Typing tool
|
|
|
|
|
|
Typing tool
|
Complete norovirus genomes
| LC790064 | GII.4 Sydney | |
|
|---|---|---|---|
| GII.P16 |
ORF1: 1..5094
ORF2: 5075..6697
ORF3: 6697..7503
LOCUS LC790064 7540 bp RNA linear VRL 13-DEC-2023
DEFINITION Norovirus GII.4 Sydney 2012 GII/Hu/JP/2023/GII.4Sydney[P16]/
TKY221394 RNA, nearly complete genome.
ACCESSION LC790064
VERSION LC790064.1
KEYWORDS .
SOURCE Norovirus GII.4 Sydney 2012
ORGANISM Norovirus GII.4 Sydney 2012
Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes;
Picornavirales; Caliciviridae; Norovirus; Norwalk virus.
REFERENCE 1
AUTHORS Asakura,H., Yokota,S., Kuroki,K., Isogai,M., Hayashi,Y.,
Fujiwara,T., Miyake,H., Nagashima,M. and Sadamasu,K.
TITLE The Detection of Norovirus in Tokyo
JOURNAL Unpublished
REFERENCE 2 (bases 1 to 7540)
AUTHORS Asakura,H., Yokota,S., Kuroki,K., Isogai,M., Hayashi,Y.,
Fujiwara,T., Miyake,H., Nagashima,M. and Sadamasu,K.
TITLE Direct Submission
JOURNAL Submitted (09-DEC-2023) Contact:Hiroyuki Asakura Tokyo Metropolitan
Institute of Public Health, Department of Microbiology; Hyakunincho
3-24-1, Shinjyuku-ku, Tokyo 169-0073, Japan URL
:https://www.tmiph.metro.tokyo.lg.jp/
FEATURES Location/Qualifiers
source 1..7540
/organism="Norovirus GII.4 Sydney 2012"
/mol_type="genomic RNA"
/isolate="GII/Hu/JP/2023/GII.4Sydney[P16]/TKY221394"
/isolation_source="feces"
/host="Homo sapiens"
/db_xref="taxon:1776356"
/country="Japan"
/collection_date="2023-01"
gene <1..5094
/gene="POL"
CDS <1..5094
/gene="POL"
/codon_start=1
/product="nonstructural polyprotein"
/protein_id="BEV21206.1"
/translation="MASNDATVAVACNNNNDKEKSSGEGLFTNMSSTLKKALGARPKQ
PAPRDEPQKPPRPPTPELIKRIPPPPPNGEEEGEPVIRYEVKSGVSGLPELTTVPQPG
VANTAFSVPPLSLRENREAKEPLTGAILEMWDGEIYHYGLYVEKGLVLGVHKPPAAIS
MARVELTPLSLYWRVVYTPQYLISPETLKRLNGEAFPYTAFDNNCYAFCCWVLDLNDS
WLSRRMVQRTTGFFRPYQEWNRKPLPTMDDSKIKKVANIFLCSLSTLFTRPIKDLIGK
IKPLNILNILATCDWTFAGIVESLILLAELFGVFWTPPDVSAMIAPLLGDYELQGPED
LAVELVPVVMGGIGLVLGFTKEKIGKMLSSAASTLRACKDLGAYGLEILKLVMKWFFP
KKEEANELAMVRAIEDAVLDLEAIENNHMTTLLKDKDSLATYMKTLDMEEEKARRLST
KSASPDIVGTINALLARIAAARSLVHRAKEELSSRIRPVVVMISGKPGIGKTHLAREV
ARKVASTLTGDQRVGLIPRNGVDHWDAYKGERVVLWDDYGMSNPIHDALRIQELADTC
PLTLNCDRIENKGKVFDSEVIIITTNLANPAPLDYVNFEACSRRIDFLVYAEAPEVEK
AKRDFPGQPDMWKDAFKPDFSHIKLQLAPQGGFDKNGNTPHGKGVMKTLTTGSLIARA
SGLLHERMDEFELQGPTITTFNFDRNRITAFRQLAAENKYGLVDTMKVGNQLKGVKTM
EELKQAIRNVTIKRCRIIYGGSTYDLESDGKGKVLVEKVKNASIQTNNELVGALHHLK
HARIRYYVKCVQEAVYSIMQIAGAAFVTTRIARRMNIQELWSKPQLDQNESESKEEAP
KPEDDEFIISSKDIKEEGKKGKNKTGRGKKHTAFSSKGLSDEEYDEYKRIREERNGKY
SIEEYLQDRDRYYEELAIAKATEEDFCEEEEIKIRQRIFRPTRKQRKEERATLGLVTG
SEIRRRNPDDFKPKGKLWADDNRSVDYNEKLDFEAPPSIWSRIVSFGSGWGFWVSPSL
FITSTHVIPVGITEAFGVPIKQIQIHKSGEFCRFRFPKPIRPDVTGMILEEGAPEGTV
ATVLIKRPTGELMPLAARMGTHATMKIQGRMVGGQMGMLLTGSNAKGMDLGTTPGDCG
CPYIYKRGNDYVVIGVHTAAARGGNTVICATQGSEGEATLEGGDDKGTYCGAPILGPG
GAPKLSTKTKFWRSSNTPLPPGTYEPAYLGGRDPRVRGGPSLQQVMRDQLKPFTEPRG
KPPRPSVLEAAKQTIINVLEQTLDPPQKWTYAQACASLDKTTSSGHPHHVRKNEFWSG
ETFTGKLADQASKANLMFEEGKHMTPVYTAALKDELVKTEKIYGKIKKRLLWGSDLST
MIRCARSFGGLMDEMKAHCISLPVRVGMNMNEDGPIIFEKHSRYKYHYDADYSRWDST
QQRAVLAAALEIMVRFSAEPQLAQIVAEDLLAPSVVDVGDFKITINEGLPSGVPCTSQ
WNSIAHWLLTLCALSEVTKLSPDIIQANSMFSFYGDDEIVSTDIKLDPEQLTAKLKEY
GLKPTRPDKTEGPLIISEDLDGLTFLRRTVTRDPAGWFGKLDQSSILRQMYWTRGPNH
EDPNETMIPHSQRPIQLMALLGEASLHGPSFYSRISKLVITELKEGGMDFYVPRQEPM
FRWMRFSDLSTWEGDRNLAPNFVNEDGVE"
gene 5075..6697
/gene="VP1"
CDS 5075..6697
/gene="VP1"
/codon_start=1
/product="capsid protein VP1"
/protein_id="BEV21207.1"
/translation="MKMASSDANPSDGSAANLVPEVNNEVMALEPVVGAAIAAPVAGQ
QNVIDPWIRNNFVQAPGGEFTVSPRNAPGEILWSAPLGPDLNPYLSHLARMYNGYAGG
FEVQVILAGNAFTAGKIIFAAVPPNFPTEGLSPSQVTMFPHIIVDVRQLEPVLIPLPD
VRNNFYHYNQSNDSTIKLIAMLYTPLRANNAGDDVFTVSCRVLTRPSPDFDFIFLVPP
TVESRTKPFSVPVLTVEEMTNSRFPIPLEKLFTGPSSAFVVQPQNGRCTTDGVLLGTT
QLSPVNICTFRGDVTHITGSHNYTMNLASQNWNNYDPTEEIPAPLGTPDFVGKIQGML
TQTTRTDGSTRGHKATVYTGSADFAPKLGRVQFETDTNHDFEANQNTKFTPVGVIQDG
STTHRNEPQQWVLPSYSGRNTHNVHLAPAVAPTFPGEQLLFFRSTMPGCSGYPNMDLD
CLLPQEWVQYFYQEAAPAQSDVALLRFVNPDTGRVLFECKLHKPGYVTVAHTGQHDLV
IPPNGYFRFDSWVNQFYTLAPMGNGTGRRRAV"
gene 6697..7503
/gene="VP2"
CDS 6697..7503
/gene="VP2"
/codon_start=1
/product="capsid protein VP2"
/protein_id="BEV21208.1"
/translation="MAGAFFAGLASDVLGSGLGSLINAGAGAINQKVEFENNRKLQQA
SFQFSSNLQQASFQHDKEMLQAQIEATKKLQQEMMRVKQAMLLEGGFSETDAARGAIN
APMTKALDWSGTRYWAPDARVTTYSAGHFSTPQPSGALPGRANLRDAAPARGPSTRPS
NSSTATSVYSNQTISTRLGSTAGSGTSVSSLPSTARTRSWVEDQNRNLSPFMRGAHNI
SFVTPPSSRSSSQGTVSTVPKEILDSWTGAFNTRRQPLFAHIRKRGESRV"
ORIGIN
1 atggcgtcta acgacgctac cgttgccgtt gcttgcaaca acaacaacga caaggaaaaa
61 tcttcaggtg aaggcttatt cacaaacatg tcttccacct taaagaaagc cctcggggct
121 aggcccaaac agcctgcccc gagagacgaa ccacaaaagc ccccaagacc accaactccc
181 gagttgatca agaggatacc cccccctcca cctaatggcg aggaagaagg agaaccagtc
241 attaggtatg aggttaagag tggggtctct ggcctgcccg agctcacaac agtcccccaa
301 ccgggcgtgg ccaacacagc atttagtgtt ccaccactga gcttgagaga aaacagggag
361 gccaaggagc cgttaacagg ggcaatacta gagatgtggg acggagagat ataccactat
421 ggcctgtacg tggagaaagg cttagtgttg ggtgtgcaca aaccacctgc agccataagc
481 atggcgagag tggagctaac gccgctgtca ttgtattggc gtgtggtgta cactccccaa
541 tacctcatct cccctgaaac tctcaagagg ctcaacggag aggcgtttcc ttacaccgct
601 ttcgacaaca actgctatgc cttttgctgc tgggtgttag acctcaatga ttcatggctt
661 agcaggagaa tggtgcaaag aacaacgggc ttcttcagac cttaccaaga gtggaacaga
721 aaacccctac ccaccatgga tgactccaaa ataaagaagg ttgcaaatat attcctatgt
781 tcattgtcca cattattcac cagacccata aaagacctca taggaaaaat taaaccatta
841 aacatattga acatcctggc aacgtgtgac tggacgtttg ccggaatagt ggagtctctg
901 atattgcttg ctgaactctt cggagttttc tggacacccc cagatgtgtc tgctatgatc
961 gctcccttac tcggggacta cgagttgcaa gggccagaag acctcgccgt tgaactcgta
1021 cctgtggtaa tgggagggat tggcttggtg ttgggattca ccaaagagaa aattggcaaa
1081 atgctatcct cagcagcatc aacactcagg gcttgtaaag atcttggtgc ctatggctta
1141 gagatactca aattggtcat gaagtggttc ttcccaaaga aagaggaggc caacgagtta
1201 gccatggtaa gggccataga ggatgccgta ctagatcttg aggcaataga aaataaccac
1261 atgacaaccc tgttgaaaga caaagacagc ttagcaacat acatgaaaac actggacatg
1321 gaggaggaga aagccagaag gttgtccaca aaatctgcat cccctgacat agttgggaca
1381 atcaacgccc tgctggctcg aatagcagcg gccaggtcat tagtccacag ggccaaggaa
1441 gaactgtcta gcaggataag gccagtagtt gttatgatat ctggtaaacc aggaataggc
1501 aaaactcatc tggccaggga ggtggcaaga aaggtggcat ccactctcac aggggatcag
1561 agagtcggac tcataccaag aaacggtgtg gatcattggg atgcatacaa aggtgagaga
1621 gtcgtgttgt gggacgacta tggcatgagt aaccccattc atgatgctct ccgcatacaa
1681 gaattggctg acacgtgccc ccttacttta aattgtgaca gaattgaaaa taagggaaaa
1741 gtttttgaca gtgaagtcat aataattaca acaaaccttg ccaacccagc cccacttgat
1801 tatgtcaact ttgaggcctg ttccaggaga attgatttcc tggtgtacgc tgaggcacca
1861 gaagtagaaa aggcaaaacg ggattttcct ggtcagccag atatgtggaa ggacgccttc
1921 aagccggact tttcacacat caagctacag cttgcacctc agggcggctt tgacaagaat
1981 ggcaacaccc cacatgggaa aggagtgatg aagaccctca ctaccggttc tctgattgcc
2041 cgtgcatcag gcctactgca tgagaggatg gatgaatttg aactccaagg tcccacaatc
2101 accactttca atttcgaccg gaacagaatc acagcattca gacaattggc tgcagaaaac
2161 aagtatggac tggtggacac catgaaagtt ggcaatcaac taaaaggagt gaaaaccatg
2221 gaagaactca aacaagcaat caggaatgtg accatcaaga ggtgccggat catctacggt
2281 ggctccacgt atgaccttga atctgatggc aagggcaaag ttttggtgga aaaggtcaag
2341 aacgcctcta tacagaccaa caacgagttg gtcggggccc tgcaccatct taaacatgcc
2401 cgaatcaggt actatgtcaa atgtgtgcaa gaagcagtct attccatcat gcaaatcgcc
2461 ggcgctgcgt ttgtcaccac gcgtattgca cgccgcatga acatacaaga actctggtcg
2521 aagccacaat tagatcaaaa tgaatcagag tccaaggaag aggcccccaa gccagaagat
2581 gacgagttca tcatatcttc taaggatatc aaggaggaag gaaagaaggg caaaaacaaa
2641 actggccgtg gcaagaaaca cactgcattc tccagcaagg gcttgagcga tgaggagtat
2701 gacgagtaca agaggataag agaagagaga aatgggaagt actctataga ggagtacctt
2761 caagacagag acaggtacta tgaggagctc gccattgcca aggccacgga agaagacttc
2821 tgtgaagagg aggagatcaa aatccgtcag agaattttcc gtcccaccag gaaacaaaga
2881 aaggaagaga gggccacact agggctggtg acaggttcag aaatcagaag aagaaaccct
2941 gatgacttca aacccaaagg gaagctgtgg gccgatgaca acagaagtgt tgactacaat
3001 gagaaactgg actttgaggc ccccccaagc atatggtcta ggattgtgag ctttggttct
3061 ggttggggct tctgggtatc accaagcctg ttcataacat caactcatgt gatccctgta
3121 ggcataacag aagcatttgg agtccccatc aaacaaattc agatccacaa atcaggtgaa
3181 ttttgtcgat tcagattccc aaaaccaatc agaccagatg tgacaggaat gatcttggaa
3241 gaaggtgcgc ctgaaggcac cgtggcaact gtgctcatca aacgccccac cggagagctc
3301 atgcctcttg cagccagaat gggaacacac gcaaccatga agattcaagg ccgcatggtt
3361 ggcggacaga tgggtatgtt gctcactgga tcaaatgcca aaggaatgga tttgggaaca
3421 acccctggtg actgtggctg cccttacatc tataaaagag gcaatgacta tgtagtcatt
3481 ggggtgcaca ctgcagcagc ccgtggtgga aacaccgtca tctgtgccac acagggaagt
3541 gagggtgagg caacccttga gggtggagat gacaaaggaa catactgtgg ggcacccatt
3601 ctaggccctg ggggcgcacc aaaattgagc accaaaacca aattttggag gtcatcgaac
3661 acgccccttc caccagggac atatgaacct gcctacctcg gtggccgtga cccacgtgtt
3721 aggggtgggc cctccttaca gcaggtaatg agagaccagt tgaagccatt cactgaaccc
3781 aggggcaagc ctccaagacc aagtgttttg gaagcagcca aacaaactat tatcaatgtc
3841 cttgaacaaa ccctggatcc tccacaaaaa tggacatacg cgcaggcgtg tgcctcactt
3901 gacaaaacca cctccagcgg gcatccccat cacgtccgaa agaatgaatt ctggagtggt
3961 gagaccttca ctggtaaatt ggctgaccaa gcatcaaaag caaacctaat gtttgaggaa
4021 gggaaacaca tgacaccagt gtacacagca gcactcaagg atgagctagt taagactgag
4081 aaaatctatg gaaaaatcaa gaagagactg ctctggggct ctgacctgtc caccatgatc
4141 cggtgcgcta ggtcatttgg tgggctcatg gacgagatga aggcacactg catatcactc
4201 ccagtacgag ttggcatgaa tatgaatgaa gatggtccaa taatatttga gaaacattcc
4261 agatacaaat atcactatga tgcagattac tctcgttggg attcaacaca acagagggca
4321 gtattagcag cagccttgga aatcatggtc agattctctg cagaaccaca attggcacaa
4381 atagtcgctg aggatctact ggcccctagt gtagtagatg taggagactt taaaatcaca
4441 ataaatgagg ggctaccatc tggcgtgcca tgcacttctc aatggaactc catcgcacac
4501 tggctgctaa ctctctgtgc cttgtctgaa gtcaccaaac tatcccctga cattatacaa
4561 gcaaattcca tgttctcatt ttacggtgat gacgagattg tcagcaccga cataaagttg
4621 gaccctgaac agttgaccgc caaattgaaa gagtacggcc tgaaaccaac ccgcccagac
4681 aagaccgagg gacccctgat catcagtgaa gatttggacg gacttacttt cctccgaagg
4741 acggtgactc gtgacccagc tggctggttt ggaaaactgg accaaagttc aattttgagg
4801 cagatgtatt ggactagagg accaaatcat gaagacccca acgagacaat gataccccat
4861 tctcaaagac ccatacagct catggcactg cttggtgaag cctctcttca cggaccctct
4921 ttctacagta gaatcagtaa attggttata actgaactta aagaaggtgg gatggacttt
4981 tacgtgccaa ggcaggaacc catgttcagg tggatgaggt tttctgactt gagcacgtgg
5041 gagggcgatc gcaatctggc tcccaatttt gtgaatgaag atggcgtcga gtgacgccaa
5101 cccatctgat gggtccgcag ccaacctcgt accagaggtc aacaatgagg ttatggcttt
5161 ggagcccgtt gttggtgccg ctattgcggc acctgtagcg ggccaacaaa atgtaattga
5221 cccctggatt agaaataatt ttgtacaagc ccctggtggg gagtttacag tgtcccccag
5281 aaatgctcca ggtgaaatac tatggagcgc gcccctaggc cctgacctaa atccctacct
5341 atcccatctg gccaggatgt acaatggtta tgcaggtggc tttgaagtgc aggtaattct
5401 cgcggggaac gcgttcaccg ccgggaagat tatatttgca gcagtcccac caaattttcc
5461 aactgaaggc ttaagtccta gccaggtcac tatgttcccc catataatag tagatgttag
5521 acaattggaa cctgtgctga tccccttgcc cgatgttagg aataatttct atcattacaa
5581 tcagtcaaat gactccacta ttaagttgat agcaatgttg tacacaccac ttagggctaa
5641 taatgctggg gatgatgttt tcacagtctc gtgtcgagtt ctcacgaggc catcccccga
5701 ttttgatttc atattcctag taccacccac agttgagtca agaaccaaac cattctccgt
5761 cccagtttta actgttgagg agatgaccaa ctcaagattc cccatccctt tggaaaagtt
5821 gttcacaggc cccagcagtg catttgttgt tcaaccacaa aacggcagat gcacaactga
5881 tggcgtgctc ctaggcacca cccaactttc tcctgtcaac atctgcacct tcagagggga
5941 tgtcacccac atcacaggca gtcacaacta cactatgaat ttggcttctc aaaattggaa
6001 caactacgac ccgacagaag aaatcccagc tcccctagga actccagatt ttgtggggaa
6061 gattcaaggc atgctcaccc aaaccacaag gacagatggt tcaacacgcg gccacaaagc
6121 tacagtgtac actgggagcg ccgactttgc tccaaaactg ggtagagttc aatttgaaac
6181 tgacacaaac catgattttg aagccaatca aaacacaaag ttcaccccag tcggtgtcat
6241 ccaagatggt agcaccaccc accgaaacga accccaacag tgggtgctcc caagttactc
6301 aggcagaaat actcacaatg tacatttagc ccccgctgta gcccccacct ttccgggtga
6361 gcaacttctc ttctttagat ctaccatgcc cggatgcagc gggtacccca acatggattt
6421 ggactgtctg ctcccccagg aatgggtgca gtacttttac caagaggcag ccccagcaca
6481 atctgatgtg gctctgctaa gatttgtgaa tccagacaca ggtagggttt tgtttgagtg
6541 caagcttcac aaaccaggct atgttacagt ggctcacact ggccaacatg atttggttat
6601 cccccccaat ggttacttta ggtttgactc ctgggtcaac cagttctaca cgcttgcccc
6661 catgggaaat ggaacggggc gtagacgtgc agtataatgg ctggagcttt ctttgctgga
6721 ttggcatctg atgtccttgg ctctggactt ggttccctta tcaatgctgg ggctggggcc
6781 atcaaccaaa aagttgagtt tgaaaataac agaaaattgc aacaggcatc cttccaattt
6841 agcagcaatt tgcaacaggc ttcctttcaa catgataaag agatgctcca agcacaaatt
6901 gaggccacca aaaagctaca acaggaaatg atgagagtta agcaggcaat gctcctagag
6961 ggtgggttct ctgagacaga tgcggcccgc ggggcaatta acgcccccat gacaaaggct
7021 ttggactgga gcgggacaag gtactgggct ccagatgcta gagttacaac atacagtgca
7081 ggccactttt ccacccctca accatcgggg gcactgccag gaagagctaa tcttagggat
7141 gctgcccctg ctcggggacc ctccaccaga ccttctaact cttctactgc cacctctgtg
7201 tattcaaatc aaactatttc aacgagactt ggttctacag ctggttctgg aaccagtgtc
7261 tcgagcctcc cgtcaactgc aaggactagg agctgggttg aggatcaaaa taggaatttg
7321 tctcctttca tgaggggggc ccacaacata tcatttgtca ccccaccatc tagcagatcc
7381 tctagccaag gcacagtctc aaccgtgcct aaagaaattt tggactcctg gactggcgct
7441 ttcaacacgc gcaggcagcc tctcttcgct cacattcgta agcgagggga gtcacgggtg
7501 taatgtgaaa agacaaaact gattattttc tttttctttt
//