Typing tool
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Typing tool
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Complete norovirus genomes
| PQ196516 | GII.4 Sydney | |
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| GII.P16 |
ORF1: 1..5100
ORF2: 5081..6703
ORF3: 6703..7509
LOCUS PQ196516 7524 bp RNA linear VRL 27-MAR-2025
DEFINITION Norovirus GII isolate Hu/GII.4
Sydney[P16]/SantaBarbara0198/2023/USA nonstructural polyprotein
(ORF1), VP1 (ORF2), and VP2 (ORF3) genes, complete cds.
ACCESSION PQ196516
VERSION PQ196516.1
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]/SantaBarbara0198/2023/USA"
/isolation_source="stool"
/host="Homo sapiens"
/db_xref="taxon:122929"
/geo_loc_name="USA"
/collection_date="10-May-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="XEJ39576.1"
/translation="MKMASNDASAAVACNNNNDKEKSSGEGLFTNMSSTLKKALGARP
KQPAPRGGPQKPPRPPTPELVKRIPPPPPNGEEEEEPVIRYEVKSGISGLPELTTVPQ
PDVANTAFSVPPLSLRENREAKEPLTGAILEMWDGEIYHYGLYVEKGLVLGVHKPPAA
ISMARVELAPLSLYWRVVYTPQYLISPETLRRLNGEAFPYTAFDNNCYAFCCWVLDLN
DSWLSRRMVQRTTGFFRPYQEWNRKPLPTMDDSKIKKVANIFLCSLSTLFTRPIKDLI
GKIKPLNILNILATCDWTFAGIVESLILLAELFGVFWTPPDVSAMIAPLLGDYELQGP
EDLAVELVPVVMGGIGLVLGFTKEKIGKMLSSAASTLRACKDLGAYGLEILKLVMKWF
FPKKEEANELAMVRAIEDAVLDLEAIENNHMTTLLKDKDSLATYMKTLDMEEEKARRL
STKSASPDIVGTINALLARIAAARSLVHRAKEELSSRIRPVVVMISGKPGIGKTHLAR
EVARKVASTLTGDQRVGLIPRNGVDHWDAYKGERVVLWDDYGMSNPIHDALRIQELAD
TCPLTLNCDRIENKGKVFDSEVIIITTNLANPAPLDYVNFEACSRRIDFLVYAEAPEV
EKAKRDFPGQPDMWKDAFKPDFSHIKLQLAPQGGFDKNGNTPHGKGVMKTLTTGSLIA
RASGLLHERMDEFELQGPTTTTFNFDRNRITAFRQLAAENKYGLVDTMKVGNQLKGVK
TMEELKQAIRNVTIKRCRIIYGGSTYDLESDGKGKVLVEKVKNTSIQTNNELAGALHH
LKHARIRYYVKCVQEAVYSIIQIAGAAFVTTRIARRMNIQELWSKPQLDQNESETKEE
TPKPEEDEFIISSKDIKEEGKKGKNKTGRGKKHTAFSSKGLSDEEYDEYKRIREERNG
KYSIEEYLQDRDRYYEELAIAKATEEDFCEEEEIKIRQRIFRPTRKQRKEERATLGLV
TGSEIRRRNPDDFKPKGKLWADDNRSVDYNEKLDFEAPPSIWSRIVSFGSGWGFWVSP
SLFITSTHVIPAGITEAFGVPIKQIQIHKSGEFCRFRFPKPIRPDVTGMILEEGAPEG
TVATVLIKRPTGELMPLAARMGTHATMKIQGRMVGGQMGMLLTGSNAKGMDLGTTPGD
CGCPYIYKRGNDYIVIGVHTAAARGGNTVICATQGSEGEATLEGGDDKGTYCGAPILG
PGGAPKLSTKTKFWRSSNTPLPPGTYEPAYLGGRDPRVKGGPSLQQVMRDQLKPFTEP
RGKPPRPSVLEAAKQTIINVLEQTLDPPQKWTYAQACASLDKTTSSGHPHHVRKNEFW
NGETFTGKLADQASKANLMFEEGKHMTPVYTAALKDELVKTEKIYGKVKKRLLWGSDL
STMIRCARSFGGLMDEMKAHCISLPVRVGMNMNEDGPIIFEKHSRYKYHYDADYSRWD
STQQRAVLAAALEIMVRFSAEPQLAQIVAEDLLAPSVVDVGDFKITINEGLPSGVPCT
SQWNSIAHWLLTLCALSEVTKLSPDIIQANSLFSFYGDDEIVSTDIKLDPEQLTAKLK
EYGLKPTRPDKTEGPLIISEDLNGLTFLRRTVTRDPAGWFGKLDQSSILRQMYWTRGP
NHEDPNETMIPHSQRPIQLMALLGEASLHGPSFYSRISKLVIAELKEGGMDFYVPRQE
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="XEJ39577.1"
/translation="MKMASSDANPSDGSAANLVPEVNNEVMALEPVVGAAIAAPVAGQ
QNVIDPWIRSNFVQAPGGEFTVSPRNAPGEILWSAPLGPDLNPYLSHLARMYNGYAGG
FEVQVILAGNAFTAGKIISAAVPPNFPTEGLSPSQVTMFPHIIVDVRQLEPVLIPLPD
VRNNFYHYNQSNDSTIKLIAMLYTPLRANNAGDDVFTVSCRVLTRPSPDFDFIFLVPP
TVESRTKPFSVPVLTVEEMTNSRFPIPLEKLFTGPSSAFVVQPQNGRCTTDGVLLGTT
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="XEJ39578.1"
/translation="MAGAFFAGLASDVLGSGLGSLINAGAGAINQKVEFENNRKLQQA
SFQFSSNLQQASFQHDKEMLQAQIEATKKLQQEMMRVKQAMLLEGGFSETDAARGAIN
APMTKALDWSGTRYWAPDARITTYNAGHFSTPQPSGALPGRANLRDAAPARGPSTKPS
NFSTATSVYSNQTISTRLGSTAGSGTSVSSLPSTARTRSWVEDQNRNLSPFMRGAHNI
SFVTPPSSRSSSQGTVSTVPKEILDSWTGAFNTRRQPLFAHIRKRGESRV"
ORIGIN
1 atgaagatgg cgtctaacga cgcttccgct gccgttgctt gcaacaacaa caacgacaag
61 gaaaaatctt caggtgaagg cttattcaca aatatgtctt ccaccttaaa gaaagccctc
121 ggggctaggc ccaaacagcc tgccccgaga ggtggaccac aaaagccccc aagaccacca
181 actcccgagt tggtcaagag gataccccct cctccaccta atggcgaaga agaagaagaa
241 ccagtcatta ggtatgaggt taagagtggg atctctggcc tgcccgagct cacaacagtc
301 ccccaaccgg acgtggccaa cacagcattt agtgttccac cactgagctt gagagaaaac
361 agggaggcca aggaaccgct gacaggggca atactagaga tgtgggacgg agagatatac
421 cactatggcc tgtacgtgga gaaaggctta gtgttgggtg tgcacaaacc acctgcagcc
481 ataagcatgg caagagtgga gctggcaccg ctgtcattgt attggcgtgt ggtgtacact
541 ccccaatacc tcatctcccc tgagactctc aggaggctca acggagaggc gtttccttac
601 accgcttttg acaacaactg ctacgctttt tgctgctggg tgttagacct caatgactca
661 tggcttagca ggaggatggt gcaacgaacc acgggcttct tcaggcctta ccaagagtgg
721 aacagaaaac ccctacccac catggatgac tccaaaataa agaaggtagc aaatatattc
781 ctatgttcat tgtccacatt attcaccaga cccataaaag acctcatagg aaaaattaaa
841 ccattaaaca tattgaacat cctggcaacg tgtgattgga cgtttgccgg aatagtggag
901 tctctgatat tgcttgccga actcttcgga gttttctgga cacccccaga tgtgtctgct
961 atgatcgctc ccttacttgg ggattacgag ttgcaggggc cagaggacct cgccgttgaa
1021 ctcgtacctg tggtaatggg agggattggt ttggtgttgg gattcaccaa agagaaaatt
1081 ggcaaaatgt tgtcctcagc agcatcaaca ctcagggctt gtaaagatct tggtgcctat
1141 ggcttagaga tactcaaatt ggtcatgaag tggtttttcc caaagaaaga agaggccaat
1201 gagctagcta tggtgagggc catagaggat gccgtactag atcttgaggc aatagaaaac
1261 aaccacatga caaccctgtt gaaagacaaa gacagcttag caacatacat gaaaacactg
1321 gacatggagg aggagaaagc cagaaggttg tccacaaaat ctgcatcccc tgacatagtt
1381 gggacaatca acgccctgct ggctcgaata gcagcagcca ggtcattagt ccacagggcc
1441 aaggaagaac tgtctagcag gataagacca gtagttgtta tgatatctgg caaaccagga
1501 ataggcaaaa ctcatctagc cagagaggtg gcaagaaagg tggcatccac tctcacaggg
1561 gatcaaagag tcggactcat accaagaaac ggtgtggacc attgggatgc 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 attttctggt gtacgctgag
1861 gcaccagaag tagaaaaggc aaaacgggat tttcctggtc agccagatat gtggaaggac
1921 gccttcaagc cggacttttc gcacatcaag ctacagcttg cacctcaggg cggctttgac
1981 aagaatggta acaccccaca tgggaaaggg gtgatgaaga ccctcactac cggttctctg
2041 attgcccgtg catcaggcct actgcacgag aggatggatg agtttgaact ccaaggtccc
2101 acaaccacca ctttcaactt cgaccggaac agaatcacag cattcagaca attggctgca
2161 gaaaacaagt atggactggt ggacaccatg aaagttggca atcaactaaa aggagtgaaa
2221 accatggaag aactcaaaca agcaatcagg aatgtgacca tcaagaggtg ccggatcatc
2281 tacggtggct ccacgtatga ccttgaatct gatggcaagg gcaaagtttt ggtcgaaaag
2341 gtcaagaaca cctctataca gaccaacaac gagttggccg gggccctgca tcatctcaaa
2401 catgcccgaa tcaggtacta tgtcaaatgt gtgcaagaag cagtctattc catcatacaa
2461 attgccggcg ctgcgtttgt caccacgcgc attgcacgcc gcatgaacat acaagagctc
2521 tggtcgaagc cacaattaga tcaaaatgaa tcagagacta aggaagagac ccccaagcca
2581 gaagaagacg agttcatcat atcttctaag gatatcaagg aggaaggaaa gaagggcaaa
2641 aacaaaactg gccgtggcaa gaaacacacc gcattctcca gcaagggttt aagcgatgag
2701 gagtatgacg agtacaagag gataagagaa gagagaaatg ggaagtactc tatagaagag
2761 tatcttcaag acagagacag gtattatgag gagctcgcca ttgccaaggc cacggaagaa
2821 gacttctgtg aagaggagga gatcaaaata cgccagagaa ttttccgtcc caccaggaaa
2881 caaagaaagg aagagagggc cacactaggg ctggtaacag gttcagaaat cagaagaaga
2941 aaccctgacg atttcaaacc caaagggaag ctgtgggccg atgacaacag aagtgttgac
3001 tacaatgaga aactggattt tgaggccccc ccaagcatat ggtctaggat tgtgagcttt
3061 ggttctggct ggggcttctg ggtatcacca agcctgttca taacatcaac tcatgtgatc
3121 cctgcaggca taacagaagc atttggagtc cccatcaaac agattcagat ccacaaatca
3181 ggtgaatttt gccgattcag attcccaaaa ccaatcagac cagatgtgac aggaatgatc
3241 ttggaagaag gtgcgcctga aggcaccgtg gcaactgtgc tcatcaaacg ccccaccgga
3301 gagctcatgc cccttgcagc tagaatggga acacacgcaa ccatgaagat tcaaggccgc
3361 atggttggtg gacagatggg tatgctgctc actggatcaa atgccaaagg gatggatttg
3421 ggaacaactc ctggtgactg tggctgccct tacatctata aaaggggcaa tgactatata
3481 gtcattgggg tgcacaccgc agcagcccgt ggtggaaaca ccgtcatctg tgccacacag
3541 ggaagtgagg gtgaggcaac tcttgaaggt ggagatgaca aaggaacata ctgtggggca
3601 cccattctag gccctggggg tgcaccaaaa ttgagcacta aaaccaaatt ttggaggtca
3661 tcgaacacgc cccttccacc agggacgtac gaacctgcct acctcggtgg ccgtgacccg
3721 cgtgttaagg gtgggccctc attacaacag gtaatgagag accagttgaa gccattcact
3781 gaacccaggg gcaaacctcc aagaccaagt gttttggaag cagccaaaca aaccattatc
3841 aatgtccttg aacaaaccct ggatcctcca caaaagtgga catacgcaca ggcgtgtgcc
3901 tcacttgaca aaactacctc cagcgggcat ccccaccatg tccgaaagaa tgaattctgg
3961 aatggtgaga ccttcactgg taaactggca gaccaagcat caaaagcaaa cctaatgttt
4021 gaggaaggga aacacatgac accagtgtac acagcagcac tcaaggacga gctagtcaag
4081 actgagaaaa tctatggaaa ggtcaagaag aggctgctct ggggctctga cttgtccacc
4141 atgatccggt gcgctaggtc atttggtggg ctcatggacg agatgaaggc gcactgcata
4201 tcactcccag tacgagttgg catgaacatg aatgaagatg gcccaataat atttgagaaa
4261 cattccaggt acaaatatca ctatgatgca gactactctc gttgggattc aacacagcag
4321 agggcagtat tagcagcagc cttggaaatt atggtcagat tctctgcaga accacaattg
4381 gcacaaatag tcgctgagga tctactggcc cctagtgtag tagatgtagg agactttaaa
4441 attacaataa atgaagggct cccatctggc gtgccatgca cttctcaatg gaactccatt
4501 gcacactggc tgctaactct ctgtgccttg tctgaagtca ccaaactgtc ccctgacatt
4561 atacaagcaa attccttgtt ctcattttac ggtgatgacg agattgtcag caccgacata
4621 aaattggacc ctgaacagtt gaccgccaag ttgaaggagt acggcctgaa accaacccgc
4681 ccagacaaga ccgagggacc tctgattatc agtgaagatt tgaacggact cactttcctc
4741 cgaaggacgg tgactcgtga cccagctggc tggtttggaa aactggacca aagttcaatt
4801 ttgaggcaga tgtactggac tagaggacca aatcatgaag accccaatga gacaatgata
4861 ccccattctc agaggcccat acagctcatg gcactgcttg gtgaagcctc tcttcacgga
4921 ccctctttct acagtagaat cagtaaattg gtcatagctg aacttaaaga aggtgggatg
4981 gacttttacg tgccaaggca ggaacccatg ttcaggtgga tgaggttctc tgacttgagc
5041 acgtgggagg gcgatcgcaa tctggctccc aactttgtga atgaagatgg cgtcgagtga
5101 cgccaaccca tctgatgggt ccgcagccaa cctcgtacca gaggtcaaca atgaggttat
5161 ggctttggaa cccgttgttg gtgccgctat tgcggcacct gtagcgggcc aacaaaatgt
5221 aattgacccc tggattagaa gtaattttgt acaagctcct ggtggggagt ttacagtatc
5281 ccctagaaat gctccaggtg aaatactatg gagcgcgccc ctaggtcctg acctaaatcc
5341 ctacctatcc catttggcca gaatgtacaa tggttatgca ggtggttttg aagtgcaggt
5401 aattctcgcg gggaacgcgt tcaccgccgg gaagattata tctgcagcag tcccaccaaa
5461 tttcccaact gaaggcttaa gccctagtca ggtcactatg tttccccata taatagtaga
5521 tgttagacaa ttggaacctg tgctgatccc cttacccgat gttaggaata acttctatca
5581 ttacaatcag tcaaatgact ccactattaa gttgatagcg atgttgtaca caccacttag
5641 ggctaataat gctggagatg atgttttcac agtttcgtgc cgagttctca cgagaccatc
5701 ccccgatttt gatttcatat tcttagtacc acctacagtt gagtcaagaa ctaaaccatt
5761 ctctgtccca gttttaactg ttgaggagat gaccaattca agattcccca tccctttgga
5821 aaagttgttc acaggcccca gcagtgcatt tgttgttcaa ccacaaaacg gcagatgcac
5881 aactgatggc gtgctcctag gcaccaccca actttctcct gtcaacatct gcaccttcag
5941 gggggacgtc acccacatca caggcagtca caacttcact atgaatttgg cttctcaaaa
6001 ttggaacaac tatgacccaa cagaagaaat cccagccccc ctaggaactc cagattttgt
6061 ggggaagatc caaggcatgc tcacccaaac cacaaggaca gatggttcaa cacgcggcca
6121 caaagctaca gtgtacactg ggagcgccga ctttgctcca aaactgggta gagtccaatt
6181 tgaaactgac acaaaccatg actttgaagc taatcaaaac acaaagttca ccccagtcgg
6241 tgtcattcaa gatggcagca ccacccaccg aaacgaaccc caacagtggg tgctcccaag
6301 ttactcaggc agaaacactc acaatgtaca tttggccccc gctgtagccc ccacctttcc
6361 gggtgagcaa ctcctcttct tcagatccac catgcccgga tgcagcgggt atcccaacat
6421 ggatttggac tgtctgctcc cccaggaatg ggtgcagtac ttctaccaag aggcagcccc
6481 agcacaatct gatgtggctc tgctaagatt tgtgaatcca gacacaggta gggttctgtt
6541 tgagtgcaag cttcacaaat caggctatgt tacagtggct cacactggcc aacatgattt
6601 ggttatcccc cccaatggtt actttaggtt tgattcctgg gtcaaccagt tctacacgct
6661 tgcccccatg ggaaatggaa cggggcgtag acgtgcagta taatggctgg agctttcttt
6721 gctggattgg catctgatgt ccttggctct ggacttggtt cccttatcaa tgctggggct
6781 ggggccatca accaaaaagt tgagtttgaa aataacagaa aattgcaaca agcatccttc
6841 caatttagca gcaatttgca acaggcttcc tttcaacatg ataaagagat gctccaagca
6901 caaattgagg ccaccaaaaa gctacagcag gaaatgatga gagttaagca ggcaatgctc
6961 ctagagggtg ggttctctga gacagatgca gcccgcgggg caattaacgc ccccatgaca
7021 aaggctttgg actggagcgg aacaaggtac tgggctccag atgctagaat tacaacatac
7081 aatgcaggcc acttttccac ccctcaacca tcgggggcac tgccaggaag agctaatctt
7141 agggatgctg cccctgctcg tggaccctcc accaaacctt ctaacttttc tactgccacc
7201 tctgtgtact caaatcaaac tatttcaacg agacttggtt ctacagctgg ttctggaacc
7261 agtgtctcga gcctcccgtc aactgcaaga actaggagct gggttgagga tcagaatagg
7321 aatttgtcac ctttcatgag gggggcccac aacatatcat ttgtcacccc accatctagc
7381 agatcctcta gccaaggcac agtctcaacc gtgcctaaag aaattttgga ctcctggact
7441 ggcgctttca acacgcgcag gcagcctctc ttcgctcaca ttcgtaagcg aggggagtca
7501 cgggtgtaat gtgaaaagac aaaa
//