Typing tool
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Typing tool
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Complete norovirus genomes
| MK616584 | GII.1 | |
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| GII.P33 |
ORF1: 1..5064
ORF2: 5045..6652
ORF3: 6652..7425
LOCUS MK616584 7452 bp RNA linear VRL 17-MAR-2019
DEFINITION Norovirus GII isolate CA-RGDS-1021 nonstructural polyprotein (ORF1)
gene, partial cds; and VP1 (ORF2) and VP2 (ORF3) genes, complete
cds.
ACCESSION MK616584
VERSION MK616584.1
KEYWORDS .
SOURCE Norovirus GII
ORGANISM Norovirus GII
Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes;
Picornavirales; Caliciviridae; Norovirus; Norwalk virus.
REFERENCE 1 (bases 1 to 7452)
AUTHORS Pan,C.-Y., Huynh,T., Castro,C.J., Ng,T.F., Marine,R.L. and
Wadford,D.A.
TITLE Norovirus GII.Pg-GII.1 genomes from gastroenteritis outbreaks,
California, 2018
JOURNAL Unpublished
REFERENCE 2 (bases 1 to 7452)
AUTHORS Pan,C.-Y., Huynh,T., Castro,C.J., Ng,T.F., Marine,R.L. and
Wadford,D.A.
TITLE Direct Submission
JOURNAL Submitted (11-MAR-2019) 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..7452
/organism="Norovirus GII"
/mol_type="genomic RNA"
/isolate="CA-RGDS-1021"
/isolation_source="stool"
/host="Homo sapiens"
/db_xref="taxon:122929"
/country="USA: CA"
/collection_date="Feb-2018"
/note="genotype: GII.Pg-GII.1"
gene <1..5064
/gene="ORF1"
CDS <1..5064
/gene="ORF1"
/codon_start=1
/product="nonstructural polyprotein"
/protein_id="QBL14409.1"
/translation="TSNNDNAKSSSDGVLSSMAVTFKRALGARPKQPPPRETEQKQKP
PRPPTPELIKKIPPPPPNGEDDIVVSYSAKDGVSGLPELSTVRQPDGTNTAFSVPPLN
QRENKDAKEPLPGTILEMWDGEIYHYGLYVERGLVLGVHKPPAAISLAKVELTPLSLY
WRPVYTPQYLISPETLKKLHGETFPYTAFDNNCYAFCCWVLDLNDSWLSRRMIQRTTG
FFRPYQDWNRKPLPTMDDSKLKKVANIVLCALSSLFTRPIKDIIGKLRPLNILNILAS
CDWTFAGIVESLILLAELFGVFWTPPDVSAMIAPLLGDYELQGPEDLAVELVPVVMGG
IGLVLGFTKEKIGKMLSSAASTLRACRDLGAYGLEILKLVMKWFFPKKDEANELAMVR
SIEDAVLDLEAIENNHMTTLLKDKDSLATYMKTLDLEEEKARKLSTKSASPDIVGTIN
SLLARIAAARSLVHRAKEELSSRPRPVVVMISGKPGIGKTHLARDLAKKVAATLTGDQ
RVGLIPRNGVDHWDAYKGERVVLWDDYGMSNPIHDALRLQELADTCPLTLNCDRIENK
GKVFDSDAIIITTNLANPAPLDYVNFEACSRRIDFLVYADAPDVEKAKRDFPGQPDMW
KDAFRPDFSHIKLMLAPQGGFDKNGNTPHGRGVMKTLTSGSLIARASGLLHERLDEYE
LQGPTPTTFNFDQNKVFAFRQLAAENKYGLVDTMRVGSQLKNVKTVSELKQALKNISI
RRCQIVYGGLTYSLESDGKGNVRVEKVQSPAVQTNNELTGALHHLRCARIRYYVKCVQ
EALYSIIQIAGAAFVTTRIAKRMNIQNLWSRPQVDDEEETTSKDGCPKPKDEEEFVIS
SEDIKAEGKKGKNKSGRGKKHTAFSSKGLSDEEYDEYKRIREERNGKYSIEEYLQDRD
KYYEEVAIARATEEDFCEEEEAKIRQRIFRPTRKQRKEERVSLGLVTGSEIRKRNPDD
FKPKGKLWADDDRSVDYNEKLSFEAPPSIWSRIVNFGSGWGFWVSPSLFITSTHVIPQ
GAQEFFGVSIKQIQIHKSGEFCRLRFPKPIRTDVTGMILEEGAPEGTVATLLIKRPTG
ELMPLAARMGTHATMKIQGRTVGGQMGMLLTGSNAKSMDLGTTPGDCGCPYIYKRGND
YVVIGVHTAAARGGNTVICATQGSEGEAVLEGGDNKGTYCGAPILGPGNAPKLSTKTK
FWRSSTAPLPPGTYEPAYLGGKDPRVKGGPSLQQVMRDQLKPFTEPRGKPPKPSVLEA
AKKTIINVLEQTIDPPQKWTFAQACASLDKTTSSGYPHHVRKNEHWNGESFTGKLADQ
ASKANLMFEEGKHMTPVYTGALKDELVKTDKIYGKIKKRLLWGSDLATMIRCARAFGG
LMDELKAHCVTLPIRVGMNMNEDGPIIFGKHSRYTYHYDADYSRWDSTQQRAVLASAL
EIMVKFSPEPHLAQIVAEDLLSPSVMDVGDFKISITEGLPSGVPCTSQWNSIAHWLLT
LCALSEVTDLSPDIIQANSLFSFYGDDEIVSTDIKLDPERLTAKLKEYGLKPTRPDKT
EGPLVISEDLDGLTFLRRTVTRDPAGWFGKLEQSSILRQMYWTRGPNHEDPSETMIPH
SQRPIQLMSLLGEAALHGPSFYSKISKLVISELKEGGMDFYVPRQEPMFRWMRFSDLS
TWEGDRNLAPSFVNEDGVE"
mat_peptide <1..954
/gene="ORF1"
/product="p48"
mat_peptide 955..2052
/gene="ORF1"
/product="NTPase"
mat_peptide 2053..2589
/gene="ORF1"
/product="p22"
mat_peptide 2590..2988
/gene="ORF1"
/product="VPg"
mat_peptide 2989..3531
/gene="ORF1"
/product="Pro"
mat_peptide 3532..5061
/gene="ORF1"
/product="RdRp"
gene 5045..6652
/gene="ORF2"
CDS 5045..6652
/gene="ORF2"
/note="major capsid protein"
/codon_start=1
/product="VP1"
/protein_id="QBL14407.1"
/translation="MKMASNDAAPSNDGAAGLVPEVNNETMALEPVAGASIAAPLTGQ
NNVIDPWIRMNFVQAPNGEFTVSPRNSPGEVLLNLELGPELNPFLAHLSRMYNGYAGG
VEVQVLLAGNAFTAGKLVFAAIPPHFPLENLSPGQITMFPHVIIDVRTLEPVLLPLPD
VRNNFFHYNQQPEPRMRLVAMLYTPLRSNGSGDDVFTVSCRVLTRPSPDFDFNYLVPP
TVESKTKPFTLPILTIGELSNSRFPVPIDELYTSPNEGVVVQPQNGRSTLDGELLGTT
QLVPSNICALRGRINAQVPDDHHQWNLQVTNANGTPFDPTEDVPAPLGMPDFLANIYG
VTSQRNPDNTCRAHDGVLATWSPKFTPKLGSVVLGTWEEQDLDLNQPTRFTPVGLYDT
NHFDQWILPNYSGRLTLNMNLAPSVAPLFPGEQILFFRSHIPLKGGTSNGAIDCLLPQ
EWIQHFYQESAPSPTDVALIRYTNPDTGRVLFEAKLHRQGFITVANSGSRPIVVPPNG
YFRFDSWVNQFYSLAPMGTGNGRRRVQ"
gene 6652..7425
/gene="ORF3"
CDS 6652..7425
/gene="ORF3"
/note="minor structural protein; small basic protein"
/codon_start=1
/product="VP2"
/protein_id="QBL14408.1"
/translation="MAGAFVAGLAGDIVTNSIGSLVNAGANAINQKVDFENNKQLQQA
SFNHDKEMLQAQIQATKQLQADMIALRQGVLTAGGFSPTDAARGAVNVPMTQVLDWNG
TRYWAPGATKTTAFSGGFTSSPNTRTVDLPRKTSTTPAPTPISRPSSSASTVSTRSTI
ISGTSGLSSLTRSSFNSQPTSSSSRTSEWVRGQNRALEPYMRGALQTAYVTPPSSRAS
SNGTVSTVPKEVLDSWTSVFNTHRQPLFAHLRRRGESQV"
ORIGIN
1 accagcaaca acgacaacgc aaaatcttca agtgacggag tactaagtag tatggctgtc
61 acttttaaac gagccctcgg ggcccggcct aaacagccgc ccccgaggga aacagaacaa
121 aaacaaaaac ctccacgacc gcccaccccg gagttaatca aaaagattcc acctcccccg
181 cccaacgggg aggacgatat agtggtatcc tatagtgcca aagatggtgt ctccggcctg
241 cctgagctat ccaccgtcag gcagccagat gggacaaaca cagcatttag tgtcccccca
301 ctcaaccaga gggaaaacaa agatgctaaa gaaccgctgc ctggcaccat cttggaaatg
361 tgggacggag agatttacca ctacggcttg tacgtggagc ggggcttggt gcttggggtg
421 cacaaaccac cagcggctat tagccttgca aaggttgaac taacaccact gtctctgtac
481 tggaggccag tgtacacccc tcagtacctc atatccccag aaactctcaa aaagttacat
541 ggagagacat tcccttacac ggcctttgac aacaactgtt acgccttttg ttgttgggtc
601 ttggatctaa atgactcttg gctcagcagg aggatgatac agagaacaac tggcttcttc
661 agaccctacc aggactggaa caggaaacct ctccccacca tggatgattc caaattgaaa
721 aaggtggcta atatagtcct gtgtgcattg tcatcattat tcaccaggcc cattaaggac
781 ataataggaa aactaaggcc cctaaacata ctcaatatac tagcttcctg cgactggact
841 ttcgcgggaa tagtagaatc cctaattctc cttgcagaac tcttcggagt tttctggaca
901 cccccagatg tgtctgcgat gatcgccccc ttactaggcg actacgaact acagggacct
961 gaagatctcg ctgtggaact cgtgccagta gtgatggggg ggataggttt ggttctaggt
1021 ttcaccaagg agaagattgg caagatgcta tcatctgccg cgtccaccct cagagcttgt
1081 agagatctcg gagcatatgg attggaaatt ctaaagttgg tcatgaagtg gttcttcccg
1141 aagaaggatg aggcgaatga acttgcaatg gtgagatcca ttgaggatgc agtgctagac
1201 cttgaagcaa ttgagaacaa tcacatgaca accctactca aagacaaaga cagcttagca
1261 acctacatga agactctgga ccttgaggag gagaaagcca ggaaactctc caccaaatct
1321 gcttctcctg atattgtggg cactatcaat tcacttctgg cacggattgc agctgcccgt
1381 tccctggtac atcgggcaaa agaagagctt tccagtaggc caagacccgt tgttgtcatg
1441 atatcaggaa agccagggat agggaaaacc caccttgcca gagatttggc aaagaaagtt
1501 gcagccaccc tcacagggga ccagagggta ggcctcatcc cacggaatgg tgtcgatcac
1561 tgggacgcgt acaaaggtga gagagtcgtc ctttgggatg actatggaat gagtaacccc
1621 atccacgacg cccttaggct acaagaactt gctgacactt gccccctaac attaaattgt
1681 gatagaattg agaacaaagg aaaggtcttt gacagtgatg ccataattat cacaactaat
1741 ctggctaacc cggcaccact ggactatgtt aattttgaag catgttcgag gcgcatcgac
1801 ttcctagtgt atgctgatgc ccccgatgtt gaaaaagcaa aacgcgactt cccagggcag
1861 cctgacatgt ggaaggatgc ttttagacct gacttctcac acataaaatt gatgttggct
1921 cctcagggtg gttttgataa gaatggtaac accccacatg gaagaggtgt catgaaaacc
1981 ctcacatctg gctccctcat tgcccgtgct tcaggactcc tccacgaaag actggatgag
2041 tacgagttac aagggccaac acccacaacc ttcaatttcg accaaaacaa ggtgttcgcc
2101 tttagacagc ttgccgctga aaacaagtac gggctggtgg acaccatgag agtaggaagc
2161 cagctcaaga atgtcaagac cgtgtcagag cttaaacagg cacttaagaa catttcaatt
2221 agaaggtgcc agatagtcta tggtggtctc acctattcac ttgaatctga tggcaaaggt
2281 aatgtgaggg ttgagaaggt gcaaagtcca gctgtgcaga ccaacaatga gctaactggc
2341 gcactacacc acttgaggtg cgctaggatt agatattatg ttaagtgtgt ccaggaagct
2401 ttgtattcca tcatccaaat tgctggagcc gcgtttgtca ccacgcgcat tgcaaagcgc
2461 atgaacatac aaaacctctg gtccagacca caggtagatg atgaggaaga gaccaccagc
2521 aaagacgggt gcccaaaacc aaaggatgag gaggagtttg tcatctcgtc tgaagacatc
2581 aaagctgaag gtaagaaggg aaagaacaag tctggccgcg gcaagaaaca cacagccttc
2641 tcgagtaagg gtcttagtga tgaggagtac gatgagtaca agagaatcag agaagaaaga
2701 aatggcaagt actccataga ggaatacctc caagatagag acaagtacta tgaggaggtt
2761 gccatagcca gggccactga agaggacttt tgtgaggaag aagaggccaa gatccggcag
2821 aggattttca gaccaacaag gaaacaacgc aaggaggaga gggtttcact cggactggtc
2881 acaggctcgg aaatcaggaa aaggaacccg gatgacttca aacctaaagg aaagttgtgg
2941 gctgatgacg acaggagtgt cgattacaat gaaaaactca gttttgaagc tcccccaagc
3001 atctggtcga gaatagtcaa ctttggatca ggttggggct tctgggtctc accaagcctt
3061 tttataacat ccactcatgt catacctcaa ggggcacaag agttcttcgg tgtatccatc
3121 aaacagatcc aaattcacaa gtcaggtgag ttctgccgac taagattccc aaagccaatc
3181 agaactgatg tgacaggcat gatcctagag gaaggggccc ctgaaggcac cgtggccaca
3241 ctgctcataa agaggccaac tggagagctg atgccactag cggctagaat gggcacccat
3301 gcaactatga agatccaagg ccgaactgtc gggggacaga tggggatgct cctgacagga
3361 tccaacgcca agagcatgga tttgggtact acaccaggtg attgtggatg cccatatatc
3421 tacaaaagag gaaatgacta cgtagtcatc ggggtccaca cagctgccgc ccgcggaggg
3481 aacactgtta tctgtgcaac ccaaggaagt gagggcgagg ccgttcttga aggtggtgac
3541 aacaaaggca cctattgtgg cgccccaatc ctaggtccag gaaatgcccc caaactcagt
3601 actaaaacta aattctggag gtcctcaaca gcaccactcc cgcctggcac atatgaacca
3661 gcttacctcg gaggtaaaga ccccagggtg aagggtggtc cctcattaca acaagttatg
3721 agagaccaat tgaaaccgtt cacagaaccc agaggtaagc caccaaagcc tagtgtattg
3781 gaagcagcca aaaagacaat tattaacgtc cttgagcaaa ctatagatcc accccagaaa
3841 tggacgttcg cacaggcgtg cgcctccctt gataaaacaa cctctagtgg ctatccgcac
3901 cacgtgcgga agaatgaaca ttggaatggg gaatctttca cagggaagtt ggctgatcag
3961 gcttcaaagg ctaatttgat gtttgaggaa ggaaaacaca tgacaccagt ctatacagga
4021 gctctcaagg atgagttagt caaaactgac aaaatatatg gtaagatcaa gaaaaggtta
4081 ttatggggct cagatctggc aaccatgatt cgttgtgctc gagcgttcgg agggttgatg
4141 gatgagctca aggcccattg tgtcacactc cccatcaggg tggggatgaa catgaatgaa
4201 gatggtccca tcatttttgg gaaacactct aggtacacct accattatga tgcagactac
4261 tctcgatggg actcaacaca gcagagagct gttttagctt cagccctaga gatcatggta
4321 aagttttccc cagaaccaca cctggctcaa attgtcgcag aagatctcct atctcccagc
4381 gtgatggacg tgggcgattt taaaatatca atcactgaag gactcccctc tggggtgcct
4441 tgcacctcac aatggaactc cattgctcat tggcttctca cgctctgtgc gctctctgag
4501 gtgacagatc tatctcctga catcatccaa gcaaactcac ttttctcttt ctatggtgat
4561 gatgaaattg tgagcactga tattaaatta gatccagaaa ggctaacagc caaactaaaa
4621 gagtatggcc tcaagccaac ccgcccggac aagactgaag ggcctttggt catttctgag
4681 gacttagatg gtctgacctt tttgcggaga actgtgaccc gtgatccagc aggttggttt
4741 ggaaaattgg aacaaagctc aatactaaga cagatgtatt ggaccagggg ccccaaccat
4801 gaagacccct ctgagacaat gataccacat tctcaacgac ccatacagtt gatgtcccta
4861 ttgggtgaag ctgcattgca tggcccatcg ttctacagca aaatcagcaa attggtcatc
4921 tcagagttga aagaaggtgg catggacttt tacgtgccaa gacaagagcc aatgttccgg
4981 tggatgaggt tctcagactt gagcacgtgg gagggcgatc gcaatctggc tcccagtttt
5041 gtgaatgaag atggcgtcga atgacgccgc tccatctaat gatggtgcag ccggtctcgt
5101 accagaggtc aacaacgaga cgatggcact tgagccggtg gctggggcct ctatagctgc
5161 ccctttgacc ggccaaaata atgtgataga cccctggatt agaatgaatt ttgtccaagc
5221 tccaaatggt gaatttacag tgtccccccg taattcccca ggtgaagttt tgttgaattt
5281 ggaattaggc cctgaactaa atccattctt ggcacatctt tcaagaatgt ataatggtta
5341 tgctggtggg gttgaagtgc aggtgctact tgctgggaat gcgttcacag caggaaaact
5401 agtgttcgcg gcaatccccc cgcacttccc tcttgagaat ctaagtcctg gtcaaattac
5461 aatgttccct cacgtgatta ttgatgttag aactttagaa cctgttcttt tgcctttacc
5521 agatgttagg aataatttct ttcattacaa tcagcagcct gagccccgta tgagacttgt
5581 ggctatgttg tatactcctc ttagatctaa tggctctggt gatgatgtgt tcacagtctc
5641 ttgtagggtc ctcacccgcc cctctccaga ttttgatttt aattatttgg ttcccccaac
5701 tgtggaatct aaaactaaac cattcaccct gccaatattg accattggag aattgtcaaa
5761 ttctaggttc ccagtgccaa tagatgaatt gtacaccagc cccaatgaag gagtggttgt
5821 gcaacctcaa aatggcagat caacacttga tggtgaactg cttggcacaa cacaacttgt
5881 accatcaaac atctgtgcct tgcgagggcg catcaacgcc caagtgccag acgaccacca
5941 tcaatggaac ttgcaggtta caaacgcaaa tgggactccc ttcgacccca ctgaagatgt
6001 ccctgcacca ttgggcatgc cagacttcct ggcaaacatc tacggagtta ctagccagag
6061 gaaccctgac aacacttgcc gtgcccatga tggggtcttg gcaacctgga gccctaaatt
6121 tacacctaag ttaggatctg tggttttggg cacttgggaa gaacaagatc ttgatctcaa
6181 ccaacctacc agattcacac ctgtcggttt gtatgataca aaccactttg atcagtggat
6241 tctacccaac tattctggaa gattaacctt aaacatgaat ttggcgccct ccgttgctcc
6301 ccttttccca ggtgaacaaa tactcttctt taggtcccac ataccactta aaggaggcac
6361 ttccaatggt gccattgact gtctactccc tcaggagtgg atccagcatt tctatcagga
6421 atcagccccg tcacccacag atgttgctct gattaggtac accaaccctg acacgggccg
6481 tgtccttttt gaggccaaac tacataggca ggggttcatt acagtagcaa attctggttc
6541 tagacctatt gttgtccccc ctaatggtta ttttaggttt gattcttggg ttaatcagtt
6601 ttattctctc gcccccatgg gaactgggaa tgggcgcaga agggtgcagt aatggctgga
6661 gcttttgtag caggtcttgc cggtgacata gtcaccaata gcattggttc acttgtgaac
6721 gctggagcca atgcaataaa ccaaaaagta gactttgaaa acaacaaaca actacagcag
6781 gcctctttca accatgataa ggaaatgttg caagctcaaa ttcaggccac aaaacaatta
6841 caggctgaca tgattgcgct cagacaaggg gtgttgaccg caggcggctt ctcccctact
6901 gatgcagcaa gaggggcggt taatgtgccc atgacgcaag tcttggactg gaatgggact
6961 aggtactggg cccccggagc caccaaaaca actgctttct ccggtgggtt cacaagctct
7021 cccaatacca ggactgttga tttgcctagg aaaacatcaa ccacaccagc ccccacacct
7081 atatccagac ctagttcttc tgcttctact gtttctaccc gctcaacaat tattagcggg
7141 acttctggcc tttcttcttt gactaggagc tcttttaatt cccagcccac ctcctcttct
7201 tctcggacta gcgaatgggt gcgtggtcaa aacagggcgc tggagcccta catgagggga
7261 gcgctgcaaa ctgcttacgt gacgcctccc tctagtagag cgtctagcaa tggcacagtc
7321 tcaaccgtgc caaaagaagt tttggactcc tggacatctg tgttcaacac ccacagacaa
7381 ccgcttttcg ctcatctccg tcggagaggg gagtcacagg tttagtgaaa agatgatttt
7441 tctttcttcc ac
//