Typing tool
|
Complete norovirus genomes
OP686904 | GII.8 | ||
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GII.P8 |
ORF1: 5..5104 ORF2: 5085..6698 ORF3: 6698..7471LOCUS OP686904 7533 bp RNA linear VRL 25-OCT-2022 DEFINITION Norovirus GII isolate Hu/US/2020/GII.8[P8]/CA-RGDS-1153, complete genome. ACCESSION OP686904 VERSION OP686904.1 KEYWORDS . SOURCE Norovirus GII ORGANISM Norovirus GII Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes; Picornavirales; Caliciviridae; Norovirus; Norwalk virus. REFERENCE 1 (bases 1 to 7533) 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..7533 /organism="Norovirus GII" /mol_type="genomic RNA" /strain="CA-RGDS-1153" /isolate="Hu/US/2020/GII.8[P8]/CA-RGDS-1153" /isolation_source="stool" /host="Homo sapiens" /db_xref="taxon:122929" /country="USA: CA" /collection_date="Feb-2020" /note="Amplicon sequencing:first 35 nt does represent primer sequence; genotype: GII.8[P8]" gene 5..5104 /gene="ORF1" CDS 5..5104 /gene="ORF1" /codon_start=1 /product="nonstructural polyprotein" /protein_id="UYL06246.1" /translation="MKMASNDASAAAGNFNIANNSESTPPPIKEEASVLSNVKVGFKK ILGAVPKQPKPPEVKTKDQPRVLVNGKALEVPPPPPNGEDVVYYNSKDDTVHGLPNLT TVSCEGENLPYTVPPLSEREHRAAPEPLPGTILEMWDGEFYHYAIYVSGGKAIGVHKP PAAISLATIELTPISLYWRPVYVPNYLVHPDTLKSLAGEKFPYTAFSNNCYNFCCWVL DLKDSWLNRRSITRTTGFFKPYQTWNKKPLPTVDDGKIKKVANAVLCALGSLFSKPIK DLIGKLKPLNFLNLLASCDWTFSGVVETVILAAELFGVFWTPPDVSNFIASLIGDFEL QGPEDLAVELVPIIMGGIGMVLGFTAEKIGRMLSSAASTLRACKDLGNYALDILKLVM KWFFPKKEEKAEMETLRAIEDAVLDMEAIGNNHLTALLKDRDSLLTYMKTLDLEEEKA RKLSTKSSSPDIVGTINAILARIAAARSLLHRAKEEMYSRPRPVVVMISGRPGVGKTH MARHLAKSVAGTMSGDQRVGLIPRNGVDHWDAYRGERVVLWDDYGMGNPVKDALALQE LADTCPVTLNCDRIENKGKMFDSEVIIITTNLANPAPLDYVNFEACSRRIDFLVYAEA PTIEKAKKDFPGQPDMWKEHFKADFSHLKLTLAPQGGFDKNGNTPHGKGTMKTLTQGS LTARVAGLVHERKDEFQLQGGELQVYNFDTNKVSAFRKLAADNNYGFLETMRVGTSLK DVKTVEDLKCALKSVSFKECEIIYRNVKYRISSDGCGKVSIEKLADNNSQTTREIITA VTRLRQARARYYISCFQDLVYTLLQVAGASFVINRIVKKFNWERWVKTPETDEPTPSN DKPDTEEEWEIAPKDVDSEGKKGKNKKGRGRKHTAFSSKGLSDEEYDEFKRLREEKQG RYTIEEYLQDRDRYYEELAVARATEENFCEEEEIKIRQRIFRPTKKQRKEERGVLGLV TGADIRKRRPDDFQPKGKLWADDSRSVDYNEKIEFEAPPSVWSRIVPLGTGWGFWVSS NLLITTTHVLPKGIKELFGVDIKQVQVHKSGEFCRFRFPKPVRPDVSGLVLEEGAPEG TVCSVLIKRSTGEMIPLAVRMGTHASMKIQGRTVGGQMGMLLTGANAKNMDLGTGPGD CGCPYIYKRGNDIVVAGVHTAAARGGNTVICATQGPDGEAVLEGGEDHGTYCGAPILA PGKAPKLSTKTKFWRSSPDSLPPGTYEPAYLGGKDPRVEKGPSLQQVMRDQLKPFTEP RGKPPRPSVLEEAKKTVMNVLEQTIEPAKPWTYSQACASLDKTTSSGSPHHVRKNEHW NGESFTGPLADQASKANLMYEEGKHMDPMYTAALKDELVKTDKIYKKIKKRLLWGSDL GTMVRCARAFGGLLDSMKESCISLPCRVGMNINEDGPLIFEKHSKYTYHYDADYSRWD STQQRAVLSAAMEVMVKFSAEPELAQVVAEDLLAPSRLDVGDFVVSVQEGLPSGVPCT SQWNSIAHWILTLSAMSEVSGLSPEVVQANSCFSFYGDDEIVSTDINLDPEKLTRKLR EYGLVPTRPDKTEGPLVITQDLNGLTFLRRTIVRDPAGWFGKLDRDSILRQLYWTRGP NHENPFESMIPHSQRATQLMALLGEASLHGPQFYKKVSKMVINEIKSGGLEFYVPRQE AMFRWMRFSDLSTWEGDRNLAPENVNEDGVE" mat_peptide 5..1009 /gene="ORF1" /product="p48" mat_peptide 1010..2107 /gene="ORF1" /product="NTPase" mat_peptide 2108..2629 /gene="ORF1" /product="p22" mat_peptide 2630..3028 /gene="ORF1" /product="VPg" mat_peptide 3029..3571 /gene="ORF1" /product="Pro" mat_peptide 3572..5101 /gene="ORF1" /product="RdRp" gene 5085..6698 /gene="ORF2" CDS 5085..6698 /gene="ORF2" /note="major capsid protein" /codon_start=1 /product="VP1" /protein_id="UYL06247.1" /translation="MKMASNDAAPSNDGAAGLVPEINHEVMAIEPVAGASLAAPVVGQ LNIIDPWIRNNFVQAPAGEFTVSPRNAPGEFLLDLELGPELNPYLAHLARMYNGHAGG MEVQIVLAGNAFTAGKILFAVIPPGFPYENLSPAQLTMCPHVVVDVRQLEPILLPMPD IRNTFFHYNQSNGPKLRLVAMLYTPLRANNAGDDVFTVSCRVLTRPSPDFEFNFLVPP SVESKTKAFTLPILKTSEMTNSRFPIPVDQMYTSRNENIVVQPQNGRVTLDGELQGTT TLQPVSICGFRGTLQTRLADQPNYTYQVHLENLDGSPVDPTDEVPAPLGTPDFQAQLF GVVSQRSSDNATRAHEARVNTNDPTFAPQIAQVRFKSPSHDFFDNEPIKFTPVGISVD SENSYNQWLLPRYGGHLTNNTHLAPSVSPMFPGEQILFFRSFMPGASGHTDGAIDCLL PQEWVAHFYQEAATAQTDVALIRFVNPDTGRVLFEGKLHKQGFITISNSGDHPIVMPA NGYFRFEAWVNQFYSLAPVGTGSGRRRIQ" gene 6698..7471 /gene="ORF3" CDS 6698..7471 /gene="ORF3" /note="minor structural protein; small basic protein" /codon_start=1 /product="VP2" /protein_id="UYL06248.1" /translation="MAGAFLAGLAGDVVTSGIGSLINAGANAVNQKVEYDFNRQLQEA SFKHDKEMLNAQINATTKLQRDMIAIKQGVLTAGGFSPTDAARGSINAPTTKILDWNG SRYWAPGSMRTTAYSGNFISQGVKQPTPIVKSVEPQVQQSPAPSSVYSVGSVKSQSTQ STQLTGSGTVSRAPTPSTTTTLSRTSEWVRSQNDRLSPFMGGALQTAFITPPSSKASS SSGTVSTVPREILDSWTPVFNTRRQPLFAHMRRRGESRA" ORIGIN 1 gtgaatgaag atggcgtcta acgacgcttc cgctgccgct ggcaacttta acattgccaa 61 caacagtgaa agcactcccc ctcccattaa ggaagaggcg agtgtcctat ccaacgtaaa 121 agttggattc aagaaaatat tgggggctgt gcctaagcag cccaagccac cagaagtgaa 181 aaccaaagat caacccaggg tgctggtcaa tggtaaggcc ctggaggtgc cgcccccacc 241 accaaatggt gaagacgtgg tttactataa cagcaaggat gacactgtgc acggcctacc 301 aaatctaaca acagtcagct gtgaaggtga aaaccttccg tacacagttc ctcctctcag 361 cgagagagag cacagggcag caccagaacc attacctggc accatactag agatgtggga 421 tggtgaattc taccattatg cgatatatgt ctctggtggt aaggccatag gggtgcacaa 481 acccccagct gcaatcagcc ttgctaccat cgagcttaca cccatatcgc tttactggag 541 gcctgtctat gtccccaatt acttggtcca ccctgacaca ctcaagagct tagctggtga 601 aaaatttcca tacaccgcat ttagcaacaa ttgttacaat ttctgttgct gggttcttga 661 cttgaaagac tcgtggctta accgcaggtc aataactaga acaaccggtt tcttcaagcc 721 ttatcaaacc tggaacaaga aaccactccc gacggtggat gatggaaaaa tcaagaaagt 781 cgccaatgca gtcctgtgtg cccttggttc actattctca aaacctatta aggacttgat 841 cgggaagctg aaaccattga atttcttgaa tctcctcgct tcgtgcgatt ggacattctc 901 cggagtggtt gagaccgtca tactagctgc tgaactattc ggagtgtttt ggacccctcc 961 cgacgtgtcg aacttcatcg cgtcactcat cggggacttt gagttgcagg gtccagagga 1021 tttagctgtg gagttggtgc cgattatcat gggcggcatc gggatggtgc tgggattcac 1081 cgccgagaag atcggccgaa tgctatcatc agctgcgtcg acccttaggg cctgtaaaga 1141 cctaggtaac tatgcccttg acatacttaa attggtcatg aagtggttct tcccaaagaa 1201 ggaggaaaag gcagagatgg agaccttgag ggccatagag gatgctgttt tggacatgga 1261 ggcgattgga aataatcacc tcactgctct gttgaaagac agggacagtc tcctaaccta 1321 catgaagact ctagacctcg aagaggaaaa ggcaagaaag ttatccacaa aatcatcttc 1381 ccctgacatc gtgggtacca tcaatgccat actagccaga attgccgcgg ctaggtctct 1441 cctacacaga gctaaagaag aaatgtacag cagacctagg cctgtcgtgg tgatgatatc 1501 aggaagacca ggggttggca aaacccatat ggctagacac ctcgccaaga gtgtggcggg 1561 caccatgagc ggtgaccaaa gggtgggcct catcccccgt aatggagttg atcactggga 1621 tgcctacagg ggggaacgag tagtcttgtg ggacgactat ggcatgggca acccagtgaa 1681 ggacgccctt gctctgcaag aactagcaga cacttgtcca gtcaccctca attgtgacag 1741 gatagagaat aagggaaaga tgtttgatag cgaggtaata attataacaa ccaatctggc 1801 caaccccgcc ccgcttgatt atgtcaactt tgaggcatgt tcccgcagaa ttgacttcct 1861 cgtctacgca gaggccccga ccattgagaa ggcgaagaaa gatttccccg gacaaccaga 1921 catgtggaag gagcacttca aagcagactt ctctcatctc aaactcacac tggccccaca 1981 aggcggtttt gacaagaacg gcaacacgcc acatgggaag gggactatga agaccttgac 2041 acagggttcc ctcacagcaa gagtggctgg gcttgtgcat gaaaggaaag acgagttcca 2101 gttacagggt ggagagttgc aggtctacaa ctttgacaca aacaaggtat cggctttcag 2161 gaagcttgct gcagacaaca actatgggtt tctggagaca atgagagtcg gcacctcact 2221 caaggacgtc aagacagtgg aagaccttaa atgtgcactc aagagtgtca gtttcaaaga 2281 atgtgaaata atctacagga atgtcaagta ccgcatatca tcagacggtt gcggtaaggt 2341 cagcatagag aaactggcag ataacaactc ccaaacaacc agagagatta tcacggccgt 2401 cactagacta cgacaggctc gtgctaggta ctacattagc tgcttccaag acctagtcta 2461 cacactcttg caggttgccg gagcctcatt tgtcattaat agaatagtta agaagttcaa 2521 ctgggaacga tgggtcaaga ccccagaaac ggatgaaccc acaccaagta atgacaagcc 2581 cgacactgaa gaggaatggg agatcgcccc caaagatgtg gactctgagg gtaaaaaggg 2641 gaagaacaag aagggcagag gacgtaagca cactgcattc tccagcaaag ggcttagtga 2701 tgaggagtat gatgaattca aaaggctgag ggaagagaaa cagggccgct acacaataga 2761 ggagtacctc caggacagag accggtacta tgaagagctg gcagtggccc gggccactga 2821 agagaacttc tgtgaagagg aagagataaa gatcaggcaa agaatattcc gccccaccaa 2881 aaagcagagg aaggaggaga ggggggttct gggactcgtc acaggagcag acatcaggaa 2941 acggagaccc gatgatttcc aaccaaaagg aaaactgtgg gcagatgatt ctaggagcgt 3001 cgactacaat gagaagatcg agtttgaagc tcctcctagc gtctggtcaa gaatcgtccc 3061 gcttgggact ggttggggat tctgggtctc atccaactta ctaatcacca ccacacatgt 3121 gctgcccaaa ggcattaaag agctttttgg ggtggacatc aaacaagtcc aagtccacaa 3181 atcaggtgaa ttttgcagat tcaggttccc aaaaccagtg aggccagatg tctctgggtt 3241 ggtactagaa gaaggggccc ccgaaggcac agtgtgctct gttctcatca agaggtcaac 3301 aggagagatg atcccccttg cagtcaggat gggcacccac gcctctatga agatccaggg 3361 gcgcactgtt ggcggccaga tgggcatgct gctcactgga gccaacgcta agaacatgga 3421 tttaggcacc ggccccgggg attgtggttg cccgtacata tacaagaggg gcaatgacat 3481 cgtggtggcc ggcgtccaca cagcagcagc gcgcgggggc aacacggtca tctgcgcaac 3541 ccaaggacct gatggtgagg cagtgttgga agggggagag gaccacggca cttattgtgg 3601 agctccaata ttggcccctg gtaaagcgcc gaagcttagc acaaagacta agttttggcg 3661 ctcatcccct gattcccttc cccctgggac gtatgaacca gcttaccttg ggggtaagga 3721 tccccgtgtg gagaaagggc cgtcactcca acaagtgatg cgagaccaac taaaaccctt 3781 cacagaaccc aggggcaagc cacctaggcc gtcagtgctg gaggaagcca agaagacagt 3841 catgaatgta ctggagcaga ccatagaacc agctaagcca tggacctact ctcaagcctg 3901 tgcttcattg gataaaacaa catccagtgg cagtcctcac cacgtcagga agaatgaaca 3961 ctggaacggg gagtctttca ctgggcctct tgcagatcaa gcctcaaaag ccaacctgat 4021 gtatgaggag ggtaaacaca tggaccctat gtacacagca gccctcaagg acgagttggt 4081 gaaaactgac aaaatctata agaaaatcaa gaagaggttg ttgtgggggt ctgatctggg 4141 gacaatggta aggtgtgctc gagcgtttgg aggattgctc gacagcatga aagagagttg 4201 catctcctta ccctgtaggg ttggcatgaa cataaacgaa gatggaccac tcatatttga 4261 aaaacattcc aaatacacct atcactatga tgctgactac tctaggtggg actcaacgca 4321 acagagggct gtcctgagtg cagccatgga ggtaatggtg aagttctctg ctgagccgga 4381 actggctcag gtggttgccg aagacctcct tgcacccagc cgtcttgacg tgggtgactt 4441 cgtcgtctcc gtccaagaag gtcttccatc gggtgtcccc tgcacgtcac agtggaactc 4501 aatcgctcac tggatcctga ctcttagtgc tatgtctgag gtctctggtc tttcccctga 4561 ggttgtgcaa gccaactcct gtttctcatt ctatggggat gatgaaatag tcagcacaga 4621 tataaaccta gacccagaaa aactcaccag gaaactgagg gagtatggcc tcgtcccaac 4681 aaggccagac aaaactgagg gcccacttgt gatcactcag gatttgaatg gtctcacatt 4741 cttgaggcgg accatagtgc gggaccccgc aggttggttt ggaaaattgg atcgtgattc 4801 cattctaagg cagttatact ggaccagagg acccaatcat gagaacccct ttgaaagtat 4861 gattccccac tcccagagag caacccagtt aatggccctt cttggggaag cctcgttgca 4921 tggtccccaa ttttacaaga aggtgagtaa aatggtcatc aatgagatca agagtggtgg 4981 tctggagttt tacgtgccca gacaggaggc catgtttaga tggatgagat tttcagacct 5041 cagcacgtgg gagggcgatc gcaatctggc tcccgagaat gtgaatgaag atggcgtcga 5101 atgacgcagc tccatcgaat gatggcgcgg ctggcctcgt accagagatc aaccatgagg 5161 tcatggccat agagcctgtt gcaggggcct ctctagcagc ccctgtcgta ggacaactta 5221 atataattga tccctggatt agaaataatt ttgtacaagc ccctgctgga gaattcactg 5281 tttcgcctag aaatgctcca ggtgaatttt tgttagattt agagttaggt ccagaattga 5341 atccttatct tgctcacctt gcacgcatgt ataatgggca tgcaggtggt atggaggtgc 5401 agatagtgct tgctgggaat gcgttcacag cgggcaaaat actgtttgca gtcataccac 5461 ctggattccc ctatgaaaat ttgtcacctg cacaattgac catgtgccca cacgtagtgg 5521 tggatgtgag gcagctagaa ccaatactgc tgcccatgcc agacatccgt aatacattct 5581 tccattacaa tcagagcaat gggccaaaac tcagattagt agctatgctt tacacacccc 5641 taagggctaa caatgctggt gatgatgtct tcacagtctc ctgcagggtt ctgactcgtc 5701 catcaccaga ttttgaattc aactttcttg tccccccatc tgttgaatct aagactaaag 5761 ctttcactct tccaattctt aagacatctg agatgacaaa ttcaagattt cccataccag 5821 ttgaccagat gtatactagt aggaatgaaa atatagttgt tcaaccacag aatggcaggg 5881 tgacacttga tggagagtta cagggcacaa ccacactcca accggtgtcc atttgtggct 5941 ttcgggggac gctgcagacc aggctggcag atcaaccaaa ttacacatac caagtgcacc 6001 ttgagaattt ggacggctca cccgtcgatc cgacagatga agtcccagcc cccctgggga 6061 cgccagattt tcaggcccaa ctgtttggag ttgtcagcca aaggagtagt gataatgcca 6121 ccagggcaca tgaggctagg gtcaacacca acgatcctac cttcgcgccc cagatcgccc 6181 aggtgcgttt caaatcacca tcccacgact tctttgacaa tgaacccatc aagttcacac 6241 cagttggaat tagtgttgat agcgaaaaca gctacaacca atggctcctt cccaggtatg 6301 gcgggcactt gacaaacaac actcacctgg ccccctctgt gtccccaatg ttccccggcg 6361 agcagattct cttcttccgc tcgttcatgc caggtgccag tggtcatact gatggcgcta 6421 ttgactgcct tttaccacaa gagtgggttg cccacttcta tcaggaggcc gcaactgccc 6481 aaacagatgt ggctctgatt agatttgtga accccgacac aggcagagtg ctatttgaag 6541 ggaagctaca caagcagggc tttataacca tctccaacag tggggaccac cccattgtta 6601 tgcctgctaa tggatacttc aggtttgagg catgggtcaa ccaattttac tctctcgccc 6661 ccgtgggaac cggaagtggg cgcagaagga ttcaataatg gctggagctt ttcttgcggg 6721 tctggctggt gatgtggtga cctctggcat cgggtcgctc atcaatgcag gtgccaatgc 6781 agtaaaccaa aaggttgaat atgatttcaa taggcaactt caagaagctt cttttaaaca 6841 tgacaaggag atgttgaatg ctcaaattaa tgccactacc aaattgcaga gggacatgat 6901 tgccatcaag cagggggttt tgaccgctgg cggcttttcc cccactgatg ctgcaagagg 6961 ttccatcaat gctccaacca ccaaaattct tgactggaat ggatctaggt actgggcgcc 7021 aggatcaatg agaacaacag catactctgg caatttcata tcacagggag ttaagcagcc 7081 tacacccatt gttaaatctg tggaacccca agtacagcaa tctcctgccc cttcttctgt 7141 ttattctgta ggttctgtta agtcacaatc aacacaatca actcaattaa cagggtcagg 7201 gactgtgtca agggcaccca ccccctcaac aaccacaaca ctgtccagaa caagtgagtg 7261 ggtgaggagc cagaatgata ggctgagccc ctttatggga ggcgcactcc agacagcttt 7321 catcacgccc ccatcgagta aggcttcatc ctcatcagga acagtctcaa ccgttcctag 7381 agaaattttg gactcctgga ctcctgtatt taacacacgc aggcagccgc tcttcgccca 7441 catgcgtagg cgaggggagt cacgggctta gtgaaaagaa tgatttggtt agattatatc 7501 tttttcttac ctattctatc ttttaaaaaa aaa //