Typing tool

Complete norovirus genomes

JQ798158  GII.4 Farmington Hills
 GII.P4 Farmington Hills

Length: 7,558 | 3 CDS

ORF1: 5..5104
ORF2: 5085..6707
ORF3: 6707..7513
LOCUS       JQ798158                7558 bp    RNA     linear   VRL 23-AUG-2012
DEFINITION  Norovirus Hu/GII.4/5M/USA/2004, complete genome.
ACCESSION   JQ798158
VERSION     JQ798158.1
KEYWORDS    .
SOURCE      Norovirus Hu/GII.4/5M/USA/2004
  ORGANISM  Norovirus Hu/GII.4/5M/USA/2004
            Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes;
            Picornavirales; Caliciviridae; Norovirus.
REFERENCE   1  (bases 1 to 7558)
  AUTHORS   Dicaprio,E., Ma,Y., Purgianto,A., Hughes,J. and Li,J.
  TITLE     Internalization and dissemination of human norovirus and animal
            caliciviruses in hydroponically grown romaine lettuce
  JOURNAL   Appl. Environ. Microbiol. 78 (17), 6143-6152 (2012)
   PUBMED   22729543
REFERENCE   2  (bases 1 to 7558)
  AUTHORS   Ma,Y., Hughes,J.H. and Li,J.
  TITLE     Sequence analysis of norovirus GII.4
  JOURNAL   Unpublished
REFERENCE   3  (bases 1 to 7558)
  AUTHORS   Ma,Y., Hughes,J.H. and Li,J.
  TITLE     Direct Submission
  JOURNAL   Submitted (19-MAR-2012) Department of Food Science and Technology,
            The Ohio State University, 2015 Fyffe Road, Columbus, OH 43210, USA
FEATURES             Location/Qualifiers
     source          1..7558
                     /organism="Norovirus Hu/GII.4/5M/USA/2004"
                     /mol_type="genomic RNA"
                     /strain="Hu/GII.4/5M/USA/2004"
                     /isolate="5M"
                     /host="Homo sapiens"
                     /db_xref="taxon:1195791"
                     /country="USA"
                     /collection_date="2004"
                     /note="genotype: GII.4"
     CDS             5..5104
                     /note="ORF1"
                     /codon_start=1
                     /product="non-structural polyprotein"
                     /protein_id="AFL70022.1"
                     /translation="MKMASNDASAAAVANSNNDTAKSSSDGVLSSMAVTFKRALGARS
                     KQPPPRETPQRPPRPPTPELVKKIPPPPPNGEDEIVVSYSVKDGVSGLPELSTVRQPE
                     EANTAFSVPPLNQRENRDAKEPLTGTILEMWDGEIYHYGLYVDRGLVLGVHKPPAAIS
                     LAKVELTPLSLFWRPVYTPQYLTSPDTLKKLHGETFPYTAFDNNCYAFCCWVLDLNDS
                     WLSRRMIQRTTGFFRPYQDWNRKPLPTVDDSKLKKVANIFLCALSSLFTRPIKDIIGK
                     LKPLNILNILASCDWTFAGIVESLILLAELFGVFWTPPDVSAMIAPLLGDYELQGPED
                     LAVELVPVVMGGIGLVLGFTKEKIGKMLSSAASTLRACKDLGAYGLEILKLVMKWFFP
                     KKEEANELAMVRSIEDAVLDLEAIENNHMTTLLKDKDSLATYMRTLDLEEEKARKLST
                     KSASPDIVGTINALLARIAAARSLVHRAKEELSSRPRPVVLMISGRPGIGKTHLAREV
                     AKRIAASLTGDQRVGLIPRNGVDHWDAYKGERVVLWDDYGMSNPIHDALRLQELADTC
                     PLTLNCDRIENKGKVFDSDVIIITTNLANPAPLDYVNFEACSRRIDFLVYAEAPEVEK
                     AKRDFPGQPDMWKNAFSSDFSHIKLALAPQGGFDKNGNTPHGKGVMKTLTTGSLIARA
                     SGLLHEKLDEFELQGPALTTFNFDRNKVLAFRQLAAENKYGLMDTMRVGRQLKDVRTM
                     PELKQALKNISIKKCQIVYSGCTYTLESDGKGNVKVDRVQSTSVQTSNELTGALHHLR
                     CARIRYYVRCVQEALYSIIQIAGAAFVTTRIVKRMNIQDLWSKPQVENTEEVTNKDGC
                     PKPKDDEEFVISSDDIKTEGKKGKNKTGRGKKHTAFSSKGLSDEEYDEYKRIREERNG
                     KYSIEEYLQDRDKYYEEVAIARATEEDFCEEEEAKIRQRIFRPTRKQRKEERASLGLV
                     TGSEIRKRNPDDFKPKGKLWADDNRSVDYNEKLSFEAPPGIWSRIVNFGSGWGFWVSP
                     SLFITSTHVIPQGAKEFFGVPIKQIQVHKSGEFCRLRFPKPIRTDVTGMILEEGAPEG
                     TVVTLLIKRSTGELMPLAARMGTHATMKIQGRTVGGQMGMLLTGSNAKSMDLGTTPGD
                     CGCSYIYKRGNDYVVIGVHTAAARGGNTVICATQGSEGEATLEGGDSKGTYCGAPILG
                     PGSAPKLSTKTKFWRSSTAPLPPGTYEPAYLGGKDPRVKGGPSLQQVMRDQLKSFTEP
                     RGKPPKPSVLEAAKKTIINVLEQTIDPPEKWSFAQACASLDKTTSSGHPHHMRKNDCW
                     NGESFTGKLADQASKANLMFEEGKNMTPVYTGALKDELVKTDKIYGKIKKRLLWGSDL
                     ATMIRCARAFGGLMDELKAHCVTLPIRVGMNMNEDGPIIFERHSRYRYHYDADYSRWD
                     STQQRAVLAAALGIMVKFSSEPHLAQVVAEDLLSPSVVDVGDFTISINEGLPSGVPCT
                     SQWNSIAHWLLTLCALSEVTNLSPDIIQANSLFSFYGDDEIVSTDIKLDPEKLAAKLR
                     EYGLKPTRPDKTEGPLVISEDLNGLTFLRRTVTRDPAGWFGKLEQSSILRQMYWTRGP
                     NHEDPSETMIPHSQRPIQLMSLLGEAALHGPAFYSKISKLVIAELKEGGMDFYVPRQE
                     PMFRWMRFSDLSTWEGDRNLAPSFVNEDGVE"
     CDS             5085..6707
                     /note="capsid protein; ORF2"
                     /codon_start=1
                     /product="VP1"
                     /protein_id="AFL70023.1"
                     /translation="MKMASNDANPSDGSTANLVPEVNNEVMALEPVVGAAIAAPVAGQ
                     QNVIDPWIRNNFVQAPGGEFTVSPRNAPGEILWSAPLGPDLNPYLAHLARMYNGYAGG
                     FEVQVILAGNAFTAGKIIFAAVPPNFPTEGLSPSQVTMFPHIVVDVRQLEPVLIPLPD
                     VGNNFYHYNQSNDPTIKLIAMLYTPLRANNAGEDVFTVSCRVLTRPSPDFDFIFLVPP
                     TVESRTKPFTVPILTVEEMTNSRFPIPLEKLFTGPSGAFVVQPQNGRCTTDGVLLGTT
                     QLSPVNICTFRGDVTHIAGTHNYTMNLASQNWNNYDPTEEIPAPLGTPDFVGRIQGML
                     TQTTRGDGSTRGHKATVSTGDVHFTPKLGSIQFNTDTNNDFETGQNTKFTPVGVVQDG
                     NGAHQNEPQQWVLPSYSGRTGHNVHLAPAVAPTFPGEQLLFFRSTMPGCSGYPNMNLD
                     CLLPQEWVQHFYQEAAPAQSDVALLRFVNPDTGRVLFECKLHKSGYVTVAHTGQHDLV
                     IPPNGYFRFDSWVNQFYTLAPMGNGTGRRRAL"
     CDS             6707..7513
                     /note="ORF3"
                     /codon_start=1
                     /product="VP2"
                     /protein_id="AFL70024.1"
                     /translation="MAGAFFAGLASDVLGSGLGSLISAGAGAINQKVEFENNRKLQQA
                     SFQFSSNLQQASFQHDKEMLQAQIEATKKLQQGMMEVKRAMLLEGGFSETDASRGAIN
                     APMTKALDWSGTRYWAPDARTTTYNAGRFSTPQPSGALPGRTNPRATVPARGFSNAPS
                     NTSTATSVYSNQTISTRLGSTAGSGTSVSSLPSTARTRSWVEDQNRNLSPFMRGAHNI
                     SFVTPPSSRSSSQGTVSTVPKEVLDSWTGAFNTRRQPLFAHIRKRGESRA"
ORIGIN      
        1 gtgaatgaag atggcgtcta acgacgcttc cgctgccgct gttgctaaca gcaacaacga
       61 caccgcaaaa tcttcaagtg acggagtgct ttctagcatg gctgtcactt ttaaacgagc
      121 cctcggggcg cggtctaaac agcccccccc gagggaaaca ccacaaagac ccccacgacc
      181 acctactcca gaactggtca aaaagatccc tcctcccccg cccaacggag aggatgaaat
      241 agtggtttct tatagtgtca aagatggcgt ttccggtttg cctgagctct ccaccgttag
      301 gcaaccggaa gaagccaata cggccttcag tgtccccccg ctcaatcaga gggagaatag
      361 ggatgctaag gagccactga ctggaacaat tctggaaatg tgggatgggg aaatctacca
      421 ttacggcctt tatgtggatc gaggtcttgt actaggcgtg cacaagccac cagctgccat
      481 tagcctcgcc aaggtcgaac taacaccact ctccttgttc tggagacctg tgtatactcc
      541 tcagtacctc acctctccag acactctcaa gaaattacac ggagaaacgt tcccttacac
      601 agcctttgac aacaattgct atgccttttg ctgctgggtc ctggacctaa acgactcgtg
      661 gctgagtagg agaatgatcc agagaacaac cggctttttc agaccctacc aagattggaa
      721 taggaaaccc ctccccactg tggatgattc caagttaaag aaggtagcta atatattcct
      781 gtgtgctctg tcttcgctgt tcaccaggcc cataaaagac ataataggga agctaaagcc
      841 tcttaacatc ctcaacatct tggcctcatg tgattggact ttcgcaggca tagtggagtc
      901 cttgatactc ctggcagagc tctttggagt tttctggaca cccccagatg tgtctgcgat
      961 gattgccccc ttactcggtg actacgagtt acaaggaccc gaggaccttg cagtggagct
     1021 cgtccctgta gtgatggggg gaattggttt ggtgctggga ttcaccaaag agaagattgg
     1081 aaaaatgttg tcatctgctg cgtccacctt gagagcttgc aaagatcttg gtgcatatgg
     1141 gctagagatc ctaaagttgg tcatgaagtg gttcttcccg aagaaagagg aagcaaatga
     1201 actggctatg gtgagatcca tagaggatgc agtgctggac ctcgaggcaa ttgaaaacaa
     1261 ccatatgacc accttgctca aagacaaaga cagtctggca acctacatga gaacccttga
     1321 ccttgaggag gagaaagcca gaaaactctc aaccaagtct gcttcacctg acatcgtggg
     1381 cacaatcaat gcccttctgg cgagaatcgc tgctgcacgt tccctggtgc atcgagcgaa
     1441 ggaggagctt tccagcagac caagacctgt ggtcttgatg atatcaggta gaccaggaat
     1501 agggaagacc caccttgcta gggaagtggc taagagaatc gcagcctccc tcacaggaga
     1561 ccagcgtgtg ggcctcatcc cacgcaatgg cgtcgaccac tgggatgcgt acaaggggga
     1621 gagggtcgtt ctatgggacg actatggaat gagcaatccc atccacgatg ccctcaggtt
     1681 gcaagaactc gctgacactt gccccctcac tctaaactgt gacaggattg agaataaagg
     1741 aaaggtcttt gacagcgatg tcatcattat cactactaac ctggccaacc cggcaccact
     1801 ggactatgtc aactttgagg catgctcgag gcgcatcgat ttcctcgtgt atgcagaagc
     1861 ccctgaagtc gaaaaggcga agcgtgactt cccaggccaa cctgacatgt ggaagaacgc
     1921 ctttagttct gatttttcac acataaaact agcactggct ccacagggtg gcttcgataa
     1981 aaacgggaac accccgcacg ggaagggcgt catgaagact ctcaccactg gttcccttat
     2041 tgcccgggca tcagggctac tccatgagaa gctagatgag tttgaactac agggcccagc
     2101 tctcaccacc ttcaactttg accgcaacaa agtgcttgcc tttaggcaac ttgctgctga
     2161 aaacaaatat gggttgatgg acacaatgag agttgggagg cagctcaagg atgtcagaac
     2221 catgccagag cttaaacaag cactcaagaa tatctcgatc aagaagtgcc agatagtgta
     2281 cagtggttgc acctacacac ttgagtctga cggcaagggc aatgtgaaag ttgacagagt
     2341 tcagagcacc tccgtgcaga ccagcaatga gctgactggc gccctgcacc acctaaggtg
     2401 tgccagaatc aggtactatg tcaggtgtgt ccaggaggcc ctgtattcca tcatccagat
     2461 tgccggggct gcatttgtca ccacgcgcat cgtcaagcgc atgaacatac aagacctatg
     2521 gtccaagcca caagtggaaa acacagagga ggttaccaac aaggacgggt gcccaaaacc
     2581 caaagatgat gaggagttcg tcatttcatc tgacgacatt aaaactgagg gcaagaaagg
     2641 gaagaacaag actggtcgcg gcaagaagca cacagccttc tcaagcaaag gtctcagtga
     2701 tgaagagtat gatgagtaca agaggattag agaagagagg aatggcaagt attccataga
     2761 agagtacctc caggacaggg acaaatacta tgaggaggtg gccattgcca gggcgaccga
     2821 ggaagacttc tgtgaagagg aggaggccaa gatccggcaa aggatcttta ggccaacaag
     2881 aaaacaacgc aaggaggaaa gagcttctct cggtttagtc acaggttctg aaattaggaa
     2941 aagaaaccca gatgatttca agcccaaggg gaaactgtgg gctgacgata atagaagtgt
     3001 ggactacaat gagaaactca gctttgaggc cccaccaggc atctggtcga ggatagtcaa
     3061 ctttggttca ggttggggct tctgggtctc ccccagcctg ttcataacat caacccatgt
     3121 cataccccag ggcgcaaagg agttctttgg agttcccatc aaacaaattc aggtacacaa
     3181 atcaggcgaa ttctgccgct tgagattccc aaaaccaatc aggactgatg tgacgggtat
     3241 gatcttagaa gaaggtgcgc ccgaaggcac cgtggtcaca ctactcataa aaaggtctac
     3301 aggagaactc atgcccctag cagctagaat ggggacccat gcaaccatga aaattcaagg
     3361 gcgcactgtt ggaggtcaga tgggcatgct tctgacagga tctaacgcta aaagcatgga
     3421 cctaggcacc acaccaggtg attgcggctg ttcctacatc tacaagagag gaaatgacta
     3481 tgtggtcatt ggagtccaca cggctgccgc tcgtggggga aacactgtca tatgtgccac
     3541 ccaggggagt gagggggagg ctacgcttga aggtggtgac agtaagggaa catactgcgg
     3601 tgcaccaatc ttaggtccag ggagtgcccc aaaacttagc accaagacca aattctggag
     3661 atcgtccaca gcaccactcc cacctggcac ctatgaacca gcctatcttg gcggcaagga
     3721 ccccagggtc aagggtggcc cttcattgca gcaagtcatg agggatcagt tgaaatcatt
     3781 tacagagccc aggggaaagc caccaaagcc aagtgtgtta gaagctgcca agaaaaccat
     3841 tattaatgtc cttgagcaaa caattgatcc acctgagaaa tggtcgttcg cacaagcttg
     3901 cgcgtccctc gacaaaacca cttccagtgg ccatccgcac cacatgcgga aaaacgactg
     3961 ctggaacggg gaatctttca caggcaagct ggcggatcag gcttccaagg ccaacctgat
     4021 gttcgaagaa gggaagaaca tgaccccagt ctacacaggt gcgcttaagg atgaattggt
     4081 caaaactgat aaaatttatg gtaagatcaa gaagaggctt ctctggggct cggatttagc
     4141 gaccatgatc cgatgtgctc gagcattcgg aggcctaatg gatgaactca aagcacactg
     4201 tgtcacactt cctatcagag ttggtatgaa tatgaatgag gatggcccca tcatattcga
     4261 gaggcattcc aggtacagat atcactatga tgctgattac tctcggtggg attcaacaca
     4321 acagagagct gtgttggcag cagctctagg aatcatggtt aaattctcct cagaaccaca
     4381 tttggctcag gtagtcgcag aagaccttct ttctcctagc gtggtggatg tgggtgactt
     4441 cacaatatca atcaacgagg gtctcccctc tggggtgccc tgcacctccc aatggaactc
     4501 catcgcccac tggcttctca ctctctgtgc gctctctgaa gttacaaatc tgtcccctga
     4561 catcatacag gctaattccc tcttctcctt ttatggtgat gatgaaatcg ttagcacgga
     4621 cataaaattg gacccagaga agttggcagc aaagctcagg gaatatgggc tgaaaccaac
     4681 ccgccctgac aaaactgaag ggccccttgt tatctctgaa gacttaaatg gtctgacttt
     4741 cctgcggaga actgtgaccc gcgacccagc tggttggttt ggaaaactgg agcagagttc
     4801 aatactcagg caaatgtact ggactagggg ccccaaccat gaagacccat ctgaaacaat
     4861 gattccacac tctcaaagac ccatacagtt gatgtcctta ctgggagagg ccgcactcca
     4921 cggcccagca ttctacagca aaatcagcaa gttagtcatt gcagagctaa aagaaggtgg
     4981 catggatttt tacgtgccca ggcaagagcc aatgttcaga tggatgagat tctcagatct
     5041 gagcacgtgg gagggcgatc gcaatctggc tcccagtttt gtgaatgaag atggcgtcga
     5101 atgacgccaa cccatctgat gggtccacag ccaacctcgt cccagaggtc aacaatgagg
     5161 ttatggcttt ggagcccgtt gttggtgccg ctattgcggc acctgtagcg ggccaacaaa
     5221 atgtaattga cccctggatt agaaataatt ttgtacaagc ccctggtgga gagtttacag
     5281 tatcccctag aaacgctcca ggtgaaatac tatggagcgc gcccttgggc cccgatctga
     5341 atccctacct tgctcatttg gccagaatgt acaatggcta tgcaggtggc tttgaagtgc
     5401 aggtaatcct tgcggggaat gcgttcaccg ccggaaaaat catatttgca gcagtcccac
     5461 caaatttccc aactgaaggc ttgagcccca gccaggtcac tatgttcccc catatagtag
     5521 tagatgttag gcaactggaa cctgtgttga tccccttacc tgatgttggg aacaatttct
     5581 atcattacaa ccaatcaaat gaccccacca ttaaactgat agcaatgctg tacacaccac
     5641 ttagggctaa taatgctggg gaagatgtct ttacagtctc ttgtcgagtc ctcacgaggc
     5701 catctcccga ttttgatttc atatttttgg tgccacccac agttgagtca agaactaaac
     5761 cattcaccgt cccaatctta actgttgagg aaatgaccaa ttcaagattc cccattcctt
     5821 tggaaaagtt gttcacgggt cctagcggtg cctttgttgt tcaaccacaa aatggcaggt
     5881 gcacgactga tggcgtgctt ttaggcacta cccaactgtc tcctgtcaac atctgcacct
     5941 tcagagggga tgtcacccac attgcaggca ctcataatta cacaatgaat ttggcttctc
     6001 aaaattggaa caattatgac ccaacagaag aaatcccagc ccctctgggg accccagatt
     6061 tcgtgggaag gatccaaggc atgctcaccc aaactacaag gggagatggc tctacccgcg
     6121 gccacaaagc tacagtgagc actggggatg tccacttcac cccaaagctg ggcagtattc
     6181 agttcaacac tgatacaaac aatgattttg aaactggcca aaacacgaaa ttcaccccag
     6241 tcggtgttgt ccaggatggt aatggtgccc accaaaatga acctcaacaa tgggtgctcc
     6301 caagctactc aggtagaact ggtcataatg tacacttagc ccccgccgta gcccccactt
     6361 ttccgggtga gcaacttctt ttcttcaggt ccactatgcc cgggtgcagc gggtacccta
     6421 acatgaattt ggattgtcta ctcccccaag aatgggtgca gcacttctac caagaggcag
     6481 ccccagcaca atctgatgtg gctctgctaa gatttgtgaa tccagacaca ggtagggttc
     6541 tatttgagtg caagcttcat aaatcaggct atgtcacagt ggctcacact ggccagcatg
     6601 atttggttat cccccccaat ggctacttta gatttgattc ctgggtcaac caattctaca
     6661 cacttgcccc catgggaaat gggacggggc gtagacgtgc attataatgg ctggagcttt
     6721 cttcgccggg ctggcatctg atgtccttgg ctctggactt ggttccctaa tcagtgctgg
     6781 ggctggggcc atcaaccaga aagttgaatt tgaaaataac agaaaattgc aacaagcttc
     6841 cttccaattt agtagcaatc tacaacaggc ttcctttcaa catgataaag agatgctcca
     6901 agcacaaatt gaggccacta aaaagttaca acagggtatg atggaagtta aacgggcaat
     6961 gctcctagag ggtggattct ctgaaacaga tgcatctcgt ggggcaatca acgcccccat
     7021 gacaaaggct ttggactgga gcggaacgag gtactgggct cctgatgcta ggactacaac
     7081 atacaatgca ggccgctttt ccacccctca accctcgggg gcactgccag gaaggaccaa
     7141 tcccagggct actgtccccg ctcggggctt ctccaatgca ccctctaata cttctactgc
     7201 tacttctgtg tattcaaatc agactatttc aacgagactt ggttctacag ctggttctgg
     7261 caccagtgtc tcgagtctcc cgtcaactgc aaggactagg agctgggttg aggatcaaaa
     7321 caggaatttg tcacctttca tgaggggagc tcacaacata tcgtttgtca ccccaccatc
     7381 tagtagatcc tctagccaag gcacagtctc aaccgtgcct aaagaagttt tggactcctg
     7441 gactggcgct ttcaacacgc gcaggcagcc tctcttcgct cacattcgta agcgagggga
     7501 gtcacgggcg taatgtgaaa agacaaaact gattatcttt ctcttcttta gtgtcttt
//