Typing tool
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Typing tool
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Complete norovirus genomes
| MK616561 | GII.12 | |
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| GII.P16 |
ORF1: 1..5052
ORF2: 5033..6640
ORF3: 6640..7419
LOCUS MK616561 7466 bp RNA linear VRL 17-MAR-2019
DEFINITION Norovirus GII isolate CA-RGDS-1020 nonstructural polyprotein (ORF1)
gene, partial cds; and VP1 (ORF2) and VP2 (ORF3) genes, complete
cds.
ACCESSION MK616561
VERSION MK616561.1
KEYWORDS .
SOURCE Norovirus GII
ORGANISM Norovirus GII
Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes;
Picornavirales; Caliciviridae; Norovirus; Norovirus norwalkense.
REFERENCE 1 (bases 1 to 7466)
AUTHORS Pan,C.-Y., Huynh,T., Castro,C.J., Ng,T.F., Marine,R.L. and
Wadford,D.A.
TITLE Norovirus GII.P16-GII.12 genomes from gastroenteritis outbreaks,
California, 2018
JOURNAL Unpublished
REFERENCE 2 (bases 1 to 7466)
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..7466
/organism="Norovirus GII"
/mol_type="genomic RNA"
/isolate="CA-RGDS-1020"
/isolation_source="stool"
/host="Homo sapiens"
/db_xref="taxon:122929"
/geo_loc_name="USA: CA"
/collection_date="Aug-2018"
/note="genotype: GII.P16-GII.12"
gene <1..5052
/gene="ORF1"
CDS <1..5052
/gene="ORF1"
/codon_start=1
/product="nonstructural polyprotein"
/protein_id="QBL14290.1"
/translation="NNDKEKSSGEGLFTNMSSTLKKALGARPKQPAPRDKPQKPPRPP
TPELVKRIPPPPPNGEEEEEPVIRYEVKSGVSGLPELTTVPQPDVANTAFSVPPLSLR
ENREAKEPLTGAILEMWDGEIYHYGLYVEKGLVLGVHKPPAAISMAKVELTPLSLYWR
VVYTPQYLISPETLRRLNGEAFPYTAFDNNCYAFCCWVLDLNDSWFSRRMVQRTTGFF
RPYQEWNRKPLPTMDDSKIKKVANIFLCSLSTLFTRPIKDLIGKIKPLNILNILATCD
WTFAGIVESLILLAELFGVFWTPPDVSAMIAPLLGDYELQGPEDLAVELVPVVMGGIG
LVLGFTKEKIGRMLSSAASTLRACKDLGAYGLEILKLVMKWFFPKKEEANELAMVRAI
EDAVLDLEAIENNHMTTLLKDKDSLATYMKTLDMEEEKARRLSTKSASPDIVGTINAL
LARIAAARSLVHRAKEELSSRIRPVVVMISGKPGIGKTHLAREVARKVASTLTGDQRV
GLIPRNGVDHWDAYKGERVVLWDDYGMSNPIHDALRIQELADTCPLTLNCDRIENKGK
VFDSEVIIITTNLANPAPLDYVNFEACSRRIDFLVYAEAPDVEKAKRDFPGQPDMWKD
AFKSDFSHIKLQLAPQGGFDKNGNTPHGKGVMKTLTTGSLIARASGLLHERMDEFELQ
GPTITTFNFDRNRITAFRQLAAENKYGLVDTMKVGNQLKGVKTMEELKQAIRNVTIKR
CRIIYGGSTYDLESDGKGKVLVEKVKNASVQTNNELAGALHHLKHARIRYYVKCVQEA
VYSIIQIAGAAFVTTRIARRMNIQELWSKPQLDQNESETKEEAPKPEDDEFVISCKDI
KEEGKKGKNKTGRGKKHTAFSSKGLSDEEYDEYKRIREERNGKYSIEEYLQDRDRYYE
ELAIAKATEEDFCEEEEIKIRQRIFRPTRKQRKEERATLGLVTGSEIRKRNPDDFKPK
GKLWADDNRSVDYNEKLDFEAPPSIWSRIVSFGSGWGFWVSPSLFITSTHVIPTGITE
AFGVPIKQVQIHKSGEFCRFRFPKPIRPDVTGMILEEGAPEGTVATVLIKRPTGELMP
LAARMGTHATMKIQGRMVGGQMGMLLTGSNAKGMDLGTTPGDCGCPYIYKRGNDYIVI
GVHTAAARGGNTVICATQGSEGEATLEGGDDKGTYCGAPILGPGGAPKLSTKTKFWRS
SNTPLPPGTYEPAYLGGRDPRVKGGPSLQQVMRDQLKPFTEPRGKPPRPSVLEAAKQT
IINVLEQTLDPPQKWTYAQACASLDKTTSSGHPYHVRKNEFWNGETFTGKLADQASKA
NLMFEEGKHMTPVYTAALKDELVKTEKIYGKIKKRLLWGSDLSTMIRCARSFGGLMDE
MKAHCISLPVRVGMNMNEDGPIIFEKHSRYKYHYDADYSRWDSTQQRAVLAAALEIMV
RFSAEPQLAQIVAEDLLAPSVVDVGDFKITINEGLPSGVPCTSQWNSIAHWLLTLCAL
SEVTKLSPDIIQANSMFSFYGDDEIVSTDIKLDPEQLTAKLKEYGLKPTRPDKTEGPL
IISEDLNGLTFLRRTVTRDPAGWFGKLDQSSILRQMYWTRGPNHEDPNETMIPHSQRP
IQLMALLGEASLHGPSFYSKISKLVITELKEGGMDFYVPRQEPMFRWMRFSDLSTWEG
DRNLAPNFVNEDGVE"
mat_peptide <1..948
/gene="ORF1"
/product="p48"
mat_peptide 949..2046
/gene="ORF1"
/product="NTPase"
mat_peptide 2047..2577
/gene="ORF1"
/product="p22"
mat_peptide 2578..2976
/gene="ORF1"
/product="VPg"
mat_peptide 2977..3519
/gene="ORF1"
/product="Pro"
mat_peptide 3520..5049
/gene="ORF1"
/product="RdRp"
gene 5033..6640
/gene="ORF2"
CDS 5033..6640
/gene="ORF2"
/note="major capsid protein"
/codon_start=1
/product="VP1"
/protein_id="QBL14291.1"
/translation="MKMASNDAVPSNDGAAGLVPEVNNETMALEPVAGASIAAPLTGQ
NNVIDPWIRLNFVQAPNGEFTVSPRNSPGEVLLNLELGPELNPYLAHLSRMYNGYAGG
VEVQVLLAGNAFTAGKLVFAAVPPHFPLENISPGQITMFPHVIIDVRTLEPVLLPLPD
VRNNFFHYNQQNEPRMRLVAMLYTPLRSNGSGDDVFTVSCRVLTRPSPDFDFNYLVPP
TVESKTKPFTLPVLTIGELTNSRFPVPIDELYTSPNESLVVQPQNGRCALDGELQGTT
QLLPTAICSFRGRINQKVSGENHVWNMQVTNINGTPFDPTEDVPAPLGTPDFSGKLFG
VLSQRDHDNACRSHDAVIATDSTKFTPKLGAVQIGTWEQDDVHINQPTKFTPVGLFEN
EGFNQWTLPNYSGALTLNMGLAPPVAPTFPGEQILFFRSHIPLKGGVADPVIDCLLPQ
EWIQHLYQESAPSQTDVALIRFTNPDTGRVLFEAKLHRSGYITVANTGSRPIVVPANG
YFRFDSWVNQFYSLAPMGTGNGRRRMQ"
gene 6640..7419
/gene="ORF3"
CDS 6640..7419
/gene="ORF3"
/note="minor structural protein; small basic protein"
/codon_start=1
/product="VP2"
/protein_id="QBL14292.1"
/translation="MAGAFIAGLAGDIVTNSIGSLVNAGANAINQKVDFENNKQLQQA
SFNHDKEMLQAQIQATKQLQADMIAIRQGVLTAGGFSPTDAARGAVNAPMTQVLDWNG
TRHWAPGAAKTTAFSGGFTSASHARTVDLTKKTSATPAPMPVSRPSSIASTVSTRSTL
ISGSSDSPSSARSSSSVSSQPTSSSSRTSEWVRSQNRALEPYMNGALRTAYVTPPSSR
ASSNGTVSTVPKEVLDSWSSAFNTHRQPLFAHLRRRGESQA"
ORIGIN
1 aacaacgaca aggaaaaatc ttcaggtgaa ggcttattca caaatatgtc ttccacctta
61 aagaaagccc tcggggctag gcccaaacag cctgccccga gagacaaacc acaaaagccc
121 ccaagaccac caactcccga gttggtcaag aggatacccc ctcctccacc taacggcgaa
181 gaagaagaag aaccagtcat taggtatgag gttaagagtg gggtctctgg cctgcccgag
241 ctcacaacag tcccccaacc ggacgtggcc aacacagcat tcagtgttcc accactgagc
301 ttgagagaaa acagggaagc caaggaaccg ctgacagggg caatattaga gatgtgggat
361 ggagagatat accactacgg cctgtacgtg gagaaaggct tagtgttggg tgtacacaaa
421 ccacctgcag ccataagcat ggcaaaagtg gagctgacgc cgctgtcatt gtattggcgt
481 gtggtgtaca ctccccaata cctcatctcc cctgaaactc tcaggaggct caacggagag
541 gcattccctt acaccgcctt tgacaacaac tgctatgcct tttgctgctg ggtattagac
601 ctcaatgact catggtttag caggagaatg gtgcaaagaa caacgggctt cttcagacct
661 taccaagagt ggaacagaaa acccctgcct accatggacg actccaaaat taagaaggta
721 gcaaatatat tcctatgttc attgtccaca ttgttcacta gacccataaa agacctcata
781 ggaaaaatta aaccattaaa catattgaat atcctggcaa cgtgtgactg gacgtttgcc
841 ggaatagtgg agtctctaat actacttgct gaactcttcg gagttttctg gacaccccca
901 gatgtgtctg ctatgatcgc tcccttactt ggggattacg agttgcaagg gccagaagac
961 ctcgccgtcg aactcgtacc tgtggtgatg ggtgggattg gtttggtgtt gggattcacc
1021 aaagagaaaa ttggcagaat gttgtcctcg gcagcatcaa cactcagggc ttgcaaagac
1081 cttggtgcct atggcttaga gatactcaaa ttagtcatga agtggttctt cccaaagaaa
1141 gaggaggcca atgagctagc catggtgagg gccatagagg acgctgtact agatcttgag
1201 gcaatagaaa ataaccacat gacaaccctg ttgaaagaca aagacagctt agcaacatac
1261 atgaaaacac tggacatgga ggaggagaaa gccagaaggt tgtccacaaa atctgcatcc
1321 cctgacatag ttgggacaat caacgccctg ctggctcgaa tagcagcggc caggtcatta
1381 gtccacaggg ccaaggaaga gctatctagc aggatcagac cagtagttgt tatgatatct
1441 ggcaaaccag gaataggcaa aactcatctg gccagggaag tggcaagaaa ggtggcatcc
1501 actctcacag gggatcaaag agtcggactc ataccaagaa acggtgtgga ccattgggat
1561 gcatacaaag gtgagagagt cgtgctgtgg gacgactatg gcatgagtaa ccccattcat
1621 gatgctcttc gcatacaaga attggctgat acgtgtcccc tcaccttaaa ttgtgacaga
1681 attgaaaata aaggaaaagt ttttgacagt gaagtcataa taatcacaac aaaccttgcc
1741 aatccagccc cgcttgatta tgtcaacttt gaggcctgtt ccaggagaat tgatttcctg
1801 gtgtacgctg aggcaccaga tgtggaaaag gcaaaacggg actttcctgg tcagccagat
1861 atgtggaagg acgccttcaa atcggacttt tcacacatca agctacagct tgcacctcag
1921 ggcggctttg acaaaaacgg caacacccca catgggaaag gggtgatgaa gaccctcact
1981 accggttctt tgattgcccg tgcatcaggc ctactgcatg agaggatgga tgaatttgaa
2041 ctccaaggtc ctacaatcac caccttcaat ttcgaccgga acagaatcac agcattcaga
2101 caattggctg cagaaaacaa gtatggactg gtggacacca tgaaagtcgg caatcaatta
2161 aaaggagtga aaaccatgga agagctcaaa caagcaatca ggaatgtgac catcaagagg
2221 tgccggatca tctacggtgg ctccacatat gaccttgaat ctgatggcaa gggcaaagtt
2281 ttggtggaaa aggtcaagaa cgcctctgta cagaccaaca acgagttggc cggggccctg
2341 caccatctca aacacgcccg aatcaggtac tatgtcaagt gtgtgcaaga agcagtctat
2401 tctatcatac aaattgccgg cgctgcgttt gtcaccacgc gcattgcacg ccgcatgaac
2461 atacaagaac tctggtcgaa gccacaattg gatcaaaatg aatcagagac taaggaagag
2521 gcccccaagc cagaagatga cgagttcgtc atatcttgta aggacatcaa ggaggaagga
2581 aagaagggca aaaataaaac tggccgtggc aagaaacaca ctgcattctc cagcaagggc
2641 ttgagcgatg aggagtatga cgagtacaag aggataagag aagagagaaa tgggaagtac
2701 tctatagagg aataccttca agacagagac aggtactatg aagaactcgc cattgccaag
2761 gccacggaag aagacttctg tgaagaggag gagataaaaa tccgtcagag aattttccgt
2821 cctaccagga aacaaaggaa ggaagagagg gccacattag ggctagtaac aggttcagaa
2881 atcagaaaaa gaaatcctga tgacttcaaa cccaaaggga agctgtgggc cgatgacaac
2941 agaagtgttg actacaatga gaagctggat tttgaggccc ccccaagcat atggtctagg
3001 attgtgagct ttggttctgg ctggggcttc tgggtatcac caagcctgtt cataacatca
3061 actcatgtaa tccccacagg cataacagaa gcgtttggag tccccatcaa acaagttcaa
3121 atccacaaat caggtgaatt ttgccgattc agattcccaa agccaattag accagatgtg
3181 acaggaatga tcttggaaga aggtgcgcct gagggcaccg tggcaactgt gctcatcaaa
3241 cgccccaccg gagagctcat gcctcttgca gccagaatgg gaacacacgc aaccatgaaa
3301 attcaaggcc gcatggttgg cggacagatg ggcatgttgc tcactggatc aaatgctaaa
3361 ggaatggatt tgggaacaac tcctggagac tgtggctgtc cttacatcta taaaaggggc
3421 aatgactata tagtcattgg ggtgcacact gcagcagccc gtggtggaaa caccgtcatc
3481 tgtgccacac agggaagtga gggtgaggca actcttgagg gtggagatga caaaggaaca
3541 tattgtgggg cacccatcct aggccctggg ggtgcaccaa aattgagcac caaaaccaaa
3601 ttttggaggt catcgaacac gccccttcca ccagggacat atgagcctgc ctacctcggc
3661 ggtcgtgacc cgcgtgttaa gggtgggccc tccttgcagc aggtaatgag agaccagttg
3721 aagccattca ctgaacccag gggcaaacct ccaagaccaa gtgtattgga agcagccaaa
3781 caaaccatca tcaatgtcct cgagcaaacc ctggaccctc cacaaaaatg gacatacgca
3841 caggcgtgtg cctcacttga caaaacaacc tctagcggtc acccctatca cgttcgaaag
3901 aatgaattct ggaatggtga gaccttcact ggtaaattgg cagaccaagc atcaaaagca
3961 aacctaatgt ttgaggaagg gaaacacatg acaccagtgt atacagcagc actcaaggac
4021 gagctagtca agactgagaa aatctatgga aaaatcaaga agagactgct ctggggctct
4081 gatttgtcca ccatgatccg gtgtgctagg tcatttggtg ggctcatgga cgagatgaag
4141 gcacactgca tatcactccc agtccgagtt ggcatgaata tgaatgaaga tggcccaata
4201 atatttgaga aacattctag atacaaatat cactatgatg cagactactc tcgttgggat
4261 tcaacacaac agagggcagt actggcagca gccttggaaa tcatggtcag attctctgca
4321 gaaccacaat tggcacaaat agtcgctgag gacctactgg cccctagtgt agtagatgta
4381 ggagacttta aaatcacaat aaatgagggg ctcccctctg gtgtgccatg cacttctcaa
4441 tggaactcca tcgcacactg gttgctaact ctctgtgcct tgtctgaagt cactaagctg
4501 tcacctgaca ttatacaggc aaattccatg ttctcatttt acggtgatga cgagattgtc
4561 agcaccgaca taaaattgga ccccgaacag ttaaccgcca aattgaagga gtacggtcta
4621 aaaccaaccc gcccagacaa aaccgaggga cccctgatca tcagtgaaga tttgaacgga
4681 ctcactttcc tccgaaggac ggtgactcgt gacccagctg gctggtttgg aaaactggac
4741 caaagctcaa ttttgaggca gatgtactgg actagaggac caaatcatga agaccccaat
4801 gagacaatga taccccattc tcaaaggccc atacagctca tggcactgct tggtgaagcc
4861 tctcttcacg gaccctcttt ctacagtaaa atcagtaaat tggtcataac tgaactcaaa
4921 gaaggtggga tggactttta cgtgccaagg caggaaccca tgttcaggtg gatgaggttt
4981 tctgacctga gcacgtggga gggcgatcgc aatctggctc ccaattttgt gaatgaagat
5041 ggcgtcgaat gacgccgttc catctaatga tggtgcagcc ggtctcgtac cagaggtcaa
5101 caatgagacc atggcacttg aaccggtggc tggggcttcg atagccgccc cactcaccgg
5161 ccaaaataat gttatagacc cctggattag attaaatttt gtgcaggccc ctaatggaga
5221 gtttacagtc tcaccccgca actcgcctgg ggaagtccta ctcaatttgg aattaggtcc
5281 cgaattgaat ccatatttgg cacacctttc tagaatgtat aatggttatg caggtggagt
5341 tgaggtacaa gtgctactgg ctgggaacgc gttcacggct ggaaaattgg tatttgctgc
5401 agttccccct cattttccat tagagaatat aagccctggt caaataacca tgttccctca
5461 tgtaattatt gatgttagga ctttggaacc agttttattg cctctaccag atgtcagaaa
5521 taacttcttc cattacaacc agcaaaatga gccgaggatg aggcttgttg caatgcttta
5581 tacccctctt agatctaatg gttctggtga tgatgtgttc accgtctcct gtagggtgct
5641 cactcgaccc tctcctgatt ttgattttaa ttatttggtg cccccaacag ttgaatctaa
5701 aacaaaacca ttcacactcc ctgtcttgac cattggggag ttaaccaatt ccaggttccc
5761 tgtgcccata gatgaactct acactagccc caatgagagt ttggtggttc aaccccagaa
5821 tgggaggtgc gcgctggatg gggagttgca gggcaccacc cagctccttc ccacggcgat
5881 ttgctcgttc aggggtcgga tcaatcagaa agtgagtgga gagaatcatg tttggaacat
5941 gcaagtcacc aacattaacg gaaccccttt tgatccaaca gaggatgttc cagcccctct
6001 gggcacgcca gacttttctg gcaagctctt tggtgtccta agccagaggg accatgataa
6061 tgcctgcagg agtcatgatg cagtgattgc aactgattct accaaattta ccccaaaatt
6121 gggtgctgta caaattggca catgggaaca agatgatgta cacatcaacc aacccaccaa
6181 gtttactcca gttggattgt ttgagaatga aggttttaat caatggacac ttcctaatta
6241 ttctggagct ttaacactca atatggggtt ggccccccct gtggccccca cattccctgg
6301 tgagcaaatt ctcttcttca ggtcccacat tccccttaaa ggaggtgttg cagacccagt
6361 tattgattgt cttctacccc aagagtggat ccagcacctt tatcaggagt cagccccttc
6421 acaaacagat gtggcactga ttagattcac aaatccagac acagggcgtg tcctatttga
6481 agcaaaattg cacaggagtg gttacatcac agtggccaac actggtagca gaccaattgt
6541 ggtgccagct aatggttatt tcaggtttga ctcttgggtt aatcagtttt actctcttgc
6601 ccccatggga actgggaatg ggcgcagaag gatgcagtaa tggctggagc tttcatagca
6661 gggcttgccg gtgacatagt caccaacagc attggctcac tcgtgaacgc tggggccaat
6721 gcaataaacc agaaagtaga ctttgaaaac aacaagcaac tacaacaggc atcttttaac
6781 catgacaaag agatgttgca agctcaaatt caggccacca aacaactaca ggctgatatg
6841 attgcgatca gacaaggggt gttgaccgca ggcggcttct cccctactga tgcagcaaga
6901 ggtgcagtca acgcgcccat gactcaagtc ttggattgga atgggaccag acattgggcc
6961 cccggagccg cgaaaacaac tgctttctcc ggtgggttta ccagtgcctc tcatgccagg
7021 accgttgacc tgaccaagaa gacatcagcc acaccagccc ctatgcctgt ttctaggccc
7081 agttctattg cttccactgt ttctactcgc tctactttga ttagtgggtc ctctgattct
7141 ccttcttcag ctaggagctc ttctagtgtt tcttcccaac ccacttcctc atcctcccga
7201 actagtgagt gggtacgcag tcaaaatagg gcgctggagc cttatatgaa tggggcgctg
7261 cgtacagcct acgtgacgcc tccatccagt agggcttcta gcaatggcac agtctcaacc
7321 gtgccaaaag aggttttgga ctcctggtcg tctgcgttta atacacacag acagccgctg
7381 tttgctcatc tccgtcggag aggggagtca caagcttagt gaaaagatgg tcttttcttt
7441 ctttcctttg aaaaaccctg tcttct
//