Typing tool
|
Complete norovirus genomes
KT780406 | GII.17 | ||
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GII.P17 |
ORF1: 1..5106 ORF2: 5087..6709 ORF3: 6709..7488LOCUS KT780406 7559 bp RNA linear VRL 08-MAR-2016 DEFINITION Norovirus Hu/GII.17/CUHK-NS-600/HKG/2015 nonstructural polyprotein (ORF1) gene, partial cds; and viral protein 1 (VP1) and viral protein 2 (VP2) genes, complete cds. ACCESSION KT780406 VERSION KT780406.1 KEYWORDS . SOURCE Norovirus Hu/GII.17/CUHK-NS-600/HKG/2015 ORGANISM Norovirus Hu/GII.17/CUHK-NS-600/HKG/2015 Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes; Picornavirales; Caliciviridae; Norovirus; Norwalk virus. REFERENCE 1 (bases 1 to 7559) AUTHORS Chan,M.C., Lee,N., Hung,T.N., Kwok,K., Cheung,K., Tin,E.K., Lai,R.W., Nelson,E.A., Leung,T.F. and Chan,P.K. TITLE Rapid emergence and predominance of a broadly recognizing and fast-evolving norovirus GII.17 variant in late 2014 JOURNAL Nat Commun 6, 10061 (2015) PUBMED 26625712 REMARK Publication Status: Online-Only REFERENCE 2 (bases 1 to 7559) AUTHORS Chan,M.C.W., Hung,T.T.N., Kwok,K.T.T., Cheung,K.K.W. and Chan,P.K.S. TITLE Direct Submission JOURNAL Submitted (18-SEP-2015) Department of Microbiology, The Chinese University of Hong Kong, CUHK, Shatin 852, Hong Kong COMMENT ##Assembly-Data-START## Sequencing Technology :: Sanger dideoxy sequencing ##Assembly-Data-END## FEATURES Location/Qualifiers source 1..7559 /organism="Norovirus Hu/GII.17/CUHK-NS-600/HKG/2015" /mol_type="genomic RNA" /strain="Hu/GII.17/CUHK-NS-600/HKG/2015" /isolate="CUHK-NS-600" /host="Homo sapiens" /db_xref="taxon:1760902" /country="Hong Kong" /collection_date="2015" /note="genotype: GII.17" gene <1..5106 /gene="ORF1" CDS <1..5106 /gene="ORF1" /note="contains RNA-dependent RNA polymerase; RdRp" /codon_start=1 /product="nonstructural polyprotein" /protein_id="ALP48637.1" /translation="KMASNDASAAVAGKNNNNDKEKSSSDSLFANMSVTFKKALGARS KQPPPGETKQIQKPPRPPTPELVKRIPPPPPNGEDEPGIVYKVGEGVSGLPDLTTVVQ PDAQNTAYSVPPLSQREVGEAKEPLPGSILEMWDGEIYHYGLYVERGHVLGVHKPPAA ISLAKIEITPLSLYWRVVYTPQYLIDPGTLKNLSGETFPYTAFDNNCYAFCCWVLDLN DSWLSRRMIQRTTGFFKPYQDWNRKPLPTMDEPKIKKAANAVLCALSSLFTRPIKDII GKLRPLNILNILATCDWTFAGIVESLILLAELFGVFWTPPDVSAMIAPLLGDYEMQGP EDLAVELVPVVMGGIGLVLGFTKEKIGKMLSSAATTLRACKDLGSYGLEILKLVMKWF FPKKEEANELAMVRAIEDAVLDLEAIENNHMTTLLKDKDSLATYMRTLDLEEEKARKL STKSASPDIVGTINALLARIAAARSLVHKAKEELSSRQRPVVVMISGRPGIGKTHLAR ELAKKVASTLSGDQRIGLVPRNGVDHWDAYKGERVVLWDDYGMSNPIQDALRLQELAD TCPLTLNCDRIENKGKVFDSDAIIITTNLANPAPLDYVNFEACSRRIDFLVYADAPDI EKAKRDFPGQPDMWKDHFRPDFSHIKLQLAPQGGFDKNGNTPHGKGVVKSLTIGSLIA RASGLLHERMDEFELQGSDLPTFNFDRNKVAAFRQLAAENKYGLMDTLRVGNQLKSVK TLDELKQAIKNISIKKCQIVYNGCTYTMESDGRGKVVVEKVQNATVQTNNELVGALHH LRSARIRYYVKCFQEAIYSLLQIAGAAFVTSRIVRRMNISNLWSKPPIEEGDEPEDRG GCPKPRDEDDLTIDSRDIKVEGKKGKNKSGRGKKHTAFSSKGLSDEEYDEYKRIREER NGKYSIEEYLQDRDKYYEELAIAKATEEDFCEEEEIKIRQRIFRPTRKQRKEERATLG LVTGSEIRKRNPDDFKPKGKLWADDNRSVDYNERIDFEAPPSVWSRIVNFGTGWGFWV SPSLFVTSTHVIPKGITEAFGVPINQIQIHKSGEFCRLRFPKPIRPDVSGMILEEGAP EGTVVSILIKRTTGELMPLAVRMGTHATMKIQGRTVGGQMGMLLTGSNAKSMDLGTTP GDCGCPYMYKRGNDLVVIGVHTAAARGGNTVICATQGSEGEATLEGGDNKGTYCGAPI LGPGNAPKLSTKTKFWRSSNAPLPPGTYEPAYLGGRDPRVKGGPSLQQVMRDQLKPFT EPRGKPPNPNVLESAKKTIINVLEQTIDPPQKWSYAQACASLDKTTSSGYPHHVRKND YWSGESFTGKLADQASKANLMYEEGKHMQPVYTAALKDELVKTDKIYGKIKKRLLWGS DLSTMIRCARAFGGLMDEFKANCITLPIRVGMNMNEDGPIIFEKHSRYRYHYDADYSR WDSTQQRAVLEAALEIMVRFSAEPQLAQIVAEDLLSPSVVDVGDFKIAINEGLPSGVP CTSQWNSIAHWLLTLCALSEVTGLGPDIIQANSMYSFYGDDEIVSTDIKLDPEKLTAK LKEYGLKPTRPDKTEGPLVISEDLNGLTFLRRTVTRDPAGWFGKLDQNSILRQLYWTR GPNHEDPSETMIPHAQRPVQLMALLGESSLHGPSFYSKVSKLVISELKEGGMDFYVPR QESMFRWMRFSDLSTWEGDRNLAPSFVNEDGVE" primer_bind 1..21 gene 5087..6709 /gene="VP1" CDS 5087..6709 /gene="VP1" /codon_start=1 /product="viral protein 1" /protein_id="ALP48638.1" /translation="MKMASNDAAPSNDGAAGLVPEGNNETLPLEPVAGAAIAAPVTGQ NNIIDPWIRTNFVQAPNGEFTVSPRNSPGEILLNLELGPDLNPYLAHLSRMYNGYAGG VEVQVLLAGNAFTAGKILFAAVPPNFPVEFLSPAQITMLPHLIVDVRTLEPIMIPLPD VRNTFFHYSNQPNSRMRLVAMLYTPLRSNGSGDDVFTVSCRVLTRPTPDFEFTYLVPP SVESKTKPFSLPILTLSELTNSRFPVPIDSLFTAQNNVLQVQCQNGRCTLDGELQGTT QLLPSGICAFRGRVTAQINQRDRWHMQLQNLNGTTYDPTDDVPAPLGTPDFKGVVFGM VSQRNVGNDAPGSTRAQQAWVSTYSPQFVPKLGSVNLRISDNDDFQFQPTKFTPVGVN DDDDGHPFRQWELPNYSGELTLNMNLAPPVAPNFPGEQLLFFRSFVPCSGGYNQGIID CLIPQEWIQHFYQESAPSQSDVALIRYVNPDTGRTLFEAKLHRSGYITVSHSGDYPLV VPANGHFRFDSWVNQFYSLAPMGTGNGRRRAQ" gene 6709..7488 /gene="VP2" CDS 6709..7488 /gene="VP2" /codon_start=1 /product="viral protein 2" /protein_id="ALP48639.1" /translation="MAGAFIAGLAGDMLTSSVGSLVNAGANAINQKIDFENNKQLQSA SFQHDKEMLQAQVRATKQLQSEMIALKQGVLAAGGFSLTDAARGSIGAPMTKVLDWSG TRYWAPNSTRTTGYSGQFTSSPVHMSSPNAPQSKPAKPRSLAPSSSSSSVYSMYTQST HLTSGSSSNASSASTKLTNLSSGSSQNRTAEWVNQQRSLSPFMSGALNISHVTPPSSR ASSSGTVSTVPKEVLDSWTSAFNTHRQPLFAHLRVRGESRV" ORIGIN 1 aagatggcgt ctaacgacgc ttccgctgcc gttgctggca aaaacaacaa caacgacaag 61 gaaaaatctt caagtgacag cttgtttgct aacatgtctg tcacttttaa gaaagccctc 121 ggggcgcggt ctaaacaacc gcccccggga gaaacaaaac aaatacaaaa accaccaagg 181 ccaccgacac cggaattggt gaagagaata cctccacccc cacccaatgg cgaggatgaa 241 ccagggatag tgtacaaggt gggagagggt gtgtctgggc tgcccgacct aacaactgtg 301 gtacaacctg acgcacaaaa cacagcttat agtgttcccc cacttagcca gagagaagtc 361 ggcgaagcta aagaaccgct gcctggctcc attctggaaa tgtgggatgg tgagatctac 421 cactatgggc tgtatgttga gcgggggcat gtgctcggag tacacaaacc acctgctgca 481 ataagccttg ccaaaattga aataacaccg ctgtctctct actggagagt ggtctacact 541 ccccagtatt tgatagatcc aggaactctt aagaacttga gtggagagac tttcccatac 601 acggcctttg acaacaactg ttatgccttc tgttgttggg tcctagacct caacgactcc 661 tggcttagca ggagaatgat ccaaagaaca actggattct tcaaacctta tcaggattgg 721 aacagaaaac ccttaccaac catggatgaa ccgaaaatca agaaggccgc gaatgctgtc 781 ctatgcgctc tctcctcact cttcactaga cccattaagg acatcattgg aaagcttaga 841 ccactgaaca ttcttaatat actggcaacc tgcgattgga cttttgcagg catagtggaa 901 tccttgatcc ttcttgctga actctttggg gtgttctgga cacccccaga tgtgtctgcg 961 atgattgctc ccttactcgg tgactacgag atgcaaggcc ccgaagacct ggccgtggaa 1021 cttgtgcccg tggtgatggg aggaataggt ttggtgttag gattcaccaa agaaaagatc 1081 ggcaagatgc tttcatcagc tgcgaccaca cttagggcct gcaaggatct aggatcttat 1141 gggttggaga tactcaaatt ggtcatgaag tggttcttcc ccaagaagga ggaggctaac 1201 gaactagcca tggtgagggc cattgaggat gcagtcctgg atttggaggc aatagaaaac 1261 aatcacatga ccacccttct caaggataaa gacagcctgg ccacatacat gaggactctt 1321 gacttggaag aagagaaagc aaggaaactg tcaaccaaat cggcgtcacc tgacatcgtg 1381 ggtacaataa acgcattatt ggctaggata gcagccgcca ggtcactggt ccacaaggct 1441 aaggaggagc tctcgagcag acagagacct gttgttgtaa tgatatcagg tagaccaggt 1501 ataggaaaga cccatctggc cagagagcta gccaagaaag ttgcgtcaac actgtcaggc 1561 gaccaaagga ttggactggt acctagaaat ggcgtcgacc attgggacgc ctacaaggga 1621 gaaagggtgg ttctgtggga tgattatggt atgagcaacc ctatacagga cgcactgagg 1681 ctccaagaat tggctgacac ctgtcctctg accctaaatt gtgataggat tgaaaacaaa 1741 ggaaaagtgt tcgacagtga tgccataatt ataacaacca accttgcaaa cccagcacca 1801 ctagactatg tcaactttga ggcctgctct agacgcatag acttcttggt gtatgcagac 1861 gcacctgaca ttgagaaggc taagcgtgac ttccctggcc aaccagatat gtggaaagac 1921 catttcagac cagacttctc acacattaaa cttcagctgg caccacaggg aggttttgac 1981 aaaaatggca acaccccaca tggcaaaggt gtggtgaagt ccctgacgat tggttctctg 2041 atcgccaggg cctccggctt gctccacgag agaatggatg aattcgagct ccaaggctct 2101 gacctgccaa ccttcaattt tgaccgcaac aaagtcgccg ccttcagaca attagcagct 2161 gaaaacaaat atggtcttat ggacacactg agggtcggca accaattgaa aagtgttaag 2221 accctggatg agctgaagca ggccataaag aacatcagta tcaagaagtg tcagatagtg 2281 tataatggat gcacctatac catggaatct gatgggaggg gcaaggttgt ggttgaaaag 2341 gtacaaaacg caacagttca aaccaacaat gaacttgtag gggcgctcca ccacctgaga 2401 tctgcaagga taagatacta tgttaaatgt ttccaagaag ccatttactc tctactccaa 2461 attgctggtg cagccttcgt cacctcacgc atcgtgaggc gcatgaacat atcaaacctc 2521 tggtcgaagc cacccatcga ggagggtgat gagcctgaag acagaggagg atgccccaag 2581 cccagggatg aagatgacct cactattgac tctagagaca ttaaagtgga agggaagaag 2641 ggcaagaaca agtctggccg gggcaagaaa cacacagcct tctcttccaa gggcctcagt 2701 gatgaagagt acgatgagta caagagaatc agagaggaga gaaatggcaa atactcaata 2761 gaggaatacc tccaagatag ggacaaatac tatgaagagc ttgccattgc taaggccact 2821 gaggaggact tctgtgagga ggaggagatc aaaatccgcc agagaatctt ccgacccacc 2881 aggaagcagc ggaaagagga aagggccacg cttgggcttg tcacaggatc ggaaatcaga 2941 aagaggaatc cagatgactt taaaccaaaa ggaaaattgt gggctgatga caacaggagc 3001 gtggattaca atgagaggat agattttgag gctcccccga gtgtttggtc taggatagtc 3061 aactttggca caggctgggg attctgggtt tctccaagtc tctttgtaac ttcaacacac 3121 gtcataccaa aaggaatcac tgaggccttt ggagtgccca taaaccaaat ccaaattcac 3181 aaatctggag aattttgccg cttgcggttt ccaaagccaa ttagaccaga cgtgagtggg 3241 atgatcttgg aagagggcgc ccctgaaggc actgttgtgt ctattctcat caaaaggaca 3301 acaggggagc tgatgccact tgcagtcaga atggggactc atgccacaat gaaaatccaa 3361 ggtagaacgg tgggtggtca gatgggtatg cttctcactg gctcaaatgc taaaagcatg 3421 gatctaggca caacgccagg tgactgcgga tgtccataca tgtacaaaag gggcaatgac 3481 cttgtggtca ttggggtgca cactgcagca gctcgtggag gcaacacggt catatgtgcc 3541 acacagggaa gtgaaggtga agccactctt gaaggaggtg acaacaaggg tacctattgt 3601 ggagccccca ttttgggacc tggcaatgca ccaaaattga gcacaaagac aaaattctgg 3661 agatcctcta acgcaccgct tcccccaggt acttatgaac cagcatacct tggtgggaga 3721 gacccgcgcg tgaagggagg cccatctctg caacaagtta tgagagacca acttaaacct 3781 tttacagagc ccagagggaa gccaccaaac ccaaatgtct tagagtcagc aaagaagact 3841 atcatcaatg ttctggaaca aaccattgac ccccctcaaa agtggtcata tgcccaagct 3901 tgtgcatccc tcgacaagac aacctccagt ggatacccgc accacgtccg gaagaatgac 3961 tattggagtg gtgaatcctt cacaggaaaa cttgcagatc aggcctcaaa agcaaatctc 4021 atgtatgagg aaggcaagca catgcaacca gtttacaccg cagcactcaa agacgagctc 4081 gtgaaaactg acaaaattta tggcaaaatc aagaaaagac tcctgtgggg ttctgacctc 4141 tccacaatga ttcgatgcgc cagagcattt ggtggtctca tggatgaatt caaagcaaat 4201 tgtattacac tccctatcag agttggtatg aatatgaatg aagatggtcc cataatattt 4261 gagaaacact ccaggtacag gtaccactat gatgctgatt actcccgctg ggactccaca 4321 caacagcggg cagtgctgga agcggcactt gaaatcatgg tgagattttc tgctgagcca 4381 cagctggcac aaatagtggc agaggacctg ctgtcaccaa gtgtggttga tgtgggcgat 4441 ttcaaaatcg ctatcaatga aggcctacca tctggcgtgc cttgcacctc acaatggaat 4501 tctattgccc actggttact taccttgtgt gccctttctg aagtgacagg attaggtcct 4561 gacatcatac aagctaactc catgtactct ttctatggtg atgatgagat tgtgagcaca 4621 gacataaaat tggacccaga gaaattgacc gcaaagctca aagaatatgg ccttaaaccc 4681 actcggcccg acaaaactga ggggccgttg gtgattagtg aggacctgaa tgggttgact 4741 ttcctccgcc gaacagtcac ccgtgatcca gcaggttggt ttggaaagtt ggaccaaaac 4801 tccatcctca ggcagttgta ctggacaaga ggacccaacc atgaagaccc cagtgagacc 4861 atgataccac acgcacaaag acctgtgcag ctcatggcac tactaggaga atcctcccta 4921 catggaccct cattttacag caaggttagc aaattagtca tatctgaact taaagaggga 4981 ggaatggatt tttatgtgcc cagacaagag tcaatgttca gatggatgag gttctcagat 5041 ctaagcacat gggagggcga tcgcaatctg gctcccagtt ttgtgaatga agatggcgtc 5101 gaatgacgcc gctccatcta atgatggtgc tgctggtctc gtaccagagg gcaacaacga 5161 gacccttccc ctagaaccag ttgcgggcgc agctatagcc gcacccgtca ctggccaaaa 5221 taacataatt gacccctgga ttagaacaaa ttttgtgcaa gcaccaaatg gagagttcac 5281 agtgtcaccc agaaactctc ctggagaaat tttattaaac ttagagttgg gccctgattt 5341 gaacccttat ttggctcatt tgtcaaggat gtacaatggg tatgctggtg gagtggaagt 5401 tcaggttctc ctggcaggga acgcgttcac tgccggaaag atcctcttcg ccgccgtccc 5461 gccaaatttc ccagtggaat tcttaagccc agcccagatc acaatgctcc cacatttaat 5521 agtagatgtt aggactcttg aaccaattat gatcccactc cctgatgtta ggaatacatt 5581 cttccattat agtaaccagc ctaacagccg catgagatta gtggctatgc tctatacccc 5641 actcagatct aatggctcag gtgatgatgt ctttactgtc tcttgcaggg ttttgactag 5701 gcctactcct gattttgagt tcacttattt agtgccacct tctgttgaat ctaaaactaa 5761 gcctttttcc ttacctattt taaccctttc tgagctcaca aactcgaggt tcccagtccc 5821 catcgattcg cttttcaccg cccagaataa tgtgttgcag gtgcagtgtc aaaatggcag 5881 gtgtacactt gatggtgagt tacaaggcac aacccagttg ctcccatctg gcatctgtgc 5941 attcagagga cgggtgacag cacaaattaa ccaacgtgac aggtggcaca tgcaactgca 6001 aaacctcaat ggtacaacat atgacccaac tgatgatgtg ccagccccgc tgggtacacc 6061 tgacttcaag ggcgtcgtgt ttgggatggt aagccaaaga aatgtgggta atgatgcgcc 6121 tggctcaacc agagcccaac aggcgtgggt ttcaacctat agcccccaat ttgtccccaa 6181 attaggttct gtcaacctta gaattagtga taatgatgat ttccaattcc agccgacaaa 6241 attcacacca gtgggcgtca atgatgacga tgatggccac ccgttcagac aatgggaact 6301 accaaactat tcaggggaac ttaccttgaa tatgaatctt gcccccccag ttgctccaaa 6361 ttttcctggt gaacaattgt tattcttcag atctttcgtg ccatgctcag gaggttacaa 6421 ccaaggtatt atagattgtc ttattcccca agaatggatc caacacttct atcaggaatc 6481 agcaccctcc cagtcagacg tggccctaat caggtatgtc aaccccgata cgggacgtac 6541 actgtttgaa gcaaaattgc acagatctgg ttacattact gtgtctcact ctggagacta 6601 tcctcttgtt gttccggcta atggacactt tagatttgat tcttgggtaa atcagtttta 6661 ctcactcgcc ccaatgggaa ctgggaatgg gcgaaggagg gctcagtaat ggctggggct 6721 ttcattgcag gattggcagg cgacatgctc acgtcatctg tgggctccct tgtgaacgca 6781 ggggcaaacg ccatcaacca aaagatagac tttgaaaaca acaaacaact ccagtctgct 6841 tcctttcagc atgataaaga gatgctccaa gcgcaggtga gggcaaccaa gcagctgcaa 6901 tctgaaatga tagccctaaa acagggggtt ttggccgcag gcggcttttc cctcactgat 6961 gcagcaaggg gatccattgg tgcacccatg acaaaggtgc ttgactggtc tggcactcga 7021 tactgggcgc ccaattccac aaggacaact ggctattcgg gacaattcac ctcttcacct 7081 gtgcatatgt ctagcccaaa tgctccacaa tcaaaacctg caaagcctag gtctctagct 7141 ccttcctctt cttctagcag tgtctatagt atgtacactc aatctactca tttaacatct 7201 ggctcttcta gtaatgcttc ttctgcctcc acaaaattga caaatttaag ctctggctcc 7261 tctcaaaaca gaacagcaga gtgggtaaat caacagagaa gtcttagccc tttcatgagt 7321 ggcgcactta acatctcaca tgtcacgcca ccctcaagta gggcttccag ttctgggacg 7381 gtctcgaccg tgcccaagga agttttggac tcctggacgt ctgcgtttaa cacacacaga 7441 cagccgctct tcgcacacct cagagtgagg ggggagtcac gtgtttagtg aaaagaaata 7501 attggctata atgtgatttc tttctaaatt tggctaattt gtatctttta aaaaaaaaa //