Typing tool
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Typing tool
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Complete norovirus genomes
| PP658559 | GII.4 Sydney | |
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| GII.P16 |
ORF1: 4..5103
ORF2: 5084..6706
ORF3: 6706..7512
LOCUS PP658559 7526 bp RNA linear VRL 01-JUN-2024
DEFINITION Norovirus GII isolate PBH23425-STN nonstructural polyprotein
(ORF1), VP1 (ORF2), and VP2 (ORF3) genes, complete cds.
ACCESSION PP658559
VERSION PP658559.1
KEYWORDS .
SOURCE Norovirus GII
ORGANISM Norovirus GII
Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes;
Picornavirales; Caliciviridae; Norovirus; Norovirus norwalkense.
REFERENCE 1 (bases 1 to 7526)
AUTHORS Doungngern,P., Pittayawong-anont,C., Kraipatanapong,S.,
Waikhruea,K., Menkoon,K., Rattanatumhi,K., Supataragul,A.,
Thippamom,N., Khunnawutmanotham,W., Hirunpatrawong,P.,
Wacharapluesadee,S., Sereewit,J., Sobolik,E.B., Roychoudhury,P.,
Greninger,A.L. and Putcharoen,O.
TITLE Direct Submission
JOURNAL Submitted (13-APR-2024) Virology, University of Washington, 850
Republican St, Seattle, WA 98109, USA
COMMENT ##Assembly-Data-START##
Assembly Method :: Geneious v. 2023; metaspades v. 2024
Sequencing Technology :: Illumina
##Assembly-Data-END##
FEATURES Location/Qualifiers
source 1..7526
/organism="Norovirus GII"
/mol_type="genomic RNA"
/isolate="PBH23425-STN"
/isolation_source="Rectal swab"
/host="Homo sapiens"
/db_xref="taxon:122929"
/geo_loc_name="Thailand"
/collection_date="2023-06-21"
/note="genotype: GII"
gene 4..5103
/gene="ORF1"
CDS 4..5103
/gene="ORF1"
/codon_start=1
/product="nonstructural polyprotein"
/protein_id="WZF77178.1"
/translation="MKMASNDATVAVACNNNNDKEKSSGEGLFTNMSSTLKKALGARP
KQPAPRDKPQKPPRPPTPELVKRIPPPPPNGEEEEEPVIRYEVKSGISGLPELTTVPQ
PDVANTAFSVPPLSLRENREAKEPLTGAILEMWDGEIYHYGLYVEKGLVLGVHKPPAA
ISMARVELTPLSLYWRVVYTPQYLISPETLRRLNGEAFPYTAFDNNCYAFCCWVLDLN
DSWLSRRMVQRTTGFFRPYQEWNRKPLPTMDDSKIKKVANIFLCSLSTLFTRPIKDLI
GKIKPLNILNILATCDWTFAGIVESLILLAELFGVFWTPPDVSAMIAPLLGDYELQGP
EDLAVELVPVVMGGIGLVLGFTKEKIGKMLSSAASTLRACKDLGAYGLEILKLVMKWF
FPKKEEANELAMVRAIEDAVLDLEAIENNHMTTLLKDKDSLATYMKTLDMEEEKARRL
STKSASPDIVGTINALLARIAAARSLVHRAKEELSSRIRPVVVMISGKPGIGKTHLAR
EVARKVASTLTGDQRVGLIPRNGVDHWDAYKGERVVLWDDYGMSNPIHDALRIQELAD
TCPLTLNCDRIENKGKVFDSEVIIITTNLANPAPLDYVNFEACSRRIDFLVYAEAPEV
EKAKRDFPGQPDMWKDAFKPDFSHIKLQLAPQGGFDKNGNTPHGKGVMKTLTTGSLIA
RASGLLHERMDEFELQGPTITTFNFDRNRIAAFRQLAAENKYGLVDTMKVGNQLKGVK
TMEELKQAIRNVTIKRCRIIYGGSTYELESDGKGKVLVEKVKNTSVQTNNELAGALHH
LKHARIRYYVKCVQEAVYSIIQIAGAAFVTTRIARRMNIQELWSKPQLDQSEPETKEE
ALKSEDDEFVISSKDIKEEGKKGKNKTGRGKKHTAFSSKGLSDEEYDEYKRIREERNG
KYSIEEYLQDRDRYYEELAIAKATEEDFCEEEEIKIRQRIFRPTRKQRKEERATLGLV
TGSEIRKRNPDDFKPKGKLWADDNRSVDYNEKLDFEAPPSIWSRIVSFGSGWGFWVSP
SLFITSTHVIPAGITEAFGVSIKQIQIHKSGEFCRFRFPKPIRPDVTGMILEEGAPEG
TVATVLIKRPTGELMPLAARMGTHATMKIQGRMVGGQMGMLLTGSNAKGMDLGTTPGD
CGCPYIYKRGNDYIVIGVHTAAARGGNTVICATQGSEGEATLEGGDDKGTYCGAPILG
PGGAPKLSTKTKFWRSSNTPLPPGTYEPAYLGGRDPRIKGGPSLQQVMRDQLKPFTEP
RGKPPRPSVLEAAKQTIINVLEQTLDPPQKWTYAQACASLDKTTSSGNPHHVRKNEFW
NGETFTGKLADQASKANLMYEEGKHMTPVYTAALKDELVKTEKIYGKIKKRLLWGSDL
STMVRCARSFGGLMDEMKAHCISLPVRVGMNMNEDGPIIFEKHSRYKYHYDADYSRWD
STQQRAVLAAALEIMVRFSAEPQLAQIVAEDLLAPSVVDVGDFKITINEGLPSGVPCT
SQWNSIAHWLLTLCALSEVTKLSPDIIQANSMFSFYGDDEIVSTDIKLDPEQLTAKLK
EYGLKPTRPDKTEGPLIISEDLDGLTFLRRTVTRDPAGWFGKLDQSSILRQMYWTRGP
NHEDPNETMIPHSQRPIQLMALLGEASLHGPSFYSKISKLVITELKEGGMDFYVPRQE
PMFRWMRFSDLSMWEGDRNLAPNFVNEDGVE"
mat_peptide 4..999
/gene="ORF1"
/product="p48"
mat_peptide 1000..2097
/gene="ORF1"
/product="NTPase"
mat_peptide 2098..2628
/gene="ORF1"
/product="p22"
mat_peptide 2629..3027
/gene="ORF1"
/product="VPg"
mat_peptide 3028..3570
/gene="ORF1"
/product="Pro"
mat_peptide 3571..5100
/gene="ORF1"
/product="RdRp"
gene 5084..6706
/gene="ORF2"
CDS 5084..6706
/gene="ORF2"
/note="major capsid protein"
/codon_start=1
/product="VP1"
/protein_id="WZF77179.1"
/translation="MKMASSDANPSDGSAANLVPEVNNEVMALEPVVGAAIAAPVAGQ
QNVIDPWIRNNFVQAPGGEFTVSPRNAPGEILWSAPLGPDLNPYLSHLARMYNGYAGG
FEVQVILAGNAFTAGKIIFAAVPPNFPTEGLSPSQVTMFPHIIVDVRQLEPVLIPLPD
VRNNFYHYNQSNDSTIKLIAMLYTPLRANNAGDDVFTVSCRVLTRPSPDFDFIFLVPP
TVESRTKPFSVPVLTVEEMTNSRFPIPLEKLFTGPSSAFVVQPQNGRCTTDGVLLGTT
QLSPVNICTFRGDVTHITGSHNYTMNLASQNWNNYDPTEEIPAPLGTPDFVGKIQGML
TQTTRTDGSTRGHKATVYTGSADFAPKLGRVQFETDTNHDFEANQNTKFTPVGVIQDG
STTHRNEPQQWVLPSYSGRNTHNVHLAPAVAPTFPGEQLLFFRSTMPGCSGYPNMDLD
CLLPHEWVQYFYQEAAPAQSDVALLRFVNPDTGRVLFECKLHKSGYVTVAHTGQHDLV
IPPNGYFRFDSWVNQFYTLAPMGNGTGRRRAV"
gene 6706..7512
/gene="ORF3"
CDS 6706..7512
/gene="ORF3"
/note="minor structural protein; small basic protein"
/codon_start=1
/product="VP2"
/protein_id="WZF77180.1"
/translation="MAGAFFAGLASDVLGSGLGSLINAGAGAINQKVEFENNRKLQQA
SFQFSSNLQQASFQHDKEMLQAQIEATKKLQQEMMRVKQAMLLEGGFSETDAARGAIN
APMTKALDWSGTRYWAPDARITTYNAGHFSTPQPSGALPGRANFRDAVPARGPSTRLS
NSSTATSVYSNQTISTRLGSTAGSGTSVSSLPSTARTRSWVEDQNKNLSPFMRGAHNI
SFVTPPSSRSSSQGTVSTVPKEILDSWTGAFNTRRQPLFAHIRKRGESRV"
ORIGIN
1 tgaatgaaga tggcgtctaa cgacgctacc gttgccgttg cttgcaacaa caacaacgac
61 aaggaaaaat cttcaggtga aggcttattc acaaatatgt cttccacctt aaagaaagcc
121 ctcggggcta ggcccaaaca gcctgccccg agagacaaac cacaaaagcc cccaagacca
181 ccaactcctg agttggtcaa gaggataccc cctcctccac ctaatggcga agaagaagaa
241 gaaccagtca ttaggtatga ggttaagagc ggaatctctg gcctgcccga gctcacaaca
301 gtcccccaac cggatgtggc caacacagca ttcagtgttc caccactgag cttgagagaa
361 aacagggagg ccaaggaacc gctaacaggg gcaatattag agatgtggga tggagagata
421 taccactatg gcctatacgt ggagaaaggc ctagtgttgg gtgtgcacaa accacctgca
481 gccataagca tggcaagagt ggaactgacg ccgctgtcat tatactggcg tgtagtgtac
541 actccccaat acctcatctc ccctgaaact cttaggaggc tcaacggaga ggctttccct
601 tacaccgcct ttgacaacaa ctgctatgcc ttttgttgct gggtgctaga cctcaacgac
661 tcatggctta gcaggagaat ggtgcagaga acaacgggct tcttcagacc ttaccaagag
721 tggaacagaa aacccctgcc taccatggat gactccaaaa ttaagaaggt ggcaaacata
781 ttcctatgtt cattgtctac attattcacc aggcccataa aagatctcat aggaaaaatt
841 aaaccattaa atatattgaa cattctggca acgtgtgact ggacgtttgc tgggatagtg
901 gagtctctaa tattacttgc tgaactcttc ggagttttct ggacaccccc agatgtgtct
961 gctatgatcg ctcccttgct cggggactac gagttgcagg ggccagagga cctcgccgtt
1021 gaactcgtgc ctgtggtaat gggagggatt ggtttggtgt tgggattcac caaagagaaa
1081 attggcaaaa tgttgtcttc agcagcatca acactcaggg cttgcaaaga tcttggtgcc
1141 tatggcttag agatactaaa attggtcatg aagtggttct tcccaaagaa agaggaggcc
1201 aatgagctag ccatggtgag ggccatagag gatgctgtac tagatcttga ggcaatagaa
1261 aataaccaca tgacaaccct gttgaaagac aaagacagcc tagcaacata catgaagaca
1321 ctagacatgg aggaggagaa agccagaaga ttgtccacaa aatctgcatc ccctgacata
1381 gttgggacaa tcaacgccct actggctcga atagcagcgg ccaggtcatt agtccacagg
1441 gccaaggaag agctatctag caggataaga ccagtagttg ttatgatatc tggcaaacca
1501 ggaataggca aaactcatct ggccagggag gtggcaagaa aggtggcttc cactcttaca
1561 ggggaccaga gagtcggact cattccaaga aacggtgtgg accattggga tgcatacaaa
1621 ggcgagagag tcgtgctgtg ggacgactat ggcatgagta atcccatcca tgatgctctt
1681 cgcatacaag aattggctga tacgtgtccc ctcaccttaa attgtgacag aattgaaaac
1741 aaaggaaaag tttttgacag tgaagtcata ataattacaa caaaccttgc caacccagcc
1801 ccacttgatt atgtcaactt tgaggcttgc tccaggagaa ttgacttcct ggtgtacgct
1861 gaggcaccag aagtagagaa ggcaaagcgg gacttccctg gtcagccaga tatgtggaag
1921 gacgccttca agccggactt ttcacacatc aagctgcaac ttgcacctca gggcggcttt
1981 gacaagaatg gcaacacccc acatgggaaa ggagtgatga agaccctcac taccggctct
2041 ctgatcgctc gtgcatcagg cctactgcat gagaggatgg atgaatttga actccaaggc
2101 cccacaatca ccaccttcaa tttcgaccgg aacagaatcg cagcattcag acaactggct
2161 gcagaaaaca agtatggatt agtggacacc atgaaagttg gcaaccaatt aaaaggagtg
2221 aaaaccatgg aagaactcaa acaagcaatc aggaatgtga ccatcaagag gtgccggatc
2281 atttacggtg gctctacgta tgaacttgaa tctgacggca agggcaaagt tttggtggaa
2341 aaggtcaaga acacctctgt acagaccaac aacgagttgg ccggggcctt gcaccatctc
2401 aaacacgccc gaatcagata ctatgtcaaa tgcgtgcaag aagcagtcta ttccatcata
2461 caaattgccg gcgctgcgtt tgtcaccacg cgcattgcac gccgcatgaa catacaagaa
2521 ctctggtcga agccacaatt agatcaaagt gaaccagaga ctaaggaaga ggccctcaag
2581 tcagaagacg acgagttcgt catatcttct aaggacatca aggaggaagg aaagaagggc
2641 aaaaataaaa ctggccgtgg caagaaacac actgcattct ccagcaaggg cttgagtgat
2701 gaggagtatg acgagtataa gaggataaga gaagagagaa atgggaagta ctctatagag
2761 gagtatcttc aagacagaga caggtactat gaagagctcg ccattgccaa ggccacggaa
2821 gaagacttct gtgaagagga ggagatcaaa atccgtcaga gaattttccg tcccaccagg
2881 aaacaaagaa aggaagagag ggccacatta gggctagtaa cgggttcaga aatcagaaag
2941 agaaaccctg atgacttcaa acccaaaggg aagctgtggg ccgatgacaa cagaagtgtt
3001 gactacaatg aaaaactgga ctttgaggcc cccccaagca tatggtctag gatcgtgagt
3061 tttggttctg gctggggctt ctgggtatca ccaagcctgt ttataacatc aactcatgtg
3121 atccccgcgg gcataacaga agcatttggg gtctccatca aacaaattca gatccacaaa
3181 tcaggtgaat tttgccggtt caggttccca aaaccaatta gaccagatgt tacaggaatg
3241 atcttggaag aaggtgcgcc tgaaggtacc gtggcaactg tgctcatcaa acgccccacc
3301 ggagagctca tgcctcttgc agccagaatg ggaacacacg caaccatgaa aattcaaggc
3361 cgcatggttg gcgggcagat gggtatgttg ctcactggat caaatgctaa aggaatggat
3421 ttggggacaa cccctggtga ctgtggctgc ccctacatct acaaaagagg caacgactat
3481 atagtcattg gggtgcacac tgcagcagcc cgtggtggaa acaccgtcat ctgtgccaca
3541 cagggaagtg agggtgaggc aactcttgag ggtggagatg acaaaggaac atactgtggg
3601 gcacccattc tgggccctgg gggcgcacca aaattgagca ccaaaaccaa attttggagg
3661 tcatcgaaca cgccccttcc accagggacg tatgagcctg cctacctcgg cggccgtgat
3721 ccacgtatca agggcgggcc ctccttgcag caggtaatga gagatcagtt gaagccattc
3781 actgaaccca ggggcaaacc tccaagacca agtgtattag aagcagccaa acaaaccatc
3841 atcaatgtcc tcgaacaaac cctggatcct ccacaaaaat ggacatacgc acaggcgtgt
3901 gcctcacttg acaaaaccac ctccagcggg aacccccatc acgtccgaaa gaatgaattc
3961 tggaatggtg agacctttac tggaaaattg gcagaccaag catcaaaagc aaatttaatg
4021 tatgaggaag ggaaacatat gacaccagtg tatacagcag cactcaagga cgagctagtt
4081 aagactgaga aaatctatgg aaagatcaag aagaggctgc tctggggctc tgacttgtcc
4141 accatggtcc ggtgtgctag gtcatttggt gggctcatgg atgagatgaa ggcacactgc
4201 atatcactcc cagtccgagt tggcatgaat atgaatgaag atggcccaat aatatttgag
4261 aaacattcca gatacaagta ccactatgat gcagactact ctcgttggga ttcaacacaa
4321 cagagggcag tactggcagc agccttggaa atcatggtca gattctctgc agaaccacaa
4381 ctggcacaaa tagtcgctga ggatctgctg gcccctagtg tagtagatgt gggagacttc
4441 aaaattacaa taaatgaagg gctcccctct ggtgttccat gtacttctca atggaactcc
4501 attgcacact ggctgctaac tctctgtgcc ttgtctgaag tcaccaaact gtcccctgac
4561 attatacagg caaattccat gttctcattt tacggtgatg atgagattgt cagcaccgac
4621 ataaaattag accctgaaca gttaaccgcc aaattgaagg agtacggcct gaaaccaacc
4681 cgcccagaca aaaccgaggg acccctgatc atcagtgaag atttggacgg actcactttc
4741 ctccgaagga cggtgactcg tgacccagct ggctggtttg gtaaactgga ccagagctcc
4801 attttgaggc agatgtactg gactagaggg ccaaatcatg aagaccccaa tgagacaatg
4861 ataccccatt ctcagagacc catacagctc atggcactgc ttggtgaagc ctctcttcac
4921 ggaccctctt tctatagtaa aatcagcaaa ttagtcataa ctgaactcaa ggaaggtggg
4981 atggacttct acgtgccaag acaggaaccc atgttcaggt ggatgaggtt ttctgacttg
5041 agcatgtggg agggcgatcg caatctggct cccaattttg tgaatgaaga tggcgtcgag
5101 tgacgccaac ccatctgatg ggtccgcagc caacctcgta ccagaggtca acaatgaggt
5161 tatggctttg gagcccgttg ttggtgccgc tattgcggca cctgtagcgg gccaacaaaa
5221 tgtaattgac ccctggatta gaaataattt tgtacaagcc cctggtgggg agtttacagt
5281 gtcccctaga aatgctccag gtgaaatact atggagcgcg cccttaggcc ctgacctaaa
5341 tccctaccta tcccatttgg ccaggatgta caatggttat gcaggtggct ttgaagtgca
5401 ggtaattctc gcggggaacg cgttcaccgc tgggaagatt atatttgcag cagtcccacc
5461 aaattttcca actgaaggct taagccctag ccaggtcact atgttccccc atataatagt
5521 agatgttaga caattggaac ctgtgctgat ccccttaccc gatgttagga ataatttcta
5581 tcactacaat cagtcaaatg actccactat taagttgata gcaatgttgt acacaccact
5641 tagggctaat aatgctggag atgatgtttt cacagtctcg tgccgagttc tcacgagacc
5701 atcccccgat tttgatttca tattcttagt accacccaca gttgagtcaa gaactaaacc
5761 attctccgtc ccagttttaa ctgttgagga gatgaccaat tcaagattcc ctatcccttt
5821 ggaaaagttg ttcacaggcc ccagcagtgc atttgttgtt caaccacaaa acggcaggtg
5881 cacaactgat ggcgtgcttc taggcaccac ccaactttct cctgtcaaca tctgcacctt
5941 cagaggggat gtcacccaca tcacaggtag tcacaactac actatgaatt tggcttctca
6001 aaattggaac aactacgacc caacagaaga aatcccagct cccctaggaa ctccagattt
6061 tgtggggaag atccaaggca tgctcaccca aaccacaagg acagatggtt caacacgcgg
6121 ccacaaagct acagtgtaca ctgggagcgc cgactttgct ccaaaactgg gtagagttca
6181 atttgaaact gacacaaacc atgattttga agctaatcaa aacacaaagt tcaccccagt
6241 cggtgttatc caagatggta gcaccaccca ccgaaacgaa ccccaacagt gggtgcttcc
6301 aagttactca ggcagaaata cccacaatgt acatttggcc cccgctgtag cccccacctt
6361 tccgggtgag caacttctct tctttagatc taccatgccc ggatgtagcg ggtaccccaa
6421 catggatttg gactgtctgc tcccccatga atgggtgcag tatttctacc aagaggcagc
6481 cccagcacaa tctgatgtgg ctctgctaag atttgtgaat ccagacacag gtagggtttt
6541 gtttgagtgt aagcttcaca aatcaggcta tgttacagtg gctcacactg gccaacatga
6601 tttggttatc ccccccaatg gttactttag gtttgattcc tgggtcaacc agttctacac
6661 gcttgccccc atgggaaacg gaacggggcg tagacgtgca gtataatggc tggagctttc
6721 tttgctggat tggcatctga tgtccttggc tccggacttg gttcccttat caatgctggg
6781 gctggggcca tcaaccaaaa agttgagttt gaaaataaca gaaaattgca acaagcatcc
6841 ttccaattta gcagcaattt gcaacaggct tcctttcaac atgataaaga gatgctccaa
6901 gcacaaattg aggccaccaa aaaactacaa caggaaatga tgagagttaa gcaggcaatg
6961 ctcctagagg gtgggttctc tgagacagat gcggcccgcg gggcaattaa cgcccccatg
7021 acaaaggctt tggactggag cgggacaagg tactgggctc cagatgctag aattacaaca
7081 tacaatgcag gccacttttc cacccctcaa ccatcggggg cactgccagg aagagctaat
7141 tttagggatg ctgtccctgc tcggggaccc tccaccagac tttctaactc ttctactgcc
7201 acctctgtgt attcaaatca aactatttca acgagacttg gttctacagc tggttctgga
7261 accagtgtct cgagcctccc gtcaactgca aggactagga gctgggttga ggatcaaaat
7321 aagaatttgt ctcctttcat gaggggggcc cacaacatat catttgtcac cccaccatct
7381 agcagatcct ctagccaagg cacagtctca accgtgccta aagaaatttt ggactcctgg
7441 actggcgctt tcaatacgcg caggcagcct ctcttcgctc acattcgtaa gcgaggggag
7501 tcacgggtgt aatgtgaaaa gacaaa
//