Typing tool

Complete norovirus genomes

KY486271  GII.4 Sydney
 GII.P31

Length: 7,551 | 3 CDS

ORF1: 1..5094
ORF2: 5075..6697
ORF3: 6697..7503
LOCUS       KY486271                7551 bp    RNA     linear   VRL 19-SEP-2018
DEFINITION  Norovirus GII strain Hu/GII.Pe-GII.4-Sydney/2013/USA, complete
            genome.
ACCESSION   KY486271
VERSION     KY486271.1
DBLINK      BioProject: PRJNA490509
            BioSample: SAMN10060453
KEYWORDS    .
SOURCE      Norovirus GII
  ORGANISM  Norovirus GII
            Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes;
            Picornavirales; Caliciviridae; Norovirus.
REFERENCE   1  (bases 1 to 7551)
  AUTHORS   Yang,Z., Vinje,J. and Kulka,M.
  TITLE     Complete Genome Sequence of Human Norovirus GII.Pe-GII.4 Sydney
            from the United States
  JOURNAL   Genome Announc 5 (15), e00159-17 (2017)
   PUBMED   28408676
  REMARK    Publication Status: Online-Only
REFERENCE   2  (bases 1 to 7551)
  AUTHORS   Yang,Z. and Kulka,M.
  TITLE     Direct Submission
  JOURNAL   Submitted (18-JAN-2017) Molecular Virology Team/Division of
            Molecular Biology, OARSA/CFSAN/Food and Drug Administration, 8301
            Muirkirk Road, Laurel, MD 20708, USA
COMMENT     ##Assembly-Data-START##
            Assembly Method       :: CLC Genomics Workbench v. 8.0.1
            Coverage              :: 66,490 X
            Sequencing Technology :: Illumina
            ##Assembly-Data-END##
FEATURES             Location/Qualifiers
     source          1..7551
                     /organism="Norovirus GII"
                     /mol_type="genomic RNA"
                     /strain="Hu/GII.Pe-GII.4-Sydney/2013/USA"
                     /isolation_source="stool"
                     /host="Homo sapiens"
                     /db_xref="taxon:122929"
                     /country="USA"
                     /collection_date="06-Jan-2013"
                     /note="genotype: GII.Pe-GII.4-Sydney"
     CDS             1..5094
                     /note="ORF1"
                     /codon_start=1
                     /product="non-structrual polyprotein"
                     /protein_id="AQN80591.1"
                     /translation="MASNDASVAAVANSNNDIAKSSSDGVFSNMAVTFKRALGARPKQ
                     PPPKEIPPRPPRPPTPELVKKIPPPPPNGEDELVVSYSAKDGVSGLPELTTVRQPEET
                     NTAFSVPPLNQRESRDAKEPLTGTIIEMWDGEIYHYGLYVERGLILGVHKPPAAISLA
                     KVELTPLSLFWRPVYTPQYLISPDTLRRLHGESFPYTAFDNNCYAFCCWVLDLNDSWL
                     SRRMIQRTTGFFRPYQDWNRKPLPTMDDSKLKKVANIFLCTLSSLFTRPIKDVIGKLK
                     PLNILNILATCDWTFAGIVESLILLAELFGVFWTPPDVSAMIAPLLGDYELQGPEDLA
                     VELVPIVMGGIGLVLGFTKEKIGKMLSSAASTLRACKDLGAYGLEILKLVMKWFFPKK
                     EEVNELAMVRSIEDAVLDLEAIENNHMTTLLKDKDSLATYMRTLDLEEEKARKLSTKS
                     ASPDIVGTINSLLARIAAARSLVHRAKEELSSRPRPVVVMISGRPGIGKTHLARELAK
                     KIAASLTGDQRVGLIPRNGVDHWDAYKGERVVLWDDYGMSNPIHDALRLQELADTCPL
                     TLNCDRIENKGKVFDSDAIIITTNLANPAPLDYVNFEACSRRIDFLVYAEAPEVEKAK
                     RDFPGQPDMWKNAFSPDFSHIKLSLAPQGGFDKNGNTPHGKGVMKTLTTGSLIARASG
                     LLHERLDEYELQGPALTTFNFDRNKILAFRQLAAENKYGLMDTMRVGKQLKDVKTMSD
                     LKQALKNIAIKKCQIVYNGSTYTLEADGKGSVKVDKVQSVTVQTNNELAGALHHLRCA
                     RIRYYVKCVQEALYSIIQIAGAAFVTTRIAKRMNIQNLWSKPQVEDTEEMTNKDGCLK
                     PKDDEEFVVSSDDIKTEGKKGKNKSGRGKKHTAFSSKGLSDEEYDEYKRIREERNGKY
                     SIEEYLQDRDRYYEEVAIARATEEDFCEEEEAKIRQRIFRPTRKQRKEERASLGLVTG
                     SEIRKRNPEDFKPKGKLWADDDRSVDYNEKLNFEAPPSIWSRIVNFGSGWGFWVSPSL
                     FITSTHVIPQGAKEFFGVPIKQIQIHKSGEFCRLRFPKPIRTDVTGMILEEGAPEGTV
                     ATLLIKRPTGELMPLAARMGTHATMKIQGRTVGGQMGMLLTGSNAKSMDLGTTPGDCG
                     CPYIYKRGNDYVVIGVHTAAARGGNTVICATQGSEGEATLEGGDSKGTYCGAPILGPG
                     SAPKLSTKTKFWRSSTTPLPPGTYEPAYLGGKDPRVKGGPSLQQVMRDQLKPFTEPRG
                     KPPRPNVLEAAKKTIINVLEQTIDPPQKWSFAQACASLDKTTSSGHPHHMRKNDCWNG
                     ESFTGKLADQASKANLMFEEGKNMTPVYTGALKDELVKTDKVYGKIKKRLLWGSDLAT
                     MIRCARAFGGLMDELKAHCVTLPVRVGMNMNEDGPIIFEKHSRYRYHYDADYSRWDST
                     QQRDVLAAALEIMVKFSPEPHLAQVVAEDLLSPSVMDVGDFQISISEGLPSGVPCTSQ
                     WNSIAHWLLTLCALSEVTDLSPDIIQANSLFSFYGDDEIVSTDIKLDPEKLTAKLKEY
                     GLKPTRPDKTEGPLVISEDLDGLTFLRRTVTRDPAGWFGKLEQSSILRQMYWTRGPNH
                     EDPFETMIPHSQRPIQLMSLLGEAALHGPAFYSKISKLVIAELKEGGMDFYVPRQEPM
                     FRWMRFSDLSTWEGDRNLAPSFVNEDGVE"
     CDS             5075..6697
                     /note="ORF2"
                     /codon_start=1
                     /product="major capsid protein"
                     /protein_id="AQN80592.1"
                     /translation="MKMASSDANPSDGSAANLVPEVNNEVMALEPVVGAAIAAPVAGQ
                     QNVIDPWIRNNFVQAPGGEFTVSPRNAPGEILWSAPLGPDLNPYLSHLARMYNGYAGG
                     FEVQVILAGNAFTAGKVIFAAVPPNFPTEGLSPSQVTMFPHIVVDVRQLEPVLIPLPD
                     VRNNFYHYNQSNDPTIKLIAMLYTPLRANNAGDDVFTVSCRVLTRPSPDFDFIFLVPP
                     TVESRTKPFSVPVLTVEEMTNSRFPIPLEKLFTGPSSAFVVQPQNGRCTTDGVLLGTT
                     QLSPVNICTFRGDVTHITGSRNYTMNLASQNWNNYDPTEEIPAPLGTPDFVGKIQGML
                     TQTTRADGSTRGHKATVYTGSADFAPKLGRVQFETDTDHDFEANQNTKFTPVGVIQDG
                     STTHRNEPQQWVLPSYSGRNTHNVHLAPAVAPTFPGEQLLFFRSTMPGCSGYPNMDLD
                     CLLPQEWVQYFYQEAAPAQSDVALLRFVNPDTGRVLFECKLHKSGYVTVAHTGQHDLV
                     IPPNGYFRFDSWVNQFYTLAPMGNGTGRRRAV"
     CDS             6697..7503
                     /note="ORF3"
                     /codon_start=1
                     /product="minor capsid protein"
                     /protein_id="AQN80593.1"
                     /translation="MAGAFFAGLASDVLGSGLGSLINAGAGAINQKVEFENNRKLQQA
                     SFQFSSNLQQASFQHDKEMLQAQIEATKKLQQEMMKVKQAMLLEGGFSETDAARGAIN
                     APMTKALDWSGTRYWAPDARTTTYNAGRFSTPQPSGALPGRANLRDAVPARGSSSKSS
                     NSSTATSVYSNQTTSTRLGSTAGSGTSVSSLPSTARTRSWVEDQSGNLSPFMRGAHNI
                     SFVTPPSSRSSSQGTVSTVPKEVLDSWTGAFNTRRQPLFAHIRKRGESRV"
     3'UTR           7504..7551
ORIGIN      
        1 atggcgtcta acgacgcttc cgttgccgct gttgccaaca gcaacaacga catcgcaaaa
       61 tcttcaagtg acggtgtgtt ttctaacatg gctgtcactt ttaagcgggc cctcggggcg
      121 cggcctaaac agccgccccc gaaggagata ccacccagac ccccgcgacc acccacacca
      181 gaattggtca aaaagatccc tcctccccca cccaacgggg aggatgaact agtggtctct
      241 tacagcgcca aagatggcgt ttccggactg cctgagctca ccactgtcag acaaccggaa
      301 gaaaccaaca cggcgttcag tgtcccccca ctcaaccaaa gggagagcag ggacgccaag
      361 gagccactaa ctggaacaat tattgaaatg tgggatggag aaatctacca ttacggcctg
      421 tacgtggaac gaggtcttat acttggtgtg cacaagccac cggcagccat cagccttgcc
      481 aaggtcgagc taacaccgct ctctttgttc tggagacctg tatacacccc ccagtatctc
      541 atctctccag acactcttag gagattacat ggggagtcat tcccctacac tgcatttgac
      601 aacaattgct acgccttttg ttgttgggta ttagacctaa acgactcatg gttaagcagg
      661 agaatgattc agagaacaac aggtttcttc aggccgtacc aggattggaa caggaagccc
      721 ctccccacta tggatgattc caaattaaag aaggtagcca acatattctt gtgcactttg
      781 tcttcactat tcaccagacc cattaaggac gtaataggga agttgaaacc tcttaacatc
      841 cttaacattc tggctacatg tgattggacc ttcgcaggca tagtggaatc tttaatactc
      901 ttagcagaac tctttggagt tttctggaca cccccagatg tgtctgcgat gatcgccccc
      961 ttgctaggtg attatgaact gcaaggacct gaggaccttg cagtggaact ggtcccaata
     1021 gtgatggggg ggataggttt ggtgctagga tttaccaaag agaaaattgg aaagatgcta
     1081 tcatccgctg catccacttt aagagcttgt aaagacctcg gtgcatacgg actggaaatc
     1141 ttaaaattgg tcatgaagtg gttcttccca aagaaagagg aagtaaatga actggctatg
     1201 gtgagatcca tcgaggatgc agtgctagac ctcgaggcaa ttgaaaacaa ccacatgacc
     1261 accctactca aagacaaaga cagcttggca acctacatga gaacccttga ccttgaggag
     1321 gagaaagcca gaaaactctc aaccaaatct gcttcacccg atattgtggg cacaatcaac
     1381 tctcttctgg caagaatcgc tgctgcacgc tccctagtgc atcgggcgaa agaagagctc
     1441 tccagcaggc cgagacctgt cgttgtgatg atatcgggaa gaccagggat agggaaaact
     1501 caccttgcca gggagctggc caagaagatc gcggcctccc tcacagggga ccagcgtgtg
     1561 ggtcttatcc cacgcaatgg tgtcgaccac tgggacgcat acaagggcga aagagttgtc
     1621 ctatgggacg actatggaat gagcaacccc atccatgatg ccctcaggtt gcaggagctt
     1681 gctgacactt gccccctcac gctaaattgt gacagaattg agaacaaagg gaaagtcttt
     1741 gacagtgatg ccataattat caccaccaat ctggccaacc cagcaccact ggactatgtc
     1801 aactttgaag cgtgctcgag acgtattgac ttcctcgtgt acgcagaagc ccctgaggtg
     1861 gagaaggcaa agcgcgactt cccaggtcaa cctgacatgt ggaagaacgc tttcagtcct
     1921 gacttctcac acataaaact gtcattggct ccacagggtg gttttgacaa gaacggcaac
     1981 accccgcatg gaaaaggggt catgaagacc ctcaccactg gctccctcat cgcccgagca
     2041 tcagggttac tccatgagag gctagatgaa tatgaactgc aaggcccagc cctcaccact
     2101 ttcaactttg accgcaacaa gatacttgct tttagacagc ttgctgctga aaacaagtat
     2161 gggctgatgg acacaatgag agttggaaaa cagctcaagg atgtcaagac catgtcagac
     2221 ctcaaacaag cactcaagaa catcgcgatc aagaagtgcc agatagtgta caatggtagc
     2281 acctacacac ttgaggccga tggcaagggt agtgtgaaag ttgacaaagt gcaaagtgtc
     2341 actgtgcaga ccaacaatga actagccggt gccctacacc acctaaggtg cgctagaatc
     2401 agatactatg ttaagtgcgt ccaggaggca ctgtattcca tcatccaaat cgctggggct
     2461 gcattcgtca ccacgcgcat cgctaagcgc atgaatatac agaacctctg gtccaagcca
     2521 caggtggaag acacagaaga gatgaccaac aaagatggtt gcctaaaacc caaagatgat
     2581 gaagagtttg tcgtctcatc cgacgacatc aaaactgagg gcaagaaagg gaagaacaag
     2641 tccggccgtg gcaagaagca cacagccttt tcaagcaaag ggctcagtga tgaggagtac
     2701 gatgagtaca agagaatcag agaagaaagg aatggtaagt actccataga agagtacctt
     2761 caggacagag acaggtacta cgaggaggtg gccattgcca gggcaaccga agaggacttc
     2821 tgtgaagaag aagaggccaa aatccgacag agaattttca gaccaacaag gaaacaacgc
     2881 aaagaagaga gggcctctct cggcttggtc acaggctctg aaatcaggaa gagaaaccca
     2941 gaagacttca aacccaaggg aaagctgtgg gctgatgatg acagaagtgt tgactacaat
     3001 gagaaactca actttgaggc cccaccaagc atctggtcgc ggatagtcaa ctttggttca
     3061 ggctggggct tctgggtctc ccccagtctg tttataacat caacccatgt cataccccaa
     3121 ggtgcaaaag agttcttcgg agtccctatc aagcaaatcc agatacacaa atcaggtgaa
     3181 ttctgccggt tgagattccc aaagccaatc agaactgatg tgacgggcat gattctagaa
     3241 gaaggtgcgc ccgaggggac cgtggccaca ctgctcatca agagaccaac aggagagctc
     3301 atgcctttgg cagccagaat ggggacccat gcaaccatga aaattcaggg gcgcacagtt
     3361 ggagggcaaa tgggtatgct cctgacagga tccaacgcca agagtatgga cctaggcaca
     3421 acaccaggcg actgcggttg cccctacatc tacaagaggg ggaatgacta cgtggtcata
     3481 ggagtccaca cggccgctgc ccgtggagga aacactgtca tatgtgccac ccaggggagt
     3541 gagggagaag ccacacttga aggaggtgac agtaaaggga catactgtgg cgcaccaatc
     3601 ttgggcccag ggagcgctcc aaagctcagt accaagacta agttttggag atcatccaca
     3661 acaccactcc cacctggcac ctacgaacca gcctacctcg gtggcaaaga ccccagagtc
     3721 aaaggtggcc cttcattgca acaagttatg agggaccagc tgaagccatt cacagaaccc
     3781 agaggcaaac caccaagacc aaatgtgttg gaagctgcca agaaaaccat catcaatgtc
     3841 cttgagcaaa caattgatcc accccaaaaa tggtcatttg cgcaggcttg cgcatctctt
     3901 gacaaaacca cctccagcgg ccacccgcac cacatgcgga aaaacgattg ttggaatggg
     3961 gagtccttca caggaaaatt ggctgatcaa gcctccaagg ccaacctaat gtttgaagag
     4021 ggaaagaaca tgactccagt ctacacaggt gcacttaaag atgagttggt aaagaccgat
     4081 aaagtttatg gtaagatcaa gaagaggctt ctgtggggtt cagatctggc gaccatgata
     4141 cggtgtgccc gagcttttgg aggccttatg gatgaactca aggcgcactg tgtcacactt
     4201 cctgtcagag ttggtatgaa catgaatgag gatggcccca tcatctttga gaagcactcc
     4261 aggtatagat atcactatga tgctgattat tcccggtggg actcaacaca acaaagggat
     4321 gtgctagcag cagcactaga aatcatggtt aagttctctc cagaaccaca cctggcccag
     4381 gtagttgcag aagacctcct ttcccctagc gtgatggatg taggtgactt tcaaatatca
     4441 ataagtgagg gtcttccctc tggggtacct tgtacctccc agtggaattc catcgcccac
     4501 tggctcctca ctctttgtgc actctctgaa gtcacggacc tgtcccctga catcattcag
     4561 gccaactccc ttttctcctt ctatggtgat gatgagattg taagcacaga cataaagttg
     4621 gacccagaga agctgacagc aaagctcaag gagtacgggc tgaaaccaac ccgccccgac
     4681 aaaactgaag gaccccttgt tatctctgaa gacctggatg gcctgacatt cctccggaga
     4741 actgtgaccc gtgatccagc tggctggttt ggaaaattgg aacaaagttc aattctcaga
     4801 caaatgtact ggaccagggg tcccaaccat gaagatccat ttgaaacaat gataccacac
     4861 tcccaaagac ccatacaatt gatgtccttg ctgggcgagg ctgcactcca cggcccggca
     4921 ttttacagca aaattagcaa attagtcatt gcagagctga aggaaggtgg catggatttt
     4981 tacgtgccca gacaagagcc aatgttcaga tggatgagat tctcagatct gagcacgtgg
     5041 gagggcgatc gcaatctggc tcccagtttt gtgaatgaag atggcgtcga gtgacgccaa
     5101 cccatctgat gggtccgcag ccaacctcgt cccagaggtc aacaatgagg ttatggctct
     5161 ggagcccgtt gttggtgccg ccattgcggc acctgtagcg ggccaacaaa atgtaattga
     5221 cccctggatt agaaacaatt ttgtacaagc ccctggtgga gagtttacag tgtcccctag
     5281 aaacgctcca ggtgaaatac tatggagcgc gcccttgggc cctgatctaa atccctacct
     5341 atcccatttg gccagaatgt acaatggtta tgcaggtggt tttgaagtgc aggtaattct
     5401 cgcggggaac gcgttcaccg ccgggaaggt catatttgca gcagtcccac caaactttcc
     5461 aactgaaggc ttgagcccca gccaggtcac tatgttcccc catatagtag tagatgttag
     5521 gcaactagaa cctgtgttga ttcccttacc cgatgttagg aataatttct atcattataa
     5581 tcaatcaaat gaccccacca ttaagttgat agcaatgttg tacacaccac ttagggctaa
     5641 taatgctggg gatgatgtct tcacagtttc ttgccgagtt ctcacgagac catcccccga
     5701 ttttgatttc atatttctag tgccacccac agttgagtca agaactaaac cattctctgt
     5761 cccagtttta actgttgagg agatgaccaa ttcaagattc cccattcctt tggaaaagtt
     5821 gttcacgggt cccagcagtg cctttgttgt ccaaccacaa aacggcaggt gcacgactga
     5881 tggcgtgctc ctaggcacaa cccaactgtc tcctgtcaac atctgcacct tcagaggaga
     5941 tgtcacccat atcacaggta gtcgtaacta cacaatgaat ttggcttctc aaaattggaa
     6001 caattatgac ccaacagaag aaatcccagc ccctctagga actccagact ttgtggggaa
     6061 gattcaaggc atgctcaccc aaaccacaag ggcagatggc tcaacacgcg gccacaaagc
     6121 cacagtgtac actgggagcg ccgactttgc tccaaaactg ggtagagttc aatttgagac
     6181 tgacacagac catgattttg aagctaacca aaacacaaag ttcaccccag tcggtgtcat
     6241 ccaagatggt agcaccaccc accgaaatga accccaacag tgggtgctcc caagttactc
     6301 aggcagaaat actcataatg tgcatctggc ccccgctgta gcccccactt ttccgggtga
     6361 gcaacttctc ttcttcagat ccaccatgcc cggatgcagc gggtacccta acatggattt
     6421 ggactgtctg ctcccccagg aatgggtgca gtacttctac caagaggcag cccccgcaca
     6481 atctgatgtg gctctgctaa gatttgtgaa tccagacaca ggtagggttt tgtttgagtg
     6541 taagcttcat aaatcaggct atgttacagt ggctcacact ggccaacatg atttggttat
     6601 tccccccaat ggttatttta gatttgattc ctgggtcaac cagttctaca cgcttgcccc
     6661 catgggaaat ggaacggggc gtagacgtgc agtataatgg ctggagcttt ctttgctgga
     6721 ttggcatctg atgtccttgg ctctggactt ggttccctta tcaatgctgg ggctggggcc
     6781 atcaaccaaa aagttgagtt tgaaaataac agaaaattgc aacaagcatc cttccaattt
     6841 agcagcaatc tacaacaggc ttcctttcaa catgacaaag agatgctcca agcacaaatt
     6901 gaggccacca aaaagctaca acaggaaatg atgaaagtta agcaggcaat gctcctagag
     6961 ggtgggttct ctgagacaga tgcagcccgc ggggcaatca acgcccccat gacaaaagct
     7021 ttggactgga gtgggacaag gtactgggct cccgatgcta ggactacaac atacaatgca
     7081 ggccgctttt ccacccctca accatcgggg gcactgccag gaagagctaa tcttagggat
     7141 gctgtccctg ctcggggttc ctccagtaaa tcttctaatt cttctactgc tacttctgtg
     7201 tactcaaatc aaactacttc aacgagactt ggttctacag ctggttctgg taccagtgtc
     7261 tcgagcctcc cgtcaactgc aaggactagg agctgggttg aggatcaaag tgggaatttg
     7321 tcacctttca tgaggggggc ccacaacata tcttttgtca ccccaccatc tagcagatcc
     7381 tctagccaag gcacagtctc aaccgtgcct aaagaggttt tggactcctg gactggcgct
     7441 ttcaacacgc gcaggcagcc actcttcgct cacattcgta agcgagggga gtcacgggtg
     7501 taatgtgaaa agacaaaatt gattatcttt ctttttcttt agtgtctttt a
//