Typing tool
|
Complete norovirus genomes
OL685302 | GIX.1 | ||
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GII.P15 |
ORF1: 1..5091 ORF2: 5072..6739 ORF3: 6739..7467LOCUS OL685302 7542 bp RNA linear VRL 28-OCT-2022 DEFINITION Norovirus GIX isolate Hu/US/2021/GIX.1[GII.P15]/CA-RGDS-1145 nonstructural polyprotein (ORF1) gene, partial cds; and VP1 (ORF2) and VP2 (ORF3) genes, complete cds. ACCESSION OL685302 VERSION OL685302.1 KEYWORDS . SOURCE Norovirus GIX ORGANISM Norovirus GIX Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes; Picornavirales; Caliciviridae; Norovirus; Norwalk virus. REFERENCE 1 (bases 1 to 7542) AUTHORS Osborn,B., Pan,C.Y., Hatada,A., Hatfield,J., Wagner,J., Oakeson,K., Montmayeur,A., Morales,C. and Vinje,J. TITLE Cluster of Norovirus Genogroup IX Outbreaks in Long-Term Care Facilities, Utah, USA, 2021 JOURNAL Emerg Infect Dis 28 (11), 2312-2315 (2022) PUBMED 36286223 REFERENCE 2 (bases 1 to 7542) AUTHORS Pan,C.-Y., Hatada,A., Wagner,J.M., Oakeson,K.F., Montmayeur,A.M., Vinje,J., Padilla,T., Wadford,D.A. and Morales,C. TITLE Direct Submission JOURNAL Submitted (30-NOV-2021) Viral and Rickettsial Disease Laboratory, California Department of Public Health, 850 Marina Bay Parkway, Richmond, CA 94804, USA COMMENT ##Assembly-Data-START## Assembly Method :: SPAdes v. 3.6; Geneious v. R10 Sequencing Technology :: Illumina ##Assembly-Data-END## FEATURES Location/Qualifiers source 1..7542 /organism="Norovirus GIX" /mol_type="genomic RNA" /isolate="Hu/US/2021/GIX.1[GII.P15]/CA-RGDS-1145" /isolation_source="stool" /host="Homo sapiens" /db_xref="taxon:2594528" /country="USA: UT" /collection_date="Apr-2021" /note="genotype: GIX.1[GII.P15]" gene <1..5091 /gene="ORF1" CDS <1..5091 /gene="ORF1" /codon_start=1 /product="nonstructural polyprotein" /protein_id="UFP63609.1" /translation="MASNDVVTALGSQKATNDSYSTPPPNKEEASVLANVKVGFKKIL GAVPKAPKQHGSIQKPPIVEIDGVTMRVPSPPPNGEDAVHFVKETETIKGLPDLSTVE NESEHSPYTVPPLSEREHRPATEPLPGTILEMWDGEFYHYSIYVDNGKALGVHKPPAA ISLATIDLTPISLYWRPVYTPPYLVHPETLKGLAGEKFPYTAFSNNCYNFCCWVLDLN DSWLNRRSITRTTGFFKPYQSWNRKPLPTVDDGKIKKVANAVLCALGSLFSKPIKDLL GKLKPLNLLNLLASCDWTFAGVVETVILAAELFNVFWTPPDVSNFIASIIGDFEMQGP EDLAVELVPVIMGGIGMVLGFTAEKIGRMLSSAASTLRACKDLGNYALDILKLVMKWF FPKKEEKAEMETLRAIEDAVLDMEAIGNNHLTTLLKDKDSLSAYMKTLDMEEEKARRL STKSSSPDIVGTINAILARIAAARSLLHKAKEEMFSRARPVVVMVSGRPGIGKTYLAR QLAKSIANSMSGDQRVGLVPRNGVDHWDAYRGERVVLWDDYGMGNTIKDALTLQELAD TCPVTLNCDRIENKGKMFDSDVIIITTNLVNPAPLDYVNFEACCRRIDFLVYAEAPDI EKVKKDFPGQPDMWRDHFKADSSHIKLSLAPQGGFDKNGNTPHGKGTMKTLTLHSLTA RVMGLVCERKDEFQLQGDELQVYNFDTNKVSAFRKLAADNKYSFVETMKVGAVLKNVK TLEDLKSALKGVKFKECEIIYKGAKYRVASDGCGSVSVSKIKDVVSQTSNEVHTALLR LRQARARYYISCFQDLIYTLIQVAGASFVVHRISKRFSWDRWVKPSDSPQEEEQPSSE VATGRWEIEPKDTDPEGKKGKNKKGRGRKHTAFSSKGLSDEEYDEFKRIREEKNGKYS IEEYLQDRDRFYEEVAVARATEEDFCEEEVAKIRQRIFRPTKKQRKEERGVLGLVTGS EIRKRRPDDFQPKGNLWADDTRSVDYNEKLEFEAPPSVWSRIVPLGTGWGFWVSSNLL ITTTHVLPKGLKELFGVDIKQVQIHKSGEFCRFRFPRPIRPDVTGLILEEGAPEGTVC SILVKRPTGEMIPLAVRMGTHASMKIQGRTVGGQMGMLLTGANAKNMDLGTNPGDCGC PYIFKRGNDIVVAGVHTAAARGGNTVICATQGADGEAVLEGGEDKGTYCGAPILGLGK APKLSTKTKFWRSSPDALPPGTYEPAYLGGKDPRVEKGPSLQQVMREQLKPFTEPRGK PPKPNVLDEAKKTVMNVLEQTINPAKPWSYSQACASLDKTTSSGSPHHLRKNDHWNGE SFTGPLADQASKANLMYEQAKHMSPVYTAALKDELVKTDKIYKKIKKRLLWGSDLGTM VRCARAFGGLMDSMKESCVMLPCRVGMNMNEDGPIIFDKHAKYKYHYDADYSRWDSTQ QRSILSAAMEVMVKFSAEPELAQVVAEDLLAPSQLDVGDFVVSVQEGLPSGVPCTSQW NSIAHWIITLSAMAEVSGLSPDVIQAHSCFSFYGDDEIVSTDINLDPAKLTLKLREYG LVPTRPDKTEGPLVITEDLHGLTFLRRHITRDPAGWFGKLDQDSILRQLYWTRGPNHE NPYECMVPHSQRATQLMALLGEASLHGPQFYKKVSKMVINEIKSGGLEFYVPRQEAMF RWMRFSDLSTWEGDRNLAPDGVNEDGVE" mat_peptide <1..996 /gene="ORF1" /product="p48" mat_peptide 997..2094 /gene="ORF1" /product="NTPase" mat_peptide 2095..2616 /gene="ORF1" /product="p22" mat_peptide 2617..3015 /gene="ORF1" /product="VPg" mat_peptide 3016..3558 /gene="ORF1" /product="Pro" mat_peptide 3559..5088 /gene="ORF1" /product="RdRp" gene 5072..6739 /gene="ORF2" CDS 5072..6739 /gene="ORF2" /note="major capsid protein" /codon_start=1 /product="VP1" /protein_id="UFP63610.1" /translation="MRMASSDAPVSGTDGAAGLVPESQQEVLPLEPVAGVQLAAPVAG QSNIIDPWIRMNFVQAPAGEFTVSPRNAPGEVLIDLELGPELNPYLNHLARMYNGYVG GMEVEVVLAGNAFTAGKILFAAVPPSFPTHGISAAQATMLPHVIVDVRQLEPVRLPLP DVRNVMFHFCQENKEPRMRIVAILYTPLRANGAGDDVFTVSCRVLTRPSPDFDFIFLV PPSVESKLKQFTLPNLQPNEMTNSRFPTGITQLYTSPNTNLVVQFQNGRCLLDGTLLG TTPVRAADICSFRGVTSTEVDATDSPRVAGSHRIMVQLKEPDGEEFSPTGPNPAPVGT PDFQAAIFGTLSQRNTGGAGQNSNRAHFAYFYTRNPTFAPGIGTVVFSFDTTDFQNRQ PTKFSPSGVFDDDSSEPFNQFSLPYYNGSLGAVDAGKLAPPVAPNYPGEQILYFRGNI PFKGGYGEGEIDSLLPQEWITHFYAEQAPTQGDAALLRYYNPDTGRVLFECKLHREGF ITINYTGSNALAVPVNGVFRFEGWVNKFYTLTPMGNGNGRRGRRREL" gene 6739..7467 /gene="ORF3" CDS 6739..7467 /gene="ORF3" /note="minor structural protein; small basic protein" /codon_start=1 /product="VP2" /protein_id="UFP63611.1" /translation="MAGAFFAGLASDVLGSGLSSLIGAGANAINQKVEYDYNRHLQSA SFQHDKDMLNSQVEATKHLQREMMAIKEGMLLKGGFSPTDAARGAVNAPMTQILDWNG TRYWAPGAMKTTAYSGRFVSQSTHRPIPNVAHKSDGPIHQTGSTTGSISSLSTSSTHV PSSTSSSSASRTRDWVSEQQRLSPFMRGSLHTAYVTPPSSSASSVSSVSTVPHYVLDS WTPSFNTKHLPLFAHVRKRGQSQV" ORIGIN 1 atggcgtcga atgacgtcgt tactgccctt ggcagccaaa aagctaccaa tgacagctac 61 agcacacctc cccccaacaa ggaggaggct agtgtgcttg ccaacgttaa agttggcttt 121 aaaaagatcc tcggggccgt ccctaaggct ccgaaacagc atggcagcat acaaaaaccg 181 ccgatcgtcg agatcgatgg tgtgaccatg cgtgtaccct ctccccctcc aaacggtgag 241 gacgcagtcc acttcgtgaa ggaaacggag accatcaagg gactgccaga cttgtccacc 301 gtggagaacg agtctgaaca ctctccgtac acagtccccc cgttgagtga gagggagcac 361 aggccagcaa cagagccatt gcccggcact atacttgaga tgtgggatgg tgagttctac 421 cactactcca tatacgtgga caatggcaag gcccttggag ttcacaaacc accagcagca 481 attagcctag caacgataga tttaacacct atatcgttgt actggagacc ggtttacaca 541 ccgccgtacc ttgtccaccc agagacgctc aagggactgg ctggcgaaaa attcccctac 601 acggccttca gcaacaactg ctacaacttc tgttgctggg ttctggacct caatgactcg 661 tggttgaacc ggagatccat aactagaaca actggtttct tcaaacccta ccaatcctgg 721 aacaggaagc ccctcccaac tgtggatgat ggcaagatca agaaggtcgc gaatgcagtt 781 ctgtgtgccc taggatcact tttctccaag cccattaagg acctccttgg caaattaaaa 841 cccctcaatc tcctgaactt gcttgcatca tgtgactgga cctttgctgg cgtggtggaa 901 acagtcattc ttgctgcaga gctcttcaat gtcttctgga ctccacctga tgtctccaac 961 ttcattgctt ccataattgg cgacttcgag atgcaaggac cagaggatct tgctgtggag 1021 cttgtccctg ttatcatggg aggcattggt atggtgttag ggtttacagc tgagaagata 1081 gggcgtatgt tatcatctgc agcatccacc ctcagggctt gtaaggacct tggcaattac 1141 gccttagaca tcctgaaact agtcatgaag tggtttttcc ctaaaaagga ggaaaaggcc 1201 gagatggaga ccctgagggc cattgaggac gctgtccttg acatggaggc aattggaaac 1261 aaccacctca caacgctgct caaagacaaa gatagcttga gcgcctatat gaagaccttg 1321 gacatggagg aggagaaggc caggaggctc tccaccaaat catcatcacc cgacattgtt 1381 ggcaccatca acgcgatcct cgcacgcatt gctgccgcaa ggtcactcct acacaaagcc 1441 aaagaggaaa tgttcagtcg agcgaggcct gttgtcgtta tggtgtctgg aaggcccggt 1501 atcgggaaga catatctggc cagacagctt gccaaatcga ttgcaaacag catgagtggt 1561 gatcagagag tgggactcgt cccccgcaat ggggttgacc actgggatgc ctataggggt 1621 gaaagagttg tcctatggga tgactacggc atgggaaata caatcaaaga tgccctgacc 1681 ctacaagagt tggctgacac ctgcccagtt accctcaact gtgacaggat cgaaaacaag 1741 gggaagatgt ttgacagcga tgtcattata ataacaacca atcttgtcaa ccccgctccc 1801 ctcgattatg ttaattttga ggcttgctgt aggcgaattg acttccttgt ttatgccgag 1861 gcaccggaca ttgagaaagt caaaaaggat ttccctggac aacctgacat gtggcgtgac 1921 cattttaaag ctgactcgtc acacataaag ttatcactag ccccacaggg tggctttgac 1981 aagaacggaa acacccctca cgggaagggc accatgaaaa ctctcacgct gcactcactc 2041 actgcacgtg tgatgggttt agtgtgtgag aggaaggatg agttccaact gcagggtgat 2101 gaactacagg tttataactt tgacacaaac aaggtctctg catttagaaa actagcagct 2161 gacaacaagt acagctttgt ggagacaatg aaagtcggtg cagtcctcaa gaatgtaaaa 2221 accctggaag atctgaaatc tgccctcaag ggagttaaat tcaaagagtg tgaaataatt 2281 tacaaggggg ccaagtatag agtcgcctcg gatggttgtg gcagtgtctc agtttccaag 2341 atcaaggatg ttgtatcgca gacatccaac gaagtgcaca cagcgctcct gagattgagg 2401 caagcccggg ccaggtatta tatcagctgc ttccaagatc tcatatacac cctaatacag 2461 gttgctggag cctcatttgt ggtacatagg atctcaaaga gattctcatg ggaccgctgg 2521 gtcaaaccca gtgacagccc tcaggaggaa gaacaaccca gtagtgaggt ggccacaggg 2581 agatgggaaa ttgagccaaa agacacagat cctgaaggca aaaagggtaa aaacaagaag 2641 ggaaggggaa ggaaacacac ggctttctct agtaagggtc ttagtgatga agagtatgat 2701 gagttcaaaa gaatcagaga agagaagaac ggcaaatact ccatagaaga atacctccag 2761 gaccgtgaca gattttacga ggaagtggca gttgcaaggg caacggagga ggatttctgt 2821 gaggaagaag tggcaaagat cagacagaga atcttcaggc ccacaaagaa gcaaaggaag 2881 gaggagcgag gcgtcctagg gctggtcact ggttcagaaa tcaggaagag aagaccagat 2941 gacttccagc ctaaaggtaa cttgtgggct gatgacacca ggagcgtgga ctacaacgaa 3001 aagctggagt ttgaggcccc tccgagcgtg tggtcacgta tcgtacccct cggcactggc 3061 tggggtttct gggtctcctc caaccttctc ataacaacaa cacatgtcct gccaaaagga 3121 ttgaaggagc tgtttggggt tgatatcaaa caagtccaga tacacaagtc aggtgagttc 3181 tgcaggttca ggtttccaag accaatcaga ccagatgtca caggcctcat ccttgaagaa 3241 ggggcccctg aaggcacggt gtgttctatc cttgtcaaaa gaccgactgg ggagatgata 3301 ccgcttgcag tgaggatggg cacccacgct tccatgaaga tccagggtag aacggttggt 3361 ggtcaaatgg gcatgctgct cacaggagca aacgccaaaa acatggattt gggcacgaac 3421 cctggtgatt gtggatgccc gtacattttt aagaggggca atgacattgt ggtagctggg 3481 gtccacactg cagctgcacg gggtggcaac actgtgatct gtgccacgca aggagctgac 3541 ggagaggccg tccttgaagg aggagaggac aaagggacgt actgtggtgc cccaatactt 3601 ggactcggga aggcccccaa actcagtacc aagacaaagt tctggcggtc ctcccctgat 3661 gcgcttcccc cgggaacgta tgagccagca tacctaggtg gaaaagaccc aagggttgag 3721 aagggcccgt cactccagca ggtcatgaga gaacaactta aacctttcac cgaacccaga 3781 ggaaaacccc caaaacccaa cgttcttgat gaggcaaaga aaactgtgat gaacgtgttg 3841 gagcagacta taaaccctgc caaaccctgg tcatactccc aagcatgtgc ttcgcttgac 3901 aagacaactt caagtggtag cccccaccac ctgagaaaga atgaccattg gaatggtgaa 3961 tctttcaccg gtcctttggc cgatcaagct tcaaaagcaa acctaatgta tgaacaggca 4021 aaacacatga gccccgttta cactgcagcc cttaaagatg aactggtcaa gaccgacaag 4081 atctacaaga aaataaagaa gaggctgctg tggggctctg acctgggtac tatggtcagg 4141 tgtgctaggg cttttggtgg gttgatggat agcatgaaag agagttgtgt gatgttgccc 4201 tgcagagttg gcatgaacat gaatgaagat ggaccaatca tttttgacaa acatgcaaaa 4261 tacaaatatc actatgatgc agattactcc agatgggatt ccacacaaca aaggagcatc 4321 ttatctgctg ctatggaggt tatggtgaag ttctcagctg aaccggaact ggcacaagtg 4381 gtcgctgaag acttactcgc cccaagccaa ctcgacgtgg gcgactttgt ggtgtcagtc 4441 caagaaggtc tcccctcagg tgttccgtgc acttcccaat ggaactccat agcacattgg 4501 atcatcaccc ttagtgcaat ggcagaagtt tctggtctct ccccagatgt gatccaagct 4561 cactcatgct tctctttcta tggtgatgat gagatagtta gcacagacat caacttggac 4621 ccagcaaagc taaccttaaa actcagagaa tatggattgg tccccaccag accagacaaa 4681 actgaaggcc cattagtcat cacagaggat ctccatggat tgacctttct acgcagacac 4741 atcacacgag atcctgctgg atggtttgga aaattagacc aggattcaat cttgaggcaa 4801 ctctattgga ctagaggacc caaccatgaa aatccctacg agtgcatggt cccacactca 4861 cagcgtgcaa ctcagttaat ggcgctgttg ggtgaggcat cattgcacgg tccccagttc 4921 tacaagaaag tcagcaagat ggttatcaat gagattaaga gtggtggtct ggaattttac 4981 gtgcccagac aggaggccat gttcagatgg atgagattct ctgacctcag cacgtgggag 5041 ggcgatcgca atctggctcc cgacggtgtg aatgaggatg gcgtcgagtg acgcgcccgt 5101 ttctggcacc gatggtgcgg caggactcgt cccagagagt caacaagaag tcttgccttt 5161 agagcccgtc gcgggagttc agctggctgc tcccgtagca gggcaaagta atataattga 5221 cccctggatt agaatgaatt ttgtgcaagc cccggccggt gagttcactg tttcccctcg 5281 gaacgcaccg ggtgaggtgc ttattgattt agaattagga ccagaattaa atccctatct 5341 caatcacctt gcgagaatgt acaatgggta tgtgggagga atggaggtgg aagttgtcct 5401 tgccgggaat gcgttcacgg cgggtaagat cttattcgca gctgtgcccc ccagcttccc 5461 aacccatggc atttctgcag cacaggcaac tatgttacca catgtgattg tggatgtcag 5521 gcagctggag cctgtccggc tccctcttcc tgatgtcagg aatgtgatgt tccatttctg 5581 tcaagaaaat aaggagccgc gcatgagaat tgtggcaata ttgtacaccc cactccgtgc 5641 caacggtgcg ggtgatgatg tcttcactgt ctcatgtcgt gtgctgacaa ggccctcccc 5701 agattttgat tttattttct tggttccccc ctctgtagag agtaagttga aacagtttac 5761 ccttccaaac ctgcagccaa atgaaatgac caattcaaga ttccccactg gcatcacaca 5821 actctacacc agtccaaata ccaatttggt tgttcagttc caaaatggca ggtgtctgct 5881 tgatggtaca cttctcggca ccacccctgt cagagctgct gacatctgca gtttcagagg 5941 agtcacctca actgaagttg atgcaactga cagccccaga gtggcagggt cccatagaat 6001 tatggtgcag ctcaaggagc cagatggaga ggagttttca cccacaggtc ctaaccctgc 6061 ccctgttggc actccagact ttcaagcagc catatttggc acccttagtc aaagaaacac 6121 tggcggggct ggacagaact ccaacagagc ccacttcgca tacttctaca ctagaaaccc 6181 cacatttgca ccaggtatag ggacagttgt gttttctttt gatactactg attttcaaaa 6241 tcgccaacct accaaattct ctccttctgg tgtgtttgat gatgattctt ctgaaccctt 6301 taatcaattt tctctaccat actataatgg atcactcggt gcagtggatg ctggaaaact 6361 ggctccgcct gtggcaccca actacccagg tgagcagatt ctttatttta gagggaatat 6421 tcccttcaaa ggtgggtatg gagagggtga gattgatagc ttgcttcccc aggagtggat 6481 cacccacttt tatgcagagc aggctcctac acaaggtgac gcagccctgc tgcgttacta 6541 caaccctgac actggcagag tcctttttga gtgcaaactc caccgcgagg gattcatcac 6601 aatcaattac acagggtcca atgctcttgc tgtaccagtc aatggagtct tcaggtttga 6661 gggctgggtt aacaaattct acacacttac ccccatggga aatggcaacg gccgcagggg 6721 tagaagaagg gagttataat ggctggagct ttctttgcag gtcttgcttc tgatgttctc 6781 ggcagtggtt tgtcttcact tatcggtgcc ggtgccaatg ccataaacca aaaggttgaa 6841 tatgattaca ataggcactt gcagtctgct tctttccaac atgataagga catgctcaac 6901 tcacaggtgg aagccacaaa gcacttacaa agagagatga tggccatcaa ggaaggcatg 6961 ctgctcaagg gtgggttctc ccccactgat gcagcaagag gagctgtcaa cgcccctatg 7021 acacaaattt tggattggaa tggcaccaga tactgggccc cgggtgcaat gaaaaccacg 7081 gcttactcag gccgttttgt tagccaatcc actcacaggc ctattcccaa tgttgctcac 7141 aagagtgatg gacccataca ccaaactggg tcaaccacag ggtccatttc ctctctctcc 7201 acatcatcca cccatgttcc atcatctaca tcctcatcta gtgcttctag aacaagggac 7261 tgggtgtctg aacagcaaag actcagtcct ttcatgagag gctctcttca cactgcatat 7321 gtgactcctc cctcaagctc tgcctcctca gttagttctg tttctacagt cccacactat 7381 gttttagatt catggacccc ttcttttaac actaaacatc tacctttgtt tgctcatgtt 7441 agaaagaggg gacaatctca agtttaatct accactcatg gtttgattga tttgttttgt 7501 aattagtgaa atgttgattc tttctaattc ggcatttaaa aa //