Typing tool
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Typing tool
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Complete norovirus genomes
| MT362915 | GII.2 | |
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| GII.P16 |
ORF1: 1..5088
ORF2: 5069..6697
ORF3: 6697..7476
LOCUS MT362915 7500 bp RNA linear VRL 01-JUN-2020
DEFINITION Norovirus GII isolate 813-2 nonstructural polyprotein (ORF1) gene,
partial cds; and VP1 (ORF2) and VP2 (ORF3) genes, complete cds.
ACCESSION MT362915
VERSION MT362915.1
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 7500)
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JOURNAL Unpublished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 7500)
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..7500
/organism="Norovirus GII"
/mol_type="genomic RNA"
/isolate="813-2"
/isolation_source="stool"
/host="Homo sapiens"
/db_xref="taxon:122929"
/country="USA"
/collection_date="11-Apr-2018"
/note="genotype: GII.2[P16]"
gene <1..5088
/gene="ORF1"
CDS <1..5088
/gene="ORF1"
/codon_start=1
/product="nonstructural polyprotein"
/protein_id="QJC69089.1"
/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..984
/gene="ORF1"
/product="p48"
mat_peptide 985..2082
/gene="ORF1"
/product="NTPase"
mat_peptide 2083..2613
/gene="ORF1"
/product="p22"
mat_peptide 2614..3012
/gene="ORF1"
/product="VPg"
mat_peptide 3013..3555
/gene="ORF1"
/product="Pro"
mat_peptide 3556..5085
/gene="ORF1"
/product="RdRp"
gene 5069..6697
/gene="ORF2"
CDS 5069..6697
/gene="ORF2"
/note="major capsid protein"
/codon_start=1
/product="VP1"
/protein_id="QJC69090.1"
/translation="MKMASNDAAPSTDGAAGLVPESNNEVMALEPVAGAALAAPVTGQ
TNIIDPWIRANFVQAPNGEFTVSPRNAPGEVLLNLELGPELNPYLAHLARMYNGYAGG
MEVQVMLAGNAFTAGKLVFAAVPPHFPVENLSPQQITMFPHVIIDVRTLEPVLLPLPD
VRNNFFHYNQKDDPKMRIVAMLYTPLRSNGSGDDVFTVSCRVLTRPSPDFDFTYLVPP
TVESKTKPFTLPILTLGELSNSRFPVSIDQMYTSPNEIISVQCQNGRCTLDGELQGTT
QLQVSGICAFKGEVTAHLHDNDHLYNVTITNLNGSPFDPSEDIPAPLGVPDFQGRVFG
IISQRDKHNSPGHNEPANRGHDAVVPTYTAQYTPKLGQIQIGTWQTDDLTVNQPVKFT
PVGLNDTEHFNQWVVPRYAGALNLNTNLAPSVAPVFPGERLLFFRSYIPLKGGYGNPA
IDCLLPQEWVQHFYQEAAPSMSEVALVRYINPDTGRALFEAKLHRAGFMTVSSNTSAP
VVVPANGYFRFDSWVNQFYSLAPMGTGNGRRRVQ"
gene 6697..7476
/gene="ORF3"
CDS 6697..7476
/gene="ORF3"
/note="minor structural protein; small basic protein"
/codon_start=1
/product="VP2"
/protein_id="QJC69091.1"
/translation="MAGAFVAGLAGDVLSNGLSSLINAGANAINQRAEFDFNQKLQQN
SFNHDKEMLQAQIQATKQLQADMMAIKQGVLTAGGFSPADAARGAVNAPMTQALDWNG
TRYWAPNSMRTTSYSGKFTSTTPVRQADFQHTQSRPSSGSSVSSFATQSSRPTLTTTT
GSSHGTASSNSTRSTSLSQSTVSRATSRTGEWVRDQNRNLEPYMHGALQTAFVTPPSS
RASDGTVSTVPKGVLDSWTPAFNTRRQPLFAHLRKRGESQA"
ORIGIN
1 tctaacgacg ctaccgttgc cgttgcttgc aacaacaaca acgacaaaga aaaatcttca
61 ggtgaaggct tattcacaaa tatgtcttcc accttaaaga aagccctcgg ggctaggccc
121 aaacagcctg ccccgggaga caaaccacaa aagcccccaa gaccaccaac tcccgagttg
181 gtcaagagga taccccctcc tccacctaac ggcgaagaag aagaggaacc agtcattagg
241 tatgaggtta agagtgggat ctctggcctg cccgagctca caacagtccc ccaaccggac
301 gtggtcaaca cagcattcag tgttccacca ctgagcttga gagaaaacag ggaggccaag
361 gagccgctaa caggggcagt attagagatg tgggatggag agatatacca ctatggcctg
421 tacgtggaga aaggcttagt gttgggtgtg cacaaaccac ctgcagccat aagcatggca
481 agagtggagc tgacgccgtt gtcattgtac tggcgtgtgg tgtacactcc ccaatacctc
541 atctcccctg aaaccctcag gaggctcaac ggagaggcat tcccttacac cgcctttgac
601 aacaactgct atgccttttg ctgctgggta ttagacctca atgactcatg gcttagcagg
661 aggatggtac aaagaacaac gggcttcttc agaccttacc aagagtggaa cagaaaaccc
721 ctgcctacca tggatgactc caaaattaag aaggtagcaa atatatttct atgttcattg
781 tccacattat tcaccagacc cataaaagac ctcataggaa aaattaaacc attgaacata
841 ttaaatatcc tggcaacgtg tgactggact tttgccggaa tagtggagtc tctgatatta
901 tttgctgaac tcttcggagt tttctggaca cccccagatg tgtctgctat gatcgctccc
961 ttactcgggg actacgagtt acaagggcca gaagacctcg ccgttgaact cgtacctgtg
1021 gtaatggggg ggattggttt ggtgttggga ttcaccaaag agaaaattgg caaaatgttg
1081 tcctcagcag catcaacact cagggcttgc aaagatcttg gtgcctatgg cttagagata
1141 ctcaaattgg tcatgaaatg gttcttccca aagaaagagg aggccaatga gctagctatg
1201 gtgagagcca tagaggatgc tgtactagac cttgaggcaa tagaaaataa ccacatgaca
1261 accctgttga aagacaaaga cagcttagca acatacatga aaacactgga catggaggag
1321 gagaaagcca ggaggttgtc cacaaaatct gcatcccctg acatagttgg gacaatcaac
1381 gccctgctgg ctcgaatagc agcggccagg tcattagtcc acagggccaa ggaagagcta
1441 tctagcagga taaggccagt agttgttatg atatctggca aaccaggaat aggcaaaact
1501 catctggcca gggaggtggc aagaaaggtg gcatccactc tcacagggga tcaaagagtc
1561 ggactcatac cacgaaacgg tgtggaccat tgggatgcat acaaaggtga gagagtcgtg
1621 ctgtgggacg actatggcat gagtaaccct attcatgatg ctcttcgcat acaagaattg
1681 gctgatacgt gtccccttac cttaaattgt gacagaattg aaaataaggg aaaagttttt
1741 gacagtgaag tcataataat tacaacaaac ctcgccaatc cagccccact tgattatgtc
1801 aactttgagg cctgttccag gagaattgat ttcctggtgt acgctgaggc accagaagta
1861 gaaaaggcaa aacgggactt tcctggtcag ccagatatgt ggaaggacgc cttcaagccg
1921 gacttttcac acatcaagct acagcttgca ccccagggcg gctttgacaa gaatggcaac
1981 accccacatg ggaaaggagt gatgaagacc ctcactaccg gttctctgat tgcccgtgca
2041 tcaggcctac tgcatgagag gatggatgaa tttgaactcc aaggtcccac aatcaccacc
2101 ttcaatttcg accggaacag aatcacggca ttcagacaat tggctgcaga aaacaagtat
2161 ggattggtgg ataccatgaa agttggtaat caattaaaag gagtgaaaac catggaagaa
2221 ctcaaacaag caatcaggaa tgtgaccatc aagaggtgcc agatcatcta cggtggttcc
2281 acgtatgacc ttgaatctga tggcaagggc aaagttttgg tggaaaaggt caagaacacc
2341 tctgtacaga ccaataacga gttggctggg gccctgcacc atctcaaaca tgcccgaatc
2401 aggtactatg tcaaatgtgt gcaagaagca gtctattcca tcatacaaat tgccggcgct
2461 gcgtttgtca ccacgcgcat tgcacgccgc atgaacatac aagaactctg gtcgaagcca
2521 caattagatc aaaatgaatc agagactaag gaagaggccc ccaagtcaga agatgacgag
2581 ttcatcatat cttctaagga catcaaggag gaaggaaaga agggcaaaaa caaaactggc
2641 cgtggcaaga aacacactgc attctccagc aagggcttga gcgatgagga gtatgacgag
2701 tacaagagga taagagaaga gagaaatggg aagtactcta tagaggagta tcttcaagac
2761 agagacaggt actatgagga gctcgccatt gccaaggcca cggaagaaga cttctgtgaa
2821 gaggaggaga tcaaaatccg tcagagaatt ttccgtccta ccaggaaaca aagaaaggaa
2881 gagagggcca cattagggct agtaacaggt tcagaaatca gaaaaagaaa ccctgatgac
2941 ttcaaaccca aagggaagct gtgggccgat gacaacagga gtgttgacta caatgagaaa
3001 ctggactttg aggccccccc aagcatatgg tccaggattg tgagctttgg ttctggctgg
3061 ggcttctggg tgtcaccaag cctttttata acatcaactc atgtaatccc cgcaggcata
3121 acagaagcat ttggagtccc catcaaacaa attcagatcc acaaatcagg cgaattttgc
3181 cgattcagat tcccaaaacc aattagacca gacgtgacag gaatgatctt ggaagaaggt
3241 gcgcctgagg gcaccgtggc aactgtgctc atcaaacgcc ccaccggaga gctcatgcct
3301 cttgcagcca gaatgggaac acacgcaacc atgaaaattc aaggccgcat ggttggcgga
3361 cagatgggta tgttgctcac tggatcaaac gctaaaggaa tggacttggg aacaactcct
3421 ggtgactgtg gctgtcctta catctataaa aggggcaatg actatatagc cattggggtg
3481 cacactgcag cagcccgtgg tggaaacact gtcatctgtg ccacacaggg aagtgagggt
3541 gaggcaactc ttgagggtgg agatgacaaa ggaacatact gtggggcacc cattctaggc
3601 cctgggggtg caccaaaatt gagcaccaaa accaaatttt ggaggtcatc gaacacgccc
3661 cttccaccag ggacatatga gcctgcctac ctcggtggcc gtgatccgcg tgttaagggt
3721 gggccttccc tgcagcaggt aatgagagac cagttgaagc ctttcactga acccaggggc
3781 aaacctccaa gaccaagtgt attggaagca gccaaacaaa ccatcatcaa tgtcctcgaa
3841 caaaccctgg accctccaca aaaatggaca tacgcacagg cgtgtgcctc acttgacaaa
3901 accacatcca gcgggcaccc ctatcacgtc cgaaagaatg aattctggaa tggtgagacc
3961 ttcactggta aactggcaga ccaagcatca aaagcaaatc taatgtttga ggaagggaaa
4021 cacatgacgc cagtgtacac agcagcactc aaggacgagc tagtcaagac tgagaaaatc
4081 tatggaagga tcaagaagag actgctctgg ggctctgact tgtccaccat gatccggtgc
4141 gctaggtcat ttggtgggct tatggacgag atgaaggcac actgcatatc actcccagtc
4201 cgagttggca tgaatatgaa tgaagatggc ccaataatat ttgagaaaca ttccagatac
4261 aaatatcact atgatgcaga ctactctcgt tgggattcaa cacaacagag ggcagtacta
4321 gcagcagcct tggaaatcat ggtcagattc tctgcagaac cacaattggc acaaatagtc
4381 gctgaggatc tgctggcccc tagtgtagta gatgtaggag actttaaaat tacaataaat
4441 gaagggctcc cttctggtgt gccatgcact tctcaatgga actccatcgc acactggctg
4501 ctaactctct gtgccttgtc tgaagtcacc aaactgtccc ctgacattat acaggcaaat
4561 tccatgttct cattttacgg tgatgacgag attgtcagca ccgacataaa attggaccct
4621 gaacagttaa ccgccaaatt gaaggagtac ggcctgaaac caacccgccc agacaaaacc
4681 gagggacccc tgattatcag tggggatttg aacggtctca ctttcctccg aaggacggtg
4741 actcgtgacc cagctggctg gtttggaaaa ctggatcaaa gctcaatttt gaggcagatg
4801 tactggacta gaggaccaaa tcatgaagac cccaatgaga caatgatacc ccattctcaa
4861 agacccatac agctcatggc actgcttggt gaagcctctc ttcacggacc ctctttctac
4921 agtaaaatca gtaaattggt cataactgaa ctcaaagaag gtgggatgga cttttacgtg
4981 ccaaggcagg aacccatgtt caggtggatg aggttttctg acttgagcac gtgggagggc
5041 gatcgcaatc tggctcccaa ttttgtgaat gaagatggcg tcgaatgacg ccgctccatc
5101 tactgatggt gcagccggcc tcgtgccaga aagtaacaat gaggtcatgg cccttgaacc
5161 cgtggctggt gccgccttgg cagccccggt caccggtcaa acaaatatta tagacccttg
5221 gattagagca aattttgtcc aggcccccaa tggtgaattt acagtctctc cccgaaatgc
5281 ccctggtgaa gtgctactga atctagagtt gggtccagaa ttaaatcctt atctggcaca
5341 tttagcaaga atgtacaatg ggtatgccgg tgggatggag gtgcaggtca tgttggctgg
5401 gaacgcgttc acagccggca agttggtctt cgccgccgtg ccaccccact tcccggttga
5461 aaaccttagc ccacagcaaa tcaccatgtt ccctcatgtg atcatagatg tgagaacctt
5521 ggaacctgtt ttattaccac tccctgatgt taggaataac ttcttccatt ataaccagaa
5581 agatgatccc aagatgagaa ttgtggctat gctttatacc cccctcaggt ctaatggttc
5641 aggtgatgat gtgtttacag tctcctgtag agtgttgact agaccttccc ctgactttga
5701 cttcacatac ctggtgccac caacagtgga gtctaaaaca aagccattca ccctcccaat
5761 cctcacactt ggggaacttt ccaattctag gttcccagtg tccatagacc agatgtacac
5821 cagccctaat gaaattatat cagtgcagtg tcaaaatggt aggtgcacac tggacgggga
5881 gctccaaggg acaacacaac tccaagtcag tggcatttgt gctttcaaag gtgaagtaac
5941 cgcccacttg catgacaatg atcacctata taatgtcacc atcacaaact tgaatgggtc
6001 cccttttgat ccctccgagg atatccctgc ccctctgggt gtgcctgact tccagggaag
6061 ggtttttggt atcatctccc aaagagataa acacaatagt cctgggcata atgaaccagc
6121 aaacagggga cacgacgctg tggtccccac ttacacagca cagtatactc caaaacttgg
6181 acaaattcaa attggcacat ggcaaactga cgaccttaca gtcaaccaac cagtcaaatt
6241 caccccagtt ggactcaatg acactgaaca ctttaaccaa tgggtggtcc ctaggtatgc
6301 tggtgcccta aacctcaata caaaccttgc cccttctgtt gctccagtat ttccaggaga
6361 gcgcttgctc ttcttcagat catacattcc cctcaagggc ggttatggaa acccagccat
6421 tgattgccta ctaccacaag agtgggtgca acacttctat caggaagcag ccccttcaat
6481 gagtgaggtg gccctcgtca gatacatcaa cccggacact ggtcgggcac tgtttgaggc
6541 caagctccac agagctggtt tcatgacagt ctcgagcaac accagtgccc cggtggttgt
6601 gcctgccaac gggtacttca gatttgattc ttgggtgaac caattttatt ctctcgcccc
6661 catgggaact gggaatgggc gtagaagggt tcaataatgg ctggagcttt tgtagctggt
6721 cttgcagggg acgtgctcag caatgggctt agttcattaa tcaatgcagg tgctaatgca
6781 ataaatcaga gggcagaatt tgattttaat cagaaattgc agcaaaattc ttttaatcat
6841 gataaggaga tgttgcaggc tcagattcag gcaactaagc agctgcaggc agacatgatg
6901 gctataaaac aaggggtctt gaccgctggc ggcttttccc ctgctgatgc agccagaggt
6961 gccgtgaacg cgcccatgac acaggcgctg gattggaatg gcacaaggta ttgggcacca
7021 aactccatga ggaccacatc ttattctgga aaatttacat caaccacccc agtgaggcag
7081 gctgacttcc agcacaccca aagccggcct tcgagtggct cctctgtgtc ttcctttgcc
7141 actcagtctt caaggccaac tctgaccaca accactggtt cctcacatgg cacagcctca
7201 tcaaattcaa ctcgcagcac aagcctctcc caatcaacgg tctccagagc tacatctagg
7261 actggtgagt gggttagaga tcaaaataga aatttggaac cctacatgca tggtgcctta
7321 cagacagcct ttgtcacccc accttccagt agggcatctg acgggacagt ctcaaccgtc
7381 cctaaaggtg ttttggactc ctggacacct gcgttcaaca cccgcaggca gccgcttttt
7441 gcacacctcc gtaagagggg ggagtcacaa gcttagtgaa aaggtgaaaa tctatttagg
//