Typing tool
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Typing tool
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Complete norovirus genomes
| PQ213803 | GII.4 Den Haag | |
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| GII.P4 Den Haag |
ORF1: 1..5025
ORF2: 5006..6628
ORF3: 6628..7362
LOCUS PQ213803 7362 bp RNA linear VRL 01-JAN-2025
DEFINITION Norovirus GII isolate Hu/GII.4 Den Haag[P4]/Rutherford0455/2013/USA
nonstructural polyprotein (ORF1) gene, partial cds; VP1 (ORF2)
gene, complete cds; and VP2 (ORF3) gene, partial cds.
ACCESSION PQ213803
VERSION PQ213803.1
KEYWORDS .
SOURCE Norovirus GII
ORGANISM Norovirus GII
Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes;
Picornavirales; Caliciviridae; Norovirus; Norovirus norwalkense.
REFERENCE 1 (bases 1 to 7362)
AUTHORS Barclay,L., Montmayeur,A.M., Cannon,J.L., Mallory,M.L., Reyes,Y.I.,
Lindesmith,L., Wall,H., Baric,R.S., Vinje,J. and Chhabra,P.
TITLE Norovirus GII.4 evolution in the United States since emergence of
GII.4 Sydney
JOURNAL Unpublished
REFERENCE 2 (bases 1 to 7362)
AUTHORS Dill,J., Barclay,L., Montmayeur,A.M., Vinje,J. and Chhabra,P.
TITLE Direct Submission
JOURNAL Submitted (21-AUG-2024) Viral Gastroenteritis Branch, Centers for
Disease Control and Prevention, 1600 Clifton Road NE, Atlanta, GA
30329, USA
COMMENT ##Assembly-Data-START##
Assembly Method :: Geneious v. v. 11.1.2; SPAdes v. v. 3.6
Sequencing Technology :: 454; Illumina
##Assembly-Data-END##
FEATURES Location/Qualifiers
source 1..7362
/organism="Norovirus GII"
/mol_type="genomic RNA"
/isolate="Hu/GII.4 Den Haag[P4]/Rutherford0455/2013/USA"
/isolation_source="stool"
/host="Homo sapiens"
/db_xref="taxon:122929"
/geo_loc_name="USA"
/collection_date="29-Jan-2013"
/note="genotype: GII.4 Den Haag[P4]"
gene <1..5025
/gene="ORF1"
CDS <1..5025
/gene="ORF1"
/codon_start=1
/product="nonstructural polyprotein"
/protein_id="XEQ87059.1"
/translation="DGVFSSMAVTFKRALGARPKQPPPREIPQRPPRPPTPELVKKIP
PPPPNGEDEVVVSYSAKDGVSGLPELSTVRQPEETNTAFSVPPLNQRENRDAKEPLTG
TILEMWDGEIYHYGLYVERGLVLGVHKPPAAISLAKVELTPLSLFWRPVYTPQYLISP
DTLKKLHGETFPYTAFDSNCYAFCCWVLDLNDSWLSRRMIQRTTGFFRPYQDWNRKPL
PTMDDSKLKKVANIFLCALSSLFTRPIKDIIGKLRPLNIINILASCDWTFAGIVESLI
LLAELFGVFWTPPDVSAMIAPLLGDFELQGPEDLVVELVPVVMGGIGLVLGFTKEKIG
KMLSSAATTLRACKDLGAYGLEILKLVMKWFFPKKEEANELAMVRSIEDAVLDLEAIE
NNHMTTLLKDKDSMATYMRTLDLEEEKARKLSTKSASPDIVGTINALLARIAAARSLV
HRAKEELSSRPRPVVLMISGRPGIGKTHLAREVAKRIATSLTGDQRVGLIPRNGVDHW
DAYKGERVVLWDDYGMSNPIHDALRLQELADTCPLTLNCDRIENKGKVFDSDVIIITT
NLANPAPLDYVNFEACSRRIDFLVYAEAPEVEKAKRDFPGQPDMWKNAFSSDFSHIKL
ALAPQGGFDKNGNTPHGKGVMKTLTTGSLIARASGLLHERLDEFELQGPALTTFNFDR
NKVLAFRQLAAENKYGLMDTMKVGRQLKDVKTMPELKQALKNISIKKCQIVYSGCTYT
LESDGKGNVKVDRVQSISVQTNNELAGALHHLRCARIRYYVKCVQEALYSIIQIAGAA
FVTTRIIKRVNIQDLWSKPQVENTEEATSKDGCPKPKDDEEFVISSDDIKTEGKKGKN
KTGRGKKHTAFSSKGLSDEEYDEYKRIREERNGKYSIEEYLQDRDKYYEEVAIARATE
EDFCEEEEAKIRQRIFRPTRKQRKEERASLGLVTGSEIRKRNPEDFKPKGKLWADDDR
SVDYSEKLSFEAPPSIWSRIVNFGSGWGFWVSPSLFITSTHVIPQGAKEFFGVPIKQI
QVHKSGEFCRLRFPKPIRTDVTGMILEEGAPEGTVVTLLIKRSTGELMPLAARMGTHA
TMRIQGRTVGGQMGMLLTGSNAKSMDLGTTPGDCGCPYIYKRGNDYVVIGVHTAAARG
GNTVICATQGGEGEATLEGGDSKGTYCGAPILGPGSAPKLSTKTKFWRSSTAPLPPGT
YEPAYLGGKDPRVKGGPSLQQVMRDQLKPFTEPRGKPPKPSVLEAAKKTIINVLEQTI
DPPEKWSFAQACASLDKTTSSGHPHHVRKNDCWNGESFTGKLADQASKANLMFEEGKN
MTPVYTGALKDELVKTDKIYGKIKKRLLWGSDLATMIRCARAFGGLMDELKAHCVTLP
VRVGMNMNEDGPIIFEKHSRYRYHYDVDYSRWDSTQQRAVLAAALEIMVKFSSEPHLA
QVVAEDLLSPSVVDVGDFTISINEGLPSGVPCTSQWNSIAHWLLTLCALSEVTNLSPD
IIQANSLFSFYGDDEIVSTDIKLDPEKLTAKLKEYGLKPTRPDKTEGPLVISEDLDGL
TFLRRTVTRDPAGWFGKLEQSSILRQMYWTRGPNHEDPSESMIPHSQRPIQLMSLLGE
AALHGPTFYSKISKLVIAELKEGGMDFYVPRQESMFRWMRFSDLSTWEGDRNLAPSFV
NEDGVE"
mat_peptide <1..915
/gene="ORF1"
/product="p48"
mat_peptide 916..2013
/gene="ORF1"
/product="NTPase"
mat_peptide 2014..2550
/gene="ORF1"
/product="p22"
mat_peptide 2551..2949
/gene="ORF1"
/product="VPg"
mat_peptide 2950..3492
/gene="ORF1"
/product="Pro"
mat_peptide 3493..5022
/gene="ORF1"
/product="RdRp"
gene 5006..6628
/gene="ORF2"
CDS 5006..6628
/gene="ORF2"
/note="major capsid protein"
/codon_start=1
/product="VP1"
/protein_id="XEQ87060.1"
/translation="MKMASNDANPSDGSAASLVPEVNNEVMALEPVVGAAIAAPVAGQ
QNVIDPWIRNNFVQAPGGEFTVSPRNAPGEILWSAPLGPDLNPYLSHLARMYNGYAGG
FEVQVILAGNAFTAGKIIFAAVPPNFPTEGLSPSQVTMFPHIIVDVRQLEPVLIPLPD
VRNNFYHYNQSNDSTIKLIAMLYTPLRANNAGDDVFTVSCRVLTRPSPDFDFIFLVPP
TVESRTKPFTVPILTVEEMTNSRFPIPLEKLFTGPSSAFVVQPQNGRCTTDGVLLGTT
QLSPVNICTFRGDVTHIAGSRNYTMNLASLNWNNYDPTEEIPAPLGTPDFVGKIQGVL
TQTTKGDGSTRGHKATVYTGSADFTPKLGSVQFATDTENDFETHQNTKFTPVGVIQDG
GTTHRNEPQQWVLPSYSGRNVHNVHLAPAVAPNFPGEQLLFFRSTMPGCSGYPNTDLD
CLLPQEWVQHFYQEAAPAQSDVALLRFVNPDTGRVLFECKLHKSGYVTVAHTGQHDLV
IPPNGYFRFDSWVNQFYTLAPMGNGTGRRRAL"
gene 6628..>7362
/gene="ORF3"
CDS 6628..>7362
/gene="ORF3"
/note="minor structural protein; small basic protein"
/codon_start=1
/product="VP2"
/protein_id="XEQ87061.1"
/translation="MAGAFFAGLASDVLSSGLGSLINAGAGAINQKIDFENNRKLQQA
SFQFSSNLQQASFQHDKEMLQAQIEATKKLQQEMMKVKQAMLLEGGFSETDAARGAIN
APMTKTLDWSGTRYWAPDARTTTYNAGRFSTPQPSGALPGRINPRTPAPARGSPNILS
NVSTATSVYSNQTGSTRLGSTAGSGTNVSSLPSTARTRSWVEDQNRNLSPFMRGAHNI
SFVTPPSSRSSSQGTVSTVPKEVLDSW"
ORIGIN
1 gacggtgtgt tttctagcat ggctgtcact tttaaacgag ccctcggggc gcggcctaaa
61 cagccccccc cgagggaaat accacaaaga cccccacgac caccaactcc agaactggtc
121 aaaaagatcc ctcctccccc gcccaacgga gaggatgaag tagtggtttc ttacagtgcc
181 aaggatggcg tttccggttt gcctgagctt tccaccgtca ggcaaccgga agaaaccaat
241 acggccttca gtgtccctcc actcaaccag agggagaata gggatgctaa ggaaccactg
301 actggaacaa ttctggaaat gtgggatgga gagatctacc attatggcct gtatgttgag
361 cgaggtcttg tgctgggtgt acacaaacca ccagctgcca ttagcctcgc caaggtcgaa
421 ctaacaccac tctccttgtt ctggagacct gtgtacactc ctcagtacct catttctcca
481 gacactctca agaaattaca cggagaaaca tttccctaca cagcctttga cagcaattgc
541 tatgcctttt gttgctgggt cctggatcta aacgactcgt ggttgagtag gagaatgatc
601 cagaggacaa ctggcttctt cagaccctac caagattgga ataggaaacc cctccccact
661 atggatgatt ccaaattaaa gaaagtagcc aacatattcc tgtgcgccct gtcttcgcta
721 ttcaccaggc ccataaaaga cataatagga aagttgaggc ctctcaacat catcaacatc
781 ctggcttcat gtgattggac tttcgcaggc atagtggagt ccttgatact cttggcagag
841 ctctttggag ttttctggac acccccagat gtgtctgcga tgattgcccc cttactcggt
901 gatttcgagt tacaaggacc tgaggacctt gtagtggagc tcgtccctgt agtaatgggg
961 gggattggtt tggtgctagg attcaccaaa gagaagattg gaaaaatgtt gtcatctgct
1021 gcaaccaccc tgagagcttg taaagacctc ggtgcatatg ggctagagat cctaaagtta
1081 gtcatgaagt ggttcttccc gaagaaagag gaagcgaatg aactggctat ggtgaggtcc
1141 atcgaggacg cagtactgga ccttgaggca attgaaaaca accacatgac caccttgctc
1201 aaagacaaag acagcatggc aacctacatg agaacccttg acctcgagga agagaaggcc
1261 agaaaactct caaccaagtc tgcttcacct gacatcgtgg gcacgatcaa cgcccttctg
1321 gcgagaatcg ccgctgcacg ttccctggtg caccgagcga aggaggagct ttccagcaga
1381 ccaagacctg tagtcttgat gatatcaggc aggccaggaa tagggaagac ccaccttgct
1441 agggaagtgg ctaagaggat cgcaacatcc ctcacaggag accagcgcgt aggcctcatc
1501 ccacgcaatg gcgtcgatca ctgggatgcg tacaaggggg agagggtcgt cctatgggac
1561 gactatggaa tgagcaatcc catccacgac gccctcaggt tgcaagaact cgctgacact
1621 tgccccctca ctctaaactg tgacaggatt gagaataaag gaaaggtctt tgacagcgat
1681 gtcatcatca tcactactaa tctggccaac ccagcaccac tggactatgt caactttgaa
1741 gcgtgctcga gacgcatcga tttcctcgtg tatgcagaag cccccgaggt cgaaaaggcg
1801 aagcgcgact ttccgggcca acctgacatg tggaaaaacg cttttagttc tgatttctca
1861 cacataaaat tggcactggc tccacaaggt ggctttgata agaacgggaa caccccacac
1921 gggaagggcg tcatgaagac tctcaccact ggctccctca ttgcccgggc atcagggctg
1981 ctccatgaga ggttggatga gtttgaacta cagggcccag ctcttaccac cttcaacttt
2041 gaccgcaaca aagtgcttgc cttcaggcag cttgctgctg aaaacaaata tgggctgatg
2101 gacacaatga aagttgggag gcagctcaag gatgttaaaa ccatgccaga actcaaacaa
2161 gcactcaaga atatctcaat caagaagtgc cagatcgtgt acagtggttg cacctacaca
2221 cttgagtctg atggcaaggg caatgtgaaa gttgacagag ttcagagtat ctccgttcag
2281 accaacaatg agttggctgg cgccctgcac catctaagat gcgccagaat caggtactat
2341 gtcaagtgtg ttcaggaggc tctgtattct atcatccaga ttgctggggc tgcgtttgtc
2401 accacgcgca tcatcaagcg tgtgaacatt caagatttat ggtccaagcc acaagtggaa
2461 aacacagagg aggctaccag caaggacggg tgcccaaaac ccaaagatga tgaggagttc
2521 gtcatttcat ctgacgacat taaaactgag ggtaagaaag ggaagaacaa gactggccgt
2581 ggcaagaagc acacagcctt ctcaagtaaa ggtctcagtg atgaagagta tgatgagtac
2641 aagagaatta gagaggaaag aaatggcaag tactccatag aagagtacct tcaggacagg
2701 gacaaatact atgaggaggt ggccattgcc agggcgaccg aggaagactt ctgtgaagag
2761 gaggaggcca agatccggca aaggatcttc agaccaacaa ggaaacaacg caaggaagaa
2821 agagcctctc tcggtttagt cacaggttct gaaattagga aaagaaatcc agaagacttc
2881 aagcccaagg ggaaactgtg ggctgacgat gacagaagtg tggactacag tgaaaaactc
2941 agctttgagg ccccaccaag catctggtca aggatagtca attttggctc aggttggggc
3001 ttctgggtct cccccagtct gttcataaca tcaacccacg tcatacccca gggcgcaaag
3061 gagttctttg gagtccccat caaacaaatt caggtgcaca agtcaggcga attctgtcgc
3121 ttgaggttcc caaaaccaat caggactgat gtgactggca tgatcttgga agaaggtgcg
3181 cctgaaggca ccgtggtcac actactcatc aaaaggtcta ctggagaact catgccccta
3241 gcagctagaa tggggaccca tgcaaccatg agaattcaag ggcgcactgt tggaggtcag
3301 atgggcatgc ttctgacagg atccaacgcc aaaagcatgg atctaggcac cacaccaggt
3361 gattgcggct gtccctacat ctacaagaga ggaaacgact atgtggtcat tggagtccac
3421 acggctgccg ctcgtggggg aaacactgtc atatgtgcca cccagggggg tgagggggaa
3481 gctacacttg aaggtggtga cagtaaggga acatactgtg gtgcaccaat cctaggccca
3541 gggagtgccc caaaacttag caccaaaacc aaattctgga gatcatccac agcaccactc
3601 ccacctggca cctatgaacc agcctacctt ggtggcaaag accccagagt caagggtggc
3661 ccctcgttgc agcaagtcat gagggaccag ctgaaaccat ttacagagcc taggggtaag
3721 ccaccaaagc caagtgtgtt agaagctgcc aagaaaacca tcattaatgt ccttgaacag
3781 acaattgacc cacctgagaa gtggtcgttc gcacaagctt gcgcgtccct tgacaagacc
3841 acttctagcg gccatccgca ccacgtgcgg aaaaacgact gctggaacgg ggaatccttc
3901 acaggcaagc tggcagacca ggcttccaag gccaacctga tgtttgaaga agggaagaac
3961 atgaccccag tctacacagg tgcacttaag gatgaattag tcaaaactga caaaatttat
4021 ggtaagatca agaagaggct tctctggggc tcggatttag caaccatgat ccggtgtgct
4081 cgagcattcg gaggcctgat ggatgaactc aaagcacact gcgtcacact tcctgtcaga
4141 gttggtatga acatgaacga ggatggcccc atcatcttcg agaagcactc caggtacaga
4201 taccactatg atgttgatta ctctcgatgg gattcaacac aacagagagc cgtgctggca
4261 gctgctctag aaatcatggt taaattctcc tcagaaccac acttggctca ggttgtagca
4321 gaagaccttc tttctcctag cgtggtggat gtgggtgact tcacaatatc aatcaacgag
4381 ggccttccct ctggggtgcc ctgcacctcc caatggaact ccatcgccca ctggcttctc
4441 actctctgtg cactctccga agtcacaaat ttgtccccag acatcataca ggctaattct
4501 ctcttctcct tctatggtga tgatgaaatt gttagtacag acataaaatt agacccagag
4561 aagttgacag caaagcttaa ggaatatggg ttgaaaccaa cccgccctga caaaactgaa
4621 ggacctcttg ttatttctga agacttagac ggtttgactt tcctgcggag aactgtgacc
4681 cgcgacccag ctggttggtt tggaaaattg gagcagagct caatactcag gcaaatgtac
4741 tggactaggg gccccaatca tgaagaccca tctgaatcaa tgatcccaca ctctcaaaga
4801 cccatacaat tgatgtcctt actaggagag gccgcactcc acggcccaac attctacagt
4861 aaaatcagca aattagttat tgcagagcta aaagaaggtg gcatggattt ttacgtgccc
4921 aggcaagagt caatgttcag atggatgaga ttctcggatc tgagcacgtg ggagggcgat
4981 cgcaatctgg ctcccagttt tgtgaatgaa gatggcgtcg aatgacgcca acccatctga
5041 tgggtccgca gccagcctcg tcccagaggt caacaatgag gttatggctt tggagcccgt
5101 tgtcggtgcc gctattgcgg cgcctgtagc gggccaacaa aatgtaattg acccctggat
5161 tagaaataat tttgtacaag cccctggtgg agagttcaca gtatccccta gaaacgctcc
5221 aggtgaaata ctatggagcg cacccttagg ccctgatttg aatccctacc tatctcattt
5281 ggccagaatg tataatggtt atgcaggtgg ttttgaagtg caggtgatcc tcgcggggaa
5341 cgcgttcacc gccggaaaaa ttatatttgc agcagtccca ccaaattttc caactgaagg
5401 cttgagtccc agccaggtca ctatgttccc ccacataata gtagatgtta ggcaattgga
5461 acccgtgttg atccccttac ctgatgttag gaataacttc tatcactata atcagtcaaa
5521 tgattctact attaaattga tagcaatgct gtatacacca cttagggcca ataatgctgg
5581 ggatgatgtc ttcacagtct cttgtcgagt cctcacgagg ccatcccctg attttgactt
5641 tatatttttg gtgccaccta cagttgagtc aagaactaag ccatttactg tcccaatctt
5701 aactgttgaa gaaatgacca attcaagatt ccccattcct ttggaaaaat tgttcacggg
5761 tcccagcagt gcctttgttg tccaaccaca aaatggcaga tgcacgactg atggcgtgct
5821 cttaggcacc acccaactgt ctcctgtcaa catctgcacc ttcagagggg acgtcaccca
5881 cattgcgggt tctcgtaatt acacaatgaa tttggcctct ctaaattgga acaattatga
5941 cccaacagag gaaattccag cccctctggg aactccagat ttcgtgggaa agatccaagg
6001 tgtgctcact caaaccacaa agggagatgg ctcgacccgg ggccataaag ctacagttta
6061 cactgggagt gccgacttta ctccaaagct gggcagtgtt caatttgcta ctgatacaga
6121 aaatgatttt gaaacccacc aaaacacaaa attcacccca gtcggtgtca tccaggatgg
6181 tggcaccacc catcgaaatg aaccccaaca atgggtgctc ccaagttatt caggtagaaa
6241 tgtccataat gtacacctag cccctgctgt agcccccaat tttccgggtg aacaacttct
6301 tttcttcagg tccactatgc ccggatgcag cgggtatccc aacacggatt tggattgcct
6361 actcccccag gagtgggtgc agcacttcta ccaagaggca gctccagcac aatctgatgt
6421 ggctctattg agatttgtga atccagacac gggtagggtc ctgtttgagt gcaaacttca
6481 taaatcaggc tatgtcacag tggcccacac cggccaacat gatttggtca tcccccccaa
6541 tggctatttt agatttgatt cctgggttaa ccagttctac acacttgccc ccatgggaaa
6601 tggaacgggg cgtagacgtg ctttataatg gctggagctt tctttgctgg attggcatct
6661 gatgtcctta gctctggact tggttcccta atcaatgctg gggccggggc tatcaaccaa
6721 aagattgatt ttgaaaataa tagaaaattg cagcaagctt ccttccagtt tagcagtaat
6781 ctacaacagg cttcctttca acatgataaa gagatgctcc aagcacaaat tgaggccact
6841 aaaaagttgc agcaggaaat gatgaaagtc aaacaggcaa tgctcttaga aggtggattc
6901 tctgaaacag atgcagcccg tggggcaatc aacgccccca tgacaaagac tttggactgg
6961 agcggaacaa ggtactgggc ccctgatgct aggactacaa catacaatgc aggccgcttc
7021 tccacccctc aaccttcggg ggcactgcca ggaagaatca atcccaggac tcctgccccc
7081 gcccggggct cccccaatat actttccaac gtttctactg ctacttctgt atattcaaat
7141 caaactggtt caacgagact tggttctaca gctggttctg gcaccaatgt ctcgagtctc
7201 ccgtcaactg caaggactag gagttgggtt gaggatcaaa acagaaattt gtcacctttc
7261 atgagggggg ctcacaacat atcgtttgtc accccaccat ctagcagatc ctccagccaa
7321 ggcacagtct caaccgtgcc taaagaagtt ttggactcct gg
//