Typing tool
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Typing tool
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Complete norovirus genomes
| OP690505 | GII.3 | |
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| GII.P25 |
ORF1: 5..5140
ORF2: 5121..6767
ORF3: 6767..7531
LOCUS OP690505 7573 bp RNA linear VRL 25-OCT-2022
DEFINITION Norovirus GII isolate Hu/US/2022/GII.3[P25]/CA-RGDS-1158, complete
genome.
ACCESSION OP690505
VERSION OP690505.1
KEYWORDS .
SOURCE Norovirus GII
ORGANISM Norovirus GII
Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes;
Picornavirales; Caliciviridae; Norovirus; Norwalk virus.
REFERENCE 1 (bases 1 to 7573)
AUTHORS Pan,C.-Y., Hatada,A., Morales,C., Montmayeur,A.M., Chhabra,P. and
Vinje,J.
TITLE Direct Submission
JOURNAL Submitted (20-OCT-2022) Viral and Rickettsial Disease Laboratory,
California Department of Public Health, 850 Marina Bay Parkway,
Richmond, CA 94804, USA
COMMENT ##Assembly-Data-START##
Assembly Method :: Geneious v. R10; SPAdes v. 3.6
Sequencing Technology :: Illumina
##Assembly-Data-END##
FEATURES Location/Qualifiers
source 1..7573
/organism="Norovirus GII"
/mol_type="genomic RNA"
/strain="CA-RGDS-1158"
/isolate="Hu/US/2022/GII.3[P25]/CA-RGDS-1158"
/isolation_source="stool"
/host="Homo sapiens"
/db_xref="taxon:122929"
/country="USA: CA"
/collection_date="Mar-2022"
/note="Amplicon sequencing:first 35 nt does represent
primer sequence;
genotype: GII.3[P25]"
gene 5..5140
/gene="ORF1"
CDS 5..5140
/gene="ORF1"
/codon_start=1
/product="nonstructural polyprotein"
/protein_id="UYL33179.1"
/translation="MKMASNDASAATAGKTSTNSEIHNQDVNTTSSLFANMTVGLKRA
LGARPKQSAPRASSPNREGKSETTTRTPPLNKGGRDNTPQIPPPPPNGEDIIIKYTKQ
DDVIAGVPTVATVDVPPTHNTAYSVPPLDQREKVEAKEPLTGSIIEMWDGEIFHYGLY
VEKGLVLGVHKPPAAISFARIELTPLSLYWRTVYTPPYLVAPETLRRLHGESFPYNAF
DNNCYSFCCWVLDLNDSWLNRKFVSRTTGFYRPYQEWNRKPLPTMDEGKLKKVANVLL
CGLSGLFTRPIKDLIGKLRPLNILNIITNCDWTFPGVVEALILLAELFGVFWTPPDIS
TFIASLLGDYEMQGPEDIAVEVVPVILGGIGMVLGFTKERIGRLLSSAASSLRACREI
GNYGIEVVKLVMKWFFPTKDETNEMDMVRAIEDAVLDFEAIQNNHMTALLKDKNSLAT
FLRELDMEEEKARKLSTKSASPDIIGTINALLARIAAARSLVHKAKEEMSSRMRPVVI
MISGRPGIGKTHLARDLAKKMAATLSGDQRVGLVPRNGVDHWDAYKGERIVLWDDYGM
SNPVTDALRLQELADTCPLTLNCDRIENKGKVFDSDTIIITTNLANPAPLDYVNFEAC
SRRIDFLVYADSPSVDKAKRDFPGQPDMWKDAFKPDFSHIKLQLAPQGGFDKNGNTPH
GKGVMKSLTTHSLIARATGLLHERLDEFDLQGPELPVYNFDQNRVAAFRKLAADNKYG
LVETIKVGNKLKSVRTLEQLKDALKDISIKPCRIIYNSMAYDLDSNGSGRVNVKKVVD
HKVQTNNELNSALNNLRGARVRYYVKCVQEMVYSLLQIAGAAFVTSRMTRRLNVSGIW
ARPEKQVEAIEEPPVPPSEDWTITPSDAIQEGKKGKNKSGRGKKHTAFSSKGLSDEEY
DEFKRIREERQGKYSIEEYLQDRDRYYEELAIAKATEENFCEEEEIKIRQRVFRPTRK
QRREERATLGLVTGSEIRKRNPDDFKPKGKLWADDDRSVNYNEKIDFEAPPSLWSRIV
NFGSGWGFWVSSNLLITSTHVIPPNMTEAFGVPISQIQIHRSGEFCKMRFPKAIRPDV
SGMILEEGAPEGTVVTILIKRTTGELMPLAARMGTHATMKIQGKMLGGQMGMLLTGSN
AKNMDLGTIPGDCGCPYVYKRGNDWVVIGVHTAAARGGNTVICATQGPDGEATLEGGD
NHGTYCGAPILGPGNAPKLSTKTKFWRSSNAPLPPGTYEPAYLGGKDPRVKGGPSLQQ
VMRDQLKPFTAPRGKPPRPAILEAAKETICNVLEQVIEPPQKWSYAQACASLDKTTSS
GHPHHMKKNDNWNGESFTGVLADQASKANLMFEQGKHMQPVYTAALKDELVKTSKIYE
NIKKRLLWGSDLGTMIRCARAFGGLMDEMEANCVNLLIRVGMNMNEDGPIIFEKHSKY
KYHYDADYSRWDSTQQRHILGSALEIMVRFSAEPELAQIVSEDLLAPSVVDVGDFKIT
INEGLPSGVPCTSQWNSISHWLITLCAISEVSGLSPDVVQTNSCFSFYGDDEIVSTDI
KLDPMKLTNKLKEYGLIPTRPDKTEGPLIIKESLEGLTFLRRDVCRDPAGWYGKLDQS
SIMRQLYWTKGTNHDDPNETMIPHSQRPIQLMSLLGEAALHGPTFYKKVSKLVITELK
EGGMDFYVPRQEPMFRWMRFSDLSTWEGDRNLAPEGVNEDGVE"
mat_peptide 5..1045
/gene="ORF1"
/product="p48"
mat_peptide 1046..2143
/gene="ORF1"
/product="NTPase"
mat_peptide 2144..2680
/gene="ORF1"
/product="p22"
mat_peptide 2681..3064
/gene="ORF1"
/product="VPg"
mat_peptide 3065..3607
/gene="ORF1"
/product="Pro"
mat_peptide 3608..5137
/gene="ORF1"
/product="RdRp"
gene 5121..6767
/gene="ORF2"
CDS 5121..6767
/gene="ORF2"
/note="major capsid protein"
/codon_start=1
/product="VP1"
/protein_id="UYL33180.1"
/translation="MKMASNDAAPSSDGAAGLVPEINNEAMALEPVAGAAIAAPLTGQ
QNIIDPWIMNNFVQAPGGEFTVSPRNSPGEVLLNLELGPEINPYLAHLSRMYNGYAGG
FEVQVVLAGNAFTAGKVIFAAIPPNFPIDNLSAAQITMCPHVIVDVRQLEPINLPMPD
VRNNFFHYNQGSDSRLRLIAMLYTPLRANNSGDDVFTVSCRVLTRPSPDFSFNFLVPP
TVESKTKPFTLPILTISEMSNSRFPVPIDSLHTSPTDNVIVQCQNGRVTLDGELMGTT
QLLPSQICAFRGTLTTSTNRDRDQPDAAAPRIFDHRWHIQLDNLNGTPYDPAEDIPAP
LGTPDFQGKVFGVASQRNPDGTTRAHEAKVDTTSGRFTPKLGSLEIITESGDFNPNMP
TKFTPVGVGVDTDEEFQQWVLPRYSGQVTHNMNLAPAVAPNFPGEQLLFFRSQLPSSG
GTSSGTLDCLVPQEWVQHFYQESAPAQTQVALVRYVNPDTGRVLFEAKLHKLGFITIA
KNGDSPITVPPNGYFRFESWVNPFYTLAPMGTGNGRRRIQ"
gene 6767..7531
/gene="ORF3"
CDS 6767..7531
/gene="ORF3"
/note="minor structural protein; small basic protein"
/codon_start=1
/product="VP2"
/protein_id="UYL33181.1"
/translation="MAGAFVAGLAGDILTNTVGSLVSAGANAINQKVDFENNKYLQNA
SFNHDKEMLNAQIEATKRLQADMIAIKQGVLTASGFSPADAARGAINAPVTKVLDWSG
TRYWAPNATSTTSMSGGFTSQVVHRTTPNFKMSQTPKPPPSSGSSVRSNSTQLTSLSS
HSSGSSRSSGSMVISSLPSSSRTRDWVNQQNFNLEPHMPGSLRTAFVTPPSSTVSSSD
TVSTVPKSVLDSWTSAFNTRRQPLFAHLRRRGESNA"
ORIGIN
1 gtgaatgaag atggcgtcta acgacgcttc cgctgcgacc gctggcaaaa ccagcacaaa
61 cagtgaaatt cacaaccaag atgtaaacac tacatcaagc ctcttcgcca acatgaccgt
121 tggcttgaag agggccctgg gggcgaggcc aaaacagtct gcccccaggg cttcctcccc
181 caatagggag gggaagtctg aaaccaccac taggactccc cccctaaaca agggaggaag
241 ggacaacacc ccccaaatac cccccccgcc acccaatggt gaggacataa tcatcaaata
301 caccaaacag gatgatgtga ttgcaggggt gcccactgtc gctacggtgg acgtcccccc
361 aacacacaac accgcctaca gtgtccctcc cttggatcag agggagaagg ttgaggcaaa
421 ggaacccctg acaggctcaa taattgagat gtgggatggt gaaattttcc attatgggct
481 ctatgttgag aagggcttgg ttcttggagt gcacaaaccc ccggctgcca taagctttgc
541 acgcatagag ctcacccccc tctctttata ctggagaaca gtctacacac caccttatct
601 agtggcccca gaaacactta ggagactcca cggggagtcg ttcccataca atgcatttga
661 caataattgc tactccttct gctgttgggt cttggacctg aacgattcct ggcttaacag
721 aaagtttgtt tcgagaacta caggtttcta cagaccctac caagagtgga acagaaagcc
781 cctaccgacc atggatgagg gaaaactcaa gaaagtggcc aatgtgctac tgtgtggtct
841 ctccggtctt ttcaccagac caatcaagga cctcataggg aaactaagac cattgaacat
901 actcaatatc atcaccaatt gtgattggac ttttcccggg gttgtggaag ctctcatatt
961 acttgcagaa ctcttcggag tcttctggac accaccagac atttctactt ttatagcatc
1021 acttctgggt gattatgaaa tgcagggccc cgaggacatt gcagttgaag ttgtgccagt
1081 aattctcggt ggcataggca tggtgctcgg gttcaccaaa gagagaatcg gccggttgct
1141 gagctctgcc gcttcttcgc ttagggcgtg cagagagatc ggcaattacg gaatagaagt
1201 ggtaaagttg gtgatgaaat ggtttttccc caccaaagat gagacaaatg agatggacat
1261 ggtgagggca atagaggatg ccgtgctcga ctttgaggcc atacaaaaca accacatgac
1321 agcattactc aaagacaaaa atagcctagc aaccttcctt agggagttag acatggaaga
1381 ggagaaagcg cggaagttat caacaaagtc cgcgtcccca gacatcattg gcaccataaa
1441 cgcccttcta gccaggattg ccgccgctag gtccctagtc cacaaggcca aagaagaaat
1501 gtcatctagg atgcgtcctg ttgtcattat gatctctggc cgacctggga taggaaagac
1561 acatctagcc cgcgacctgg ccaaaaagat ggcggcaacc ctctcaggtg accagagggt
1621 agggctcgtg ccaaggaacg gtgtcgatca ttgggacgca tacaaagggg agagaattgt
1681 gctctgggat gactatggaa tgagcaaccc tgtgaccgac gcgctgcggc tccaagagct
1741 tgccgacaca tgccccttga cgctcaactg tgataggata gagaacaagg ggaaggtctt
1801 tgatagtgac actataatta tcaccaccaa tttggccaat cctgcccctc tagattatgt
1861 taattttgaa gcttgctctc gccgaattga tttccttgtc tatgcggact ccccctcggt
1921 tgataaggcg aagagagact tccccggcca accagatatg tggaaggacg catttaaacc
1981 agacttttcc cacataaaac tccaactggc accacaaggg ggctttgata agaacggaaa
2041 caccccccat gggaagggtg tcatgaaatc actgactaca cattccctta ttgcccgtgc
2101 cacgggtctg ttacatgaga ggttggatga gttcgaccta caggggcctg aactacctgt
2161 gtacaatttt gaccaaaaca gggtggccgc ttttagaaag cttgcggctg acaacaagta
2221 cgggctcgtg gaaaccataa aagtgggcaa caaactgaag agtgtcagga ctctagaaca
2281 acttaaggat gccttaaaag acataagtat caagccttgc agaataatct acaactccat
2341 ggcttatgat ctcgactcga atgggtcagg aagggttaac gtcaaaaagg ttgtggatca
2401 taaagtccaa actaacaatg aactcaactc cgcgcttaac aacctgcgtg gcgccagggt
2461 aagatactat gtcaagtgtg ttcaagagat ggtgtactct ctcctccaga tcgctggcgc
2521 ggccttcgtc acttcaagaa tgacgcgaag attaaacgtc agtggtatct gggccaggcc
2581 agaaaaacag gtggaggcca ttgaagaacc cccagtcccc ccatctgaag attggactat
2641 aaccccatca gatgcaatcc aagagggcaa gaagggcaag aacaaaagtg gcagaggtaa
2701 gaaacacact gccttctcca gcaaaggcct gagcgatgag gagtatgatg aatttaaaag
2761 aatcagggaa gagaggcagg gaaaatattc catagaagaa tacctccagg acagagaccg
2821 gtactatgag gaattggcca tagccaaagc tacagaagaa aacttctgtg aggaggaaga
2881 aataaaaatt agacagaggg tcttccgccc aaccagaaaa caacgtaggg aagaaagggc
2941 gaccctagga ctggtcacgg gtagtgaaat caggaaaagg aacccagatg acttcaaacc
3001 aaaaggaaaa ttgtgggctg atgatgaccg cagtgtaaac tacaatgaga aaatagattt
3061 cgaggcccct cctagccttt ggtcccgaat agtgaatttt gggtcaggat ggggtttctg
3121 ggtgtcttct aacctgttga tcacatcaac acatgtcatc cccccgaaca tgactgaggc
3181 ttttggtgta ccaataagcc agatacaaat acacagaagt ggagagttct gcaaaatgag
3241 gttccccaag gctataagac ctgatgtctc gggcatgatc ctagaggaag gagcacctga
3301 aggaacggtg gtgaccatac tgattaagag aaccaccggt gagctcatgc cattggctgc
3361 ccgaatgggc acccacgcca ccatgaagat acaagggaaa atgcttggag gtcaaatggg
3421 aatgctcctc acggggtcca acgccaagaa tatggacctc ggcaccattc ctggagactg
3481 tggttgcccc tatgtgtaca agagaggtaa tgattgggtg gtcataggag tgcacaccgc
3541 agctgccaga ggtggcaaca ctgtgatctg cgccacccag gggccagatg gtgaggccac
3601 actcgaggga ggagacaatc acgggaccta ctgtggtgca ccaatacttg gaccaggaaa
3661 tgcaccaaag ctcagcacca aaaccaagtt ttggaggtca tccaacgccc cactcccacc
3721 tggtacttat gagcctgctt acctaggagg aaaggaccca agggtaaaag ggggtccgtc
3781 attacaacag gttatgaggg atcaactcaa acccttcacc gccccccgag ggaaaccacc
3841 gcgaccagcg attttagagg cagccaaaga gaccatctgc aatgtgcttg agcaagtcat
3901 tgaaccaccc caaaaatggt cttatgctca ggcctgtgct tcattggata agacaacatc
3961 tagtggtcac ccccaccaca tgaaaaagaa tgacaattgg aacggagagt ctttcactgg
4021 tgtattggct gatcaggcct ctaaggccaa tctcatgttt gaacagggaa aacacatgca
4081 acccgtgtac actgctgctc tcaaagatga gctcgtcaag actagtaaga tctatgaaaa
4141 cattaagaaa agacttctat ggggatcaga tctgggcaca atgatccgtt gtgctagggc
4201 attcggtggc ctcatggatg agatggaggc aaattgtgtg aatttactaa ttagagttgg
4261 catgaacatg aatgaagatg gacccatcat atttgagaag cattcaaaat acaaatacca
4321 ttatgatgct gactattcca ggtgggactc aacccaacag aggcacatcc ttgggtctgc
4381 ccttgaaata atggttagat tttcagctga acctgaatta gcacaaatag tgtctgaaga
4441 tctcctagcc cccagtgtgg tggacgttgg cgacttcaaa atcaccataa atgaaggatt
4501 gccctctgga gtgccgtgta catcacagtg gaactcaatt tcccactggc tcataacact
4561 gtgtgccata tcagaagttt caggactgtc gccagacgta gtgcaaacaa actcctgctt
4621 ctccttctac ggggatgatg agatagtcag caccgacatc aagttagatc ccatgaagct
4681 gaccaacaag ttgaaagagt atgggttgat tccaacaagg ccagacaaga cagaggggcc
4741 gctcataatt aaagagagtc ttgagggcct aactttcctg aggagggacg tgtgtcgaga
4801 cccagctggt tggtatggga aacttgacca atcctcaatc atgagacaac tgtattggac
4861 taagggaacc aaccatgatg atcccaatga gacaatgatt ccacactctc agagacccat
4921 acaattgatg tcactgctag gggaggcagc actgcatggc ccaactttct acaagaaagt
4981 cagcaaattg gtcatcactg agctcaaaga aggtgggatg gatttctatg taccaagaca
5041 ggaacctatg ttcagatgga tgagattctc ggatctcagt acttgggagg gcgatcgcaa
5101 tcttgctccc gaaggtgtga atgaagatgg cgtcgaatga cgctgctcca tctagtgatg
5161 gtgccgccgg cctcgtccca gagatcaaca atgaggcaat ggcgctagaa ccagtggcgg
5221 gcgcagcaat agcagcaccc ctcactggtc agcaaaatat aattgatccc tggattatga
5281 acaattttgt gcaagcacct ggtggtgagt ttacagtgtc ccccagaaat tcccctggtg
5341 aagtgttact taatctggaa ctaggcccag aaataaatcc ttacctggcc cacctttcta
5401 gaatgtacaa tggctatgca ggtgggtttg aagtgcaggt ggtcctagct ggaaatgcat
5461 tcacagcagg aaaggtaatc tttgcagcca taccccccaa ttttcctatt gataatctga
5521 gtgcagcaca gatcacaatg tgcccgcatg tgattgtgga tgttaggcag ttagaaccaa
5581 tcaacctccc aatgcctgat gttcgcaata atttctttca ttataatcaa gggtctgatt
5641 caagattacg cttgatcgca atgttgtata cacctcttag agcaaataat tctggtgatg
5701 atgttttcac tgtgtcttgt agagttttaa ccaggcctag tcctgatttc tctttcaact
5761 ttcttgtacc acctactgtg gaatcaaaga caaagccttt cacccttcct attctgacca
5821 tctcggagat gtccaattct aggtttccag tgccaattga ttctctacac accagcccaa
5881 ccgacaatgt tattgtccaa tgtcaaaacg ggcgcgtcac tctcgatggc gagctgatgg
5941 gtaccactca actattacca agccaaatat gtgctttcag gggcacgctc acaacatcaa
6001 caaataggga cagggaccaa cctgatgcag cagcccccag gatattcgac catcgttggc
6061 atattcaatt ggataacctg aatggcaccc cttatgatcc tgcagaggac ataccagctc
6121 ccttgggtac gccagatttt cagggtaagg tctttggtgt ggctagccag aggaaccccg
6181 atggcacaac aagagcacat gaggcaaaag tggacacaac atctggccgc tttactccaa
6241 agttgggttc cctagaaata atcactgaat ctggtgattt taatccaaat atgccaacaa
6301 aattcacccc agttggtgtt ggagttgaca ctgatgaaga attccaacaa tgggtattgc
6361 ctagatattc tggccaggtc acccacaaca tgaatctggc cccagctgtt gcccccaact
6421 tccctggtga gcagcttctt ttcttccgct cacagctacc atcttctggt gggacgtcca
6481 gcgggacttt ggactgcttg gtcccccagg agtgggttca gcatttctac caggaatcag
6541 cccctgccca gacacaggtg gccctggtca gatatgtcaa ccctgacact ggtagggtgt
6601 tgtttgaggc caaacttcat aaattgggtt ttataaccat agcaaagaat ggtgactctc
6661 caataactgt ccccccaaat gggtatttta gatttgaatc ttgggtgaac cccttttata
6721 cacttgcccc catgggaact ggcaacgggc gcagaaggat tcaataatgg caggagcatt
6781 tgtggcagga ttggctggtg acatactcac aaacactgtg ggatctttgg tgagtgcagg
6841 ggctaatgct attaatcaga aggttgattt tgagaataat aaatatttgc aaaatgcatc
6901 ttttaatcat gataaggaga tgttgaatgc acaaattgag gcaacaaaaa ggctgcaggc
6961 tgatatgatt gctatcaaac aaggggtctt gaccgctagc ggcttttccc ctgctgatgc
7021 agcccgtggg gcaatcaatg ctccagtgac aaaagtcctg gactggagtg gaacaaggta
7081 ctgggcacca aacgccacct ccacaacttc aatgtcaggt ggctttacaa gccaagttgt
7141 gcacaggacc acaccaaatt tcaagatgag ccagactccc aagcccccac ccagcagcgg
7201 gtcttcagtg agatcaaact caacacagct cactagcctg agctcacact catccgggtc
7261 atctcgatcc agtgggtcca tggttatcag ctcactacca tcttccagca ggaccagaga
7321 ttgggttaat caacaaaatt tcaatttgga accacacatg cctgggtctc ttaggacagc
7381 ttttgtcact ccaccatcta gcacagtttc tagttcagac acggtctcaa ccgtgcccaa
7441 aagtgttttg gactcctgga catctgcgtt taacacacgc agacagccgc tgtttgcaca
7501 ccttcgtaga aggggggagt caaatgctta gtgaaaagat tatctttgaa tttgatttag
7561 attagatttg att
//