Typing tool
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Typing tool
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Complete norovirus genomes
| OP689689 | GII.17 | |
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| GII.P17 |
ORF1: 5..5113
ORF2: 5094..6710
ORF3: 6710..7489
LOCUS OP689689 7565 bp RNA linear VRL 25-OCT-2022
DEFINITION Norovirus GII isolate Hu/US/2022/GII.17[P17]/CA-RGDS-1164, complete
genome.
ACCESSION OP689689
VERSION OP689689.1
KEYWORDS .
SOURCE Norovirus GII
ORGANISM Norovirus GII
Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes;
Picornavirales; Caliciviridae; Norovirus; Norovirus norwalkense.
REFERENCE 1 (bases 1 to 7565)
AUTHORS Pan,C.-Y., Hatada,A., Morales,C., Montmayeur,A.M., Chhabra,P. and
Vinje,J.
TITLE 2022 WA oyster Outbreak
JOURNAL Unpublished
REFERENCE 2 (bases 1 to 7565)
AUTHORS Pan,C.-Y., Hatada,A., Morales,C., Montmayeur,A.M., Chhabra,P. and
Vinje,J.
TITLE Direct Submission
JOURNAL Submitted (20-OCT-2022) Viral and Rickettsial Disease Laboratory,
California Department of Public Health, 850 Marina Bay Parkway,
Richmond, CA 94804, USA
COMMENT ##Assembly-Data-START##
Assembly Method :: Geneious v. R10; SPAdes v. 3.6
Sequencing Technology :: Illumina
##Assembly-Data-END##
FEATURES Location/Qualifiers
source 1..7565
/organism="Norovirus GII"
/mol_type="genomic RNA"
/strain="CA-RGDS-1164"
/isolate="Hu/US/2022/GII.17[P17]/CA-RGDS-1164"
/isolation_source="stool"
/host="Homo sapiens"
/db_xref="taxon:122929"
/geo_loc_name="USA: CA"
/collection_date="Apr-2022"
/note="Amplicon sequencing:first 35 nt does represent
primer sequence;
genotype: GII.17[P17]"
gene 5..5113
/gene="ORF1"
CDS 5..5113
/gene="ORF1"
/codon_start=1
/product="nonstructural polyprotein"
/protein_id="UYL27250.1"
/translation="MKMASNDASAAVAGKNNNNDKEKSSSDSLFSNMTVTLKKALGAR
SKQPPPGETKQTQRPPRPPTPELVKKIPPPPPNGEDEPKIAYKVGEGVSGLPDLTTVA
QPDAQNTAYSVPPLSQREVGEAKEPLPGSILEMWDGEIYHYGLYVERGLVLGVHKPPA
AISLAKIELTPLSLYWRVVYTPQYLIAPETLKNLNGEAFPYTAFDNNCYAFCCWVLDL
NDSWLSRRMIQRTTGFFRPYQDWNRKPLPTMDEPKIKKAANAVLCALSSLFTRPIKDV
IGKLKPLNIMNILAICDWTFAGIVESMILLAELFGVFWTPPDVSAMIAPLLGDYEMQG
PEDLAVELVPVVMGGIGLVLGFTKEKIGKMLSSAATTLRACKDLGSYGLEILKLVMKW
FFPKKEEASELAMVRAIEDAVLDLEAIENNHMTTLLKDKDSLATYMRSLDLEEEKARK
LSSKSASPDIVGTVNALLARIAAARSLVHKAKEELSSRQRPVVVMISGRPGIGKTHLA
RELAKKVASTLSGDQRIGLIPRNGVDHWDAYKGERVVLWDDYGMSNPIQDALRLQELA
DTCPLTLNCDRIENKGKVFDSDAIIITTNLANPAPLDYVNFEACSRRIDFLVYADAPD
IEKAKRDFPGQPDMWKDHYRSDFSHIKLQLAPQGGFDKNGNTPHGKGVVKSLTIGSLI
ARASGLLHERMDEFELQGSDLPTFNFDRNKVAAFRQLAAENKYGLVDTLRVGNQLKSV
KTLDELKQAIKNITIKKCQIVYNGCTYTMESDGRNKVVVEKVQNATVQTNNELAGALH
HLRSARIRYYVKCFQEAIYSLLQIAGAAFVTTRIVRRMNISNLWSKPPVEEGDEPEDK
GGCPKPRDEDDLTIDSKDIKEEGKKGKNKSGRGKKHTAFSSKGLSDEEYDEYKRIREE
RNGKYSIEEYLQDRDRYYEELAIAKATEEDFCEEEEIKIRQRIFRPTRKQRREERATL
GLVTGSEIRKRNPDDFKPKGKLWADDNRSVDYNERIDFEAPPSVWSRIVNFGTGWGFW
VSPSLFITSTHVIPKGITEAFGVPINQIQIHKSGEFCRLRFPKPIRPDVSGMILEEGA
PEGTVVSILIKRTTGELMPLAVRMGTHATMKIQGRTVGGQMGMLLTGSNAKSMDLGTT
PGDCGCPYIYKRGNDFVVIGVHTAAARGGNTVICATQGSEGEATLEGGDNKGTYCGAP
ILGPGNAPKLSTKTKFWRSSNAPLPPGTYEPAYLGGKDPRVKGGPSLQQVMRDQLKPF
TEPRGKPPKPSVLESAKKTIINVLEQTIDPPEKWSYAQACASLDKTTSSGYPHHVRKN
DYWSGESFTGKLADQASKANLMYEEGKHMQPVYTAALKDELVKTDKIYGKIKKRLLWG
SDLSTMIRCARAFGGLMDELKANCITLPIRVGMNMNEDGPIIFEKHSRYRYHYDADYS
RWDSTQQRAVLEAALEIMVRFSAEPQLAQIVAEDLLSPSVVDVGDFKITINEGLPSGV
PCTSQWNSIAHWLLTLCALSEVTGLGPDIIQANSMYSFYGDDEIVSTDIKLDPEKLTA
KLKEYGLKPTRPDKTEGPLVISEDLNGLTFLRRTVTRDPAGWFGKLDQNSILRQLYWT
RGPNHEDPSETMIPHAQRPVQLMALLGESSLHGPSFYSKVSKLVISELKEGGMDFYVP
RQESMFRWMRFSDLSTWEGDRNLAPSFVNEDGVE"
mat_peptide 5..1003
/gene="ORF1"
/product="p48"
mat_peptide 1004..2101
/gene="ORF1"
/product="NTPase"
mat_peptide 2102..2638
/gene="ORF1"
/product="p22"
mat_peptide 2639..3037
/gene="ORF1"
/product="VPg"
mat_peptide 3038..3580
/gene="ORF1"
/product="Pro"
mat_peptide 3581..5110
/gene="ORF1"
/product="RdRp"
gene 5094..6710
/gene="ORF2"
CDS 5094..6710
/gene="ORF2"
/note="major capsid protein"
/codon_start=1
/product="VP1"
/protein_id="UYL27251.1"
/translation="MKMASNDAAPSNDGAAGLVPEGNNETLPLEPVAGAAIAAPVTGQ
NNIIDPWIRTNFVQAPNGEFTVSPRNSPGEILLNLELGPDLNPYLAHLSRMYNGYAGG
VEVQVLLAGNAFTAGKILFAAVPPNFPVEFLSPAQITMLPHIIVDVRTLEPIMIPLPD
VRNTFFHYNNQPNSRMRLVAMLYTPLRSNGSGDDVFTVSCRVLTRPTPDFEFTYLVPP
SVESKTKPFSLPILTLSELTNSRFPVPIDSLFTAQNNVLQVQCQNGRCTLDGELQGTT
QLLPSGICAFRGRVTAETDNPDKWHMQLQNLNGTTYDPTDDVPAPLGTPDFKGVVFGM
ASQRNVGNDAPGSTRAHEAVISTYSPRFVPKLGSVNFKSNDDDFQLQPTRFTPVGIND
DGDHPFRQWELPDYSGVLTLNMNLAPPVAPNFPGEQLLLFRSSVPCSGGYNQGIIDCL
IPQEWIQHFYQESAPSQSDVALIRYVNPDTGRTLFEAKLHRSGYITVAHSGDYPLVVP
ANGYFRFDSWVNQFYSLAPMGTGNGRRRAQ"
gene 6710..7489
/gene="ORF3"
CDS 6710..7489
/gene="ORF3"
/note="minor structural protein; small basic protein"
/codon_start=1
/product="VP2"
/protein_id="UYL27252.1"
/translation="MAGAFIAGLAGDMLTSSVGSLVNAGANAISQKIDFENSKQLQSA
SFQHDKEMLQEQVNATKQLQSEMIALKQGVLAAGGFSPTDAARGAIGAPMTRVLDWSG
TRYWAPNSTKTTGYSGQFTSSPVHMPSPSAPQSKPAKPRSLGSSSSSSSVYSMSTQST
SLTSGSSSNASSASTKLTNLSSGSSQNRTAEWVNQQRSLSPFMSGALNISHVTPPSSR
ASSSGTVSTVPKGVLDSWTSAFNTRRQPLFAHLRVRGESRV"
ORIGIN
1 gtgaatgaag atggcgtcta acgacgcttc cgctgccgtt gctggcaaaa acaacaacaa
61 cgacaaggaa aaatcttcaa gtgacagctt gttttctaac atgactgtta ctcttaagaa
121 agccctcggg gcgcggtcta aacagccgcc cccgggagaa acaaaacaaa cacaaagacc
181 accaaggcca ccgacaccgg aattggtgaa gaagataccc ccaccccccc ccaatggcga
241 ggatgaacca aagatagcgt ataaggtggg agaaggtgtg tctgggctgc ccgacttaac
301 aaccgtggca caacctgacg cacagaacac agcctatagt gtccccccac tcagccagag
361 agaggtcggc gaggctaaag aaccgttgcc tggctccatt ctggaaatgt gggatggtga
421 gatctaccac tatgggctgt atgttgagcg ggggcttgta ctgggagtgc acaaaccacc
481 tgccgcaata agccttgcca aaattgaatt aacaccgctg tctctctact ggagagtggt
541 ttacactccc cagtatttga tagctccaga gacccttaag aatttaaacg gagaggcttt
601 cccatacacg gcctttgaca acaactgtta tgccttctgt tgttgggtcc tagacctcaa
661 cgactcctgg cttagcagaa gaatgatcca aagaacaact ggattcttca gaccgtatca
721 ggactggaat agaaaaccct tgccaaccat ggatgaacca aaaatcaaga aggccgcgaa
781 tgctgttctg tgtgctctct cctcactctt cactaggccc atcaaagatg tcattggaaa
841 gcttaaacca ctgaacatta tgaacatact ggcaatttgt gattggactt ttgcgggtat
901 agtggaatcc atgatccttc ttgctgagct ctttggagtg ttctggacgc ccccagatgt
961 gtctgcaatg attgctccct tactcggtga ctacgagatg caaggccccg aagacttggc
1021 cgtggaactt gtgcccgtgg taatgggagg aataggtctg gtgttaggat tcaccaagga
1081 aaagatcggc aagatgcttt catcagccgc gaccacactc agggcctgta aggatctagg
1141 atcttatggg ttggagatac tcaaactggt catgaagtgg ttcttcccca agaaggagga
1201 ggccagcgag ttagccatgg tgagggccat tgaggatgca gttctggatt tggaggcaat
1261 agaaaacaac cacatgacca ctctccttaa ggacaaagac agcctggcca catacatgag
1321 gtctcttgac ttggaagaag aaaaagcaag gaaactgtca tccaaatcgg cgtcacctga
1381 catcgtgggc acagtaaacg cattattggc gaggatagca gccgccaggt cactggtcca
1441 caaggctaag gaagagctct cgagcagaca gaggcctgtt gttgtaatga tatcaggtag
1501 gccaggtata ggaaagaccc atctggccag agagctagcc aagaaggttg cgtcaacact
1561 gtcaggcgac caaaggattg gactgatacc tagaaatggc gtcgaccatt gggacgccta
1621 caaaggagag cgggtggttc tgtgggatga ctatggcatg agcaacccta tacaggacgc
1681 actgaggctc caagaattgg ctgacacctg tcctctgacc ctaaattgtg acaggattga
1741 aaacaaagga aaagtgttcg acagtgacgc cataatcata acaaccaacc ttgcaaaccc
1801 agcaccactg gattatgtca actttgaggc ttgttccagg cgcatagact tcttggtgta
1861 tgcagacgca cctgacatcg agaaagctaa gcgtgacttc cctggccaac cagatatgtg
1921 gaaagaccat tacagatcag acttctcaca cattaaactt cagctggcac cacagggagg
1981 ctttgataag aatggcaaca ccccacatgg caaaggtgtg gttaagtctc tgacgattgg
2041 ttctctgatc gccagggctt ctggcttgct ccatgagaga atggatgaat tcgagctcca
2101 aggctctgac ttaccaacct tcaatttcga ccgtaacaaa gttgccgcct tcagacaatt
2161 ggcagctgaa aacaaatatg gtcttgtgga cacactgagg gtcggcaacc aactgaaaag
2221 tgtcaaaacc ctggatgagc tgaagcaggc tataaagaac atcaccatca agaagtgcca
2281 gatagtgtac aatggatgca cctacaccat ggaatctgat gggaggaaca aggttgtggt
2341 tgaaaaggtt caaaatgcaa cagtccaaac caacaatgaa cttgcaggag cactccacca
2401 cctgagatct gcaaggataa ggtattatgt caaatgtttc caagaagcta tttactctct
2461 actccaaatt gctggtgcag ccttcgtcac cacacgcatc gtgaggcgca tgaacatctc
2521 aaacctctgg tcgaagccac ccgtcgaaga gggtgacgag cctgaagaca aaggggggtg
2581 ccccaagccc agggatgaag atgacctcac tattgactct aaggacatta aagaagaagg
2641 gaagaagggc aagaacaagt ctggccgggg caagaaacac acagctttct catccaaggg
2701 cctcagtgat gaggagtacg atgagtacaa gagaatcagg gaggagagaa atggcaaata
2761 ctcaatagaa gaatacctcc aggataggga tagatactat gaagagcttg ccattgctaa
2821 ggccactgag gaagacttct gtgaagagga ggaaatcaaa attcgccaga gaatcttccg
2881 gcccaccagg aagcaacgga gagaggaaag agccacgctt gggcttgtca caggatcgga
2941 aatcagaaag aggaacccag atgactttaa gccaaaagga aaattgtggg ctgatgacaa
3001 cagaagtgtg gactacaatg agaggataga ttttgaggct cccccgagtg tttggtctag
3061 gatagtcaac tttggtacag gatggggatt ctgggtctcc ccaagtctct ttataacttc
3121 aacacatgtc ataccaaaag gaatcactga ggcctttgga gttcccatta accaaattca
3181 aattcacaaa tctggagagt tttgccgctt gcggtttcca aaaccaatca ggccagacgt
3241 gagtggaatg atcttggaag agggtgcccc tgaaggcact gttgtgtcca ttctcatcaa
3301 gagaacaaca ggggaactga tgcctctcgc agttagaatg ggaactcatg ccacaatgaa
3361 aatccaaggt agaacggtgg gtggtcaaat gggcatgctt ctcactggct caaacgctaa
3421 aagcatggac ctaggcacaa caccaggtga ctgtgggtgc ccatacatat acaaaagagg
3481 caatgacttc gtggtcattg gggtgcacac tgcagcagcc cgtggaggca acacggtcat
3541 atgtgccaca cagggaagtg aaggcgaagc caccctcgaa ggaggtgaca ataagggcac
3601 ctattgtgga gcccccatct tgggacctgg caacgcacca aaattgagca caaaaacaaa
3661 gttctggaga tcttctaacg cgccgcttcc tccaggcacc tatgaaccag cataccttgg
3721 tggaaaagac ccgcgtgtga agggaggccc atctctacaa caggttatga gagaccaact
3781 taaacctttt acagagccca gagggaagcc cccaaaacca agtgtcctag aatcagcaaa
3841 gaagaccatc attaatgtcc tggaacaaac cattgacccc cctgaaaagt ggtcatatgc
3901 ccaagcttgt gcatctctcg acaagacaac ctccagtgga tacccgcatc acgttcggaa
3961 gaatgactat tggagtggtg aatccttcac ggggaaactt gcagaccagg cctcaaaagc
4021 aaaccttatg tatgaggaag gcaaacacat gcaaccagtt tacaccgcag cactcaaaga
4081 cgagctcgtg aaaactgaca aaatttatgg caagatcaag aaaagactcc tgtggggctc
4141 tgacctatcc accatgattc ggtgcgccag ggcatttggt ggcctcatgg atgagctcaa
4201 agcaaattgt attacactcc ctatcagagt tggtatgaac atgaatgaag atggtcccat
4261 aatatttgaa aagcactcca ggtacaggta ccactatgat gctgattact cccgctggga
4321 ttccacacaa cagcgggcag tactggaagc ggcacttgaa atcatggtga gattttctgc
4381 tgagccacag ttggcacaaa tagtggcaga ggacctgcta tcaccaagtg tggttgatgt
4441 gggcgatttc aaaattacta tcaatgaagg cctaccatct ggcgtgcctt gcacttcaca
4501 atggaattct attgcccact ggttactcac cctgtgtgcc ctgtctgaag taacaggact
4561 aggccctgac atcatacaag ccaactccat gtactctttc tatggtgatg atgagattgt
4621 gagcacagac ataaaattgg acccagagaa attgactgca aaactcaaag aatatggtct
4681 taaacccacc cggcctgaca agactgaggg gccactggta attagtgagg acctgaatgg
4741 gttgactttc ctccgccgaa cagtcacccg cgatccagcg ggttggtttg gaaagttgga
4801 ccaaaactcc atcctcaggc agctgtactg gacaagggga cccaaccatg aagatcccag
4861 tgagactatg ataccacacg cacagagacc tgtgcagctc atggcactgc taggagagtc
4921 ctccctacat ggaccctcat tttacagcaa agttagcaag ctggtcatat ctgaacttaa
4981 agagggggga atggattttt atgtgcccag acaagagtca atgttcagat ggatgagatt
5041 ctcagatcta agcacatggg agggcgatcg caatctggct cccagttttg tgaatgaaga
5101 tggcgtcgaa tgacgccgct ccatctaatg atggtgctgc tggtctcgta ccagagggca
5161 ataacgagac ccttccccta gaaccagttg cgggcgcagc tatagccgca cccgttactg
5221 gccaaaataa tataattgac ccctggatta gaacaaattt tgtgcaagca ccaaatggag
5281 agttcacagt gtcacctaga aactctcctg gagaaatttt gctaaaccta gagttgggcc
5341 ctgatttgaa cccttatttg gctcatttgt caaggatgta caatgggtat gctggtggag
5401 ttgaagttca ggttctcctg gcagggaacg cgttcactgc cgggaagatc ctcttcgccg
5461 ctgtcccgcc aaatttccca gtggaattct taagcccagc ccagattaca atgctcccac
5521 atataatagt agatgttagg actcttgaac caattatgat cccattacct gatgttagga
5581 acacattctt ccactataat aaccagccca acagccgcat gagattagtg gctatgctct
5641 atacccccct tagatctaat ggttcaggtg atgatgtttt cactgtttct tgcagggttt
5701 tgactaggcc tactcctgat tttgagttca cttatctagt gccaccctct gttgaatcta
5761 agactaagcc cttttcttta cccattctaa ccctttctga gctcacaaat tcgaggttcc
5821 cggtccccat tgattcgctt ttcaccgccc agaataatgt gttgcaggtg cagtgtcaaa
5881 atggcaggtg cacacttgac ggtgagctac aaggcacaac ccagttgctc ccatctggca
5941 tctgtgcgtt cagaggacgg gtgacagcag aaactgacaa tcctgacaag tggcacatgc
6001 aactgcaaaa cctcaatggc acaacatatg acccaactga tgatgtgcca gccccactgg
6061 gtacacctga cttcaagggc gtcgtgtttg ggatggcaag ccaaagaaat gtgggcaacg
6121 atgcgcccgg ctcaaccagg gcccatgagg cggtgatttc aacctacagc cccagatttg
6181 ttcccaaatt aggctctgtc aattttaaaa gtaatgacga tgatttccaa ttgcagccaa
6241 caagattcac accagtgggc attaatgatg atggcgacca cccgttcaga caatgggaac
6301 tgccagacta ttcaggggtg cttaccttga atatgaacct tgcccccccg gttgctccaa
6361 atttccctgg tgaacaatta ttactcttca gatcttccgt gccatgttca ggaggttaca
6421 accaaggtat tatagattgt cttatccccc aagaatggat ccaacacttc taccaggaat
6481 cagcaccttc tcagtcagac gtggccctga tcaggtacgt caaccccgac acgggtcgca
6541 cactgtttga ggcaaaactg cacagatctg gctatatcac tgtggctcac tctggagact
6601 atcctcttgt tgttccggct aatggatact ttagatttga ctcttgggta aatcagtttt
6661 actcactcgc cccaatggga actgggaatg ggcgaaggag ggctcagtaa tggctggagc
6721 cttcattgca ggattggcgg gtgacatgct cacgtcatcc gtgggctccc tggtgaacgc
6781 aggggcaaac gccatcagcc aaaagataga ctttgaaaac agcaagcaac tccagtctgc
6841 ttcttttcaa catgataaag agatgctcca agaacaggtg aatgcaacca agcagctgca
6901 atctgagatg atagccctaa aacagggggt tttggccgca ggcggctttt cccccactga
6961 tgcagcgagg ggggccatcg gtgcacccat gacaagggtg cttgactggt ctggcactcg
7021 atactgggct cccaattcta caaagacaac tggttattcg gggcaattca cctcctcacc
7081 tgtgcacatg cccagcccga gcgctccaca atcaaaaccc gcaaagccca ggtctctagg
7141 ttcttcttct tcttctagta gtgtttatag tatgtctacc caatcaactt ctctaacatc
7201 tggctcttct agtaatgctt cttctgcttc tactaaactg acaaatctaa gctctggctc
7261 ctctcaaaac agaacagcag agtgggtgaa ccaacagaga agtctcagcc ctttcatgag
7321 tggcgcactc aatatctcac atgtcacgcc accttcaagt agggcctcca gttctgggac
7381 ggtctcaacc gtgcccaagg gagttttgga ctcctggaca tctgcattca acacacgcag
7441 acagccgctc ttcgcacacc tcagagtgag gggggagtca cgtgtttagt gaaaagaaac
7501 aattggctat aatatgattt ctttaaaaat ttaaatttgg ctaatttgta tcttttaaaa
7561 aaaaa
//