Typing tool
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Typing tool
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Complete norovirus genomes
| OR685283 | GII.17 | |
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| GII.P17 |
ORF1: 1..5109
ORF2: 5090..6715
ORF3: 6715..7494
LOCUS OR685283 7494 bp RNA linear VRL 22-OCT-2023
DEFINITION Norovirus GII isolate Hu/USA/2023/GII.17[P17]/CA-RGDS-1180
nonstructural polyprotein (ORF1), VP1 (ORF2), and VP2 (ORF3) genes,
complete cds.
ACCESSION OR685283
VERSION OR685283.1
KEYWORDS .
SOURCE Norovirus GII
ORGANISM Norovirus GII
Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes;
Picornavirales; Caliciviridae; Norovirus; Norovirus norwalkense.
REFERENCE 1 (bases 1 to 7494)
AUTHORS Pan,C.-Y., Hatada,A., Padilla,T., Wright,C. and Morales,C.
TITLE Direct Submission
JOURNAL Submitted (17-OCT-2023) 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 Prime v. 2022.0.2; SPAdes v. 3.6
Sequencing Technology :: Illumina
##Assembly-Data-END##
FEATURES Location/Qualifiers
source 1..7494
/organism="Norovirus GII"
/mol_type="genomic RNA"
/isolate="Hu/USA/2023/GII.17[P17]/CA-RGDS-1180"
/isolation_source="stool"
/host="Homo sapiens"
/db_xref="taxon:122929"
/geo_loc_name="USA: CA"
/collection_date="Mar-2023"
/note="genotype: GII.17[P17]"
gene 1..5109
/gene="ORF1"
CDS 1..5109
/gene="ORF1"
/codon_start=1
/product="nonstructural polyprotein"
/protein_id="WOC94336.1"
/translation="MKMASNDASAAVAGKNNNNDKEKSSSDNLFSNMTVTFKKALGAR
SKQPPPGEVKQTQKPPRPPTPELVKRIPPPPPNGEDGPQIVYKVGEGVSGLPDLTTVT
RPDTQDTAYSVPPLSQREAGEAKEPLPGSILEMWDGEIYHYGLYVERGNVLGVHKPPA
AVSLAKIELTPLSLYWRVVYTPQYLISPDTLKGLSGETFPYTAFDNNCYAFCCWVLDL
NDSWLSRRMIQRTTGFFRPYQDWNRKPLPTMDEPKIKKAANAVLCALSSLFTRPIKDI
IGKLRPLNILNILATCDWTFAGIVESMILLAELFGVYWTPPDVSAMIAPLLGDYEMQG
PEDLAVELVPVVMGGIGLVLGFTKEKVGKMLSSAATTLRACKDLGSYGLEILKLIMKW
FFPKKEEASELAMVRAIEDAVLDLEAIENNHMTTLLKDKDSLATYMRTLDLEEEKARK
LSTKSASPDIVGTINALLARIAAARSLVHKAKEELSSRQRPVVVMLSGRPGIGKTHLA
RELAKKVASTLSGDQRIGLVPRNGVDHWDAYKGERVVLWDDYGMSNPIQDALRLQELA
DTCPLTLNCDRIENKGKVFDSDVIVITTNLANPAPLDYVNFEACSRRIDFLVYAEAPD
IEKAKRDFPGQPDMWKDHYRPDFTHIKLQLAPQGGFDKNGNTPHGKGVMKSLTVGSLI
ARASGLLHERMDEFELQGSDLPTFNFDRNKVAAFRQLAAENKYGLMDTLRVGNQLKSV
KTLDELKQAIKNISIKKCQIVYNGCTYTMESDGRGKVVVEKVQNATVQTNNELTGALH
HLRSARIRYYVKCFQEAIYSLLQIAGAAFVTSRIVKRMNISNLWSKPPVEEGDEPEDK
GGCPKPRDEDDLTIDSKDIKVEGKKGKNKSGRGKKHTAFSSKGLSDEEYDEYKRIREE
RNGKYSIEEYLQDRDRYYEELAIAKAIEEDFCEEEEIKIRQRIFRPTRKQRKEERATL
GLVTGSEIRKRNPDDFKPKGKLWADDNRSVDYNERIDFEAPPSVWSRIVNFGTGWGFW
VSPSLFITSTHVIPKGITEAFGVPMSQIQIHKSGEFCRLRFPKPIRPDVSGMILEEGA
PEGTVVSILIKRTTGELMPLAVRMGTHATMKIQGRMVGGQMGMLLTGSNAKSMDLGTT
PGDCGCPYIYKRGNDFVVIGVHTAAARGGNTVICATQGSEGEATLEGGDNKGTYCGAP
ILGPGSAPKLSTKTKFWRSSNTPLPPGTYEPAYLGGRDPRVKGGPSLQQVMRDQLKPF
TEPRGKPPNPNVLESAKKTIINVLEQTIDPPQKWSYAQACASLDKTTSSGYPHHARKN
DYWNGETFTGKLADQASKANLMYEEGKHMQPVFTAALKDELVKTDKIYGKIKKRLLWG
SDLSTMIRCARAFGGLMDELKANCIALPVRVGMNMNEDGPIIFEKHSRYRYHYDADYS
RWDSTQQRAVLEAALEIMVRFSAEPQLAQIVAEDLLSPSVVDVGDFKIAINEGLPSGV
PCTSQWNSIAHWLLTLCALSEVTGLGPDIIQANSIYSFYGDDEIVSTDIKLDPEKLTA
KLKEYGLKPTRPDKTEGPLVISEDLNGLTFLRRTVTRDPAGWFGKLDQSSILRQIYWT
RGPNHEDPSETMIPHAQRPVQLMALLGESSLHGPAFYSKVSKLVISELKEGGMDFYVP
RQESMFRWIRFSDLSTWEGDRNLAPSFVNEDGVE"
mat_peptide 1..999
/gene="ORF1"
/product="p48"
mat_peptide 1000..2097
/gene="ORF1"
/product="NTPase"
mat_peptide 2098..2634
/gene="ORF1"
/product="p22"
mat_peptide 2635..3033
/gene="ORF1"
/product="VPg"
mat_peptide 3034..3576
/gene="ORF1"
/product="Pro"
mat_peptide 3577..5106
/gene="ORF1"
/product="RdRp"
gene 5090..6715
/gene="ORF2"
CDS 5090..6715
/gene="ORF2"
/note="major capsid protein"
/codon_start=1
/product="VP1"
/protein_id="WOC94337.1"
/translation="MKMASNDAAPSNDGATGLVPEINTETLPLEPVAGASLAAAVTGQ
NNIIDPWIRTNFVQAPNGEFTVSPRNSPGEILLNLELGPDLNPYLAHLSRMYNGYAGG
VEVQVLLAGNAFTAGKILFAAVPPNFPVEFLSPAQITMLPHLIVDVRTLEPIMIPLPD
VRNTFFHYNNRPSERMRLVAMLYTPLRSNGSGDDVFTVSCRVLTRPTPDFEFTYLVPP
SVESKTKPFSLPILTISELTNSRFPAPIDSLFTAQNNVLNVQCQNGRCTLDGELQGTT
QLLPTGICAFRGKITADVENQHDDRWHLSITNLNGTPFDPTEDVPAPLGTPDFTGLLF
GVASQRNVGGSGNNTTRAHEAVISTTSTQFVPKLGSVNFGSQSDDFQVSQPTKFTPVG
IKIETGHPFEQWRLPNYAGALTLNMNLAPPIAPNFPGEQLLFFRSNIPCAGGISDGVI
DCLLPQEWIQHFYQESAPSQSDVALIRYVNPDTGRTLFEAKLHRTGYITVAHTGDYPL
VVPSNGFFRFDSWVNQFYSLAPMGTGNGRRRIQ"
gene 6715..7494
/gene="ORF3"
CDS 6715..7494
/gene="ORF3"
/note="minor structural protein; small basic protein"
/codon_start=1
/product="VP2"
/protein_id="WOC94338.1"
/translation="MAGAFIAGLAGDMLTSTVGSLANAGANAINQKIDFENNKQLQAA
SFQHDKDMLLAQVNATKQLQSDMIAIKQGILTAGGFSPTDAARGAVGAPMTKVLDWSG
TRYWAPNSTKTTSYSGQFTSTPVHTPNLSSKPKTTSVKSPSPSSSSGSVYSLATQSTS
LSGPSSGSSASSASTQSTKLSSTSSMSRTIDWVNQQRSLSPYMSGALNISHVTPPSSR
ASSSGTVSTVPKEVLDSWTSAFNTHRQPLFAHLRVRGESRV"
ORIGIN
1 atgaagatgg cgtctaacga cgcttccgct gccgttgctg gcaaaaacaa caacaacgac
61 aaggaaaaat cttcaagtga caacttgttt tctaacatga ctgtcacttt taagaaagcc
121 ctcggggcgc ggtctaaaca gccgcccccg ggagaagtaa aacaaacaca gaaaccacca
181 agaccaccga caccggaatt ggtgaagaga atacccccac ccccacccaa tggcgaggat
241 ggaccacaaa tagtgtataa ggtgggggag ggtgtgtctg ggctacccga cctaacaacc
301 gtgacgcggc ctgacacaca agacacagct tatagtgttc ccccgctaag ccagagagaa
361 gccggcgaag ctaaagaacc actgcctggt tccattcttg agatgtggga tggtgagatc
421 taccattatg ggctgtatgt tgaacgggga aatgtactcg gggtgcacaa accacctgct
481 gcagtaagcc tcgccaaaat tgaattaaca cctctgtctc tctactggag agtggtatac
541 actccccagt atctgatatc tccagacact cttaagggct tgagcggaga gactttccca
601 tacacggcct ttgataacaa ctgctatgcc ttctgttgtt gggtcctaga cctcaatgac
661 tcctggctca gcaggaggat gatccaaaga acaactggat ttttcagacc gtatcaggat
721 tggaacagaa agcctttgcc aaccatggat gagccgaaaa tcaagaaggc cgcaaatgct
781 gtcctttgtg ctctctcctc actctttacc agacccatta aggatatcat tggaaaactc
841 aggccattaa acatcctcaa cattctggca acatgtgact ggacttttgc aggcatagtg
901 gaatccatga tccttcttgc tgaactcttt ggggtgtact ggactccccc agacgtgtct
961 gcgatgattg ctcccttact cggtgactac gaaatgcaag gccccgaaga cctggccgtg
1021 gaacttgtgc ccgtggtaat gggaggaata ggcttggtgt taggattcac caaagaaaag
1081 gtcggcaaga tgctttcatc agctgcaacc acacttaggg cctgtaaaga cctaggttct
1141 tatggactgg agatactcaa attaatcatg aagtggttct tccccaagaa ggaagaggct
1201 agtgaactag ccatggtgag ggccattgag gatgcagtcc tggatttgga ggcgatagaa
1261 aataaccaca tgaccaccct cctcaaggac aaagatagcc tggccacata catgagaact
1321 cttgacttgg aggaagagaa agcaaggaaa ctatcaacca aatcggcatc acctgacatc
1381 gtgggcacaa taaacgcatt attggcaagg attgcagctg ctaggtcact ggtccacaag
1441 gccaaggagg agctctcgag cagacagagg cctgttgttg taatgttatc aggtagacca
1501 ggcataggaa agacccacct tgccagagag ctagccaaga aagttgcatc tacactgtca
1561 ggtgaccaaa gaattggatt ggtgcctaga aatggcgtcg atcactggga tgcctacaag
1621 ggagaaaggg tagtcctgtg ggatgactac ggtatgagca accctataca ggacgcattg
1681 aggctccaag aattggctga cacatgccca ctaaccctaa attgtgacag gattgaaaac
1741 aaaggaaaag tgttcgacag tgatgtcata gtcataacaa ccaaccttgc aaacccagca
1801 ccactagatt atgtcaactt tgaggcctgc tctagacgca tagacttctt ggtgtatgca
1861 gaagcacctg acatcgagaa ggctaagcgt gatttccctg gccaaccaga tatgtggaaa
1921 gaccactata gaccagactt cacacacatt aaacttcaac tggcaccaca aggaggtttt
1981 gacaagaatg gtaacacccc acatggcaaa ggtgtgatga agtcactgac ggttggttct
2041 ctgatcgcca gggcttctgg cttgctccac gaaagaatgg atgaatttga gctccagggc
2101 tctgacctgc caaccttcaa ctttgaccgt aacaaagtcg ccgccttcag gcaattggca
2161 gctgaaaata aatatggtct tatggacaca ctgagggtcg gcaaccaact gaagagtgtc
2221 aaaaccctag atgagctgaa gcaggccata aagaacatca gcatcaagaa gtgccaaata
2281 gtgtataatg gctgtacata caccatggaa tctgatggga ggggcaaggt tgtggttgaa
2341 aaggtgcaaa atgcaacagt ccaaaccaat aacgaactca caggagcact ccatcacctg
2401 aggtctgcaa ggataagata ttatgtcaaa tgtttccaag aagccattta ctccttactc
2461 caaatcgctg gtgcagcctt tgttacttca cgcatcgtga aacgcatgaa catctcaaat
2521 ctctggtcaa aaccacccgt cgaagagggt gatgaacctg aagacaaagg aggatgccct
2581 aaacccaggg atgaagatga cctcaccatt gactctaaag acataaaagt ggaagggaaa
2641 aagggcaaaa acaagtctgg tcggggcaag aaacacacag ccttctcatc caagggcctc
2701 agtgatgaag agtacgatga gtacaagaga atcagagagg agaggaatgg taaatactca
2761 atagaggaat acctccaaga tagagacaga tactatgaag aacttgccat tgctaaggcc
2821 attgaagagg acttctgtga agaggaggaa atcaaaatcc gccagagaat cttccgaccc
2881 accaggaagc aacgaaaaga ggagagggcc acgctcggac tcgtcacagg atcagaaatc
2941 aggaaaagaa acccagatga ctttaaacca aaaggaaaat tgtgggctga tgacaacagg
3001 agtgtggatt acaatgagag aatagatttt gaggcccccc cgagcgtttg gtctagaata
3061 gtcaattttg gcacaggttg gggattctgg gtttctccaa gtctctttat aacttcaaca
3121 catgtcatac caaaaggaat tactgaagcc tttggagtgc ccatgagtca aatccagatt
3181 cacaaatccg gagaattttg ccgcttgcgg tttccaaaac caattagacc agacgtgagt
3241 gggatgatct tggaagaggg tgcccctgaa ggcactgttg tgtctattct catcaaaagg
3301 acaacagggg agctgatgcc tcttgcagtc agaatgggaa cccatgccac aatgaaaatt
3361 caaggtagaa tggtgggtgg tcagatgggt atgcttctca ctggttcaaa tgccaaaagc
3421 atggatttgg gtacaacgcc aggtgattgc gggtgtccat acatctacaa aaggggcaat
3481 gacttcgtgg tcattggggt gcacactgca gcagcacgtg gaggcaacac agtcatatgt
3541 gccacacagg gaagtgaagg tgaggccact cttgaaggag gtgacaacaa gggcacctac
3601 tgtggagcac ccattctggg acctggcagt gcaccaaaac tgagcacaaa aacaaaattc
3661 tggagatctt ccaatacgcc gcttccccca ggcacctatg aaccagcgta ccttggtggg
3721 agagacccgc gtgtgaaggg aggcccgtct ctgcagcagg ttatgagaga tcaactcaaa
3781 ccctttacag aacccagagg gaagccacca aacccaaatg tcctggagtc agcaaagaag
3841 actattatca atgttttgga acaaaccatc gacccccctc agaagtggtc gtatgcccaa
3901 gcttgtgcat ctcttgacaa aacgacctcc agtggatacc cacaccacgc ccggaagaat
3961 gattattgga atggtgaaac attcacaggg aaactcgcag accaggcttc aaaggcaaat
4021 ctcatgtatg aagaaggcaa gcacatgcaa ccagttttca ctgcagcact caaagacgag
4081 cttgtaaaaa ctgataaaat ttatggtaaa atcaagaaaa gactcctgtg gggttctgac
4141 ctctccacca tgattcgttg cgctagagca ttcggtggtc tcatggacga gcttaaagca
4201 aactgcattg cactccctgt cagagttggt atgaatatga atgaagatgg tcccataata
4261 tttgagaaac actctaggta cagataccac tatgatgcag attactcccg ctgggattcc
4321 acacaacagc gggcagtgct ggaagcggca cttgaaatta tggtgagatt ttctgctgaa
4381 ccacagctgg cacaaatagt ggcagaggat ctgctgtcac caagtgtggt ggatgtgggc
4441 gacttcaaaa tcgcaatcaa tgaaggccta ccatctggtg tgccttgcac ctcacaatgg
4501 aactctattg cccactggct actcaccctg tgtgcccttt ctgaagtgac aggactaggc
4561 cccgacatca tacaagccaa ctccatatac tctttctatg gtgatgatga gattgtgagc
4621 acggacataa aattggaccc agagaaatta actgcaaaac tcaaagaata tggccttaaa
4681 cccacacggc ccgacaaaac tgagggaccg ctggtgatca gtgaggacct gaatgggtta
4741 acattcctac gccggacagt gacccgcgac ccagcaggct ggtttggaaa attggaccaa
4801 agttctatcc tcaggcagat ttattggaca aggggaccca accatgaaga tcccagtgaa
4861 accatgatac cacacgcaca gagacctgtg cagctcatgg cattattagg agaatcctcc
4921 ctacatggac cagcatttta cagcaaggtc agcaagctgg tcatatctga actcaaagag
4981 ggaggaatgg atttttatgt gcccagacaa gagtcaatgt tcagatggat aaggttctcg
5041 gatctaagca catgggaggg cgatcgcaat ctggctccca gttttgtgaa tgaagatggc
5101 gtcgaatgac gccgctccat ctaatgatgg tgctacgggc ctcgtcccag agatcaacac
5161 cgagaccctt cctttggaac cagtggctgg tgcatccctt gcagcagctg tcactggtca
5221 aaacaatata attgatccct ggattagaac aaattttgta caagcaccca atggggaatt
5281 tactgtatca cccagaaatt ccccaggaga gattcttcta aatttggaat taggtcctga
5341 tttaaatcct tatttggcac acctgtctag aatgtacaat ggctacgctg gcggagttga
5401 agtccaggtg ctcttggcgg ggaatgcgtt caccgctgga aagatccttt tcgccgctgt
5461 gccaccaaat tttccagttg aatttcttag tcctgctcaa ataactatgc ttccacattt
5521 gatagttgat gttagaactc ttgagccaat catgatacct cttcctgatg tgagaaatac
5581 cttcttccac tacaacaacc gtccctctga gcgcatgcgc ttagtggcta tgctgtatac
5641 tcctttaaga tccaatggtt caggtgatga tgtcttcaca gtctcgtgta gagttttaac
5701 caggcctacc ccagactttg agttcactta tttagtccca ccttcagttg aatctaaaac
5761 aaaacctttt tctctcccta tcctgactat ctctgagctg accaattcaa gattcccagc
5821 acctattgat tcactgttta ctgctcaaaa taatgtcctt aatgtccagt gtcaaaatgg
5881 ccggtgcact ctggatggag agctgcaagg aaccacccaa ttacttccaa ctggaatatg
5941 tgccttcagg ggaaagataa cagcagatgt agaaaatcag catgatgaca ggtggcactt
6001 gagtataaca aacctcaatg gaactccttt tgatccaaca gaagatgtcc cagccccatt
6061 aggcacccct gacttcacag gcctcctctt cggagttgca agccaaagaa atgtcggtgg
6121 gtcaggcaac aacaccacca gggcacatga ggctgtgata tcaacaacca gcacacaatt
6181 tgttccaaaa ttaggttctg tcaactttgg gagtcagagt gacgattttc aggtttctca
6241 gccaactaag ttcacaccag ttgggatcaa aattgaaact ggacaccctt ttgaacaatg
6301 gagattaccc aactatgctg gagcactgac acttaatatg aaccttgccc cacctatcgc
6361 tcccaacttt ccaggtgagc aattgctttt ctttaggtct aatatccctt gtgctggtgg
6421 tatcagtgac ggtgtcattg actgtctgct tcctcaggag tggatacaac acttctacca
6481 ggagtctgct ccttctcaat cagatgtggc tctaatcagg tacgtcaacc ctgacacggg
6541 tcgcactctc tttgaggcga agctccacag gaccggatac atcactgttg cccacaccgg
6601 cgattaccct cttgttgtcc cctctaatgg cttcttcaga tttgactctt gggtaaacca
6661 gttttactca cttgccccca tgggaactgg gaatgggcgt agaaggattc agtaatggca
6721 ggagctttta tagcaggtct tgcaggtgac atgctcacca gtactgttgg ctctctggcg
6781 aatgccggag caaacgccat aaaccaaaag atagactttg agaacaacaa acaattgcaa
6841 gctgcctctt tccaacatga caaagacatg ctcctcgcac aggtgaatgc aaccaaacaa
6901 ctgcagtcag acatgatcgc catcaagcag gggatattga ccgcgggcgg cttttcccct
6961 actgatgcag caaggggggc cgtgggggca cccatgacaa aagttctcga ttggtctggc
7021 actcgctatt gggcaccaaa ctccaccaag acaacaagct attcagggca attcacatca
7081 acgcctgtgc atacaccaaa tttgagtagc aagcccaaga ccacaagtgt caaatcccca
7141 tctccttctt cttcctctgg tagtgtttat agtctagcaa ctcagtcaac ttcactgtcc
7201 ggaccttctt caggttcctc tgcttcttct gcttcaacac aatcaacaaa attaagctca
7261 acttcttcta tgagtagaac aattgattgg gtcaatcaac aaagaagtct cagcccatac
7321 atgagtggag ctcttaacat ctcccatgtg acacctccat caagtagagc atctagttcg
7381 ggaacagtct caactgtccc caaagaagtt ttggactcct ggacatctgc atttaacaca
7441 cacagacagc cgctcttcgc acaccttagg gtaagggggg agtcacgtgt ttag
//