Typing tool
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Typing tool
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Complete norovirus genomes
| MT362914 | GII.2 | |
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| GII.P16 |
ORF1: 1..5077
ORF2: 5058..6686
ORF3: 6686..7465
LOCUS MT362914 7489 bp RNA linear VRL 01-JUN-2020
DEFINITION Norovirus GII isolate 813-1 nonstructural polyprotein (ORF1) gene,
partial cds; and VP1 (ORF2) and VP2 (ORF3) genes, complete cds.
ACCESSION MT362914
VERSION MT362914.1
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 7489)
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JOURNAL Unpublished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 7489)
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..7489
/organism="Norovirus GII"
/mol_type="genomic RNA"
/isolate="813-1"
/isolation_source="stool"
/host="Homo sapiens"
/db_xref="taxon:122929"
/country="USA"
/collection_date="11-Apr-2018"
/note="genotype: GII.2[P16]"
gene <1..5077
/gene="ORF1"
CDS <1..5077
/gene="ORF1"
/codon_start=2
/product="nonstructural polyprotein"
/protein_id="QJC69086.1"
/translation="TVAVACNNNNDKEKSSGEGLFTNMSSTLKKALGARPKQPAPGDK
PQKPPRPPTPELVKRIPPPPPNGEEEEEPVIRYEVKSGISGLPELTTVPQPDVVNTAF
SVPPLSLRENREAKEPLTGAVLEMWDGEIYHYGLYVEKALVLGVHKPPAAISMARVEL
TPLSLYWRVVYTPQYLISPETLRRLNGEAFPYTAFDNNCYAFCCWVLDLNDSWLSRRM
VQRTTGFFRPYQEWNRKPLPTMDDSKIKKVANIFLCSLSTLFTRPIKDLIGKIKPLNI
LNILATCDWTFAGIVESLILFAELFGVFWTPPDVSAMIAPLLGDYELQGPEDLAVELV
PVVMGGIGLVLGFTKEKIGKMLSSAASTLRACKDLGAYGLEILKLVMKWFFPKKEEAN
ELAMVRAIEDAVLDLEAIENNHMTTLLKDKDSLATYMKTLDMEEEKARRLSTKSASPD
IVGTINALLARIAAARSLVHRAKEELSSRIRPVVVMISGKPGIGKTHLAREVARKVAS
TLTGDQRVGLIPRNGVDHWDAYKGERVVLWDDYGMSNPIHDALRIQELADTCPLTLNC
DRIENKGKVFDSEVIIITTNLANPAPLDYVNFEACSRRIDFLVYAEAPEVEKAKRDFP
GQPDMWKDAFKPDFSHIKLQLAPQGGFDKNGNTPHGKGVMKTLTTGSLIARASGLLHE
RMDEFELQGPTITTFNFDRNRITAFRQLAAENKYGLVDTMKVGNQLKGVKTMEELKQA
IRNVTIKRCQIIYGGSTYDLESDGKGKVLVEKVKNTSVQTNNELAGALHHLKHARIRY
YVKCVQEAVYSIIQIAGAAFVTTRIARRMNIQELWSKPQLDQNESETKEEAPKSEDDE
FIISSKDIKEEGKKGKNKTGRGKKHTAFSSKGLSDEEYDEYKRIREERNGKYSIEEYL
QDRDRYYEELAIAKATEEDFCEEEEIKIRQRIFRPTRKQRKEERATLGLVTGSEIRKR
NPDDFKPKGKLWADDNRSVDYNEKLDFEAPPSIWSRIVSFGSGWGFWVSPSLFITSTH
VIPAGITEAFGVPIKQIQIHKSGEFCRFRFPKPIRPDVTGMILEEGAPEGTVATVLIK
RPTGELMPLAARMGTHATMKIQGRMVGGQMGMLLTGSNAKGMDLGTTPGDCGCPYIYK
RGNDYIAIGVHTAAARGGNTVICATQGSEGEATLEGGDDKGTYCGAPILGPGGAPKLS
TKTKFWRSSNTPLPPGTYEPAYLGGRDPRVKGGPSLQQVMRDQLKPFTEPRGKPPRPS
VLEAAKQTIINVLEQTLDPPQKWTYAQACASLDKTTSSGHPYHVRKNEFWNGETFTGK
LADQASKANLMFEEGKHMTPVYTAALKDELVKTEKIYGRIKKRLLWGSDLSTMIRCAR
SFGGLMDEMKAHCISLPVRVGMNMNEDGPIIFEKHSRYKYHYDADYSRWDSTQQRAVL
AAALEIMVRFSAEPQLAQIVAEDLLAPSVVDVGDFKITINEGLPSGVPCTSQWNSIAH
WLLTLCALSEVTKLSPDIIQANSMFSFYGDDEIVSTDIKLDPEQLTAKLKEYGLKPTR
PDKTEGPLIISGDLNGLTFLRRTVTRDPAGWFGKLDQSSILRQMYWTRGPNHEDPNET
MIPHSQRPIQLMALLGEASLHGPSFYSKISKLVITELKEGGMDFYVPRQEPMFRWMRF
SDLSTWEGDRNLAPNFVNEDGVE"
mat_peptide <1..973
/gene="ORF1"
/product="p48"
mat_peptide 974..2071
/gene="ORF1"
/product="NTPase"
mat_peptide 2072..2602
/gene="ORF1"
/product="p22"
mat_peptide 2603..3001
/gene="ORF1"
/product="VPg"
mat_peptide 3002..3544
/gene="ORF1"
/product="Pro"
mat_peptide 3545..5074
/gene="ORF1"
/product="RdRp"
gene 5058..6686
/gene="ORF2"
CDS 5058..6686
/gene="ORF2"
/note="major capsid protein"
/codon_start=1
/product="VP1"
/protein_id="QJC69087.1"
/translation="MKMASNDAAPSTDGAAGLVPESNNEVMALEPVAGAALAAPVTGQ
TNIIDPWIRANFVQAPNGEFTVSPRNAPGEVLLNLELGPELNPYLAHLARMYNGYAGG
MEVQVMLAGNAFTAGKLVFAAVPPHFPVENLSPQQITMFPHVIIDVRTLEPVLLPLPD
VRNNFFHYNQKDDPKMRIVAMLYTPLRSNGSGDDVFTVSCRVLTRPSPDFDFTYLVPP
TVESKTKPFTLPILTLGELSNSRFPVSIDQMYTSPNEIISVQCQNGRCTLDGELQGTT
QLQVSGICAFKGEVTAHLHDNDHLYNVTITNLNGSPFDPSEDIPAPLGVPDFQGRVFG
IISQRDKHNSPGHNEPANRGHDAVVPTYTAQYTPKLGQIQIGTWQTDDLTVNQPVKFT
PVGLNDTEHFNQWVVPRYAGALNLNTNLAPSVAPVFPGERLLFFRSYIPLKGGYGNPA
IDCLLPQEWVQHFYQEAAPSMSEVALVRYINPDTGRALFEAKLHRAGFMTVSSNTSAP
VVVPANGYFRFDSWVNQFYSLAPMGTGNGRRRVQ"
gene 6686..7465
/gene="ORF3"
CDS 6686..7465
/gene="ORF3"
/note="minor structural protein; small basic protein"
/codon_start=1
/product="VP2"
/protein_id="QJC69088.1"
/translation="MAGAFVAGLAGDVLSNGLSSLINAGANAINQRAEFDFNQKLQQN
SFNHDKEMLQAQIQATKQLQADMMAIKQGVLTAGGFSPADAARGAVNAPMTQALDWNG
TRYWAPNSMRTTSYSGKFTSTTPVRQADFQHTQSRPSSGSSVSSFATQSSRPTLTTTT
GSSHGTASSNSTRSTSLSQSTVSRATSRTGEWVRDQNRNLEPYMHGALQTAFVTPPSS
RASDGTVSTVPKGVLDSWTPAFNTRRQPLFAHLRKRGESQA"
ORIGIN
1 taccgttgcc gttgcttgca acaacaacaa cgataaagaa aaatcttcag gtgaaggctt
61 attcacaaat atgtcttcca ccttaaagaa agccctcggg gctaggccca aacagcctgc
121 cccgggagac aaaccacaaa agcccccaag accaccaact cccgagttgg tcaagaggat
181 accccctcct ccacctaacg gcgaagaaga agaggaacca gtcattaggt atgaggttaa
241 gagtgggatc tctggcctgc ccgagctcac aacagtcccc caaccggacg tggtcaacac
301 agcattcagt gttccaccac tgagcttgag agaaaacagg gaggccaagg agccgctaac
361 aggggcagta ttagagatgt gggatggaga gatataccac tatggcctgt acgtggagaa
421 agccttagtg ttgggtgtgc acaaaccacc tgcagccata agcatggcaa gagtggagct
481 gacgccgttg tcattgtact ggcgtgtggt gtacactccc caatacctca tctcccctga
541 aaccctcagg aggctcaacg gagaggcatt cccttacacc gcctttgaca acaactgcta
601 tgccttttgc tgctgggtat tagacctcaa tgactcatgg cttagcagga ggatggtaca
661 aagaacaacg ggcttcttca gaccttacca agagtggaac agaaaacccc tgcctaccat
721 ggatgactcc aaaattaaga aggtagcaaa tatatttcta tgttcattgt ccacattatt
781 caccagaccc ataaaagacc tcataggaaa aattaaacca ttgaacatat taaatatcct
841 ggcaacgtgt gactggactt ttgccggaat agtggagtct ctgatattat ttgctgaact
901 cttcggagtt ttctggacac ccccagatgt gtctgctatg atcgctccct tactcgggga
961 ctacgagtta caagggccag aagacctcgc cgttgaactc gtacctgtgg taatgggggg
1021 gattggtttg gtgttgggat tcaccaaaga gaaaattggc aaaatgttgt cctcagcagc
1081 atcaacactc agggcttgca aagatcttgg tgcctatggc ttagagatac tcaaattggt
1141 catgaaatgg ttcttcccaa agaaagagga ggccaatgag ctagctatgg tgagagccat
1201 agaggatgct gtactagacc ttgaggcaat agaaaataac cacatgacaa ccctgttgaa
1261 agacaaagac agcttagcaa catacatgaa aacactggac atggaggagg agaaagccag
1321 gaggttgtcc acaaaatctg catcccctga catagttggg acaatcaacg ccctgctggc
1381 tcgaatagca gcggccaggt cattagtcca cagggccaag gaagagctat ctagcaggat
1441 aaggccagta gttgttatga tatctggcaa accaggaata ggcaaaactc atctggccag
1501 ggaggtggca agaaaggtgg catccactct cacaggggat caaagagtcg gactcatacc
1561 acgaaacggt gtggaccatt gggatgcata caaaggtgag agagtcgtgc tgtgggacga
1621 ctatggcatg agtaacccta ttcatgatgc tcttcgcata caagaattgg ctgatacgtg
1681 tccccttacc ttaaattgtg acagaattga aaataaggga aaagtttttg acagtgaagt
1741 cataataatt acaacaaacc tcgccaatcc agccccactt gattatgtca actttgaggc
1801 ctgttccagg agaattgatt tcctggtgta cgctgaggca ccagaagtag aaaaggcaaa
1861 acgggacttt cctggtcagc cagatatgtg gaaggacgcc ttcaagccgg acttttcaca
1921 catcaagcta cagcttgcac cccagggcgg ctttgacaag aatggcaaca ccccacatgg
1981 gaaaggagtg atgaagaccc tcactaccgg ttctctgatt gcccgtgcat caggcctact
2041 gcatgagagg atggatgaat ttgaactcca aggtcccaca atcaccacct tcaatttcga
2101 ccggaacaga atcacggcat tcagacaatt ggctgcagaa aacaagtatg gattggtgga
2161 taccatgaaa gttggtaatc aattaaaagg agtgaaaacc atggaagaac tcaaacaagc
2221 aatcaggaat gtgaccatca agaggtgcca gatcatctac ggtggttcca cgtatgacct
2281 tgaatctgat ggcaagggca aagttttggt ggaaaaggtc aagaacacct ctgtacagac
2341 caataacgag ttggctgggg ccctgcacca tctcaaacat gcccgaatca ggtactatgt
2401 caaatgtgtg caagaagcag tctattccat catacaaatt gccggcgctg cgtttgtcac
2461 cacgcgcatt gcacgccgca tgaacataca agaactctgg tcgaagccac aattagatca
2521 aaatgaatca gagactaagg aagaggcccc caagtcagaa gatgacgagt tcatcatatc
2581 ttctaaggac atcaaggagg aaggaaagaa gggcaaaaac aaaactggcc gtggcaagaa
2641 acacactgca ttctccagca agggcttgag cgatgaggag tatgacgagt acaagaggat
2701 aagagaagag agaaatggga agtactctat agaggagtat cttcaagaca gagacaggta
2761 ctatgaggag ctcgccattg ccaaggccac ggaagaagac ttctgtgaag aggaggagat
2821 caaaatccgt cagagaattt tccgtcctac caggaaacaa agaaaggaag agagggccac
2881 attagggcta gtaacaggtt cagaaatcag aaaaagaaac cctgatgact tcaaacccaa
2941 agggaagctg tgggccgatg acaacaggag tgttgactac aatgagaaac tggactttga
3001 ggccccccca agcatatggt ccaggattgt gagctttggt tctggctggg gcttctgggt
3061 gtcaccaagc ctttttataa catcaactca tgtaatcccc gcaggcataa cagaagcatt
3121 tggagtcccc atcaaacaaa ttcagatcca caaatcaggc gaattttgcc gattcagatt
3181 cccaaaacca attagaccag acgtgacagg aatgatcttg gaagaaggtg cgcctgaggg
3241 caccgtggca actgtgctca tcaaacgccc caccggagag ctcatgcctc ttgcagccag
3301 aatgggaaca cacgcaacca tgaaaattca aggccgcatg gttggcggac agatgggtat
3361 gttgctcact ggatcaaacg ctaaaggaat ggacttggga acaactcctg gtgactgtgg
3421 ctgtccttac atctataaaa ggggcaatga ctatatagcc attggggtgc acactgcagc
3481 agcccgtggt ggaaacactg tcatctgtgc cacacaggga agtgagggtg aggcaactct
3541 tgagggtgga gatgacaaag gaacatactg tggggcaccc attctaggcc ctgggggtgc
3601 accaaaattg agcaccaaaa ccaaattttg gaggtcatcg aacacgcccc ttccaccagg
3661 gacatatgag cctgcctacc tcggtggccg tgatccgcgt gttaagggtg ggccttccct
3721 gcagcaggta atgagagacc agttgaagcc tttcactgaa cccaggggca aacctccaag
3781 accaagtgta ttggaagcag ccaaacaaac catcatcaat gtcctcgaac aaaccctgga
3841 ccctccacaa aaatggacat acgcacaggc gtgtgcctca cttgacaaaa ccacatccag
3901 cgggcacccc tatcacgtcc gaaagaatga attctggaat ggtgagacct tcactggtaa
3961 actggcagac caagcatcaa aagcaaatct aatgtttgag gaagggaaac acatgacgcc
4021 agtgtacaca gcagcactca aggacgagct agtcaagact gagaaaatct atggaaggat
4081 caagaagaga ctgctctggg gctctgactt gtccaccatg atccggtgcg ctaggtcatt
4141 tggtgggctt atggacgaga tgaaggcaca ctgcatatca ctcccagtcc gagttggcat
4201 gaatatgaat gaagatggcc caataatatt tgagaaacat tccagataca aatatcacta
4261 tgatgcagac tactctcgtt gggattcaac acaacagagg gcagtactag cagcagcctt
4321 ggaaatcatg gtcagattct ctgcagaacc acaattggca caaatagtcg ctgaggatct
4381 gctggcccct agtgtagtag atgtaggaga ctttaaaatt acaataaatg aagggctccc
4441 ttctggtgtg ccatgcactt ctcaatggaa ctccatcgca cactggctgc taactctctg
4501 tgccttgtct gaagtcacca aactgtcccc tgacattata caggcaaatt ccatgttctc
4561 attttacggt gatgacgaga ttgtcagcac cgacataaaa ttggaccctg aacagttaac
4621 cgccaaattg aaggagtacg gcctgaaacc aacccgccca gacaaaaccg agggacccct
4681 gattatcagt ggggatttga acggtctcac tttcctccga aggacggtga ctcgtgaccc
4741 agctggctgg tttggaaaac tggatcaaag ctcaattttg aggcagatgt actggactag
4801 aggaccaaat catgaagacc ccaatgagac aatgataccc cattctcaaa gacccataca
4861 gctcatggca ctgcttggtg aagcctctct tcacggaccc tctttctaca gtaaaatcag
4921 taaattggtc ataactgaac tcaaagaagg tgggatggac ttttacgtgc caaggcagga
4981 acccatgttc aggtggatga ggttttctga cttgagcacg tgggagggcg atcgcaatct
5041 ggctcccaat tttgtgaatg aagatggcgt cgaatgacgc cgctccatct actgatggtg
5101 cagccggcct cgtgccagaa agtaacaatg aggtcatggc ccttgaaccc gtggctggtg
5161 ccgccttggc agccccggtc accggtcaaa caaatattat agacccttgg attagagcaa
5221 attttgtcca ggcccccaat ggtgaattta cagtctctcc ccgaaatgcc cctggtgaag
5281 tgctactgaa tctagagttg ggtccagaat taaatcctta tctggcacat ttagcaagaa
5341 tgtacaatgg gtatgccggt gggatggagg tgcaggtcat gttggctggg aacgcgttca
5401 cagccggcaa gttggtcttc gccgccgtgc caccccactt cccggttgaa aaccttagcc
5461 cacagcaaat caccatgttc cctcatgtga tcatagatgt gagaaccttg gaacctgttt
5521 tattaccact ccctgatgtt aggaataact tcttccatta taaccagaaa gatgatccca
5581 agatgagaat tgtggctatg ctttataccc ccctcaggtc taatggttca ggtgatgatg
5641 tgtttacagt ctcctgtaga gtgttgacta gaccttcccc tgactttgac ttcacatacc
5701 tggtgccacc aacagtggag tctaaaacaa agccattcac cctcccaatc ctcacacttg
5761 gggaactttc caattctagg ttcccagtgt ccatagacca gatgtacacc agccctaatg
5821 aaattatatc agtgcagtgt caaaatggta ggtgcacact ggacggggag ctccaaggga
5881 caacacaact ccaagtcagt ggcatttgtg ctttcaaagg tgaagtaacc gcccacttgc
5941 atgacaatga tcacctatat aatgtcacca tcacaaactt gaatgggtcc ccttttgatc
6001 cctccgagga tatccctgcc cctctgggtg tgcctgactt ccagggaagg gtttttggta
6061 tcatctccca aagagataaa cacaatagtc ctgggcataa tgaaccagca aacaggggac
6121 acgacgctgt ggtccccact tacacagcac agtatactcc aaaacttgga caaattcaaa
6181 ttggcacatg gcaaactgac gaccttacag tcaaccaacc agtcaaattc accccagttg
6241 gactcaatga cactgaacac tttaaccaat gggtggtccc taggtatgct ggtgccctaa
6301 acctcaatac aaaccttgcc ccttctgttg ctccagtatt tccaggagag cgcttgctct
6361 tcttcagatc atacattccc ctcaagggcg gttatggaaa cccagccatt gattgcctac
6421 taccacaaga gtgggtgcaa cacttctatc aggaagcagc cccttcaatg agtgaggtgg
6481 ccctcgtcag atacatcaac ccggacactg gtcgggcact gtttgaggcc aagctccaca
6541 gagctggttt catgacagtc tcgagcaaca ccagtgcccc ggtggttgtg cctgccaacg
6601 ggtacttcag atttgattct tgggtgaacc aattttattc tctcgccccc atgggaactg
6661 ggaatgggcg tagaagggtt caataatggc tggagctttt gtagctggtc ttgcagggga
6721 cgtgctcagc aatgggctta gttcattaat caatgcaggt gctaatgcaa taaatcagag
6781 ggcagaattt gattttaatc agaaattgca gcaaaattct tttaatcatg ataaggagat
6841 gttgcaggct cagattcagg caactaagca gctgcaggca gacatgatgg ctataaaaca
6901 aggggtcttg accgctggcg gcttttcccc tgctgatgca gccagaggtg ccgtgaacgc
6961 gcccatgaca caggcgctgg attggaatgg cacaaggtat tgggcaccaa actccatgag
7021 gaccacatct tattctggaa aatttacatc aaccacccca gtgaggcagg ctgacttcca
7081 gcacacccaa agccggcctt cgagtggctc ctctgtgtct tcctttgcca ctcagtcttc
7141 aaggccaact ctgaccacaa ccactggttc ctcacatggc acagcctcat caaattcaac
7201 tcgcagcaca agcctctccc aatcaacggt ctccagagct acatctagga ctggtgagtg
7261 ggttagagat caaaatagaa atttggaacc ctacatgcat ggtgccttac agacagcctt
7321 tgtcacccca ccttccagta gggcatctga cgggacagtc tcaaccgtcc ctaaaggtgt
7381 tttggactcc tggacacctg cgttcaacac ccgcaggcag ccgctttttg cacacctccg
7441 taagaggggg gagtcacaag cttagtgaaa aggtgaaaat ctatttagg
//