Typing tool
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Typing tool
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Complete norovirus genomes
| MK340748 | GII.2 | |
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| GII.P16 |
ORF1: 1..5094
ORF2: 5075..6703
ORF3: 6703..7473
LOCUS MK340748 7473 bp RNA linear VRL 30-JAN-2019
DEFINITION Norovirus GII nonstructural polyprotein (ORF1) gene, partial cds;
VP1 (ORF2) gene, complete cds; and VP2 (ORF3) gene, partial cds.
ACCESSION MK340748
VERSION MK340748.1
KEYWORDS .
SOURCE Norovirus GII
ORGANISM Norovirus GII
Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes;
Picornavirales; Caliciviridae; Norovirus; Norwalk virus.
REFERENCE 1 (bases 1 to 7473)
AUTHORS Pan,C.-Y., Huynh,T., Ng,T.F., Marine,R.L., Castro,C.J. and
Wadford,D.A.
TITLE Multiple foodborne outbreaks with norovirus GII.P16-GII.2
associated with Washington state oysters, 2017
JOURNAL Unpublished
REFERENCE 2 (bases 1 to 7473)
AUTHORS Pan,C.-Y., Huynh,T., Ng,T.F., Marine,R.L., Castro,C.J. and
Wadford,D.A.
TITLE Direct Submission
JOURNAL Submitted (21-DEC-2018) 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..7473
/organism="Norovirus GII"
/mol_type="genomic RNA"
/isolation_source="Hu/US/2017/GII.P16-GII.2/San
Francisco-RGDS-1007"
/isolation_source="stool"
/host="Homo sapiens"
/db_xref="taxon:122929"
/country="USA: CA,San Francisco"
/collection_date="24-Feb-2017"
/note="genotype: GII.P16-GII.2"
gene <1..5094
/gene="ORF1"
CDS <1..5094
/gene="ORF1"
/codon_start=1
/product="nonstructural polyprotein"
/protein_id="QAT98173.1"
/translation="MASNDATVAVACNNNNDKEKSSGEGLFTNMSSTLKKALGARPKQ
PAPRDKPQKPPRPPTPELVKRIPPPPPNGEEEEEPTIRYEVKSGVSGLPELTTVPQPD
VANTAFSVPPLSLRENREAKEPLTGAILEMWDGEIYHYGLYVEKGLVLGVHKPPAAVS
MARVELTPLSLYWRVVYTPQYLISPETLRRLNGEAFPYTAFDNNCYAFCCWVLDLNDS
WLNRRMVQRTTGFFRPYQEWNRKPLPTMDDSKIKKVANIFLCSLSTLFTRPIKDLVGK
IKPLNILNILATCDWTFAGIVESLILLAELFGVFWTPPDVSAMIAPLLGDYELQGPED
LAVELVPVVMGGIGLVLGFTKEKIGKMLSSAASTLRACKDLGAYGLEILKLVMKWFFP
KKEEANELAMVRAIEDAVLDLEAIENNHMTTLLKDKDSLATYMKTLDMEEEKARRLST
KSASPDIVGTINALLARIAAARSLVHRAKEELSSRMRPVVVMISGKPGIGKTHLAREV
ARKVASTLTGDQRVGLIPRNGVDHWDAYKGERVVLWDDYGMSNPIHDALRIQELADTC
PLTLNCDRIENKGKVFDSEVIIITTNLANPAPLDYVNFEACSRRIDFLVYAEAPEVEK
AKRDFPGQPDMWKDAFKPDFSHIKLQLAPQGGFDKNGNTPHGKGVMKTLTTGSLIARA
SGLLHERMDEFELQGPTTTTFNFDRNRITAFRQLAAENKYGLVDTMKVGNQLKGVKTM
EELKQAIRNVTIKKCRIIYGGSTYDLESDGKGKVLVEKVKNTSVQTNNELAGALHHLK
HARIRYYVKCVQEAVYSIIQIAGAAFVTTRIARRMNIQELWSKPQLDQNESETKEEAP
KSEDDEFIISSKDIKEEGKKGKNKTGRGKKHTAFSSKGLSDEEYDEYKRIREERNGKY
SIEEYLQDRDRYYEELAIAKATEEDFCEEEEIKIRQRIFRPTRKQRKEERATLGLVTG
SEIRKRNPDDFKPKGKLWADDNRSVDYNEKLDFEAPPSIWSRIVSFGSGWGFWVSPSL
FITSTHVIPAGITEAFGVPIKQIQIHKSGEFCRFRFPKPIRPDVTGMILEEGAPEGTV
ATVLIKRPTGELMPLAARMGTHATMRIQGRMVGGQMGMLLTGSNAKGMDLGTTPGDCG
CPYIYKRGNDYIVIGVHTAAARGGNTVICATQGSEGEATLEGGDDKGTYCGAPILGPG
GAPKLSTKTKFWRSSNTPLPPGTYEPAYLGGRDPRVKGGPSLQQVMRDQLKPFTEPRG
KPPRPSVLEAAKQTIINVLEQTLDPPQKWTYAQACASLDKTTSSGHPYHVRKNEFWNG
ETFTGKLADQASKANLMFEEGKHMTPVYTAALKDELVKTEKIYGKIKKRLLWGSDLST
MIRCARSFGGLMDEMKAHCISLPVRVGMNMNEDGPIIFEKHSRYKYHYDADYSRWDST
QQRAVLAAALEIMVRFSAEPQLAQIVAEDLLAPSVVDVGDFKITINEGLPSGVPCTSQ
WNSIAHWLLTLCALSEVTKLSPDIIQANSVFSFYGDDEIVSTDIKLDPEQLTAKLKEY
GLKPTRPDKTEGPLIISEDLNGLTFLRRTVTRDPAGWFGKLDQSSILRQMYWTRGPNH
EDPNETMIPHSQRPIQLMALLGEASLHGPSFYSKISKLVITELKEGGMDFYVPRQEPM
FRWMRFSDLSTWEGDRNLAPNFVNEDGVE"
mat_peptide <1..990
/gene="ORF1"
/product="p48"
mat_peptide 991..2088
/gene="ORF1"
/product="NTPase"
mat_peptide 2089..2619
/gene="ORF1"
/product="p22"
mat_peptide 2620..3018
/gene="ORF1"
/product="VPg"
mat_peptide 3019..3561
/gene="ORF1"
/product="Pro"
mat_peptide 3562..5091
/gene="ORF1"
/product="RdRp"
gene 5075..6703
/gene="ORF2"
CDS 5075..6703
/gene="ORF2"
/note="major capsid protein"
/codon_start=1
/product="VP1"
/protein_id="QAT98174.1"
/translation="MKMASNDAAPSTDGAAGLVPESNNEVMALEPVAGVALAAPVTGQ
TNIIDPWIRANFVQAPNGEFTVSPRNAPGEVLLSLELGPELNPYLAHLARMYNGYAGG
MEVQVMLAGNAFTAGKLVFAAVPPHFPVENLSPQQITMFPHVIIDVRTLEPVLLPLPD
VRNNFFHYNQKDDPKMRIVAMLYTPLRSNGSGDDVFTVSCRVLTRPSPDFDFTYLVPP
TVESKTKPFTLPILTLGELSNSRFPVSIDQMYTSPNEVISVQCQNGRCTLDGELQGTT
QLQVSGICAFKGEVTAHLHDNDHLYNVTITNLNGSPFDPSEDIPAPLGVPDFQGRVFG
IISQRDKHNSPGHNEPANRGHDAVVPTYTAQYTPKLGQIQIGTWQTDDLTVNQPVKFT
PVGLNDTEHFNQWVVPRYAGALNLNTNLAPSVAPVFPGERLLFFRSYIPLKGGYGNPA
IDCLLPQEWVQHFYQEAAPSMSEVALVRYINPDTGRALFEAKLHRAGFMTVSSNTSAP
VVVPANGYFRFDSWVNQFYSLAPMGTGNGRRRVQ"
gene 6703..>7473
/gene="ORF3"
CDS 6703..>7473
/gene="ORF3"
/note="minor structural protein; small basic protein"
/codon_start=1
/product="VP2"
/protein_id="QAT98175.1"
/translation="MAGAFVAGLAGDVLSNGLSSLINAGANAINQRAEFDFNQKLQQN
SFNHDKEMLQAQIQATKQLQADMMAIKQGVLTAGGFSPADAARGAVNAPMTQALDWNG
TRYWAPNSMRTTSYSGKFTSTAPVRQADFQHTQSRPSSGSSVSSFATQSSRPTLTTTT
GSSHGTVSSNSTRSTSLSQSTVSRATSRTSEWVRDQNRNLEPYMHGALQTAFVTPPSS
RASDGTVSTVPKGVLDSWTPAFNTRRQPLFAHLRKRGES"
ORIGIN
1 atggcgtcta acgacgctac cgttgccgtt gcttgcaaca acaacaacga caaagaaaaa
61 tcttcaggtg aaggcttatt cacaaatatg tcttccacct taaagaaagc cctcggggct
121 aggcccaaac agcctgcccc gagagacaaa ccacaaaagc ccccaagacc accaactccc
181 gagttggtca agaggatacc ccctcctcca cctaatggcg aagaagaaga agaaccaacc
241 attaggtatg aggttaagag tggggtctct ggcctgcccg agctcacaac agtcccccaa
301 ccggacgtgg ccaacacagc attcagtgtt ccaccactga gcttgagaga aaacagggag
361 gccaaggaac cgctaacagg ggcaatatta gagatgtggg atggagagat ataccattat
421 ggcctgtacg tggagaaagg cttagtgttg ggtgtgcaca aaccacctgc agccgtaagc
481 atggcaagag tggagttgac gccgctgtca ttgtactggc gtgtggtgta cactccccaa
541 tacctcatct cccctgaaac tctcaggaga ctcaacggag aggcattccc ttacaccgcc
601 tttgacaata actgctatgc cttttgctgc tgggtgttag acctcaatga ctcatggctt
661 aacaggagga tggtgcaaag aacaacgggc ttctttagac cttaccaaga gtggaacaga
721 aaacccctgc ccaccatgga tgactccaaa attaagaagg tagcaaatat attcctatgc
781 tcattgtcca cattattcac cagacccata aaagacctcg taggaaaaat taaaccatta
841 aacatattga atatcctggc aacgtgtgac tggacttttg ccggaatagt ggagtctctg
901 atattacttg ctgaactctt cggagttttc tggacacccc cagatgtgtc tgctatgatc
961 gctcccttac tcggggatta cgagttgcag gggccagaag acctcgccgt tgaactcgta
1021 cccgtggtaa tgggggggat tggtttggtg ttgggattca ccaaagagaa aattggcaaa
1081 atgttgtcct cagcagcatc aacactcagg gcttgcaaag atcttggtgc ctatggctta
1141 gagatactca aattggtcat gaagtggttc ttcccaaaga aagaggaggc caatgagcta
1201 gccatggtga gggccataga ggatgctgta ctagatcttg aggcaataga aaataaccac
1261 atgacaaccc tgttaaaaga caaagacagc ttagcaacat acatgaaaac actggacatg
1321 gaggaggaga aagccaggag gttgtccaca aaatctgcat cccctgacat agttgggaca
1381 atcaacgccc tgctggctcg aatagcagcg gccaggtcat tagtccacag ggccaaggaa
1441 gagctatcta gcaggatgag accagtagtt gttatgatat ctggcaaacc aggaataggc
1501 aaaactcatc tggccaggga ggtggcaaga aaggtggcat ccactctcac aggggatcaa
1561 agagtcggac tcataccaag aaacggtgtg gaccattggg atgcatacaa aggtgagaga
1621 gtcgtgctgt gggacgacta tggcatgagt aaccccattc atgatgctct tcgcatacaa
1681 gaattggctg atacgtgtcc ccttacctta aattgtgaca gaattgaaaa taagggaaaa
1741 gtttttgaca gcgaggtcat aataattaca acaaaccttg ccaatccagc cccacttgat
1801 tatgttaact ttgaggcctg ttccaggaga attgatttcc tggtgtacgc tgaggcacca
1861 gaagtagaaa aggcaaaacg ggactttcct ggtcagccag atatgtggaa ggatgccttc
1921 aagcccgact tttcacacat caagctacag cttgcacccc agggcggctt tgacaagaat
1981 ggcaacaccc cacatgggaa aggagtgatg aagaccctca ctaccggttc tctgattgcc
2041 cgtgcatcag gcctactgca tgagaggatg gatgaatttg aactccaagg tcccacaacc
2101 accaccttca atttcgaccg gaacagaatc acagcattca gacaattggc tgcagaaaac
2161 aagtatggat tggtggatac catgaaagtt ggtaatcaac taaaaggagt gaaaaccatg
2221 gaggaactta aacaagcaat caggaatgtg accatcaaga agtgccggat catctacggt
2281 ggctccacgt atgaccttga atctgatggc aagggcaaag ttttggtgga aaaggtcaag
2341 aacacctctg tacagaccaa caacgagttg gctggggccc tgcaccatct caaacacgcc
2401 cgaatcaggt actatgtcaa atgtgtgcaa gaagcagtct attccatcat acaaattgcc
2461 ggcgctgcgt ttgtcaccac gcgcattgca cgccgcatga acatacaaga actctggtcg
2521 aagccacaat tagatcaaaa tgaatcagag actaaggaag aggcccccaa gtcagaagat
2581 gacgagttca tcatatcttc taaggacatc aaggaggaag gaaagaaggg caaaaacaaa
2641 actggccgtg gcaagaaaca cactgcattc tccagcaagg gcttgagcga tgaggagtat
2701 gacgagtaca agaggataag agaagagagg aatgggaagt actccataga ggagtatctt
2761 caagatagag acaggtacta tgaggagctc gccattgcca aggccacgga agaagacttc
2821 tgtgaagaag aggagatcaa aatccgtcag agaattttcc gtcccaccag gaaacaaaga
2881 aaggaagaga gggccacatt agggctagta acaggttcag aaatcagaaa aagaaaccct
2941 gatgacttca aacccaaagg gaagctgtgg gctgatgaca acaggagtgt tgactacaat
3001 gagaaactgg actttgaggc ccccccaagc atatggtcta ggattgtgag ctttggttct
3061 ggctggggct tctgggtgtc accaagcctt ttcataacat caactcatgt aatccccgca
3121 ggcataacag aagcatttgg agtccccatc aaacaaattc agatccacaa atcaggtgaa
3181 ttttgccgat tcagattccc aaaaccaatt agaccagatg taacagggat gatcttggaa
3241 gaaggtgcgc ctgagggcac cgtggcaact gtgctcatca aacgccccac cggggagctc
3301 atgcctcttg cagccagaat gggaacacac gcaaccatga gaattcaagg ccgcatggtt
3361 ggcggacaga tgggtatgtt gctcactgga tcaaatgcta aaggaatgga tttgggaaca
3421 actcctggtg actgtggctg cccttacatc tacaaaagag gcaatgacta tatagtcatt
3481 ggggtgcaca ctgcagcagc ccgtggtgga aacaccgtca tctgtgccac acagggaagt
3541 gagggtgagg caactcttga gggtggagat gacaaaggaa catactgtgg ggcacccatc
3601 ctaggccctg ggggtgcacc aaaattgagc accaaaacca aattttggag gtcatcgaac
3661 acgccccttc caccagggac atatgagcct gcctacctcg gtggccgtga tccgcgtgtt
3721 aagggtgggc cctccctgca gcaggtaatg agagaccagt tgaagccatt cactgaaccc
3781 aggggcaaac ctccaagacc aagtgtattg gaagcagcca aacaaaccat catcaatgtc
3841 ctcgaacaaa ccctggaccc tccacaaaaa tggacatacg cacaggcgtg tgcctcactt
3901 gacaaaacca cctccagcgg gcatccctat cacgtccgaa agaatgaatt ctggaatggt
3961 gagaccttca ctggaaaatt ggcagaccaa gcatcaaaag caaacctaat gtttgaggaa
4021 gggaaacaca tgacaccagt gtacacagca gcactcaagg atgagctagt caagactgag
4081 aaaatctatg gaaagatcaa gaagagactg ctctggggct ctgacttgtc cactatgatc
4141 cggtgcgcta ggtcatttgg tgggctcatg gacgagatga aggcacactg catatcactc
4201 ccagtccgag ttggcatgaa tatgaatgaa gatggcccaa taatatttga gaaacattcc
4261 agatacaaat accactatga tgcagactac tctcgttggg attcaacaca acagagggca
4321 gtactagcag cagccttgga aattatggtc agattctctg cagaaccaca attggcacaa
4381 atagtcgctg aggatctgct ggcccctagt gtagtagatg taggagactt taaaattaca
4441 ataaatgaag ggctcccctc tggtgtgcca tgcacttctc aatggaactc catcgcacac
4501 tggctgctaa ctctctgtgc cttgtctgaa gtcaccaaac tgtcccctga cattatacag
4561 gcaaattccg tgttctcatt ttacggtgat gacgagattg tcagcaccga cataaaattg
4621 gaccctgaac agttaaccgc caaattgaaa gagtacggcc tgaaaccaac ccgcccagac
4681 aaaaccgagg gacccctgat tatcagtgaa gatttgaacg gactcacttt cctccgaagg
4741 acggtgactc gtgacccagc tggctggttt ggaaaattgg accaaagctc aattttgagg
4801 cagatgtact ggactagagg accaaatcat gaagacccca atgagacaat gataccccat
4861 tctcaaagac ccatacagct catggcactg cttggtgaag cctctcttca cggaccctct
4921 ttctacagta aaatcagtaa attggtcata actgaactca aagaaggtgg gatggacttt
4981 tacgtgccaa ggcaggaacc catgttcagg tggatgaggt tttctgactt gagcacgtgg
5041 gagggcgatc gcaatctggc tcccaatttt gtgaatgaag atggcgtcga atgacgccgc
5101 tccatctact gatggtgcag ccggcctcgt gccagaaagt aacaatgagg tcatggctct
5161 tgaacccgtg gctggtgtcg ccttggcagc cccggtcact ggtcagacaa atattataga
5221 cccttggatt agagcaaatt ttgtccaggc ccccaatggt gaatttacag tctctccccg
5281 taatgcccct ggtgaagtgc tactgagtct agagttgggt ccagaattaa atccttatct
5341 ggcacattta gcaagaatgt acaatgggta tgccggtggg atggaggtgc aggtcatgtt
5401 ggctgggaac gcgttcacag ccggcaagtt ggtcttcgcc gccgtgccac ctcacttccc
5461 ggttgaaaac cttagcccac agcaaatcac catgttccct catgtgatca tagatgtgag
5521 aaccttggaa cctgttttat taccactccc tgatgttaga aataatttct tccattataa
5581 tcagaaagat gatcccaaga tgagaattgt ggctatgctt tacacccccc tcaggtctaa
5641 tggttcaggt gatgatgtgt ttacagtctc ctgcagagtg ttgactagac cttcccctga
5701 ctttgacttc acatacctgg tgccaccaac agtggagtct aaaacaaaac cattcactct
5761 cccaatcctc acacttgggg aactttccaa ttccaggttc ccagtgtcca tagaccagat
5821 gtataccagc cctaatgaag ttatatcagt gcagtgtcaa aatggtaggt gcacactgga
5881 cggggagctc caggggacaa cacaactcca agtcagtggc atttgtgctt tcaaaggtga
5941 agtgaccgcc cacttgcatg acaatgatca cctatacaat gttaccatca caaacttgaa
6001 tgggtcccct tttgatccct ccgaggacat ccctgcccct ctgggtgtgc ctgacttcca
6061 gggaagggtt tttggtatca tctcccaaag agacaaacac aatagtcctg ggcataatga
6121 accagcaaac aggggacacg acgctgtggt tcccacttac acagcacagt acactccaaa
6181 actgggacaa attcaaattg gcacatggca gactgatgat cttacagtca accaaccagt
6241 caaattcacc ccagttggac tcaatgacac tgaacatttc aaccaatggg tggtccctag
6301 gtatgctggt gccctaaacc tcaatacaaa ccttgcccct tctgttgctc cagtatttcc
6361 aggagagcgt ctgctcttct tcagatcata cattcccctc aagggcggtt atggaaaccc
6421 agccattgat tgcctactac cacaagagtg ggtgcaacac ttctatcagg aagcagcccc
6481 ttcaatgagt gaggtggccc tcgtcaggta catcaacccg gacactggtc gggcactgtt
6541 tgaggccaag ctccacagag ctggtttcat gacagtctcg agcaacacca gtgccccggt
6601 ggttgtgcct gccaacggat acttcagatt tgattcttgg gtgaaccaat tctattctct
6661 cgcccccatg ggaactggga atgggcgtag aagggttcaa taatggctgg agcttttgta
6721 gctggtcttg caggggatgt gctcagcaat gggcttagtt cattaatcaa tgcaggtgct
6781 aatgcaataa atcagagggc agaatttgat tttaatcaga agttgcagca aaattctttt
6841 aatcatgata aagagatgtt gcaggctcag attcaggcaa ctaagcagct gcaggcagac
6901 atgatggcta taaaacaagg ggtcttgacc gctggcggct tttcccctgc tgatgcagcc
6961 agaggtgctg tgaacgcgcc catgacacaa gcgctggatt ggaatggtac aaggtattgg
7021 gcaccaaact ccatgaggac cacatcttac tctggaaaat tcacatcaac cgccccagtg
7081 aggcaggccg acttccagca cacccaaagc cggccttcga gtggctcctc tgtgtcttcc
7141 tttgccactc agtcttcaag gccaactctg accacaacca ctggttcctc acatggcaca
7201 gtctcatcaa attcaactcg cagcacaagc ctctcccaat caacggtctc cagagccaca
7261 tctaggacta gtgagtgggt tagagatcaa aatagaaatt tagaacccta catgcatggt
7321 gccttacaga cagcctttgt caccccacca tccagcaggg catctgacgg gacagtctca
7381 accgtcccga aaggtgtttt ggactcctgg acacctgcgt ttaacacccg caggcagccg
7441 ctttttgcac acctccgtaa gaggggggag tca
//