Typing tool
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Typing tool
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Complete norovirus genomes
| OR262327 | GII.4 San Francisco | |
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| GII.P31 |
ORF1: 1..5088
ORF2: 5069..6694
ORF3: 6694..7500
LOCUS OR262327 7546 bp RNA linear VRL 11-DEC-2023
DEFINITION Norovirus GII isolate Hu/GII.4 San
Francisco[P31]/WT-NORO-1808/2021/UK nonstructural polyprotein
(ORF1) gene, partial cds; and VP1 (ORF2) and VP2 (ORF3) genes,
complete cds.
ACCESSION OR262327
VERSION OR262327.1
KEYWORDS .
SOURCE Norovirus GII
ORGANISM Norovirus GII
Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes;
Picornavirales; Caliciviridae; Norovirus; Norovirus norwalkense.
REFERENCE 1 (bases 1 to 7546)
AUTHORS Chhabra,P., Tully,D.C., Mans,J., Niendorf,S., Barclay,L.,
Cannon,J.L., Montmayeur,A.M., Pan,C.Y., Page,N., Williams,R.,
Tutill,H., Roy,S., Celma,C., Beard,S., Mallory,M.L., Manouana,G.P.,
Velavan,T.P., Adegnika,A.A., Kremsner,P.G., Lindesmith,L.C.,
Hue,S., Baric,R.S., Breuer,J. and Vinje,J.
TITLE Emergence of Novel Norovirus GII.4 Variant
JOURNAL Emerg Infect Dis 30 (1) (2023) In press
PUBMED 38063078
REMARK Publication Status: Available-Online prior to print
REFERENCE 2 (bases 1 to 7546)
AUTHORS Tutill,H.J., Williams,R.J., Roy,S. and Breuer,J.
TITLE Direct Submission
JOURNAL Submitted (12-JUL-2023) Viral Gastroenteritis Branch, Centers for
Disease Control and Prevention, 1600 Clifton Road NE, Atlanta, GA
30329, USA
COMMENT ##Assembly-Data-START##
Assembly Method :: CLC Genomics Workbench v. 11.0.01
Sequencing Technology :: Illumina
##Assembly-Data-END##
FEATURES Location/Qualifiers
source 1..7546
/organism="Norovirus GII"
/mol_type="genomic RNA"
/isolate="Hu/GII.4 San
Francisco[P31]/WT-NORO-1808/2021/UK"
/isolation_source="stool"
/host="Homo sapiens"
/db_xref="taxon:122929"
/geo_loc_name="United Kingdom"
/collection_date="Jul-2021"
/note="genotype: GII.4 San Francisco[P31]"
gene <1..5088
/gene="ORF1"
CDS <1..5088
/gene="ORF1"
/codon_start=1
/product="nonstructural polyprotein"
/protein_id="WKD81254.1"
/translation="SNDASAAAAANSNNDIEKSSSDGVFSNMAVTFKRALGARPKQPP
PKEIPPRPPRPPTPELAKKIPPPPPNGEDELVVSYSAKGGVSGLPELTTVSQPEENNT
AFSVPPLNQRENRDAKEPLTGTIIEMWDGEIYHYGLYVERGLILGVHKPPAAISLAKV
ELAPLSLFWRPVYTPQYLISPDTLKRLHGELFPYTAFDNNCYAFCCWVLDLNDSWLSR
RMIQRTTGFFRPCQEWNRKPLPTMDDSKLKKVANIFLCTLSSLFTRPIKDIIGKLKPL
NILNILATCDWTFPGIVESLILLAELFGVFWTPPDVSAMIAPLLGDYELQGPEDLAVE
LVPVVMGGIGLVLGFTKEKIGKMLSSAASTLRACKDLGAYGLEILKLVMKWFFPKKEE
ANELAMVRSIEDAVLDLEAIENNHMTTLLKDKDSLATYMRTLDLEEEKARKLSTKSAS
PDIVGTINALLARIAAARSLVHRAKEELSSRLRPVVVMISGKPGIGKTHLARELAKKI
AASLTGDQRVGLIPRNGVDHWDAYKGERVVLWDDYGMSNPIHDALRLQELADTCPLTL
NCDRIENKGKVFDSDAIIITTNLANPAPLDYVNFEACSRRIDFLVYAEAPGVEKAKHD
FPGQPDMWKNAFSSDFSHIKLALAPQGGFDKNGNTPHGKGVMKTLTTGSLIARASGLL
HERLDEYELQGPALTTFNFDRNKVLAFRQLAAENKYGLMDTMRVGKQLKDVKTMSDLK
QALKNVSIKKCQIVYNGGTYTLEADGKGSVKVDKVQSATVQTNNELAGALHHLRCARI
RYYVKCVQEALYSIIQIAGAAFVTTRIAKRMNIQNLWSKPQVEDTEETTNKDGCPKPK
EDEEFVVSSDDIKTEGKKGKNKSGRGKKHTAFSSKGLSDEEYDEYKRIREERNGKYSI
EEYLQDRDKYYEEVAIARATEEDFCEEEEAKIRQRIFRPTRKQRKEERASLGLVTGSE
IRKRNPEDFKPKGKLWADDDRSVDYNEKLNFEAPPSIWSRIVNFGSGWGFWVSPSLFI
TSTHVIPQGANEFFGVPIKQIQIHKSGEFCRLRFPKPIRTDVTGMILEEGAPEGTVAT
LLIKRPTGELMPLAARMGTHATMRIQGRTVGGQMGMLLTGSNAKSMDLGTTPGDCGCP
YIYKRGNDYVVIGVHTAAARGGNTVICATQGSEGEATLEGGDNKGTYCGAPILGPGSA
PKLSTKTKFWRSSTTPLPPGTYEPAYLGGKDPRVKGGPSLQQVMRDQLKPFTEPRGKP
PRPSVLEAAKKTIINVLEQTIDPPQKWSFAQACASLDKTTSSGHPHHMRKNDCWNGES
FTGKLADQASKANLMFEEGKNMTPVYTGALKDELVKTDKIYGKIKKRLLWGSDLATMI
RCARAFGGLMDELKAHCVTLPVRVGMNMNEDGPIIFEKHSRYKYHYDADYSRWDSTQQ
RDVLAAALEIMVKFSPEPHLAQIVAEDLLSPSVMDVGDFQILISEGLPSGVPCTSQWN
SIAHWLLTLCALSEVTDLSPDIIQANSLFSFYGDDEIVSTDIKLDPEKLTAKLKEYGL
KPTRPDKTEGPLVISEDLDGLTFLRRTVTRDPAGWFGKLEQSSILRQMYWTRGPNHED
PSETMIPHSQRPIQLMSLLGEAALHGPSFYSKISKLVIAELKEGGMDFYVPRQEPMFR
WMRFSDLSTWEGDRNLAPSFVNEDGVE"
mat_peptide <1..978
/gene="ORF1"
/product="p48"
mat_peptide 979..2076
/gene="ORF1"
/product="NTPase"
mat_peptide 2077..2613
/gene="ORF1"
/product="p22"
mat_peptide 2614..3012
/gene="ORF1"
/product="VPg"
mat_peptide 3013..3555
/gene="ORF1"
/product="Pro"
mat_peptide 3556..5085
/gene="ORF1"
/product="RdRp"
gene 5069..6694
/gene="ORF2"
CDS 5069..6694
/gene="ORF2"
/note="major capsid protein"
/codon_start=1
/product="VP1"
/protein_id="WKD81255.1"
/translation="MKMASSDANPSDGSAANLVPEVNNEVMALEPVVGAAIAAPVAGQ
QNVIDPWIRNNFVQAPGGEFTVSPRNAPGEILWSAPLGPDLNPYLSHLARMYNGYAGG
FEVQVILAGNAFTAGKIIFAAVPPNFPTEGLSPSQVTMFPHIIVDVRQLEPVLIPLPD
VRNNFYHYNQSNDPTIKLIAMLYTPLRANNAGDDVFTVSCRVLTRPSPDFDFIFLVPP
TVESRTKPFSVPILTVEEMTNSRFPIPLEKLFTGPSSTFVVQPQNGRCTTDGVLLGTT
QLSPVNICTFRGSVTQTATGSHNYTMNLASQNWNSYDPTEDIPAPLGTPDFVGKIQGV
LTQTTRGDGSTRGHKATLYTGSNDFTPKLGRVQFETDTNHDFEANQNTKFTPVGVIQN
GDTAHRNEPQQWVLPSYSGRNTHNVHLAPVVAPTFPGEQLLFFRSTLPGCSGYPNMDL
DCLLPQEWVQYFYQEAAPAQSEVALLRFVNPDTGRVLFECKLHKSGYVTVAHTGQHDL
VIPPNGYFRFDSWVNQFYTLAPMGNGTGRRRAL"
gene 6694..7500
/gene="ORF3"
CDS 6694..7500
/gene="ORF3"
/note="minor structural protein; small basic protein"
/codon_start=1
/product="VP2"
/protein_id="WKD81256.1"
/translation="MAGAFFAGLASDVLGSGLGSLINAGAGAINQKIEFENNRKLQQA
SFQFSSNLQQASFQHDKEMLQAQIEATKKLQQEMMKVKQAVLLEGGFSETDAARGAIN
APMTKALDWSGTRYWAPDARTTTYNAGRFSTPQPSGALPGRANFRNAAPARGSSSTPS
NSSIATSVYSNQTASTRLGSTAGSGTSVSSPPSTARTRSWVEDQNRNLSPFMRGAHNI
SFVTPPSSRSSSQGTVSTVPKEVLDSWTGAFNTHRQPLFAHIRRRGESRV"
ORIGIN
1 tctaacgacg cttccgctgc cgctgctgct aacagcaaca acgacatcga aaaatcttca
61 agtgacggtg tgttttctaa catggctgtc acttttaagc gggccctcgg ggcgcggccc
121 aaacagccgc ccccgaagga aataccaccc agacccccac gaccacccac accagagttg
181 gccaaaaaga tcccacctcc cccacccaat ggggaggatg aactagtggt ttcttacagc
241 gccaaaggcg gcgtttccgg attgcctgag ctcaccaccg tcagccaacc agaagaaaac
301 aacacggcgt tcagtgttcc cccgctcaat caaagggaga atagggacgc taaggaacca
361 ctaactggaa cgatcattga gatgtgggat ggggaaatct atcattacgg cctgtacgta
421 gaacgaggcc ttatacttgg tgtgcacaag ccaccggcag ccatcagcct tgccaaagtt
481 gagctagcac cactctctct gttctggaga cctgtgtata ccccccagta cctcatctct
541 ccagacactc ttaagagact acatggagag ttattcccct acaccgcatt tgacaacaac
601 tgctacgcct tctgctgttg ggtgttagac ctaaacgact catggttaag taggagaatg
661 attcagagaa caacaggttt cttcaggcca tgccaagagt ggaacaggaa acccctcccc
721 actatggatg actccaaatt gaagaaggta gccaacatat tcttgtgcac tttgtcttca
781 ctattcacca ggcccattaa ggacataata ggaaaattga aacctctcaa catcctcaat
841 attctggcca catgtgattg gaccttccca ggcatagtgg aatccctgat actcttggca
901 gaactctttg gagttttctg gacaccccca gatgtgtctg cgatgatcgc ccccttacta
961 ggtgattatg aactgcaagg gcctgaggac cttgcagtag aactggtccc agtggtaatg
1021 ggggggatag gtttggtgct aggattcacc aaagagaaaa ttggaaagat gctgtcgtcc
1081 gctgcatcca ccttgagagc ttgcaaagac cttggtgcat acggactgga aattttgaaa
1141 ctagtcatga agtggttctt tccaaagaaa gaggaagcaa atgaactggc tatggtgaga
1201 tccatcgagg acgcagtgct agacctcgag gcaatcgaaa acaaccatat gaccaccctg
1261 ctcaaggaca aagacagctt ggcaacctac atgagaaccc ttgaccttga ggaggagaaa
1321 gccagaaaac tctcaaccaa gtccgcttca cctgatattg tgggcacaat caacgctctt
1381 ctggcacgaa tcgccgctgc acgctcccta gtgcatcggg cgaaagagga gctctccagc
1441 aggctgagac ctgttgttgt gatgatatcg ggaaaaccag ggatagggaa aactcacctt
1501 gccagggagt tggccaaaaa gatcgcagcc tccctcacag gggaccagcg tgtgggtttg
1561 atcccacgca acggcgtcga ccactgggat gcatacaagg gtgaaagagt tgtcctttgg
1621 gacgactatg ggatgagtaa ccccatacac gatgccctca ggttgcagga acttgctgac
1681 acttgccccc tcacactaaa ttgtgatagg attgagaaca aaggaaaagt ctttgatagc
1741 gatgccataa ttattaccac caatctggcc aacccagcac cactggatta tgtcaatttt
1801 gaagcgtgtt cgaggcgcat tgacttcctc gtgtacgcgg aagctcctgg ggtggagaag
1861 gcaaaacacg acttcccagg ccaacctgac atgtggaaga acgctttcag ctctgacttc
1921 tcacacataa aactggcatt ggctccacag ggtggttttg acaagaacgg taacaccccg
1981 catggaaaag gtgtcatgaa gaccctcacc actggctctc tcatcgcccg agcatcaggg
2041 ttactccacg agaggctaga tgaatatgaa ttacaaggcc ctgccctcac cactttcaac
2101 tttgaccgca ataaggtact tgcttttagg cagctcgctg ctgaaaacaa gtatggtcta
2161 atggacacaa tgagagttgg aaaacagctc aaggatgtca aaactatgtc agaccttaaa
2221 caagcactca agaatgtttc gatcaagaaa tgccagatag tgtacaatgg tggcacctac
2281 acacttgaag ccgacggcaa gggtagtgtg aaagttgaca aggtgcaaag tgccaccgtg
2341 caaaccaaca atgaactagc cggcgccctg caccacctaa ggtgcgccag aattaggtat
2401 tatgtcaagt gtgtccagga ggcgctgtac tccatcatcc aaatcgctgg ggctgcgttt
2461 gtcaccacgc gcatcgccaa gcgcatgaat atacaaaatc tctggtccaa gccacaggtg
2521 gaagacacag aagagacaac caacaaagat ggttgcccaa aacccaaaga ggatgaagag
2581 ttcgtcgttt catccgacga cattaaaact gagggcaaga aagggaagaa caagtccggc
2641 cgtggcaaga agcacacagc cttctcaagt aaagggctca gtgatgaaga gtacgatgag
2701 tacaagagaa ttagagaaga gaggaatggt aagtactcca ttgaggagta cctccaggac
2761 agagacaaat actatgagga agtggccatt gccagggcaa ctgaagagga cttctgtgaa
2821 gaagaagagg ccaaaatccg gcagagaatc ttcaggccaa caaggaaaca acgtaaagaa
2881 gagagggcct ctctaggctt ggtcacaggc tcagaaatca ggaagagaaa cccagaagac
2941 ttcaaaccca agggaaagct gtgggctgat gatgacagaa gtgttgacta caacgagaag
3001 ctcaactttg aggccccacc aagcatctgg tcgcggatag tcaactttgg ttcaggttgg
3061 ggtttctggg tctcccccag tctgtttata acgtcaaccc atgtcatacc ccaaggtgca
3121 aacgagttct tcggagtccc catcaaacaa atccagatac acaaatcagg tgaattctgc
3181 cgactgagat tcccaaaacc aatcagaact gatgtgacgg gcatgattct ggaagaaggt
3241 gcgccagaag gaaccgtggc cacactgctc atcaagagac caactggaga gctcatgcct
3301 ttggcagcca gaatgggaac ccatgcaacc atgaggattc aggggcgcac ggttggagga
3361 caaatgggta tgctcttgac aggatccaac gccaagagta tggacttggg cacaacgcca
3421 ggcgactgtg gctgtcccta catctacaaa agagggaacg actacgtggt tataggagtc
3481 catacagccg ctgcccgtgg agggaacact gtcatctgcg ccacccaggg tagtgaagga
3541 gaagccacac ttgaaggagg tgacaataaa ggaacgtact gtggtgcacc aattttgggc
3601 ccagggagtg ctccgaaact cagtactaaa accaagtttt ggagatcatc cacaacgcca
3661 ctcccaccag gcacctacga accagcctac ctcggtggca aggaccccag agtcaaaggt
3721 ggcccttcat tgcaacaagt tatgagggac caactaaaac cattcacaga acccagaggc
3781 aaaccgccaa gaccaagtgt gttggaagct gccaagaaaa ccatcattaa tgtccttgag
3841 caaacaattg acccacccca aaaatggtcg ttcgcgcaag cttgcgcatc ccttgacaaa
3901 accacctcca gcggccatcc gcatcacatg cggaaaaacg actgctggaa tggggaatcc
3961 tttacaggaa aattggcaga tcaggcctcc aaggccaacc taatgtttga agagggtaag
4021 aacatgactc cagtctacac aggtgcgctt aaagatgaat tagtgaagac tgacaagatt
4081 tatggtaaga tcaagaagag gctcctgtgg ggctcggacc tggcgaccat gatacggtgc
4141 gcccgggctt tcgggggcct tatggatgaa ctcaaggcac attgtgtcac ccttcctgtc
4201 agagttggta tgaacatgaa tgaagatggc cccataatct ttgagaagca ctccagatat
4261 aagtatcatt atgatgctga ttactccagg tgggactcga cacaacaaag ggatgtgcta
4321 gcagcagcac tagaaatcat ggttaagttt tctccagaac cacacttggc ccagatagtt
4381 gcagaagacc tcctttcccc tagtgtaatg gatgtgggtg acttccagat attaataagt
4441 gaaggactcc cctctggagt accttgcacc tcccagtgga actccatcgc ccactggctc
4501 ctcacccttt gtgcactctc tgaagtcacg gacctgtccc ctgacatcat tcaggccaac
4561 tcccttttct ccttctatgg tgatgatgag attgtgagta cagacataaa gttggaccca
4621 gagaagctga cggcaaaact caaggagtac gggctgaagc caacccgccc cgacaaaact
4681 gaaggacccc ttgtcatctc tgaagatctg gatggcctga cattcctccg gaggactgtg
4741 acccgtgacc cagctggctg gtttggaaaa ttggaacaaa gttcgattct caggcaaatg
4801 tactggacca ggggtcccaa ccatgaagac ccatctgaaa caatgatacc acactcccaa
4861 aggcccatac aattgatgtc cttgctaggc gaggctgcac tccacggccc atcattttac
4921 agcaaaatta gcaaattggt cattgcagaa ttgaaggaag gtggcatgga tttttacgtg
4981 cccagacaag agccaatgtt cagatggatg agattctcag atctgagcac gtgggagggc
5041 gatcgcaatc tggctcccag ttttgtgaat gaagatggcg tcgagtgacg ccaacccatc
5101 tgatgggtcc gcagccaacc tcgtcccaga ggtcaacaat gaggttatgg ctctggagcc
5161 cgttgttggt gccgctattg cggcgcctgt agcgggccaa caaaatgtga ttgacccctg
5221 gattagaaat aattttgtgc aagcccctgg tggagagttt acagtatccc ctagaaacgc
5281 tccaggtgaa atactatgga gcgcaccctt aggccctgat ctaaacccct acctatccca
5341 tttggctaga atgtataatg gttatgcagg tggttttgaa gtgcaggtaa ttcttgcggg
5401 gaatgcgttc accgccggaa agatcatatt tgcagcagtc ccaccaaatt tcccaactga
5461 aggcttgagc ccaagccagg tcactatgtt cccccatata atagtagatg ttagacaact
5521 ggagcctgtg ttgatcccct tacccgatgt taggaataat ttctatcact ataaccaatc
5581 aaatgacccc accattaagt tgatagcaat gttgtataca ccacttaggg ctaataatgc
5641 tggggatgat gtcttcacgg tttcttgccg agtcctcacg agaccatccc ctgattttga
5701 tttcatattc ttagtaccac ccacagttga atcaagaact aaaccattct ctgtcccaat
5761 tttaactgtt gaggagatga ctaattcaag attccccatt cctttggaaa aattgttcac
5821 aggtcccagc agtacctttg ttgttcaacc acagaatggt aggtgtacga ctgatggcgt
5881 gctcctaggt accacccaat tgtcacctgt caacatctgc accttcagag ggagtgtcac
5941 ccaaacagcg acaggtagtc ataactacac aatgaatctg gcttcccaaa attggaacag
6001 ttatgatcca acagaagaca tcccagcccc tctaggaact ccagatttcg tagggaagat
6061 tcaaggtgtg ctcacccaga ccacaagagg agatggctca acacgcggcc acaaagccac
6121 attgtatact gggagcaacg atttcactcc aaaactgggt agggtccaat ttgaaactga
6181 cacaaaccac gattttgagg ccaaccaaaa cacaaagttc actccggtcg gcgtcatcca
6241 gaacggagac actgcccacc gaaatgaacc tcaacaatgg gtgctcccaa gttattcagg
6301 cagaaacact cataatgtgc atctggcccc cgttgtagct cccacttttc cgggcgagca
6361 gctcctcttc ttcagatcta ccttgcctgg atgcagcggg tatcccaaca tggatttgga
6421 ttgtctactc ccccaggaat gggtgcagta cttctatcaa gaggcagccc cagcacaatc
6481 tgaagtggct ctgttgaggt ttgtgaatcc agacacaggt agggttttgt ttgagtgtaa
6541 gctccacaaa tcgggctatg tcacagtggc ccacactggc caacatgatt tggttatccc
6601 ccccaatggt tatttcagat ttgattcctg ggtcaaccaa ttctacacgc ttgcccccat
6661 gggaaatgga acggggcgca gacgtgcatt ataatggctg gagctttctt tgctggattg
6721 gcatctgatg tccttggctc tggacttggt tccctgatca acgctggggc tggggccatc
6781 aatcaaaaga ttgaatttga aaacaacaga aaattgcaac aagcttcatt ccaatttagt
6841 agcaacctac aacaggcttc ctttcaacat gacaaagaga tgctccaagc acaaattgag
6901 gccaccaaaa agctgcaaca ggaaatgatg aaagttaagc aggcagtgct cctagagggt
6961 gggttttctg agacagatgc agcccgcgga gcaatcaacg cccctatgac aaaagctttg
7021 gactggagcg gtacaaggta ttgggcaccc gatgctagga ctacaacata caatgcaggc
7081 cgcttctcta ccccccaacc atcgggggca ctgccaggaa gagctaactt caggaatgct
7141 gcccccgctc ggggttcctc tagtacaccc tccaattcct ctattgctac ttctgtgtac
7201 tcaaatcaaa ctgcttcaac gagacttggt tctacagccg gttctgggac cagtgtctcg
7261 agccccccgt caactgcaag gactaggagc tgggttgagg atcaaaacag gaatctgtcg
7321 cctttcatga ggggggccca caacatatcg tttgtcaccc caccatctag cagatcctct
7381 agccaaggca cagtctcaac cgtgcctaaa gaagttttgg actcctggac tggtgctttc
7441 aacacgcaca ggcagcctct cttcgctcac attcgtaggc gaggggagtc acgggtgtaa
7501 tgtgaaaaga caaaattgat tatctttctt ttctttagtg tctttt
//