Typing tool
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Typing tool
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Complete norovirus genomes
| MT362916 | GII.2 | |
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| GII.P16 |
ORF1: 1..5089
ORF2: 5070..6698
ORF3: 6698..7477
LOCUS MT362916 7507 bp RNA linear VRL 01-JUN-2020
DEFINITION Norovirus GII isolate 813-3 nonstructural polyprotein (ORF1) gene,
partial cds; and VP1 (ORF2) and VP2 (ORF3) genes, complete cds.
ACCESSION MT362916
VERSION MT362916.1
DBLINK BioProject: PRJNA604000
KEYWORDS .
SOURCE Norovirus GII
ORGANISM Norovirus GII
Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes;
Picornavirales; Caliciviridae; Norovirus; Norwalk virus.
REFERENCE 1 (bases 1 to 7507)
AUTHORS Silva,A., Wolfe,J., Yang,Z., Hirneisen,K. and Ruelle,S.
TITLE Application of whole-genome sequencing for Norovirus outbreak
tracking and surveillance efforts in Orange County, CA
JOURNAL Unpublished
REFERENCE 2 (bases 1 to 7507)
AUTHORS Silva,A., Wolfe,J., Yang,Z., Hirneisen,K. and Ruelle,S.
TITLE Direct Submission
JOURNAL Submitted (21-APR-2020) Schmid College of Science and Technology,
Chapman University, 1 University Drive, Orange, CA 94526, USA
COMMENT ##Assembly-Data-START##
Assembly Method :: CLC Genomics Workbench v. 11
Sequencing Technology :: Illumina
##Assembly-Data-END##
FEATURES Location/Qualifiers
source 1..7507
/organism="Norovirus GII"
/mol_type="genomic RNA"
/isolate="813-3"
/isolation_source="stool"
/host="Homo sapiens"
/db_xref="taxon:122929"
/country="USA"
/collection_date="11-Apr-2018"
/note="genotype: GII.2[P16]"
gene <1..5089
/gene="ORF1"
CDS <1..5089
/gene="ORF1"
/codon_start=2
/product="nonstructural polyprotein"
/protein_id="QJC69092.1"
/translation="SNDATVAVACNNNNDKEKSSGEGLFTNMSSTLKKALGARPKQPA
PGDKPQKPPRPPTPELVKRIPPPPPNGEEEEEPVIRYEVKSGISGLPELTTVPQPDVV
NTAFSVPPLSLRENREAKEPLTGAVLEMWDGEIYHYGLYVEKGLVLGVHKPPAAISMA
RVELTPLSLYWRVVYTPQYLISPETLRRLNGEAFPYTAFDNNCYAFCCWVLDLNDSWL
SRRMVQRTTGFFRPYQEWNRKPLPTMDDSKIKKVANIFLCSLSTLFTRPIKDLIGKIK
PLNILNILATCDWTFAGIVESLILFAELFGVFWTPPDVSAMIAPLLGDYELQGPEDLA
VELVPVVMGGIGLVLGFTKEKIGKMLSSAASTLRACKDLGAYGLEILKLVMKWFFPKK
EEANELAMVRAIEDAVLDLEAIENNHMTTLLKDKDSLATYMKTLDMEEEKARRLSTKS
ASPDIVGTINALLARIAAARSLVHRAKEELSSRIRPVVVMISGKPGIGKTHLAREVAR
KVASTLTGDQRVGLIPRNGVDHWDAYKGERVVLWDDYGMSNPIHDALRIQELADTCPL
TLNCDRIENKGKVFDSEVIIITTNLANPAPLDYVNFEACSRRIDFLVYAEAPEVEKAK
RDFPGQPDMWKDAFKPDFSHIKLQLAPQGGFDKNGNTPHGKGVMKTLTTGSLIARASG
LLHERMDEFELQGPTITTFNFDRNRITAFRQLAAENKYGLVDTMKVGNQLKGVKTMEE
LKQAIRNVTIKRCQIIYGGSTYDLESDGKGKVLVEKVKNTSVQTNNELAGALHHLKHA
RIRYYVKCVQEAVYSIIQIAGAAFVTTRIARRMNIQELWSKPQLDQNESETKEEAPKS
EDDEFIISSKDIKEEGKKGKNKTGRGKKHTAFSSKGLSDEEYDEYKRIREERNGKYSI
EEYLQDRDRYYEELAIAKATEEDFCEEEEIKIRQRIFRPTRKQRKEERATLGLVTGSE
IRKRNPDDFKPKGKLWADDNRSVDYNEKLDFEAPPSIWSRIVSFGSGWGFWVSPSLFI
TSTHVIPAGITEAFGVPIKQIQIHKSGEFCRFRFPKPIRPDVTGMILEEGAPEGTVAT
VLIKRPTGELMPLAARMGTHATMKIQGRMVGGQMGMLLTGSNAKGMDLGTTPGDCGCP
YIYKRGNDYIAIGVHTAAARGGNTVICATQGSEGEATLEGGDDKGTYCGAPILGPGGA
PKLSTKTKFWRSSNTPLPPGTYEPAYLGGRDPRVKGGPSLQQVMRDQLKPFTEPRGKP
PRPSVLEAAKQTIINVLEQTLDPPQKWTYAQACASLDKTTSSGHPYHVRKNEFWNGET
FTGKLADQASKANLMFEEGKHMTPVYTAALKDELVKTEKIYGRIKKRLLWGSDLSTMI
RCARSFGGLMDEMKAHCISLPVRVGMNMNEDGPIIFEKHSRYKYHYDADYSRWDSTQQ
RAVLAAALEIMVRFSAEPQLAQIVAEDLLAPSVVDVGDFKITINEGLPSGVPCTSQWN
SIAHWLLTLCALSEVTKLSPDIIQANSMFSFYGDDEIVSTDIKLDPEQLTAKLKEYGL
KPTRPDKTEGPLIISGDLNGLTFLRRTVTRDPAGWFGKLDQSSILRQMYWTRGPNHED
PNETMIPHSQRPIQLMALLGEASLHGPSFYSKISKLVITELKEGGMDFYVPRQEPMFR
WMRFSDLSTWEGDRNLAPNFVNEDGVE"
mat_peptide <1..985
/gene="ORF1"
/product="p48"
mat_peptide 986..2083
/gene="ORF1"
/product="NTPase"
mat_peptide 2084..2614
/gene="ORF1"
/product="p22"
mat_peptide 2615..3013
/gene="ORF1"
/product="VPg"
mat_peptide 3014..3556
/gene="ORF1"
/product="Pro"
mat_peptide 3557..5086
/gene="ORF1"
/product="RdRp"
gene 5070..6698
/gene="ORF2"
CDS 5070..6698
/gene="ORF2"
/note="major capsid protein"
/codon_start=1
/product="VP1"
/protein_id="QJC69093.1"
/translation="MKMASNDAAPSTDGAAGLVPESNNEVMALEPVAGAALAAPVTGQ
TNIIDPWIRANFVQAPNGEFTVSPRNAPGEVLLNLELGPELNPYLAHLARMYNGYAGG
MEVQVMLAGNAFTAGKLVFAAVPPHFPVENLSPQQITMFPHVIIDVRTLEPVLLPLPD
VRNNFFHYNQKDDPKMRIVAMLYTPLRSNGSGDDVFTVSCRVLTRPSPDFDFTYLVPP
TVESKTKPFTLPILTLGELSNSRFPVSIDQMYTSPNEIISVQCQNGRCTLDGELQGTT
QLQVSGICAFKGEVTAHLHDNDHLYNVTITNLNGSPFDPSEDIPAPLGVPDFQGRVFG
IISQRDKHNSPGHNEPANRGHDAVVPTYTAQYTPKLGQIQIGTWQTDDLTVNQPVKFT
PVGLNDTEHFNQWVVPRYAGALNLNTNLAPSVAPVFPGERLLFFRSYIPLKGGYGNPA
IDCLLPQEWVQHFYQEAAPSMSEVALVRYINPDTGRALFEAKLHRAGFMTVSSNTSAP
VVVPANGYFRFDSWVNQFYSLAPMGTGNGRRRVQ"
gene 6698..7477
/gene="ORF3"
CDS 6698..7477
/gene="ORF3"
/note="minor structural protein; small basic protein"
/codon_start=1
/product="VP2"
/protein_id="QJC69094.1"
/translation="MAGAFVAGLAGDVLSNGLSSLINAGANAINQRAEFDFNQKLQQN
SFNHDKEMLQAQIQATKQLQADMMAIKQGVLTAGGFSPADAARGAVNAPMTQALDWNG
TRYWAPNSMRTTSYSGKFTSTTPVRQADFQHTQSRPSSGSSVSSFATQSSRPTLTTTT
GSSHGTASSNSTRSTSLSQSTVSRATSRTGEWVRDQNRNLEPYMHGALQTAFVTPPSS
RASDGTVSTVPKGVLDSWTPAFNTRRQPLFAHLRKRGESQA"
ORIGIN
1 gtctaacgac gctaccgttg ccgttgcttg caacaacaac aacgacaaag aaaaatcttc
61 aggtgaaggc ttattcacaa atatgtcttc caccttaaag aaagccctcg gggctaggcc
121 caaacagcct gccccgggag acaaaccaca aaagccccca agaccaccaa ctcccgagtt
181 ggtcaagagg ataccccctc ctccacctaa cggcgaagaa gaagaggaac cagtcattag
241 gtatgaggtt aagagtggga tctctggcct gcccgagctc acaacagtcc cccaaccgga
301 cgtggtcaac acagcattca gtgttccacc actgagcttg agagaaaaca gggaggccaa
361 ggagccgcta acaggggcag tattagagat gtgggatgga gagatatacc actatggcct
421 gtacgtggag aaaggcttag tgttgggtgt gcacaaacca cctgcagcca taagcatggc
481 aagagtggag ctgacgccgt tgtcattgta ctggcgtgtg gtgtacactc cccaatacct
541 catctcccct gaaaccctca ggaggctcaa cggagaggca ttcccttaca ccgcctttga
601 caacaactgc tatgcctttt gctgctgggt attagacctc aatgactcat ggcttagcag
661 gaggatggta caaagaacaa cgggcttctt cagaccttac caagagtgga acagaaaacc
721 cctgcctacc atggatgact ccaaaattaa gaaggtagca aatatatttc tatgttcatt
781 gtccacatta ttcaccagac ccataaaaga cctcatagga aaaattaaac cattgaacat
841 attaaatatc ctggcaacgt gtgactggac ttttgccgga atagtggagt ctctgatatt
901 atttgctgaa ctcttcggag ttttctggac acccccagat gtgtctgcta tgatcgctcc
961 cttactcggg gactacgagt tacaagggcc agaagacctc gccgttgaac tcgtacctgt
1021 ggtaatgggg gggattggtt tggtgttggg attcaccaaa gagaaaattg gcaaaatgtt
1081 gtcctcagca gcatcaacac tcagggcttg caaagatctt ggtgcctatg gcttagagat
1141 actcaaattg gtcatgaaat ggttcttccc aaagaaagag gaggccaatg agctagctat
1201 ggtgagagcc atagaggatg ctgtactaga ccttgaggca atagaaaata accacatgac
1261 aaccctgttg aaagacaaag acagcttagc aacatacatg aaaacactgg acatggagga
1321 ggagaaagcc aggaggttgt ccacaaaatc tgcatcccct gacatagttg ggacaatcaa
1381 cgccctgctg gctcgaatag cagcggccag gtcattagtc cacagggcca aggaagagct
1441 atctagcagg ataaggccag tagttgttat gatatctggc aaaccaggaa taggcaaaac
1501 tcatctggcc agggaggtgg caagaaaggt ggcatccact ctcacagggg atcaaagagt
1561 cggactcata ccacgaaacg gtgtggacca ttgggatgca tacaaaggtg agagagtcgt
1621 gctgtgggac gactatggca tgagtaaccc tattcatgat gctcttcgca tacaagaatt
1681 ggctgatacg tgtcccctta ccttaaattg tgacagaatt gaaaataagg gaaaagtttt
1741 tgacagtgaa gtcataataa ttacaacaaa cctcgccaat ccagccccac ttgattatgt
1801 caactttgag gcctgttcca ggagaattga tttcctggtg tacgctgagg caccagaagt
1861 agaaaaggca aaacgggact ttcctggtca gccagatatg tggaaggacg ccttcaagcc
1921 ggacttttca cacatcaagc tacagcttgc accccagggc ggctttgaca agaatggcaa
1981 caccccacat gggaaaggag tgatgaagac cctcactacc ggttctctga ttgcccgtgc
2041 atcaggccta ctgcatgaga ggatggatga atttgaactc caaggtccca caatcaccac
2101 cttcaatttc gaccggaaca gaatcacggc attcagacaa ttggctgcag aaaacaagta
2161 tggattggtg gataccatga aagttggtaa tcaattaaaa ggagtgaaaa ccatggaaga
2221 actcaaacaa gcaatcagga atgtgaccat caagaggtgc cagatcatct acggtggttc
2281 cacgtatgac cttgaatctg atggcaaggg caaagttttg gtggaaaagg tcaagaacac
2341 ctctgtacag accaataacg agttggctgg ggccctgcac catctcaaac atgcccgaat
2401 caggtactat gtcaaatgtg tgcaagaagc agtctattcc atcatacaaa ttgccggcgc
2461 tgcgtttgtc accacgcgca ttgcacgccg catgaacata caagaactct ggtcgaagcc
2521 acaattagat caaaatgaat cagagactaa ggaagaggcc cccaagtcag aagatgacga
2581 gttcatcata tcttctaagg acatcaagga ggaaggaaag aagggcaaaa acaaaactgg
2641 ccgtggcaag aaacacactg cattctccag caagggcttg agcgatgagg agtatgacga
2701 gtacaagagg ataagagaag agagaaatgg gaagtactct atagaggagt atcttcaaga
2761 cagagacagg tactatgagg agctcgccat tgccaaggcc acggaagaag acttctgtga
2821 agaggaggag atcaaaatcc gtcagagaat tttccgtcct accaggaaac aaagaaagga
2881 agagagggcc acattagggc tagtaacagg ttcagaaatc agaaaaagaa accctgatga
2941 cttcaaaccc aaagggaagc tgtgggccga tgacaacagg agtgttgact acaatgagaa
3001 actggacttt gaggcccccc caagcatatg gtccaggatt gtgagctttg gttctggctg
3061 gggcttctgg gtgtcaccaa gcctttttat aacatcaact catgtaatcc ccgcaggcat
3121 aacagaagca tttggagtcc ccatcaaaca aattcagatc cacaaatcag gcgaattttg
3181 ccgattcaga ttcccaaaac caattagacc agatgtgaca ggaatgatct tggaagaagg
3241 tgcgcctgag ggcaccgtgg caactgtgct catcaaacgc cccaccggag agctcatgcc
3301 tcttgcagcc agaatgggaa cacacgcaac catgaaaatt caaggccgca tggttggcgg
3361 acagatgggt atgttgctca ctggatcaaa cgctaaagga atggacttgg gaacaactcc
3421 tggtgactgt ggctgtcctt acatctataa aaggggcaat gactatatag ccattggggt
3481 gcacactgca gcagcccgtg gtggaaacac tgtcatctgt gccacacagg gaagtgaggg
3541 tgaggcaact cttgagggtg gagatgacaa aggaacatac tgtggggcac ccattctagg
3601 ccctgggggt gcaccaaaat tgagcaccaa aaccaaattt tggaggtcat cgaacacgcc
3661 ccttccacca gggacatatg agcctgccta cctcggtggc cgtgatccgc gtgttaaggg
3721 tgggccttcc ctgcagcagg taatgagaga ccagttgaag cctttcactg aacccagggg
3781 caaacctcca agaccaagtg tattggaagc agccaaacaa accatcatca atgtcctcga
3841 acaaaccctg gaccctccac aaaaatggac atacgcacag gcgtgtgcct cacttgacaa
3901 aaccacatcc agcgggcacc cctatcacgt ccgaaagaat gaattctgga atggtgagac
3961 cttcactggt aaactggcag accaagcatc aaaagcaaat ctaatgtttg aggaagggaa
4021 acacatgacg ccagtgtaca cagcagcact caaggacgag ctagtcaaga ctgagaaaat
4081 ctatggaagg atcaagaaga gactgctctg gggctctgac ttgtccacca tgatccggtg
4141 cgctaggtca tttggtgggc ttatggacga gatgaaggca cactgcatat cactcccagt
4201 ccgagttggc atgaatatga atgaagatgg cccaataata tttgagaaac attccagata
4261 caaatatcac tatgatgcag actactctcg ttgggattca acacaacaga gggcagtact
4321 agcagcagcc ttggaaatca tggtcagatt ctctgcagaa ccacaattgg cacaaatagt
4381 cgctgaggat ctgctggccc ctagtgtagt agatgtagga gactttaaaa ttacaataaa
4441 tgaagggctc ccttctggtg tgccatgcac ttctcaatgg aactccatcg cacactggct
4501 gctaactctc tgtgccttgt ctgaagtcac caaactgtcc cctgacatta tacaggcaaa
4561 ttccatgttc tcattttacg gtgatgacga gattgtcagc accgacataa aattggaccc
4621 tgaacagtta accgccaaat tgaaggagta cggcctgaaa ccaacccgcc cagacaaaac
4681 cgagggaccc ctgattatca gtggggattt gaacggtctc actttcctcc gaaggacggt
4741 gactcgtgac ccagctggct ggtttggaaa actggatcaa agctcaattt tgaggcagat
4801 gtactggact agaggaccaa atcatgaaga ccccaatgag acaatgatac cccattctca
4861 aagacccata cagctcatgg cactgcttgg tgaagcctct cttcacggac cctctttcta
4921 cagtaaaatc agtaaattgg tcataactga actcaaagaa ggtgggatgg acttttacgt
4981 gccaaggcag gaacccatgt tcaggtggat gaggttttct gacttgagca cgtgggaggg
5041 cgatcgcaat ctggctccca attttgtgaa tgaagatggc gtcgaatgac gccgctccat
5101 ctactgatgg tgcagccggc ctcgtgccag aaagtaacaa tgaggtcatg gcccttgaac
5161 ccgtggctgg tgccgccttg gcagccccgg tcaccggtca aacaaatatt atagaccctt
5221 ggattagagc aaattttgtc caggccccca atggtgaatt tacagtctct ccccgaaatg
5281 cccctggtga agtgctactg aatctagagt tgggtccaga attaaatcct tatctggcac
5341 atttagcaag aatgtacaat gggtatgccg gtgggatgga ggtgcaggtc atgttggctg
5401 ggaacgcgtt cacagccggc aagttggtct tcgccgccgt gccaccccac ttcccggttg
5461 aaaaccttag cccacagcaa atcaccatgt tccctcatgt gatcatagat gtgagaacct
5521 tggaacctgt tttattacca ctccctgatg ttaggaataa cttcttccat tataaccaga
5581 aagatgatcc caagatgaga attgtggcta tgctttatac ccccctcagg tctaatggtt
5641 caggtgatga tgtgtttaca gtctcctgta gagtgttgac tagaccttcc cctgactttg
5701 acttcacata cctggtgcca ccaacagtgg agtctaaaac aaagccattc accctcccaa
5761 tcctcacact tggggaactt tccaattcta ggttcccagt gtccatagac cagatgtaca
5821 ccagccctaa tgaaattata tcagtgcagt gtcaaaatgg taggtgcaca ctggacgggg
5881 agctccaagg gacaacacaa ctccaagtca gtggcatttg tgctttcaaa ggtgaagtaa
5941 ccgcccactt gcatgacaat gatcacctat ataatgtcac catcacaaac ttgaatgggt
6001 ccccttttga tccctccgag gatatccctg cccctctggg tgtgcctgac ttccagggaa
6061 gggtttttgg tatcatctcc caaagagata aacacaatag tcctgggcat aatgaaccag
6121 caaacagggg acacgacgct gtggtcccca cttacacagc acagtatact ccaaaacttg
6181 gacaaattca aattggcaca tggcaaactg acgaccttac agtcaaccaa ccagtcaaat
6241 tcaccccagt tggactcaat gacactgaac actttaacca atgggtggtc cctaggtatg
6301 ctggtgccct aaacctcaat acaaaccttg ccccttctgt tgctccagta tttccaggag
6361 agcgcttgct cttcttcaga tcatacattc ccctcaaggg cggttatgga aacccagcca
6421 ttgattgcct actaccacaa gagtgggtgc aacacttcta tcaggaagca gccccttcaa
6481 tgagtgaggt ggccctcgtc agatacatca acccggacac tggtcgggca ctgtttgagg
6541 ccaagctcca cagagctggt ttcatgacag tctcgagcaa caccagtgcc ccggtggttg
6601 tgcctgccaa cgggtacttc agatttgatt cttgggtgaa ccaattttat tctctcgccc
6661 ccatgggaac tgggaatggg cgtagaaggg ttcaataatg gctggagctt ttgtagctgg
6721 tcttgcaggg gacgtgctca gcaatgggct tagttcatta atcaatgcag gtgctaatgc
6781 aataaatcag agggcagaat ttgattttaa tcagaaattg cagcaaaatt cttttaatca
6841 tgataaggag atgttgcagg ctcagattca ggcaactaag cagctgcagg cagacatgat
6901 ggctataaaa caaggggtct tgaccgctgg cggcttttcc cctgctgatg cagccagagg
6961 tgccgtgaac gcgcccatga cacaggcgct ggattggaat ggcacaaggt attgggcacc
7021 aaactccatg aggaccacat cttattctgg aaaatttaca tcaaccaccc cagtgaggca
7081 ggctgacttc cagcacaccc aaagccggcc ttcgagtggc tcctctgtgt cttcctttgc
7141 cactcagtct tcaaggccaa ctctgaccac aaccactggt tcctcacatg gcacagcctc
7201 atcaaattca actcgcagca caagcctctc ccaatcaacg gtctccagag ctacatctag
7261 gactggtgag tgggttagag atcaaaatag aaatttggaa ccctacatgc atggtgcctt
7321 acagacagcc tttgtcaccc caccttccag tagggcatct gacgggacag tctcaaccgt
7381 ccctaaaggt gttttggact cctggacacc tgcgttcaac acccgcaggc agccgctttt
7441 tgcacacctc cgtaagaggg gggagtcaca agcttagtga aaaggtgaaa atctatttag
7501 gatgtat
//