Typing tool
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Typing tool
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Complete norovirus genomes
| PQ196524 | GII.4 Sydney | |
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| GII.P16 |
ORF1: 1..3491
ORF2: 3472..5094
ORF3: 5094..5900
LOCUS PQ196524 5915 bp RNA linear VRL 27-MAR-2025
DEFINITION Norovirus GII isolate Hu/GII.4
Sydney[P16]/SanLuisObispo0257/2023/USA nonstructural polyprotein
(ORF1) gene, partial cds; and VP1 (ORF2) and VP2 (ORF3) genes,
complete cds.
ACCESSION PQ196524
VERSION PQ196524.1
KEYWORDS .
SOURCE Norovirus GII
ORGANISM Norovirus GII
Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes;
Picornavirales; Caliciviridae; Norovirus; Norovirus norwalkense.
REFERENCE 1 (bases 1 to 5915)
AUTHORS Barclay,L., Montmayeur,A.M., Cannon,J.L., Mallory,M.L., Reyes,Y.I.,
Wall,H., Baric,R.S., Lindesmith,L.C., Vinje,J. and Chhabra,P.
TITLE Molecular Evolution and Epidemiology of Norovirus GII.4 Viruses in
the United States
JOURNAL J Infect Dis (2025) In press
PUBMED 40036172
REMARK Publication Status: Available-Online prior to print
REFERENCE 2 (bases 1 to 5915)
AUTHORS Pan,C.Y., Barclay,L., Montmayeur,A.M., Vinje,J. and Chhabra,P.
TITLE Direct Submission
JOURNAL Submitted (16-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 :: Sanger dideoxy sequencing; Illumina
##Assembly-Data-END##
FEATURES Location/Qualifiers
source 1..5915
/organism="Norovirus GII"
/mol_type="genomic RNA"
/isolate="Hu/GII.4 Sydney[P16]/SanLuisObispo0257/2023/USA"
/isolation_source="stool"
/host="Homo sapiens"
/db_xref="taxon:122929"
/geo_loc_name="USA"
/collection_date="07-Jun-2023"
/note="genotype: GII.4 Sydney[P16]"
gene <1..3491
/gene="ORF1"
CDS <1..3491
/gene="ORF1"
/codon_start=3
/product="nonstructural polyprotein"
/protein_id="XEJ39600.1"
/translation="YKGERVVLWDDYGMSNPIHDALRIQELADTCPLTLNCDRIENKG
KVFDSEVIIITTNLANPAPLDYVNFEACSRRIDFLVYAEAPEVEKAKRDFPGQPDMWK
DAFKPDFSHIKLQLAPQGGFDKNGNTPHGKGVMKTLTTGSLIARASGLLHERMDEFEL
QGSTITTFNFDRNRITAFRQLAAENKYGLVDTMKVGNQLKGVKTMEELKQAIRNVTIK
RCRIIYGGSTYDLESDGKGKVLVEKVKNTSIQTNNELTGALHHLKHARIRYYVKCVQE
AVYSIIQIAGAAFVTTRIARRMNIQELWSKPQLDQNESETKEEAPKSEDDEFIISSKD
IKEEGKKGKNKTGRGKKHTAFSSKGLSDEEYDEYKRIREERNGKYSIEEYLQDRDRYY
EELAIAKATEEDFCEEEEIKIRQRIFRPTRKQRKEERATLGLVTGSEIRKRNPDDFKP
KGKLWADDNRSVDYNEKLDFEAPPSIWSRIVSFGSGWGFWVSPSLLITSTHVIPAGIT
EAFGVPIKQIQIHKSGEFCRFRFPKPIRPDVTGMILEEGAPEGTVATVLIKRPTGELM
PLAARMGTHATMKIQGRMVGGQMGMLLTGSNAKGMDLGTTPGDCGCPYIYKRGNDYIV
IGVHTAAARGGNTVICATQGSEGEATLEGGDDKGTYCGAPILGPGGAPKLSTKTKFWR
SSNTPLPPGTYEPAYLGGRDPRVKGGPSLQQVMRDQLKPFTEPRGKPPRPSVLEAAKQ
TIINVLEQTLDPPQKWTYAQACASLDKTTSSGHPHHVRKNEFWNGETFTGKLADQASK
ANLMFEEGKHMTPVYTAALKDELVKTEKIYGKIKKRLLWGSDLSTMIRCARSFGGLMD
EMKAHCISLPVRVGMNMNEDGPIIFEKHSRYKYHYDADYSRWDSTQQRAVLAAALEIM
VRFSAEPQLAQIVAEDLLAPSVVDVGDFKIAINEGLPSGVPCTSQWNSIAHWLLTLCA
LSEVTKLSPDIIQANSMFSFYGDDEIVSTDIKLDPEQLTAKLKEYGLKPTRPDKTEGP
LIISEDLDGLTFLRRTVTRDPAGWFGKLDQSSILRQMYWTRGPNHEDPNETMIPHSQR
PIQLMALLGEASLHGPSFYSRISKLVITELKEGGMDFYVPRQEPMFRWMRFSDLSTWE
GDRNLAPNFVNEDGVE"
mat_peptide <1..485
/gene="ORF1"
/product="NTPase"
mat_peptide 486..1016
/gene="ORF1"
/product="p22"
mat_peptide 1017..1415
/gene="ORF1"
/product="VPg"
mat_peptide 1416..1958
/gene="ORF1"
/product="Pro"
mat_peptide 1959..3488
/gene="ORF1"
/product="RdRp"
gene 3472..5094
/gene="ORF2"
CDS 3472..5094
/gene="ORF2"
/note="major capsid protein"
/codon_start=1
/product="VP1"
/protein_id="XEJ39601.1"
/translation="MKMASNDANPSDGSAANLVPEVNNEVMALEPVVGAAIAAPVAGQ
QNVIDPWIRNNFVQAPGGEFTVSPRNAPGEILWSAPLGPDLNPYLSHLARMYNGYAGG
FEVQVILAGNAFTAGKIIFAAVPPNFPTEGLSPSQVTMFPHIIVDVRQLEPVLIPLPD
VRNNFYHYNQSNDSTIKLIAMLYTPLRANNAGDDVFTVSCRVLTRPSPDFDFIFLVPP
TVESRTKPFSVPILTVEEMTNSRFPIPLEKLFTGPSSAFVVQPQNGRCTTDGVLLGTT
QLSPVNICTFRGDVTHITGSHNFTMNLASQNWNNYDPTEEIPAPLGTPDFVGKIQGML
TQTTRTDGSTRGHKATVYTGSADFAPKLGRVQFETDTNHDFEANQNTKFTPVGVIQDG
STTHRNEPQQWVLPSYSGRNTHNVHLAPAVAPTFPGEQLLFFRSTMPGCSGYPNMDLD
CLLPQEWVQYFYQEAAPAQSDVALLRFVNPDTGRVLFECKLHKSGYVTVAHTGQHDLV
IPPNGYFRFDSWVNQFYTLAPMGNGTGRRRAV"
gene 5094..5900
/gene="ORF3"
CDS 5094..5900
/gene="ORF3"
/note="minor structural protein; small basic protein"
/codon_start=1
/product="VP2"
/protein_id="XEJ39602.1"
/translation="MAGAFFAGLASDVLGSGLGSLINAGAGAINQKVEFENNRKLQQA
SFQFSSNLQQASFQHDKEMLQAQIEATKKLQQEMMRVKQAMLLEGGFSETDAARGAIN
APMTKALDWSGTRYWAPDARITTYNAGHFSTPQPSGALPGRANLRDAVPARGPSTKPS
NSPTATSVHSNQTVSTRLGSTAGSGTSVSSLPSTARTRSWVEDQNRNLSPFMKGAYNI
SFVTPPSSRSSSQGTVSTVPKEILDSWTGAFNTRRQPLFAHIRKRGESRV"
ORIGIN
1 catacaaagg tgagagagtc gtgctgtggg acgactatgg tatgagtaac cccattcatg
61 atgctctccg catacaagaa ttggctgata cgtgtcccct taccttaaat tgcgacagaa
121 ttgaaaataa ggggaaagtt tttgacagtg aagtcataat aattacaaca aacctcgcca
181 acccagcccc actagattat gtcaactttg aggcctgctc caggagaatt gatttcctgg
241 tgtacgctga ggcaccagaa gtagaaaagg caaaacggga ttttcctggt cagccagata
301 tgtggaagga cgccttcaag ccggactttt cgcacatcaa gctacagctt gcacctcagg
361 gcggttttga caagaatggc aacacccctc atgggaaagg agtgatgaag accctcacta
421 ccggttctct gattgcccgt gcatcaggcc tactgcatga gaggatggat gaatttgaac
481 tccaaggttc cacaatcacc actttcaatt tcgaccggaa cagaatcaca gcattcagac
541 aattggctgc agaaaacaag tatggactgg tggacaccat gaaagttggc aatcaactaa
601 aaggagtgaa aaccatggaa gaactcaaac aagcaatcag gaatgtgacc atcaagaggt
661 gccggataat ctacggtggc tccacgtatg accttgagtc tgatggcaag ggcaaagttt
721 tggtggaaaa ggtcaagaac acctctatac agaccaacaa cgagttgacc ggggccctgc
781 atcatctcaa gcatgcccga atcaggtact atgtcaaatg tgtgcaagag gcagtctatt
841 ccatcataca aattgccggc gctgcgtttg tcaccacgcg cattgcacgc cgcatgaaca
901 tacaagagct ctggtcgaag ccacaattag accaaaatga atcagagact aaggaagagg
961 cccccaagtc agaagatgac gagttcatca tatcttctaa ggatatcaag gaggaaggaa
1021 agaagggcaa aaacaaaact ggccgtggca agaaacacac cgcattctcc agcaagggct
1081 taagcgatga ggagtatgac gagtacaaga ggataagaga agagagaaat gggaagtact
1141 ccatagaaga gtatcttcaa gacagagaca ggtattatga ggagctcgcc attgccaagg
1201 ccacggaaga agacttctgt gaagaggagg agatcaaaat ccgtcagagg atttttcgtc
1261 ccaccaggaa acaaagaaag gaagagaggg ccacactagg gctggtaact ggctcagaaa
1321 tcagaaaaag aaaccctgat gatttcaaac ccaaagggaa gctgtgggcc gatgacaaca
1381 gaagtgtcga ctacaatgag aaactggatt ttgaggctcc cccaagcata tggtctagga
1441 ttgtgagctt tggttctggc tggggcttct gggtatcacc aagcctgctc ataacgtcaa
1501 ctcatgtgat ccctgcaggc ataacagaag catttggagt ccccatcaaa caaatccaga
1561 tccacaaatc aggtgaattt tgccgattca gattcccaaa accaatcaga ccagatgtga
1621 caggaatgat cttggaagaa ggtgcgcctg aaggcaccgt ggcaactgtg ctcatcaaac
1681 gccccaccgg agagctcatg cctcttgcag ccagaatggg aacacacgca accatgaaga
1741 ttcaaggccg catggttggt ggacagatgg gtatgctgct cactgggtca aatgctaaag
1801 ggatggattt gggaacaact cctggtgact gtggctgccc ttacatctat aaaaggggca
1861 atgactatat agtcattggg gtgcacaccg cagcagcccg tggtggaaac accgtcatct
1921 gtgccacaca gggaagtgag ggtgaggcaa ctcttgaggg tggagatgac aaaggaacat
1981 actgtggggc acccattcta ggccctggag gtgcaccaaa attgagcact aaaaccaaat
2041 tttggaggtc atcgaacacg ccccttccac cggggacgta cgaacctgcc tacctcggtg
2101 gtcgtgaccc gcgtgttaag ggtgggccct ccttacaaca ggtaatgaga gatcagttga
2161 agccattcac tgaacccagg ggcaaacctc caagaccaag tgttttggaa gcagccaaac
2221 aaaccattat caatgtcctt gaacaaaccc tggatcctcc acaaaagtgg acatacgcac
2281 aggcgtgtgc ctcacttgac aaaaccacct ccagcgggca tccccaccat gtccgaaaga
2341 atgaattctg gaatggtgag accttcactg gtaaattggc agaccaagca tcaaaagcaa
2401 acctaatgtt tgaggaaggg aaacacatga caccagtgta cacagcagca ctcaaggacg
2461 agctagtcaa gactgagaaa atctatggaa agatcaagaa gagactgctc tggggctctg
2521 acttgtccac catgatccgg tgcgctaggt catttggtgg gctcatggac gagatgaagg
2581 cacactgtat atcactccca gtgcgagttg gcatgaatat gaatgaagat ggcccaataa
2641 tatttgagaa acattctagg tacaaatatc actatgatgc agactactct cgttgggatt
2701 cgacacagca aagggcagta ttagcagcag ccttggaaat tatggtcaga ttctctgcag
2761 aaccacaatt ggcacaaata gtcgctgagg atctactggc ccctagtgta gtagatgtag
2821 gagactttaa aattgcaata aatgaagggc tcccatctgg cgtgccatgc acttctcaat
2881 ggaactccat tgcacactgg ctgctaactc tctgtgcctt gtctgaagtc accaaactgt
2941 cccctgacat tatacaagca aattccatgt tctcatttta cggtgatgac gagattgtca
3001 gcaccgacat aaaattagac cctgaacagt tgaccgccaa gttgaaggag tacggcctga
3061 aaccaacccg cccagacaag actgagggac ctctgatcat cagtgaagat ttggacggac
3121 tcactttcct ccgaaggacg gtgactcgtg acccagctgg ctggtttgga aaactggacc
3181 aaagttcaat tttgaggcag atgtattgga ctagaggacc aaatcatgaa gaccccaatg
3241 agacaatgat accccattcc cagaggccca tacagctcat ggcactgctt ggtgaagcct
3301 ctcttcacgg accctctttc tacagtagaa tcagtaaatt ggttataact gaactcaaag
3361 aaggtgggat ggacttttac gtgccaaggc aggaacccat gttcaggtgg atgaggttct
3421 ctgacttgag cacgtgggag ggcgatcgca atctggctcc caactttgtg aatgaagatg
3481 gcgtcgaatg acgccaaccc atctgatggg tccgcagcca acctcgtacc agaggtcaac
3541 aatgaggtta tggctttgga gcccgttgtt ggtgccgcta ttgcggcacc cgtagcgggc
3601 caacaaaatg taattgaccc ctggattaga aataattttg tacaagcccc tggtggggag
3661 ttcacagtat cccctagaaa tgctccaggt gaaatactgt ggagcgcacc cctaggccct
3721 gacctaaatc cctacctatc ccatttggcc agaatgtaca atggttatgc aggtggtttc
3781 gaagtgcagg taattctcgc ggggaacgcg ttcaccgcag ggaagattat atttgcagca
3841 gtcccaccaa attttccaac tgaaggctta agccctagcc aggttaccat gtttccccat
3901 ataatagtag atgttagaca attggaacct gtgctgatcc ccttacccga tgttaggaat
3961 aacttctatc attacaatca gtcaaatgac tccactatca agttgatagc aatgttgtac
4021 acaccactta gggctaataa tgctggggat gatgttttca cagtttcgtg tcgagttctc
4081 acgagaccat cccccgattt tgattttata ttcttagtac cacccacagt tgagtcaaga
4141 actaaaccat tctctgtccc aattttaact gttgaggaga tgaccaactc aagattcccc
4201 atccctttgg aaaagttgtt cacaggcccc agcagtgcat ttgttgttca accacaaaac
4261 ggcagatgca caactgatgg cgtgctccta ggtaccaccc aactttctcc tgtcaacatc
4321 tgcaccttca gaggggacgt cactcatatc acaggtagtc acaacttcac tatgaatttg
4381 gcttctcaaa attggaacaa ctatgaccca acagaagaaa tcccagcccc cctaggaact
4441 ccagattttg tggggaagat ccaaggcatg ctcacccaaa ccacaaggac agatggttca
4501 acacgcggcc acaaagctac agtgtacact gggagcgccg actttgctcc aaaactgggt
4561 agagttcaat ttgaaactga cacaaaccat gactttgaag ccaatcagaa cacaaagttc
4621 accccagtcg gtgtcattca agatggtagc accacccacc gaaacgaacc ccaacagtgg
4681 gtgctcccaa gttactcagg cagaaatact cacaatgtac atttggcccc agctgtggcc
4741 cccacctttc cgggtgagca actcctcttc tttagatcca ccatgcccgg atgcagcggg
4801 taccccaaca tggacttgga ctgtctgctc ccccaggaat gggtgcagta cttctaccaa
4861 gaggcagccc cagcacaatc tgatgtggct ctgctaagat ttgtaaaccc agacacaggt
4921 agggttctgt ttgagtgcaa gcttcacaaa tcaggctatg ttacagtggc ccacactggt
4981 caacatgatt tggttatccc ccccaatggt tactttaggt ttgattcctg ggtcaaccag
5041 ttctacacgc ttgcccccat gggaaatgga acggggcgta gacgtgcagt ataatggctg
5101 gagctttctt tgctggattg gcatctgatg tccttggctc cggacttggt tctcttatca
5161 atgctggggc tggggccatc aaccaaaaag ttgagtttga aaataacaga aaattgcaac
5221 aagcatcctt ccaatttagc agcaatttgc aacaggcttc ctttcaacat gataaggaga
5281 tgctccaagc acaaattgag gccaccaaaa agctacagca ggaaatgatg agagttaagc
5341 aagcaatgct cttagagggt gggttctctg agacagatgc agcccgcggg gcaattaacg
5401 cccccatgac aaaggctttg gactggagcg ggacaaggta ctgggctcca gatgctagaa
5461 ttacaacata caatgcaggc cacttttcca cccctcaacc atcgggggca ctgccaggaa
5521 gagctaatct cagggatgct gtccctgctc gtgggccctc caccaaacct tctaactctc
5581 ctactgccac ctctgtgcac tcaaaccaaa ctgtttcaac gagacttggt tctacagctg
5641 gttctggaac cagtgtctcg agcctcccgt caactgcaag aactaggagc tgggttgagg
5701 atcagaatag gaatttgtca cctttcatga agggggccta caacatatca tttgtcaccc
5761 caccatctag cagatcctct agccagggca cagtctcaac cgtgcccaaa gaaattttgg
5821 actcctggac tggcgctttc aacacgcgca ggcagcctct cttcgctcac attcgtaagc
5881 gaggggagtc acgggtgtaa tgtgaaaaga caaaa
//