Typing tool

Complete norovirus genomes

MN493873  GII.2
 GII.P16

Length: 7,530 | 3 CDS

ORF1: 3..5102
ORF2: 5083..6711
ORF3: 6711..7490
LOCUS       MN493873                7530 bp    RNA     linear   VRL 28-SEP-2019
DEFINITION  Norovirus GII isolate Hu/US/2017/GII.P16-GII.2/CA-RGDS-1075
            nonstructural polyprotein (ORF1), VP1 (ORF2), and VP2 (ORF3) genes,
            complete cds.
ACCESSION   MN493873
VERSION     MN493873.1
KEYWORDS    .
SOURCE      Norovirus GII
  ORGANISM  Norovirus GII
            Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes;
            Picornavirales; Caliciviridae; Norovirus.
REFERENCE   1  (bases 1 to 7530)
  AUTHORS   Pan,C.-Y., Huynh,T., Castro,C.J., Marine,R.L., Ng,T.F., Morales,C.
            and Wadford,D.A.
  TITLE     Norovirus GII.2[P16] from a large foodborne outbreak associated
            with contaminated Washington state oysters, California, 2017
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 7530)
  AUTHORS   Pan,C.-Y., Huynh,T., Castro,C.J., Marine,R.L., Ng,T.F., Morales,C.
            and Wadford,D.A.
  TITLE     Direct Submission
  JOURNAL   Submitted (22-SEP-2019) Viral and Rickettsial Disease Laboratory,
            California Department of Public Health, 850 Marina Bay Parkway,
            Richmond, CA 94804, USA
COMMENT     ##Assembly-Data-START##
            Assembly Method       :: SPAdes v. 3.6; Geneious v. R10
            Sequencing Technology :: Illumina
            ##Assembly-Data-END##
FEATURES             Location/Qualifiers
     source          1..7530
                     /organism="Norovirus GII"
                     /mol_type="genomic RNA"
                     /isolate="Hu/US/2017/GII.P16-GII.2/CA-RGDS-1075"
                     /isolation_source="stool"
                     /host="Homo sapiens"
                     /db_xref="taxon:122929"
                     /country="USA: CA"
                     /collection_date="Feb-2017"
                     /note="genotype: GII.P16-GII.2"
     gene            3..5102
                     /gene="ORF1"
     CDS             3..5102
                     /gene="ORF1"
                     /codon_start=1
                     /product="nonstructural polyprotein"
                     /protein_id="QER77272.1"
                     /translation="MKMASNDATVAVACNNNNDKEKSSGEGLFTNMSSTLKKALGARP
                     KQPAPRDKPQKPPRPPTPELVKRIPPPPPNGEEEEEPVIRYEVKSGVSGLPELTTVPQ
                     PDVANTAFSVPPLSLRENREAKEPLTGAILEMWDGEIYHYGLYVEKGLVLGVHKPPAA
                     VSMARVELTPLSLYWRVVYTPQYLISPETLRRLNGEAFPYTAFDNNCYAFCCWVLDLN
                     DSWLSRRMVQRTTGFFRPYQEWNRKPLPTMDDSKIKKVANIFLCSLSTLFTRPIKDLV
                     GKIKPLNILNILATCDWTFAGIVESLILLAELFGVFWTPPDVSAMIAPLLGDYELQGP
                     EDLAVELVPVVMGGIGLVLGFTKEKIGKMLSSAASTLRACKDLGAYGLEILKLVMKWF
                     FPKKEEANELAMVRAIEDAVLDLEAIENNHMTTLLKDKDSLATYMKTLDMEEEKARRL
                     STKSASPDIVGTINALLARIAAARSLVHRAKEELSSRIRPVVVMISGKPGIGKTHLAR
                     EVARKVASTLTGDQRVGLIPRNGVDHWDAYKGERVVLWDDYGMSNPIHDALRIQELAD
                     TCPLTLNCDRIENKGKVFDSEVIIITTNLANPAPLDYVNFEACSRRIDFLVYAEAPEV
                     EKAKRDFPGQPDMWKDAFKPDFSHIKLQLAPQGGFDKNGNTPHGKGVMKTLTTGSLIA
                     RASGLLHERMDEFELQGPTITTFNFDRNRITAFRQLAAENKYGLVDTMKVGNQLKGVK
                     TMEELKQAIRNVTIKRCRIIYGGSTYDLESDGKGKVLVEKVKNTSVQTNNELAGALHH
                     LKHARIRYYVKCVQEAVYSIIQIAGAAFVTTRIARRMNIQELWSKPQLDQNESETKEE
                     APKSEDDEFIISSKDIKEEGKKGKNKTGRGKKHTAFSSKGLSDEEYDEYKRIREERNG
                     KYSIEEYLQDRDRYYEELAIAKATEEDFCEEEEIKIRQRIFRPTRKQRKEERATLGLV
                     TGSEIRKRNPDDFKPKGKLWADDNRSVDYNEKLDFEAPPSIWSRIVSFGSGWGFWVSP
                     SLFITSTHVIPAGITEAFGVPIKQIQIHKSGEFCRFRFPKPIRPDVTGMILEEGAPEG
                     TVATVLIKRPTGELMPLAARMGTHATMRIQGRMVGGQMGMLLTGSNAKGMDLGTTPGD
                     CGCPYIYKRGNDYIVIGVHTAAARGGNTVICATQGSEGEATLEGGDDKGTYCGAPILG
                     PGGAPKLSTKTKFWRSSNTPLPPGTYEPAYLGGRDPRVKGGPSLQQVMRDQLKPFTEP
                     RGKPPRPSVLEAAKQTIINVLEQTLDPPQKWTYAQACASLDKTTSSGHPYHVRKNEFW
                     NGETFTGKLADQASKANLMFEEGKHMTPVYTAALKDELVKTEKIYGKIKKRLLWGSDL
                     STMIRCARSFGGLMDEMKAHCISLPVRVGMNMNEDGPIIFEKHSRYKYHYDADYSRWD
                     STQQRAVLAAALEIMVRFSAEPQLAQIVAEDLLAPSVVDVGDFKITINEGLPSGVPCT
                     SQWNSIAHWLLTLCALSEVTKLSPDIIQANSMFSFYGDDEIVSTDIKLDPEQLTTKLK
                     EYGLKPTRPDKTEGPLIISEDLNGLTFLRRTVTRDPAGWFGKLDQSSILRQMYWTRGS
                     NHEDPNETMIPHSQRPIQLMALLGEASLHGPSFYSKISKLVITELKEGGMDFYVPRQE
                     PMFRWMRFSDLSTWEGDRNLAPNFVNEDGVE"
     mat_peptide     3..998
                     /gene="ORF1"
                     /product="p48"
     mat_peptide     999..2096
                     /gene="ORF1"
                     /product="NTPase"
     mat_peptide     2097..2627
                     /gene="ORF1"
                     /product="p22"
     mat_peptide     2628..3026
                     /gene="ORF1"
                     /product="VPg"
     mat_peptide     3027..3569
                     /gene="ORF1"
                     /product="Pro"
     mat_peptide     3570..5099
                     /gene="ORF1"
                     /product="RdRp"
     gene            5083..6711
                     /gene="ORF2"
     CDS             5083..6711
                     /gene="ORF2"
                     /note="major capsid protein"
                     /codon_start=1
                     /product="VP1"
                     /protein_id="QER77273.1"
                     /translation="MKMASNDAAPSTDGAAGLVPESNNEVMALEPVAGAALAAPVTGQ
                     TNIIDPWIRANFVQAPNGEFTVSPRNAPGEVLLSLELGPELNPYLAHLARMYNGYAGG
                     MEVQVMLAGNAFTAGKLVFAAVPPHFPVENLSPQQITMFPHVIIDVRTLEPVLLPLPD
                     VRNNFFHYNQKDDPKMRIVAMLYTPLRSNGSGDDVFTVSCRVLTRPSPDFDFTYLVPP
                     TVESKTKPFTLPILTLGELSNSRFPVSIDQMYTSPNEVISVQCQNGRCTLDGELQGTT
                     QLQVSGICAFKGEVTAHLHDNDHLYNVTITNLNGSPFDPSEDIPAPLGVPDFQGRVFG
                     IISQRDKHNSPGHNEPANRGHDAVVPTYTAQYTPKLGQIQIGTWQTDDLTVNQPVKFT
                     PVGLNDTEHFNQWVVPRYAGALNLNTNLAPSVAPVFPGERLLFFRSYIPLKGGYGNPA
                     IDCLLPQEWVQHFYQEAAPSMSEVALVRYINPDTGRALFEAKLHRAGFMTVSSNTSAP
                     VVVPANGYFRFDSWVNQFYSLAPMGTGNGRRRVQ"
     gene            6711..7490
                     /gene="ORF3"
     CDS             6711..7490
                     /gene="ORF3"
                     /note="minor structural protein; small basic protein"
                     /codon_start=1
                     /product="VP2"
                     /protein_id="QER77274.1"
                     /translation="MAGAFVAGLAGDVLSNGLSSLINAGANAINQRAEFDFNQKLQQN
                     SFNHDKEMLQAQIQATKQLQADMMAIKQGVLTAGGFSPADAARGAVNAPMTQALDWNG
                     TRYWAPNSMRTTSYSGKFTSTAPVRQADFQHTQSRPSSGSSVSSFATQSSRPTLTTTT
                     GSSHGTVSSNSTRSTSLSQSTVSRATSRTGEWVRDQNRNLEPYMHGALQTAFVTPPSS
                     RASDGTVSTVPKGVLDSWTPAFNTRRQPLFAHLRKRGESQA"
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 gggtctctgg cctgcccgag ctcacaacag
      301 tcccccaacc ggacgtggcc aacacagcat tcagtgttcc accactgagc ttgagagaaa
      361 acagggaggc caaggaaccg ctaacagggg caatattaga gatgtgggat ggagagatat
      421 accactatgg cctgtacgtg gagaaaggct tagtgttggg tgtgcacaaa ccacctgcag
      481 ccgtaagcat ggcaagagtg gagctgacgc cgctgtcatt gtactggcgt gtggtgtaca
      541 ctccccaata cctcatctcc cctgaaactc tcaggagact caacggagag gcattccctt
      601 acaccgcctt tgacaataac tgctatgcct tttgctgctg ggtgttagac ctcaatgact
      661 catggcttag caggaggatg gtgcaaagaa caacgggctt ctttagacct taccaagagt
      721 ggaacagaaa acccctgccc accatggatg actccaaaat taagaaggta gcaaatatat
      781 tcctatgctc attgtccaca ttattcacca gacccataaa agacctcgta ggaaaaatta
      841 aaccattaaa catattgaat atcctggcaa cgtgtgactg gacttttgcc ggaatagtgg
      901 agtctctgat attacttgct gaactcttcg gagttttctg gacaccccca gatgtgtctg
      961 ctatgatcgc tcccttactc ggggactacg agttgcaggg gccagaagac ctcgccgttg
     1021 aactcgtacc cgtggtaatg ggggggattg gtttggtgtt 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 ttaaaagaca aagacagctt agcaacatac atgaaaacac
     1321 tggacatgga ggaggagaaa gccaggaggt tgtccacaaa atctgcatcc cctgacatag
     1381 ttgggacaat caacgccctg cttgctcgaa tagcagcggc caggtcatta gtccacaggg
     1441 ccaaggaaga gctatctagc aggataagac cagtagttgt tatgatatct ggcaaaccag
     1501 gaataggcaa aactcatctg gccagggagg tggcaagaaa ggtggcatcc actctcacag
     1561 gggatcaaag agtcggactc ataccaagaa acggtgtgga ccattgggat gcatacaaag
     1621 gtgagagagt cgtgctgtgg gacgactatg gcatgagtaa ccccattcat gatgctcttc
     1681 gcatacaaga attggctgat acgtgtcccc ttaccttaaa ttgtgacaga attgaaaata
     1741 agggaaaagt ttttgacagc gaggtcataa taattacaac aaaccttgcc aatccagccc
     1801 cacttgatta tgttaacttt gaggcctgtt ccaggagaat tgatttcctg gtgtacgctg
     1861 aggcaccaga agtagaaaag gcaaaacggg actttcctgg tcagccagat atgtggaagg
     1921 atgccttcaa gcccgacttt tcacacatca agctacagct tgcaccccag ggcggctttg
     1981 acaagaatgg caacacccca catgggaaag gagtgatgaa gaccctcact accggttctc
     2041 tgattgcccg cgcatcaggc ctactgcatg agaggatgga tgaatttgaa ctccaaggtc
     2101 ccacaatcac caccttcaat ttcgaccgga acagaatcac agcattcaga caattggctg
     2161 cagaaaacaa gtatggattg gtggatacca tgaaagttgg caatcaacta aaaggagtga
     2221 aaaccatgga ggaacttaaa caagcaatca ggaatgtgac catcaagagg tgccggatca
     2281 tctacggtgg ctccacgtat gaccttgaat ctgatggcaa gggcaaagtt ttggtggaaa
     2341 aggtcaagaa cacctctgta cagaccaaca acgagttggc tggggccctg caccatctca
     2401 aacacgcccg aatcaggtac tatgtcaaat gtgtgcaaga agcagtctat tccatcatac
     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 ttgagcgatg
     2701 aggagtatga cgagtacaag aggataagag aagagaggaa tgggaagtac tccatagagg
     2761 agtatcttca agacagagac aggtactatg aggagctcgc cattgccaag gccacggaag
     2821 aagacttctg tgaagaagag gagatcaaaa tccgtcagag aattttccgt cccaccagga
     2881 aacaaagaaa ggaagagagg gccacattag ggctagtaac 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 cataacagaa gcatttggag tccccatcaa acaaattcag atccacaaat
     3181 caggtgaatt ttgccgattc agattcccaa aaccaattag accagatgta acagggatga
     3241 tcttggaaga aggtgcgcct gagggcaccg tggcaactgt gctcatcaaa cgccccaccg
     3301 gggagctcat gcctcttgca gccagaatgg gaacacacgc aaccatgaga attcaaggcc
     3361 gcatggttgg cggacagatg ggtatgttgc tcactggatc aaatgctaaa ggaatggatt
     3421 tgggaacaac tcctggtgac tgtggctgcc cttacatcta taaaagaggc aatgactata
     3481 tagtcattgg ggtgcacact gcagcagccc gtggtggaaa caccgtcatc tgtgccacac
     3541 agggaagtga gggtgaggca actcttgagg gtggagatga caaaggaaca tactgtgggg
     3601 cacccattct aggccctggg ggtgcaccaa aattgagcac caaaaccaaa ttttggaggt
     3661 catcgaacac gccccttcca ccagggacat atgagcctgc ctacctcggt ggccgtgatc
     3721 cgcgtgttaa gggtgggccc tccctgcagc aggtaatgag agaccagttg aagccattca
     3781 ctgaacccag gggcaaacct ccaagaccaa gtgtattgga agcagccaaa caaaccatca
     3841 tcaatgtcct cgaacaaacc ctggaccctc cacaaaaatg gacatacgca caggcgtgtg
     3901 cctcacttga caaaaccacc tccagcgggc atccctatca cgtccgaaag aatgaattct
     3961 ggaatggtga gaccttcact ggaaaattgg cagaccaagc atcaaaagca aacctaatgt
     4021 ttgaggaagg gaaacacatg acaccagtgt acacagcagc actcaaggac gagctagtca
     4081 agactgagaa aatctatgga aagatcaaga agagactgct ctggggctct gacttgtcca
     4141 ctatgatccg gtgcgctagg tcatttggtg ggctcatgga cgagatgaag gcacactgca
     4201 tatcactccc agtccgagtt ggcatgaata tgaatgaaga tggcccaata atatttgaga
     4261 aacattccag atacaaatac cactatgatg cagactactc tcgttgggat tcaacacaac
     4321 agagggcagt actagcagca gccttggaaa ttatggtcag attctctgca gaaccacaat
     4381 tggcacaaat agtcgctgag gatctgctgg cccctagtgt agtagatgta ggagacttta
     4441 aaattacaat aaatgaaggg ctcccctctg gtgtgccatg cacttctcaa tggaactcca
     4501 tcgcacactg gctgctaact ctctgtgcct tgtctgaagt caccaaactg tcccctgaca
     4561 ttatacaggc aaattccatg ttctcatttt acggtgatga cgagattgtc agcaccgaca
     4621 taaaattgga ccctgaacag ttaaccacca aattgaaaga gtacggcctg aaaccaaccc
     4681 gcccagacaa aaccgaggga cccctgatta tcagtgaaga tttgaacggt ctcactttcc
     4741 tccgaaggac ggtgactcgt gacccagctg gctggtttgg aaaattggac caaagctcaa
     4801 ttttgaggca gatgtactgg actagaggat 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 cggtcactgg tcaaacaaat
     5221 attatagacc cttggattag agcaaatttt gtccaggccc ccaatggtga atttacagtc
     5281 tctccccgta atgcccctgg tgaagtgcta ctgagtctag agttgggtcc agaattaaat
     5341 ccttatctgg cacatttagc aagaatgtac aatgggtatg ccggtgggat ggaggtgcag
     5401 gtcatgttgg ctgggaacgc gttcacagcc ggcaagttgg tcttcgccgc cgtgccacct
     5461 cacttcccgg ttgaaaacct tagcccacag caaatcacca tgttccctca tgtgatcata
     5521 gatgtgagaa ccttggaacc tgttttatta ccactccctg atgttagaaa taatttcttc
     5581 cattataatc agaaagatga tcccaagatg agaattgtgg ctatgcttta tacccccctc
     5641 aggtctaatg gttcaggtga tgatgtgttt acagtctcct gcagagtgtt gactagacct
     5701 tcccctgact ttgacttcac atacctggtg ccaccaacag tggagtctaa aacaaaacca
     5761 ttcaccctcc caatcctcac acttggggag ctttccaatt ccaggttccc agtgtccata
     5821 gaccagatgt ataccagccc taatgaagtt atatcagtgc agtgtcaaaa tggtaggtgc
     5881 acactggacg gggagctcca ggggacaaca caactccaag tcagtggcat ttgtgctttc
     5941 aaaggtgaag tgaccgccca cttgcatgac aatgatcacc tatataatgt taccatcaca
     6001 aacttgaatg ggtccccttt tgatccctcc gaggatatcc ctgcccctct gggtgtgcct
     6061 gacttccagg gaagggtttt tggtatcatc tcccaaagag acaaacacaa tagtcctggg
     6121 cataatgaac cagcaaacag gggacacgac gctgtggttc ccacttacac agcacagtac
     6181 actccaaaac tgggacaaat tcaaattggc acatggcaga ctgacgatct tacagtcaac
     6241 caaccagtca aattcacccc agttggactc aatgacactg aacatttcaa ccaatgggtg
     6301 gtccctaggt atgctggtgc cctaaacctt aatacaaacc ttgccccttc tgttgctcca
     6361 gtatttccag gagagcgtct gctcttcttc agatcataca ttcccctcaa gggcggttat
     6421 ggaaacccag ccattgattg cctactacca caagagtggg 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 gggcgtagaa gggttcaata atggctggag
     6721 cttttgtagc tggtcttgca ggggatgtgc tcagcaatgg gcttagttca ttaatcaatg
     6781 caggtgctaa tgcaataaat cagagggcag aatttgattt taatcagaaa ttgcagcaaa
     6841 attcttttaa tcatgataag gagatgttgc aggctcagat tcaggcaact aagcagctgc
     6901 aggcagacat gatggctata aaacaagggg tcttgaccgc tggcggcttt tcccctgctg
     6961 atgcagccag aggtgctgtg aacgcgccca tgacacaagc gctagattgg aatggtacaa
     7021 ggtattgggc accaaactcc atgaggacca catcttactc tggaaaattc acatcaaccg
     7081 ccccagtgag gcaggccgac ttccagcaca cccaaagccg gccttcgagt ggctcctctg
     7141 tgtcttcctt tgccactcag tcttcaaggc caactctgac cacaaccact ggttcctcac
     7201 atggcacagt ctcatcaaat tcaactcgca gcacaagcct ctcccaatca acggtctcca
     7261 gagccacatc 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 tgaaaaggtg
     7501 aaaatttatt taggatgaat tgattttacc
//