt
     5941 tcaaaggtga ggtgaccgcc cacttgcatg acaatgatca cctatataat gtcaccatca
     6001 caaacttgaa tgggtcccct tttgatccct ccgaggatat ccctgcccct ttgggtgtgc
     6061 ctgatttcca gggaagggtt tttggtatca tctcccaaag agataaacac aatagtcctg
     6121 ggcataatga accagcaaac aggggacacg acgctgtggt tcctacttac acagcacagt
     6181 acactccaaa acttggacaa attcaaattg gcacatggca aactgacgac cttacagtca
     6241 accaaccagt caaattcacc ccagttggac tcaatgacac tgaacacttt aaccaatggg
     6301 tggtccctag gtatgctggt gccctaaacc ttaatacaaa ccttgcccct tctgttgctc
     6361 cagtatttcc aggagagcgc ctgctcttct tcagatcata cattcccctc aagggcggtt
     6421 atggaaaccc agccattgat tgcctactac cacaagagtg ggtgcaacac ttctatcagg
     6481 aagcagcccc ttcaatgagt gaggtggccc tcgtcagata catcaacccg gacactggtc
     6541 gggcactgtt tgaggccaag ctccacagag ctggtttcat gacagtctcg agcaacacca
     6601 gtgccccggt ggttgtgcct gccaacgggt acttcagatt tgattcttgg gtgaaccaat
     6661 tttattctct cgcccccatg ggaactggga atgggcgtag aagggttcaa taatggctgg
     6721 agcttttgta gctggtcttg caggggacgt gctcagcaat gggcttagtt cattaatcaa
     6781 tgcaggtgct aatgcaataa atcagagggc agaattcgat tttaatcaaa aattgcagca
     6841 aaattctttt aatcatgata aggagatgtt gcaggctcag attcaggcaa ctaagcagct
     6901 gcaggcagac atgatggcta taaaacaagg ggtcttgacc gctggcggct tttcccctgc
     6961 tgatgcagcc agaggtgctg taaacgcgcc catgacacag gcgctggatt ggaatggcac
     7021 aaggtattgg gcaccaaact ccatgaggac cacatcttat tctggaaaat tcacatcaac
     7081 cgccccagtg aggcaggctg acttccagca cacccaaagc cggccttcga gtggctcctc
     7141 tgtgtcttcc tttgccactc agtcttcaag gccaactctg accacaacca ctggttcctc
     7201 acatggcaca gcctcatcaa attcaactcg cagcacaagc ctctcccaat caacggtctc
     7261 cagagctaca tctaggactg gtgagtgggt tagagatcaa aatagaaatt tggaacccta
     7321 catgcatggt gccttacaga cagcctttgt caccccacct tccagcaggg catctaacgg
     7381 gacagtctca accgtcccta aaggtgtttt ggactcctgg acacctgcgt ttaacacccg
     7441 caggcagccg ctttttgcac acctccgtaa gaggggggag tcacaagctt agtgaaaag
//