Typing tool
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Typing tool
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Complete norovirus genomes
| PQ196544 | GII.4 Sydney | |
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| GII.P16 |
ORF1: 1..4998
ORF2: 4979..6601
ORF3: 6601..7407
LOCUS PQ196544 7422 bp RNA linear VRL 27-MAR-2025
DEFINITION Norovirus GII isolate Hu/GII.4 Sydney[P16]/SanDiego0245/2023/USA
nonstructural polyprotein (ORF1) gene, partial cds; and VP1 (ORF2)
and VP2 (ORF3) genes, complete cds.
ACCESSION PQ196544
VERSION PQ196544.1
KEYWORDS .
SOURCE Norovirus GII
ORGANISM Norovirus GII
Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes;
Picornavirales; Caliciviridae; Norovirus; Norovirus norwalkense.
REFERENCE 1 (bases 1 to 7422)
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 7422)
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..7422
/organism="Norovirus GII"
/mol_type="genomic RNA"
/isolate="Hu/GII.4 Sydney[P16]/SanDiego0245/2023/USA"
/isolation_source="stool"
/host="Homo sapiens"
/db_xref="taxon:122929"
/geo_loc_name="USA"
/collection_date="30-May-2023"
/note="genotype: GII.4 Sydney[P16]"
gene <1..4998
/gene="ORF1"
CDS <1..4998
/gene="ORF1"
/codon_start=1
/product="nonstructural polyprotein"
/protein_id="XEJ39660.1"
/translation="TLKKALGARPKQPAPRGEPQKPPRPPTPELVKRIPPPPPNGEEE
DEPVIRYEVKSGISGLPELTTVPQPDVANTAFSVPPLSMRENREAKEPLTGAILEMWD
GEIYHYGLYVEKGLVLGVHKPPAAISMARVELAPLSLYWRVVYTPQYLISPETLRRLN
GEAFPYTAFDNNCYAFCCWVLDLNDSWLSRRMVQRTTGFFRPYQEWNRKPLPTMDDSK
IKKVANIFLCSLSTLFTRPIKDLIGKIKPLNILNILATCDWTFAGIVESLILLVELFG
VFWTPPDVSAMIAPLLGDYELQGPEDLAVELVPVVMGGIGLVLGFTKEKIGKMLSSAA
STLRACKDLGAYGLEILKLVMKWFFPKKEEANELAMVRAIEDAVLDLEAIENNHMTAL
LKDKDSLATYMKTLDMEEEKARRLSTKSASPDIVGTINALLARIAAARSLVHRAKEEL
SSRIRPVVVMISGKPGIGKTHLAREVARKVASTPTGDQRVGLIPRNGVDHWDAYKGER
VVLWDDYGMSNPIHDALRIQELADTCPLTLNCDRIENKGKVFDSEVIIITTNLANPAP
LDYVNFEACSRRIDFLVYAEAPEVEKAKRDFPGQPDMWKDAFKPDFSHIKLQLAPQGG
FDKNGNTPHGKGVMKTLTTGSLIARASGLLHERMDEFELQGPTITTFNFDRNRITAFR
QLAAENKYGLVDTMKVGNQLKGVKTMEELKQAIRNVTIKRCRIIYGGSTYDLESDGKG
KVLVEKVKNTSIQTNNELTGALHHLKHARIRYYVKCVQEAVYSIIQIAGAAFVTTRIA
RRMNIQELWSKPQLDQNESETKEEAPKSEDDEFIISSKDIKEEGKKGKNKTGRGKKHT
AFSSKGLSDEEYDEYKRIREERNGKYSIEEYLQDRDRYYEELAIAKATEEDFCEEEEI
KIRQRIFRPTRKQRKEERATLGLVTGSEIRRRNPDDFKPKGKLWADDNRSVDYNEKLD
FEAPPSIWSRIVSFGSGWGFWVSPSLFITSTHVIPAGITEAFGVPIKQIQIHKSGEFC
RFRFPKPIRPDVTGMILEEGAPEGTVATVLIKRPTGELMPLAARMGTHATMKIQGRMV
GGQMGMLLTGSNAKGMDLGTTPGDCGCPYIYKRGNDYIVIGVHTAAARGGNTVICATQ
GSEGEATLEGGDDKGTYCGAPILGPGGAPKLSTKTKFWRSSNTPLPPGTYEPAYLGGR
DPRVKGGPSLQQVMRDQLKPFTEPRGKPPRPSVLEAAKQTIINVLEQTLDPPQKWTYA
QACASLDKTTSSGHPHHVRKNEFWNGETFTGKLADQASKANLMFEEGKHMTPVYTAAL
KDELVKTEKIYGKIKKRLLWGSDLSTMIRCARSFGGLMDEMKAHCISLPVRVGMNMNE
DGPIIFEKHSRYKYHYDADYSRWDSTQQRAVLAAALEIMVRFSAEPQLAQIVAEDLLA
PSVVDVGDFKIAINEGLPSGVPCTSQWNSIAHWLLTLCALSEVTKLSPDIIQANSMFS
FYGDDEIVSTDIKLDPEQLTAKLKEYGLKPTRPDKTEGPLIISEDLDGLTFLRRTVTR
DPAGWFGKLDQSSILRQMYWTRGPNHEDPNETMIPHSQRPIQLMALLGEASLHGPSFY
SRISKLVITELKEGGMDFYVPRQEPMFRWMRFSDLSTWEGDRNLAPNFVNEDGVE"
mat_peptide <1..894
/gene="ORF1"
/product="p48"
mat_peptide 895..1992
/gene="ORF1"
/product="NTPase"
mat_peptide 1993..2523
/gene="ORF1"
/product="p22"
mat_peptide 2524..2922
/gene="ORF1"
/product="VPg"
mat_peptide 2923..3465
/gene="ORF1"
/product="Pro"
mat_peptide 3466..4995
/gene="ORF1"
/product="RdRp"
gene 4979..6601
/gene="ORF2"
CDS 4979..6601
/gene="ORF2"
/note="major capsid protein"
/codon_start=1
/product="VP1"
/protein_id="XEJ39661.1"
/translation="MKMASNDANPSDGSAANLVPEVNNEVMALEPVVGAAIAAPVAGQ
QNVIDPWIRNNFVQAPGGEFTVSPRNAPGEILWSAPLGPDLNPYLSHLARMYNGYAGG
FEVQVILAGNAFTAGKIIFAAVPPNFPTEGLSPSQVTMFPHIIVDVRQLEPVLIPLPD
VRNNFYHYNQSNDSTIKLIAMLYTPLRANNAGDDVFTVSCRVLTRPSPDFDFIFLVPP
TVESRTKPFSVPILTVEEMTNSRFPIPLEKLFTGPSSAFVVQPQNGRCTTDGVLLGTT
QLSPVNICTFRGDVTHITGSHNFTMNLASQNWNNYDPTEEIPAPLGTPDFVGKIQGVL
TQTTRTDGSTRGHKATVYTGSADFAPKLGRVQFETDTNHDFEANQNTKFTPVGVIQDG
STTHRNEPQQWVLPSYSGRNTHNVHLAPAVAPTFPGEQLLFFRSTMPGCSGYPNMDLD
CLLPQEWVQYFYQEAAPAQSDVALLRFVNPDTGRVLFECKLHKSGYVTVAHTGQHDLV
IPPNGYFRFDSWVNQFYTLAPMGNGTGLRRAV"
gene 6601..7407
/gene="ORF3"
CDS 6601..7407
/gene="ORF3"
/note="minor structural protein; small basic protein"
/codon_start=1
/product="VP2"
/protein_id="XEJ39662.1"
/translation="MAGAFFAGLASDVLGSGLGSLINAGAGAINQKVEFENNRKLQQA
SFQFSSNLQQASFQHDKEMLQAQIEATKKLQQEMMRVKQAMLLEGGFSETDAARGAIN
APMTKALDWSGTRYWAPDARITTYNAGHFSTPQPSGALPGRANLRDAVPARGPSTKPS
NSPTATSVHSNQTVSTRLGSTAGSGTSVSSLPSTARTRSWVEGQNRNLSPFMKGAYNI
SFVTPPSSRSSSQGTVSTVPKEILDSWTGAFNTRRQPLFAHIRKRGESRV"
ORIGIN
1 accttaaaga aagccctcgg ggctaggccc aaacagcctg ccccgagagg tgaaccacaa
61 aagcccccaa gaccaccaac tcccgagttg gtcaagagga taccccctcc tccacctaat
121 ggcgaagaag aagacgaacc agtcattagg tatgaggtta agagtgggat ctctggccta
181 cccgagctca caacagtccc ccaaccggac gtggccaaca cagcatttag tgttccacca
241 ctgagcatga gagaaaacag ggaggccaaa gaaccgctga caggggcaat actagagatg
301 tgggatggag agatatacca ctatggcctg tacgtggaga aaggcttagt gttgggtgtg
361 cacaaaccac ctgcagccat aagcatggca agagtggagc tggcgccgct gtcattgtac
421 tggcgtgtgg tgtacactcc ccaatacctc atctcccctg agactctcag gaggcttaac
481 ggtgaggcgt ttccttacac cgcttttgac aacaactgct acgctttttg ctgctgggtg
541 ttagacctca atgactcatg gcttagcagg aggatggtgc aacgaaccac gggcttcttc
601 aggccttacc aagagtggaa cagaaaaccc ttacccacca tggatgactc caaaataaag
661 aaggtagcaa atatattcct gtgctcattg tccacattat tcaccaggcc cataaaagac
721 ctcataggaa aaattaaacc attaaacata ttgaacatcc tggcaacgtg tgactggacg
781 tttgccggaa tagtggagtc tctgatattg cttgtcgaac tcttcggagt tttctggaca
841 cccccagatg tgtctgctat gattgctccc ttacttgggg actacgagtt gcaggggcca
901 gaagacctcg ccgttgaact cgtacctgtg gtaatgggag ggattggttt ggtgttggga
961 ttcaccaaag agaaaattgg caaaatgttg tcctcagcag catcaacact cagagcttgt
1021 aaagatcttg gtgcctatgg cttagagata ctcaaattgg tcatgaagtg gtttttccca
1081 aagaaagaag aggccaatga gctagctatg gtgagggcca tagaggatgc cgtactagat
1141 cttgaggcaa tagaaaacaa ccacatgaca gccctgttga aagacaaaga cagcttagca
1201 acatacatga aaacactgga catggaggag gagaaagcca gaaggttgtc cacaaaatct
1261 gcatcccctg acatagttgg gacaatcaac gccctgctgg ctcgaatagc agcagccagg
1321 tcattagtcc acagggccaa ggaagaactg tctagcagga taaggccagt agttgttatg
1381 atatctggca aaccaggaat aggcaaaact catctagcca gagaggtggc aagaaaggtg
1441 gcatccactc ccacagggga ccaaagagtc ggactcatac caagaaacgg tgtggaccac
1501 tgggatgcat acaaaggtga gagagtcgtg ctgtgggacg actatggcat gagtaacccc
1561 attcatgatg ctctccgcat acaagaattg gctgatacgt gtccccttac cttaaattgc
1621 gacagaattg aaaataaggg gaaagttttt gacagtgaag tcataataat tacaacaaac
1681 ctcgccaacc cagccccact tgattatgtc aactttgagg cctgctccag gaggattgat
1741 ttcctggtgt acgctgaggc accagaagta gaaaaggcaa aacgggattt tcctggtcag
1801 ccagatatgt ggaaggacgc cttcaagccg gacttttcgc acatcaagct acagcttgca
1861 cctcagggcg gctttgacaa gaatggcaac acccctcatg ggaaaggagt gatgaagacc
1921 ctcactaccg gttctctgat tgcccgtgca tcaggcctac tgcatgagag gatggatgaa
1981 tttgaactcc aaggtcccac aatcaccact ttcaatttcg accggaacag aatcacagca
2041 ttcagacaat tggctgcaga aaacaagtat ggactggtgg acaccatgaa agttggcaat
2101 caactaaaag gagtgaaaac catggaagaa ctcaaacaag caatcaggaa tgtgaccatc
2161 aagaggtgcc ggataatcta cggtggctcc acgtatgacc ttgagtctga tggcaagggc
2221 aaagttttgg tggaaaaggt caagaacacc tctatacaga ccaacaacga gttgaccggg
2281 gccctgcatc atctcaagca tgcccgaatc aggtactatg tcaaatgtgt gcaagaggca
2341 gtctattcca tcatacaaat tgccggcgct gcgtttgtca ccacgcgcat tgcacgccgc
2401 atgaacatac aagagctctg gtcgaagcct caattagacc aaaatgaatc agagactaag
2461 gaagaggccc ccaagtcaga agatgacgag ttcatcatat cttctaagga tatcaaggag
2521 gaaggaaaga agggcaaaaa caaaactggc cgtggcaaga aacacaccgc attctccagc
2581 aagggcttaa gcgatgagga gtatgacgag tacaagagga taagagaaga gagaaatggg
2641 aagtactcca tagaagagta tcttcaagac agagacaggt attacgagga gctcgccatt
2701 gccaaggcca cggaagaaga cttctgtgaa gaggaggaga tcaaaatccg tcagaggatt
2761 tttcgtccca ccaggaaaca aagaaaggaa gagagggcca cactagggct ggtaactggc
2821 tcagaaatca gaagaagaaa ccctgatgat ttcaaaccca aagggaagct gtgggccgat
2881 gacaacagaa gtgttgacta caatgagaaa ctggattttg aggctccccc aagcatatgg
2941 tctaggattg tgagctttgg ttctggctgg ggcttctggg tatcaccaag cctgttcata
3001 acgtcaactc atgtgatccc tgcaggcata acagaagcat ttggagtccc catcaaacaa
3061 atccagatcc acaaatcagg tgaattttgc cgattcagat tcccaaaacc aatcagacca
3121 gatgtgacag gaatgatctt ggaagaaggt gcgcctgaag gcaccgtggc aactgtgctc
3181 atcaaacgcc ccaccggaga gctcatgcct cttgcagcca gaatgggaac acacgcaacc
3241 atgaagattc aaggccgcat ggttggtgga cagatgggta tgctgctcac tgggtcaaat
3301 gctaaaggga tggatttggg aacaactcct ggtgactgtg gctgccctta catctataaa
3361 aggggcaatg actatatagt cattggggtg cacaccgcag cagcccgtgg tggaaacacc
3421 gtcatctgtg ccacacaggg aagtgagggt gaggcaactc ttgagggtgg agatgacaaa
3481 ggaacatact gtggggcacc cattctaggc cctggaggtg caccaaaatt gagcactaaa
3541 accaaatttt ggaggtcatc gaacacgccc cttccaccgg ggacttacga acctgcctac
3601 ctcggtggcc gtgacccgcg tgttaagggt gggccctcct tacaacaggt aatgagagat
3661 cagttgaagc cattcactga acccaggggc aaacctccaa gaccaagtgt tttggaagca
3721 gccaaacaaa ccattatcaa tgtccttgaa caaaccctgg atcctccaca aaagtggaca
3781 tacgcacagg cgtgtgcctc acttgacaaa accacctcca gcgggcatcc ccaccatgtc
3841 cgaaagaatg agttctggaa tggtgagacc ttcactggta agttggcaga ccaagcatca
3901 aaagcaaacc taatgtttga ggaagggaaa cacatgacac cagtgtacac agcagcactc
3961 aaggacgagc tagtcaagac tgagaaaatc tatggaaaga tcaagaagag actgctctgg
4021 ggctctgact tgtccaccat gatccggtgc gctaggtcat ttggtgggct catggacgag
4081 atgaaggcac actgtatatc actcccagtg cgagttggca tgaatatgaa tgaagatggc
4141 ccaataatat ttgagaaaca ttctaggtac aaatatcact atgatgcaga ctactctcgt
4201 tgggattcaa cacagcaaag ggcagtatta gcagcagcct tggaaattat ggtcagattc
4261 tctgcagaac cacaattggc acaaatagtc gctgaggatc tactggcccc tagtgtagta
4321 gatgtaggag actttaaaat tgcaataaat gaagggctcc catctggcgt gccatgcact
4381 tctcaatgga actccattgc acactggctg ctaactctct gtgccttgtc tgaagtcacc
4441 aaactgtccc ctgacattat acaagcaaat tccatgttct cattttacgg tgatgacgag
4501 attgtcagca ccgacataaa attagaccct gaacagttga ccgccaagtt gaaggagtac
4561 ggcctgaaac caacccgccc agacaagact gagggacctc tgatcatcag tgaagatttg
4621 gacggactca ctttcctccg aaggacggtg actcgtgacc cagctggctg gtttggaaaa
4681 ctggaccaaa gttcaatttt gaggcagatg tattggacta gaggaccaaa tcatgaagac
4741 cccaatgaga caatgatacc ccattcccag aggcccatac agctcatggc actgcttggt
4801 gaagcctctc ttcacgggcc ctctttctac agtagaatca gtaaattggt tataactgaa
4861 ctcaaagaag gtgggatgga cttttacgtg ccaaggcagg aacccatgtt caggtggatg
4921 aggttctctg acttgagcac gtgggagggc gatcgcaatc tggctcccaa ctttgtgaat
4981 gaagatggcg tcgaatgacg ccaacccatc tgatgggtcc gcagccaacc tcgtaccaga
5041 ggtcaacaat gaggttatgg ctttggagcc cgttgttggt gccgctattg cggcacccgt
5101 agcgggccaa caaaatgtaa ttgacccctg gattagaaat aattttgtac aagcccctgg
5161 tggggagttc acagtatccc ctagaaatgc tccaggtgaa atactgtgga gcgcaccctt
5221 aggccctgac ctaaatccct acctatccca tttggccaga atgtacaatg gttatgcagg
5281 tggtttcgaa gtgcaggtaa ttctcgcggg gaacgcgttc accgcaggga agattatatt
5341 tgcagcagtc ccaccaaatt ttccaactga aggcttaagc cctagccagg ttaccatgtt
5401 tccccatata atagtagatg ttagacaatt ggaacctgtg ctgatcccct tacccgatgt
5461 taggaataac ttctatcatt acaatcagtc aaatgactcc actatcaagt tgatagcaat
5521 gttgtacaca ccacttaggg ctaataatgc tggggatgat gttttcacag tttcgtgccg
5581 agttctcacg agaccatccc ccgattttga ttttatattc ttagtaccac ccacagttga
5641 gtcaagaact aaaccattct ctgtcccaat tttaactgtc gaggagatga ccaattcaag
5701 attccccatc cctttggaaa agttgttcac aggccccagc agtgcatttg ttgttcaacc
5761 acaaaacggc agatgcacaa ctgatggcgt gctcctaggt accacccaac tttctcctgt
5821 caacatctgc accttcagag gggacgtcac ccatatcaca ggtagtcaca acttcactat
5881 gaatttggct tctcaaaact ggaacaacta tgacccaaca gaagaaatcc cagcccccct
5941 aggaactcca gattttgtgg ggaagatcca aggcgtgctc acccaaacca caaggacaga
6001 tggttcaaca cgcggccaca aagctacagt gtacactggg agcgccgact ttgctccaaa
6061 actgggtaga gttcaatttg aaactgacac aaaccatgac tttgaagcca atcagaacac
6121 aaagttcacc ccagtcggcg tcattcaaga tggtagcacc acccaccgaa acgaacccca
6181 acagtgggtg ctcccaagtt actcaggcag aaatactcac aatgtacact tggcccccgc
6241 tgtagccccc acctttccgg gtgagcaact cctcttcttt agatccacca tgcccggatg
6301 cagcgggtac cccaacatgg acttggactg tctgctcccc caggaatggg tgcagtactt
6361 ctaccaagag gcagccccag cacaatctga tgtggctctg ctaagatttg taaacccaga
6421 cacaggtagg gttctgtttg agtgcaagct tcacaaatca ggctatgtta cagtggctca
6481 cactggtcaa catgatttgg ttatcccccc caatggttac tttaggtttg attcctgggt
6541 caaccagttc tacacgcttg cccccatggg aaatggaacg gggcttagac gtgcagtata
6601 atggctggag ctttctttgc tggattggca tctgatgtcc ttggctccgg acttggttct
6661 cttatcaatg ctggggctgg ggccatcaac caaaaagttg agtttgaaaa taacagaaaa
6721 ttgcaacaag catccttcca atttagtagc aatttgcaac aggcttcctt tcaacatgat
6781 aaagagatgc tccaagcaca aattgaggcc accaaaaagc tacagcagga aatgatgaga
6841 gttaagcagg caatgctctt agagggtggg ttctctgaga cagatgcagc ccgcggggca
6901 attaacgccc ccatgacaaa ggctttggac tggagcggga caaggtactg ggctccagat
6961 gctagaatta caacatacaa tgcaggccac ttttccaccc ctcaaccatc gggggcactg
7021 ccaggaagag ctaatctcag ggatgctgtc cctgctcgtg ggccctccac caaaccttct
7081 aactctccta ctgccacctc tgtgcactca aaccaaactg tttcaacgag acttggttct
7141 acagctggtt ctggaaccag tgtctcgagc ctcccgtcaa ctgcaagaac taggagctgg
7201 gttgagggtc agaataggaa tttgtcacct ttcatgaagg gggcctacaa catatcattt
7261 gtcaccccac catctagcag atcctctagc cagggcacag tctcaaccgt gcccaaagaa
7321 attttggact cctggactgg cgctttcaac acgcgcaggc agcctctctt cgctcacatt
7381 cgtaagcgag gggagtcacg ggtgtaatgt gaaaagacaa aa
//