Typing tool
|
Complete norovirus genomes
OP205537 | GII.17 | ||
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GII.P17 |
ORF1: 1..5108 ORF2: 5089..6711 ORF3: 6711..7490LOCUS OP205537 7490 bp RNA linear VRL 21-JUN-2023 DEFINITION Norovirus GII isolate RIVM-NOV-2016-0128_R02-13_major nonstructural polyprotein (ORF1) gene, partial cds; and VP1 (ORF2) and VP2 (ORF3) genes, complete cds. ACCESSION OP205537 VERSION OP205537.1 KEYWORDS . SOURCE Norovirus GII ORGANISM Norovirus GII Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes; Picornavirales; Caliciviridae; Norovirus; Norwalk virus. REFERENCE 1 (bases 1 to 7490) AUTHORS Schmitz,D., Zwagemaker,F., van der Veer,B., Vennema,H., Bosch,T., Laros,J.F., Koopmans,M.P., de Graaf,M. and Kroneman,A. TITLE Shotgun whole genome sequencing for gastroenteritis surveillance using Norovirus as a model JOURNAL Unpublished REFERENCE 2 (bases 1 to 7490) AUTHORS Schmitz,D., Zwagemaker,F., van der Veer,B., Vennema,H., Bosch,T., Laros,J.F., Koopmans,M.P., de Graaf,M. and Kroneman,A. TITLE Direct Submission JOURNAL Submitted (05-AUG-2022) Center for Infectious Diseases, Rijksinstituut voor Volksgezondheid en Milieu, Antonie van Leeuwenhoeklaan 9, Bilthoven, Utrecht 3721 MA, Netherlands COMMENT ##Assembly-Data-START## Assembly Method :: SPAdes v. v3.11.0 Sequencing Technology :: Illumina ##Assembly-Data-END## FEATURES Location/Qualifiers source 1..7490 /organism="Norovirus GII" /mol_type="genomic RNA" /isolate="RIVM-NOV-2016-0128_R02-13_major" /isolation_source="Human feces" /host="Homo sapiens" /db_xref="taxon:122929" /country="Netherlands" /collection_date="2016-03-30" /note="genotype: GII.17[P17]" gene <1..5108 /gene="ORF1" CDS <1..5108 /gene="ORF1" /codon_start=3 /product="nonstructural polyprotein" /protein_id="UUV60912.1" /translation="KMASNDASAAVAGKNNNNDKEKSSSDSLFANMSVTFKKALGARS KQPPPGETKQIQKPPRPPTPELVKRIPPPPPNGEDEPGVVYKVGEGVSGLPDLTTVVQ PDAQNTAYSVPPLSQREVGEAKEPLPGSILEMWDGEIYHYGLYVERGHVLGVHKPPAA ISLAKIEITPLSLYWRVVYTPQYLIDPGTLKSLSGETFPYTAFDNNCYAFCCWVLDLN DSWLSRRMIQRTTGFFKPYQDWNRKPLPTMDEPKIKKAANAVLCALSSLFTRPIKDII GKLRPLNILNILATCDWTFAGIVESLILLAELFGVFWTPPDVSAMIAPLLGDYEMQGP EDLAVELVPVVMGGIGLVLGFTKEKIGKMLSSAATTLRACKDLGSYGLEILKLVMKWF FPKKEEANELAMVRAIEDAVLDLEAIENNHMTTLLKDKDSLATYMRTLDLEEEKARKL STKSASPDIVGTINALLARIAAARSLVHKAKEELSSRQRPVVVMISGRPGIGKTHLAR ELAKKVASTLSGDQRIGLVPRNGVDHWDAYKGERVVLWDDYGMSNPIQDALRLQELAD TCPLTLNCDRIENKGKVFDSDAIIITTNLANPAPLDYVNFEACSRRIDFLVYADAPDI EKAKRDFPGQPDMWKDHFRPDFSHIKLQLAPQGGFDKNGNTPHGKGVVKSLTIGSLIA RASGLLHERMDEFELQGSDPPTFNFDRNKVAAFRQLAAENKYGLMDTLRVGNQLKSVK TLDELKQAIKNISIKKCQIVYNGCTYTMESDGRGKVVVEKVQNATVQTNNELVGALHH LRSARIRYYVKCFQEAIYSLLQIAGAAFVTSRIVRRMNISNLWSKPPIEEGDEPEDRG GCPKPRDEDDLTIDSRDIKVEGKKGKNKSGRGKKHTAFSSKGLSDEEYDEYKRIREER NGKYSIEEYLQDRDRYYEELAIAKATEEDFCEEEEIKIRQRIFRPTRKQRKEERATLG LVTGSEIRKRNPDDFKPKGKLWADDNRSVDYNERIDFEAPPSVWSRIVNFGTGWGFWV SPSLFITSTHVIPKGITEAFGVPINQIQIHKSGEFCRLRFPKPIRPDVSGMILEEGAP EGTVVSILIKRTTGELMPLAVRMGTHATMKIQGRTVGGQMGMLLTGSNAKSMDLGTTP GDCGCPYIYKRGNDLVVIGVHTAAARGGNTVICATQGSEGEATLEGGDNKGTYCGAPI LGPGNAPKLSTKTKFWRSSNAPLPPGTYEPAYLGGRDPRVKGGPSLQQVMRDQLKPFT EPRGKPPNPNVLESAKKTIINVLEQTIDPPQKWSYAQACASLDKTTSSGYPHHVRKND YWSGESFTGKLADQASKANLMYEEGKHMQPVYTAALKDELVKTDKIYGKIKKRLLWGS DLSTMIRCARAFGGLMDEFKANCITLPIRVGMNMNEDGPIIFEKHSRYRYHYDADYSR WDSTQQRAVLEAALEIMVRFSAEPQLAQIVAEDLLSPSVVDVGDFKIAINEGLPSGVP CTSQWNSIAHWLLTLCALSEVTGLGPDIIQANSMYSFYGDDEIVSTDIKLDPEKLTAK LKEYGLKPTRPDKTEGPLVISEDLNGLTFLRRTVTRDPAGWFGKLDQNSILRQLYWTR GPNHEDPSETMIPHAQRPVQLMALLGESSLHGPSFYSKVSKLVISELKEGGMDFYVPR QESMFRWMRFSDLSTWEGDRNLAPSFVNEDGVE" mat_peptide <1..998 /gene="ORF1" /product="p48" mat_peptide 999..2096 /gene="ORF1" /product="NTPase" mat_peptide 2097..2633 /gene="ORF1" /product="p22" mat_peptide 2634..3032 /gene="ORF1" /product="VPg" mat_peptide 3033..3575 /gene="ORF1" /product="Pro" mat_peptide 3576..5105 /gene="ORF1" /product="RdRp" gene 5089..6711 /gene="ORF2" CDS 5089..6711 /gene="ORF2" /note="major capsid protein" /codon_start=1 /product="VP1" /protein_id="UUV60913.1" /translation="MKMASNDAAPSNDGAAGLVPEGNNETLPLEPVAGAAIAAPVTGQ NNIIDPWIRTNFVQAPNGEFTVSPRNSPGEILLNLELGPDLNPYLAHLSRMYNGYAGG VEVQVLLAGNAFTAGKILFAAVPPNFPVEFLSPAQITMLPHLIVDVRTLEPIMIPLPD VRNTFFHYSNQPNSRMRLVAMLYTPLRSNGSGDDVFTVSCRVLTRPTPDFEFTYLVPP SVESKTKPFSLPILTLSELTNSRFPVPIDSLFTAQNNVLQVQCQNGRCTLDGELQGTT QLLPSGICAFRGRVTAQINQRDRWHMQLQNLNGTTYDPTDDVPAPLGTPDFKGVVFGM VSQRNVGNDAPGSTRAQQAWVSTYSPQFVPKLGSVNLRISDNDDFQFQPTKFTPVGVN DDDDGHPFRQWELPNYSGELTLNMNLAPPVAPNFPGEQLLFFRSFVPCSGGYNQGIID CLIPQEWIQHFYQESAPSQSDVALIRYVNPDTGRTLFEAKLHRSGYITVAHSGDYPLV VPANGHFRFDSWVNQFYSLAPMGTGNGRRRAQ" gene 6711..7490 /gene="ORF3" CDS 6711..7490 /gene="ORF3" /note="minor structural protein; small basic protein" /codon_start=1 /product="VP2" /protein_id="UUV60914.1" /translation="MAGAFIAGLAGDMLTSSVGSLVNAGANAINQKIDFENNKQLQSA SFQHDKEMLQAQVRATKQLQSEMIALKQGVLAAGGFSPTDAARGSIGAPMTKVLDWSG TRYWAPNSTKTTGYSGQFTSSPVHMSSPNVPQSKPAKPRSLAPSSSSSSVYSMYTQST HLTSGSSSNASSASTKLTNLSSGSSQNRTAEWVNQQRSLSPFMSGALNISHVTPPSSR ASSSGTVSTVPKEVLDSWTSAFNTHRQPLFAHLRVRGESRV" ORIGIN 1 tgaagatggc gtctaacgac gcttccgctg ccgttgctgg caaaaacaac aacaacgaca 61 aggaaaaatc ttcaagtgac agcttgtttg ctaacatgtc tgtcactttt aagaaagccc 121 tcggggcgcg gtctaaacaa ccgcccccgg gagaaacaaa acaaatacaa aaaccaccaa 181 ggccaccgac accggaattg gtgaagagaa tacctccacc cccacccaat ggcgaggatg 241 aaccaggggt agtgtacaag gtgggagagg gtgtgtctgg gctgcccgac ctaacaactg 301 tggtacaacc tgacgcacaa aacacagctt atagtgttcc cccacttagc cagagagaag 361 tcggcgaagc taaagaaccg ctgcctggct ccattctgga aatgtgggat ggtgagatct 421 accactatgg gctgtatgtt gagcgggggc atgtgctcgg agtacacaaa ccacctgctg 481 caataagcct tgccaaaatt gaaataacac cgctgtctct ctactggaga gtggtctaca 541 ctccccagta tttgatagat ccaggaactc ttaagagctt gagtggagag actttcccat 601 acacggcctt tgacaacaac tgttatgcct tctgttgttg ggtcctagac ctcaacgact 661 cctggcttag caggagaatg atccaaagaa caactggatt cttcaaacct tatcaggatt 721 ggaacagaaa acccttacca accatggatg aaccgaaaat caagaaggcc gcgaatgctg 781 tcctatgcgc tctctcctca ctcttcacta gacccattaa ggacatcatt ggaaagctta 841 gaccactgaa cattcttaat atactggcaa cctgcgattg gactttcgca ggcatagtgg 901 agtccttgat ccttcttgct gaactctttg gggtgttctg gacaccccca gatgtgtctg 961 cgatgattgc tcccttactc ggtgactacg agatgcaagg ccccgaagac ctggccgtgg 1021 aacttgtgcc cgtggtgatg ggaggaatag gtttggtgtt aggattcacc aaagaaaaga 1081 tcggcaagat gctttcatca gctgcgacca cacttagggc ctgcaaggat ctaggatctt 1141 atggattgga gatactcaaa ttggtcatga agtggttctt ccccaagaag gaggaggcta 1201 acgaactagc catggtgagg gccattgagg atgcagtcct ggatttggag gcaatagaaa 1261 acaatcacat gaccaccctt ctcaaggata aagacagcct ggccacatac atgaggactc 1321 ttgacttgga agaagagaaa gcaaggaaac tgtcaaccaa atcggcgtca cctgacatcg 1381 tgggtacaat aaacgcatta ttggctagga tagcagccgc caggtcactg gtccacaagg 1441 ctaaggagga gctctcgagc agacagagac ctgttgttgt aatgatatca ggtagaccag 1501 gtataggaaa gacccatctg gccagagagc tagccaagaa agttgcgtca acattgtcag 1561 gcgaccaaag gattggactg gtacctagaa atggcgtcga ccattgggac gcctacaagg 1621 gagaaagggt ggttctgtgg gatgattatg gtatgagcaa ccctatacag gacgcactga 1681 ggctccaaga attggctgac acctgtcctc tgaccctaaa ttgtgatagg attgaaaaca 1741 aaggaaaagt gttcgacagt gatgccataa ttataacaac caaccttgca aacccagcac 1801 cactagacta tgtcaacttt gaggcctgct ctagacgcat agacttcttg gtgtatgcag 1861 acgcacctga cattgagaag gctaagcgtg acttccctgg ccaaccagat atgtggaaag 1921 accatttcag gccagacttc tcacacatta aacttcagct ggcaccacag ggaggttttg 1981 acaaaaatgg caacacccca catggcaaag gtgtggtgaa gtccctgacg attggttctc 2041 tgatcgccag ggcctccggc ttgctccacg agagaatgga tgaattcgag ctccaaggct 2101 ctgacccgcc aaccttcaat tttgaccgca acaaagtcgc cgccttcaga caattagcag 2161 ctgaaaacaa atatggtctt atggacacac tgagggtcgg caaccaactg aaaagtgtta 2221 agaccctgga tgagctgaag caggccataa agaacatcag tatcaagaag tgtcagatag 2281 tgtataatgg atgcacctat accatggaat ctgatgggag gggcaaggtt gtggttgaaa 2341 aggtacaaaa cgcaacagtt caaaccaaca atgaacttgt aggggcgctc caccacctga 2401 gatctgcaag gataagatac tatgtcaaat gtttccaaga agccatttac tctctactcc 2461 aaattgctgg tgcagccttc gtcacctcac gcatcgtgag gcgcatgaac atatcaaacc 2521 tctggtcgaa gccacccatc gaggagggtg atgagcctga agacagagga ggatgcccca 2581 agcccaggga tgaagatgac ctcactattg actctagaga cattaaagtg gaagggaaga 2641 agggcaagaa caagtctggc cggggcaaga aacacacagc cttctcttcc aagggcctca 2701 gtgatgaaga gtacgatgag tacaagagaa tcagagagga gagaaatggc aaatactcaa 2761 tagaggaata cctccaagat agggacagat actatgaaga gcttgccatt gctaaggcca 2821 ctgaggagga cttctgtgag gaggaggaga tcaaaatccg ccagagaatc ttccgaccca 2881 ccaggaagca gcggaaagag gaaagggcca cgcttgggct tgtcacagga tcggaaatca 2941 gaaagaggaa tccagatgac tttaaaccaa aaggaaaatt gtgggctgat gacaacagga 3001 gcgtggatta caatgagagg atagattttg aggctccccc gagtgtttgg tctaggatag 3061 tcaactttgg cacaggctgg ggattctggg tttctccaag tctctttata acttcaacac 3121 acgtcatacc aaaaggaatc actgaggcct ttggagtgcc cataaaccaa atccaaattc 3181 acaaatctgg agaattttgc cgcttgcggt ttccaaagcc aattagacca gacgtgagtg 3241 ggatgatctt ggaagagggc gcccctgaag gcactgttgt gtctattctc atcaaaagga 3301 caacagggga gctgatgcct cttgcagtca gaatggggac tcatgccaca atgaaaatcc 3361 aaggtagaac ggtgggtggt cagatgggta tgcttctcac tggctcaaat gctaaaagca 3421 tggatctagg cacaacgcca ggtgactgcg gatgcccata catatacaaa aggggcaatg 3481 accttgtggt catcggggtg cacactgcag cagctcgtgg aggcaacacg gtcatatgtg 3541 ccacacaggg aagtgaaggt gaagccactc ttgaaggagg tgacaacaag ggtacctatt 3601 gtggagcccc cattttggga cctggcaatg caccaaaatt gagcacaaag acaaaattct 3661 ggagatcctc taacgcaccg cttcccccag gtacttatga accagcatac cttggtggga 3721 gagacccgcg cgtgaaggga ggcccatctc tgcaacaagt tatgagagac caacttaaac 3781 cttttacaga gcccagaggg aagccaccaa acccaaatgt cttagagtca gcaaagaaga 3841 ctatcatcaa tgttctggaa caaaccattg acccccctca aaaatggtca tatgcccaag 3901 cttgtgcatc cctcgacaag acaacctcca gtggataccc gcaccacgtc cggaagaatg 3961 actattggag tggtgaatcc ttcacaggaa aacttgcaga tcaggcttca aaagcgaatc 4021 tcatgtatga ggaaggcaag cacatgcaac cagtttacac cgcagcactc aaagacgagc 4081 tcgtgaaaac tgacaaaatt tatggcaaaa tcaagaaaag actcctgtgg ggttctgacc 4141 tctccacaat gattcgatgc gccagagcat ttggtggtct catggatgaa ttcaaagcaa 4201 attgtattac actccctatc agagttggta tgaatatgaa tgaagatggt cccataatat 4261 ttgagaaaca ctccaggtac aggtaccact atgatgctga ttactcccgc tgggactcca 4321 cacaacagcg ggcagtgctg gaagcggcac ttgaaatcat ggtgagattt tctgctgagc 4381 cacagctggc acaaatagtg gcagaggacc tgctgtcacc aagtgtggtt gatgtgggcg 4441 atttcaaaat cgctatcaat gaaggcctac catctggcgt gccttgcacc tcacaatgga 4501 attctattgc ccactggtta cttaccttgt gtgccctttc tgaagtgaca ggattaggtc 4561 ctgacatcat acaagctaac tccatgtact ctttctatgg tgatgatgag attgtgagca 4621 cagacataaa attggaccca gagaaattga ccgcaaagct caaagaatat ggccttaaac 4681 ccactcggcc cgacaaaact gaggggccgt tggtgattag tgaggacctg aatgggttga 4741 ctttcctccg ccgaacagtc acccgtgatc cagcaggttg gtttggaaag ttggaccaaa 4801 actccatcct caggcagttg tactggacaa gaggacccaa ccatgaagac cccagtgaga 4861 ccatgatacc acacgcacaa agacctgtgc agctcatggc actactagga gaatcctccc 4921 tacatggacc ctcattttac agcaaggtta gcaaattagt catatctgaa cttaaagagg 4981 gaggaatgga tttttatgtg cccagacaag agtcaatgtt cagatggatg aggttctcag 5041 atctaagcac atgggagggc gatcgcaatc tggctcccag ttttgtgaat gaagatggcg 5101 tcgaatgacg ccgctccatc taatgatggt gctgctggtc tcgtaccaga gggcaacaac 5161 gagacccttc ccctagaacc agttgcgggc gcagctatag ccgcacccgt cactggccaa 5221 aataacataa ttgacccctg gattagaaca aattttgtgc aagcaccaaa tggagagttc 5281 acagtgtcac ccagaaactc tcctggagaa attttattaa acttagagtt gggccctgat 5341 ttgaaccctt atttggctca tttgtcaagg atgtacaatg ggtatgctgg tggagtggaa 5401 gttcaggttc tcctggcagg gaacgcgttc actgccggaa agatcctctt cgccgccgtc 5461 ccgccaaatt tcccagtgga attcttgagc ccagcccaga tcacaatgct cccacattta 5521 atagtagatg ttaggactct tgaaccaatt atgatcccac tccctgatgt taggaataca 5581 ttcttccatt atagtaacca gcctaacagc cgcatgagat tagtggctat gctctatacc 5641 ccactcagat ctaatggctc aggtgatgat gtctttactg tctcttgcag ggttttgact 5701 aggcctactc ctgattttga gttcacttat ttagtgccac cttctgttga atctaaaact 5761 aagccttttt ccttacctat tttaaccctt tctgagctca caaattcgag gttcccagtc 5821 cccatcgatt cgcttttcac cgcccagaat aatgtgttgc aggtgcagtg tcaaaatggc 5881 aggtgtacac ttgatggtga gttacaaggc acaacccagt tgctcccatc tggcatctgt 5941 gcattcagag gacgggtgac agcacaaatt aaccaacgtg acaggtggca catgcaactg 6001 caaaacctca atggtacaac atatgatcca actgatgatg tgccagcccc gctgggtaca 6061 cctgacttca agggcgtcgt gtttgggatg gtaagccaaa gaaatgtggg taatgatgca 6121 cctggctcaa ccagagccca acaggcgtgg gtttcaacct atagccccca atttgtcccc 6181 aaattaggtt ctgtcaatct tagaattagt gataatgatg atttccaatt ccagccgaca 6241 aaattcacac cagtgggcgt caatgatgac gatgacggcc acccgttcag acaatgggaa 6301 ctaccaaact attcagggga gcttaccttg aatatgaatc ttgccccccc agttgctcca 6361 aattttcctg gtgaacaatt gttattcttc aggtctttcg tgccatgctc aggaggttac 6421 aaccaaggta ttatagattg tcttattccc caagaatgga tccaacactt ctatcaggaa 6481 tcagcaccct cccagtcaga cgtggcccta atcaggtatg tcaaccccga tacgggacgt 6541 acactgtttg aagcaaaatt gcacagatct ggttacatta ctgtggctca ctctggagac 6601 tatcctcttg ttgttccagc taatggacac tttagatttg actcttgggt aaatcagttt 6661 tactcactcg ccccaatggg aactgggaat gggcgaagga gggctcagta atggctgggg 6721 ctttcattgc aggattggca ggcgacatgc tcacgtcatc tgtgggctcc cttgtgaacg 6781 caggggcaaa cgccatcaac caaaagatag actttgaaaa caacaaacaa ctccagtctg 6841 cttcctttca gcatgataaa gagatgctcc aagcgcaggt gagggcaacc aagcagctgc 6901 aatctgaaat gatagcccta aaacaggggg tcttggccgc aggcggcttt tcccccactg 6961 atgcagcaag gggatccatt ggtgcaccca tgacaaaggt gcttgactgg tctggcactc 7021 gatactgggc gcccaattcc acaaagacaa ctggctattc gggacaattc acctcttcac 7081 ctgtgcatat gtctagccca aatgttccac aatcaaaacc tgcaaagcct aggtctctag 7141 ctccttcctc ttcttctagc agtgtttata gtatgtatac tcaatctact catttaacat 7201 ctggctcttc tagtaatgct tcttctgcct ccacaaaatt gacaaattta agctctggct 7261 cctctcaaaa cagaacagca gagtgggtaa atcaacagag aagtcttagc cctttcatga 7321 gtggcgcact taacatctca catgtcacgc caccctcaag tagggcttcc agttctggga 7381 cggtctcgac cgtgcccaag gaagttttgg actcctggac gtctgcgttt aacacacaca 7441 gacagccgct cttcgcacac ctcagagtga ggggggagtc acgtgtttag //