Typing tool
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Typing tool
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Complete norovirus genomes
| PQ209095 | GII.4 Sydney | |
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| GII.P16 |
ORF1: 1..5094
ORF2: 5075..6697
ORF3: 6697..7503
LOCUS PQ209095 7528 bp RNA linear VRL 01-JAN-2025
DEFINITION Norovirus GII isolate Hu/GII.4 Sydney[P16]/Clackamas0041/2019/USA
nonstructural polyprotein (ORF1) gene, partial cds; and VP1 (ORF2)
and VP2 (ORF3) genes, complete cds.
ACCESSION PQ209095
VERSION PQ209095.1
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.,
Lindesmith,L., Wall,H., Baric,R.S., Vinje,J. and Chhabra,P.
TITLE Norovirus GII.4 evolution in the United States since emergence of
GII.4 Sydney
JOURNAL Unpublished
REFERENCE 2 (bases 1 to 7528)
AUTHORS Tsaknaridis,L.J., Barclay,L., Montmayeur,A.M., Vinje,J. and
Chhabra,P.
TITLE Direct Submission
JOURNAL Submitted (20-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]/Clackamas0041/2019/USA"
/isolation_source="stool"
/host="Homo sapiens"
/db_xref="taxon:122929"
/geo_loc_name="USA"
/collection_date="07-Feb-2019"
/note="genotype: GII.4 Sydney[P16]"
gene <1..5094
/gene="ORF1"
CDS <1..5094
/gene="ORF1"
/codon_start=1
/product="nonstructural polyprotein"
/protein_id="XEO40396.1"
/translation="MASNDASAAVACNNNNDKEKSSGEGLFTNMSSTLKKALGAKPKQ
PAPRVEPQKPPRPPTPELVKRIPPPPPNGEEEEEPVIRYEVKSGISGLPELTTVPQPD
VANTAFSVPPLSLRENREAKEPLTGAILEMWDGEIYHYGLYVEKGLVLGVHKPPAAIS
MARVELTPLSLYWRVVYTPQYLISPETLRRLNGEAFPYTAFDNNCYAFCCWVLDLNDS
WLSRRMVQRTTGFFRPYQEWNRKPLPTMDDSKIKKVANIFLCSLSTLFTRPIKDLIGK
IKPLNILNILATCDWTFAGVVESLILLAELFGVFWTPPDVSAMIAPLLGDYELQGPED
LAVELVPVVMGGIGLVLGFTKEKIGKMLSSAASTLRACKDLGAYGLEILKLVMKWFFP
KKEEANELAMVRAIEDAVLDLEAIENNHMTTLLKDKDSLATYMKTLDMEEEKARRLST
KSASPDIVGTINALLARIAAARSLVHRAKEELSSRIRPVVVMISGKPGIGKTHLAREV
ARKVASTLTGDQRVGLIPRNGVDHWDAYKGERVVLWDDYGMSNPIHDALRIQELADTC
PLTLNCDRIENKGKVFDSEVIIITTNLANPAPLDYVNFEACSRRIDFLVYAEAPEVEK
AKRDFPGQPDMWKDAFKPDFSHIKLQLAPQGGFDKNGNTPHGKGVMKTLTTGSLIARA
SGLLHERMDEFELQGPTITTFNFDRNRITAFRQLAAENKYGLVDTMKVGNQLKGVKTM
EELKQAIRNVTIKRCRIIYGGSTYDLESDGKGKVLVEKVKNTSVQTNNELAGALHHLK
HARVRYYVKCVQEAVYSIIQIAGAAFVTTRIARRMNIQELWSKPQLDQNESETKEEAP
KSEDDEFIISSKDIKEEGKKGKNKTGRGKKHTAFSSKGLSDEEYDEYKRIREERNGKY
SIEEYLQDRDRYYEELAIAKATEEDFCEEEEIKIRQRIFRPTRKQRKEERATLGLVTG
SEIRKRNPDDFKPKGKLWADDNRSVDYNEKLDFEAPPSIWSRIVSFGSGWGFWVSPSL
FITSTHVIPAGITEAFGVPIKQIQIHKSGEFCRFRFPKPIRPDVTGMILEEGAPEGTV
ATVLIKRPTGELMPLAARMGTHATMKIQGRMVGGQMGMLLTGSNAKGMDLGTTPGDCG
CPYIYKRGNDYIVIGVHTAAARGGNTVICATQGSEGEATLEGGDDKGTYCGAPILGPG
GAPKLSTKTKFWRSSNTPLPPGTYEPAYLGGRDPRVKSGPSLQQVMRDQLKPFTEPRG
KPPRPSVLEAAKQTIINVLEQTLDPPQKWTYAQACASLDKTTSSGHPHHVRKNEFWNG
ETFTGKLADQASKANLMFEEGKHMTPVYTAALKDELVKTEKIYGKIKKRLLWGSDLST
MIRCARSFGGLMDEMKAHCISLPVRVGMNMNEDGPIIFEKHSRYKYHYDADYSRWDST
QQRAVLAAALEIMVRFSAEPQLAQIVAEDLLAPSVVDVGDFKITINEGLPSGVPCTSQ
WNSIAHWLLTLCALSEVTKLSPDIIQANSMFSFYGDDEIVSTDIKLDPEQLTAKLKEY
GLKPTRPDKTEGPLIISEDLNGLTFLRRTVTRDPAGWFGKLDQSSILRQMYWTRGPNH
EDPNETMIPHSQRPIQLMALLGEASLHGPSFYSRISKLVITELKEGGMDFYVPRQEPM
FRWMRFSDLSTWEGDRNLAPNFVNEDGVE"
mat_peptide <1..990
/gene="ORF1"
/product="p48"
mat_peptide 991..2088
/gene="ORF1"
/product="NTPase"
mat_peptide 2089..2619
/gene="ORF1"
/product="p22"
mat_peptide 2620..3018
/gene="ORF1"
/product="VPg"
mat_peptide 3019..3561
/gene="ORF1"
/product="Pro"
mat_peptide 3562..5091
/gene="ORF1"
/product="RdRp"
gene 5075..6697
/gene="ORF2"
CDS 5075..6697
/gene="ORF2"
/note="major capsid protein"
/codon_start=1
/product="VP1"
/protein_id="XEO40397.1"
/translation="MKMASSDANPSDGSAANLVPEVNNEVMALEPVVGAAIAAPVAGQ
QNVIDPWIRNNFVQAPGGEFTVSPRNAPGEILWSAPLGPDLNPYLSHLARMYNGYAGG
FEVQVILAGNAFTAGKIIFAAVPPNFPTEGLSPSQVTMFPHIIVDVRQLEPVLIPLPD
VRNNFYHYNQSNDSTIKLIAMLYTPLRANNAGDDVFTVSCRVLTRPSPDFDFIFLVPP
TVESRTKPFSVPVLTVEEMTNSRFPIPLEKLFTGPSSAFVVQPQNGRCTTDGVLLGTT
QLSPVNICTFRGDVTHITGSRNYTMNLASQNWNNYDPTEEIPAPLGTPDFVGKIQGML
TQTTRTDGSTRGHKATVYTGSADFAPKLGRVQFETDTDHDFEANQNTKFTPIGVIQDG
STTHRNEPQQWVLPSYSGRNTHNVHLAPAVAPTFPGEQLLFFRSTMPGCSGYPNMDLD
CLLPQEWVQYFYQEAAPAQSDVALLRFVNPDTGRVLFECKLHKSGYVTVAHIGQHDLV
IPPNGYFRFDSWVNQFYTLAPMGNGTGRRRAV"
gene 6697..7503
/gene="ORF3"
CDS 6697..7503
/gene="ORF3"
/note="minor structural protein; small basic protein"
/codon_start=1
/product="VP2"
/protein_id="XEO40398.1"
/translation="MAGAFFAGLASDVLGSGLGSLINAGAGAINQKVEFENNRKLQQA
SFQFSSNLQQASFQHDKEMLQAQIEATKKLQQEMMKVKQAMLLEGGFSETDAARGAIN
APMTKALDWSGTRYWAPDARITTYNAGHFSTPQSSGALPGRANLRDAVPVRGPSTKSS
NSSTATSVYSNQTISTRLGSTAGSGTSVSSLPSTARTRSWVEGQNRNLSPFMRGAHNI
SFVTPPSSRSSSQGTVSTVPKEILDSWTGAFNTRRQPLFAHIRKRGESRV"
ORIGIN
1 atggcgtcta acgacgcttc cgctgccgtt gcttgcaaca acaacaacga caaggaaaaa
61 tcttcaggtg aaggcttatt cacaaatatg tcttccacct taaagaaagc cctcggggct
121 aagcccaaac agcctgcccc gagagtcgaa ccacaaaagc ccccaagacc accaactccc
181 gagttggtca agaggatacc cccccctcca cctaatggcg aagaagaaga agaaccagtc
241 attaggtatg aggttaagag tgggatctct ggcctgcccg agctcacaac agtcccccaa
301 ccggacgtgg ccaacacagc atttagtgtt ccaccactga gcttgagaga aaacagggag
361 gccaaggaac cgctaacagg ggcaatacta gagatgtggg acggagagat ataccactat
421 ggcctgtacg tggagaaagg cttagtgttg ggtgtgcaca aaccacctgc agccataagc
481 atggcaagag tggagctgac gccgctgtca ttgtactggc gtgtggtgta cactccccaa
541 tacctcatct cccctgagac cctcaggagg ctcaacggag aggcgtttcc ttacaccgcc
601 ttcgacaaca actgctacgc cttttgctgc tgggtgttag acctcaatga ctcatggctt
661 agcaggagga tggtgcaaag aacaacgggc ttcttcagac cttaccaaga gtggaacaga
721 aaacccttgc ccaccatgga tgactccaaa ataaagaagg tagcaaatat attcttatgt
781 tcattgtcca cattattcac cagacccata aaagacctca taggaaaaat taaaccatta
841 aacatattga acatcctggc aacgtgtgac tggacgtttg ccggagtagt agagtctctg
901 atattgcttg ccgaactctt cggagttttc tggacacccc cagatgtgtc tgctatgatc
961 gctcccttac tcggggacta cgagttacaa gggccagaag acctcgccgt tgaactcgta
1021 cctgtggtaa tgggagggat tggtttggtg ttgggattca ccaaagagaa aattggcaaa
1081 atgttgtcct cagcagcatc aacactcagg gcttgtaaag atcttggtgc ctatggctta
1141 gagatactca aattggtcat gaagtggttc ttcccaaaga aagaggaggc caatgagcta
1201 gccatggtga gggccataga ggatgccgta ctagatcttg aggcaataga aaataaccac
1261 atgacaaccc tgttgaaaga caaagacagc ttagcaacat acatgaaaac actggacatg
1321 gaggaggaga aagccagaag gttgtccaca aaatctgcat cccctgacat agttgggaca
1381 atcaacgccc tgttggctcg aatagcagcg gctaggtcat tagtccacag ggccaaggaa
1441 gagctgtcta gcaggataag accagtagtt gttatgatat ctggcaaacc gggaataggc
1501 aaaactcatc tggccaggga ggtggcaaga aaggtggcat ccactctcac aggggatcaa
1561 agagtcggac tcataccaag aaacggtgtg gaccattggg atgcatacaa aggtgagaga
1621 gtcgtgctgt gggacgacta tggcatgagt aaccccattc atgatgctct tcgcatacaa
1681 gaattggctg atacatgtcc ccttacctta aattgtgaca gaattgaaaa taagggaaaa
1741 gtttttgaca gtgaagtcat aataattaca acaaaccttg ccaacccagc cccacttgat
1801 tatgtcaact ttgaggcctg ttccaggaga attgatttcc tggtgtacgc tgaggcacca
1861 gaagtagaaa aggcaaaacg ggattttcct ggtcagccag atatgtggaa agacgccttc
1921 aagccggact tttcacacat caagctacag cttgcacctc agggcggctt tgacaagaat
1981 ggtaacaccc cacatgggaa aggagtgatg aagaccctca ctaccggttc tctgattgcc
2041 cgtgcatcag gcctactgca tgagaggatg gatgaatttg aactccaagg ccccacaatc
2101 accactttca atttcgaccg gaacagaatc acagcattca gacaactggc tgcagaaaac
2161 aagtatggat tggtggatac catgaaagtt ggcaatcaat taaaaggagt gaaaaccatg
2221 gaagaactca aacaagcaat caggaatgtg accatcaaga ggtgccggat catctacggt
2281 ggctccacgt atgaccttga atctgatggc aaaggcaaag ttttggtgga aaaggtcaag
2341 aacacctctg tacagaccaa caatgagttg gccggggccc tgcaccatct taaacacgcc
2401 cgagtcaggt actatgtcaa atgtgtgcaa gaagcagtct attccatcat acaaattgcc
2461 ggcgccgcgt ttgtcaccac gcgcattgca cgccgcatga acatacaaga actctggtcg
2521 aagccacaat tagatcaaaa tgaatcagag actaaggaag aggcccccaa gtcagaagat
2581 gacgagttca tcatatcttc taaggacatc aaggaggaag gaaagaaggg caaaaacaaa
2641 actggccgtg gcaagaaaca cactgcattc tccagcaagg gcttgagcga tgaggagtat
2701 gacgagtaca agaggataag agaagagaga aatgggaagt actctataga ggagtatctt
2761 caagatagag acaggtacta tgaggagctc gccattgcca aggccacgga agaagacttc
2821 tgtgaagagg aggagatcaa aatccgtcag agaattttcc gtcccaccag gaaacaaaga
2881 aaggaagaga gggccacatt agggctggta acaggttcgg aaatcagaaa aagaaaccct
2941 gatgatttca aacccaaagg gaagctgtgg gccgatgaca acagaagtgt tgactacaat
3001 gagaaactgg actttgaggc ccccccaagc atatggtcta ggattgtgag ctttggttct
3061 ggctggggct tctgggtatc accaagcctg ttcataacgt caactcatgt aatccccgca
3121 ggcataacgg aagcatttgg agtccccatc aaacaaattc agatccacaa atcaggtgaa
3181 ttttgccgat tcagattccc aaaaccaatt agaccagatg tgacaggaat gatcttggaa
3241 gaaggtgcgc ctgaaggcac cgtggcaact gtgctcatca aacgccccac cggagagctc
3301 atgcctcttg cagccagaat gggaacacac gcaaccatga agattcaagg ccgcatggtt
3361 ggcggacaga tgggtatgtt gctcactggg tcaaatgcta aaggaatgga tttgggaaca
3421 actcctggtg actgtggctg cccttacatc tataaaaggg gcaatgacta tatagtcatt
3481 ggggtgcaca ctgcagcagc ccgtggtgga aacaccgtca tctgtgccac acagggaagt
3541 gagggtgagg caactcttga gggtggagat gacaaaggaa catactgtgg ggcacccatt
3601 ctaggccctg ggggtgcacc aaaattgagc accaaaacca aattttggag gtcatcgaac
3661 acgccccttc caccagggac atatgagcct gcctacctcg gtggccgcga tccgcgtgtt
3721 aagagtgggc cctccttaca gcaggtaatg agagaccagt tgaagccatt cactgaaccc
3781 aggggcaaac ctccaagacc aagtgttttg gaagcagcca aacaaaccat tatcaatgtc
3841 ctcgaacaaa ccctggatcc tccacaaaaa tggacatacg cacaggcgtg tgcctcactt
3901 gacaaaacca cctccagcgg gcatccccac cacgtccgaa agaatgaatt ctggaatggt
3961 gagaccttca ctggtaaatt ggcagaccaa gcatcaaaag caaacctaat gtttgaggaa
4021 gggaaacaca tgacaccagt gtatacggca gcactcaagg atgagctagt caagactgag
4081 aaaatctatg gaaagatcaa gaaaagactg ctctggggct ctgacttgtc caccatgatc
4141 cggtgcgcta ggtcatttgg tgggctcatg gacgagatga aggcacactg catatcactc
4201 ccagtacgag ttggcatgaa tatgaatgaa gatggcccaa taatatttga gaaacattcc
4261 agatacaaat atcactatga tgcagactac tctcgttggg attcaacaca acagagggca
4321 gtactagcag cagccttgga aatcatggtc agattctctg cagaaccaca attggcacaa
4381 atagtcgctg aggatctact ggcccctagt gtagtagatg taggagactt taaaatcaca
4441 ataaatgaag ggctcccatc tggtgtgcca tgcacttctc aatggaactc catcgcgcac
4501 tggctgctaa ctctctgtgc cttgtctgaa gtcaccaaac tgtctcctga cattatacaa
4561 gcaaattcca tgttctcatt ttacggtgat gacgagattg tcagcaccga cataaaattg
4621 gaccctgaac agttaaccgc caagttgaag gagtacggcc tgaaaccaac ccgcccagac
4681 aagaccgagg gacccctgat catcagtgaa gatttgaacg gactcacttt cctccgaagg
4741 acggtgactc gtgacccagc tggctggttt ggaaaactgg accaaagttc aattttgagg
4801 cagatgtact ggactagagg accaaatcat gaagacccca atgagacaat gataccccat
4861 tctcaaagac ccatacagct catggcactg cttggtgaag cctctcttca cggaccctct
4921 ttctacagta gaatcagcaa attggtcata actgaactca aagaaggtgg gatggacttt
4981 tacgtgccaa ggcaggaacc catgttcagg tggatgaggt tttctgactt gagcacgtgg
5041 gagggtgatc gcaatctggc tcccaatttt gtgaatgaag atggcgtcga gtgacgccaa
5101 cccatctgat gggtccgcag ccaacctcgt accagaggtc aacaatgagg ttatggcttt
5161 ggagcccgtt gttggtgccg ctattgcggc acctgtagcg ggccaacaaa atgtaattga
5221 cccctggatt agaaataatt ttgtacaagc ccctggtggg gagtttacag tatcccctag
5281 aaatgctcca ggtgaaatac tatggagcgc gcccctaggc cctgacctaa atccctatct
5341 atcccatttg gccagaatgt acaatggtta tgcaggtggt tttgaagtgc aggtaattct
5401 cgcggggaac gcgttcaccg ccgggaagat tatatttgca gcagtcccac caaattttcc
5461 aactgaaggc ttaagtccta gccaggtcac tatgttcccc catataatag tagatgttag
5521 acaattagaa cctgtgctga ttcccttacc cgatgttagg aacaatttct atcattacaa
5581 tcagtcaaat gattccacca ttaagttgat agcaatgttg tacacaccac ttagggctaa
5641 taatgctggg gacgatgttt tcacagtttc gtgccgagtt ctcacgagac catcccctga
5701 ttttgatttc atatttttag tgccacccac agttgagtca agaactaaac cattctctgt
5761 tccagtttta actgttgagg agatgaccaa ttcaagattc cccatccctt tggaaaagtt
5821 gttcacaggc cccagcagtg cctttgttgt ccaaccacaa aacggcagat gcacaactga
5881 tggcgtgctc ctaggcacca cccaactttc tcctgtcaac atctgcacct tcagagggga
5941 tgtcacccac atcacaggta gtcgcaacta cacaatgaat ttggcttctc aaaattggaa
6001 caactatgac ccaacagaag aaatcccagc ccctctagga actccagatt ttgtggggaa
6061 gattcaaggc atgctcaccc aaaccacaag gacagatggt tcaacacgcg gtcacaaagc
6121 tacagtgtat actgggagcg ccgactttgc cccaaaactg ggtagagttc aatttgaaac
6181 tgacacagac catgattttg aagctaacca aaacacaaag ttcaccccaa tcggtgtcat
6241 ccaagatggt agcaccaccc accgaaacga accccagcag tgggtgctcc caagttattc
6301 aggcagaaac actcacaatg tacatctggc ccccgctgta gcccccacct ttccgggtga
6361 gcaacttctc ttcttcagat ccaccatgcc cggatgcagc gggtacccca acatggattt
6421 agactgtctg ctcccccagg aatgggtgca gtacttctac caagaggcag ccccagcaca
6481 atctgatgtg gccctgctaa gatttgtgaa tccagacaca ggtagggttt tgtttgagtg
6541 caagcttcac aaatcaggtt atgttacagt ggctcacatt ggccaacatg acttggttat
6601 cccccccaat ggttacttca ggtttgattc ctgggtcaat cagttctaca cgcttgcccc
6661 catgggaaat ggaacggggc gtagacgtgc agtataatgg ccggagcttt ctttgctgga
6721 ttggcatctg atgtcctcgg ctctggactt ggttccctta tcaatgctgg ggctggggcc
6781 atcaaccaaa aagttgagtt tgaaaataac agaaaattgc aacaagcatc cttccaattt
6841 agcagcaatt tgcaacaggc ttcctttcaa catgataaag agatgctcca agcacaaatt
6901 gaggccacca aaaagctaca acaggaaatg atgaaagtta agcaggcaat gctcctagag
6961 ggtgggttct ctgagacaga tgcagcccgc ggggcaatta acgcccccat gacaaaagct
7021 ttggactgga gcgggacaag gtactgggct ccagatgcta gaattacaac atacaatgca
7081 ggccactttt ccacccctca atcatcgggg gcactgccag gaagggctaa tcttagggat
7141 gctgtccctg ttcggggacc ttctaccaag tcttctaact cttctactgc cacctctgtg
7201 tactcaaatc aaactatttc aacgagactt ggttctacag ctggttctgg aaccagtgtc
7261 tcaagcctcc cgtcaactgc aaggactagg agctgggttg agggtcaaaa taggaatttg
7321 tcacctttca tgaggggggc ccacaacata tcatttgtca ccccaccatc cagcagatcc
7381 tctagccaag gcacagtctc aaccgtgcct aaagaaattt tggactcctg gactggcgct
7441 ttcaacacgc gcaggcagcc tctcttcgct cacattcgta agcgagggga gtcacgggtg
7501 taatgtgaaa agacaaaatt gattatct
//