Typing tool
|
Complete norovirus genomes
MW581012 | GII.4 Yerseke | ||
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GII.P4 New Orleans |
ORF1: 5..5104 ORF2: 5085..6707 ORF3: 6707..7468LOCUS MW581012 7479 bp RNA linear VRL 01-MAR-2022 DEFINITION Norovirus GII isolate Hu/NL/2018/GII.4[P4]/Rotterdam/17016 nonstructural polyprotein (ORF1), VP1 (ORF2), and VP2 (ORF3) genes, complete cds. ACCESSION MW581012 VERSION MW581012.1 KEYWORDS . SOURCE Norovirus GII ORGANISM Norovirus GII Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes; Picornavirales; Caliciviridae; Norovirus; Norwalk virus. REFERENCE 1 (bases 1 to 7479) AUTHORS de Graaf,M. TITLE Treatment of chronic norovirus infection: lessons learned from a patient with common variable immunodeficiency JOURNAL Unpublished REFERENCE 2 (bases 1 to 7479) AUTHORS de Graaf,M. TITLE Direct Submission JOURNAL Submitted (08-FEB-2021) Viroscience, Erasmus MC, Wytemaweg 80, Rotterdam 3015CN, Netherlands COMMENT ##Assembly-Data-START## Assembly Method :: SPAdes v. v3.11.0 Sequencing Technology :: Illumina ##Assembly-Data-END## FEATURES Location/Qualifiers source 1..7479 /organism="Norovirus GII" /mol_type="genomic RNA" /isolate="Hu/NL/2018/GII.4[P4]/Rotterdam/17016" /isolation_source="feces" /host="Homo sapiens" /db_xref="taxon:122929" /country="Netherlands" /collection_date="29-May-2018" /note="genotype: GII.4[P4]" gene 5..5104 /gene="ORF1" CDS 5..5104 /gene="ORF1" /codon_start=1 /product="nonstructural polyprotein" /protein_id="QRI43772.1" /translation="MKMASNDAFTAAVANSNNDNAKSSSDGVFSNMAVTFKRALGARP KQPPLREKPQRPPRPPTPELVKNIPPPPPNGEDEMVVSYSVKDGVSGLPDLSTVRQPE ETNTAFSVPPLNQRENRDAKEPLTGTILEMWDGEIYHYGLYVERGLVLGVHKPPAAIS LAKIELTPLSLYWRPVYTPQYLISPDTLKRLSGETFPYVAFDNNCYTFCCWVLDLNDS WLSRRMIQRTTGFFRPYQDWNRKPLPTMDDSKIKKVANIFMCALSSLFTRPIKDIIGK LKPLNILNILASCDWTFAGIVESLILLAELFGVFWTPPDVSAMIAPLLGDYELQGPED LAVELVPVVMGGIGLVLGFTKEKIGKMLSSAASTLRACKDLGAYGLEILKLVMKWFFP KKEEANELAIVRSIEDAVLDLEAIENNHMTTLLKDKDTMATYMRVLDLEEEKARKLST KSASPDIVGTINALLARIAAARSLVHRAKEELSSRPRPVVLMISGKPGIGKTHLAREV AKRIAASLTGDQRVGLIPRNGVDHWDAYKGERVVLWDDYGMSNPIHDALRLQELADTC PLTLNCDRIENKGKVFDSDVIIITTNLANPAPLDYVNFEACSRRIDFLVYAEAPEVEK AKRDFPGQPDMWKNAFSSDFSHIRLSLAPQGGFDKNGNTPHGKGVMKTLTTGSLIARA SGLLHERLDEFELQGPALTTFNFDRNKVLAFRQLAAENKYGLMDTMRVGKQLKDVRTM PELKQAIKNISIKKCQIVYGGCTYILESDGKGNVKVDRVQSAAVQTNNELAGALHHLR SARIRYYVKCVQEALYSIIQIAGAAFVTSRIAKRMNIQNLWSKPQVEDTEEITSKDGC PMPKDEEEFVVSSDDIKPEGKKGKNKTGRGKKHTAFSSKGLSDEEYDEYKRIREERNG KYSIEEYLQDRDKYYEELAIARATEEDFCEEEEAKIRQRIFRPTRKQRKEERASLGLV TGAEIRKRNPDDFKPKGKLWADDDRGVDYNEKLSFEAPPSIWSRIVNFGSGWGFWVSP SLFITSTHVIPQGAKEFFGVPIKQIQVHKSGEFCRLRFPKPIRTDVTGMILEEGAPEG TVVTLLIKRPTGELMPLAARMGTHATMKIQGRTVGGQMGMLLTGSNAKSMDLGTTPGD CGCPYIYKRGNDYVVIGVHTAAARGGNTVICATQGSEGEATLEGGDNKGTYCGAPILG PGSAPTLSTKTKFWRSSTAPLPPGTYEPAYLGGKDPRVKGGPSLQQVMREQLKPFTEP RGKPPKPSVLEAAKKTIINVLEQTIDPPEKWSFAQACASLDKTTSSGHPHHVRKNDCW NGESFTGKLADQASKANLMYEEGKNMTPVYTAALKDELVKTDKIYGKIKKRLLWGSDL ATMIRCARAFGGLMDELKAHCVTLPVRVGMNMNEDGPIIFERHSRYTYHYDADYSRWD STQQRAVLEAALEIMVKFSPEPHLAQVVAEDLLSPSVVDVGDFTISINEGLPSGVPCT SQWNSIAHWLLTLCALSEVTNLSPDIIQANSLFSFYGDDEIVSTDIKLDPEKLTTKLR EYGLKPTRPDKTEGPLVISEDLNGLTFLRRTVTRDPAGWFGKLEQSSILRQMYWTRGP NHGDPSETMIPHSQRPIQLMSLLGEAALHGPAFYSKISKLVIAELKEGGMDFYVPRQE PMFRWMRFSDLSTWEGDRNLAPSFVNEDGVE" mat_peptide 5..994 /gene="ORF1" /product="p48" mat_peptide 995..2092 /gene="ORF1" /product="NTPase" mat_peptide 2093..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..6707 /gene="ORF2" CDS 5085..6707 /gene="ORF2" /note="major capsid protein" /codon_start=1 /product="VP1" /protein_id="QRI43773.1" /translation="MKMASSDANPSDGSSANLVPEVNNEVMALEPVAGAAIAAPVAGQ QNVIDPWIRNNFVQAPGGEFTVSPRNAPGEILWSAPLGPDLNPYLSHLARMYNGYAGG FEVQVILAGNAFTAGKIIFAAVPPNFPTEGLSPSQITMFPHVITDVRQLEPVMIPLPD VRNNFYHYNQTNDPTLKLVAMLYTPLRANNAGDDVFTVSCRVLTRPSPDFDFIFLVPP SVESRTKPFSIPILTVEEMTNSRFPIPLERLFTGPSNAFVVQPQNGRCTIDGVLQGTT QLSPVNICTFRGDVTHISGSRNFTMNLASQNWNSYDPTEEIPAPLGTPDFVGKIQGML TQTTRGDGSTRAHKATVYTGSAPFSPKLGRIQFETDTDRDLEANQNTKFTPVGVIQDG GTAARNEPQQWVLPSYSGRSTHNVHLAPAVAPTFPGEQLLFFRSTMPGCSGYPNMDLD CLLPQEWVQHFYQEAAPAQSDVALLRFVNPDTGRVLFECKLHKSGYVTVAHTGQHDLV IPPNGYFRFDSWVNQFYTLAPMGNGTGRRRAL" gene 6707..7468 /gene="ORF3" CDS 6707..7468 /gene="ORF3" /note="minor structural protein; small basic protein" /codon_start=1 /product="VP2" /protein_id="QRI43774.1" /translation="MAGAAIAGLASDVLSSGLGSLINAGAGVINQKVDFENNRKLQQD SFQFSSKLQQASFQHDKEMLQSQIEATKRLQQELMKLKQAMLLEGGFSGTDAARGAIN APMTKALDWSGTRYWAPDARTTTSNAGRFSTPQPSGALPGRARAAAPTRGSSSMSSIS SSATSVYSNQTTSTRLSSTAGSGTSVSSLPSTARTRSWVEGQNRGFTPPSSRSSSQGT VSTVPKEVLDSWTGAFNTRRQPLFAHIRRRGESRV" ORIGIN 1 gtgaatgaag atggcgtcta acgacgcttt caccgccgct gttgccaaca gcaacaacga 61 caacgcaaaa tcttcaagtg acggagtgtt ttctaacatg gctgtcactt ttaaacgagc 121 cctcggggcg cggcctaaac agccccccct gagggaaaaa ccacaaagac ccccacgacc 181 acctacccca gaactggtca aaaacatccc ccctccccca cccaacgggg aggatgaaat 241 ggtggtttct tacagtgtca aagatggtgt ttccggcttg cctgacctct ccaccgtcag 301 gcaaccggaa gaaaccaaca cggcatttag tgtccctcca ctcaatcaga gggagaacag 361 agatgctaag gagccactca ctgggacaat tctggaaatg tgggatgggg agatctacca 421 ttatggcctg tacgtggagc gaggtcttgt actaggtgtg cacaaaccac cagctgccat 481 cagccttgct aagatagagc taacaccact ctccttatac tggaggcctg tgtacactcc 541 tcagtacctc atctctccgg acactctcaa gagattgtcc ggagaaacat tcccctacgt 601 ggcctttgac aacaactgtt acaccttctg ttgctgggtc ctggatctaa atgattcgtg 661 gctgagcagg agaatgattc agagaacaac tggcttcttc aggccctacc aagactggaa 721 caggaagccc cttcccacca tggatgactc taaaataaag aaggtggcca acatattcat 781 gtgtgctctg tcctcgctgt tcaccaggcc cataaaagac ataataggga agttaaagcc 841 tctcaacatc ctcaacatct tggcctcatg tgattggact tttgcgggca tagtggagtc 901 cctgatactc ttggcagaac tctttggagt tttctggaca cccccagatg tgtctgcgat 961 gattgccccc ttactcggcg actacgagct acaagggcct gaggaccttg cagtggagct 1021 cgtccccgtg gtaatggggg gaattggttt ggtgctggga ttcaccaaag agaagattgg 1081 gaaaatgctg tcatcagcag cgtccacctt gagagcttgc aaagaccttg gtgcatatgg 1141 actagagatc ctgaagctgg ttatgaaatg gttcttcccg aaaaaggagg aggcaaatga 1201 gctggctata gtgaggtcca tcgaggatgc agtcctggac ctcgaggcaa ttgaaaacaa 1261 ccatatgacc accttgctca aggacaaaga cactatggca acctacatga gggtgcttga 1321 cctcgaagag gagaaagcca ggaaactctc aaccaagtcc gcctcacccg acatcgtggg 1381 cacgatcaac gctctcctgg cgagaattgc tgccgcacgt tctctggtgc atcgcgcaaa 1441 ggaggagctt tccagcagac caagacctgt ggtgctgatg atatcaggca agccaggaat 1501 aggtaagacc cacctcgcta gggaagtggc caagaggatc gcagcctccc ttacaggaga 1561 ccagcgcgtg ggcctcattc cacgcaatgg cgtcgaccat tgggacgcgt acaaagggga 1621 gagagtcgtt ctatgggacg actatggaat gagcaaccct atccacgatg ccctcaggct 1681 gcaagaactc gctgacacct gccccctcac tctaaactgt gacaggattg aaaacaaagg 1741 aaaggtcttt gacagtgatg tcatcattat caccactaac ctggccaacc cagcaccatt 1801 ggactatgtc aactttgaag catgttcgag gcgcatcgac ttcctcgtgt atgcagaagc 1861 ccctgaagtt gaaaaggcga agcgtgactt cccgggccag cctgacatgt ggaagaacgc 1921 tttcagttct gacttctcac acataagact gtcactggcc ccacagggtg gtttcgacaa 1981 gaacgggaac accccacacg gaaagggcgt catgaaaacc ctcaccactg gctccctcat 2041 cgcccgggca tcagggctgc ttcatgagag gctagatgag tttgaactac agggcccagc 2101 cctcaccacc ttcaatttcg atcgcaacaa agtgctcgcc ttcagacaac ttgctgctga 2161 gaataaatat ggactgatgg acacaatgag ggtcgggaaa cagctcaagg acgtcagaac 2221 catgccagag ctcaaacaag caatcaagaa catttcaatc aagaagtgcc aaatagtgta 2281 tggtggttgc acctacattc ttgagtctga tggtaagggc aatgtgaagg tcgacagggt 2341 ccagagcgcc gccgtgcaga ccaacaacga gctggccggt gccctgcacc acttgaggag 2401 cgctagaatc aggtactatg tcaagtgtgt ccaagaggcc ttgtattcca tcatccaaat 2461 tgctggggct gcattcgtca cctctcgcat cgccaagcgc atgaacatac aaaatctgtg 2521 gtccaagcca caggtggaag acacagagga gatcaccagt aaggacgggt gcccaatgcc 2581 taaggacgaa gaggagttcg tcgtttcatc cgacgacatc aaacctgagg gcaagaaggg 2641 gaagaacaag actggccgcg gcaagaaaca cacagctttt tcaagcaaag gcctcagtga 2701 tgaagagtac gacgagtaca agaggatcag ggaggaaagg aatggcaagt actccataga 2761 agaatacctc caggacaggg acaagtacta tgaggagttg gccattgcca gggcgaccga 2821 ggaagacttc tgtgaagagg aggaggccaa gatccggcaa aggatcttca ggccaacgag 2881 gaaacaacgc aaggaggaga gagcctctct cggtctggtc acaggcgctg aaatcaggaa 2941 aaggaaccca gatgacttca aacctaaggg aaaattgtgg gctgatgatg acaggggtgt 3001 ggactacaat gagaaactca gcttcgaggc cccaccaagc atctggtcga gaatagtcaa 3061 ctttggctca ggctggggtt tctgggtctc ccccagtttg ttcataacat caacccatgt 3121 cataccccag ggtgcaaagg agttctttgg agtgcccatc aaacaaatac aggtgcacaa 3181 gtcaggcgag ttctgtcgct tgagattccc aaaaccaatc aggactgatg tgacgggcat 3241 gatcttagaa gagggcgcac ctgagggcac cgtggtcaca ctactcatca aaaggcccac 3301 tggggagctc atgcccctgg cagctaggat ggggacccat gcgaccatga agatccaagg 3361 gcgcactgtt ggaggccaga tgggcatgct cctgacggga tccaacgcca agagcatgga 3421 cctgggtact acaccaggtg actgtggctg cccctatatc tacaagagag gtaatgacta 3481 tgtggtcatt ggagtccaca cggctgccgc acgtggagga aacactgtca tatgtgccac 3541 ccaggggagt gaaggagagg ccacacttga aggtggtgac aacaagggga catactgtgg 3601 tgcaccaata ttaggcccag ggagtgcccc aacactcagc accaaaacca aattttggag 3661 atcgtccaca gcaccgctcc cacctggcac ctatgaacca gcctatcttg gtggcaagga 3721 ccctagagtc aagggtggcc cttcactgca gcaagtcatg agggaacagc tgaagccatt 3781 cacagaacca aggggcaaac caccaaagcc aagtgtgctg gaggctgcca agaagaccat 3841 catcaatgtc cttgagcaaa cgattgaccc acccgagaaa tggtcgttcg cacaagcctg 3901 cgcgtccctt gacaagacca cttccagtgg tcatccgcac cacgtgcgga aaaacgactg 3961 ctggaacggg gagtccttca caggcaagtt agcagaccag gcttccaagg ccaacctgat 4021 gtatgaagaa gggaagaaca tgaccccagt ctacacagcc gcgctcaagg atgagctggt 4081 caagactgac aagatttatg gtaaaatcaa gaagaggctg ctctggggct cggacttggc 4141 gaccatgatc cggtgtgctc gagcgttcgg aggcctaatg gatgagctca aagctcactg 4201 tgtcacactc cccgttaggg ttggtatgaa tatgaatgag gatggcccca tcatcttcga 4261 gaggcactcc aggtacacat accactatga tgctgactac tcacggtggg actcaacaca 4321 acagagggcc gtgttggaag cagctctaga aatcatggtc aaattctccc cagaaccaca 4381 cttggctcag gtagtcgcag aagacctcct ttctcccagc gtggtggacg tgggcgactt 4441 cacaatatca atcaacgagg gtcttccctc tggggtgccc tgcacctccc aatggaactc 4501 catcgcccac tggctcctca ctctctgtgc gctctctgaa gtcacaaact tatcccctga 4561 catcatacag gccaactccc tcttctcctt ctacggagat gatgaaattg tcagcacaga 4621 cataaaattg gatccagaga aattgacaac aaagctcaga gagtacggat tgaaaccaac 4681 tcgccctgac aaaactgaag gacctcttgt catctctgaa gacctgaatg gcctgacctt 4741 cctgcggaga actgtgaccc gtgacccagc tggttggttt ggaaaactgg agcaaagctc 4801 aatactcagg caaatgtact ggactagggg ccccaaccac ggagacccat ctgaaacaat 4861 gattccacac tcccaaaggc ccatacaatt gatgtcccta ctgggggagg ccgctctcca 4921 cggcccagcc ttttacagca aaatcagcaa gctggtcatt gcagagctaa aggaaggtgg 4981 catggatttt tacgtgccta gacaagagcc aatgttcaga tggatgaggt tctcagatct 5041 gagcacgtgg gagggcgatc gcaatctggc tcccagtttt gtgaatgaag atggcgtcga 5101 gtgacgccaa cccatctgat gggtcctcag ccaacctcgt cccagaggtc aacaatgagg 5161 ttatggcttt ggagcccgta gccggcgccg ctattgcggc acctgtggcg ggccaacaaa 5221 atgtaattga cccctggatt agaaataatt ttgtacaagc ccctggtgga gagtttacag 5281 tatcccctag aaacgctcca ggtgaaatac tatggagcgc acccttgggc cctgatttga 5341 acccctacct ttcccatttg gctagaatgt acaatggcta tgcaggtggc tttgaagtgc 5401 aggtaatcct cgcggggaac gcgttcaccg ctggaaagat catatttgca gcagtcccac 5461 caaattttcc aactgaaggt ttgagcccca gccagatcac tatgttcccc catgtgataa 5521 cagatgttag gcaattggaa cctgtgatga tccccctacc cgatgttagg aacaatttct 5581 accattacaa ccagacaaat gaccccaccc tcaaattggt agcaatgttg tacacaccac 5641 tcagggctaa taatgccggg gacgatgtct tcacagtctc ttgtcgagtt ctcacgagac 5701 catcccccga ttttgatttc atatttctgg tgccaccctc agttgaatca agaactaaac 5761 cattctctat cccaattcta actgttgagg agatgaccaa ttcaaggttc cccattcccc 5821 tggaaaggct gttcacgggc cccagcaatg cctttgttgt ccaaccacaa aatggcaggt 5881 gcacgattga tggcgtgctc caaggtacca cccaactgtc ccctgtcaac atctgcactt 5941 tcagagggga tgtcacccac atctcaggca gtcgtaactt cacaatgaat ttggcctccc 6001 aaaactggaa cagttacgac ccaacagaag aaatcccagc ccctctggga accccagatt 6061 tcgtggggaa gatccaaggc atgctcaccc aaaccacaag gggagatggc tcgacccgtg 6121 ctcacaaagc cacagtgtac actgggagcg cccccttttc cccaaaattg ggcagaatcc 6181 agtttgaaac cgacacggac cgtgaccttg aagccaacca aaacacaaag ttcaccccag 6241 tcggtgtcat ccaggatggc ggcaccgccg cccgaaatga accccagcaa tgggtgctcc 6301 caagctactc gggcagaagc actcacaacg tgcacctggc ccccgctgtg gcccccacct 6361 tcccgggcga gcagctcctc ttcttcagat ccaccatgcc cggatgcagc gggtacccca 6421 acatggattt ggactgcctg ctccctcagg agtgggtgca gcacttctac caagaggcag 6481 ccccagcaca atctgatgtg gctttgttga gatttgtgaa tccagataca ggcagagttt 6541 tgtttgagtg caagcttcat aaatcaggct atgtcacagt ggctcacact ggtcaacatg 6601 atttggttat cccccccaat ggctatttta gatttgattc ctgggtcaac caattctaca 6661 cgcttgcccc catgggaaat ggaacggggc gtagacgtgc attgtaatgg ctggagccgc 6721 cattgctgga ttggcatccg atgtccttag ctctggactt ggttccctaa tcaatgctgg 6781 ggctggggtc atcaaccaaa aagttgattt tgagaacaac agaaaattgc agcaagattc 6841 cttccaattt agcagtaaat tgcagcaggc ttcctttcaa catgacaaag agatgctcca 6901 atcacaaatt gaggccacca aaaggttgca acaggaactg atgaagctca agcaagcaat 6961 gctcctagag ggcgggttct ctgggacaga cgcagctcgt ggggcaatca acgcccccat 7021 gacaaaagct ctggactgga gcgggacaag gtactgggct cccgatgcta ggaccacaac 7081 atccaatgca ggccgcttct ctacccccca accctcgggg gcgctgccag gaagagctag 7141 ggctgccgcc cctacccggg gttcctccag catgtcttct atctcctctt ctgctacctc 7201 tgtgtattca aatcaaacca cttcaacgag gcttagttct acagctggtt ctggaactag 7261 tgtctcgagc ctcccgtcaa ctgcaaggac taggagttgg gtcgagggtc agaatagggg 7321 tttcacccca ccatctagca gatcctccag ccaaggcaca gtctcaaccg tgcccaaaga 7381 agttttggac tcctggactg gcgctttcaa cacgcgcagg cagcctctct tcgcccacat 7441 tcgcaggcga ggggagtcac gggtgtaaag tgaaaagac //