Typing tool
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Typing tool
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Complete norovirus genomes
| PQ196520 | GII.4 Sydney | |
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| GII.P16 |
ORF1: 5..5104
ORF2: 5085..6707
ORF3: 6707..7513
LOCUS PQ196520 7528 bp RNA linear VRL 27-MAR-2025
DEFINITION Norovirus GII isolate Hu/GII.4 Sydney[P16]/SanMateo0195/2023/USA
nonstructural polyprotein (ORF1), VP1 (ORF2), and VP2 (ORF3) genes,
complete cds.
ACCESSION PQ196520
VERSION PQ196520.1
KEYWORDS .
SOURCE Norovirus GII
ORGANISM Norovirus GII
Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes;
Picornavirales; Caliciviridae; Norovirus; Norovirus norwalkense.
REFERENCE 1 (bases 1 to 7528)
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 7528)
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..7528
/organism="Norovirus GII"
/mol_type="genomic RNA"
/isolate="Hu/GII.4 Sydney[P16]/SanMateo0195/2023/USA"
/isolation_source="stool"
/host="Homo sapiens"
/db_xref="taxon:122929"
/geo_loc_name="USA"
/collection_date="16-May-2023"
/note="genotype: GII.4 Sydney[P16]"
gene 5..5104
/gene="ORF1"
CDS 5..5104
/gene="ORF1"
/codon_start=1
/product="nonstructural polyprotein"
/protein_id="XEJ39588.1"
/translation="MKMASNDASAAVACDNNNDKEKSSGEGLFTNMSSTLKKALGARP
KQSAPRGEPQKPPRPPTPELVKRIPPPPPNGEEEEEPVIRYEVKSGISGLPELTTVPQ
PDVANTAFSVPPLSLRENREAKEPLTGAILEMWDGEIYHYGLYVEKGLVLGVHKPPAA
ISMARVELVPLSLYWRVVYTPQYLISPETLRRLNGEAFPYTAFDNNCYAFCCWVLDLN
DSWLSRRMVQRTTGFFRPYQEWNRKPLPTMDDSKIKKVANIFLCSLSTSFTRPIKDLI
GKIKPLNILNILATCDWTFAGIVESLILLAELFGVFWTPPDVSAMIAPLLGDYELQGP
EDLAVELVPVVMGGIGLVLGFTKEKIGKMLSSAASTLRACKDLGAYGLEILKLVMKWF
FPKKEEANELAMVRAIEDAVLDLEAIENNHMTTLLKDKDSLATYMKTLDMEEEKARRL
STKSASPDIVGTINALLARIAAARSLVHRAKEELSSRIRPVVVMISGKPGIGKTHLAR
EVARKVASTLTGDQRVGLIPRNGVDHWDAYKGERVVLWDDYGMSNPIHDALRIQELAD
TCPLTLNCDRIENKGKVFDSEVIIITTNLANPAPLDYVNFEACSRRIDFLVYAEAPEV
EKAKRDFPGQPDMWKDAFKPDFSHIKLQLAPQGGFDKNGNTPHGKGVMKTLTTGSLIA
RASGLLHERMDEFELQGPTITTFNFDRNRITAFRQLAAENKYGLVDTMKVGNQLKGVK
TMEELKQAIRNVTIKRCRIIYGGSTYDLESDGKGKVLVEKVKNTSIQTNNELAGALHH
LKHARIRYYVKCVQEAVYSIIQIAGAAFVTTRIARRMNIQELWSKPQLDQNESETKEE
APKPEDDEFIISSKDIKEEGKKGKNKTGRGKKHTAFSSKGLSDEEYDEYKRIREERNG
KYSIEEYLQDRDRYYEELAIAKATEEDFCEEEEIKIRQRIFRPTRKQRKEERATLGLV
TGSEIRRRNPDDFKPKGKLWADDNRSVDYNEKLDFEAPPSIWSRIVSFGSGWGFWVSP
SLFITSTHVIPAGITEAFGVPIKQIQIHKSGEFCRFRFPKPIRPDVTGMILEEGAPEG
TVVTVLIKRPTGELMPLAARMGTHATMKIQGRMVGGQMGMLLTGSNAKGMDLGTTPGD
CGCPYIYKRGNDYIVIGVHTAAARGGNTVICATQGSEGEATLEGGDDKGTYCGAPILG
PGGAPKLSTKTKFWRSSNTPLPPGTYEPAYLGGRDPRVKGGPSLQQVMRDQLKPFTEP
RGKPPRPSVLEAAKQTIVNVLEQTLDPPQKWTYAQACASLDKTTSSGHPHHVRKNEFW
NGETFTGKLADQASKANLMFEEGKHMTPVYTAALKDELVKTEKIYGKIKKRLLWGSDL
STMIRCARSFGGLMDEMKAHCISLPVRVGMNMNEDGPIIFEKHSRYKYHYDADYSRWD
STQQRAVLAAALEIMVRFSAEPQLAQIVAEDLLAPSVVDVGDFKITINEGLPSGVPCT
SQWNSIAHWLLTLCALSEVTKLSPDIIQANSMFSFYGDDEIVSTDIKLDPEQLTAKLK
EYGLKPTRPDKTEGPLIISEDLNGLTFLRRTVARDPAGWFGKLDQSSILRQMYWTRGP
NHEDPNETMIPHSQRPIQLMALLGEASLHGPSFYSRISKLVITELKEGGMDFYVPRQE
PMFRWMRFSDLSTWEGDRNLAPNFVNEDGVE"
mat_peptide 5..1000
/gene="ORF1"
/product="p48"
mat_peptide 1001..2098
/gene="ORF1"
/product="NTPase"
mat_peptide 2099..2629
/gene="ORF1"
/product="p22"
mat_peptide 2630..3028
/gene="ORF1"
/product="VPg"
mat_peptide 3029..3571
/gene="ORF1"
/product="Pro"
mat_peptide 3572..5101
/gene="ORF1"
/product="RdRp"
gene 5085..6707
/gene="ORF2"
CDS 5085..6707
/gene="ORF2"
/note="major capsid protein"
/codon_start=1
/product="VP1"
/protein_id="XEJ39589.1"
/translation="MKMASSDANPSDGSAANLVPEVNNEVMALEPVVGAAIAAPVAGQ
QNVIDPWIRSNFVQAPGGEFTVSPRNAPGEILWSAPLGPDLNPYLSHLARMYNGYAGG
FEVQVILAGNAFTAGKIIFAAVPPNFPTEGLSPSQVTMFPHLIVDVRQLEPVLIPLPD
VRNNFYHYNQSNDSTIRLIAMLYTPLRANNAGDDVFTVSCRVLTRPSPDFDFIFLVPP
TVESRTKPFSVPVLTVEEMTNSRFPIPLEKLFTGPSSAFVVQPQNGRCTTDGVLLGTT
QLSPVNICTFRGDVTHITGSHNFTMNLASQNWNNYDPTEEIPAPLGTPDFVGKIQGML
TQTTRTDGSTRGHKATVYTGSADFAPKLGRVQFETDTNHDFEANQNTKFTPVGVIQDG
STTHRNEPQQWVLPSYSGRNTHNVHLAPAVAPTFPGEQLLFFRSTMPGCSGYPNMDLD
CLLPQEWVQYFYQEAAPAQSDVALLRFVNPDTGRVLFECKLHKSGYVTVAHTGQHDLV
IPPNGYFRFDSWVNQFYTLAPMGNGTGRRRAV"
gene 6707..7513
/gene="ORF3"
CDS 6707..7513
/gene="ORF3"
/note="minor structural protein; small basic protein"
/codon_start=1
/product="VP2"
/protein_id="XEJ39590.1"
/translation="MAGAFFAGLASDVLGSGLGSLINAGAGAINQKVEFENNRKLQQA
SFQFSSNLQQASFQHDKEMLQAQIEATKKLQQEMMRVKQAMLLEGGFSETDAARGAIN
APMTKALDWSGTRYWAPDARITTYNAGHFSTPQPSGALPGRVNLRDAAPARGPSTKPS
NSSTATSVYSNQTISTRLGSTAGSGTSVSSLPSTARTRSWVEDQNRNLSPFMRGAHNI
SFVTPPSSRSSSQGTVSTVPKEILDSWTGAFNTRRQPLFAHIRRRGESRV"
ORIGIN
1 gtgaatgaag atggcgtcta acgacgcttc cgctgccgtt gcttgcgaca acaacaacga
61 caaggaaaaa tcttcaggtg aaggcttatt cacaaatatg tcttccacct taaagaaagc
121 cctcggggct aggcccaaac agtctgcccc gagaggtgaa ccacaaaagc ccccaagacc
181 accaactccc gagttggtca agaggatacc ccctcctcca cctaatggcg aagaagaaga
241 agaaccagtc attaggtatg aggttaagag tgggatctct ggcctgcccg agctcacaac
301 agtcccccaa ccggacgtgg ccaacacagc atttagtgtt ccaccactga gcttgagaga
361 aaacagggag gccaaggaac cgctgacagg ggcaatacta gagatgtggg acggagagat
421 ataccactat ggcctgtacg tggagaaagg cttagtgttg ggtgtacaca aaccacctgc
481 agccataagc atggcaagag tggagctggt gccgctgtca ttgtactggc gtgtggtgta
541 cactccccaa tacctcatct cccctgagac tctcaggagg ctcaacggag aggcgtttcc
601 ttacaccgct tttgacaaca actgctacgc tttttgctgc tgggtgttag acctcaatga
661 ctcatggctt agcaggagga tggtgcaacg aaccacgggc ttcttcaggc cttaccaaga
721 gtggaacaga aaacccttac ccaccatgga tgactccaaa ataaagaagg tagcaaatat
781 attcctatgt tcattgtcca catcattcac cagacccata aaagacctca taggaaaaat
841 taaaccatta aacatattga acatcctggc gacgtgtgat tggacgtttg ccggaatagt
901 ggagtctctg atattgcttg ccgaactctt cggagttttc tggacacccc cagatgtgtc
961 tgctatgatc gctcccttac ttggggacta cgagttgcag gggccagaag acctcgccgt
1021 tgaactcgta cctgtggtaa tgggagggat tggtttggtg ttaggattca ccaaagagaa
1081 aattggcaaa atgttgtcct cagcagcatc aacactcagg gcttgtaaag atcttggtgc
1141 ctatggctta gagatactca aattggtcat gaagtggttt ttcccaaaga aagaagaggc
1201 caatgagcta gctatggtga gggccataga ggatgccgta ctagatcttg aggcaataga
1261 aaacaaccac atgacaaccc tgttgaaaga caaagacagc ttagcaacat acatgaaaac
1321 actggacatg gaggaggaga aagccagaag gttgtccaca aaatctgcat cccctgacat
1381 agttgggaca atcaacgccc tgctggctcg aatagcagca gccaggtcat tagtccacag
1441 ggccaaggaa gaactgtcta gcaggataag gccagtagtt gttatgatat ctggcaaacc
1501 aggaataggc aaaactcacc tagccagaga ggtggcaaga aaggtggcat ccactctcac
1561 aggggatcaa agagtcggac tcataccaag aaacggtgtg gaccattggg atgcatacaa
1621 aggtgagaga gtcgtgttgt gggacgacta tggcatgagt aatcccattc atgatgctct
1681 ccgcatacaa gaattggctg atacgtgtcc cctcacctta aattgcgaca gaattgaaaa
1741 taaggggaaa gtttttgaca gtgaagtcat aataattaca acaaacctcg ccaacccagc
1801 cccacttgat tatgtcaact ttgaggcctg ctccaggaga attgatttcc tggtgtacgc
1861 tgaggcacca gaagtagaaa aggcaaaacg ggattttcct ggtcagccag atatgtggaa
1921 ggacgccttc aagccggact tttcgcacat caagctacag cttgcacctc agggcggctt
1981 tgacaagaat ggtaacaccc cgcatgggaa aggagtgatg aagactctca ctaccggttc
2041 tctgattgcc cgtgcatcag gcctactgca tgagaggatg gatgaatttg aacttcaagg
2101 tcccacaatc accactttca atttcgaccg gaacagaatc acagcattca gacaattggc
2161 tgcagaaaac aagtatggac tggtggacac catgaaagtt ggcaatcaac taaaaggagt
2221 gaaaaccatg gaagaactca aacaagcaat caggaatgtg accatcaaga ggtgccggat
2281 catctacggt ggctccacgt atgatcttga atctgatggc aagggcaaag ttttggtgga
2341 aaaggtcaag aacacctcta tacagaccaa caacgagttg gccggggccc tgcatcatct
2401 caaacatgcc cgaatcaggt actatgtcaa atgtgtgcaa gaagcagtct attccatcat
2461 acaaattgcc ggcgctgcgt ttgtcaccac gcgcattgca cgccgcatga acatacaaga
2521 gctctggtcg aagccacaat tagatcaaaa tgaatcagag actaaggaag aggcccccaa
2581 gccagaagat gacgagttca tcatatcttc taaggatatc aaggaggaag gaaagaaggg
2641 caaaaacaaa actggccgtg gcaagaaaca caccgcattc tccagcaagg gcttaagcga
2701 tgaggagtat gacgagtaca agaggataag agaagagaga aatgggaagt actctataga
2761 agagtatctt caagacagag acaggtatta tgaggagctc gccattgcca aggccacgga
2821 agaagacttc tgtgaagagg aggagatcaa aatccgtcag agaattttcc gtcccaccag
2881 gaaacaaaga aaggaagaga gggccacact agggctggta acaggttcag aaatcagaag
2941 aagaaaccct gatgatttca aacccaaagg gaagctgtgg gccgatgaca acagaagtgt
3001 tgactacaat gagaaactgg attttgaggc ccccccaagc atatggtcta ggattgtgag
3061 ctttggttct ggctggggct tctgggtatc accaagcctg ttcataacat caactcacgt
3121 gatccctgca ggcataacag aagcatttgg agtccccatc aaacagattc agatccacaa
3181 atcaggtgaa ttttgccgat tcagattccc aaaaccaatc agaccagatg tgacaggaat
3241 gatcttggaa gaaggtgcgc ctgagggcac cgtggtaact gtgctcatca aacgccccac
3301 cggagagctc atgcctcttg cagccagaat gggaacacac gcaaccatga agattcaagg
3361 ccgcatggtt ggtggacaga tgggtatgct gctcactgga tcaaatgcta aagggatgga
3421 tttgggaaca acacctggtg actgtggctg cccttacatc tataaaaggg gcaatgacta
3481 tatagtcatt ggggtgcaca ccgcagcagc ccgtggtgga aacaccgtca tctgtgccac
3541 acagggaagt gagggtgagg caactcttga gggtggagat gacaaaggaa catactgtgg
3601 ggcacccatt ctaggccctg ggggtgcacc aaaattgagc actaaaacca aattttggag
3661 gtcatcgaac acgccccttc caccagggac gtacgaacct gcctacctcg gtggccgtga
3721 cccgcgtgtt aagggtgggc cctcattaca acaggtaatg agagaccagt tgaagccatt
3781 cactgaaccc aggggcaaac ctccaagacc aagtgttttg gaagcagcca aacaaaccat
3841 tgtcaatgtc cttgaacaaa ccctggatcc tccacaaaag tggacatacg cacaggcgtg
3901 tgcctcactt gacaaaacca cctccagcgg gcatccccac catgtccgaa agaatgaatt
3961 ctggaatggt gagaccttca ctggtaaatt agcagaccaa gcatcaaaag caaacctaat
4021 gtttgaggaa gggaaacaca tgacaccagt gtacacagca gcactcaagg acgagctagt
4081 caagactgag aaaatctatg gaaagatcaa gaagagactg ctctggggct ctgacttgtc
4141 caccatgatc cggtgcgcta ggtcatttgg tgggctcatg gacgagatga aggcacactg
4201 catatcactc ccagtacgag ttggcatgaa tatgaatgaa gatggcccaa taatatttga
4261 gaaacattcc aggtacaaat atcactatga tgcagactac tctcgttggg attcaacaca
4321 gcagagggca gtattagcag cagccttgga aattatggtc agattctctg cagaaccaca
4381 attggcacaa atagtcgctg aggatctact ggcccctagt gtagtagatg taggagactt
4441 taaaattaca ataaatgaag ggctcccatc tggcgtgcca tgcacttctc aatggaactc
4501 cattgcacac tggctgctaa ctctctgtgc cttgtctgaa gtcaccaaac tgtcccctga
4561 cattatacaa gcaaattcca tgttctcatt ttacggtgat gacgagattg tcagcaccga
4621 cataaaattg gaccctgaac agttgaccgc caagttgaag gagtacggcc tgaaaccaac
4681 ccgcccagac aagaccgagg gacctctgat tatcagtgaa gatttgaacg gactcacttt
4741 cctccgaagg acggtggctc gtgacccagc tggctggttt ggaaaactgg accaaagttc
4801 aattttgagg cagatgtact ggactagagg accaaatcat gaagacccca atgagacaat
4861 gataccccat tctcagaggc ccatacagct catggcactg cttggtgaag cctctcttca
4921 cggaccctct ttctacagta gaatcagtaa attggtcata actgaactta aagaaggtgg
4981 gatggatttt tacgtgccaa ggcaggaacc catgttcagg tggatgaggt tctctgactt
5041 gagcacgtgg gagggcgatc gcaatctggc tcccaacttt gtgaatgaag atggcgtcga
5101 gtgacgccaa cccatctgat gggtccgcag ccaacctcgt accagaggtc aacaatgagg
5161 ttatggcttt ggagcccgtt gttggtgccg ctattgcggc acctgtagcg ggccaacaaa
5221 atgtaattga cccctggatt agaagtaatt ttgtacaagc tcctggtggg gagtttacag
5281 tatcccctag aaatgctcca ggtgaaatac tatggagcgc gcccctaggt cctgacctaa
5341 atccctacct atcccatttg gccagaatgt acaatggtta tgcaggtggt tttgaagtgc
5401 aggtaattct cgcggggaac gcgttcaccg ccgggaagat tatatttgca gcagtcccac
5461 caaattttcc aactgaaggc ttaagcccta gtcaggtcac tatgtttccc catctaatag
5521 tagatgttag acaattggaa cctgtgctga tccccttacc cgatgttagg aataacttct
5581 atcattacaa tcagtcaaat gactccacta ttaggttgat agcaatgttg tacacaccac
5641 ttagggctaa taatgctgga gatgatgttt tcacagtttc gtgccgagtt ctcacgagac
5701 catcccccga ttttgatttc atattcttag taccacccac agttgaatca agaactaaac
5761 cattctctgt cccagtttta actgttgagg agatgaccaa ttcaagattc cccatccctt
5821 tggaaaagct gttcacaggc cccagcagtg catttgttgt tcaaccacaa aacggcagat
5881 gcacaactga tggcgtgctc ctaggcacca cccaactttc tcctgtcaac atctgcacct
5941 tcagagggga cgtcacccat atcacaggta gtcacaactt cactatgaat ttggcctctc
6001 aaaattggaa caactatgac ccaacagaag aaatcccagc ccccctagga actccagatt
6061 ttgtggggaa gatccaaggc atgctcaccc aaaccacaag gacagatggt tcaacacgcg
6121 gccacaaagc tacagtgtac actgggagcg ccgactttgc tccaaaactg ggtagagttc
6181 aatttgaaac tgacacaaac catgactttg aagctaatca aaacacaaag ttcaccccgg
6241 tcggtgtcat tcaagatggt agcaccaccc accgaaatga gccccaacaa tgggtgctcc
6301 caagttactc aggcagaaat actcacaatg tgcatttggc ccccgctgta gcccccacct
6361 ttccgggtga gcaactcctc tttttcagat ccaccatgcc cggatgcagc gggtacccca
6421 acatggattt ggactgtcta ctcccccagg aatgggtgca gtacttctac caagaggcag
6481 ccccagcaca atctgatgtg gctctgctaa gatttgtgaa tccagacaca ggtagggttc
6541 tgtttgagtg caagcttcac aaatcaggct atgttacagt ggctcacact ggccaacatg
6601 atttggttat cccccccaat ggttacttta ggtttgattc ctgggtcaac cagttctaca
6661 cgcttgcccc catgggaaat ggaacggggc gtagacgtgc agtataatgg ctggagcttt
6721 ctttgctgga ttggcatctg atgtccttgg ctctgggctt ggctccctta tcaatgctgg
6781 ggctggggcc atcaaccaaa aagttgagtt tgaaaataac agaaaattgc aacaggcatc
6841 cttccaattt agcagcaatt tgcaacaggc ttcctttcaa catgataaag agatgctcca
6901 agcacaaatt gaggccacca aaaagctaca gcaggaaatg atgagagtta agcaggcaat
6961 gctcctagag ggtgggttct ctgagacaga tgcagcccgc ggggcaatta atgcccccat
7021 gacaaaggct ttggactgga gcgggacaag gtactgggct ccagatgcta gaattacaac
7081 atacaatgca ggccactttt ccacccctca accatcgggg gcactgccag gaagagttaa
7141 tcttagggat gctgcccctg ctcgtggacc ctccaccaaa ccttctaact cttctactgc
7201 cacctctgtg tactcaaatc aaactatttc aacgagactt ggttctacag ctggttctgg
7261 aactagtgtc tcgagcctcc cgtcaactgc aagaactagg agctgggttg aggatcagaa
7321 taggaatttg tcacctttca tgaggggggc ccacaacata tcatttgtca ccccaccatc
7381 tagcagatcc tctagccaag gcacagtctc aaccgtgcct aaagaaattt tggactcctg
7441 gactggcgct ttcaacacgc gcaggcagcc tctcttcgct cacattcgta ggcgagggga
7501 gtcacgggtg taatgtgaaa agacaaaa
//