Typing tool
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Typing tool
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Complete norovirus genomes
| KT780411 | GII.17 | |
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| GII.P17 |
ORF1: 1..5106
ORF2: 5087..6709
ORF3: 6709..7488
LOCUS KT780411 7559 bp RNA linear VRL 08-MAR-2016
DEFINITION Norovirus Hu/GII.17/CUHK-NS-643/HKG/2015 nonstructural polyprotein
(ORF1) gene, partial cds; and viral protein 1 (VP1) and viral
protein 2 (VP2) genes, complete cds.
ACCESSION KT780411
VERSION KT780411.1
KEYWORDS .
SOURCE Norovirus Hu/GII.17/CUHK-NS-643/HKG/2015
ORGANISM Norovirus Hu/GII.17/CUHK-NS-643/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-643/HKG/2015"
/mol_type="genomic RNA"
/strain="Hu/GII.17/CUHK-NS-643/HKG/2015"
/isolate="CUHK-NS-643"
/host="Homo sapiens"
/db_xref="taxon:1760918"
/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="ALP48652.1"
/translation="KMASNDASAAVAGKNNNNDKEKSSSDSLFANMSVTFKKALGARS
KQPPPGETKQIQKPPRPPTPELVKRIPPPPPNGEDEPGIVYKVGEGVSGLPDLTTVVQ
PDAQNTAYSVPPLSQREVGEAKEPLPGSILEMWDGEIYHYGLYVERGHVLGVHKPPAA
ISLAKIEITPLSLYWRVVYTPQYLIDPGTLKNLSGETFPYTAFDNNCYAFCCWVLDLN
DSWLSRRMIQRTTGFFKPYQDWNRKPLPTMDEPKIKKAANAVLCALSSLFTRPIKDII
GKLRPLNILNILATCDWTFAGIVESLILLAELFGVFWTPPDVSAMIAPLLGDYEMQGP
EDLAVELVPVVMGGIGLVLGFTKEKIGKMLSSAATTLRACKDLGSYGLEILKLVMKWF
FPKKEEANELAMVRAIEDAVLDLEAIENNHMTTLLKDKDSLATYMRTLDLEEEKARKL
STKSASPDIVGTINALLARIAAARSLVHKAKEELSSRQRPVVVMISGRPGIGKTHLAR
ELAKKVASTLSGDQRIGLVPRNGVDHWDAYKGERVVLWDDYGMSNPIQDALRLQELAD
TCPLTLNCDRIENKGKVFDSDAIIITTNLANPAPLDYVNFEACSRRIDFLVYADAPDI
EKAKRDFPGQPDMWKDHFRPDFSHIKLQLAPQGGFDKNGNTPHGKGVVKSLTIGSLIA
RASGLLHERMDEFELQGSDLPTFNFDRNKVAAFRQLAAENKYGLMDTLRVGNQLKSVK
TLDELKQAIKNISIKKCQIVYNGCTYAMESDGRGKVVVEKVQNATVQTNNELVGALHH
LRSARIRYYVKCFQEAIYSLLQIAGAAFVTSRIVRRMNISNLWSKPPIEEGDEPEDRG
GCPKPRDEDDLTIDSRDIKVEGKKGKNKSGRGKKHTAFSSKGLSDEEYDEYKRIREER
NGKYSIEEYLQDRDRYYEELAIAKATEEDFCEEEEIKIRQRIFRPTRRQRKEERATLG
LVTGSEIRKRNPDDFKPKGKLWADDNRSVDYNERIDFEAPPSVWSRIVNFGTGWGFWV
SPSLFITSTHVIPKGITEAFGVPINQIQIHKSGEFCRLRFPKPIRPDVSGMILEEGAP
EGTVVSILIKRTTGELMPLAVRMGTHATMKIQGRTVGGQMGMLLTGSNAKSMDLGTTP
GDCGCPYIYKRGNDLVVIGVHTAAARGGNTVICATQGSEGEATLEGGDNKGTYCGAPI
LGPGNAPKLSTKTKFWRSSNAPLPPGTYEPAYLGGRDPRVKGGPSLQQVMRDQLKPFT
EPRGKPPNPNVLESAKKTIINVLEQTIDPPQKWSYAQACASLDKTTSSGYPHHVRKND
YWSGESFTGKLADQASKANLMYEEGKHMQPVYTAALKDELVKTDKIYGKIKKRLLWGS
DLSTMIRCARAFGGLMDEFKANCITLPIRVGMNMNEDGPIIFEKHSRYRYHYDADYSR
WDSTQQRAVLEAALEIMVRFSAEPQLAQIVAEDLLSPSVVDVGDFKIAINEGLPSGVP
CTSQWNSIAHWLLTLCALSEVTGLGPDIIQANSMYSFYGDDEIVSTDIKLDPEKLTAK
LKEYGLKPTRPDKTEGPLVVSEDLNGLTFLRRTVTRDPAGWFGKLDQNSILRQLYWTR
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="ALP48653.1"
/translation="MKMASNDAAPSNDGAAGLVPEGNNETLPLEPVAGAAIAAPVTGQ
NNIIDPWIRTNFVQAPNGEFTVSPRNSPGEILLNLELGPDLNPYLAHLSRMYNGYAGG
VEVQVLLAGNAFTAGKILFAAVPPNFPVEFLSPAQITMLPHLIVDVRTLEPIMIPLPD
VRNTFFHYSNQPNSRMRLVAMLYTPLRSNGSGDDVFTVSCRVLTRPTPDFEFTYLVPP
SVESKTKPFSLPILTLSELTNSRFPVPIDSLFTAQNNVLQVQCQNGRCTLDGELQGTT
QLLPSGICAFRGRVTAQINQRDRWHMQLQNLNGTTYDPTDDVPAPLGTPDFKGVVFGM
VSQRNVGNDAPGSTRAQQAWVSTYSPQFVPKLGSVNLRISDNDDFQFQPTKFTPVGVN
DDDDGHPFRQWELPNYSGELTLNMNLAPPVAPNFPGEQLLFFRSFVPCSGGYNQGIID
CLIPQEWIQHFYQESAPSQSDVALIRYVNPDTGRTLFEAKLHRSGYITVAHSGDYPLV
VPANGHFRFDSWVNQFYSLAPMGTGNGRRRAQ"
gene 6709..7488
/gene="VP2"
CDS 6709..7488
/gene="VP2"
/codon_start=1
/product="viral protein 2"
/protein_id="ALP48654.1"
/translation="MAGAFIAGLAGDMLTSSVGSLVNAGANAINQKIDFENNKQLQSA
SFQHDKEMLQAQVRATKQLQSEMIALKQGVLAAGGFSPTDAARGSIGAPMTKVLDWSG
TRYWAPNSTKTTGYSGQFTSSPVHMSSPNAPQSKPAKPRSLAPSSSSSSVYSMYTQST
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 ctatgccttc 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 ggattggaga 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 ggcacaataa 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 ggcctgttct 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 accaactgaa aagtgttaag
2221 accctggatg agctgaagca ggccataaag aacatcagta tcaagaagtg tcagatagtg
2281 tataatggat gcacctatgc 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 ggaatggcaa atactcaata
2761 gaggaatacc tccaagatag ggacagatac tatgaagagc ttgccattgc taaggccact
2821 gaggaggact tctgtgagga ggaggagatc aaaatccgcc agagaatctt ccgacccacc
2881 aggaggcagc ggaaagagga aagggccacg cttgggcttg tcacaggatc ggaaatcaga
2941 aagaggaatc cagatgactt taaaccaaaa gggaaattgt gggctgatga caacaggagc
3001 gtggattaca atgagaggat agattttgag gctcccccga gtgtttggtc taggatagtc
3061 aactttggca caggctgggg attctgggtt tctccaagtc tctttataac ttcaacacac
3121 gtcataccaa aaggaatcac tgaggccttt ggagtgccca taaaccaaat ccaaattcac
3181 aaatctggag aattttgccg cttgcggttt ccaaagccaa ttagaccaga cgtgagtggg
3241 atgatcttgg aagagggcgc ccctgaaggc actgttgtgt ctattctcat caaaaggaca
3301 acaggggagc tgatgcctct tgcagtcaga atggggactc atgccacaat gaaaatccaa
3361 ggtagaacgg tgggtggtca gatgggtatg cttctcactg gctcaaatgc taaaagcatg
3421 gatctaggca caacgccagg tgactgcgga tgtccataca tatacaaaag 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 atcacgtccg gaagaatgac
3961 tattggagtg gtgaatcctt cacaggaaaa cttgcagatc aggcttcaaa 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 gtggttagtg 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 gaacccttac 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 aattcgaggt 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 gtcaatctta gaattagtga taatgatgat ttccaattcc agccgacaaa
6241 attcacacca gtgggcgtca atgatgacga tgatggccac ccgttcagac aatgggaact
6301 accaaactat tcaggggagc ttaccttgaa tatgaatctt gcccccccag ttgctccaaa
6361 ttttcctggt gaacaattgt tattcttcag atctttcgtg ccatgctcag gaggttacaa
6421 ccaaggtatt atagattgtc ttattcccca agaatggatc caacacttct atcaggaatc
6481 agcaccctcc cagtcagacg tggccctaat caggtatgtc aaccccgata cgggacgcac
6541 actgtttgaa gcaaaattgc acagatctgg ttacattact gtggctcact ctggagacta
6601 tcctcttgtt gttccggcta atggacactt tagatttgat tcttgggtaa atcagtttta
6661 ctcactcgcc ccaatgggaa ctgggaatgg gcgaaggagg gctcagtaat ggctggggct
6721 ttcattgcag gattggcggg cgacatgctc acgtcatctg tgggctccct tgtgaacgca
6781 ggggcaaacg ccatcaacca aaagatagac tttgaaaaca acaaacaact ccagtctgct
6841 tcctttcagc atgataaaga gatgctccaa gcgcaggtga gggcaaccaa gcagctgcaa
6901 tctgaaatga tagccctaaa acagggggtt ttggccgcag gcggcttttc ccccactgat
6961 gcagcaaggg gatccattgg tgcacccatg acaaaggtgc ttgactggtc tggcactcga
7021 tactgggcgc ccaattccac aaagacaact ggctattcgg gacaattcac ctcttcacct
7081 gtgcatatgt ctagcccaaa tgctccacaa tcaaaacctg caaagcctag gtctctagct
7141 ccttcctctt cttctagcag tgtctatagt atgtatactc aatctactca tttaacatct
7201 ggctcctcta gtaatgcttc ttctgcctct 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
//