Typing tool

Complete norovirus genomes

KM198573  GII.3
 GII.P21

Length: 7,421 | 3 CDS

ORF1: 1..5100
ORF2: 5081..6727
ORF3: 6727..7419
LOCUS       KM198573                7421 bp    RNA     linear   VRL 13-NOV-2014
DEFINITION  Norovirus Hu/GII/C2H-45/2011/VNM nonstructural polyprotein, capsid
            protein VP1, and capsid protein VP2 genes, complete cds.
ACCESSION   KM198573
VERSION     KM198573.1
KEYWORDS    .
SOURCE      Norovirus Hu/GII/C2H-45/2011/VNM
  ORGANISM  Norovirus Hu/GII/C2H-45/2011/VNM
            Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes;
            Picornavirales; Caliciviridae; Norovirus.
REFERENCE   1  (bases 1 to 7421)
  AUTHORS   Cotten,M., Petrova,V., Phan,M.V., Rabaa,M.A., Watson,S.J.,
            Ong,S.H., Kellam,P. and Baker,S.
  TITLE     Deep sequencing of norovirus genomes defines evolutionary patterns
            in an urban tropical setting
  JOURNAL   J. Virol. 88 (19), 11056-11069 (2014)
   PUBMED   25056894
REFERENCE   2  (bases 1 to 7421)
  AUTHORS   Cotten,M.L., Petrova,V., Phan,M.V.T., Rabaa,M.A., Watson,S.J.,
            Kellam,P. and Baker,S.
  TITLE     Direct Submission
  JOURNAL   Submitted (13-JUL-2014) Virus Genomics, The Wellcome Trust Sanger
            Institute, Hinxton CB10 1SA, United Kingdom
COMMENT     ##Assembly-Data-START##
            Assembly Method       :: SPAdes v. 2.4.0
            Sequencing Technology :: Illumina
            ##Assembly-Data-END##
FEATURES             Location/Qualifiers
     source          1..7421
                     /organism="Norovirus Hu/GII/C2H-45/2011/VNM"
                     /mol_type="genomic RNA"
                     /isolate="Hu/GII/C2H-45/2011/VNM"
                     /host="Homo sapiens"
                     /db_xref="taxon:1527019"
                     /country="Viet Nam"
                     /collection_date="02-Nov-2011"
                     /note="genotype: GII"
     CDS             1..5100
                     /note="ORF1"
                     /codon_start=1
                     /product="nonstructural polyprotein"
                     /protein_id="AII02847.1"
                     /translation="MKMASNDASAAAAANSNNDNAKSSSDGVFSNMAVTFKRALGARP
                     KQPPPGDKPPKPPRPPTPELVKAIPPPPPNGEDEPIISYNVKEGVSGLPELSTVTQPE
                     ESSTAFSVPPLSQRENRDAKEPLTGTILEMWDGEIYHYGLYVERGLVLGVHKPPAAIS
                     LAKVELTPLSLYWRPVYTPQYLISPDTLKKLHGETFPYTAFDNNCYAFCCWVLDLNDS
                     WLSRRMIQRTTGFFRPYQDWNRKPLPTMDDSKVKKVANVVLCALSSLFTRPIKDIIGK
                     LKPLNILNILATCDWTFAGIVESLILLAELFGVFWTPPDVSAMIAPLLGDYELQGPED
                     LAVELVPVVMGGIGLVLGFTKEKIGKMLSSAASTLRACKDLGAYGLEILKLVMKWFFP
                     KKEEKNELAMVRSIEDAVLDLEAIENNHMTALLKDKDSLATYMRTLDMEEEKARKLST
                     KSASPDIVGTINALLSRIAAARSLVHRAKEELSSRPRPVVVMISGRPGIGKTHLAREL
                     AKKIASSLTGDQRVGLIPRNGVDHWDAYKGERVVLWDDYGMSNPIHDALRLQELADTC
                     PLTLNCDRIENKGKVFDSDAIIITTNLANPAPLDYVNFEACSRRIDFLVYADAPEVEK
                     AKRDFPGQPDMWKDTFKPDFSHIKLALAPQGGFDKNGNTPHGKGVMKTLTASSLVARA
                     SGLLHERLDEYELQGPTPTTFNFDRNKVLAFRQLAAENKYGLVDTMRVGSQLKNVKTM
                     TELKQALKNISVKKCQLVYGGGTYTLESDGKGNVHVEKVNNASVQTNNELSGALHHLR
                     CARIRYYVKCVQEALYSILQIAGAAFITTRIAKRMNIQNLWSKPQAEDLEETSNEEGC
                     PKPKNDEEFVISSDDIKTEGKKGKNKTGRGKKHTAFSSKGLSDEEYDEYKRIREERNG
                     KYSIEEYLQDRDKYYEEVAIARATEEDFCEEEEAKIRQRIFRPTRKQRKEERASLGLV
                     TGSEIRKRNPDDFKPKGKLWADDDRSVDYNERLSFEAPPSIWSRIVNFGSGWGFWVSP
                     SLFITSTHVIPQGAQEFFGVPIKQIQIHKSGEFCRLRFPKPIRTDVTGMILEEGAPEG
                     TVATLLIKRPTGELMPLAARMGTHATMKIQGRTVGGQMGMLLTGSNAKSMDLGTTPGD
                     CGCPYIYKRGNDYVVIGVHTAAARGGNTVICATQGNEGEAMLEGGDNKGTYCGAPILG
                     PGNAPKLSTKTKFWRSSTTPLPPGTYEPAYLGGKDPRVKGGPSLQQVMRDQLKPFTEP
                     RGKPPKPSVLEAAKKTIINVLEQTIDPPQKWTYAQACASLDKTTSSGHPYHMRKNDCW
                     NGETFTGKLADQASKANLMFEEGKNMTPVYTGALKDELVKTDKIYGTIKKRLLWGSDL
                     STMIRCARAFGGLMDELKAHCVTLPVRVGMNMNEDGPIIFEKHSRYKYHYDADYSRWD
                     STQQRAVLAAALEIMVKFSPEPHLAQVVAEDLLSPSVMDVGDFKISINEGLPSGVPCT
                     SQWNSIAHWLLTLCALSEVTDLSPDIIQANSLFSFYGDDEIVSTDIKLDPEKLTTKLK
                     EYGLKPTRPDKTEGPLIISEDLDGLTFLRRTVTRDPAGWFGKLDQSSILRQMYWTRGP
                     NHEDPFETMIPHSQRPIQLMSLLGEAALHGPSFYSKISKLVISELKEGGMDFYVPRQE
                     PMFRWMRFSDLSTWEGDRNLAPSFVNEDGVE"
     CDS             5081..6727
                     /note="ORF2"
                     /codon_start=1
                     /product="capsid protein VP1"
                     /protein_id="AII02848.1"
                     /translation="MKMASNDAAPSNDGAAGLVPEINSEAMALEPVAGAAIAAPLTGQ
                     QNIIDPWIMNNFVQAPGGEFTVSPRNSPGEVLLNLELGPEINPYLAHLARMYNGYAGG
                     FEVQVVLAGNAFTAGKIIFAAIPPNFPIDNLSAAQITMCPHVIVDVRQLEPVNLPMPD
                     VRNNFFHYNQGSDSRLRLIAMLYTPLRANNSGDDVFTVSCRVLTRPSPDFSFNFLVPP
                     TVESKTKPFSLPILTISEMSNSRFPVPIDSLHTSPTENIVVQCQNGRVTLDGELMGTT
                     QLLPSQICAFRGMLTRSTSRASDQADTATPRLFNYYWHIQLDNLNGTPYDPAEDIPGP
                     LGTPDFRGKVFGVASQRNPDATTRAHEAKIDTTSGRFTPKLGSLEISTESGDFDQNQP
                     TRFTPVGIGVDHEADFQQWTLPDYAGQFTHNMNLAPAVAPNFPGEQLLFFRSQLPSSG
                     GRSNGILDCLVPQEWVQHFYQESAPSQTQVALVRYVNPDTGRVLFEAKLHKLGFMTIA
                     KSGDSPITVPPNGYFRFESWVNPFYTLAPMGTGNGRRRIQ"
     CDS             6727..7419
                     /note="ORF3"
                     /codon_start=1
                     /product="capsid protein VP2"
                     /protein_id="AII02849.1"
                     /translation="MAGAFIAGLAGDMLTNTVGSLVNAGANAINQTIDFENNKYLQNA
                     SFNHDKEMLNAQIEATKRLQADMIAIKQGVLTAGGFSPTDAARGAINAPMTKVLDWNG
                     TRYWAPGATSTTSMSGGFINQTVHRSTPNFKTNQAPKPAPSSGSSVRSNSTQITSLSS
                     HSSGSSRSSGSTVVSSIPSSNRTRDWVNQQNFNLEPHMPGSLRTAFVTPPSSTASSSG
                     TVSTVPKNVLDS"
ORIGIN      
        1 atgaagatgg cgtctaacga cgcttccgct gccgctgctg ccaacagcaa caacgacaac
       61 gcaaaatctt caagtgacgg agtattttct aatatggctg tcacttttaa acgagccctc
      121 ggggcgcggc ctaaacagcc gcccccgggg gacaaaccac caaaaccccc aagaccaccc
      181 acaccagagt tggttaaagc aatcccccct cccccaccca acggggagga cgaaccaatc
      241 atttcttaca acgtcaaaga gggggtttct ggtctgcctg aactctcaac tgtcacccaa
      301 ccggaagaga gctctacagc attcagcgtt ccccctctta gccagaggga gaacagagat
      361 gcaaaggaac cactgactgg aaccatcctg gagatgtggg acggggagat ctaccattat
      421 ggcttatatg tggaacgagg gttagtgcta ggtgtacaca aaccaccagc agccatcagc
      481 cttgctaagg ttgagctgac ccccttgtct ttgtattgga gaccagtgta caccccacag
      541 tacctcattt cccctgacac tctcaaaaag ttgcatgggg agacattccc ttatacagcc
      601 tttgataaca actgttatgc cttctgctgc tgggtacttg acttgaacga ttcatggctg
      661 agtagaagga tgatacagag gacaacaggc ttcttccgac cctaccagga ctggaacagg
      721 aaacccctcc ccacgatgga tgactccaaa gtgaaaaagg tggccaatgt tgtcctctgt
      781 gctctctcgt cattgtttac aagaccaatt aaggacatta ttgggaagtt gaaaccccta
      841 aacatcctca acatcctagc cacatgtgat tggacttttg caggcatagt agaatccctg
      901 atccttttgg ctgaactgtt tggagttttc tggacacccc cagatgtgtc tgcaatgatc
      961 gctcccttac tgggtgatta tgagctgcag ggacccgagg acctcgctgt ggaactcgta
     1021 cccgtagtaa tgggagggat aggtttggtg ttgggattca ccaaagagaa aatcggcaaa
     1081 atgctttcat ctgctgcttc aaccctgagg gcatgtaaag atctcggtgc atatgggttg
     1141 gagatcctca agttggtcat gaagtggttt ttcccaaaga aagaagagaa aaacgaattg
     1201 gcaatggtga gatccatcga ggatgcagtg ctagatcttg aggccattga gaacaaccac
     1261 atgacagctc tactcaagga caaagacagc cttgcaacct acatgaggac tcttgacatg
     1321 gaggaggaga aggcgaggaa actttccacc aagtctgcct caccggatat tgtgggcacg
     1381 ataaatgccc tactgtcaag gattgcagct gcccggtctc tagtgcacag ggctaaggag
     1441 gaactgtcaa gcaggccccg accggtcgtt gtgatgattt cagggagacc aggcataggg
     1501 aaaacccacc tagctagaga gctggcaaag aagatcgcct cctcactcac aggtgaccag
     1561 agggtgggtc ttatcccgcg caacggggtc gaccactggg atgcatacaa aggtgaaagg
     1621 gtcgttctct gggacgacta cgggatgagc aaccctatcc acgacgccct cagactccag
     1681 gagctcgctg atacctgtcc tcttacactt aactgtgaca ggattgagaa caaaggcaaa
     1741 gtctttgaca gtgacgccat aataataacc accaatctgg ccaacccagc gccactggat
     1801 tacgtcaact ttgaagcctg ctcaagacgc atagacttcc tcgtctatgc tgatgcccct
     1861 gaagttgaga aggctaaacg ggacttccca ggccaaccag acatgtggaa agacaccttt
     1921 aaacctgact tctcacacat aaaactggca ttagccccgc aaggaggttt tgacaagaat
     1981 ggtaacactc ctcatgggaa gggtgtcatg aagaccctca ctgctagttc cctcgttgcc
     2041 cgagcatcgg gactcctcca cgagagatta gacgaatacg agctgcaggg cccaactccc
     2101 acaacattca acttcgaccg caacaaggtg cttgccttta ggcagcttgc tgctgaaaac
     2161 aagtatggcc ttgttgacac aatgagggtc ggatcacagc tcaagaacgt caaaactatg
     2221 acagaactca agcaggctct taagaacatc tcagtcaaga aatgtcagct tgtgtatggt
     2281 gggggcacgt acacactcga atctgatggc aaaggcaatg tgcatgtcga gaaggtgaac
     2341 aacgccagtg tgcaaactaa caacgagctc tccggggctt tgcaccatct caggtgtgcc
     2401 agaatcaggt actatgttaa gtgtgtccag gaagctctct actccatctt gcaaattgct
     2461 ggggctgcat tcatcaccac gcgcattgca aagcgcatga acatacaaaa cctctggtcc
     2521 aaaccacagg cagaagatct ggaggagact agtaatgagg agggttgtcc aaaacctaaa
     2581 aatgatgagg agtttgtcat ctcctctgat gacatcaaaa ctgagggtaa gaaaggaaag
     2641 aacaagaccg gccgtggcaa gaagcacaca gccttttcca gcaaaggact cagtgatgag
     2701 gagtacgatg aatataaaag aatcagggaa gaaaggaatg gcaagtactc catagaggaa
     2761 tacctacagg atagagacaa gtactatgag gaggtggcca tagccagggc aactgaggaa
     2821 gacttctgtg aagaagagga ggcaaaaatc cggcaaagga tatttagacc gacaaggaaa
     2881 caacgcaaag aggaaagggc ctctcttggt ttggttacag gttctgagat caggaagaga
     2941 aacccagatg acttcaagcc caaagggaaa ctgtgggccg atgatgacag gagtgttgac
     3001 tacaatgaga gacttagttt cgaggctcca ccaagcattt ggtcacgaat agtcaacttt
     3061 ggctcagggt ggggcttttg ggtctcgccc agcctcttca taacatcaac ccatgtcatt
     3121 ccccaaggcg cacaggagtt ctttggagtg cccatcaaac aaatacaaat tcacaagtca
     3181 ggtgagttct gccggcttag attcccaaaa ccaatcagga cagatgtcac aggcatgatc
     3241 ctggaggaag gtgctccaga aggcactgtt gccacacttc tcatcaagag accaactggg
     3301 gaactcatgc ccttggcagc cagaatgggc acccacgcga ccatgaaaat tcagggtcgc
     3361 actgttggtg gacagatggg catgttactt acagggtcta acgctaagag tatggacctg
     3421 ggtacaactc ctggcgattg tggttgtccc tacatctaca agagggggaa cgactacgtg
     3481 gtcattgggg ttcacactgc cgccgctcgt ggaggaaaca ccgtcatctg tgcaactcaa
     3541 ggaaacgagg gtgaggccat gttagaaggt ggtgacaaca agggaactta ctgtggagca
     3601 ccaatattgg gccctggaaa tgcccccaaa ctcagcacca aaaccaaatt ttggagatct
     3661 tctaccaccc ccctgccacc cggaacctat gagccagcct atctgggtgg caaggaccct
     3721 agagtgaaag gtggcccctc actgcaacag gttatgaggg accaactaaa accattcact
     3781 gagcccagag gcaaaccacc caaaccaagt gtgctagaag ccgccaagaa gactataatc
     3841 aatgtgcttg aacaaacaat agacccacct cagaaatgga catacgcaca ggcgtgtgca
     3901 tcactagaca agaccacttc cagcggccac ccttaccaca tgcggaagaa cgattgctgg
     3961 aatggggaga ctttcacagg aaaactggca gaccaggcct caaaggctaa cctaatgttt
     4021 gaggaaggaa agaacatgac cccagtatac acaggagctc tgaaagatga gttagtcaag
     4081 actgataaga tctatggaac aatcaagaag agactccttt ggggttcaga cctatcgacc
     4141 atgatacggt gtgcacgagc tttcggtggg ctaatggacg aactcaaggc ccattgcgtc
     4201 acactaccag tcagggttgg tatgaacatg aatgaggatg gacccataat ctttgagaaa
     4261 cattccagat acaaatatca ttatgatgca gactactccc gttgggattc aacacaacaa
     4321 agagcagtgt tggctgcagc cctggaaata atggtcaaat tctcaccaga accccatctg
     4381 gctcaagtgg ttgcagaaga cctcttatcc cccagtgtga tggatgtggg tgacttcaag
     4441 atatcaatca acgaggggtt accctctggt gttccctgca cctcacaatg gaactccatt
     4501 gcccactggc tcctcacact gtgtgcactg tctgaggtta cagacctgtc tcctgacatc
     4561 atccaggcaa attccctgtt ctccttttat ggtgatgatg aaatagtgag tacagatatc
     4621 aaactggacc cagaaaaatt aacaacaaaa ttgaaggaat acgggctaaa gccaacccgt
     4681 cctgacaaaa cagaaggacc cttaatcatc tctgaagatt tggatggcct gaccttctta
     4741 cggagaacgg taacccgtga tccggccggg tggtttggca aattggacca aagttcaata
     4801 ctcaggcaga tgtactggac caggggacca aaccatgagg accccttcga aacaatgata
     4861 ccacactccc aaagacccat acaactgatg tcattattgg gtgaagctgc gttgcatggt
     4921 ccatcattct acagtaaaat cagcaaattg gtcatctcag aattgaaaga gggtggaatg
     4981 gatttttacg tgcccagaca agaaccaatg ttcaggtgga tgagattctc agatttgagc
     5041 acgtgggagg gcgatcgcaa tctggctccc agttttgtga atgaagatgg cgtcgaatga
     5101 cgccgctcca tctaatgatg gtgccgccgg cctcgtccca gagatcaaca gtgaggcaat
     5161 ggcgctagag ccagtggcgg gtgcagcgat agcagcaccc ctcactggtc agcaaaatat
     5221 aattgatccc tggattatga ataattttgt gcaagcacct ggtggtgagt tcacagtatc
     5281 ccctagaaat tcccctggtg aagttcttct caatttggaa ttgggtccag aaataaatcc
     5341 ctacttggcc catcttgcta gaatgtataa tggttatgca ggtggatttg aagtgcaggt
     5401 ggtcctagct ggaaatgcgt ttacagcagg aaagataatc tttgcagcta ttccccctaa
     5461 ttttccaatt gataatctaa gtgcagcaca gatcacaatg tgcccacatg tgattgtgga
     5521 tgttagacag ctggaaccag tcaacctccc gatgcctgac gttcgcaata actttttcca
     5581 ttacaatcag gggtctgatt cgagattgcg cctaattgca atgctgtata cacctcttag
     5641 ggcaaataac tctggggatg atgttttcac tgtgtcttgc agagtgctaa ctagacctag
     5701 tcctgacttc tcatttaatt tccttgtgcc acccactgtg gagtcaaaga caaaaccctt
     5761 ttccctcccc attctgacta tctctgaaat gtccaattct aggttcccag taccaattga
     5821 ttctctgcac accagtccta ctgagaacat tgttgtccag tgccagaacg gacgcgtcac
     5881 ccttgatggt gagttgatgg gcaccactca acttttacct agccaaatct gtgctttcag
     5941 gggcatgctc accaggtcaa caagcagggc cagtgaccag gccgatacag caacccctag
     6001 attgtttaat tattattggc atatacaatt ggataaccta aatggaactc cttatgaccc
     6061 tgcagaagat ataccaggcc ccctagggac accagatttc cggggcaaag tctttggcgt
     6121 ggccagccag agaaatcctg atgccacgac tagggcacat gaagcaaaga tagacacaac
     6181 atctggccgc ttcactccaa aattaggctc actagagatt tccactgagt ctggagattt
     6241 tgatcaaaac caaccaacaa gattcacccc agttggcatt ggggttgacc atgaggcaga
     6301 ttttcaacaa tggactcttc ccgactacgc tggtcagttc acccacaaca tgaacttagc
     6361 cccagctgtt gcccccaact tccccggtga gcagctcctt ttctttcgct cacagttgcc
     6421 atcttctggc ggtcggtcca acgggattct agactgcctg gtcccccaag aatgggtaca
     6481 gcacttctat caagaatcag ccccctccca aactcaagtg gccctggtta ggtatgtcaa
     6541 ccctgacact ggtagagtgt tatttgaggc caagctgcac aaattaggtt tcatgactat
     6601 agccaagagt ggtgactctc caataactgt ccccccaaat ggatacttca ggtttgaatc
     6661 ttgggtgaac cccttttata cacttgcccc catgggaact gggaatgggc gtagaaggat
     6721 tcaataatgg ctggagcttt tatagcagga ttggctggtg acatgctcac aaatactgta
     6781 ggatctttag ttaatgcagg ggctaatgcc attaatcaaa caattgattt tgaaaataat
     6841 aaatatttgc aaaatgcctc ttttaatcat gataaggaga tgttgaatgc acaaattgag
     6901 gcaacaaaga ggttacaggc tgacatgatt gctatcaaac aaggggtgtt gaccgctggc
     6961 ggcttctccc ccactgatgc agcccgcggg gcaattaatg cccccatgac aaaagtccta
     7021 gattggaatg gaacgagata ctgggcgcca ggcgccacct ccacaacctc gatgtcgggt
     7081 ggcttcataa atcaaactgt gcacagatcc acaccaaatt ttaaaacgaa ccaggccccc
     7141 aaacccgcac ccagcagtgg gtcttcagtg aggtcaaatt caacccaaat cactagcctg
     7201 agctcacact cgtccgggtc gtctcgatcc agcgggtcta cagttgtcag ctcaataccg
     7261 tcctctaaca ggactaggga ctgggttaac caacaaaatt ttaatttgga accacacatg
     7321 cctggatctc ttaggacagc ttttgtcact ccaccatcta gtacagcctc tagctcaggc
     7381 acagtctcaa ctgtgcccaa aaatgttttg gactcctaga c
//