Typing tool
|
|
|
|
|
|
Typing tool
|
Complete norovirus genomes
| OP649637 | GI.6 | |
|
|---|---|---|---|
| GI.P6 |
ORF1: 5..5368
ORF2: 5352..6974
ORF3: 6974..7603
LOCUS OP649637 7727 bp RNA linear VRL 22-OCT-2022
DEFINITION Norovirus GI strain CA-RGDS-1149 nonstructural polyprotein (ORF1),
VP1 (ORF2), and VP2 (ORF3) genes, complete cds.
ACCESSION OP649637
VERSION OP649637.1
KEYWORDS .
SOURCE Norovirus GI
ORGANISM Norovirus GI
Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes;
Picornavirales; Caliciviridae; Norovirus; Norwalk virus.
REFERENCE 1 (bases 1 to 7727)
AUTHORS Pan,C.-Y., Hatada,A., Morales,C., Montmayeur,A.M., Chhabra,P. and
Vinje,J.
TITLE 2018 LTCF outbreak California
JOURNAL Unpublished
REFERENCE 2 (bases 1 to 7727)
AUTHORS Pan,C.-Y., Hatada,A., Morales,C., Montmayeur,A.M., Chhabra,P. and
Vinje,J.
TITLE Direct Submission
JOURNAL Submitted (13-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..7727
/organism="Norovirus GI"
/mol_type="genomic RNA"
/strain="CA-RGDS-1149"
/isolate="HU/US/2018/GI.6[P6]/CA-RGDS-1149"
/isolation_source="stool"
/host="Homo sapiens"
/db_xref="taxon:122928"
/country="USA: CA"
/collection_date="Aug-2018"
/note="Amplicon sequencing:first 35 nt does represent
primer sequence;
genotype: GI.6[P6]"
gene 5..5368
/gene="ORF1"
CDS 5..5368
/gene="ORF1"
/codon_start=1
/product="nonstructural polyprotein"
/protein_id="UYG09757.1"
/translation="MMMASNDAIAATAASVSSTGDNSNTMKDRFLAKLKSLGNTKPIK
IENTQMALGLLSREPSPSPNRDPPKQQRDRVPRNVAETQQAMGWADPPVDQNLPTWEE
LSQSEKQKIMAENSRWFDAGGLGPATLPTNYCRVQDSSDGDHQVKWSAKDGVNLGVDT
LTTVQGPPWNLCPLPPADQRNSGAAKEPLIGDMIEFYEGHIYHYAMYIGQGKTIGVHS
PRAAFSIPRITIHPIAAWWRVCYVPTQEQRLSYDQLKELENEPWPYAAVTNNCYEFCC
RIMDLQDTWLERRLVTSGRFNHPTQDWSKDTPDFQQDSKLEVVRDAVLAAINGLVSRP
FKNLLNKLKPLNILNLLSNCDWTFMGIVETIILLMELFGVFWDPPDVSNFIASLLPDM
HLQGPEDLAKDLIPLILGGIGLAIGFTKDKVTKVMKSAVDGLRAATQLGQYGLEVFAV
IKKYFFGGDQTEKTLKDIETAVIDMEVISTTAITQLVRDKQSARTYMAILDAEEEKAR
KLSVKHADPHVVSTTNALISRISMARSALAKAQAELTNRVKPVVIMMCGPPGIGKTKA
AEYLAKRLANEIRPGGKVGLVPREAVDHWDGYHGEEVMLWDDYGMSKIADDCNKLQAI
ADTAPLTLNCDRIEKKGMQFVSDAIVITTNAPGPAPVDFVNLGPVCRRVDFLVYCSAP
EVEQVRRVSPGDTGALKDCFKDDFSHLKMEIAPQGGFDNQGNTPFGKGVMRPTTINRL
LIQAVALTMERQDEFQMQGPTYDFDSDRISAFTSLAKANGLSLIGMASLGKRLRSVNS
VHGLKNALTGYTITPCTIKWQARFYDIESDGSVVKICENTTAQTQRQQSIDTAVLALT
RLRAARAAAYASCLQSAITTVLQMAGSALVIHRAVKRMFGTHTNAVSLEGPDREHRCR
VHQAKANGRGPIGHDDVIEKYGLCETEDESTQEQEATMELPTASHEGKNKGKTKKGRG
RRANYNAFSRRGLSDEEYEEYKKVREEKGGNYSIQEYLEDRQRYEEEMAEVQAGGDGG
IGETEMEIRHRVFFKSKTKKNRQEERRQLGLVTGSEIRKRKPIDWTPPKNEWADDDRE
VDYNEKINFEAPPTMWSRVTRFGSGWGFWVSPTVFITTTHVIPTGAKEFFGEPLDSIA
IHRAGEFTQFRFSRKIRPDLTGMVLEEGCPEGVVCSILIKRDSGELLPLAVRMGAIAS
MKIQGRLVHGQSGMLLTGANAKGMDLGTLPGDCGAPYVYKRNNDWVVCGVHAAATKSG
NTVVCAVQAGEGETTLEGGDRGHYAGHEIVRNSKGPALSSKTKFWRSTPEPLPPGVYE
PAYLGGKDPRVKGGPSLHQVLRDQLKPFAEPRGRMPEPGLLEAAVETVTSMLEQVMDT
PTPWSYADACQSLDKTTSSGHPYHKRKNDDWNGTTFVGELGEQAAHANNMYEQGKSMK
PLYTAALKDELVKPEKIYQKIKKRLLWGADLSTVIRSARAFGPFCDAIKSHVIKLPIK
VGMNSIEDGPLIYAEHAKYKNHFDADYSAWDSTQNRQIMMESFSIMCRLTASPDLAAV
VARDLLAPSEMDVGDFVIRVKEGLPSGFPCTSQVNSINHWLITLCALSEVTGLAPDVI
QSQSYFSFYGDDEIVSTDIDFDPVRLTQVLREYGLRPTRPDKSEGPIILRRNVDGLVF
LRRTISKDAAGYQGRLDRNSIERQLWWTRGPNHDDPNETLIPHPQRKVQLISLLGEAS
LHGEKFYRKISGRVIQEIKTGGLEMYVPGWQAMFRWMRFHDLGLWTGDRDLLPEFVND
DGV"
gene 5352..6974
/gene="ORF2"
CDS 5352..6974
/gene="ORF2"
/note="major capsid protein"
/codon_start=1
/product="VP1"
/protein_id="UYG09758.1"
/translation="MMMASKDAPTSPDGASGAGQLVPEVNTADQISMDPVAGASTAVA
TAGQVNMIDPWIFNNFVQAPQGEFTISPNNTPGDILFDLQLGPHLNPFLAHLSQMYNG
WVGNMRVRILLAGNAFTAGKIIICCVPPGFDARILTIAQATLFPHMIADVRTLEPVEL
PLEDVRNVLYHNNSQPQPTMRLVAMLYTPLRTGGGSGGTDAFVVAGRVLTCPAPDFSF
LFLVPPSVEQKTRVFSVPNIPLKDLSNSRVPTLIQGMFVSPDVNQSVQFQNGRCQIDG
QLQGTTPVSLSQLCKIRGRTSSNARVLNLSEVDGTPFVPLESPAPVGFPDLGGCDWHV
GFTFEARDQDPSQNVTFATNDSSFVPYLGSISPHNGDGFHSGDIIGSLDWISAPSDGS
TLDVWSIPKYGSSLPDVTHLAPAVFPPGFGEVILYFHSKFPGSGPTDKLRVPCLIPQE
FITHFCNEQAPIAGEAALLHYVDPDTGRNLGEFKLYPDGFMTCVPNSISSGPQTLPTN
GVFVFVSWVSRFYQLKPVGTASMARRLGLRRI"
gene 6974..7603
/gene="ORF3"
CDS 6974..7603
/gene="ORF3"
/note="minor structural protein; small basic protein"
/codon_start=1
/product="VP2"
/protein_id="UYG09759.1"
/translation="MAQAIIGAIAASAAGSILGAGIQAGAEAGLQAQRYQQDLQLQQN
TFQHDREMIGYQVQASNALLAKNLNTRYTLLQAGGLSSADAARAVAGAPVTRIVDWNG
TRVAAPTSSATTLKSGGFMPVPVPLTQKSKQPLMTGQDNPNYAASSISRTASWVQSQN
SLRSMPPFHNDALRTVWVTPPGSSSTSSVQSSYYGVFNTDRLPLFANRR"
ORIGIN
1 gtgaatgatg atggcgtcta acgacgctat tgcagctact gctgccagtg tttcaagcac
61 tggtgacaac agtaacacaa tgaaggatcg cttcttagcg aaactcaaga gtttgggcaa
121 caccaaaccc ataaaaattg aaaacacaca gatggctctt gggcttctga gccgggaacc
181 gtcgccatcg cccaaccgtg acccccctaa acaacaacgg gacagggtgc cacggaatgt
241 ggctgaaacc cagcaggcaa tgggatgggc agacccacct gttgaccaaa atctgccaac
301 atgggaggag ctcagccagt ctgagaaaca gaagatcatg gctgagaatt caagatggtt
361 tgatgctggt ggcctaggtc cagctaccct accaacgaat tactgtcgtg tacaagacag
421 tagcgatggt gaccatcagg ttaaatggag tgctaaggat ggtgtcaatc tgggagttga
481 caccttgaca accgttcagg gccccccatg gaacttgtgc ccgcttcctc cagctgacca
541 acgcaatagc ggggcagcta aagagcccct gattggagac atgattgagt tttatgaagg
601 gcacatatac cattatgcca tgtacatagg ccagggaaaa acgattggtg tgcactcccc
661 tagggctgct ttttccatac ctaggattac catacaccca atcgctgctt ggtggagggt
721 gtgctatgtc cccacccaag agcagagact aagttatgat caactcaagg aacttgaaaa
781 tgaaccttgg ccatatgcag ctgtcaccaa caactgctac gagttctgct gcaggataat
841 ggatctgcag gacacttggt tggagaggag actggtgaca tcaggccgct ttaaccaccc
901 aacccaggac tggtccaagg acaccccaga tttccaacaa gatagcaagc tagaggttgt
961 tcgtgatgcc gttttagcag ctattaatgg cctggtctca cgcccgttca agaacttgct
1021 aaataagctc aaaccactaa acatcctcaa cctcctatcc aattgtgatt ggaccttcat
1081 gggaatagtt gaaaccataa tattgctaat ggagctcttt ggggtctttt gggatccccc
1141 tgacgtgtcc aacttcatag cttccctcct tcctgacatg cacctccaag gcccagaaga
1201 tctggccaag gatctgatac cacttatatt gggtggaatc gggttggcca taggcttcac
1261 taaggataaa gtgacaaagg tgatgaaaag tgcagttgat ggtctacgtg cagccactca
1321 actagggcaa tatggcttgg aggtcttcgc agtcatcaag aaatacttct ttgggggtga
1381 tcagacagag aagacactta aagatattga gacagcagtt attgacatgg aggtcatctc
1441 cacgacagcc ataacacaat tggtcaggga caaacaatcc gccaggacct atatggccat
1501 actagatgct gaagaggaaa aggcccgaaa gttgtctgtg aagcatgctg acccccacgt
1561 ggtatcaacc accaacgcac tgatttcgcg catctcaatg gcgcgttctg ccctggctaa
1621 agcgcaagct gagttgacaa acagagttaa gccagtggtg ataatgatgt gtggccctcc
1681 tggtataggc aagacgaagg ctgccgagta cctagccaaa cggcttgcca atgaaatacg
1741 tccaggtggg aaggttggtc tggtcccacg tgaagctgtc gaccactggg atggatacca
1801 tggtgaggag gttatgttgt gggatgacta tgggatgtca aagatagcag atgactgtaa
1861 taaactgcaa gcaattgctg acacagcccc attgacactt aattgtgacc ggatagaaaa
1921 gaaaggtatg cagtttgtgt cagatgccat tgttataacc accaatgccc cagggccagc
1981 ccctgttgac tttgtcaatt taggacctgt ctgtcggcgt gtcgacttcc tggtctattg
2041 ttctgcccca gaagtcgaac aggtgcgccg tgttagtccc ggagacactg gcgcgctcaa
2101 agattgcttc aaggacgact tctctcacct taaaatggaa attgcaccac agggaggatt
2161 tgacaatcaa gggaacacac catttggcaa gggcgtcatg cgccctacca ccataaatag
2221 acttttgatt caggcggttg ctctcaccat ggaacgccag gatgagttcc agatgcaagg
2281 accaacctac gattttgact cagacaggat ttcagctttc actagtctag ccaaagccaa
2341 tggtttaagt ctgattggta tggcaagtct tgggaagaga ctacgcagtg tcaactcagt
2401 ccatggcctc aaaaatgccc taaccggtta cactatcaca ccatgtacca taaaatggca
2461 agccaggttt tatgacatag aatctgatgg tagcgtggtc aagatatgtg agaacacaac
2521 tgcacaaacc cagcgccaac agtccattga taccgctgtc ctcgcgctca cccgactcag
2581 ggctgcgagg gccgctgcgt atgcatcctg tctgcagagt gctatcacga ccgtgttgca
2641 gatggcaggt tcagcccttg ttatacatcg agccgtcaag cgcatgttcg gcacccatac
2701 caatgctgtc tccctagagg gtcctgacag ggaacatcgc tgtcgagtgc atcaggctaa
2761 ggctaatggt cgtggcccca ttggacatga tgatgtcata gagaaatatg ggttgtgtga
2821 aacagaagat gagtctaccc aggagcagga agccaccatg gaactgccca ctgcaagcca
2881 tgaaggcaag aacaagggga agaccaagaa gggccgaggc cgaagagcca actacaatgc
2941 cttctctaga cgtggcctaa gtgatgagga gtacgaggag tacaagaagg ttagagaaga
3001 gaaaggtgga aactacagca tccaagagta ccttgaagac aggcaacgct atgaggagga
3061 gatggctgaa gtgcaggccg gcggcgatgg tggaataggt gagacggaga tggaaatacg
3121 tcatcgagtc ttctttaagt ccaaaacaaa gaagaaccgc caggaggaac gccggcagct
3181 tggcttagtc acgggcagtg agataagaaa gagaaaaccc atagattgga ccccccccaa
3241 aaatgaatgg gcagacgatg atagagaagt ggattacaat gagaaaataa attttgaagc
3301 ccctcccacc atgtggagcc gagtcacacg attcggttct gggtgggggt tttgggttag
3361 ccccacagtg ttcatcacca ccacccatgt tataccaacc ggggccaaag aattctttgg
3421 ggaaccatta gattccattg ccatacatcg tgcaggagag ttcacacaat tccgcttctc
3481 aagaaagata cggccagatc tgacagggat ggttcttgag gaagggtgtc ctgaaggagt
3541 ggtttgctca atcctgatca agcgtgactc aggtgagctg ctaccgttgg ctgtgcgcat
3601 gggggctata gcttcaatga aaatacaggg ccggttagtc catggtcagt ctggtatgct
3661 cctaactggt gccaatgcaa aaggtatgga cctgggtact ctcccaggtg attgtggggc
3721 gccctatgtc tacaagagaa acaatgattg ggtggtctgc ggtgtccacg cagcggccac
3781 caagtctggt aacactgtgg tctgtgcagt acaagcaggt gagggggaga ccactctaga
3841 aggaggtgat aggggacatt atgctgggca tgaaatagtc aggaatagca agggtcccgc
3901 actctcatcc aaaactaagt tctggagatc aacaccagag cccctgcccc caggtgtcta
3961 tgaaccagct tatctagggg gcaaagaccc tagagtcaag ggtggtcctt ctttgcacca
4021 ggtcctccgg gatcaactga aacctttcgc tgaaccacgt gggcgcatgc cagagccagg
4081 tttactggag gccgctgttg agacagtgac ctctatgctg gaacaggtta tggatacacc
4141 cacaccatgg tcgtatgcag atgcctgcca gtcattagac aagaccacca gttctggaca
4201 cccctaccac aagaggaaga atgatgattg gaatggcacc acctttgtgg gggagcttgg
4261 tgagcaggca gcccatgcaa acaacatgta tgagcaaggc aagtctatga agcccctata
4321 cacagcagcc ctcaaagatg aacttgttaa accagagaag atctatcaaa aaattaagaa
4381 aaggttgctg tggggagctg acctgtcgac cgttatacgg tccgcacggg cttttggccc
4441 cttctgtgat gcaataaaat cccatgtgat caaattaccc atcaaggttg gtatgaactc
4501 aattgaggat ggccctctaa tctatgctga acatgcaaag tataagaatc actttgatgc
4561 ggattattca gcctgggact caacacaaaa tagacaaatc atgatggagt ccttctcaat
4621 catgtgtcgc ctcactgcct caccagattt ggcagctgtt gtggctagag acctgttggc
4681 cccttctgag atggatgtgg gagactttgt aattagagtc aaggagggtc tcccatcagg
4741 attcccctgt acttcacaag tcaatagcat aaaccactgg ctcattacat tgtgtgctct
4801 atctgaggtc acgggtctgg cacccgatgt tattcagtca cagtcatatt tctccttcta
4861 tggggacgat gaaatcgtgt ccacagacat tgattttgac ccggtccggc tcacccaggt
4921 tctcagggag tatgggctgc gtccaactcg tccagacaaa agtgagggcc ccataatttt
4981 gaggagaaat gtagatggct tggtgttcct taggcgcacc atctccaaag acgcagctgg
5041 ctaccaaggc cggttggata ggaactccat agaaagacaa ctgtggtgga cccgtggccc
5101 caatcatgat gatccaaatg agacacttat tcctcacccc caaagaaagg tccagctcat
5161 atcactgcta ggagaggcat cacttcatgg ggaaaagttt tacagaaaga tttcaggtag
5221 agtcatccaa gagatcaaaa caggtggatt ggaaatgtat gtgccaggct ggcaggccat
5281 gttccgctgg atgcgttttc atgaccttgg actttggaca ggagatcgcg atctcctgcc
5341 cgaattcgta aatgatgatg gcgtctaagg acgccccaac atcgcctgat ggcgccagtg
5401 gcgctggcca gctagtgccg gaggttaata cagctgacca aatttcaatg gatcctgttg
5461 cgggtgcttc cactgcagtt gcaaccgctg gacaagttaa tatgattgac ccatggatat
5521 tcaataattt tgtccaggcc cctcagggtg aatttactat ttctccaaac aatacccccg
5581 gcgatatttt gtttgattta caattgggcc cccatctgaa ccccttctta gctcacttat
5641 cacagatgta caatgggtgg gtcggcaata tgcgggtccg tatattgctg gcaggcaatg
5701 cttttacagc tggtaagata atcatatgtt gtgtcccccc cggttttgat gctagaatac
5761 ttaccattgc tcaagctacc ctatttcccc atatgattgc tgatgttagg actcttgaac
5821 cagtagagtt acctctcgag gacgtgcgta atgtcctcta ccacaacaac agccagccac
5881 agccaaccat gcgtctggtg gctatgctat acaccccgct gcgcacaggc ggtgggtctg
5941 gaggcactga tgcttttgtg gttgctggga gagtgctgac atgtcctgca ccagacttca
6001 gttttctatt ccttgttcct ccctctgtag agcaaaagac tagggtcttc agtgtgccca
6061 atataccact caaggacctt tcaaactctc gggtgccaac cttgatacaa ggtatgtttg
6121 tttctcctga tgttaatcaa tcagtgcaat ttcaaaatgg gcggtgccaa attgatggcc
6181 agttacaagg tactactcca gtgtccctca gccaattatg taagatcagg ggtaggactt
6241 ccagcaatgc cagggtactc aaccttagtg aggttgatgg aacacctttt gtgccccttg
6301 agtcccctgc acctgtaggt ttcccagatt taggcgggtg tgattggcac gtcggcttta
6361 cttttgaggc acgagaccag gacccttccc agaatgtgac ctttgcaact aatgattcta
6421 gctttgtgcc atatcttggc agtatctcac cccataatgg tgatgggttt catagtggtg
6481 atattatagg tagtttagat tggatttcag ctccatcgga tggttccaca cttgacgtgt
6541 ggtccatacc aaaatatgga tcatccctcc cagatgtcac tcatctggcc cctgcagttt
6601 ttccccctgg ttttggtgag gtcatcctct actttcactc taaattccct ggttctggcc
6661 ctactgataa gcttagggtc ccatgtctga taccacaaga gttcataaca cacttctgca
6721 atgaacaagc acccatagcg ggggaggctg ccctccttca ctatgtggac cctgacacag
6781 gtaggaactt gggggaattc aagctttatc cagatggctt tatgacatgt gtgcctaaca
6841 gcatcagcag tggcccccag actctgccaa ctaatggtgt gtttgtgttt gtgtcctggg
6901 tgtccagatt ttaccaactt aagcctgtgg gaacggcctc aatggccagg aggcttggtc
6961 ttcggcgcat ataatggccc aagccatcat aggtgccata gcagcttctg ctgctggaag
7021 tatactcggt gctggcatac aagctggtgc tgaggctgga ctccaagccc aacggtatca
7081 acaggatctt caactacaac agaacacttt ccagcatgat agggaaatga tagggtacca
7141 agtccaagcc agcaatgccc tgttggccaa gaatcttaac actagatata ctctactgca
7201 ggcagggggt ttgtctagtg cggatgcagc tagggctgtt gcgggtgctc ctgttacacg
7261 catagtggat tggaacggga cccgtgtggc agctcccaca tcaagcgcta ccacactaaa
7321 atctggtggg tttatgcctg tccctgtacc cttaactcaa aagtctaaac aacctctaat
7381 gactgggcaa gataatccta actatgctgc ttcctctatt tctagaactg cctcatgggt
7441 gcaatcccag aattctttga ggtctatgcc cccctttcac aatgatgctc tccggactgt
7501 gtgggtcacg ccacccggtt cttcatctac atcttctgtg cagtctagtt attatggtgt
7561 ctttaataca gatagattac ccctcttcgc aaataggagg tagggttttt gtaataggat
7621 gccagtgggc accatattca gtttaatcag aatttataat taggatttat aattagaatt
7681 tataattaga atttataatt tggttaaatt ggcttttaat tggtgtt
//