Typing tool
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Typing tool
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Complete norovirus genomes
| OR262328 | GII.4 San Francisco | |
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| GII.P31 |
ORF1: 1..5093
ORF2: 5074..6699
ORF3: 6699..7505
LOCUS OR262328 7551 bp RNA linear VRL 11-DEC-2023
DEFINITION Norovirus GII isolate Hu/GII.4 San
Francisco[P31]/WT-NORO-1954/2019/UK nonstructural polyprotein
(ORF1) gene, partial cds; and VP1 (ORF2) and VP2 (ORF3) genes,
complete cds.
ACCESSION OR262328
VERSION OR262328.1
KEYWORDS .
SOURCE Norovirus GII
ORGANISM Norovirus GII
Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes;
Picornavirales; Caliciviridae; Norovirus; Norovirus norwalkense.
REFERENCE 1 (bases 1 to 7551)
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 7551)
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..7551
/organism="Norovirus GII"
/mol_type="genomic RNA"
/isolate="Hu/GII.4 San
Francisco[P31]/WT-NORO-1954/2019/UK"
/isolation_source="stool"
/host="Homo sapiens"
/db_xref="taxon:122929"
/geo_loc_name="United Kingdom"
/collection_date="21-Nov-2019"
/note="genotype: GII.4 San Francisco[P31]"
gene <1..5093
/gene="ORF1"
CDS <1..5093
/gene="ORF1"
/codon_start=3
/product="nonstructural polyprotein"
/protein_id="WKD81257.1"
/translation="ASNDASAAAAANSNNDIEKSSSDGVFSNMAVTFKRALGARPKQP
PPREKPPRPPRPPTPELVKRIPPPPPNGEDELVVSYNAKDGVSGLPELTTVSQPEENN
TAFSVPPLNQRENRDAKEPLTGTIIEMWDGEIYHYGLYVERGLILGVHKPPAAISLAK
VELTPLSLFWRPVYTPQYLISPDTLKRLHGESFPYTAFDNNCYAFCCWVLDLNDSWLS
RRMIQRTTGFFRPYQEWNRKPLPTMDDSKLKKVANIFLCTLSSLFTRPIKDIIGKLKP
LNILNILATCDWTFPGIVESLILLAELFGVFWTPPDVSAMIAPLLGDYELQGPEDLAV
ELVPVVMGGIGLVLGFTKEKIGKMLSSAASTLRACKDLGAYGLEILKLVMKWFFPKKE
ETNELAMVRSIEDAVLDLEAIENNHMTALLKDKDSLATYMKTLDLEEEKARKLSTKSA
SPDIVGTINALLARIAAARSLVHRAKEELSSRPRPVVVMISGKPGIGKTHLARELAKK
IAASLTGDQRVGLIPRNGVDHWDAYKGERVVLWDDYGMSNPIHDALRLQELADTCPLT
LNCDRIENKGKVFDSDAIIITTNLANPAPLDYVNFEACSRRIDFLVYAEAPGVEKAKH
DFPGQPDMWKNAFSPDFSHIKLALAPQGGFDKNGNTPHGKGVMKTLTTGSLIARASGL
LHERLDEYELQGPALTTFNFDRNKVLAFRQLAAENKYGLMDTMRVGKQLKDVKTMPDL
KQALKNVAIKKCQIVYNGGTYTLEADGKGGVRVDKVQSATVQTNNELAGALHHLRCAR
IRYYVKCVQEALYSIIQIAGAAFVTTRIAKRMNIQNLWSKPQVEDTEETTSKDGCPKP
KDDEEFVVSSDDIKTEGKKGKNKSGRGKKHTAFSSKGLSDEEYDEYKRIREERNGKYS
IEEYLQDRDKYYEEVAIARATEEDFCEEEEAKIRQRIFRPTRKQRKEERASLGLVTGS
EIRKRNPEDFKPKGKLWADDDRSVDYNEKLNFEAPPSIWSRIVNFGSGWGFWVSPSLF
ITSTHVIPQGAKEFFGVPIKQIQIHKSGEFCRLRFPKPIRTDVTGMILEEGAPEGTVA
TLLIKRPTGELMPLAARMGTHATMRIQGRTVGGQMGMLLTGSNAKSMDLGTTPGDCGC
PYIYKRGNDYVVIGVHTAAARGGNTVICATQGSEGEATLEGGDNKGTYCGAPILGPGS
APKLSTKTKFWRSSTTPLPPGTYEPAYLGGKDPRVKGGPSLQQVMRDQLKPFTEPRGK
PPRPNVLEAAKKTIINVLEQTIDPPQKWSFAQACASLDKTTSSGHPHHMRKNDCWNGE
SFTGKLADQASKANLMFEEGKNMTPVYTGALKDELVKTDKIYGKIKKRLLWGSDLATM
IRCARAFGGLMDELKAHCVTLPVRVGMSMNEDGPIIFEKHSRYKYHYDADYSRWDSTQ
QRDVLAAALEIMVKFSPEPHLAQIVAEDLLSPSVMDVGDFQISISEGLPSGVPCTSQW
NSIAHWLLTLCALSEVTDLSPDIIQANSLFSFYGDDEIVSTDIKLDPEKLTAKLKEYG
LKPTRPDKTEGPLVISEDLDGLTFLRRTVTRDPAGWFGKLEQSSILRQMYWTRGPNHE
DPSETMIPHSQRPIQLMSLLGEAALHGPAFYSKISKLVIAELKEGGMDFYVPRQEPMF
RWMRFSDLSTWEGDRNLAPSFVNEDGVE"
mat_peptide <1..983
/gene="ORF1"
/product="p48"
mat_peptide 984..2081
/gene="ORF1"
/product="NTPase"
mat_peptide 2082..2618
/gene="ORF1"
/product="p22"
mat_peptide 2619..3017
/gene="ORF1"
/product="VPg"
mat_peptide 3018..3560
/gene="ORF1"
/product="Pro"
mat_peptide 3561..5090
/gene="ORF1"
/product="RdRp"
gene 5074..6699
/gene="ORF2"
CDS 5074..6699
/gene="ORF2"
/note="major capsid protein"
/codon_start=1
/product="VP1"
/protein_id="WKD81258.1"
/translation="MKMASSDANPSDGSAANLVPEVNNEVMALEPVVGAAIAAPVAGQ
QNVIDPWIRNNFVQAPGGEFTVSPRNAPGEILWSAPLGPDLNPYLSHLARMYNGYAGG
FEVQVILAGNAFTAGKIIFAAVPPNFPTEGLSPNQVTMFPHIIVDVRQLEPVLIPLPD
VRNNFYHYNQSNDPTIKLIAMLYTPLRANNAGDDVFTVSCRVLTRPSPDFDFIFLVPP
TVESRTKPFSVPILTVEEMTNSRFPIPLEKLFTGPSSTFVVQPQNGRCTTDGVLLGTT
QLSPVNICTFRGSVTQTAAGTHNYTMNLASQNWNSYDPTEEIPAPLGTPDFVGKIRGM
LTQTTRGNGSTRGHIATVYTGSNDFAPKLGRVQFETDTTNDFETNQNTKFTPVGVIQD
GDTAHRNEPLQWVLPSYSGRNTHNVHLAPAVAPTFPGEQLLFFRSTLPGCSGYPNMDL
DCLLPQEWVQYFYQEAAPAQSEVALLRFVNPDTGRVLFECKLHKSGYVTVAHTGQHDL
VIPPNGYFRFDSWVNQFYTLAPMGNGTGRRRAL"
gene 6699..7505
/gene="ORF3"
CDS 6699..7505
/gene="ORF3"
/note="minor structural protein; small basic protein"
/codon_start=1
/product="VP2"
/protein_id="WKD81259.1"
/translation="MAGAFFAGLASDVLGSGLGSLINAGAGAINQKIEFENNRKLQQA
SFQFSSNLQQASFQHDKEMLQAQIEATKKLQQEMMKVKQAVLLEGGFSETDAARGAIN
APMTKALDWSGTRYWAPDARTTTYNAGRFSTPQPSGALPGRANLRNVVPARGSSSTPS
NSSIATSVHSNQTASTRLGSTAGSGTSVSSLPSTARTRSWVEDQNRNLSPFMRGAHNI
SFVTPPSSRSSSQGTVSTVPKEVLDSWTGAFNTHRQPLFAHIRRRGESRV"
ORIGIN
1 tggcgtctaa cgacgcttcc gctgccgctg ctgctaacag caacaacgac atcgaaaaat
61 cttcaagtga cggtgtgttt tctaacatgg ctgtcacttt taagcgggcc ctcggggcgc
121 ggcctaaaca gccgcccccg agggaaaaac cacccagacc cccacgacca cccacaccag
181 agttggtcaa aaggatccca cctcccccac ccaacgggga ggatgaacta gtggtttctt
241 acaacgccaa agacggcgtt tccggattgc ctgagctcac caccgtcagc caaccggaag
301 aaaacaacac ggcgttcagt gttcccccgc tcaatcaaag ggagaacagg gacgctaagg
361 aaccactaac tggaacaatc attgagatgt gggatgggga aatctatcac tacggcctgt
421 acgtagaacg aggtcttata cttggtgtgc ataagccacc ggcggccatc agtcttgcca
481 aagttgagct aacaccactc tctttgttct ggagacctgt gtataccccc cagtacctca
541 tctctccaga cactcttaag agactacatg gagagtcatt cccctacacc gcatttgaca
601 acaattgcta tgccttctgc tgttgggtgc tagacctaaa cgactcatgg ctaagtagga
661 gaatgattca gaggacaaca ggtttcttca gaccatacca agaatggaac aggaaacccc
721 tccccactat ggatgactcc aaattgaaga aggtagccaa catattcttg tgcaccttgt
781 cttcactatt caccagaccc attaaggaca taatagggaa attgaaacct cttaacatcc
841 tcaatattct ggccacatgt gattggacct tcccaggcat agtggaatcc ctaatactct
901 tggcagaact ctttggagtt ttctggacac ccccagatgt gtctgcgatg atcgccccct
961 tactaggtga ttatgaactg caaggacctg aggaccttgc agtagaactg gtcccagtgg
1021 tgatgggggg gataggtttg gtgctaggat tcaccaaaga gaaaattgga aagatgctgt
1081 cgtccgctgc atccaccttg agagcttgca aagaccttgg tgcatacgga ctggaaattt
1141 tgaaactagt catgaagtgg ttcttcccaa agaaagagga aacaaatgaa ctggctatgg
1201 tgagatccat cgaggacgca gtactagatc tcgaggcaat tgaaaacaac cacatgaccg
1261 ccctgctcaa agacaaagac agtttggcaa cctacatgaa aacccttgat cttgaggagg
1321 agaaagccag aaaactctca actaaatccg cttcacctga tattgtgggc acaatcaacg
1381 ctcttctggc acgaatcgcc gctgcacgct ccctagtgca tcgggcgaaa gaagagctct
1441 ccagcaggcc gagacctgtt gtcgtgatga tatcgggaaa accagggata gggaaaactc
1501 accttgccag ggagttggcc aaaaagatcg cagcctccct cacaggggac cagcgtgtgg
1561 gtttgatccc acgcaacggc gtcgaccact gggatgcata caagggtgaa agagttgtcc
1621 tatgggacga ctatgggatg agcaacccca tacacgatgc cctcaggttg caggaacttg
1681 ctgacacttg ccccctcaca ctaaattgtg ataggattga gaataaagga aaagtctttg
1741 atagcgatgc cataattatt accaccaatc tggccaaccc agcaccactg gactatgtta
1801 actttgaagc gtgttcgagg cgcattgact tcctcgtgta cgcggaagct cctggggtgg
1861 agaaggcaaa acacgacttc ccaggccaac ctgacatgtg gaagaacgct ttcagccctg
1921 acttctcaca cataaaactg gcattggctc cacagggagg ttttgacaag aacggcaaca
1981 ccccgcatgg aaaaggtgtc atgaagaccc tcaccactgg ctccctcatc gcccgagcat
2041 cagggttact ccatgagagg ctagatgaat atgaattgca aggcccagcc ctcaccactt
2101 tcaacttcga ccgcaacaag gtacttgctt ttagacagct tgctgctgaa aacaagtatg
2161 gcctaatgga cacaatgaga gttggaaaac agctaaagga tgttaagact atgccagacc
2221 ttaaacaagc actcaagaat gtcgcgatca agaagtgcca gatagtgtac aatggtggca
2281 cctacacact tgaggccgac ggcaagggtg gtgtgagagt tgataaagtg caaagtgcca
2341 ccgtacaaac caacaatgag ctagccggcg ccctgcacca cctaaggtgc gccagaatca
2401 ggtattatgt taagtgtgtc caggaggcac tgtactccat catccaaatc gctggggctg
2461 cgtttgtcac tacgcgcatc gccaagcgca tgaatataca aaatctctgg tctaagccac
2521 aggtggaaga cacagaagag acaaccagca aagatggttg cccaaaaccc aaagatgatg
2581 aagagttcgt cgtttcatcc gacgacatca aaactgaggg caagaaaggg aagaacaagt
2641 ccggccgtgg caagaagcac acagccttct caagtaaagg actcagtgat gaagagtatg
2701 atgagtacaa gaggattagg gaagagagga atggtaagta ctccatagag gagtacctcc
2761 aggacagaga caagtactat gaggaagtgg ccattgccag ggcaactgaa gaggacttct
2821 gtgaagaaga agaggccaaa atccggcaga gaattttcag accaacaagg aaacaacgta
2881 aagaagagag ggcctctcta ggcttggtca caggctcaga aatcaggaag agaaacccag
2941 aagacttcaa acccaaggga aagctgtggg ctgatgatga cagaagtgtt gactacaatg
3001 agaagctcaa ctttgaggcc ccaccaagca tctggtcgcg gatagtcaac tttggttcag
3061 gttggggttt ctgggtctcc cccagtctgt ttataacatc aacccatgtc ataccccaag
3121 gtgcaaaaga gttcttcgga gtccccatca aacaaatcca gatacacaaa tcaggtgaat
3181 tctgccgact gagattccca aaaccaatca gaactgatgt gacgggcatg attctggaag
3241 aaggtgcgcc agaaggaacc gtggccacac tgctcatcaa gagaccaact ggagagctca
3301 tgcctttggc agccagaatg ggaacccatg caaccatgag gattcagggg cgcacggttg
3361 gaggacaaat gggcatgctc ttgacaggat ccaacgccaa gagtatggac ttgggcacaa
3421 caccaggcga ttgtggctgt ccctacatct acaaaagagg gaatgactac gtggttatag
3481 gagtccatac agccgctgcc cgtggaggaa acactgtcat ctgcgccacc cagggtagtg
3541 aaggagaagc cacacttgaa ggaggtgaca acaaaggaac gtactgtggt gcaccaattt
3601 tgggcccagg gagtgctccg aaactcagca ctaaaactaa gttttggaga tcatccacaa
3661 cgccactccc accaggcacc tacgaaccag cttacctcgg tggcaaggac cctagagtca
3721 aaggtggccc ttcattgcaa caagttatga gggaccaact aaaaccattc acagaaccta
3781 gaggcaaacc gccaagacca aatgtgttgg aagctgccaa gaaaaccatc attaatgttc
3841 ttgagcaaac aattgaccca ccccaaaaat ggtcattcgc gcaagcttgc gcatccctcg
3901 acaaaaccac ctccagcggc catccgcacc acatgcggaa aaacgactgc tggaatgggg
3961 aatcctttac aggaaaattg gcagaccagg cctctaaggc caacctaatg tttgaagagg
4021 gaaagaacat gactccagtt tacacaggtg cacttaaaga tgagttagtg aagactgata
4081 aaatttatgg taagatcaag aagaggctcc tgtggggctc ggacctggcg accatgatac
4141 ggtgcgcccg ggctttcgga ggccttatgg atgaactcaa ggcacattgt gtcacccttc
4201 ctgttagagt tggtatgagt atgaatgaag atggccctat aatctttgag aagcactcca
4261 gatataaata tcattatgat gctgattact ccaggtggga ctcgacacaa cagagggatg
4321 tgttagcagc agcactagaa atcatggtta aattctctcc agaaccacac ttggcccaga
4381 tagttgcaga agacctcctt tcccctagtg taatggatgt gggtgacttt caaatatcaa
4441 taagcgaagg acttccctcc ggggtacctt gcacctccca gtggaattcc atcgcccact
4501 ggctcctcac cctttgtgca ctctctgaag tcacggacct gtcccctgac attattcagg
4561 ccaactccct tttctccttc tatggtgatg acgagattgt gagtacagac ataaagttgg
4621 acccagagaa gctgacggca aaactcaagg agtacggact gaagccaacc cgccccgaca
4681 agactgaagg accccttgtc atctctgaag atctggatgg cctgacattc ctccggagga
4741 ctgtgacccg tgacccagct ggctggtttg gcaaattgga acaaagttca atcctcaggc
4801 aaatgtactg gaccaggggt cccaaccatg aagacccatc tgaaacaatg ataccacact
4861 ctcaaagacc catacaattg atgtccctgc taggcgaggc tgcactccac ggcccagcat
4921 tttacagcaa aattagcaaa ttggtcatcg cagaattgaa ggaaggtggt atggactttt
4981 acgtgcccag acaagaacca atgttcagat ggatgagatt ctcagatctg agcacgtggg
5041 agggcgatcg caatctggct cccagttttg tgaatgaaga tggcgtcgag tgacgccaac
5101 ccatctgatg ggtccgcagc caacctcgtc ccagaggtca acaatgaggt tatggctctg
5161 gagcccgttg ttggtgccgc tattgcggca cctgtagcgg gccaacaaaa tgtaattgac
5221 ccctggatta gaaataattt tgtgcaagcc cctggtggag agtttacagt atcccctaga
5281 aacgctccag gtgaaatact atggagcgct cccctaggcc ctgatctaaa cccctaccta
5341 tcccatttgg ccagaatgta taatggttat gcaggtggtt ttgaagtgca ggtaatcctt
5401 gcggggaacg cgttcaccgc cggaaagatc atatttgcag cagtcccacc taattttcca
5461 actgaaggtt tgagccccaa ccaggtcact atgttccccc atataatagt agatgttaga
5521 caactggaac ctgtgttgat tcccctaccc gatgttagga ataatttcta tcactataac
5581 caatcaaacg accccaccat taagttgata gcaatgttgt atacaccact tagggctaat
5641 aatgctgggg atgatgtctt cacggtttct tgccgagtcc tcacgagacc atcccctgat
5701 tttgacttca tattcttggt gccacccaca gttgagtcaa gaactaaacc attctctgtc
5761 ccaattttaa ctgttgagga gatgactaat tcaagattcc ccattccttt ggaaaagttg
5821 ttcacaggtc ccagcagcac ctttgttgtt caaccacaaa atggcaggtg cacgactgat
5881 ggcgtgctcc tgggcaccac ccaattgtcc cctgtcaaca tctgcacctt cagagggagt
5941 gtcacccaaa cagcggcagg tactcataac tacacaatga atttggcttc ccaaaattgg
6001 aatagctatg atccaacaga agaaatccca gcccctttag gaaccccaga tttcgtaggt
6061 aagattcgag gtatgctcac ccaaaccaca aggggaaatg gctcaacacg tggccacata
6121 gccacagtgt acactgggag caacgacttt gctccaaaac tgggtagggt ccaatttgaa
6181 actgacacaa ccaacgattt tgaaactaac caaaacacaa agttcacccc ggttggcgtc
6241 atccaggatg gtgacactgc tcaccgaaat gaacccctac aatgggtgct cccaagttat
6301 tcaggcagaa atactcataa tgtgcatctg gcccccgctg tagctcccac ttttccgggc
6361 gagcagctcc tcttctttag atctaccttg cccggatgca gcgggtaccc caacatggat
6421 ttggattgtc tgcttcccca ggaatgggtg cagtacttct atcaagaggc agccccagca
6481 caatctgaag tggctctgtt aagatttgtg aatccagata caggtagggt tttgtttgag
6541 tgtaagctcc acaaatcggg ctatgtcaca gtggctcata ctggccaaca tgatttggtt
6601 atccccccca atggttattt tagatttgat tcctgggtca atcaattcta cacgcttgcc
6661 cccatgggaa atggaacggg gcgtagacgt gcattgtaat ggctggagct ttctttgctg
6721 gattggcatc tgatgtcctt ggctctggac ttggttccct gatcaacgct ggggctgggg
6781 ccatcaacca aaagattgaa tttgaaaata acagaaaatt gcaacaggca tccttccaat
6841 ttagtagcaa cctacaacag gcttcctttc aacatgacaa agagatgctc caagcacaaa
6901 ttgaggccac caaaaagctg caacaggaaa tgatgaaagt taagcaggca gtgctcttag
6961 agggcgggtt ctctgagaca gatgcagccc gcggggcaat caacgcccct atgacaaaag
7021 ctttggattg gagcggtaca aggtattggg cccctgatgc tagaactaca acatacaatg
7081 caggccgttt ctccacaccc caaccatcgg gggcactgcc aggaagagct aatctcagga
7141 atgttgtccc cgctcggggt tcctctagta caccttctaa ttcctctatt gctacttctg
7201 tgcactcaaa tcaaactgct tcaacgagac ttggttctac agctggttct gggaccagtg
7261 tctcgagcct cccgtcaact gcaaggacta ggagctgggt tgaggatcaa aataggaatc
7321 tgtcaccttt catgaggggg gcccacaaca tatcgtttgt caccccacca tctagcagat
7381 cctctagcca aggcacagtc tcaaccgtgc ctaaagaagt tttggactcc tggactggtg
7441 cttttaacac gcacaggcag cctctcttcg ctcacattcg taggcgaggg gagtcacggg
7501 tgtaatgtga aaagacaaaa ttgattatct ttctcatctt tagtgtcttt t
//