Typing tool
|
Complete norovirus genomes
MW559990 | GII.4 | ||
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GII.P31 |
ORF1: 1..5100 ORF2: 5081..6703 ORF3: 6703..7443LOCUS MW559990 7443 bp RNA linear VRL 22-FEB-2021 DEFINITION Norovirus GII isolate Hu/GII.4/P31/004/2019/KEN nonstructural polyprotein (ORF1) and VP1 (ORF2) genes, complete cds; and VP2 (ORF3) gene, partial cds. ACCESSION MW559990 VERSION MW559990.1 KEYWORDS . SOURCE Norovirus GII ORGANISM Norovirus GII Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes; Picornavirales; Caliciviridae; Norovirus; Norwalk virus. REFERENCE 1 (bases 1 to 7443) AUTHORS Lambisia,A.W., de Laurent,Z., Nokes,J.D. and Agoti,C.N. TITLE Near complete genomes of five human norovirus GII.4 recovered from diarrheal stool samples of hospitalized children in coastal Kenya in 2019 JOURNAL Unpublished REFERENCE 2 (bases 1 to 7443) AUTHORS Lambisia,A.W., de Laurent,Z., Nokes,J.D. and Agoti,C.N. TITLE Direct Submission JOURNAL Submitted (03-FEB-2021) Bioscience, KEMRI WELLCOME TRUST, KILIFI, KILIFI, KILIFI 230-80108, Kenya COMMENT ##Assembly-Data-START## Assembly Method :: SPAdes v. v3.13.2 Sequencing Technology :: Illumina ##Assembly-Data-END## FEATURES Location/Qualifiers source 1..7443 /organism="Norovirus GII" /mol_type="genomic RNA" /strain="KLF_NOV_004" /isolate="Hu/GII.4/P31/004/2019/KEN" /isolation_source="human stool" /host="Homo sapiens" /db_xref="taxon:122929" /country="Kenya" /collection_date="09-May-2019" /note="genotype: GII.4" gene 1..5100 /gene="ORF1" CDS 1..5100 /gene="ORF1" /codon_start=1 /product="nonstructural polyprotein" /protein_id="QRF49927.1" /translation="MKMASNDASAAVAANSNNDIAKSSSDGVFSNMAVTFKRALGARP KQPPPKEIPPKPPRPPTPELVRKIPPPPPNGEDELVVSYSAKDGISGLPELTTVSQPE EINTAFSVPPLNQRENRDAKEPLTGTIIEMWDGEIYHYGLYEERGLILGVHKPPAAIS LAKVELTPLSLFWRPVYTPQYLISPDTLRRLHGESFPYTAFDNNCYAFCCWVLDLNDS WFSRRMIQRTTGFFRPYQEWNRKPLPTMDDSKLKKVANIFLCTLSSLFTRPIKDIIGK LKPLNILNILATCDWTFPGIVESLILLAELFGVFWTPPDVSAMIAPLLGDYELQGPED LAVELVPVVMGGIGLVLGFTKEKIGKMLSSAASTLRACKDLGAYGLEILKLVMKWFFP KKEEANELAMVRSIEDAVLDLEAIENNHMTTLLKDKDSLATYMRTLDHEEEKARKLST KSASPDIVGTINSLLARIAAARSLVHRAKEELSSRPRPVVVMISGKPGIGKTHLAREL AKKIAASLTGDQRVGLIPRNGVDHWDAYKGERVVLWDDYGMSNPIHDALRLQELADTC PLTLNCDRIENKGKVFDSDAIIITTNLANPAPLDYVNFEACSRRIDFLVYAEAPEVEK AKRDFPGQPDMWKNAFSPDFSHIKLALAPQGGFDKNGNTPHGKGVMKTLTTGSLIARA SGLLHERLDEYELQGPALTTFNFDRNKILAFRQLAAENKYGLMDTMRVGKQLKDVRTM PDLKQALKNVAIKKCQIVYNGSTYTLEADGKGSVKVDKVQNATVQTNNELAGALHHLR CARIRYYVKCVQEALYSIIQIAGAAFVTTRIAKRMNIQNLWSKPQVEDTEETASKDGC PKPKDDEEFVVSSDDIKAEGKKGKNKSGRGKKHTAFSSKGLSDEEYDEYKRIREERNG KYSIEEYLQDRDKYYEEVAIARATEEDFCEEEEAKIRQRIFRPTRKQRKEERASLGLV TGSEIRKRNPEDFKPKGKLWADDDRSVDYNEKLNFEAPPSIWSRIVNFGSGWGFWVSP SLFITSTHVIPQGTKEFFGVPIKQIQIHKSGEFCRLRFPKPIRTDVTGMILEEGAPEG TVVTLLIKRPTGELMPLAARMGTHATMKIQGRTVGGQMGMLLTGSNAKSMDLGTTPGD CGCPYIYKRGNDYVVIGVHTAAARGGNTVICATQGSEGEATLEGGDNKGTYCGAPILG PGSAPKLSTKTKFWRSSTTPLPPGTYEPAYLGGKDPRVKGGPSLQQVMRDQLKPFTEP RGKPPRPNVLEAAKKTIINVLEQTIDPPQKWSFAQACASLDKTTSSGHPHHVRKNDCW NGDSFTGRLADQASKANLMFEEGKNMTPVYTGALKDELVKTDKIYGKIKKRLLWGSDL ATMIRCARAFGGLMDELKAHCVTLPVRVGMNMNEDGPIIFEKHSRYKYHYDADYSRWD STQQRDVLAAALEIMVKFSPEPHLAQVVAEDLLSPSVMDVGDFQISISEGLPSGVPCT SQWNSIAHWLLTLCALSEVTDLSPDIIQANSLFSFYGDDEIVSTDIKLDPEKLTAKLK EYGLKPTRPDKTEGPLVISEDLDGLTFLRRTVTRDPAGWFGKLEQSSILRQMYWTRGP NHEDPSEAMIPHSQRPIQLMSLLGEAALHGPAFYSKISKLVIAELKEGGMDFYVPRQE PMFRWMRFSDLSTWEGDRNLAPSFVNEDGVE" mat_peptide 1..990 /gene="ORF1" /product="p48" mat_peptide 991..2088 /gene="ORF1" /product="NTPase" mat_peptide 2089..2625 /gene="ORF1" /product="p22" mat_peptide 2626..3024 /gene="ORF1" /product="VPg" mat_peptide 3025..3567 /gene="ORF1" /product="Pro" mat_peptide 3568..5097 /gene="ORF1" /product="RdRp" gene 5081..6703 /gene="ORF2" CDS 5081..6703 /gene="ORF2" /note="major capsid protein" /codon_start=1 /product="VP1" /protein_id="QRF49928.1" /translation="MKMASSDANPSDGSAANLVPEVNNEVMALEPVVGAAIAAPVAGQ QNVIDPWIRNNFVQAPGGEFTVSPRNAPGEILWSAPLGPDLNPYLSHLARMYNGYAGG FEVQVILAGNAFTAGKVIFAAVPPNFPTEGLSPSQVTMFPHIVVDVRQLEPVLIPLPD VRNNFYHYNQSNDPTIKLIAMLYTPLRANNAGDDVFTVSCRVLTRPSPDFDFIFLVPP TVESRTKPFSIPVLTVEEMTNSRFPIPLEKLFTGPSSAFVVQPQNGRCTTDGVLLGTT QLSPVNICTFRGDVTHITGSHNYTMNLSSQNWNNYDPTEEIPAPLGTPDFVGKIQGML TQTTRTDGSTRGHKATVYTGSADFAPKLGRVQFETDTNHDFEANQNTKFTPVGVIQDG STTHRNEPQQWVLPSYSGRNTHNVHLAPAVAPTFPGEQLLFFRSTMPGCSGYPNMDLD CLLPQEWVQHFYQEAAPAQSDVALLRFVNPDTGRVLFECKLHKSGYVTVAHTGQHDLV IPPNGYFRFDSWVNQFYTLAPMGNGAGRRRVV" gene 6703..>7443 /gene="ORF3" CDS 6703..>7443 /gene="ORF3" /note="minor structural protein; small basic protein" /codon_start=1 /product="VP2" /protein_id="QRF49929.1" /translation="MAGAFFAGLASDVLGSGLGSLINAGAGAINQKVEFENNRKLQQA SFQFSSNLQQASFQHDKDMLQAQIEATKKLQQEMMKVKQAMLLEGGFSETDAARGAIN APMTKALDWSGTRYWAPDARTTTYNTGRFSTPQLSGAPSGRANIRDAVPARGSSNKTS NSSTATSVYSNQTTSTRLGSTAGSGTSVSSLPSTARTRSWVEDQSRNLSPFMRGAHNI SYVTPPSSRSSSQGTVSTVPKEVLDSWTG" ORIGIN 1 atgaagatgg cgtctaacga cgcttccgct gccgttgctg ccaacagcaa caacgacatc 61 gcaaaatctt caagtgacgg tgtgttttcc aacatggctg tcacttttaa acgggccctc 121 ggggcgcggc ctaaacagcc gcccccgaag gagataccac ccaaaccccc acgaccaccc 181 acgccagaat tggtcagaaa gatccctcct cccccaccca acggggagga tgaactagtg 241 gtttcttaca gtgccaaaga tggcatttcc ggattgcctg agctcaccac tgtcagccaa 301 ccggaagaaa tcaacacggc gttcagtgtc cccccgctca atcaaaggga gaacagggac 361 gccaaggaac cactgactgg aacaattatt gaaatgtggg atggagaaat ctaccattac 421 ggcctgtatg aggaacgggg tcttatactt ggtgtgcata agccaccggc agccatcagc 481 cttgccaagg tcgagctaac accgctctct ttgttctgga gacctgtgta tacccctcag 541 tacctcatct ctccagacac tcttaggaga ctacacggag aatcattccc ctacaccgca 601 tttgacaaca attgttacgc cttctgctgt tgggtattag acctaaacga ctcatggttc 661 agtagaagaa tgattcagag aacaacgggt ttcttcagac cataccagga atggaacagg 721 aaacccctcc ccactatgga tgattccaag ttaaagaagg tagccaacat attcttgtgc 781 accttgtctt cactattcac cagacccatt aaggacataa tagggaaatt gaaacctctt 841 aacatcctca atattctggc tacatgtgac tggaccttcc caggcatagt ggaatcccta 901 atactcttgg cagaactctt tggagttttc tggacacccc cagatgtgtc tgcgatgatc 961 gcccccttac taggtgatta tgaactgcaa ggacctgagg accttgcagt agaactggtc 1021 ccagtggtga tgggggggat aggcttggtg ctaggattta ccaaagagaa aattggaaag 1081 atgttgtcgt ccgctgcatc cactttgaga gcttgcaaag acctgggtgc atacggactg 1141 gaaatcttga agttagttat gaaatggttc ttcccgaaga aagaggaagc aaatgaactg 1201 gccatggtga ggtccatcga agatgcagta ctagacctcg aggcaattga aaacaaccac 1261 atgaccaccc tgctcaagga caaggatagc ttggcaactt acatgagaac cctcgaccat 1321 gaggaggaga aagccagaaa actctcaact aaatctgctt cgcctgatat cgtgggcaca 1381 atcaactctc ttctggcacg aatcgccgct gcgcgctccc tagtgcatcg agcgaaagag 1441 gagctctcca gcaggccgag acctgtcgtt gtgatgatat cgggaaaacc aggaataggg 1501 aaaactcatc ttgccaggga gttggccaag aagatcgcag cctccctcac aggtgaccag 1561 cgtgtaggtc taatcccacg caatggcgtc gaccactggg acgcatacaa gggtgaaaga 1621 gttgtcctat gggacgacta tgggatgagc aaccccatac atgatgccct caggctacag 1681 gaacttgctg acacttgccc cctcacgcta aactgtgaca ggattgagaa caaaggaaaa 1741 gtctttgaca gtgacgccat aatcatcacc accaatctgg ccaacccagc accactggat 1801 tatgtcaatt ttgaggcgtg ctcaaggcgc attgacttcc tcgtgtacgc ggaagctcct 1861 gaggtggaaa aggcaaaacg tgacttccca ggccaacctg acatgtggaa gaacgctttc 1921 agtcctgact tctcacacat aaaattggca ttggctccac agggtggttt tgacaagaac 1981 ggcaacaccc cgcatggaaa aggtgtcatg aagaccctca caactggctc cctcatcgcc 2041 cgagcatcag gactactcca tgagaggcta gatgaatatg aattacaagg cccagccctc 2101 accactttca attttgaccg caacaagata cttgctttca gacagcttgc tgctgaaaac 2161 aagtatgggc tgatggacac aatgagagtt ggaaaacagc tcaaggatgt caggaccatg 2221 ccagacctca aacaagcact caagaatgtc gcaattaaga agtgccagat agtgtacaat 2281 ggtagcacct atacgcttga agccgatggc aagggtagtg tgaaagttga caaagtgcaa 2341 aatgccaccg tgcagaccaa caatgaactg gccggcgccc tgcaccacct aaggtgcgcc 2401 agaatcaggt actatgttaa gtgtgtccag gaggcactgt attccatcat tcaaatcgct 2461 ggggctgcgt tcgtcaccac gcgcatcgcc aagcgcatga acatacaaaa tctctggtcc 2521 aagccacagg tggaagacac agaagagacg gccagcaaag atggttgccc taagcccaaa 2581 gatgatgaag agttcgtcgt ttcatccgac gacatcaaag ctgagggcaa gaaagggaag 2641 aacaagtccg gccgtggcaa gaagcacaca gccttctcaa gcaaaggact cagtgatgag 2701 gagtacgatg agtacaagag aatcagggag gaaaggaatg gcaagtactc catagaagag 2761 tacctccagg acagagacaa gtactatgag gaggtggcca ttgccagggc aactgaagag 2821 gacttctgtg aagaagaaga ggccaaaatc cggcagagaa tttttagacc aacaagaaaa 2881 caacgtaagg aagaaagggc ctctctaggc ttggtcacag gttcagaaat caggaagaga 2941 aacccagagg acttcaaacc caagggaaag ctgtgggccg atgatgacag aagtgttgac 3001 tacaacgaga aactcaactt tgaggcccca ccaagcatct ggtcgcggat agtcaacttt 3061 ggttcaggtt ggggcttctg ggtctccccc agtttgttta taacatcaac ccatgtcata 3121 ccccaaggta caaaggagtt cttcggggtc cccatcaaac aaatccagat acacaaatca 3181 ggtgaattct gtcggctgag attcccaaaa ccaatcagaa ctgatgtgac gggcatgatt 3241 ctagaagaag gtgcgccaga gggaaccgtg gtcacactgc tcatcaagag gccaactgga 3301 gagcttatgc ctttggcagc cagaatggga actcacgcaa ccatgaaaat tcaggggcgc 3361 acagttggag gacaaatggg tatgctcttg acagggtcca acgccaagag tatggacttg 3421 ggcacaacac caggcgactg cggctgtccc tacatctata aaagagggaa cgactatgtg 3481 gtcataggag tccatactgc tgctgcccgt ggagggaaca ctgtcatctg tgccacccag 3541 ggtagtgagg gggaagccac ccttgaagga ggtgacaaca aaggaacgta ctgtggtgca 3601 ccaatcttgg gtccagggag cgctccgaaa cttagcacca agactaagtt ttggaggtca 3661 tccacaacgc cactcccacc aggcacctac gaaccagcct acctcggcgg caaggatccc 3721 agagtcaaag gtggcccttc attgcaacaa gtcatgaggg accagctaaa gccattcaca 3781 gaacccagag gcaaaccacc aagaccaaat gtattggaag ccgccaagaa aaccatcatt 3841 aatgtccttg agcaaacaat tgacccaccc caaaaatggt cattcgcgca agcttgcgca 3901 tcccttgaca aaaccacctc cagcggccat ccgcaccacg tgcggaaaaa cgattgctgg 3961 aatggggact cctttacagg aagattggca gatcaggcct ccaaggccaa cctaatgttt 4021 gaggagggaa agaacatgac tccagtctac acaggtgcac ttaaagatga attggtaaag 4081 actgacaaga tttatggtaa gatcaagaag aggcttttgt ggggctcgga cttggcgacc 4141 atgatacggt gcgcccgggc ttttggaggc cttatggatg agctcaaggc acactgtgtc 4201 acccttccag tcagagttgg tatgaacatg aatgaagatg gccccataat ctttgagaag 4261 cactccagat acaagtatca ctatgatgct gattactcca ggtgggactc aacacaacaa 4321 agggatgtgc tagcagcagc actagaaatc atggttaagt tctctccaga accacacttg 4381 gcccaggtgg ttgcagaaga cctcctttcc cctagtgtaa tggatgtagg tgactttcag 4441 atatcaataa gtgaggggct cccctccggg gtgccttgca cttcccagtg gaattccatc 4501 gcccactggc tcctcaccct ttgtgcgctc tctgaagtca cggacctgtc ccctgatatc 4561 attcaggcca attccctttt ctccttctac ggtgatgatg agattgtgag tacagacata 4621 aaattggacc cagagaagct gacagcaaaa ctcaaggagt acggattgaa gccaacccgt 4681 cccgacaaaa ctgaaggacc ccttgttatc tctgaagatt tggatggcct gacattcctc 4741 cggaggactg tgacccgtga cccagctggc tggtttggaa aattggaaca aagctcaatc 4801 ctcaggcaaa tgtactggac caggggtccc aaccatgaag atccatctga agcaatgata 4861 ccacactccc aaagacccat acaattgatg tccttgctag gcgaggctgc actccacggc 4921 ccagcatttt atagcaaaat tagcaaattg gttattgcag agttgaagga aggtggcatg 4981 gatttctacg tgcccagaca agagccaatg ttcagatgga tgagattctc agatctgagc 5041 acgtgggagg gcgatcgcaa tctggctccc agttttgtga atgaagatgg cgtcgagtga 5101 cgccaaccca tctgatgggt ccgcagccaa cctcgtccca gaggtcaaca atgaggttat 5161 ggctctggag cccgttgttg gtgccgccat agcggcacct gtagcgggcc agcaaaatgt 5221 aattgacccc tggattagaa acaattttgt acaagcccct ggtggagagt ttacagtatc 5281 tcctagaaac gctccaggtg aaatactatg gagcgcgccc ttaggccctg atttaaatcc 5341 ctacctatcc catttggcca gaatgtacaa tggttatgca ggtggctttg aagtgcaggt 5401 aattctcgcg gggaacgcgt tcaccgccgg gaaggtcata tttgcagcag tcccaccaaa 5461 ttttccaact gaaggcttaa gtcccagcca ggtcaccatg ttcccccaca tagtagtaga 5521 tgttaggcaa ctagaacctg tgttgattcc cttacccgat gttaggaaca atttttacca 5581 ctacaatcaa tcaaatgacc ccactatcaa gttgatagca atgttgtata caccacttag 5641 ggctaataat gctggggatg atgtcttcac agtctcttgc cgggtcctca cgagaccatc 5701 ccccgatttt gatttcatat ttttggtgcc acccacagtt gagtcaagaa ctaagccatt 5761 ctctatccca gttttaactg ttgaggagat gaccaattca agattcccca tccctttgga 5821 gaagttattc acgggtccca gcagtgcctt tgttgttcaa ccacaaaacg gcaggtgcac 5881 gactgatggc gtgctcctag gcaccaccca attgtctcct gtcaacatct gtaccttcag 5941 aggggatgtc acccatatca caggcagtca taactacaca atgaatttgt cttctcaaaa 6001 ttggaacaat tatgacccaa cagaagaaat cccagcccct ctaggaactc cagactttgt 6061 ggggaagatc caaggcatgc tcacccaaac cacaaggaca gatggctcaa cacgcggcca 6121 caaagccaca gtgtacaccg ggagcgccga cttcgctcca aaactgggta gagttcaatt 6181 tgaaactgac acaaaccatg actttgaagc taaccaaaac acaaagttca ccccagtcgg 6241 tgtcatccaa gatggtagca ccacccaccg aaatgaaccc caacagtggg tgctcccaag 6301 ttattcaggc agaaatactc ataatgtgca tctggccccc gctgtggccc ccacttttcc 6361 aggtgagcag cttctctttt tccgatccac catgcccgga tgcagcgggt accccaacat 6421 ggatctggat tgtctcctcc cccaggaatg ggtgcagcac ttctaccaag aggcagcccc 6481 agcacaatct gatgtggccc tgctgagatt tgtgaaccca gacacaggta gggttttgtt 6541 cgagtgtaaa ctccacaaat caggttatgt tactgtggct cacactggcc aacatgattt 6601 ggttatcccc cccaatggtt attttaggtt tgattcctgg gtcaaccagt tctacacgct 6661 tgcccccatg ggaaatggag cggggcgtag acgtgtggta taatggctgg agctttcttt 6721 gctggattgg catctgatgt ccttggctct ggacttggtt ccctcatcaa tgctggggct 6781 ggggccatca accaaaaagt tgagtttgaa aataacagaa aattacaaca agcatccttc 6841 caatttagca gcaatctgca acaggcctcc tttcaacatg acaaagatat gctccaagca 6901 caaattgaag ccaccaaaaa gttacaacag gaaatgatga aggtcaagca ggcaatgctc 6961 ctagagggtg ggttctctga gacagatgca gcccgcgggg caatcaacgc ccccatgaca 7021 aaagctctgg actggagcgg gacaaggtac tgggcccccg atgctaggac tacaacatac 7081 aacacaggcc gcttttccac ccctcaacta tcgggggcac cgtcaggaag agctaatatt 7141 agggatgctg tccctgctcg gggttcctcc aataaaactt ctaattcttc tactgctact 7201 tctgtgtatt cgaatcaaac tacttcaacg agacttggtt ctacagctgg ttctggcacc 7261 agtgtctcga gcctcccgtc aactgcaagg actaggagct gggttgagga tcaaagtagg 7321 aatttgtcac ctttcatgag gggggcccac aacatttcgt atgtcacccc accatctagt 7381 agatcctcca gccaaggcac agtctcaacc gtgcctaaag aggttttgga ctcctggact 7441 ggc //