Typing tool
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Typing tool
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Complete norovirus genomes
| PQ218790 | GII.4 Sydney | |
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| GII.P16 |
ORF1: 1..5098
ORF2: 5079..6701
ORF3: 6701..7507
LOCUS PQ218790 7558 bp RNA linear VRL 01-JAN-2025
DEFINITION Norovirus GII isolate Hu/GII.4 Sydney[P16]/Arapahoe0002/2023/USA
nonstructural polyprotein (ORF1) gene, partial cds; and VP1 (ORF2)
and VP2 (ORF3) genes, complete cds.
ACCESSION PQ218790
VERSION PQ218790.1
KEYWORDS .
SOURCE Norovirus GII
ORGANISM Norovirus GII
Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes;
Picornavirales; Caliciviridae; Norovirus; Norovirus norwalkense.
REFERENCE 1 (bases 1 to 7558)
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JOURNAL Unpublished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 7558)
AUTHORS Mallal,D., Barclay,L., Montmayeur,A.M., Vinje,J. and Chhabra,P.
TITLE Direct Submission
JOURNAL Submitted (22-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. 11.0; SPAdes v. 3.5
Sequencing Technology :: Sanger dideoxy sequencing; Illumina
##Assembly-Data-END##
FEATURES Location/Qualifiers
source 1..7558
/organism="Norovirus GII"
/mol_type="genomic RNA"
/isolate="Hu/GII.4 Sydney[P16]/Arapahoe0002/2023/USA"
/isolation_source="stool"
/host="Homo sapiens"
/db_xref="taxon:122929"
/geo_loc_name="USA"
/collection_date="06-Dec-2023"
/note="genotype: GII.4 Sydney[P16]"
gene <1..5098
/gene="ORF1"
CDS <1..5098
/gene="ORF1"
/codon_start=2
/product="nonstructural polyprotein"
/protein_id="XER81190.1"
/translation="KMASNDASAAVACNNNNDKEKSSGEGLFTNMSSTLKKALGARPK
QPAPRDKPQKPPRPPTPELVKRIPPPPPNGEEEEEPVIRYEVKSGISGLPELTTVPQP
DVANTAFSVPPLSLRENREAKEPLTGAILEMWDGEIYHYGLYVEKGLVLGVHKPPAAI
SMARVELTPLSLYWRVVYTPQYLISPETLRRLNGEAFPYTAFDNNCYAFCCWVLDLND
SWLSRRMVQRTTGFFRPYQEWNRKPLPTMDDSKIKKVANIFLCSLSTLFTRPIKDLIG
KIKPLNILNILATCDWTFAGIVESLILLAELFGVFWTPPDVSAMIAPLLGDYELQGPE
DLAVELVPVVMGGIGLVLGFTKEKIGKMLSSAASTLRACKDLGAYGLEILKLVMKWFF
PKKEEANELAMVRAIEDAVLDLEAIENNHMTTLLKDKDSLATYMKTLDMEEEKARRLS
TKSASPDIVGTINALLARIAAARSLVHRAKEELSSRIRPVVVMISGKPGIGKTHLARE
VARKVASTLTGDQRVGLIPRNGVDHWDAYKGERVVLWDDYGMSNPIHDALRLQELADT
CPLTLNCDRIENKGKVFDSEVIIITTNLANPAPLDYVNFEACSRRIDFLVYAEAPEVE
KAKRDFPGQPDMWKDAFKPDFSHIKLQLAPQGGFDKNGNTPHGKGVMKTLTTGSLIAR
ASGLLHERMDEFELQGPTITTFNFDRNRIAAFRQLAAENKYGLVDTMKVGNQLKGVRT
MEELKQAIRNVTIKRCRIIYGGSTYDLESDGKGKVLVEKVKNISVQTNNELAGALHHL
KHARIRYYVKCVQEAVYSIIQIAGAAFVTTRIARRMNIQELWSKPQLGQSEPETKEEA
LKSEDDEFVISSKDIKEEGKKGKNKTGRGKKHTAFSSKGLSDEEYDEYKRIREERNGK
YSIEEYLQDRDRYYEELAIAKATEEDFCEEEEIKIRQRIFRPTRKQRKEERATLGLVT
GSEIRKRNPDDFKPKGKLWADDNRSVDYNEKLDFEAPPSIWSRIVSFGSGWGFWVSPS
LFITSTHVIPAGITEAFGVSIKQIQIHKSGEFCRFRFPKPIRPDVTGMILEEGAPEGT
VATVLIKRPTGELMPLAARMGTHATMKIQGRMVGGQMGMLLTGSNAKGMDLGTTPGDC
GCPYIYKRGNDYIVIGVHTAAARGGNTVICATQGSEGEATLEGGDDKGTYCGAPILGP
GGAPKLSTKTKFWRSSNTPLPPGTYEPAYLGGRDPRIKGGPSLQQVMRDQLKPFTEPR
GKPPRPSVLEAAKQTIINVLEQTLDPPQKWTYAQACASLDKTTSSGNPHHVRKNEFWN
GETFTGKLADQASKANLMFEEGKHMTPVYTAALKDELVKTEKIYGKIKKRLLWGSDLS
TMVRCARSFGGLMDEMKAHCISLPVRVGMNMNEDGPIIFEKHSRYKYHYDADYSRWDS
TQQRAVLAAALEIMVRFSAEPQLAQIVAEDLLAPSVVDVGDFKITINEGLPSGVPCTS
QWNSIAHWLLTLCALSEVTKLSPDIIQANSMFSFYGDDEIVSTDIKLDPEQLTAKLKE
YGLKPTRPDKTEGPLIISEDLDGLTFLRRTVTRDPAGWFGKLDQSSILRQMYWTRGPN
HEDPNETMIPHSQRPIQLMALLGEASLHGPSFYSKISKLVITELKEGGMDFYVPRQEP
MFRWMRFSDLSTWEGDRNLAPNFVNEDGVE"
mat_peptide <1..994
/gene="ORF1"
/product="p48"
mat_peptide 995..2092
/gene="ORF1"
/product="NTPase"
mat_peptide 2093..2623
/gene="ORF1"
/product="p22"
mat_peptide 2624..3022
/gene="ORF1"
/product="VPg"
mat_peptide 3023..3565
/gene="ORF1"
/product="Pro"
mat_peptide 3566..5095
/gene="ORF1"
/product="RdRp"
gene 5079..6701
/gene="ORF2"
CDS 5079..6701
/gene="ORF2"
/note="major capsid protein"
/codon_start=1
/product="VP1"
/protein_id="XER81191.1"
/translation="MKMASSDANPSDGSAANLVPEVNNEVMALEPVVGAAIAAPVAGQ
QNVIDPWIRNNFVQAPGGEFTVSPRNAPGEILWSAPLGPDLNPYLSHLARMYNGYAGG
FEVQVILAGNAFTAGKIIFAAVPPNFPTEGLSPSQVTMFPHIIVDVRQLEPVLIPLPD
VRNNFYHYNQSNDSTIKLIAMLYTPLRANNAGDDVFTVSCRVLTRPSPDFDFIFLVPP
TVESRTKPFSVPVLTVEEMTNSRFPIPLEKLFTGPSSAFVVQPQNGRCTTDGVLLGTT
QLSPVNICTFRGDVTHITGSHNYTMNLASQNWNNYDPTEEIPAPLGTPDFVGKIQGML
TQTTRTDGSTRGHKATVYTGSADFAPKLGRVQFETDTNHDFEANQNTKFTPVGVIQDG
STTHRNEPQQWVLPSYSGRNTHNVHLAPAVAPTFPGEQLLFFRSTMPGCSGYPNMDLD
CLLPQEWVQYFYQEAAPAQSDVALLRFVNPDTGRVLFECKLHKSGYVTVAHTGQHDLV
IPPNGYFRFDSWVNQFYTLAPMGNGTGRRRAV"
gene 6701..7507
/gene="ORF3"
CDS 6701..7507
/gene="ORF3"
/note="minor structural protein; small basic protein"
/codon_start=1
/product="VP2"
/protein_id="XER81192.1"
/translation="MAGAFFAGLASDVLGSGLGSLINAGAGAINQKVEFENNRKLQQA
SFQFSSNLQQASFQHDKEMLQAQIEATKKLQQEMMRVKQAMLLEGGFSETDAARGAIN
APMTKALDWSGTRYWAPDARITTYNAGHFSTPQPSGALPGRANFRDAVPARGPSTRLS
NSSTATSVYSNQTVSTRLGSTAGSGTSVSSLPSTARTRSWVEDQNRNLSPFMRGAHNI
SFVTPPSSRSSSQGTVSTVPKEILDSWTGAFNTRRQPLFAHIRKRGESRV"
ORIGIN
1 gaagatggcg tctaacgacg cttccgctgc cgttgcttgc aacaacaaca acgacaagga
61 aaaatcttca ggtgaaggct tattcacaaa tatgtcttcc accttaaaga aagccctcgg
121 ggctaggccc aaacagcctg ccccgagaga caaaccacaa aagcccccaa gaccaccaac
181 tcctgagttg gtcaagagga taccccctcc tccacctaat ggcgaagaag aagaagaacc
241 agtcattagg tatgaggtta agagcggaat ctctggcctg cccgagctca caacagtccc
301 ccaaccggac gtggccaaca cagcattcag tgttccacca ctgagcttga gagaaaacag
361 ggaggccaag gaaccgctaa caggggcaat attagagatg tgggatggag agatatatca
421 ctatggtcta tacgtggaga aaggcctagt gttgggtgtg cacaaaccac ctgcagccat
481 aagcatggca agagtggaac tgacgccgct gtcattatac tggcgtgtag tgtacactcc
541 ccaatacctc atctcccctg aaactcttag gaggctcaac ggagaggctt tcccttacac
601 cgcctttgac aacaactgct atgccttttg ttgctgggtg ctagacctca acgactcatg
661 gcttagcagg agaatggtgc agagaacaac gggcttcttc agaccttacc aagagtggaa
721 cagaaaaccc ctgcctacca tggatgactc caaaattaag aaggtggcaa acatattcct
781 atgttcattg tctacattat tcaccaggcc cataaaagat ctcataggaa aaattaaacc
841 attaaacata ttgaacattc tggcaacgtg tgactggacg tttgctggga tagtggagtc
901 tctaatatta cttgctgaac tcttcggagt tttctggaca cccccagatg tgtctgctat
961 gatcgctccc ttgctcgggg actacgagtt gcaggggcca gaggacctcg ccgttgaact
1021 cgtgcctgtg gtaatgggag ggattggttt ggtgttggga ttcaccaaag agaaaattgg
1081 caaaatgttg tcttcagcag catcaacact cagggcttgc aaagatcttg gtgcctatgg
1141 cttagagata ctaaaattgg tcatgaagtg gttcttccca aagaaagagg aggccaatga
1201 gctagccatg gtgagggcca tagaggatgc tgtactagac cttgaggcaa tagaaaataa
1261 ccacatgaca accctgttga aagacaaaga cagcttagca acatacatga agacactaga
1321 catggaggag gagaaagcca gaaggttgtc cacaaaatct gcatcccctg acatagttgg
1381 gacaatcaac gccctactgg ctcgaatagc agcggccagg tcattagtcc acagggccaa
1441 ggaagagcta tctagcagga taagaccagt agttgttatg atatctggca aaccaggaat
1501 aggcaaaact catctggcca gggaggtggc aagaaaggtg gcttccactc ttacagggga
1561 ccagagagtc ggactcattc caagaaacgg tgtggaccat tgggatgcat acaaaggcga
1621 gagagtcgtg ctgtgggacg actatggcat gagtaatccc atccatgatg ctcttcgctt
1681 acaagaattg gctgatacgt gtcccctcac cttaaattgt gacagaattg aaaacaaagg
1741 aaaagttttt gacagtgaag tcataataat tacaacaaac cttgccaacc cagcccctct
1801 tgattatgtc aactttgagg cttgttccag gagaattgac ttcctggtgt acgctgaggc
1861 accagaagta gagaaggcaa agcgggactt ccctggtcag ccagatatgt ggaaggacgc
1921 cttcaagccg gacttttcac acatcaagct gcaacttgca cctcagggcg gctttgacaa
1981 gaatggcaac accccacatg ggaaaggagt gatgaagacc ctcactaccg gctctctgat
2041 cgctcgtgca tcaggcctac tgcatgagag gatggatgaa tttgaacttc aaggccccac
2101 aatcaccacc ttcaatttcg accggaacag aatcgcagca ttcagacaac tggctgcaga
2161 aaacaagtat ggattagtgg acactatgaa agttggcaat caattaaaag gagtgagaac
2221 catggaagaa ctcaaacaag caatcaggaa tgtgaccatc aagaggtgcc ggatcattta
2281 cggtggctct acatatgacc ttgaatctga cggtaagggc aaagttttgg tggaaaaggt
2341 caagaacatc tctgtacaga ccaacaacga gttggccggg gccttgcacc atctcaaaca
2401 cgcccgaatc agatactatg tcaaatgcgt gcaagaagca gtctattcca tcatacaaat
2461 agccggcgct gcgtttgtca ccacgcgcat tgcacgccgc atgaacatac aagaactctg
2521 gtcgaagcca caattaggtc aaagtgaacc agagactaag gaggaggccc tcaagtcaga
2581 agacgacgag tttgtcatat cttctaagga catcaaggag gaaggaaaga agggcaaaaa
2641 taaaactggc cgtggcaaga aacacactgc attctccagc aagggcttga gtgatgagga
2701 gtatgacgag tataagagga taagagaaga gagaaatggg aagtactcta tagaggagta
2761 tcttcaagac agagacaggt actatgagga gctcgccatt gccaaggcca cggaagaaga
2821 cttctgtgaa gaggaggaga tcaaaatccg tcagagaatt ttccgtccca ccaggaaaca
2881 aagaaaggaa gagagggcca cactagggct agtaacgggt tcagaaatca gaaaaagaaa
2941 ccctgatgac ttcaaaccca aagggaagct gtgggccgac gacaacagaa gtgttgacta
3001 caacgaaaaa ctggactttg aggccccccc aagcatatgg tctaggatcg tgagctttgg
3061 ttctggctgg ggcttctggg tatcaccaag cctgtttata acatcaactc atgtgatccc
3121 cgcaggcata acagaagcat ttggagtctc catcaaacaa attcagatcc acaaatcagg
3181 tgaattttgc cggttcaggt tcccaaaacc aattagacca gatgttacag gaatgatctt
3241 ggaagaaggt gcgcctgagg gtaccgtggc aactgtgctc atcaaacgcc ccaccggaga
3301 gctcatgcct cttgcagcca gaatgggaac acacgcaacc atgaaaattc aaggccgcat
3361 ggttggcggg cagatgggta tgttgctcac tggatcaaat gctaaaggaa tggatttggg
3421 gacaacccct ggtgactgtg gctgccccta catctataaa agaggcaacg attatatagt
3481 cattggggtg cacactgcag cagcccgtgg tggaaacacc gtcatctgtg ccacccaggg
3541 aagtgagggt gaggcaactc ttgagggtgg agatgacaaa ggaacatact gtggggcacc
3601 cattctgggc cctgggggcg caccaaaatt gagcaccaaa accaaatttt ggaggtcatc
3661 gaatacgccc cttccaccag ggacgtatga gcctgcctac ctcggcggcc gtgatccacg
3721 tatcaagggc gggccctcct tgcagcaggt aatgagagat cagttgaagc cattcactga
3781 acccagggga aaacctccaa gaccaagtgt actagaagca gccaaacaaa ccatcatcaa
3841 tgtcctcgaa caaaccctgg atcctccaca aaaatggaca tacgcacagg cgtgtgcctc
3901 acttgacaaa accacctcca gcgggaaccc ccatcacgtc cgaaagaatg aattctggaa
3961 tggtgagacc tttactggaa aattggcaga ccaagcatca aaagcaaatc taatgtttga
4021 ggaagggaaa catatgacac cagtgtatac agcagcactc aaggacgagc tagttaagac
4081 tgagaaaatc tatggaaaga tcaagaagag gctgctctgg ggctctgact tgtccaccat
4141 ggtccggtgt gctaggtcat ttggtgggct catggacgag atgaaggcac actgcatatc
4201 actcccagtc cgagttggca tgaatatgaa tgaagatggc ccaataatat ttgagaaaca
4261 ttccagatat aagtaccact atgatgcaga ctactctcgt tgggattcaa cacaacagag
4321 ggcagtactg gcagcagcct tggaaatcat ggtcagattc tctgcagaac cacaactggc
4381 acaaatagtc gctgaggatc tgttggcccc tagtgtagta gatgtaggag acttcaaaat
4441 tacaataaat gaagggctcc cctctggtgt tccatgcact tctcaatgga actccattgc
4501 acactggctg ctaactctct gtgccttgtc tgaagtcacc aaactgtccc ctgacattat
4561 acaggcaaat tccatgttct cattttacgg tgatgacgag attgtcagca ccgatataaa
4621 attagaccct gaacagttaa ccgccaaatt gaaggagtac ggcctgaaac caacccgccc
4681 agacaaaacc gaggggcccc tgatcatcag tgaagatttg gacggactca ctttcctccg
4741 aaggacggtg actcgtgacc cagctggctg gtttggtaaa ctggaccaga gctccatttt
4801 gaggcagatg tactggacta gagggccaaa tcatgaagac cccaatgaga caatgatacc
4861 ccattctcag agacccatac agctcatggc actgcttggt gaagcctctc ttcacggacc
4921 ctctttctat agtaaaatca gcaaattggt cataactgaa ctcaaggaag gtgggatgga
4981 cttttacgtg ccaagacagg aacccatgtt caggtggatg aggttttctg acttgagcac
5041 gtgggagggc gatcgcaatc tggctcccaa ttttgtgaat gaagatggcg tcgagtgacg
5101 ccaacccatc tgatgggtcc gcagccaacc tcgtaccaga ggtcaacaat gaggttatgg
5161 ctttggagcc cgttgttggt gccgctattg cggcacctgt agcgggccaa caaaatgtaa
5221 ttgacccctg gattagaaat aattttgtac aagcccctgg tggggagttt acagtgtccc
5281 ctagaaatgc tccaggtgaa atactatgga gcgcgccctt aggccctgac ctaaatccct
5341 acctatccca tttggccagg atgtacaatg gttatgcagg tggctttgaa gtgcaggtaa
5401 ttctcgcggg gaatgcgttc accgctggga agattatatt tgcagcagtc ccaccaaatt
5461 ttccaactga aggcttaagc cctagccagg tcactatgtt cccccatata atagtagatg
5521 ttagacaatt ggaacctgtg ctgatcccct tacccgatgt taggaacaat ttctatcatt
5581 acaatcagtc aaatgattcc actattaagt tgatagcaat gttgtacaca ccacttaggg
5641 ctaataatgc tggagatgat gttttcacag tctcgtgccg agttctcacg agaccatccc
5701 ccgattttga tttcatattc ttagtaccac ccacagttga gtcaagaacc aaaccattct
5761 ccgtcccagt tttaactgtt gaggagatga ccaattcaag gttccccatc cctttggaaa
5821 agttgttcac aggccccagc agtgcatttg ttgttcaacc acaaaacggc agatgcacaa
5881 ctgatggcgt gctcctaggc accacccaac tttctcctgt caacatctgc accttcagag
5941 gggatgtcac ccacatcaca ggtagtcaca actacactat gaatttggct tctcaaaatt
6001 ggaacaacta cgacccaaca gaagaaatcc cagctcccct aggaactcca gattttgtgg
6061 ggaagattca aggcatgctc acccaaacca caaggacaga tggttcaaca cgcggccaca
6121 aagctacagt gtacactggg agcgccgact ttgctccaaa actgggtaga gttcaatttg
6181 aaactgacac aaaccatgat tttgaagcta atcaaaacac aaagttcacc ccagtcggtg
6241 ttatccaaga cggtagcacc acacaccgaa acgaacccca acagtgggtg cttccaagtt
6301 actcaggcag aaacactcac aatgtacatt tggcccccgc tgtagccccc acctttccgg
6361 gtgagcaact tctcttcttt agatctacca tgcccggatg tagcgggtac cccaacatgg
6421 atttggactg tctgctcccc caggaatggg tgcagtattt ctaccaagag gcagccccag
6481 cacaatctga tgtggccctg ctaagatttg tgaatccaga cacaggtagg gttttgtttg
6541 agtgcaagct tcacaaatca ggctatgtta cagtggctca cactggccaa catgatttgg
6601 ttatcccccc caatggttac tttaggtttg attcctgggt caaccagttc tacacgcttg
6661 cccccatggg aaatggaacg gggcgtagac gtgcagtata atggctggag ctttctttgc
6721 tggattggca tctgatgtcc ttggctccgg acttggttcc cttatcaatg ctggggctgg
6781 ggccatcaac caaaaagttg agtttgaaaa taacagaaaa ttgcaacaag catccttcca
6841 atttagcagc aatttgcaac aggcttcctt tcaacatgat aaagagatgc tccaagcaca
6901 aattgaggcc accaaaaagc tacaacagga aatgatgaga gttaagcagg caatgctcct
6961 agagggtggg ttctctgaga cagatgcggc ccgcggggca attaacgccc ccatgacaaa
7021 ggctttggac tggagcggga caaggtactg ggctccagat gctagaatta caacatacaa
7081 tgcaggccac ttttccaccc ctcaaccatc gggggcactg ccaggaagag ctaattttag
7141 ggatgctgtc cctgctcggg gaccctccac cagactttct aactcttcta ctgccacctc
7201 tgtgtattca aatcaaactg tttcaacgag acttggttct acagctggtt ctggaaccag
7261 tgtctcgagc ctcccgtcaa ctgcaaggac taggagctgg gttgaggatc aaaataggaa
7321 cttgtctcct ttcatgaggg gggcccacaa catatcattt gtcaccccac catctagcag
7381 atcctctagc caaggcacag tctcaaccgt gcctaaagaa attttggact cctggactgg
7441 cgctttcaac acgcgcaggc agcctctctt cgctcacatt cgtaagcgag gggagtcacg
7501 ggtgtaatgt gaaaagacaa aactgattat tttctttttc ttttctttag tgtctttt
//