Typing tool
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Typing tool
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Complete norovirus genomes
| MZ265142 | GII.5 | |
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| GII.P40 |
ORF1: 5..5140
ORF2: 5121..6743
ORF3: 6743..7519
LOCUS MZ265142 7540 bp RNA linear VRL 26-MAY-2021
DEFINITION Norovirus GII isolate Hu/US/2013/GII.5[P40]/CA-RGDS-1116
nonstructural polyprotein (ORF1), VP1 (ORF2), and VP2 (ORF3) genes,
complete cds.
ACCESSION MZ265142
VERSION MZ265142.1
KEYWORDS .
SOURCE Norovirus GII
ORGANISM Norovirus GII
Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes;
Picornavirales; Caliciviridae; Norovirus; Norwalk virus.
REFERENCE 1 (bases 1 to 7540)
AUTHORS Pan,C.-Y., Huynh,T., Padilla,T., Montmayeur,A.M., Chhabra,P.,
Barclay,L., Vinje,J., Wadford,D.A. and Morales,C.
TITLE Direct Submission
JOURNAL Submitted (19-MAY-2021) 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..7540
/organism="Norovirus GII"
/mol_type="genomic RNA"
/strain="CA-RGDS-1116"
/isolate="Hu/US/2013/GII.5[P40]/CA-RGDS-1116"
/isolation_source="stool"
/host="Homo sapiens"
/db_xref="taxon:122929"
/country="USA"
/collection_date="20-Jun-2013"
/note="Amplicon sequencing: first 35 nt does represent
primer sequence;
genotype: GII.5[P40]"
gene 5..5140
/gene="ORF1"
CDS 5..5140
/gene="ORF1"
/codon_start=1
/product="nonstructural polyprotein"
/protein_id="QVQ56624.1"
/translation="MKMASNDASAATAGNTSTNSVIHNQDVNSTSSLFANMTVGLKRA
LGARPKQPAPRVPSPNREGRHETTPRAPPPNKGGNANIPPIPPPPPNGEDIVIKYTKQ
DDAVEGVPTVATVDVPPTHNTAYSVPPLDQREKIEAKEPLTGSILEMWDGEIYHYGLY
VEKGLVLGVHKPPAAISFARIELTPLSLYWRTVYTPPYLIAPETLRKLHGESFPYTAF
DNNCYSFCCWVLDLNDSWLNRKFVSRTTGFYRPYQEWNRKPLPTMDEGKLKKVANVLL
CGLSGLFTRPIKDLIGKLRPLNILNIITNCDWTFPGIVEAFILLAELFGVFWTPPDIS
TFIASLLGDYEMQGPEDIAVEVVPVILGGIGMVLGFTKERIGRLLSSAASSLRACREI
GNYGIEVVKLVMKWFFPTKDETNEMDMVRAIEDAVLDFEAIQNNHMTALLKDKNSLAT
FLRELDMEEEKARKLSTKSASPDIIGTINALLARIAAARSLVHKAKEEMSSRMRPVVI
MISGRPGIGKTHLARDLAKKMAATLSGDQRVGLVPRNGVDHWDAYKGERIVLWDDYGM
SNPVTDALRLQELADTCPLTLNCDRIENKGKVFDSDTIIITTNLANPAPLDYVNFEAC
SRRIDFLVYADSPSVDKAKRDFPGQPDMWKDAFKSDFSHIKLQLAPQGGFDKNGNTPH
GKGVMKTLTTHSLIARATGLLHERLDEFDLQGPELPVYNFDHNRVAAFRRLAADNKYG
LVETIKVGNKLKSVKTLEQLKDALKDISIMPCRIVYNSMAYDLDSNGSGRVSVKKVVD
HKIQTNNELNSALNNLRGARVRYYVKCVQEMVYSLLQIAGAAFVTSRMTRRLNVSSIW
ARPEKQVEATEEPPSPPTEDWTITPANAVQEGKKGKNKSGRGKKHTAFSSKGLSDEEY
DEYKRIREERQGKYSIEEYLQDRDRYYEELAIAKATEENFCEEEEIKIRQRVFRPTRK
QRKEERATLGLVTGSEIRKRNPDDFKPRGKLWADDDRSVNYNEKIDFEAPPSLWSRIV
NFGSGWGFWVSSNLLITSTHVIPPNMTEAFGVPISQIQVHRSGEFCKMRFPKAIRPDV
SGMILEEGAPEGTVVTILIKRTTGELMPLAARMGTHATMKIQGKMLGGQMGMLLTGSN
AKNMDLGTIPGDCGCPYVYKRGNDWVVIGVHTAAARGGNTVICATQGPDGEATLEGRD
NHGTYCGAPILGPGSAPKLSTKTKFWRSSNAPLPPGTYEPAYLGGKDPRVKGGPSLQQ
VMREQLKPFTAPRGKPPRPAILEAAKETICNVLEQIIDPPQKWSYAQACASLDKTTSS
GHPHHMKKNDNWNGESFTGVLADQASKANLMFEQGKHMQPVYTAALKDELVKTSKIYE
KIKKRLLWGSDLGTMIRCARAFGGLMDEMKANCVNLPIRVGMNMNEDGPIIFEKHSKY
KYHYDADYSRWDSTQQRHILGAALEIMVRFSAEPELAQIVSEDLLAPSVVDVGDFKIT
INEGLPSGVPCTSQWNSISHWLITLCAISEISGLSPDVVQTNSCFSFYGDDEIVSTDI
KLDPMELTNKLKEYGLIPTRPDKTEGPLIIKENLDGLTFLRRDVCRDPAGWYGKLDQS
SIMRQLFWTKGPNHDDPNETMIPHSQRPIQLMSLLGEAALHGPAFYKKVSKLVITELK
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..6743
/gene="ORF2"
CDS 5121..6743
/gene="ORF2"
/note="major capsid protein"
/codon_start=1
/product="VP1"
/protein_id="QVQ56625.1"
/translation="MKMASNDASPSNDGAAGLVPESNNEAMALEPVVGASLAAPVTGQ
TNIIDPWIRTNFVQAPNGEFTVSPRNSPGEILVNLELGPELNPYLAHLARMYNGYAGG
MEVQVMLAGNAFTAGKIIFAAVPPYFPVENLSPSQITMFPHVIIDVRTLEPVLLPMPD
VRSTLFHFNQKDEPKMRLVAMLYTPLRSNGSGDDVFTVSCRILTRPSPEFDFTYLVPP
TVESKTKPFTLPVLTLGELSNSRFPISIDEMVTSPNESIVVQPQNGRVTLDGELLGTT
QLQACNICSIRGKVTGQVPNEQHMWNLEITNLNGTQFDPTDDVPAPLGVPDFAGEVFG
VLSQRNRGESNPANRAHDAVVATYSDKYTPKLGLVQIGTWNTNDVENQPTKFTPIGLN
EVANGHRFEQWTLPRYSGALTLNMNLAPAVAPLFPGERLLFFRSYVPLKGGFGNPAID
CLVPQEWVQHFYQESAPSLGDVALVRYVNPDTGRVLFEAKLHKGGFLTVSSTSTGPVV
VPANGYFRFDSWVNQFYSLAPMGTGNGRRRFQ"
gene 6743..7519
/gene="ORF3"
CDS 6743..7519
/gene="ORF3"
/note="minor structural protein; small basic protein"
/codon_start=1
/product="VP2"
/protein_id="QVQ56626.1"
/translation="MAGAFIAGLAGDVLSNGLGSLINAGANAINQRAEFDFNRQLQQN
SFNHDKEMLNAQIQATKQLQADMIAIKQGVLAAGGFSPTDAARGAVNAPMTQALDWSG
TRYWAPGSMKTTSYSGKFVSMNPVRQVEFPQPKKSTAIPSSASSVSSGRTNFTNSTQS
TVVSTSSVSPSRGSSAPSTLSRATTRTSNWVEEQNRNLEPYMRGALQTTFVTPPSSRA
SSNGTVSTVPKGVLDSWTPAFNTRRQPLFAYLRKKGESQV"
ORIGIN
1 gtgaatgaag atggcgtcta acgacgcttc cgctgcgacc gctggcaata ccagcacaaa
61 cagtgtaatt cacaaccaag atgtaaattc tacatctagc ctctttgcca acatgactgt
121 tggcctgaag agggccctgg gggcgagacc aaaacaaccc gctcccaggg ttccctcccc
181 caacagggag ggaagacatg aaaccactcc tagagctccc cctccgaaca agggaggtaa
241 tgctaacatc ccaccaatac cacccccacc gcccaacggg gaggacatag tcatcaagta
301 taccaagcag gatgacgcgg ttgaaggggt gcccaccgtc gccacggttg atgttccccc
361 cacacacaac accgcttaca gtgtcccccc cctggatcag agggaaaaga ttgaagcgaa
421 ggagcccttg acaggttcga tacttgagat gtgggacggt gagatctacc actatggtct
481 ctacgtggag aagggcttgg ttcttggtgt gcacaaacct ccagctgcca taagctttgc
541 acgcatagaa ctcactcccc tctccttata ctggagaaca gtctacaccc caccttacct
601 gatagcccca gaaaccctaa ggaagctcca cggggagtca ttcccatata cagcctttga
661 caacaattgc tactccttct gctgctgggt cctggacctg aacgattctt ggctcaacag
721 aaaatttgtg tcaaggacaa cgggtttcta cagaccctac caagagtgga atagaaagcc
781 tttgccaacc atggatgaag gaaagctcaa gaaagtggcc aatgtgcttc tatgtggtct
841 ctctgggctt ttcactaggc ccatcaagga tctcataggg aagctgaggc cactaaacat
901 actaaacatc atcaccaatt gcgactggac cttccccgga attgtggagg ctttcatact
961 gcttgcagag ctctttggag ttttctggac accaccagac atttccacct tcatagcttc
1021 acttctgggt gactatgaaa tgcagggccc tgaggatatc gctgttgaag tcgtaccggt
1081 gatcctcggc ggcataggta tggtacttgg attcaccaaa gaaagaattg gccggttgtt
1141 aagctctgcc gcttcctcac ttagagcatg cagggagatc ggcaactatg ggatagaggt
1201 agtgaagctg gtgatgaaat ggtttttccc caccaaagat gagacaaatg agatggatat
1261 ggtgagggca atagaggatg ctgttcttga ctttgaagcc atacagaaca atcacatgac
1321 agcattgctt aaagacaaaa acagccttgc aaccttcctc agggagctag atatggaaga
1381 ggaaaaggcg cggaagctat caacaaaatc tgcgtcccca gatattatcg gcaccataaa
1441 cgcccttcta gccagaattg ccgctgctag gtccctagtc cacaaggcca aggaagaaat
1501 gtcatctagg atgcgtcctg ttgtcatcat gatctccggc cgacccggga tagggaagac
1561 gcatctggcc cgcgacctgg ctaagaagat ggcggcgacc ctctcaggtg atcagagagt
1621 ggggctcgtg ccgaggaatg gtgttgacca ttgggacgca tataaaggag agaggatcgt
1681 gctctgggac gattatggaa tgagcaaccc tgtgactgat gcgctgcggc tccaggagct
1741 tgccgacaca tgccctctaa cgctcaactg tgatagaata gaaaataagg gaaaagtgtt
1801 tgacagtgac actataatca tcaccactaa tttggccaac cctgctcctc tagattatgt
1861 caactttgaa gcttgctccc gccgaatcga cttccttgtc tatgcagact ccccctcggt
1921 ggacaaggcg aagagagact tccctggtca accagacatg tggaaggatg cctttaaatc
1981 ggacttttca cacataaaac ttcagttggc accacaggga ggctttgata agaacgggaa
2041 cacccctcat gggaaaggtg tcatgaaaac gctaaccaca cactcactca ttgcccgcgc
2101 cacgggcctc ctacatgaga gattggatga atttgacctg cagggacccg agttgcccgt
2161 gtacaatttt gaccacaaca gggtggctgc tttcaggaga ctggcagctg acaacaagta
2221 tgggcttgtg gaaaccataa aggtgggtaa caaattgaaa agcgtcaaga ctctagaaca
2281 actcaaggac gctctaaaag acataagtat catgccttgc agaatagtct acaactcgat
2341 ggcttacgat ctcgattcga acggatcagg gagagtcagt gtcaaaaagg ttgtagacca
2401 caagatccag accaacaacg agctcaattc cgccctcaac aatctgcgcg gtgccagagt
2461 gagatactat gttaaatgtg ttcaagagat ggtatattcc ctccttcaaa ttgctggcgc
2521 agccttcgtc acttcaagaa tgacacggag gttgaacgtc agcagcatct gggccagacc
2581 agaaaaacaa gtggaggcca ctgaggaacc cccatccccc ccaactgagg actggactat
2641 aaccccagca aatgcagtcc aggaaggtaa aaagggcaag aacaagagcg gcagaggcaa
2701 gaaacatacc gccttctcca gtaaaggcct aagtgatgag gagtatgatg agtataaaag
2761 aatcagagaa gagagacaag gaaaatactc catagaagaa taccttcagg atagggaccg
2821 gtattatgaa gaattggcca tagccaaggc aacagaggag aacttctgtg aggaggaaga
2881 aataaaaatc agacagaggg tcttccgtcc gaccaggaaa caacgcaagg aagagagggc
2941 aactctagga ctggtcacag gtagtgaaat aaggaagagg aacccagatg atttcaagcc
3001 aagaggaaaa ttgtgggctg atgatgaccg cagtgtaaat tacaatgaga aaatagattt
3061 tgaagcgcct cccagccttt ggtctcgaat agttaacttc ggatcaggtt ggggtttttg
3121 ggtttcttcc aacttgctca tcacatcaac acatgtcatc cccccgaaca tgactgaggc
3181 ctttggtgta ccaataagtc agatacaagt acataggagt ggagagttct gtaaaatgag
3241 gttccccaaa gctataagac ctgatgtctc aggcatgatc cttgaggaag gagctcccga
3301 gggaacggtg gtgaccatac tgatcaagag gaccaccggt gagctcatgc cactggccgc
3361 ccgaatgggc acccacgcca ccatgaaaat tcaagggaaa atgcttggag gccaaatggg
3421 catgctcctc acggggtcca acgccaagaa catggacctc ggcaccattc ctggagactg
3481 tggttgtccc tatgtttaca agagaggtaa tgactgggtg gttatagggg tgcacaccgc
3541 agccgccaga ggtggcaaca ctgtgatttg tgccactcag ggtccagacg gtgaggccac
3601 gcttgagggg agagacaacc acgggactta ctgtggggca ccaatacttg gaccaggaag
3661 tgcaccaaaa ctcagcacta agactaaatt ctggaggtca tccaacgccc cactcccgcc
3721 tggcacttat gagcccgctt acctaggcgg aaaagaccca agagtcaagg ggggaccatc
3781 actacagcaa gtcatgaggg aacaactcaa acctttcaca gccccccgag ggaagccgcc
3841 acgaccggcg atcctggagg ctgctaagga aaccatctgt aatgtacttg agcagatcat
3901 tgacccaccc caaaaatggt cttatgctca ggcctgtgcc tctctggaca aaacaacatc
3961 cagtggccat ccccaccata tgaaaaagaa tgacaactgg aacggagagt ccttcaccgg
4021 tgtgttggct gaccaagctt ccaaggcaaa tctcatgttt gaacaaggga aacacatgca
4081 acctgtgtac actgccgccc tcaaagacga gctcgtcaag actagtaaga tctatgagaa
4141 aattaagaag aggctcctat ggggttcaga tctgggcaca atgatccgct gtgctagggc
4201 ttttggaggc ctcatggatg agatgaaagc aaattgtgta aacctaccaa tcagagttgg
4261 catgaacatg aatgaagatg gacccatcat tttcgagaaa cattcaaagt ataagtacca
4321 ttatgatgct gactactcta ggtgggattc aacccaacag agacacatct tgggggctgc
4381 ccttgagata atggttaggt tctcagctga acctgaattg gcccaaattg tatctgaaga
4441 tctcctagcc cccagcgtgg tggacgttgg cgacttcaag atcaccataa atgaaggttt
4501 accctctgga gtgccgtgca catcacaatg gaactcaatt tcccactggc taataacact
4561 atgtgccata tcagaaattt cagggctgtc gccagatgtg gtacaaacaa actcctgttt
4621 ctccttctat ggggatgatg agatagtcag cactgacatt aagttagatc ccatggaatt
4681 aactaacaag ttgaaggagt atggactgat cccaacaaga ccagacaaga cagaggggcc
4741 actcataatc aaagagaacc ttgatggctt gacctttctg aggagggatg tgtgtcggga
4801 cccagctggt tggtatggaa aacttgatca atcctcaatt atgagacaat tgttttggac
4861 caaggggccc aaccatgacg atcccaatga gacaatgatt ccacactccc agaggcccat
4921 acaactaatg tcattgctgg gggaggcagc attacacgga ccagctttct acaagaaagt
4981 cagtaaatta gttatcactg agctcaaaga gggtggaatg gatttttacg tgccaaggca
5041 agaacctatg tttaggtgga tgagattctc tgacctcagc acttgggagg gcgatcgcaa
5101 tcttgctccc gaaggtgtga atgaagatgg cgtcgaatga cgcttctcca tcaaatgatg
5161 gtgctgccgg cctcgtgcca gaaagtaaca atgaggcaat ggctctggaa cccgtggtgg
5221 gggcgtcttt agccgcccct gtcactggcc aaactaatat aatagacccc tggattagaa
5281 ctaattttgt ccaagcccct aatggtgaat tcacagtttc ccctagaaat tcccctggag
5341 agatattggt caatttggag ttaggtccag aactgaaccc ttatctggca catttagcta
5401 ggatgtacaa tggttatgcg ggtggtatgg aggtgcaagt gatgctcgcg gggaacgcgt
5461 tcactgctgg caagatcatc tttgccgccg tgccacctta ctttccagtg gaaaatctta
5521 gcccttccca aataacaatg ttcccacatg tgattatcga tgttagaacc ttagaacctg
5581 tactgctccc aatgcctgat gtcagaagca cccttttcca ctttaatcaa aaggatgaac
5641 ctaagatgag acttgttgcc atgctctaca cccctcttcg ttctaatggc tctggtgatg
5701 acgttttcac tgtctcatgt aggatcctca ctaggccctc tcctgaattt gatttcacat
5761 acttggtgcc accaacagtg gagtcaaaga ccaagccatt cacactacct gtgctgacat
5821 tgggagaatt gtccaattct agattcccta tctctattga tgaaatggtc accagcccta
5881 atgagtccat agttgttcag ccacagaatg gtagggtcac actagatggg gagttgttag
5941 gcacaaccca actgcaagca tgtaacattt gttccataag ggggaaagtg acaggacagg
6001 tccctaatga acaacacatg tggaacctgg agattacaaa cctaaatggg acgcaatttg
6061 accctacaga tgatgtccca gcccctcttg gtgtgcccga ctttgcaggt gaggtctttg
6121 gtgtgctcag ccagagaaat agaggtgaaa gcaatccagc aaacagggct catgatgctg
6181 ttgtggctac ctacagtgat aaatacaccc ctaaattggg cttagtgcaa attgggactt
6241 ggaataccaa cgatgttgaa aaccagccaa caaaattcac cccaattggt ttgaatgagg
6301 tcgccaatgg ccatcgattt gaacagtgga ccttgcctag gtattctggt gccctgacac
6361 taaatatgaa tttagctcct gctgtggccc ccctctttcc tggagagcgt ctccttttct
6421 tccgctctta cgtcccatta aaaggtggat ttggaaaccc tgctatagat tgtctagtgc
6481 ctcaggagtg ggtccaacat ttctatcagg aatctgcccc atctctgggg gatgtggcct
6541 tagtcaggta cgtcaaccca gacaccgggc gcgtcctttt tgaggccaaa ctccacaaag
6601 gtgggttcct gaccgtgtca agcactagca cagggcctgt tgtggtccca gccaatggtt
6661 atttcagatt tgattcttgg gttaatcaat tttactctct tgcccccatg ggaactggga
6721 atgggcgcag aaggtttcag taatggcagg agctttcata gcaggtttag caggtgatgt
6781 gcttagtaat ggcctcggtt cgctgattaa tgccggagcc aatgctatca atcaaagagc
6841 agaatttgat ttcaataggc aattgcagca aaattctttt aatcatgata aggagatgtt
6901 aaatgcccaa attcaagcaa caaaacagtt gcaggctgat atgatagcaa tcaaacaggg
6961 agtcctggct gctgggggtt tctcaccaac tgatgcagcc agaggagctg tcaatgcacc
7021 catgacccaa gcattagatt ggagtggcac taggtattgg gcccctggtt caatgaagac
7081 caccagctat tctggaaagt ttgtgtccat gaatcctgtt aggcaggttg agttcccgca
7141 gcccaaaaag agtacggcca taccatcaag tgccagctct gtgtcttctg gtaggaccaa
7201 tttcacaaat tctactcaat caactgttgt tagcacttcc tcagtatcac cttctagggg
7261 ttcttctgct ccttctactc tatcaagggc tacaaccaga acttccaatt gggttgagga
7321 acaaaacagg aatttggaac cctacatgag gggtgccctc caaacaacat ttgtcacccc
7381 cccttccagc cgggcatcta gcaacggtac agtctcaact gtaccaaaag gtgttttgga
7441 ctcctggaca cctgcgttta acacccgcag gcaaccgctt ttcgcttacc ttcgcaagaa
7501 gggggagtca caagtttagt gaaaagataa ttagtgattg
//