Typing tool
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Typing tool
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Complete norovirus genomes
| LC646333 | GII.2 | |
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| GII.P16 |
ORF1: 1..5090
ORF2: 5071..6699
ORF3: 6699..7478
LOCUS LC646333 7478 bp RNA linear VRL 05-AUG-2021
DEFINITION Norovirus GII.2 Hu/GII.2[P16]/1047F/Tokyo/2020/Japan genomic RNA,
nearly complete genome.
ACCESSION LC646333
VERSION LC646333.1
KEYWORDS .
SOURCE Norovirus GII.2
ORGANISM Norovirus GII.2
Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes;
Picornavirales; Caliciviridae; Norovirus; Norwalk virus.
REFERENCE 1
AUTHORS Yaoita,Y., Hasegawa,M., Asakura,H., Nagano,M., Hayashi,Y.,
Negishi,A., Kumagai,R., Kawakami,M., Hayashi,M., Yamazaki,T.,
Kitamura,Y., Kaku,E., Fujiwara,T., Miyake,H., Nagashima,M.,
Chiba,T., Suzuki,J. and Sadamasu,K.
TITLE A Genetic Analysis of Norovirus Cases Detected in Tokyo(April
2020-March 2021)
JOURNAL Unpublished
REFERENCE 2 (bases 1 to 7478)
AUTHORS Yaoita,Y., Hasegawa,M., Asakura,H., Nagano,M., Hayashi,Y.,
Negishi,A., Kumagai,R., Kawakami,M., Hayashi,M., Yamazaki,T.,
Kitamura,Y., Kaku,E., Fujiwara,T., Miyake,H., Nagashima,M.,
Chiba,T., Suzuki,J. and Sadamasu,K.
TITLE Direct Submission
JOURNAL Submitted (02-AUG-2021) Contact:Yuu Yaoita Tokyo Metropolitan
institute of public health, Department of Microbiology;
Hyakunincho3-24-1, Shinjyuku, Tokyo 169-0073, Japan URL
:http://www.tokyo-eiken.go.jp/
FEATURES Location/Qualifiers
source 1..7478
/organism="Norovirus GII.2"
/mol_type="genomic RNA"
/strain="Hu/GII.2[P16]/1047F/Tokyo/2020/Japan"
/host="Homo sapiens"
/db_xref="taxon:490039"
/country="Japan:Tokyo"
/collection_date="2020-11"
gene <1..5090
/gene="POL"
CDS <1..5090
/gene="POL"
/note="ORF1"
/codon_start=3
/product="nonstructural polyprotein"
/protein_id="BDA36035.1"
/translation="SNDATVAVACNNNNDKEKSSGEGLFTNMSSTLKKALGARPKQPA
PRDKPQKPPRPPTPELVKRIPPPPPNGEEEEEPVIRYEVKSGISGLPELTTVPQPDVA
NTAFSVPPLSLRENREAKEPLTGAILEMWDGEIYHYGLYVEKGLVLGVHKPPAAISMA
RVELTPLSLYWRVVYTPQYLIPPETLRRLNGEAFPYTAFDNNCYAFCCWVLDLNDSWL
SRRMIQRTTGFFRPYQEWNRKPLPTMDDSKIKKVANIFLCSLSTLFTRPIKDLIGKIK
PLNILNILATCDWTFAGIVESLILLAELFGVFWTPPDVSAMIAPLLGDYELQGPEDLA
VELVPVVMGGIGLVLGFTKEKIGKMLSSAASTLRACKDLGAYGLEILKLVMKWFFPKK
EEANELAMVRAIEDAVLDLEAIENNHMTTLLKDKDSLATYMKTLDMEEEKARRLSTKS
ASPDIVGTINALLARIAAARSLVHRAKEELSSRIRPVVVMISGKPGIGKTHLAREVAR
KVASTLTGDQRVGLIPRNGVDHWDAYKGERVVLWDDYGMSNPIHDALRIQELADTCPL
TLNCDRIENKGKVFDSEVIIITTNLANPAPLDYVNFEACSRRIDFLVYAEAPEVEKAK
RDFPGQPDMWKDAFKPDFSHIKLQLAPQGGFDKNGNTPHGKGVMKTLTTGSLIARASG
LLHERMDEFELQGPTITTFNFDRNRITAFRQLAAENKYGLVDTMKVGNQLKGVKTMEE
LKQAIRNVTIKRCQIIYGGSTYDLESDGKGRVLVEKVKNTSVQTNNELAGALHHLKHA
RIRYYVKCVQEAVYSIIQIAGAAFVTTRIARRMNIQELWSKPQLDQNESETKEEAPKS
EDDEFIISSKDIKEEGKKGKNKTGRGKKHTAFSSKGLSDEEYDEYKRIREERNGKYSI
EEYLQDRDRYYEELAIAKATEEDFCEEEEIKIRQRIFRPTRKQRKEERATLGLVTGSE
IRKRNPDDFKPKGKLWADDNRSVDYNEKLDFEAPPSIWSRIVSFGSGWGFWVSPSLFI
TSTHVIPAGITEAFGVPIKQIQIHKSGEFCRFRFPKPIRPDVTGMILEEGAPEGTVAT
VLIKRPTGELMPLAARMGTHATMKIQGRMVGGQMGMLLTGSNAKGMDLGTTPGDCGCP
YIYKRGNDYIVIGVHTAAARGGNTVICATQGSEGEATLEGGDDKGTYCGAPILGPGGA
PKLSTKTKFWRSSNTPLPPGTYEPAYLGGRDPRVKGGPSLQQVMRDQLKPFIEPRGKP
PRPSVLEAAKQTIINVLEQTLDPPQKWTYAQACASLDKTTSSGHPHHVRKNEFWNGET
FTGKLADQASKANLMFEEGKHMTPVYTAALKDELVKTEKIYGKIKKRLLWGSDLSTMI
RCARSFGGLMDEMKAHCISLPVRVGMNMNEDGPIIFEKHSRYKYHYDADYSRWDSTQQ
RAVLAAALEIMVRFSAEPQLAQIVAEDLLAPSVVDVGDFKITINEGLPSGVPCTSQWN
SIAHWLLTLCALSEVTKLSPDIIQANSMFSFYGDDEIVSTDIKLDPEQLTAKLKEYGL
KPTRPDKTEGPLIISEDLNGLTFLRRTVTRDPAGWFGKLDQSSILRQMYWTRGPNHED
PNETMIPHSQRPIQLMALLGEASLHGPSFYSKISKLVITELKEGGMDFYVPRQEPMFR
WMRFSDLSTWEGDRNLAPNFVNEDGVE"
gene 5071..6699
/gene="VP1"
CDS 5071..6699
/gene="VP1"
/note="ORF2"
/codon_start=1
/product="capsid protein VP1"
/protein_id="BDA36036.1"
/translation="MKMASNDAAPSTDGAAGLVPESNNEVMALEPVAGAALAAPVTGQ
TNIIDPWIRANFVQAPNGEFTVSPRNAPGEVLLNLELGPELNPYLAHLARMYNGYAGG
MEVQVMLAGNAFTAGKLVFAAVPPHFPVENLSPQQITMFPHVIIDVRTLEPVLLPLPD
VRNNFFHYNQKDDPKMRIVAMLYTPLRSNGSGDDVFTVSCRVLTRPSPDFDFTYLVPP
TVESKTKPFTLPILTLGELSNSRFPVSIDQMYTSPNEIISVQCQNGRCTLDGELQGTT
QLQVSGICAFKGEVTAHLHDNDHLYNVTITNLNGSPFDPSEDIPAPLGVPDFQGRVFG
IISQRDKHNSPGHNEPANRGHDAVVPTYTAQYTPKLGQIQIGTWQTDDLTVNQPVKFT
PVGLNDTEHFNQWVVPRYAGALNLNTNLAPSVAPVFPGERLLFFRSYIPLKGGYGNPA
IDCLLPQEWVQHFYQEAAPSMSEVALVRYINPDTGRALFEAKLHRAGFMTVSSNTSAP
VVVPANGYFRFDSWVNQFYSLAPMGTGNGRRRVQ"
gene 6699..7478
/gene="VP2"
CDS 6699..7478
/gene="VP2"
/note="ORF3"
/codon_start=1
/product="capsid protein VP2"
/protein_id="BDA36037.1"
/translation="MAGAFVAGLAGDVLSNGLSSLINAGANAINQRAEFDFNQKLQQN
SFNHDKEMLQAQIQATKQLQADMMAIKQGVLTAGGFSPADAARGAVNAPMTQALDWNG
TRYWAPNSMRTTSYSGKFTSTAPVRQADFQHTQSRPSGGSSVSSFATQSSRPTLTTTT
GSSHGTASSNSTRSTSLSQSTVSRATSRTGEWVRDQNRNLEPYMHGALQTAFVTPPSS
RASDGTVSTVPKGVLDSWTPAFNTRRQPLFAHLRKRGESQV"
ORIGIN
1 cgtctaacga cgctaccgtt gccgttgctt gcaacaacaa caacgacaaa gaaaaatctt
61 caggtgaagg cttattcaca aatatgtctt ccaccttaaa gaaagccctc ggggctaggc
121 ccaaacagcc tgccccgaga gacaaaccac aaaagccccc aagaccacca actcccgagt
181 tggtcaagag gataccccct cctccaccta acggcgaaga agaagaagaa ccagtcatta
241 ggtatgaggt caagagtggg atctctggcc tgcccgagct cacaacagtc ccccaaccgg
301 acgtggccaa cacagcattc agtgttccac cactgagctt gagagaaaac agggaggcca
361 aggagccgct aacaggggca atattagaga tgtgggatgg agagatatac cactatggtc
421 tgtacgtgga gaaaggctta gtgttgggtg tgcacaaacc acctgcagcc ataagcatgg
481 caagagtgga gctgacgccg ttgtcattgt actggcgtgt ggtgtacact ccccaatacc
541 tcatcccccc tgaaaccctc aggaggctca acggagaggc attcccttac accgcctttg
601 acaacaactg ctatgccttt tgctgctggg tgttagacct caatgactca tggcttagca
661 ggaggatgat acaaaggaca acgggcttct tcagacctta ccaagagtgg aacagaaaac
721 ccctgcctac catggatgac tccaaaatta agaaggtggc aaatatattc ctatgttcat
781 tgtccacatt attcaccaga cccataaaag acctcatagg aaaaatcaaa ccattgaaca
841 tattgaatat cctggcaacg tgtgactgga cttttgccgg aatagtggag tctctgatat
901 tacttgctga actcttcgga gttttctgga cacccccaga tgtgtctgct atgatcgctc
961 ccttactcgg ggactatgag ttgcaagggc cagaagacct cgccgttgaa ctcgtgcctg
1021 tggtaatggg ggggattggt ttggtgttgg gattcaccaa agagaaaatt ggcaaaatgt
1081 tgtcctcagc agcatcaaca ctcagggctt gcaaagatct tggtgcctat ggcttggaga
1141 tactcaaatt ggtcatgaag tggttcttcc caaagaaaga ggaggccaat gagctagcta
1201 tggtgagggc catagaggat gctgtattag acctcgaggc aatagaaaat aaccacatga
1261 caaccctgtt gaaagacaaa gacagcttag caacatacat gaaaacactg gatatggagg
1321 aggagaaagc caggaggttg tccacaaaat ctgcatcccc tgacatagtt gggacaatca
1381 acgccctgct ggctcgaata gcagcggcca ggtcattagt ccacagggcc aaggaagagc
1441 tatctagtag gataaggcca gtagttgtta tgatatctgg caaaccagga ataggcaaaa
1501 ctcatctggc cagggaggtg gcaagaaagg tggcatccac cctcacagga gatcaaagag
1561 tcggactcat accacgaaac ggtgtggacc attgggatgc atacaaaggt gagagagtcg
1621 tgctgtggga cgactatggc atgagtaacc ctattcatga tgctcttcgc atacaagaat
1681 tggctgacac gtgtcccctc accttaaatt gtgacagaat tgaaaataag ggaaaagttt
1741 ttgacagtga agtcataata attacaacaa accttgccaa tccagcccca cttgattatg
1801 tcaactttga ggcctgttcc aggagaattg atttcctggt gtacgctgag gcaccagaag
1861 tagaaaaggc aaaacgggac tttcctggtc agccagatat gtggaaggac gccttcaagc
1921 cggacttttc acacatcaag ctacagcttg caccccaggg cggctttgac aagaatggca
1981 acaccccaca tgggaaagga gtgatgaaga ccctcactac cggttctctg attgcccgtg
2041 catcaggcct actgcatgag aggatggatg aatttgaact ccaaggcccc acaatcacca
2101 cctttaattt cgaccgaaac agaatcacgg cattcagaca attggctgca gaaaacaagt
2161 atggattggt ggataccatg aaagttggca atcaattaaa aggagtgaaa accatggaag
2221 aactcaaaca agcaatcagg aatgtgacca ttaagaggtg ccagatcatc tacggcggtt
2281 ccacgtatga tcttgaatct gatggcaagg gcagagtttt ggtggaaaag gtcaagaaca
2341 cctctgtaca gaccaataac gagttggctg gggccctgca ccatctcaaa catgcccgaa
2401 tcaggtacta tgtaaaatgt gtgcaagaag cagtctattc catcatacaa attgccggcg
2461 ctgcgtttgt caccacgcgc atcgcacgcc gcatgaacat acaagaactc tggtcgaagc
2521 cacaactaga tcaaaatgaa tcagagacta aggaagaggc ccccaagtca gaagatgacg
2581 agttcatcat atcttctaag gacatcaagg aggaaggaaa gaagggcaaa aacaaaactg
2641 gccgtggcaa gaaacacact gcattctcca gcaagggcct gagcgatgag gagtatgacg
2701 agtacaagag gataagagaa gagagaaatg ggaagtactc tatagaggag tatcttcaag
2761 acagagacag gtactatgag gagctcgcca ttgccaaggc cacggaagaa gacttctgtg
2821 aagaggagga gatcaaaatc cgtcagagaa ttttccgtcc caccaggaaa caaagaaagg
2881 aagagagggc cacattaggg ctagtaacag gttcagaaat cagaaaaaga aaccctgatg
2941 acttcaaacc caaagggaag ctgtgggccg atgacaacag gagtgttgac tacaacgaga
3001 aactggactt tgaggccccc ccaagcatat ggtctaggat tgtgagcttt ggctctggct
3061 ggggcttctg ggtgtcacca agccttttca taacatcaac tcatgtaatc cccgcaggca
3121 taacagaagc atttggagtc cccatcaaac aaattcagat ccacaaatca ggcgaatttt
3181 gccgattcag attcccaaaa ccaattagac cagatgtgac aggaatgatc ttggaagaag
3241 gtgcgcctga gggcaccgtg gcaactgtgc tcatcaaacg ccccaccgga gagctcatgc
3301 ctcttgcagc cagaatggga acacacgcaa ccatgaaaat tcaaggccgc atggttggcg
3361 gacagatggg tatgttgctc actggatcaa atgctaaagg aatggacttg ggaacaactc
3421 ctggtgactg tggctgtcct tacatctata aaaggggcaa tgactatata gtcattgggg
3481 tgcacactgc agcagcccgt ggtggaaaca ctgtcatctg tgccacacag ggaagtgagg
3541 gtgaggcaac tcttgagggt ggagatgaca aaggaacgta ctgtggggca cccattctag
3601 gccctggggg tgcaccaaaa ttgagcacca aaaccaaatt ttggaggtca tcgaacacgc
3661 cccttccacc agggacatat gagcctgcct acctcggtgg ccgtgatccg cgtgttaagg
3721 gtgggccttc cctgcagcag gtgatgagag accagttgaa gccatttatt gaacccaggg
3781 gcaaacctcc aagaccaagt gtattggaag cagccaaaca aaccatcatc aatgtcctcg
3841 aacaaaccct ggaccctcca caaaaatgga catacgcaca ggcgtgcgcc tcacttgaca
3901 aaaccacctc cagcgggcac ccccatcacg tccgaaagaa tgaattctgg aatggtgaga
3961 ccttcactgg taaactggca gaccaagcat caaaagcaaa cctaatgttt gaggaaggga
4021 aacacatgac accagtgtac acagcagcac tcaaggacga gctagtcaag actgagaaaa
4081 tttatggaaa gatcaagaag agactgctct ggggctctga cttgtccacc atgatccggt
4141 gcgctaggtc atttggtggg cttatggacg agatgaaggc acactgcata tcactcccag
4201 tccgagttgg catgaatatg aatgaagatg gcccaataat atttgagaaa cattccagat
4261 acaaatatca ctatgatgca gactactctc gttgggattc aacacaacag agggcagttc
4321 tagcagcagc cttggaaatc atggtcagat tctctgcaga accacaattg gcacaaatag
4381 tcgctgagga tctgctggcc cctagtgtag tagatgtagg agactttaaa atcacaataa
4441 atgaagggct cccttctggt gtgccatgca cttctcaatg gaactccatc gcacactggc
4501 tgctaactct ctgtgccttg tctgaagtca ccaaactatc ccctgacatt atacaggcaa
4561 attccatgtt ctcattttac ggtgatgacg agattgtcag taccgacata aaattggacc
4621 ctgaacagtt aaccgccaaa ttgaaggagt acggcctgaa accaacccgc ccagacaaaa
4681 ccgagggacc cctgattatc agtgaagatt tgaacggtct cactttcctc cgaaggacgg
4741 tgactcgtga cccagctggc tggtttggaa aactggacca aagctcaatt ttgaggcaga
4801 tgtactggac tagaggacca aatcatgaag accccaatga gacaatgata ccccattccc
4861 aaagacccat acagctcatg gcactgcttg gtgaagcctc tcttcacgga ccctctttct
4921 acagtaaaat cagtaaattg gtcataactg aactcaaaga aggtgggatg gacttttacg
4981 tgccaaggca ggaacctatg ttcaggtgga tgaggttttc tgacttgagc acgtgggagg
5041 gcgatcgcaa tctggctccc aattttgtga atgaagatgg cgtcgaatga cgccgctcca
5101 tctactgatg gtgcagccgg cctcgtgcca gaaagtaaca atgaggtcat ggctcttgaa
5161 cccgtggctg gtgccgcctt ggcagccccg gtcaccggtc aaacaaatat tatagaccct
5221 tggattagag caaattttgt ccaggccccc aatggtgaat ttacagtctc tccccgaaat
5281 gcccctggtg aagtgctact gaatctagag ttgggtccag aattaaatcc ttatctggca
5341 catttagcaa gaatgtacaa tgggtatgcc ggtgggatgg aggtgcaggt catgttggct
5401 gggaacgcgt tcacagccgg caagttggtc ttcgccgccg tgccacccca cttcccggtt
5461 gaaaacctta gcccacagca aatcaccatg ttccctcatg tgattataga tgtgagaacc
5521 ttggaacctg ttttattacc actccctgat gttaggaata acttcttcca ttataaccag
5581 aaagatgatc ccaagatgag aattgtggct atgctttata cccccctcag gtctaatggt
5641 tcaggtgatg atgtgtttac agtctcctgt agagtgttga ctagaccttc ccctgacttt
5701 gacttcacat acctggtgcc accaacagtg gagtctaaaa caaagccatt caccctccca
5761 atcctcacac ttggggaact ttccaattct aggttcccag tatccataga ccagatgtac
5821 accagcccta atgaaattat atcagtgcag tgtcaaaatg gtaggtgcac actggacggg
5881 gagctccaag ggacaacaca actccaagtc agtggcattt gtgctttcaa aggtgaagtg
5941 accgcccact tgcatgacaa tgatcaccta tataatgtca ccatcacaaa cttgaatggg
6001 tccccttttg atccctccga ggatatccct gcccctttgg gtgtgcctga cttccaggga
6061 agggtttttg gtatcatctc ccaaagagat aaacacaata gtcctggaca taatgaacca
6121 gcaaacaggg gacacgacgc tgtggtcccc acttacacag cacagtacac tccaaaactt
6181 ggacaaattc aaattggcac atggcaaact gacgacctca cagtcaacca accagtcaaa
6241 ttcaccccag ttggactcaa tgacactgaa cactttaacc aatgggtggt ccctaggtat
6301 gctggtgccc taaacctcaa tacaaacctt gccccttctg ttgctccagt atttccagga
6361 gagcgcctgc tctttttcag atcatacatt cccctcaagg gcggttatgg aaacccagcc
6421 attgattgcc tactaccaca agagtgggtg caacacttct atcaggaagc agccccttca
6481 atgagtgagg tggccctcgt caggtacatc aacccggaca ctggtcgggc actgtttgag
6541 gccaagctcc acagagctgg tttcatgaca gtctcgagca acaccagtgc cccagtggtt
6601 gtgcctgcca acgggtactt cagatttgat tcttgggtga accaatttta ttctctcgcc
6661 cccatgggaa ctgggaatgg gcgtagaagg gttcaataat ggctggagct tttgtggctg
6721 gtcttgcagg ggacgtgctc agcaatgggc ttagttcatt aatcaatgca ggtgctaatg
6781 caataaatca gagggcagaa tttgatttta atcaaaaatt gcagcaaaat tcttttaatc
6841 atgataagga gatgttgcag gctcagattc aggcaactaa gcagctgcag gcagacatga
6901 tggctataaa acaaggggtc ttgaccgctg gcggcttttc ccctgctgat gcagccagag
6961 gtgctgtgaa cgcgcccatg acacaggcgc tggattggaa tggcacaagg tattgggcac
7021 caaactccat gaggaccaca tcttattctg gaaaattcac atcaaccgcc ccagtgaggc
7081 aggctgactt ccagcacacc caaagccggc cttcgggtgg ctcctctgtg tcttcctttg
7141 ccactcagtc ttcaaggcca actctgacca caaccactgg ctcctcacat ggcacagcct
7201 catcaaattc gactcgcagc acaagcctct cccaatcaac ggtctccaga gctacatcta
7261 ggactggtga gtgggttaga gatcaaaata gaaatttgga accctacatg catggtgcct
7321 tacagacagc ctttgttacc ccaccttcca gcagggcatc tgacgggaca gtctcaaccg
7381 tccctaaagg tgttttggac tcctggacac ctgcgtttaa cacccgcagg cagccgcttt
7441 ttgcacacct ccgtaagagg ggggagtcac aagtttag
//