Typing tool
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Typing tool
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Complete norovirus genomes
| PQ196531 | GII.4 Sydney | |
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| GII.P16 |
ORF1: 1..4914
ORF2: 4895..6517
ORF3: 6517..7323
LOCUS PQ196531 7338 bp RNA linear VRL 27-MAR-2025
DEFINITION Norovirus GII isolate Hu/GII.4 Sydney[P16]/SanJoaquin0168/2023/USA
nonstructural polyprotein (ORF1) gene, partial cds; and VP1 (ORF2)
and VP2 (ORF3) genes, complete cds.
ACCESSION PQ196531
VERSION PQ196531.1
KEYWORDS .
SOURCE Norovirus GII
ORGANISM Norovirus GII
Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes;
Picornavirales; Caliciviridae; Norovirus; Norovirus norwalkense.
REFERENCE 1 (bases 1 to 7338)
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 7338)
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..7338
/organism="Norovirus GII"
/mol_type="genomic RNA"
/isolate="Hu/GII.4 Sydney[P16]/SanJoaquin0168/2023/USA"
/isolation_source="stool"
/host="Homo sapiens"
/db_xref="taxon:122929"
/geo_loc_name="USA"
/collection_date="11-Apr-2023"
/note="genotype: GII.4 Sydney[P16]"
gene <1..4914
/gene="ORF1"
CDS <1..4914
/gene="ORF1"
/codon_start=1
/product="nonstructural polyprotein"
/protein_id="XEJ39621.1"
/translation="ELVKRIPPPPPNGEEEDEPVIRYGVKSGISGLPELTTVPQPDVA
NTAFSVPPLSMRENREAKEPLTGAILEMWDGEIYHYGLYVEKGLVLGVHKPPAAISMA
RVELAPLSLYWRVVYTPQYLISPETLRRLNGEAFPYTAFDNNCYAFCCWVLDLNDSWL
SRRMVQRTTGFFRPYQEWNRKPLPTMDDSKIKKVANIFLCSLSTLFTRPIKDLIGKIK
PLNILNILATCDWTFAGIVESLILLAELFGVFWTPPDVSAIIAPLLGGYELQGPEDLA
VELVPVVMGGIGLVLGFTKEKIGKMLSSAASTLRACKDLGAYGLEILKLVMKWFFPKK
EEANELAMVRAIEDAVLDLEAIENNHMTTLLKDKDSLATYMKTLDMEEEKARRLSTKS
ASPDIVGTINALLARIAAARSLVHRAKEELSSRIRPVVVMISGKPGIGKTHLAREVAR
KVASTLTGDQRVGLIPRNGVDHWDAYKGERVVLWDDYGMSNPIHDALRIQELADTCPL
TLNCDRIENKGKVFDSEVIIITTNLANPAPLDYVNFEACSRRIDFLVYAEAPEVEKAK
RDFPGQPDMWKDAFKPDFSHIKLQLAPQGGFDKNGNTPHGKGVMKTLTTGSLIARASG
LLHERMDEFELQGPTITTFNFDRNRIAAFRQLAAENKYGLVDTMKVGNQLKGVKTMEE
LKQAIRNVAIKRCRIIYGGSTYDLESDGKGKVLVEKVKNTSIQTNNELTGTLHHLKHA
RIRYYVKCVQEAVYSIIQIAGAAFVTTRIARRMNIQELWSKPQLDQNESETKEEAPKS
EDDEFIISSKDIKEEGKKGKNKTGRGKKHTAFSSKGLSDEEYDEYKRIREERNGKYSI
EEYLQDRDRYYEELAIAKATEEDFCEEEEIKIRQRIFRPTRKQRKEERATLGLVTGSE
IRRRNPDDFKPKGKLWADDNRSVDYNEKLDFEAPPSIWSRIVSFGSGWGFWVSPSLFI
TSTHVIPAGITEAFGVPIKQIQIHKSGEFCRFRFPKPIRPDVTGMILEEGAPEGTVAT
VLIKRPTGELMPLAARMGTHATMKIQGRMVGGQMGMLLTGSNAKGMDLGTTPGDCGCP
YIYKRGNDYIVIGVHTAAARGGNTVICATQGSEGEATLEGGDDKGTYCGAPILGPGGA
PKLSTKTKFWRSSNTPLPPGTYEPAYLGGRDPRVKGGPSLQQVMRDQLKPFTEPRGKP
PRPSVLEAAKQTIINVLEQTLDPPQKWTYAQACASLDKTTSSGHPHHVRKNEFWNGET
FTGKLADQASKANLMFEEGKHMTPVYTAALKDELVKTEKIYGKIKKRLLWGSDLSTMI
RCARSFGGLMDEMKAHCISLPVRVGMNMNEDGPIIFEKHSRYKYHYDADYSRWDSTQQ
RAVLAAALEIMVRFSAEPQLAQIVAEDLLAPSVVDVGDFKIAINEGLPSGVPCTSQWN
SIAHWLLTLCALSEVTKLSPDIIQANSMFSFYGDDEIVSTDIKLDPEQLTAKLKEYGL
KPTRPDKTEGPLIISEDLDGLTFLRRTVTRDPAGWFGKLDQSSILRQMYWTRGPNHED
PNETMIPHSQRPIQLMALLGEASLHGPSFYSRISKLVITELKEGGMDFYVPRQEPMFR
WMRFSDLSTWEGDRNLAPNFVNEDGVE"
mat_peptide <1..810
/gene="ORF1"
/product="p48"
mat_peptide 811..1908
/gene="ORF1"
/product="NTPase"
mat_peptide 1909..2439
/gene="ORF1"
/product="p22"
mat_peptide 2440..2838
/gene="ORF1"
/product="VPg"
mat_peptide 2839..3381
/gene="ORF1"
/product="Pro"
mat_peptide 3382..4911
/gene="ORF1"
/product="RdRp"
gene 4895..6517
/gene="ORF2"
CDS 4895..6517
/gene="ORF2"
/note="major capsid protein"
/codon_start=1
/product="VP1"
/protein_id="XEJ39622.1"
/translation="MKMASNDANPSDGSAANLVPEVNNEVMALEPVVGAAIAAPVAGQ
QNVIDPWIRNNFVQAPGGEFTVSPRNAPGEILWSAPLGPDLNPYLSHLARMYNGYAGG
FEVQVILAGNAFTAGKIIFAAVPPNFPTEGLSPSQVTMFPHIIVDVRQLEPVLIPLPD
VRNNFYHYNQSNDSTIKLIAMLYTPLRANNAGDDVFTVSCRVLTRPSPDFDFIFLVPP
TVESRTKPFSVPILTVEEMTNSRFPIPLEKLFTGPSSAFVVQPQNGRCTTDGVLLGTT
QLSPVNICTFRGDVTHITGSHNFTMNLASQNWNNYDPTEEIPAPLGTPDFVGKIQGML
TQTTRTDGSTRGHKATVYTGSADFAPKLGRVQFETDTNHDFEANQNTKFTPVGVIQDG
STTHRNEPQQWVLPSYSGRNTHNVHLAPAVAPTFPGEQLLFFRSTMPGCSGYPNMDLD
CLLPQEWVQYFYQEAAPAQSDVALLRFVNPDTGRVLFECKLHKSGYVTVAHTGQHDLV
IPPNGYFRFDSWVNQFYTLAPMGNGTGRRRAV"
gene 6517..7323
/gene="ORF3"
CDS 6517..7323
/gene="ORF3"
/note="minor structural protein; small basic protein"
/codon_start=1
/product="VP2"
/protein_id="XEJ39623.1"
/translation="MAGAFFAGLASDVLGSGLGSLINAGAGAINQKVEFENNRKLQQA
SFQFSSNLQQASFQHDKEMLQAQIEATKKLQQEMMRVKQAMLLEGGFSETDAARGAIN
APMTKALDWSGTRYWAPDARITTYNAGHFSTPQPSGALPGRANLRDAVPARGPSTKPS
NSPTATSVHSNQTVSTRLGSTAGSGTSVSSLPSTARTRSWVEDQNRSLSPFMKGAYNI
SFVTPPSSRSSSQGTVSTVPKEILDSWTGAFNTRRQPLFAHIRKRGESRA"
ORIGIN
1 gagttggtca agaggatacc ccctcctcca cctaatggcg aagaagaaga tgaaccagtc
61 attaggtatg gggttaagag tgggatctct ggcctgcccg agctcacaac agtcccccaa
121 ccggacgtgg ccaacacagc atttagtgtt ccaccactga gcatgagaga aaacagggag
181 gccaaagaac cgctgacagg ggcaatacta gagatgtggg atggagagat ataccactat
241 ggcctgtacg tggagaaagg cttagtgttg ggtgtgcaca aaccacctgc agccataagc
301 atggcaagag tggagctggc gccgctgtca ttgtactggc gtgtggtgta cactccccaa
361 tacctcatct cccctgagac tctcaggagg ctcaacggtg aggcgtttcc ttacaccgct
421 tttgacaaca actgctacgc tttttgctgc tgggtgttag acctcaatga ctcatggctt
481 agcaggagga tggtgcaacg aaccacgggc ttcttcaggc cttaccaaga gtggaacaga
541 aaacccttac ccaccatgga tgactccaaa ataaagaagg tagcaaatat attcctatgt
601 tcattgtcca cattattcac caggcccata aaagacctca taggaaaaat caaaccatta
661 aacatattga acatcctggc aacgtgtgac tggacgtttg ccggaatagt ggagtctctg
721 atattgcttg ccgaactctt cggagttttc tggacacccc cagatgtgtc tgctataatt
781 gctcccttac ttgggggcta cgagttgcag gggccagaag acctcgccgt tgaactcgta
841 cctgtggtaa tgggagggat tggtttggtg ttgggattca ccaaagagaa aattggcaaa
901 atgttgtcct cagcagcatc aacactcaga gcttgtaaag atcttggtgc ctatggctta
961 gagatactta aattggtcat gaagtggttt ttcccaaaga aagaagaggc caatgagcta
1021 gctatggtga gggccataga ggatgccgtg ctagatcttg aggcaataga aaacaaccac
1081 atgacaaccc tgttgaaaga caaagacagc ttagcaacat acatgaaaac actggacatg
1141 gaggaggaga aagccaggag gttgtccaca aaatctgcat cccctgacat agttgggaca
1201 atcaacgccc tgctggctcg aatagcagca gccaggtcat tagtccacag ggctaaggaa
1261 gaactgtcta gcaggataag gccagtagtt gttatgatat ctggcaaacc aggaataggc
1321 aaaactcatc tagccagaga ggtggcaaga aaggtggcat ccactctcac aggggaccaa
1381 agagtcggac tcataccaag aaacggtgtg gaccactggg atgcatacaa aggtgagaga
1441 gtcgtgctgt gggacgacta tggcatgagt aaccccattc atgatgctct ccgcatacaa
1501 gaattggctg atacgtgtcc ccttacctta aattgcgaca gaattgaaaa taaggggaaa
1561 gtttttgaca gtgaagtcat aataattaca acaaacctcg ccaacccagc cccacttgat
1621 tatgtcaact ttgaggcctg ctccaggaga attgatttcc tggtgtacgc tgaggcacca
1681 gaagtagaaa aggcaaaacg ggattttcct ggtcagccag atatgtggaa ggacgccttc
1741 aagccggact tttcgcacat caagctacag cttgcacctc agggcggctt tgacaagaat
1801 ggcaacaccc ctcatgggaa aggagtgatg aagaccctca ctaccggttc tctgattgcc
1861 cgtgcatcgg gcctactgca tgagaggatg gatgaatttg aactccaagg tcccacaatc
1921 accactttca atttcgaccg gaacagaatc gcagcattca gacaattggc tgcagaaaac
1981 aagtatggac tggtggacac catgaaagtt ggcaatcaac taaaaggagt gaaaaccatg
2041 gaagaactca aacaagcaat caggaatgtg gccattaaga ggtgccggat catctacggt
2101 ggctccacgt atgaccttga gtctgatggc aagggcaaag ttttggtgga aaaggtcaag
2161 aacacctcta tacagaccaa caacgagttg accgggaccc tgcatcatct caagcatgcc
2221 cgaatcaggt actatgtcaa atgtgtgcaa gaggcagtct attccatcat acaaattgcc
2281 ggcgctgcgt ttgtcaccac gcgcattgca cgccgcatga acatacaaga gctctggtcg
2341 aagccacaat tagatcaaaa tgaatcagag actaaggaag aggcccccaa gtcagaagat
2401 gacgagttca tcatatcttc taaggatatc aaggaggaag gaaagaaggg caaaaacaaa
2461 actggccgtg gcaagaaaca caccgcattc tccagcaagg gcttaagcga tgaggagtat
2521 gacgagtaca agaggataag agaagagaga aatgggaagt actccataga agagtatctt
2581 caagacagag acaggtatta tgaggagctc gccattgcca aggccacgga agaagacttc
2641 tgtgaagagg aggagatcaa aatccgtcag agaatttttc gtcccaccag gaaacaaaga
2701 aaggaagaga gggccacact agggctggta actggctcag aaatcagaag aagaaaccct
2761 gatgatttca aacccaaagg gaagctgtgg gccgatgaca acagaagtgt tgactacaat
2821 gagaaactgg attttgaggc tcccccaagc atatggtcta ggattgtgag ctttggttct
2881 ggctggggct tctgggtatc accaagcctg ttcataacgt caactcatgt gatccctgca
2941 ggcataacag aagcatttgg agtccccatc aaacaaatcc agatccacaa atcaggtgag
3001 ttttgccgat ttagattccc aaaaccaatc agaccagatg tgacaggaat gatcttggaa
3061 gaaggtgcgc ctgaaggcac cgtggcaact gtgctcatca aacgccccac cggagagctc
3121 atgcctcttg cagccagaat gggaacacac gcaaccatga agattcaagg ccgcatggtt
3181 ggtggacaga tgggtatgct gctcactgga tcaaatgcta aagggatgga tttgggaaca
3241 actcctggtg actgtggctg cccttacatc tataaaaggg gcaatgacta catagtcatt
3301 ggggtgcaca ccgcagcagc ccgtggtgga aacaccgtca tctgtgccac acagggaagt
3361 gagggtgagg caactcttga gggtggagat gacaaaggaa catactgtgg ggcacccatt
3421 ctaggccctg gaggtgcacc aaaattgagc actaaaacca aattttggag gtcatcgaac
3481 acgccccttc caccggggac gtacgaacct gcctacctcg gtggccgtga tccgcgtgtt
3541 aagggtgggc cctccttaca acaggtaatg agagatcagt tgaagccatt cactgaaccc
3601 aggggcaaac ctccaagacc aagtgttttg gaagcagcca aacaaaccat tatcaatgtc
3661 cttgaacaaa ccctggatcc tccacaaaaa tggacatacg cacaggcgtg tgcctcactt
3721 gacaaaacca cttccagcgg gcatccccac catgtccgaa agaatgaatt ctggaatggt
3781 gagaccttca ctggtaaatt ggcagaccaa gcatcaaaag caaacctaat gtttgaggaa
3841 gggaagcaca tgacaccagt gtacacagca gcactcaagg acgagctagt caagactgag
3901 aaaatctatg gaaagatcaa gaagagactg ctctggggct ctgacttgtc caccatgatc
3961 cggtgcgcta ggtcatttgg tgggctcatg gacgagatga aggcacactg tatatcactc
4021 ccagtgcgag ttggcatgaa tatgaatgaa gatggcccaa taatatttga gaaacactct
4081 aggtacaaat atcactatga tgcagattat tctcgttggg attcaacaca acaaagggca
4141 gtgttagcag cagccttgga aattatggtc agattctctg cagaaccaca attggcacaa
4201 atagtcgctg aggatctact ggcccctagt gtagtagatg taggagactt taaaattgca
4261 ataaatgaag ggctcccatc tggcgtgcca tgcacttctc aatggaactc cattgcacac
4321 tggctgctaa ctctctgtgc cttgtctgaa gtcaccaaac tgtcccctga cattatacaa
4381 gcaaattcca tgttctcatt ttacggtgat gacgagattg tcagcaccga cataaaatta
4441 gaccctgaac agttgaccgc caagttgaag gagtacggcc tgaaaccaac ccgcccagac
4501 aagactgagg gacctctgat catcagtgaa gatttggacg gactcacttt cctccgaagg
4561 acggtgactc gtgacccagc tggctggttt ggaaaactgg accaaagttc gattttgagg
4621 cagatgtatt ggactagagg accaaatcat gaagacccca atgagacaat gataccccat
4681 tcccagaggc ccatacagct catggcactg cttggtgaag cctctcttca cggaccctct
4741 ttctacagta gaatcagtaa attggttata actgaactca aagaaggtgg gatggacttt
4801 tacgtgccaa ggcaggaacc catgttcagg tggatgaggt tctctgactt gagcacgtgg
4861 gagggcgatc gcaatctggc tcccaacttt gtgaatgaag atggcgtcga atgacgccaa
4921 cccatctgat gggtccgcag ccaacctcgt accagaggtc aacaatgagg ttatggcttt
4981 ggagcccgtt gttggtgccg ctattgcggc acccgtagcg ggccaacaaa atgtaattga
5041 cccctggatt agaaataatt ttgtacaagc ccctggtggg gaattcacag tatcccctag
5101 aaatgctcca ggtgaaatac tgtggagcgc acccttaggc cctgacctaa atccctacct
5161 atcccatttg gccagaatgt acaatggtta tgcaggtggt ttcgaagtgc aggtaattct
5221 cgcggggaac gcgttcaccg cagggaagat tatatttgca gcagtcccac caaattttcc
5281 aactgaaggc ttaagcccta gccaggtcac catgtttccc catataatag tagatgttag
5341 acaattggaa cctgtgctga tccccttacc cgatgttagg aataatttct atcattacaa
5401 tcagtcaaat gactccacta tcaagttgat agcaatgttg tacacaccac ttagggctaa
5461 taatgctggg gatgatgttt tcacagtttc gtgccgagtt ctcacgagac catcccccga
5521 ttttgatttt atattcttag taccacccac agttgagtca agaactaaac cattctctgt
5581 cccaatttta actgttgagg agatgaccaa ttcaagattc cccatccctt tggaaaagtt
5641 gttcacaggc cccagcagtg catttgttgt tcaaccacaa aacggcagat gcacaactga
5701 tggcgtgctc ctaggtacca cccaactttc tcctgtcaat atctgcacct tcagagggga
5761 cgtcacccat atcacaggta gtcacaactt cactatgaat ttggcttctc aaaattggaa
5821 caactatgac ccaacagaag aaatcccagc ccccctagga actccagatt ttgtggggaa
5881 gatccaaggc atgctcaccc aaaccacaag gacagatggt tcaacacgcg gccacaaagc
5941 tacagtgtac actgggagtg ccgactttgc tccaaaactg ggtagagttc aatttgaaac
6001 tgacacaaac catgactttg aagccaatca gaacacaaag ttcaccccag tcggtgtcat
6061 tcaagatggt agcaccaccc accgaaacga accccaacag tgggtgctcc caagttactc
6121 aggcagaaat actcacaatg tacatttggc ccccgctgta gcccccacct ttccgggtga
6181 acaactcctc ttctttagat ccaccatgcc cggatgcagc gggtacccca acatggattt
6241 ggactgtctg ctcccccagg aatgggtgca gtacttctac caagaggcag ccccagcaca
6301 atctgatgtg gctctgctaa gatttgtaaa cccagacaca ggtagggttc tgtttgagtg
6361 caagcttcac aaatcaggct atgttacagt ggctcacact ggtcaacatg atttggttat
6421 cccccccaat ggttacttca ggtttgattc ctgggtcaac cagttctaca cgcttgcccc
6481 catgggaaat ggaacggggc gtagacgtgc agtataatgg ctggagcttt ctttgctgga
6541 ttggcatctg atgtccttgg ctccggactt ggttctctta tcaatgctgg ggctggggcc
6601 atcaaccaaa aagttgagtt tgaaaataac agaaaattgc aacaagcatc cttccaattt
6661 agcagcaatt tgcaacaggc ttcctttcaa catgataaag agatgctcca agcacaaatt
6721 gaggccacca aaaagctaca gcaggaaatg atgagagtta agcaggcaat gctcttagag
6781 ggtgggttct ctgagacaga tgcagcccgc ggggcaatta acgcccccat gacaaaggct
6841 ttggactgga gcgggacaag gtactgggct ccagatgcta gaattacaac atacaatgca
6901 ggccactttt ccacccctca accatcgggg gcactgccag gaagagctaa tctcagggat
6961 gctgtccctg ctcgtgggcc ctccaccaaa ccttctaact ctcctactgc cacttctgtg
7021 cactcaaacc aaactgtttc aacgagactt ggttctacag ctggttctgg aactagtgtc
7081 tcgagcctcc cgtcaactgc aagaactagg agctgggttg aggatcagaa taggagtttg
7141 tcacctttca tgaagggggc ctacaacata tcatttgtca ccccaccatc tagcagatcc
7201 tctagccagg gcacagtctc aaccgtgccc aaagaaattt tggactcctg gactggcgct
7261 ttcaacacgc gcaggcagcc tctcttcgct cacattcgta agcgagggga gtcacgggcg
7321 taatgtgaaa agacaaaa
//