Typing tool

Complete norovirus genomes

KY865307  GII.2
 GII.P16

Length: 7,497 | 3 CDS

ORF1: 3..5102
ORF2: 5083..6711
ORF3: 6711..7490
LOCUS       KY865307                7497 bp    RNA     linear   VRL 18-MAY-2017
DEFINITION  Norovirus GII strain Hu/USA/2016/GII.P16-GII.2/Nashville 2122
            polyprotein, VP1, and VP2 genes, complete cds.
ACCESSION   KY865307
VERSION     KY865307.1
KEYWORDS    .
SOURCE      Norovirus GII
  ORGANISM  Norovirus GII
            Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes;
            Picornavirales; Caliciviridae; Norovirus.
REFERENCE   1  (bases 1 to 7497)
  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 7497)
  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..7497
                     /organism="Norovirus GII"
                     /mol_type="genomic RNA"
                     /strain="Hu/USA/2016/GII.P16-GII.2/Nashville 2122"
                     /isolation_source="stool"
                     /host="Homo sapiens"
                     /db_xref="taxon:122929"
                     /country="USA"
                     /collection_date="21-Dec-2016"
                     /note="genotype: GII.P16-GII.2"
     5'UTR           1..2
     CDS             3..5102
                     /note="nonstructural protein; ORF1"
                     /codon_start=1
                     /product="polyprotein"
                     /protein_id="ARR95873.1"
                     /translation="MKMASNDATVAVACNNNNDKEKSSGEGLFTNMSSTLKKALGARP
                     KQPAPRDKPQKPPRPPTPELVKRIPPPPPNGEEEEEPVIRYEVKSGISGLPELTTVPQ
                     PDVANTAFSVPPLSLRENREAKEPLTGAILEMWDGEIYHYGLYVEKGLVLGVHKPPAA
                     ISMARVELTPLSLYWRVVYTPQYLISPETLRRLNGEAFPYTAFDNNCYAFCCWVLDLN
                     DSWLSRRMVQRTTGFFRPYQEWNRKPLPTMDDSKIKKVANIFLCSLSTLFTRPIKDLI
                     GKIKPLNILNILATCDWTFAGIVESLILLAELFGVFWTPPDVSAMIAPLLGDYELQGP
                     EDLAVELVPVVMGGIGLVLGFTKEKIGKMLSSAASTLRACKDLGAYGLEILKLVMKWF
                     FPKKEEANELAMVRAIEDAVLDLEAIENNHMTTLLKDKDSLATYMKTLDMEEEKARRL
                     STKSASPDIVGTINALLARIAAARSLVHRAKEELSSRIRPVVVMISGKPGIGKTHLAR
                     EVARKVASTLTGDQRVGLIPRNGVDHWDAYKGERVVLWDDYGMSNPIHDALRIQELAD
                     TCPLTLNCDRIENKGKVFDSEVIIITTNLANPAPLDYVNFEACSRRIDFLVYAEAPEV
                     EKAKRDFPGQPDMWKDAFKPDFSHIKLQLAPQGGFDKNGNTPHGKGVMKTLTTGSLIA
                     RASGLLHERMDEFELQGPTTTTFNFDRNRITAFRQLAAENKYGLVDTMKVGNQLKGVK
                     TMEELKQAIRNVTIKRCRIIYGGSTYDLESDGKGKVLVEKVKNTSVQTNNELAGALHH
                     LKHARIRYYVKCVQEAVYSIIQIAGAAFVTTRIARRMNIQELWSKPQLDQNESETKEE
                     APKSEDDEFIISSKDIKEEGKKGKNKTGRGKKHTAFSSKGLNDEEYDEYKRIREERNG
                     KYSIEEYLQDRDRYYEELAIAKATEEDFCEEEEIKIRQRIFRPTRKQRKEERATLGLV
                     TGSEIRKRNPDDFKPKGKLWADDNRSVDYNEKLDFEAPPSIWSRIVSFGSGWGFWVSP
                     SLFITSTHVIPAGITEAFGVPIKQIQIHKSGEFCRFRFPKPIRPDVTGMILEEGAPEG
                     TVATVLIKRPTGELMPLAARMGTHATMKIQGRMVGGQMGMLLTGSNAKGMDLGTTPGD
                     CGCPYIYKRGNDYIVIGVHTAAARGGNTVICATQGSEGEATLEGGDDKGTYCGAPILG
                     PGGAPKLSTKTKFWRSSNTPLPPGTYEPAYLGGRDPRVKGGPSLQQVMRDQLKPFTEP
                     RGKPPRPSVLEAAKQTIINVLEQTLDPPQKWTYAQACASLDKTTSSGYPHHVRKNEFW
                     NGETFTGKLADQASKANLMFEEGKHMTPVYTAALKDELVKTEKIYGKIKKRLLWGSDL
                     STMIRCARSFGGLMDEMKAHCISLPVRVGMNMNEDGPIIFEKHSRYKYHYDADYSRWD
                     STQQRAVLAAALEIMVRFSAEPQLAQIVAEDLLAPSVVDVGDFKITINEGLPSGVPCT
                     SQWNSIAHWLLTLCALSEVTKLSPDIIQTNSMFSFYGDDEIVSTDIKLDPEQLTAKLK
                     EYGLKPTRPDKTEGPLIISEDLNGLTFLRRTVTRDPAGWFGKLDQSSILRQMYWTRGP
                     NHEDPNETMIPHSQRPIQLMALLGEASLHGPSFYSKISKLVITELKEGGMDFYVPRQE
                     PMFRWMRFSDLSTWEGDRNLAPNFVNEDGVE"
     CDS             5083..6711
                     /note="major capsid protein; ORF2"
                     /codon_start=1
                     /product="VP1"
                     /protein_id="ARR95874.1"
                     /translation="MKMASNDAAPSTDGAAGLVPESNNEVMALEPVAGAALAAPVTGQ
                     TNIIDPWIRANFVQAPNGEFTVSPRNAPGEVLLNLELGPELNPYLAHLARMYNGYAGG
                     MEVQVMLAGNAFTAGKLVFAAVPPHFPVENLSPQQITMFPHVIIDVRTLEPVLLPLPD
                     VRNNFFHYNQKDDPKMRIVAMLYTPLRSNGSGDDVFTVSCRVLTRPSPDFDFTYLVPP
                     TVESKTKPFTLPILTLGELSNSRFPVSIDQMYTSPNEVISVQCQNGRCTLDGELQGTT
                     QLQVSGICAFKGEVTAHLHDNDHLYNVTITNLNGSPFDPSEDIPAPLGVPDFQGRVFG
                     IISQRDKHNSPGHNEPANRGHDAVVPTYTAQYTPKLGQIQIGTWQTDDLTVNQPVKFT
                     PVGLNDTEHFNQWVVPRYAGALNLNTNLAPSVAPVFPGERLLFFRSYIPLKGGYGNPA
                     IDCLLPQEWLQHFYQEAAPSMSEVALVRYINPDTGRALFEAKLHRAGFMTVSSNTSAP
                     VVVPANGYFRFDSWVNQFYSLAPMGTGNGRRRVQ"
     CDS             6711..7490
                     /note="minor structural protein; ORF3"
                     /codon_start=1
                     /product="VP2"
                     /protein_id="ARR95875.1"
                     /translation="MAGAFVAGLAGDVLSNGLSSLINAGANAINQRAEFDFNQKLQQN
                     SFNHDKEMLQAQIQATKQLQADMMAIKQGVLTAGGFSPADAARGAVNAPMTQALDWNG
                     TRYWAPNSMRTTSYSGKFTSTAPVRQADFQHTQNRPSSGSSVSSFATQSSRPTLTTTT
                     GSSHGTASSNSTRSTSLSQSTVPRATSRTGEWVRDQNRNLEPYMHGALQTAFVTPPSS
                     RASDGTVSTVPKGVLDSWTPAFNTRRQPLFAHLRKRGESQA"
     3'UTR           7491..7497
ORIGIN      
        1 gaatgaagat ggcgtctaac gacgctaccg ttgccgttgc ttgcaacaac aacaacgaca
       61 aagaaaaatc ttcaggtgaa ggcttattca caaatatgtc ttccacctta aagaaagccc
      121 tcggggctag gcccaaacag cctgccccga gagacaaacc acaaaagccc ccaagaccac
      181 caactcccga gttggtcaag aggatacccc ctcctccacc taatggcgaa gaagaagaag
      241 aaccagtcat taggtatgag gttaagagtg ggatctctgg cctgcccgag ctcacaacag
      301 tcccccagcc ggacgtggcc aacacagcat ttagtgttcc accactgagc ttgagagaaa
      361 acagggaggc caaggaaccg ctaacagggg caatattaga gatgtgggat ggagagatat
      421 accactatgg cctgtacgtg gagaaaggct tagtgttggg tgtgcacaaa ccacctgcag
      481 ccataagcat ggcaagagtg gagctgacgc cgctgtcatt gtactggcgt gtggtgtaca
      541 ctccccaata cctcatctcc cctgaaactc tcaggaggct caacggagag gcattccctt
      601 acaccgcctt tgacaacaac tgctatgcct tttgctgctg ggtgttagac cttaatgatt
      661 catggcttag caggaggatg gtacaaagaa caacgggctt cttcagacct taccaagagt
      721 ggaacagaaa acccctgcct accatggatg actccaaaat taagaaggta gcaaatatat
      781 tcctatgttc attgtccaca ttattcacca gacccataaa agacctcata ggaaaaatta
      841 aaccattaaa catattgaat atcctggcaa cgtgtgactg gacttttgcc ggaatagtgg
      901 agtctctgat attacttgct gaactcttcg gagttttctg gacaccccca gatgtgtctg
      961 ctatgatcgc tcccttactc ggggactacg agttgcaagg accagaagac ctcgccgttg
     1021 aactcgtacc tgtggtgatg ggggggattg gcttggtgtt gggattcacc aaagagaaaa
     1081 ttggcaaaat gttgtcctca gcagcatcaa cactcagggc ttgcaaagat cttggtgcct
     1141 atggcttaga gatactcaaa ttggtcatga agtggttctt cccaaagaaa gaggaggcca
     1201 atgagctagc catggtgagg gccatagagg atgctgtact agatcttgag gcaatagaaa
     1261 ataaccacat gacaaccctg ttgaaagaca aagacagctt agcaacatac atgaaaacat
     1321 tggacatgga ggaggagaaa gccaggaggt tgtccacaaa atctgcatcc cctgacatag
     1381 ttgggacaat caacgccctg ctggctcgaa tagcagcggc caggtcgtta gtccacaggg
     1441 ccaaggaaga gctatctagc aggataagac cagtagttgt tatgatatct ggcaaaccag
     1501 gaataggcaa aactcatctg gccagggagg tggcaagaaa ggtggcatcc actctcacag
     1561 gggatcaaag agtcggactc ataccacgaa acggtgtgga ccattgggat gcatacaaag
     1621 gtgagagagt cgtgctgtgg gacgactatg gcatgagtaa ccccattcat gatgctcttc
     1681 gcatacaaga attggctgat acgtgtcccc ttaccttaaa ttgtgacaga attgaaaata
     1741 agggaaaagt ttttgacagt gaagtcataa taattacaac aaaccttgcc aacccagccc
     1801 cacttgatta tgtcaacttt gaggcctgtt ccaggagaat tgatttcctg gtgtacgctg
     1861 aggcaccaga agtagaaaag gcaaaacggg actttcctgg tcagccagat atgtggaagg
     1921 acgccttcaa gccggacttt tcacacatca agctacagct tgcaccccag ggcggctttg
     1981 acaagaatgg caacacccca catgggaaag gagtgatgaa gaccctcact accggttctc
     2041 tgattgcccg tgcatcaggc ctactgcatg agaggatgga tgaatttgag ctccaaggtc
     2101 ccacaaccac caccttcaat ttcgaccgga acagaatcac agcattcaga caattggctg
     2161 cagaaaacaa gtatggattg gtggatacca tgaaagttgg caatcaatta aaaggagtga
     2221 aaaccatgga agaactcaaa caagcaatca ggaatgtgac catcaagagg tgccggatca
     2281 tctacggtgg ttccacgtat gaccttgaat ctgatggcaa gggcaaagtt ttggtggaaa
     2341 aggtcaagaa cacctctgta cagaccaaca acgagttggc tggggccctg caccatctca
     2401 aacatgcccg aatcaggtac tatgtcaaat gtgtgcaaga agcagtctat tctatcatac
     2461 aaattgccgg cgctgcgttt gtcaccacgc gcattgcacg ccgcatgaac atacaagaac
     2521 tctggtcgaa gccacaatta gatcaaaatg aatcagagac taaggaagag gcccccaagt
     2581 cagaagatga cgagttcatc atatcttcta aggacatcaa ggaggaagga aagaagggca
     2641 aaaacaaaac tggccgtggc aagaaacaca ctgcattctc cagcaagggc ttgaacgatg
     2701 aggagtatga cgagtacaag aggataagag aagagagaaa tgggaagtac tctatagagg
     2761 agtatcttca agacagagac aggtactatg aggagctcgc cattgccaag gccacggaag
     2821 aagacttctg tgaagaggag gagatcaaaa tccgtcagag aattttccgt cccaccagga
     2881 aacaaagaaa ggaagagagg gccacattag gactagtaac aggttcagaa atcagaaaaa
     2941 gaaaccctga tgacttcaaa cccaaaggga agctgtgggc cgatgacaac aggagtgttg
     3001 actacaatga gaaactggac tttgaggccc ccccaagcat atggtctagg attgtgagct
     3061 ttggttctgg ctggggcttc tgggtgtcac caagcctttt cataacatca actcatgtaa
     3121 tccccgcagg cataacagag gcatttggag tccccatcaa acaaattcag atccacaaat
     3181 caggtgaatt ttgccgattc agattcccaa aaccaattag accagatgtg acaggaatga
     3241 ttttggaaga aggtgcgcct gagggcaccg tggcaactgt gctcatcaaa cgccccaccg
     3301 gagagctcat gcctcttgca gccagaatgg gaacacacgc aaccatgaaa attcaaggcc
     3361 gcatggttgg cggacagatg ggtatgttgc tcactggatc aaatgctaaa ggaatggatt
     3421 tgggaacaac tcctggtgac tgtggctgtc cttacatcta taaaaggggc aatgactata
     3481 tagtcattgg ggtgcacact gcagcagccc gtggtggaaa caccgtcatc tgtgccacac
     3541 agggaagtga gggtgaggca actcttgagg gtggagatga caaaggaacg tactgtgggg
     3601 cacccattct aggccctgga ggtgcaccaa aattgagcac caaaaccaag ttttggagat
     3661 catcgaacac gccccttcca ccagggacat atgagcctgc ctacctcggt ggccgtgatc
     3721 cgcgtgttaa gggtgggcct tccctgcagc aggtaatgag agaccagttg aagccattca
     3781 ctgaacccag gggcaaacct ccaagaccaa gtgtattgga agcagccaaa caaaccatca
     3841 tcaatgttct cgaacaaacc ctggaccctc cacaaaaatg gacatacgca caggcgtgtg
     3901 cctcacttga caaaaccacc tccagcgggt atccccatca cgtccgaaag aatgaattct
     3961 ggaatggtga gaccttcact ggtaaactgg cagaccaagc atcaaaagca aacctaatgt
     4021 ttgaggaagg gaaacacatg acaccagtgt acacagcagc actcaaggac gagctagtca
     4081 agactgagaa aatctatgga aagatcaaga agagactgct ctggggctct gacttgtcca
     4141 ccatgatccg gtgcgctagg tcatttggtg ggctcatgga cgagatgaag gcacactgca
     4201 tatcactccc agtccgagtt ggcatgaata tgaatgaaga tggcccaata atatttgaga
     4261 aacattccag atacaaatat cactatgatg cagactactc tcgttgggat tcaacacaac
     4321 agagggcagt actagcagca gccttggaaa tcatggtcag attctctgca gaaccacaat
     4381 tggcacaaat agtcgctgag gatctgttgg cccctagtgt agtagatgta ggagacttta
     4441 aaattacaat aaatgaaggg ctcccttctg gtgtgccatg cacttctcaa tggaactcca
     4501 tcgcacactg gctgctaact ctctgtgcct tgtctgaagt caccaaactg tcccctgaca
     4561 ttatacagac aaattccatg ttctcatttt acggtgatga cgagattgtc agcaccgaca
     4621 taaaattgga ccctgaacaa ttaaccgcca aattgaagga gtacggcctg aaaccaaccc
     4681 gcccagacaa aaccgaggga cccctgatta tcagtgaaga tttgaacggt ctcactttcc
     4741 tccgaaggac ggtgactcgt gacccagctg gctggtttgg aaaactggac caaagctcga
     4801 ttttgaggca gatgtactgg actagaggac caaatcatga agaccccaat gagacaatga
     4861 taccccattc tcaaagaccc atacagctca tggcactgct tggtgaagcc tctcttcacg
     4921 gaccctcttt ctacagtaaa atcagtaaat tggtcataac tgaactcaaa gaaggtggga
     4981 tggactttta cgtgccaagg caggaaccca tgttcaggtg gatgaggttt tctgacttga
     5041 gcacgtggga gggcgatcgc aatctggctc ccaattttgt gaatgaagat ggcgtcgaat
     5101 gacgccgctc catctactga tggtgcagcc ggcctcgtgc cagaaagtaa caatgaggtc
     5161 atggctcttg aacccgtggc tggtgccgcc ttggcagccc cggtcaccgg tcaaacaaat
     5221 attatagacc cttggattag agcaaatttt gtccaggccc ccaatggtga atttacagtc
     5281 tctccccgaa atgcccctgg tgaagtgcta ttgaatctag agttgggtcc agaattaaat
     5341 ccttatctgg cacatttagc aagaatgtat aatgggtatg ccggtgggat ggaggtgcag
     5401 gtcatgttgg ctgggaacgc gttcacagcc ggcaagttgg tcttcgccgc cgtgcctcct
     5461 cacttcccgg ttgaaaacct tagcccacag caaatcacca tgttccctca tgtgatcata
     5521 gatgtgagaa ccttggaacc tgttttatta ccactccctg atgttaggaa taatttcttc
     5581 cattataatc agaaagatga tcccaagatg aggattgtgg ctatgcttta tacccccctc
     5641 aggtctaatg gttcaggtga tgatgtgttc acagtctcct gtagagtgtt gactagacct
     5701 tcccctgact ttgacttcac atacctggtg ccaccaacag tggagtctaa aacaaagcca
     5761 ttcaccctcc caatcctcac acttggggaa ctatccaatt ctaggttccc agtgtccata
     5821 gaccagatgt acaccagccc taatgaagtt atatcagtgc agtgtcaaaa tggtaggtgc
     5881 acactggacg gggagctcca aggaacaaca caactccaag tcagtggcat ttgtgctttc
     5941 aaaggtgaag tgaccgccca cttgcatgac aatgatcacc tatataatgt taccatcaca
     6001 aacttgaatg ggtccccttt tgatccctcc gaggacatcc ctgcccctct gggtgtgcct
     6061 gacttccagg gaagggtttt tggtatcatc tctcaaagag acaaacacaa tagtcctggg
     6121 cataatgaac cagcaaacag gggacacgac gctgtggtcc ctacttacac agcacagtac
     6181 actccaaaac tgggacaaat tcaaattggc acatggcaga ctgacgatct tacagtcaac
     6241 caaccagtca aattcacccc agttggactc aatgacactg aacattttaa tcaatgggtg
     6301 gtccctaggt atgctggtgc cctaaacctc aatacaaacc ttgccccttc tgttgctcca
     6361 gtatttccag gagagcgtct gctcttcttc agatcataca ttcccctcaa gggcggttat
     6421 ggaaacccag ccattgattg cctactacca caagagtggc tgcaacactt ctatcaggaa
     6481 gcagcccctt caatgagtga ggtggccctc gtcagataca tcaacccgga cactggtcgg
     6541 gcactgtttg aggccaagct ccacagagct ggtttcatga cagtctcgag caacaccagt
     6601 gccccggtgg ttgtgcctgc caacggatac ttcagatttg attcttgggt gaaccaattc
     6661 tattctctcg cccccatggg aactgggaat gggcgcagaa gggttcaata atggctggag
     6721 cttttgtagc tggtcttgca ggggacgtgc tcagcaatgg gcttagttca ttaatcaatg
     6781 cgggtgctaa tgcaataaat cagagggcag aatttgattt taatcagaaa ttgcagcaaa
     6841 attcttttaa tcatgataag gagatgttgc aggctcagat tcaggcaact aagcagctgc
     6901 aggcagacat gatggctata aaacaagggg tcttgaccgc tggcggcttt tcccctgctg
     6961 atgcagccag aggtgctgtg aacgcgccca tgacacaggc gctggattgg aatggcacaa
     7021 ggtattgggc accaaactcc atgaggacca catcttattc tggaaaattc acatcaaccg
     7081 ccccagtgag gcaggctgac ttccagcaca cccaaaaccg gccttcgagt ggctcctctg
     7141 tgtcttcctt cgccactcag tcttcaaggc caactttgac cacaaccact ggttcctcac
     7201 atggcacagc ctcatcaaat tcaactcgca gcacaagcct ctcccaatca acggtcccca
     7261 gagctacatc taggactggt gagtgggtta gagatcaaaa tagaaatttg gaaccctaca
     7321 tgcatggtgc cttacagaca gcctttgtca ccccaccttc cagcagggca tctgacggga
     7381 cagtctcaac cgtcccgaaa ggtgttttgg actcctggac acctgcgttt aacacccgca
     7441 ggcagccgct ttttgcacac ctccgtaaga ggggggagtc acaagcttag tgaaaag
//