Typing tool
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Typing tool
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Complete norovirus genomes
| OR262329 | GII.4 San Francisco | |
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| GII.P31 |
ORF1: 1..5078
ORF2: 5059..6684
ORF3: 6684..7490
LOCUS OR262329 7500 bp RNA linear VRL 11-DEC-2023
DEFINITION Norovirus GII isolate Hu/GII.4 San
Francisco[P31]/WT-NORO-2177/2021/UK nonstructural polyprotein
(ORF1) gene, partial cds; and VP1 (ORF2) and VP2 (ORF3) genes,
complete cds.
ACCESSION OR262329
VERSION OR262329.1
KEYWORDS .
SOURCE Norovirus GII
ORGANISM Norovirus GII
Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes;
Picornavirales; Caliciviridae; Norovirus; Norovirus norwalkense.
REFERENCE 1 (bases 1 to 7500)
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 7500)
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..7500
/organism="Norovirus GII"
/mol_type="genomic RNA"
/isolate="Hu/GII.4 San
Francisco[P31]/WT-NORO-2177/2021/UK"
/isolation_source="stool"
/host="Homo sapiens"
/db_xref="taxon:122929"
/geo_loc_name="United Kingdom"
/collection_date="02-Nov-2021"
/note="genotype: GII.4 San Francisco[P31]"
gene <1..5078
/gene="ORF1"
CDS <1..5078
/gene="ORF1"
/codon_start=3
/product="nonstructural polyprotein"
/protein_id="WKD81260.1"
/translation="SAAAAANSNNDIEKSSGDGVFSNMAVTFKRALGARPKQPSPREK
PPRPPRPPTPELVKRIPSPPPNGEDELVVSYSAKDGISGLPELTTVSQPEENNTAFSV
PPLNQRENRDAKEPLTGTIIEMWDGEIYHYGLYVERGLILGVHKPPAAISLAKVELAP
LSLFWRPVYTPQYLISPDTLKRLHGESFPYTAFDNNCYAFCCWVLDLNDSWLSRRMIQ
RTTGFFRPYQEWNRKPLPTMDDSKLKKVANIFLCTLSSLFTRPIKDIIGKLKPLNILN
ILATCDWTFPGIVESLILLAELFGVFWTPPDVSAMIAPLLGDYELQGPEDLAVELVPV
VMGGIGLVLGFTKEKIGKMLSSAASTLRACKDLGAYGLEILKLVMKWFFPKKEETNEL
AMVRSIEDAVLDLEAIENNHMTALLKDKDSLATYMKTLDLEEEKARKLSTKSASPDIV
GTINALLARIAAARSLVHRAKEELSSRPRPVVVMISGKPGIGKTHLARELAKKIAASL
TGDQRVGLIPRNGVDHWDAYKGERVVLWDDYGMSNPIHDALRLQELADTCPLTLNCDR
IENKGKVFDSDAIIITTNLANPAPLDYVNFEACSRRIDFLVYAEAPGVEKAKHDFPGQ
PDMWKNAFSPDFSHIKLALAPQGGFDKNGNTPHGKGVMKTLTTGSLIARASGLLHERL
DEYELQGPALTTFNFDRNKVLAFRQLAAENKYGLMDTMRVGKQLKDVKTMPDLKQALK
NVAIKKCQIVYNGGTYTLEADGKGGVRVDKVQSATVQTNNELAGALHHLRCARIRYYV
KCVQEALYSIIQIAGAAFVTTRIAKRMNIQNLWSKPQVEDTEETTSKDGCPKPKDDEE
FVVSSDDIRTEGKKGKNKSGRGKKHTAFSSKGLSDEEYDEYKRIREERNGKYSIEEYL
QDRDKYYEEVAIARATEEDFCEEEEAKIRQRIFRPTRKQRKEERASLGLVTGSEIRKR
NPEDFKPKGKLWADDDRSVDYNEKLNFEAPPSIWSRIVNFGSGWGFWVSPSLFITSTH
VIPQGAKEFFGVPIKQIQIHKSGEFCRLRFPKPIRTDVTGMILEEGAPEGTVATLLIK
RPTGELMPLAARMGTHATMRIQGRTVGGQMGMLLTGSNAKSMDLGTTPGDCGCPYIYK
RGNDYVVIGVHTAAARGGNTVICATQGSEGEATLEGGDNKGTYCGAPILGPGSAPKLS
TKTKFWRSSTTPLPPGTYEPAYLGGKDPRVKGGPSLQQVMRDQLKPFTEPRGKPPRPN
VLEAAKKTIINVLEQTIDPPQKWSFAQACASLDKTTSSGHPHHMRKNDCWNGESFTGK
LADQASKANLMFEEGKNMTPVYTGALKDELVKTDKIYGKIKKRLLWGSDLATMIRCAR
AFGGLMDELKAHCVTLPVRVGMNMNEDGPIIFEKHSRYKYHYDADYSRWDSTQQRDVL
AAALEIMVKFSPEPHLAQIVAEDLLSPSVMDVGDFQISISEGLPSGVPCTSQWNSIAH
WLLTLCALSEVTDLSPDIIQANSLFSFYGDDEIVSTDIKLDPEKLTAKLKEYGLKPTR
PDKTEGPLVISEDLDGLTFLRRTVTRDPAGWFGKLEQSSILRQMYWTRGPNHEDPSET
MIPHSQRPIQLMSLLGEAALHGPAFYSKISKLVIAELKEGGMDFYVPRQEPMFRWMRF
SDLSTWEGDRNLAPSFVNEDGVE"
mat_peptide <1..968
/gene="ORF1"
/product="p48"
mat_peptide 969..2066
/gene="ORF1"
/product="NTPase"
mat_peptide 2067..2603
/gene="ORF1"
/product="p22"
mat_peptide 2604..3002
/gene="ORF1"
/product="VPg"
mat_peptide 3003..3545
/gene="ORF1"
/product="Pro"
mat_peptide 3546..5075
/gene="ORF1"
/product="RdRp"
gene 5059..6684
/gene="ORF2"
CDS 5059..6684
/gene="ORF2"
/note="major capsid protein"
/codon_start=1
/product="VP1"
/protein_id="WKD81261.1"
/translation="MKMASSDANPSDGSAANLVPEVNNEVMALDPVVGAAIAAPVAGQ
QNVIDPWIRNNFVQAPGGEFTVSPRNAPGEILWSAPLGPDLNPYLSHLARMYNGYAGG
FEVQVILAGNAFTAGKIIFAAVPPNFPTEGLSPSQVTMFPHIIVDVRQLEPVLIPLPD
VRNNFYHYNQSNDPTIKLIAMLYTPLRANNAGDDVFTVSCRVLTRPSPDFDFIFLVPP
TVESRTKPFSVPILTVEEMTNSRFPIPLEKLFTGPSSAFVVQPQNGRCTTDGVLLGTT
QLSPVNICTFRGSVTQTAAGSHNYTMNLASQNWNSYDPTEEIPAPLGTPDFVGKIQGM
LTQTTRGDGSTRGHKATVYTGSNDFAPKLGRVQFETDTTNDFETNQNTKFTPVGVIQN
GDTAHRNEPQQWVLPSYSGRDTHNVHLAPAVAPTFPGEQLLFFRSTLPGCSGYPNMDL
DCLLPQEWVQYFYQEAAPAQSEVALLRFVNPDTGRVLFECKLHKSGYVTVAHTGQHDL
VIPPNGYFRFDSWVNQFYTLAPMGNGTGRRRAL"
gene 6684..7490
/gene="ORF3"
CDS 6684..7490
/gene="ORF3"
/note="minor structural protein; small basic protein"
/codon_start=1
/product="VP2"
/protein_id="WKD81262.1"
/translation="MAGAFFAGLASDVLGSGLGSLINAGAGAINQKIEFENNRKLQQA
SFQFSSNLQQASFQHDKEMLQAQIEATKKLQQEMMKVKQAVLLEGGFSETDAARGAIN
APMTKALDWSGTRYWAPDARTTTYNAGRFSTPQPPGALPGRANLRNAVPARGSSNTPS
NSSIATSVYSNQTASTRLGSTAGSGTSVSSLPSTARTRSWVEDQNRNLSPFMRGAHNI
SFVTPPSSRSSSQGTVSTVPKEVLDSWTGAFNTHRQPLFAHIRRRGESRV"
ORIGIN
1 cttccgctgc cgctgctgct aacagcaaca acgacatcga aaaatcttca ggtgacggtg
61 tgttttctaa catggctgtc acttttaagc gggccctcgg ggcgcggcct aaacagccgt
121 ccccgaggga aaaaccaccc agacccccac gaccacccac accagagttg gtcaaaagga
181 tcccatctcc cccacccaac ggggaggatg aactagtggt ttcttacagc gccaaagacg
241 gcatttccgg attgcctgag ctcaccaccg tcagccaacc ggaagaaaac aacacggcgt
301 tcagtgttcc cccgctcaat caaagggaga acagggacgc taaggaacca ctaactggaa
361 caatcattga gatgtgggat ggggaaatct atcattatgg cctgtacgta gaacgaggcc
421 ttatacttgg tgtgcataag ccaccggcag ccatcagtct tgccaaagtt gagctagcac
481 cactctcttt gttctggaga cctgtgtaca cccctcagta cctcatctct ccagacactc
541 ttaagagact acatggagag tcatttccct acaccgcatt tgacaacaat tgctacgcct
601 tttgctgttg ggtgttggac ctaaacgact catggctaag taggagaatg attcagagga
661 caacaggttt ctttagacca taccaagaat ggaacaggaa acccctcccc actatggatg
721 actccaaatt gaagaaggtg gccaacatat ttttgtgcac cttgtcttca ctattcacca
781 gacccattaa ggacataata ggaaaattga aacctcttaa catcctcaat attctggcca
841 catgtgattg gaccttccca ggtatagtgg agtccctaat actcttggca gaactctttg
901 gagttttctg gacaccccca gatgtgtctg cgatgatcgc ccccttacta ggtgattatg
961 aactacaagg acctgaggac cttgcagtag aactggtccc agtggtgatg ggggggatag
1021 gtttggtgct aggattcacc aaagagaaaa ttggaaagat gctgtcatcc gctgcatcca
1081 ccttgagagc ttgcaaagac cttggtgcat acggactgga aattttgaaa ctagtcatga
1141 agtggttctt cccaaagaaa gaggaaacaa atgaactggc tatggtaaga tccatcgagg
1201 acgcagtact agacctcgag gcaattgaaa acaaccacat gaccgccctg ctcaaagaca
1261 aagacagctt ggcaacctac atgaaaaccc ttgatcttga ggaggagaaa gccagaaaac
1321 tctcaactaa atccgcttca cctgatattg tgggcacaat caacgctctc ctggcacgaa
1381 tcgccgctgc acgttcccta gtgcatcggg cgaaagaaga gctctccagc aggccgagac
1441 ctgttgttgt gatgatatcg ggaaaaccag ggatagggaa aactcacctt gccagggagt
1501 tggccaaaaa gattgcagcc tccctcacag gggaccagcg tgtgggtttg atcccacgca
1561 acggcgtcga ccactgggat gcatacaagg gtgaaagagt tgtcctatgg gacgactatg
1621 ggatgagcaa ccccatacac gatgccctca ggttgcagga acttgctgac acttgccccc
1681 tcacactaaa ttgtgatagg attgagaaca aagggaaagt ctttgatagt gatgccataa
1741 ttattaccac caacctggcc aacccagcac cactggatta tgtcaacttt gaagcgtgtt
1801 cgaggcgcat tgacttcctc gtgtatgcgg aagctcctgg ggtggagaag gcaaaacacg
1861 acttcccagg ccaacctgac atgtggaaga acgctttcag ccctgacttc tcacacataa
1921 aactagcatt ggctccacag ggtggttttg acaagaacgg caacaccccg catggaaaag
1981 gtgtcatgaa gaccctcacc actggctccc tcatcgcccg agcatcaggg ttgctccatg
2041 agagactaga tgaatatgaa ttgcaaggcc cagccctcac cactttcaac ttcgaccgca
2101 acaaggtgct tgcttttaga cagctcgctg ctgaaaacaa gtatggtcta atggacacga
2161 tgagagttgg aaaacagctc aaggacgtta agactatgcc agaccttaaa caagcactca
2221 agaatgtcgc gatcaagaaa tgccagatag tgtacaatgg tggcacctac acacttgagg
2281 ccgacggtaa gggtggtgtg agagttgaca aagtgcaaag tgccaccgtg caaaccaaca
2341 atgaactagc cggcgccctg caccacctaa ggtgcgccag gatcaggtat tatgttaagt
2401 gcgtccagga agcactgtac tccatcatcc aaatcgctgg ggctgcgttt gtcaccacgc
2461 gcatcgccaa gcgcatgaat atacaaaatc tctggtccaa gccacaggtg gaagacacag
2521 aagagacaac cagcaaggat ggttgcccaa aacccaaaga tgatgaagag ttcgtcgttt
2581 catccgacga catcagaact gagggcaaga aagggaagaa caagtccggc cgtggcaaga
2641 agcacacagc cttctcaagc aaagggctca gtgatgaaga gtacgatgag tacaagagaa
2701 ttagagaaga gaggaatggt aagtactcca tagaggagta cctccaggac agagacaagt
2761 actatgagga agtggccatt gccagggcaa ctgaagagga cttctgtgaa gaagaagagg
2821 ctaaaatccg gcagagaatt ttcagaccaa caaggaaaca acgtaaagaa gagagggcct
2881 ccctaggctt ggtcacaggt tcagaaatca ggaaaagaaa cccagaagac ttcaaaccca
2941 agggaaaact atgggctgat gatgacagaa gtgttgacta caatgagaag ctcaactttg
3001 aggccccacc aagcatctgg tcgcggatag tcaactttgg ttcaggttgg ggtttctggg
3061 tctcccccag tctgtttata acatcaaccc atgtcatacc tcaaggtgca aaagagttct
3121 tcggagtccc catcaaacaa atccagatac acaaatcagg tgaattctgc cgactgagat
3181 tcccaaaacc aatcagaact gatgtgacgg gcatgattct ggaagaaggc gcgccagaag
3241 gaaccgtggc cacactgctc attaagagac caactggaga actcatgcct ttggcagcca
3301 gaatggggac ccatgcaacc atgaggattc aggggcgcac ggttggagga caaatgggta
3361 tgctcttgac aggatccaac gccaagagta tggacttggg cacaacacca ggcgactgtg
3421 gctgtcccta catctacaag agagggaatg actacgtggt tataggagtc catacagccg
3481 ctgcccgtgg aggaaacact gtcatctgcg ccacccaggg tagtgaagga gaagccacac
3541 ttgaaggagg tgacaacaaa ggaacgtact gtggtgcacc gattttgggc ccagggagtg
3601 ctccgaaact cagcactaaa actaagtttt ggagatcatc cacgacgcca ctcccaccag
3661 gcacctacga accagcttac ctcggtggca aggaccctag agtcaaaggt ggcccttcat
3721 tgcaacaagt tatgagggac caactaaaac cattcacaga acccaggggc aaaccgccaa
3781 gaccaaatgt gttggaagct gccaagaaaa ccatcattaa tgttcttgag caaacaattg
3841 acccacccca aaaatggtca ttcgcgcaag cttgcgcatc cctcgacaaa accacctcca
3901 gcggccatcc gcaccacatg cggaaaaacg actgctggaa tggggagtcc tttacaggaa
3961 aattggcaga tcaggcctct aaggccaacc taatgttcga agagggaaag aacatgactc
4021 cagtttacac aggtgcactt aaagatgagt tagtgaagac tgacaaaatt tatggtaaga
4081 tcaagaagag gctcctgtgg ggctcggacc tggcgaccat gatacggtgc gcccgggcct
4141 tcggaggcct tatggatgaa ctcaaggcgc attgtgtcac ccttcctgtc agagttggta
4201 tgaatatgaa tgaagatggc cccataatct ttgagaagca ctccagatat aaataccatt
4261 atgatgctga ttactccagg tgggactcga cacagcaaag ggatgtgtta gcagcagcac
4321 tagaaatcat ggttaagttc tctccagaac cacacttggc ccagatagtt gcagaagacc
4381 tcctttcccc tagtgtaatg gatgtgggtg actttcaaat atcaataagt gaaggactcc
4441 cctccggggt gccttgcacc tcccagtgga attccatcgc ccactggctc ctcacccttt
4501 gtgcactctc tgaagtcacg gacctgtccc ctgacatcat tcaggccaat tcccttttct
4561 ccttttatgg cgatgatgag attgtgagta cagacataaa gttggaccca gagaagctga
4621 cggcaaaact caaagagtac gggctaaagc caacccgccc cgacaagact gaaggacccc
4681 ttgtcatctc tgaagatctg gatggcctga cattcctccg gaggactgtg acccgtgacc
4741 cagctggctg gtttgggaaa ttggaacaaa gttcaatcct caggcaaatg tattggacca
4801 ggggtcccaa ccatgaagac ccatctgaaa caatgatacc acactcccaa agacccatac
4861 aattgatgtc cttgctaggc gaggctgcac tccacggccc agcattttac agcaaaatta
4921 gcaaattggt cattgcagaa ttaaaggagg gtggcatgga tttttacgtg cccaggcagg
4981 aaccaatgtt cagatggatg agattctcag atctgagcac gtgggagggc gatcgcaatc
5041 tggctcccag ttttgtgaat gaagatggcg tcgagtgacg ccaacccatc tgatgggtcc
5101 gcagccaacc tcgtcccaga ggtcaacaat gaggttatgg ctctggatcc cgttgttggt
5161 gccgctattg cggcgcctgt agcgggccaa caaaatgtaa ttgacccctg gattagaaat
5221 aattttgtgc aagcccctgg tggagagttt acagtgtcac ctagaaatgc tccaggtgaa
5281 atactatgga gcgctccctt aggccctgat ctaaacccct acctatccca tttggccaga
5341 atgtacaatg gttatgcagg tggttttgaa gtgcaggtaa tccttgcggg gaacgcgttc
5401 accgccggaa agatcatatt tgcagcagtc ccacctaatt ttccaactga aggtctgagc
5461 cccagccagg tcactatgtt cccccatata atagtagatg ttagacaact ggaacctgtg
5521 ttgattcccc tgcccgatgt taggaataat ttctatcact ataaccaatc aaacgatccc
5581 accattaagt tgatagcaat gttgtataca ccacttaggg ctaataatgc tggggatgat
5641 gtcttcacag tttcttgtcg agtcctcacg agaccatccc ctgattttga ctttatattc
5701 ttagtgccac ccacagttga gtcaagaact aaaccatttt ctgtcccaat tttaactgtt
5761 gaggagatga ctaattcaag attccccatt cctttggaaa agttgttcac aggtcccagc
5821 agtgcctttg ttgttcaacc acaaaatggc aggtgcacga ctgatggcgt gctcctaggt
5881 accacccaat tgtcccctgt caacatctgc accttcagag ggagtgtcac ccaaacagca
5941 gcaggtagtc ataactacac aatgaatttg gcctcccaaa attggaacag ttatgatcca
6001 acagaagaaa tcccagcccc tttaggaact ccagatttcg tagggaagat tcaaggtatg
6061 ctcacccaaa ccacaagagg agatggctca acacgcggcc acaaagccac agtgtacact
6121 gggagcaacg actttgctcc aaaactgggt agggttcaat ttgaaactga cacaaccaac
6181 gattttgaaa ctaaccaaaa cacaaagttc accccggtcg gcgtcatcca gaatggtgac
6241 actgcccacc gaaatgaacc ccaacaatgg gtgctcccaa gttattcagg cagagacact
6301 cataatgtgc acctggcccc cgctgtagct cccacttttc cgggagagca actcctcttc
6361 ttcagatcta ccttgcccgg atgcagcggg taccccaaca tggatttgga ttgtctgctt
6421 ccccaggagt gggtgcagta cttctatcaa gaggcagccc cagcacaatc cgaagtggct
6481 ctgttaagat ttgtgaatcc agacacaggt agggttttgt ttgagtgcaa gctccacaaa
6541 tcgggctatg tcacagtggc tcacactggc cagcatgatt tggttatccc ccccaatggt
6601 tatttcagat ttgattcctg ggttaatcaa ttctacacgc ttgcccccat gggaaatgga
6661 acggggcgta gacgtgcatt ataatggctg gagctttctt tgctggattg gcatctgatg
6721 tccttggctc tggacttggt tccctgatca atgctggggc tggggccatc aaccaaaaga
6781 ttgaatttga aaataacaga aaattgcaac aagcttcctt ccaattcagt agcaacctac
6841 aacaggcttc ctttcaacat gacaaagaga tgctccaagc acaaattgag gccaccaaaa
6901 agctgcaaca ggaaatgatg aaagttaagc aggcagtgct cttagagggc gggttctctg
6961 agacagatgc agcccgcggg gcaatcaatg cccccatgac aaaagctttg gattggagcg
7021 gtacaaggta ttgggcccct gatgctagaa ctacaacata caatgcaggc cgcttctcca
7081 caccccaacc accgggggca ctgccaggaa gagctaacct caggaatgct gtccctgctc
7141 ggggttcctc taatacacct tccaattcct ctattgctac ttctgtgtac tcaaatcaaa
7201 ctgcttcaac gagacttggt tctacagctg gttctgggac cagtgtctcg agtctcccgt
7261 caactgcaag gactaggagt tgggttgagg atcaaaatag gaatctgtca cctttcatga
7321 ggggggccca caacatatcg tttgtcaccc caccatctag cagatcctct agccaaggca
7381 cagtctcaac cgtgcctaaa gaagttttgg actcctggac tggtgctttc aacacgcaca
7441 ggcagcctct cttcgctcac attcgtaggc gaggggagtc acgggtgtaa tgtgaaaaga
//