Typing tool
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Typing tool
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Complete norovirus genomes
| MN226991 | GI.6 | |
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| GI.P11 |
ORF1: 4..5370
ORF2: 5354..6976
ORF3: 6976..7605
LOCUS MN226991 7633 bp RNA linear VRL 31-JUL-2019
DEFINITION Norovirus GI isolate Hu/US/2018/GI.Pb-GI.6/CA-RGDS-1059
nonstructural polyprotein (ORF1), VP1 (ORF2), and VP2 (ORF3) genes,
complete cds.
ACCESSION MN226991
VERSION MN226991.1
KEYWORDS .
SOURCE Norovirus GI
ORGANISM Norovirus GI
Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes;
Picornavirales; Caliciviridae; Norovirus; Norwalk virus.
REFERENCE 1 (bases 1 to 7633)
AUTHORS Pan,C.-Y., Huynh,T., Castro,C.J., Marine,R.L., Ng,T.F. and
Wadford,D.A.
TITLE Norovirus GI.Pb-GI.6 from a Long Term Care Facility Outbreak,
California, 2018
JOURNAL Unpublished
REFERENCE 2 (bases 1 to 7633)
AUTHORS Pan,C.-Y., Huynh,T., Castro,C.J., Marine,R.L., Ng,T.F. and
Wadford,D.A.
TITLE Direct Submission
JOURNAL Submitted (26-JUL-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 :: SPAdes v. 3.6; Geneious v. R10
Sequencing Technology :: Illumina
##Assembly-Data-END##
FEATURES Location/Qualifiers
source 1..7633
/organism="Norovirus GI"
/mol_type="genomic RNA"
/isolate="Hu/US/2018/GI.Pb-GI.6/CA-RGDS-1059"
/isolation_source="stool"
/host="Homo sapiens"
/db_xref="taxon:122928"
/country="USA: CA"
/collection_date="31-Aug-2018"
/note="genotype: GI.Pb-GI.6"
gene 4..5370
/gene="ORF1"
CDS 4..5370
/gene="ORF1"
/codon_start=1
/product="nonstructural polyprotein"
/protein_id="QDQ72248.1"
/translation="MMMASKDVVATNVASNNNANNTSATSRFLSRFRGLGGGASPPNP
IKIKSTEMALGLIGKTTQETAGTNGLPPKQQRDRPPRTQEEVQYGMGWTERPMDQNVK
SWEELDTSTKGEILDSHKEWFDAGGLGPCTMPSTCEQAKDDSPPGEQVRWSVRDGVDL
GVNRLTTVSGPEWNLCPLPPIDLRNMEPASEPTIGDMIEFYEGHIYHYSIYIGQGKTV
GVHSPQAAFSVARVTIQPIAAWWRVCYIPQPKHRLSYDQLKELENEPWPYAAITNNCF
EFCCQIMNLEDTWLQRRLITSGRFHHPSQSWSQQTPEFQQDSKLELVRDAILAAVNGL
VSQPFKNFLNKLKPLNILSILSNCDWTFMGVVEMVVLLLELFGVFWNPPDVSNFIASL
LPDFHLQGPEDLARDLVPVILGGIGLAIGFTRDKVTKVMKSAVDGLRAATQLGQYGLE
IFSLLKKYFFGGDQTERTLKGIEAAVIDMEVLSSTSVTQLVRDKQAAKAYMNILDNEE
EKARKLSAKNADPHVISSTNALISRIAMARSALAKAQAEMTSRMRPVVIMMCGPPGIG
KTKAAEHLAKRLANEIRPGGKVGLVPREAVDHWDGYHGEEVMLWDDYGMTKIQDDCNK
LQAIADSAPLTLNCDRIENKGMQFVSDAIVITTNAPGPAPVDFVNLGPVCRRVDFLVY
CSAPEVEQIRRVSPGDTSALKDCFKPDFSHLRMELAPQGGFDNQGNTPFGKGVMKPTT
INRLLIQAVALTMERQDEFRLQGKMYDFDDDRVSAFTTMARDNGLGILSMASLGKKLR
GVTSMEGLKNALKGYRIGACTIKWQAKVYSLESDGNSVNIREEKNVLTQQQQSVCTAS
IALTRLRAARAVAYASCIQSAITSILQIAASALVVNRAVKRMFGTRTAALSLEGPPKE
HKCRVHQAKAAGKGPIGHDDVVDKYGLCETEEDEEVVQTEMPSATMEGKNKGKNKKGR
GRKNNYNAFSRRGLNDEEYEEYKKIREEKGGNYSIQEYLEDRQRYEEELAEVQAGGDG
GIGETEMEIRHRVFYKSKSKKHHQEERRQLGLVTGSDIRKRKPIDWTPPKSAWADDER
EVDYNERINFEAPPTLWSRVTKFGSGWGFWVSPTVFITTTHVIPTSAKEFFGEPLTSI
AIHRAGEFTLFRFSKKIRPDLTGMILEEGCPEGTVCSVLIKRDSGELLPLAVRMGAIA
SMRIQGRLVHGQSGMLLTGANAKGMDLGTIPGDCGAPYVYKRANDWVVCGVHAAATKS
GNTVVCAVQASEGETTLEGGDKGHYAGHEIIKHGCGPALSTKTKFWKSSPEPLPPGVY
EPAYLGGRDPRVSGGPSLQQVLRDQLKPFAEPRGRMPEPGLLEAAVETVTSSLEQVMD
TPVPWSYSDACQSLDKTTSSGYPHHKKKNDDWNGTAFIRELGEQAAHANNMYEQGKSM
KPMYTAALKDELVKPEKVYQKVKKRLLWGADLGTVIRAARAFGPFCDAIKSHTIKLPI
KVGMNSIEDGPLIYAEHSKYKYHFDADYTAWDSTQNRQIMTESFSIMCRLTASPELAS
VVAQDLLAPSEMDVGDYVIRVKEGLPSGFPCTSQVNSINHWLITLCALSEVTGLSPDV
IQSMSYFSFYGDDEIVSTDIEFDPAKLTQVLKEYGLKPTRPDKSEGPIIVRKSVDGLV
FLRRTISRDAAGFQGRLDRASIERQIYWTRGPNHSDPFETLVPHQQRKIQLISLLGEA
SLHGEKFYRKISSKVIQEVKTGGLEMYVPGWQAMFRWMRFHDLGLWTGDRNLLPEFVN
DDGV"
mat_peptide 4..1200
/gene="ORF1"
/product="p48"
mat_peptide 1201..2289
/gene="ORF1"
/product="NTPase"
mat_peptide 2290..2886
/gene="ORF1"
/product="p22"
mat_peptide 2887..3300
/gene="ORF1"
/product="VPg"
mat_peptide 3301..3843
/gene="ORF1"
/product="Pro"
mat_peptide 3844..5367
/gene="ORF1"
/product="RdRp"
gene 5354..6976
/gene="ORF2"
CDS 5354..6976
/gene="ORF2"
/note="major capsid protein"
/codon_start=1
/product="VP1"
/protein_id="QDQ72249.1"
/translation="MMMASKDAPTSPDGASGAGQLVPEANTAEQISMDPVAGASTAVA
TAGQVNMIDPWIFNNFVQAPQGEFTISPNNTPGDILFDLQLGPHLNPFLAHLSQMYNG
WVGNMRVRILLAGNAFTAGKIIICCVPPGFDARILTIAQATLFPHLIADVRTLEPVEL
PLEDVRNVLYHNSSQPQPTMRLVAMLYTPLRTGGGSGGTDAFVVAGRVLTCPAPDFSF
LFLVPPSVEQKTRVFSVPNIPLKDLSNSRVPVPVQGMFMSPDVNQSVQFQNGRCQIDG
QLQGTTPVSLSQLCKIRGKTSSNARVLNLSEVDGTPFIPLESPAPVGFPDLGGCDWHV
NFTFQAQNQDPSQSVTFATNDASFVPYLGSISPHNGGDFHTGDIIGSLGWISAPSDNS
QLNVWTIPKYGSSLPDVTHLAPAVFPPGFGEVILYFYSTFPGSGQPSQLQVPCLLPQE
FITHFCNEQAPIAGEAALLHYVDPDTGRNLGEFKLYPDGFMTCVPNSVSSGPQTLPIN
GVFVFVSWVSRFYQLKPVGTASAARRLGLRRI"
gene 6976..7605
/gene="ORF3"
CDS 6976..7605
/gene="ORF3"
/note="minor structural protein; small basic protein"
/codon_start=1
/product="VP2"
/protein_id="QDQ72250.1"
/translation="MAQAVIGAIAASAAGSILGAGIQAGAEAGLQAQRYQQDLQLQQN
SFKHDKEMLGYQVQASNALLAKNLNTRYALLQAGGLSSADAARAVAGAPVTRIVDWNG
TRIAAPASSATTLRSGGFMAVPIPLSSKTKQPVMSGQDNPNYAASSISRTASWVQSQN
SMRSVSPFHSDALRTVWVTPPGSSSTSSVQSSFYGVFNTDRLPLFANRR"
ORIGIN
1 tgaatgatga tggcgtcgaa agacgtcgtt gcgactaatg ttgcaagcaa taacaatgct
61 aacaacacta gtgctacatc tcgattttta tcgagattca ggggtttagg tggtggcgca
121 agccccccta atcccataaa gattaaaagc acagaaatgg ccttgggttt gattggcaag
181 acaacccaag agacggcagg gaccaatggc ctgccaccta aacagcaaag agaccgaccc
241 cctaggactc aagaggaagt tcagtacggc atgggatgga ctgaacggcc tatggatcag
301 aatgtcaagt catgggagga gcttgatacc tctaccaaag gggagatctt ggacagccac
361 aaagaatggt tcgatgcagg tggtttgggc ccatgcacaa tgccctcaac ttgtgaacag
421 gctaaagatg atagcccgcc tggtgagcag gtcagatggt cagtgcgtga tggagttgac
481 cttggagtga atcgccttac aacggtgagt ggccccgagt ggaatctctg tcctttaccc
541 cctattgatc taaggaatat ggaaccagct agtgaaccca ccattggaga catgatagag
601 ttttatgaag gtcatatcta ccactactcc atatacatag gacagggaaa gacagttggt
661 gtgcactccc cacaggcggc attctctgta gccagagtga ctatccaacc catagccgct
721 tggtggaggg tctgctacat accccagccc aaacataggc tgagttacga ccagcttaag
781 gagttggaaa atgaaccttg gccatatgca gctatcacca acaattgttt tgagttttgc
841 tgtcaaatta tgaaccttga ggacacatgg ttgcagaggc gactaataac atcaggcaga
901 tttcaccatc cttcccaatc ttggtcacaa cagacccccg aatttcagca ggatagcaag
961 ctggaactgg tcagagatgc catactggcc gcggtgaatg gccttgtttc acaacctttt
1021 aaaaatttct tgaataaact caagcccctt aacatcctaa gcatcttatc taactgtgat
1081 tggactttta tgggggtggt tgaaatggtt gtactacttc ttgaactctt tggcgtgttc
1141 tggaatccgc ccgatgtgtc taattttata gcatcccttc tccctgattt tcacctccag
1201 gggccagaag acctagcccg ggatctggtg ccagtcattc ttggtggcat agggctagcc
1261 attggattta ccagagacaa ggtcactaaa gtcatgaaaa gtgctgtaga tgggctccgg
1321 gccgctacgc agttagggca atatggattg gaaatatttt cactcctcaa gaagtatttc
1381 tttggcgggg atcagactga gcgaactctc aaaggcattg aagcagcagt catagatatg
1441 gaggttttgt cctctacgtc agtaacacaa ctggtgagag acaagcaggc agctaaagct
1501 tatatgaata tcctggataa tgaagaggaa aaagctagaa aactttctgc taagaatgct
1561 gacccccatg tgatatcttc aacaaatgcc ctgatatcac gcatagccat ggctcgatcc
1621 gctctggcta aggctcaagc tgagatgacc agtcgaatga ggccagttgt cattatgatg
1681 tgtggacccc ctggaattgg aaagactaag gcagcagagc acttggcaaa acgcctggcc
1741 aatgagatca gacctggcgg caaagtggga ctggtgccac gtgaggctgt tgaccactgg
1801 gatggctacc atggtgagga ggtgatgcta tgggatgact atggcatgac aaagatacaa
1861 gatgactgca acaagctcca ggctattgct gactctgccc cactcactct caattgtgat
1921 aggattgaaa acaaggggat gcagtttgtg tcagacgcaa tagtcatcac caccaatgcc
1981 ccaggacctg cccctgtgga cttcgtcaac ctcggccctg tgtgcagacg ggtcgacttc
2041 ctagtctact gttccgcccc agaggtggag caaataagga gggttagccc tggtgacaca
2101 tcagcgctta aagactgctt caaaccagat ttctcccatc tcaggatgga gttagctcct
2161 caaggggggt ttgacaacca agggaacaca ccatttggca agggtgttat gaaaccaaca
2221 actatcaata gactcctcat acaagctgtg gctcttacca tggagagaca ggatgagttc
2281 cgactccagg gaaaaatgta tgattttgat gatgataggg tgtcagcctt taccaccatg
2341 gcacgcgata atggattggg cattctgagt atggcgagcc taggcaagaa gctgcgtggt
2401 gttacatcaa tggagggcct gaagaatgcc ttgaaggggt acagaattgg tgcgtgcaca
2461 atcaagtggc aggctaaggt gtattcacta gaatcagatg gcaacagtgt taacattagg
2521 gaggagaaga atgttttgac tcaacaacag cagtcggtgt gcactgcttc tattgcactc
2581 acccgcctgc gggccgcgcg tgcggtagca tatgcgtcat gcatccaatc agccataacc
2641 tccatactac aaatagctgc ctcagcccta gtggttaaca gagccgtaaa gagaatgttt
2701 ggtacacgca ccgctgcctt atccctagag ggccccccca aagagcacaa gtgtagggtc
2761 caccaggcta aggccgcagg gaaggggccc attggccatg atgacgtggt tgacaagtat
2821 ggtctatgtg agactgagga ggatgaagag gtggtccaaa ccgagatgcc atctgccacc
2881 atggaaggca agaataaagg taagaacaag aaagggcgtg gccgaaagaa taactataat
2941 gccttttccc gtagagggct caatgatgaa gagtatgagg agtacaagaa aatacgggaa
3001 gagaagggtg gaaattacag cattcaggag tacctagaag atagacaaag gtatgaagag
3061 gagcttgctg aggttcaagc aggtggagat ggagggatcg gcgaaaccga aatggaaatt
3121 cgccatagag tgttctacaa gtccaagagt aagaagcacc accaggaaga acggcgccaa
3181 ctaggattag tcacaggttc tgacatccgt aaaaggaaac caattgactg gaccccccct
3241 aaatcagcat gggcagatga tgagcgcgaa gtggactaca atgagagaat caactttgag
3301 gcgcccccca ccttatggag ccgagtcaca aaatttgggt ctgggtgggg cttttgggtt
3361 agtcccacag tcttcataac cacaacacac gtcataccaa ccagtgcaaa agagttcttt
3421 ggtgaacccc tcaccagtat agccattcat agggctggag aattcaccct cttcaggttc
3481 tctaagaaaa tcaggcctga tctcacgggc atgattcttg aggaaggctg cccagagggt
3541 acggtgtgct cagtgttaat aaaaagggac tccggtgagc tattaccatt ggctgtaaga
3601 atgggcgcaa tagcatcaat gcgcatacag ggccgccttg tccatggcca gtctggtatg
3661 ttgctcactg gggcgaatgc taagggcatg gaccttggaa ctatcccagg agattgtgga
3721 gctccctatg tctataagag agcaaatgac tgggtggttt gtggtgtgca tgctgctgcc
3781 actaaatcag gcaacacggt agtgtgtgcc gtccaagcta gtgaaggaga aaccacactg
3841 gaggggggtg ataaaggtca ctatgctggg catgagataa ttaagcatgg atgtgggcca
3901 gccttatcaa ccaaaacaaa gttctggaag tcgtcccctg aaccactacc ccctggagta
3961 tatgaacctg catacctcgg tggccgggac ccaagagtga gtggtggccc ctcgctccaa
4021 caggtgttgc gggaccaatt aaagccattt gctgaaccac gggggcgtat gccagagcca
4081 ggtctcctgg aggccgcagt tgagactgtg acctcatcac tggagcaggt tatggatacc
4141 ccagtgccat ggagttacag cgatgcatgt caatccttag ataaaaccac tagctcaggt
4201 taccctcacc ataagaagaa gaatgatgac tggaatggca ctgccttcat cagggaattg
4261 ggggagcaag cggcgcacgc caataacatg tatgaacaag gtaagagtat gaagcccatg
4321 tacacggcgg cgcttaagga tgaattggtg aagccagaaa aagtgtacca aaaagtgaag
4381 aagcgcttgc tttggggggc agatctagga acagtgatcc gggctgcacg agccttcggc
4441 ccattctgtg acgccataaa atcccacaca ataaaactac ctatcaaagt tgggatgaat
4501 tcaattgagg atgggccact aatttatgca gagcattcaa aatataaata tcactttgat
4561 gcagactata cagcttggga ctcaacacaa aataggcaaa ttatgactga atcattctca
4621 attatgtgcc gattgaccgc ttctccagaa ttggcctcag tggtagcaca agatctactc
4681 gcaccctcag aaatggacgt tggtgactac gtcataagag taaaggaagg ccttccatct
4741 ggctttccat gcacatcaca ggtcaatagc ataaaccatt ggttgataac tttgtgtgcc
4801 ctctctgagg tgactggcct gtcaccagat gttattcagt ctatgtcata cttctctttc
4861 tatggtgatg atgaaattgt ttccactgac atagaatttg atccagctaa attgacacaa
4921 gtccttaaag agtatggcct taagcccacc cgccccgaca agagtgaagg tccaataatt
4981 gtgaggaaga gtgtggatgg cttagtcttc ttacgccgca ccatttctcg cgatgccgcg
5041 gggttccaag ggcgactaga ccgagcgtcc attgaaaggc aaatctattg gaccagagga
5101 cccaatcact cagacccttt tgaaactttg gtgccccacc aacaaagaaa aatccagtta
5161 atatcactgt taggtgaggc ttcattgcat ggtgaaaagt tctacaggaa gatctcaagc
5221 aaagtcatcc aagaagttaa aacagggggc cttgaaatgt atgtgccagg gtggcaagcc
5281 atgttccgtt ggatgcggtt tcatgatctt ggcttgtgga caggagatcg caatctcctg
5341 cccgaattcg taaatgatga tggcgtctaa ggacgcccca acatcccctg atggcgccag
5401 tggcgccggc cagctggtac cggaggctaa cacagctgag caaatttcaa tggaccctgt
5461 cgcgggtgct tcaacagcag tcgcgacggc tggacaagta aatatgattg acccttggat
5521 tttcaataac tttgtccagg cgccccaagg agaattcact atttccccta acaatacccc
5581 cggtgatatt ttgtttgatt tacaattagg accccacctt aacccatttc tagcccatct
5641 ctcacagatg tataatggtt gggtcggcaa tatgcgtgtg cgcatactgt tggccgggaa
5701 tgcctttaca gctggaaaga taatcatttg ttgtgtcccc cctggttttg atgctagaat
5761 actcacaata gctcaagcaa ccctcttccc acacttaatt gctgatgtga ggacccttga
5821 gcctgtggag cttcctttgg aggatgtgcg caacgttctc taccacaata gtagccagcc
5881 gcaaccaaca atgcggctgg ttgctatgtt gtataccccc ctccgcactg gtggtggttc
5941 cggaggcact gatgcctttg tggtggcggg tagggtgctc acgtgccctg cccccgattt
6001 cagtttcttg tttcttgttc ccccttctgt tgaacaaaag actagagttt tcagtgtccc
6061 caacataccc ctaaaagatc tctcaaattc tcgtgtccct gtgcccgtac agggcatgtt
6121 tatgtctcca gatgttaatc agtcagtcca gttccagaat gggcgttgcc aaattgatgg
6181 tcaactccag ggcaccaccc cagtctcact cagccaactc tgcaagatta ggggtaaaac
6241 ttctagcaat gctagggtgc tcaacttaag tgaagtggat ggtacacctt ttatccccct
6301 tgaatcacca gcaccagttg gcttccccga cttgggaggc tgtgactggc atgtaaattt
6361 cactttccag gcccaaaatc aggacccatc ccaaagtgtg acctttgcaa ctaatgatgc
6421 cagctttgtc ccttacctag gtagcatctc ccctcataac gggggggact ttcatacagg
6481 tgacatcata ggcagccttg gatggatttc agcgccgtct gacaactcac aacttaatgt
6541 ttggacaata ccaaagtatg gatctagtct cccagatgtc acccatcttg ctcctgctgt
6601 attcccccca ggctttgggg aggtgatcct atatttctat tccaccttcc caggctctgg
6661 gcaacctagt caactccaag tcccatgttt gttaccccag gagttcatca cccacttctg
6721 taatgaacaa gctcccatcg ctggggaggc tgccctcctc cactacgtgg accctgatac
6781 gggccggaac ttgggagagt tcaaacttta ccctgatgga tttatgacct gtgtccccaa
6841 tagtgttagc agtggccctc aaaccctacc tatcaatgga gtctttgtct ttgtttcatg
6901 ggtgtctaga ttctatcaac ttaagcctgt gggaacggcc tcagcggcta gaaggcttgg
6961 actgcggcgc atataatggc tcaagctgtc atcggtgcca tagccgcgtc tgccgctggt
7021 agcatactag gggcaggcat acaggctggt gctgaggctg gtctccaggc tcaacggtac
7081 cagcaggatc tacaattgca gcaaaattct ttcaagcatg ataaggaaat gttaggctat
7141 caagttcagg ctagtaatgc tcttttagct aagaatctta acactagata tgcccttctg
7201 caggcagggg gcctgtctag tgctgatgct gcccgggcag tggctggtgc tcctgtcacc
7261 cgtatagtgg attggaatgg cacgcgcatt gcagctcctg cctcaagtgc cactacactt
7321 agatctggtg gtttcatggc cgtccctata ccattgtcct caaagaccaa gcaaccagtg
7381 atgtctgggc aggataatcc aaattatgct gcttcttcta tctctagaac tgcttcatgg
7441 gtgcaatctc aaaattctat gaggtctgtt tctccctttc acagtgatgc tctgaggacc
7501 gtttgggtta cgccacccgg ttcatcatca acctcatctg tgcagtctag tttttatggt
7561 gtttttaata cagatagatt acctctgttc gcaaacagaa ggtaaaattt tgtaatagga
7621 tgccagtggg cac
//