Typing tool
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Typing tool
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Complete norovirus genomes
| PQ196530 | GII.4 Sydney | |
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| GII.P16 |
ORF1: 1..5100
ORF2: 5081..6703
ORF3: 6703..7509
LOCUS PQ196530 7524 bp RNA linear VRL 27-MAR-2025
DEFINITION Norovirus GII isolate Hu/GII.4 Sydney[P16]/SanJoaquin0169/2023/USA
nonstructural polyprotein (ORF1), VP1 (ORF2), and VP2 (ORF3) genes,
complete cds.
ACCESSION PQ196530
VERSION PQ196530.1
KEYWORDS .
SOURCE Norovirus GII
ORGANISM Norovirus GII
Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes;
Picornavirales; Caliciviridae; Norovirus; Norovirus norwalkense.
REFERENCE 1 (bases 1 to 7524)
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 7524)
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..7524
/organism="Norovirus GII"
/mol_type="genomic RNA"
/isolate="Hu/GII.4 Sydney[P16]/SanJoaquin0169/2023/USA"
/isolation_source="stool"
/host="Homo sapiens"
/db_xref="taxon:122929"
/geo_loc_name="USA"
/collection_date="12-Apr-2023"
/note="genotype: GII.4 Sydney[P16]"
gene 1..5100
/gene="ORF1"
CDS 1..5100
/gene="ORF1"
/codon_start=1
/product="nonstructural polyprotein"
/protein_id="XEJ39618.1"
/translation="MKMASNDASAAVACNNNNDKEKSSGEGLFTNMSSTLKKALGARP
KQPAPRGESQKPPRPPTPELVKRIPPPPPNGEEEDEPVIRYGVKSGISGLPELTTVPQ
PDVANTAFSVPPLSMRENREAKEPLTGAILEMWDGEIYHYGLYVEKGLVLGVHKPPAA
ISMARVELAPLSLYWRVVYTPQYLISPETLRRLNGEAFPYTAFDNNCYAFCCWVLDLN
DSWLSRRMVQRTTGFFRPYQEWNRKPLPTMDDSKIKKVANIFLCSLSTLFTRPIKDLI
GKIKPLNILNILATCDWTFAGIVESLILLAELFGVFWTPPDVSAIIAPLLGGYELQGP
EDLAVELVPVVMGGIGLVLGFTKEKIGKMLSSAASTLRACKDLGAYGLEILKLVMKWF
FPKKEEANELAMVRAIEDAVLDLEAIENNHMTTLLKDKDSLATYMKTLDMEEEKARRL
STKSASPDIVGTINALLARIAAARSLVHRAKEELSSRIRPVVVMISGKPGIGKTHLAR
EVARKVASTLTGDQRVGLIPRNGVDHWDAYKGERVVLWDDYGMSNPIHDALRIQELAD
TCPLTLNCDRIENKGKVFDSEVIIITTNLANPAPLDYVNFEACSRRIDFLVYAEAPEV
EKAKRDFPGQPDMWKDAFKPDFSHIKLQLAPQGGFDKNGNTPHGKGVMKTLTTGSLIA
RASGLLHERMDEFELQGPTITTFNFDRNRIAAFRQLAAENKYGLVDTMKVGNQLKGVK
TMEELKQAIRNVAIKRCRIIYGGSTYDLESDGKGKVLVEKVKNTSIQTNNELTGTLHH
LKHARIRYYVKCVQEAVYSIIQIAGAAFVTTRIARRMNIQELWSKPQLDQNESETKEE
APKSEDDEFIISSKDIKEEGKKGKNKTGRGKKHTAFSSKGLSDEEYDEYKRIREERNG
KYSIEEYLQDRDRYYEELAIAKATEEDFCEEEEIKIRQRIFRPTRKQRKEERATLGLV
TGSEIRRRNPDDFKPKGKLWADDNRSVDYNEKLDFEAPPSIWSRIVSFGSGWGFWVSP
SLFITSTHVIPAGITEAFGVPIKQIQIHKSGEFCRFRFPKPIRPDVTGMILEEGAPEG
TVATVLIKRPTGELMPLAARMGTHATMKIQGRMVGGQMGMLLTGSNAKGMDLGTTPGD
CGCPYIYKRGNDYIVIGVHTAAARGGNTVICATQGSEGEATLEGGDDKGTYCGAPILG
PGGAPKLSTKTKFWRSSNTPLPPGTYEPAYLGGRDPRVKGGPSLQQVMRDQLKPFTEP
RGKPPRPSVLEAAKQTIINVLEQTLDPPQKWTYAQACASLDKTTSSGHPHHVRKNEFW
NGETFTGKLADQASKANLMFEEGKHMTPVYTAALKDELVKTEKIYGKIKKRLLWGSDL
STMIRCARSFGGLMDEMKAHCISLPVRVGMNMNEDGPIIFEKHSRYKYHYDADYSRWD
STQQRAVLAAALEIMVRFSAEPQLAQIVAEDLLAPSVVDVGDFKIAINEGLPSGVPCT
SQWNSIAHWLLTLCALSEVTKLSPDIIQANSMFSFYGDDEIVSTDIKLDPEQLTAKLK
EYGLKPTRPDKTEGPLIISEDLDGLTFLRRTVTRDPAGWFGKLDQSSILRQMYWTRGP
NHEDPNETMIPHSQRPIQLMALLGEASLHGPSFYSRISKLVITELKEGGMDFYVPRQE
PMFRWMRFSDLSTWEGDRNLAPNFVNEDGVE"
mat_peptide 1..996
/gene="ORF1"
/product="p48"
mat_peptide 997..2094
/gene="ORF1"
/product="NTPase"
mat_peptide 2095..2625
/gene="ORF1"
/product="p22"
mat_peptide 2626..3024
/gene="ORF1"
/product="VPg"
mat_peptide 3025..3567
/gene="ORF1"
/product="Pro"
mat_peptide 3568..5097
/gene="ORF1"
/product="RdRp"
gene 5081..6703
/gene="ORF2"
CDS 5081..6703
/gene="ORF2"
/note="major capsid protein"
/codon_start=1
/product="VP1"
/protein_id="XEJ39619.1"
/translation="MKMASNDANPSDGSAANLVPEVNNEVMALEPVVGAAIAAPVAGQ
QNVIDPWIRNNFVQAPGGEFTVSPRNAPGEILWSAPLGPDLNPYLSHLARMYNGYAGG
FEVQVILAGNAFTAGKIIFAAVPPNFPTEGLSPSQVTMFPHIIVDVRQLEPVLIPLPD
VRNNFYHYNQSNDSTIKLIAMLYTPLRANNAGDDVFTVSCRVLTRPSPDFDFIFLVPP
TVESRTKPFSVPILTVEEMTNSRFPIPLEKLFTGPSSAFVVQPQNGRCTTDGVLLGTT
QLSPVNICTFRGDVTHITGSHNFTMNLASQNWNNYDPTEEIPAPLGTPDFVGKIQGML
TQTTRTDGSTRGHKATVYTGSADFAPKLGRVQFETDTNHDFEANQNTKFTPVGVIQDG
STTHRNEPQQWVLPSYSGRNTHNVHLAPAVAPTFPGEQLLFFRSTMPGCSGYPNMDLD
CLLPQEWVQYFYQEAAPAQSDVALLRFVNPDTGRVLFECKLHKSGYVTVAHTGQHDLV
IPPNGYFRFDSWVNQFYTLAPMGNGTGRRRAV"
gene 6703..7509
/gene="ORF3"
CDS 6703..7509
/gene="ORF3"
/note="minor structural protein; small basic protein"
/codon_start=1
/product="VP2"
/protein_id="XEJ39620.1"
/translation="MAGAFFAGLASDVLGSGLGSLINAGAGAINQKVEFENNRKLQQA
SFQFSSNLQQASFQHDKEMLQAQIEATKKLQQEMMRVKQAMLLEGGFSETDAARGAIN
APMTKALDWSGTRYWAPDARITTYNAGHFSTPQPSGALPGRANLRDAVPARGPSTKPS
NSPTATSVHSNQTVSTRLGSTAGSGTSVSSLPSTARTRSWVEDQNRSLSPFMKGAYNI
SFVTPPSSRSSSQGTVSTVPKEILDSWTGAFNTRRQPLFAHIRKRGESRA"
ORIGIN
1 atgaagatgg cgtctaacga cgcttccgct gccgttgctt gcaacaacaa caacgacaag
61 gaaaaatctt caggtgaagg cttattcaca aatatgtctt ccaccttaaa gaaagccctc
121 ggggctaggc ccaaacagcc tgccccgaga ggtgaatcac aaaagccccc aagaccacca
181 actcccgagt tggtcaagag gataccccct cctccaccta atggcgaaga agaagatgaa
241 ccagtcatta ggtatggggt taagagtggg atctctggcc tgcccgagct cacaacagtc
301 ccccaaccgg acgtggccaa cacagcattt agtgttccac cactgagcat gagagaaaac
361 agggaggcca aagaaccgct gacaggggca atactagaga tgtgggatgg agagatatac
421 cactatggcc tgtacgtgga gaaaggctta gtgttgggtg tgcacaaacc acctgcagcc
481 ataagcatgg caagagtgga gctggcgccg ctgtcattgt actggcgtgt ggtgtacact
541 ccccaatacc tcatctcccc tgagactctc aggaggctca acggtgaggc gtttccttac
601 accgcttttg acaacaactg ctacgctttt tgctgctggg tgttagacct caatgactca
661 tggcttagca ggaggatggt gcaacgaacc acgggcttct tcaggcctta ccaagagtgg
721 aacagaaaac ccttacccac catggatgac tccaaaataa agaaggtagc aaatatattc
781 ctatgttcat tgtccacatt attcaccagg cccataaaag acctcatagg aaaaatcaaa
841 ccattaaaca tattgaacat cctggcaacg tgtgactgga cgtttgccgg aatagtggag
901 tctctgatat tgcttgccga actcttcgga gttttctgga cacccccaga tgtgtctgct
961 ataattgctc ccttacttgg gggctacgag ttgcaggggc cagaagacct cgccgttgaa
1021 ctcgtacctg tggtaatggg agggattggt ttggtgttgg gattcaccaa agagaaaatt
1081 ggcaaaatgt tgtcctcagc agcatcaaca ctcagagctt gtaaagatct tggtgcctat
1141 ggcttagaga tacttaaatt ggtcatgaag tggtttttcc caaagaaaga agaggccaat
1201 gagctagcta tggtgagggc catagaggat gccgtgctag atcttgaggc aatagaaaac
1261 aaccacatga caaccctgtt gaaagacaaa gacagcttag caacatacat gaaaacactg
1321 gacatggagg aggagaaagc caggaggttg tccacaaaat ctgcatcccc tgacatagtt
1381 gggacaatca acgccctgct ggctcgaata gcagcagcca ggtcattagt ccacagggct
1441 aaggaagaac tgtctagcag gataaggcca gtagttgtta tgatatctgg caaaccagga
1501 ataggcaaaa ctcatctagc cagagaggtg gcaagaaagg tggcatccac tctcacaggg
1561 gaccaaagag tcggactcat accaagaaac ggtgtggacc actgggatgc atacaaaggt
1621 gagagagtcg tgctgtggga cgactatggc atgagtaacc ccattcatga tgctctccgc
1681 atacaagaat tggctgatac gtgtcccctt accttaaatt gcgacagaat tgaaaataag
1741 gggaaagttt ttgacagtga agtcataata attacaacaa acctcgccaa cccagcccca
1801 cttgattatg tcaactttga ggcctgctcc aggagaattg atttcctggt gtacgctgag
1861 gcaccagaag tagaaaaggc aaaacgggat tttcctggtc agccagatat gtggaaggac
1921 gccttcaagc cggacttttc gcacatcaag ctacagcttg cacctcaggg cggctttgac
1981 aagaatggca acacccctca tgggaaagga gtgatgaaga ccctcactac cggttctctg
2041 attgcccgtg catcgggcct actgcatgag aggatggatg aatttgaact ccaaggtccc
2101 acaatcacca ctttcaattt cgaccggaac agaatcgcag cattcagaca attggctgca
2161 gaaaacaagt atggactggt ggacaccatg aaagttggca atcaactaaa aggagtgaaa
2221 accatggaag aactcaaaca agcaatcagg aatgtggcca ttaagaggtg ccggatcatc
2281 tacggtggct ccacgtatga ccttgagtct gatggcaagg gcaaagtttt ggtggaaaag
2341 gtcaagaaca cctctataca gaccaacaac gagttgaccg ggaccctgca tcatctcaag
2401 catgcccgaa tcaggtacta tgtcaaatgt gtgcaagagg cagtctattc catcatacaa
2461 attgccggcg ctgcgtttgt caccacgcgc attgcacgcc gcatgaacat acaagagctc
2521 tggtcgaagc cacaattaga tcaaaatgaa tcagagacta aggaagaggc ccccaagtca
2581 gaagatgacg agttcatcat atcttctaag gatatcaagg aggaaggaaa gaagggcaaa
2641 aacaaaactg gccgtggcaa gaaacacacc gcattctcca gcaagggctt aagcgatgag
2701 gagtatgacg agtacaagag gataagagaa gagagaaatg ggaagtactc catagaagag
2761 tatcttcaag acagagacag gtattatgag gagctcgcca ttgccaaggc cacggaagaa
2821 gacttctgtg aagaggagga gatcaaaatc cgtcagagaa tttttcgtcc caccaggaaa
2881 caaagaaagg aagagagggc cacactaggg ctggtaactg gctcagaaat cagaagaaga
2941 aaccctgatg atttcaaacc caaagggaag ctgtgggccg atgacaacag aagtgttgac
3001 tacaatgaga aactggattt tgaggctccc ccaagcatat ggtctaggat tgtgagcttt
3061 ggttctggct ggggcttctg ggtatcacca agcctgttca taacgtcaac tcatgtgatc
3121 cctgcaggca taacagaagc atttggagtc cccatcaaac aaatccagat ccacaaatca
3181 ggtgagtttt gccgatttag attcccaaaa ccaatcagac cagatgtgac aggaatgatc
3241 ttggaagaag gtgcgcctga aggcaccgtg gcaactgtgc tcatcaaacg ccccaccgga
3301 gagctcatgc ctcttgcagc cagaatggga acacacgcaa ccatgaagat tcaaggccgc
3361 atggttggtg gacagatggg tatgctgctc actggatcaa atgctaaagg gatggatttg
3421 ggaacaactc ctggtgactg tggctgccct tacatctata aaaggggcaa tgactacata
3481 gtcattgggg tgcacaccgc agcagcccgt ggtggaaaca ccgtcatctg tgccacacag
3541 ggaagtgagg gtgaggcaac tcttgagggt ggagatgaca aaggaacata ctgtggggca
3601 cccattctag gccctggagg tgcaccaaaa ttgagcacta aaaccaaatt ttggaggtca
3661 tcgaacacgc cccttccacc ggggacgtac gaacctgcct acctcggtgg ccgtgatccg
3721 cgtgttaagg gtgggccctc cttacaacag gtaatgagag atcagttgaa gccattcact
3781 gaacccaggg gcaaacctcc aagaccaagt gttttggaag cagccaaaca aaccattatc
3841 aatgtccttg aacaaaccct ggatcctcca caaaaatgga catacgcaca ggcgtgtgcc
3901 tcacttgaca aaaccacttc cagcgggcat ccccaccatg tccgaaagaa tgaattctgg
3961 aatggtgaga ccttcactgg taaattggca gaccaagcat caaaagcaaa cctaatgttt
4021 gaggaaggga agcacatgac accagtgtac acagcagcac tcaaggacga gctagtcaag
4081 actgagaaaa tctatggaaa gatcaagaag agactgctct ggggctctga cttgtccacc
4141 atgatccggt gcgctaggtc atttggtggg ctcatggacg agatgaaggc acactgtata
4201 tcactcccag tgcgagttgg catgaatatg aatgaagatg gcccaataat atttgagaaa
4261 cactctaggt acaaatatca ctatgatgca gattattctc gttgggattc aacacaacaa
4321 agggcagtgt tagcagcagc cttggaaatt atggtcagat tctctgcaga accacaattg
4381 gcacaaatag tcgctgagga tctactggcc cctagtgtag tagatgtagg agactttaaa
4441 attgcaataa atgaagggct cccatctggc gtgccatgca cttctcaatg gaactccatt
4501 gcacactggc tgctaactct ctgtgccttg tctgaagtca ccaaactgtc ccctgacatt
4561 atacaagcaa attccatgtt ctcattttac ggtgatgacg agattgtcag caccgacata
4621 aaattagacc ctgaacagtt gaccgccaag ttgaaggagt acggcctgaa accaacccgc
4681 ccagacaaga ctgagggacc tctgatcatc agtgaagatt tggacggact cactttcctc
4741 cgaaggacgg tgactcgtga cccagctggc tggtttggaa aactggacca aagttcgatt
4801 ttgaggcaga tgtattggac tagaggacca aatcatgaag accccaatga gacaatgata
4861 ccccattccc agaggcccat acagctcatg gcactgcttg gtgaagcctc tcttcacgga
4921 ccctctttct acagtagaat cagtaaattg gttataactg aactcaaaga aggtgggatg
4981 gacttttacg tgccaaggca ggaacccatg ttcaggtgga tgaggttctc tgacttgagc
5041 acgtgggagg gcgatcgcaa tctggctccc aactttgtga atgaagatgg cgtcgaatga
5101 cgccaaccca tctgatgggt ccgcagccaa cctcgtacca gaggtcaaca atgaggttat
5161 ggctttggag cccgttgttg gtgccgctat tgcggcaccc gtagcgggcc aacaaaatgt
5221 aattgacccc tggattagaa ataattttgt acaagcccct ggtggggaat tcacagtatc
5281 ccctagaaat gctccaggtg aaatactgtg gagcgcaccc ttaggccctg acctaaatcc
5341 ctacctatcc catttggcca gaatgtacaa tggttatgca ggtggtttcg aagtgcaggt
5401 aattctcgcg gggaacgcgt tcaccgcagg gaagattata tttgcagcag tcccaccaaa
5461 ttttccaact gaaggcttaa gccctagcca ggtcaccatg tttccccata taatagtaga
5521 tgttagacaa ttggaacctg tgctgatccc cttacccgat gttaggaata atttctatca
5581 ttacaatcag tcaaatgact ccactatcaa gctgatagca atgttgtaca caccacttag
5641 ggctaataat gctggggatg atgttttcac agtttcgtgc cgagttctca cgagaccatc
5701 ccccgatttt gattttatat tcttagtacc acccacagtt gagtcaagaa ctaaaccatt
5761 ctctgtccca attttaactg ttgaggagat gaccaattca agattcccca tccctttgga
5821 aaagttgttc acaggcccca gcagtgcatt tgttgttcaa ccacaaaacg gcagatgcac
5881 aactgatggc gtgctcctag gtaccaccca actttctcct gtcaatatct gcaccttcag
5941 aggggacgtc acccatatca caggtagtca caacttcact atgaatttgg cttctcaaaa
6001 ttggaacaac tatgacccaa cagaagaaat cccagccccc ctaggaactc cagattttgt
6061 ggggaagatc caaggcatgc tcacccaaac cacaaggaca gatggttcaa cacgcggcca
6121 caaagctaca gtgtacactg ggagtgccga ctttgctcca aaactgggta gagttcaatt
6181 tgaaactgac acaaaccatg actttgaagc caatcagaac acaaagttca ccccagtcgg
6241 tgtcattcaa gatggtagca ccacccaccg aaacgaaccc caacagtggg tgctcccaag
6301 ttactcaggc agaaatactc acaatgtaca tttggccccc gctgtagccc ccacctttcc
6361 gggtgaacaa ctcctcttct ttagatccac catgcccgga tgcagcgggt accccaacat
6421 ggatttggac tgtctgctcc cccaggaatg ggtgcagtac ttctaccaag aggcagcccc
6481 agcacaatct gatgtggctc tgctaagatt tgtaaaccca gacacaggta gggttctgtt
6541 tgagtgcaag cttcacaaat caggctatgt tacagtggct cacactggtc aacatgattt
6601 ggttatcccc cccaatggtt acttcaggtt tgattcctgg gtcaaccagt tctacacgct
6661 tgcccccatg ggaaatggaa cggggcgtag acgtgcagta taatggctgg agctttcttt
6721 gctggattgg catctgatgt ccttggctcc ggacttggtt ctcttatcaa tgctggggct
6781 ggggccatca accaaaaagt tgagtttgaa aataacagaa aattgcaaca agcatccttc
6841 caatttagca gcaatttgca acaggcttcc tttcaacatg ataaagagat gctccaagca
6901 caaattgagg ccaccaaaaa gctacagcag gaaatgatga gagttaagca ggcaatgctc
6961 ttagagggtg ggttctctga gacagatgca gcccgcgggg caattaacgc ccccatgaca
7021 aaggctttgg actggagcgg gacaaggtac tgggctccag atgctagaat tacaacatac
7081 aatgcaggcc acttttccac ccctcaacca tcgggggcac tgccaggaag agctaatctc
7141 agggatgctg tccctgctcg tgggccctcc accaaacctt ctaactctcc tactgccact
7201 tctgtgcact caaaccaaac tgtttcaacg agacttggtt ctacagctgg ttctggaact
7261 agtgtctcga gcctcccgtc aactgcaaga actaggagct gggttgagga tcagaatagg
7321 agtttgtcac ctttcatgaa gggggcctac aacatatcat ttgtcacccc accatctagc
7381 agatcctcta gccagggcac agtctcaacc gtgcccaaag aaattttgga ctcctggact
7441 ggcgctttca acacgcgcag gcagcctctc ttcgctcaca ttcgtaagcg aggggagtca
7501 cgggcgtaat gtgaaaagac aaaa
//