Typing tool
|
|
|
|
|
|
Typing tool
|
Complete norovirus genomes
| OR262326 | GII.4 San Francisco | |
|
|---|---|---|---|
| GII.P31 |
ORF1: 1..5083
ORF2: 5064..6689
ORF3: 6689..7495
LOCUS OR262326 7541 bp RNA linear VRL 11-DEC-2023
DEFINITION Norovirus GII isolate Hu/GII.4 San
Francisco[P31]/WT-NORO-1807/2021/UK nonstructural polyprotein
(ORF1) gene, partial cds; and VP1 (ORF2) and VP2 (ORF3) genes,
complete cds.
ACCESSION OR262326
VERSION OR262326.1
KEYWORDS .
SOURCE Norovirus GII
ORGANISM Norovirus GII
Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes;
Picornavirales; Caliciviridae; Norovirus; Norwalk virus.
REFERENCE 1 (bases 1 to 7541)
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 7541)
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..7541
/organism="Norovirus GII"
/mol_type="genomic RNA"
/isolate="Hu/GII.4 San
Francisco[P31]/WT-NORO-1807/2021/UK"
/isolation_source="stool"
/host="Homo sapiens"
/db_xref="taxon:122929"
/country="United Kingdom"
/collection_date="Jul-2021"
/note="genotype: GII.4 San Francisco[P31]"
gene <1..5083
/gene="ORF1"
CDS <1..5083
/gene="ORF1"
/codon_start=2
/product="nonstructural polyprotein"
/protein_id="WKD81251.1"
/translation="DASAAAAANSNNDIEKSSSDGVFSNMAVTFKRALGARPKQPPPK
EIPPRPPRPPTPELAKKIPPPPPNGEDELVVSYSAKGGVSGLPELTTVSQPEENNTAF
SVPPLNQRENRDAKEPLTGTIIEMWDGEIYHYGLYVERGLILGVHKPPAAISLAKVEL
APLSLFWRPVYTPQYLISPDTLKRLHGELFPYTAFDNNCYAFCCWVLDLNDSWLSRRM
IQRTTGFFRPCQEWNRKPLPTMDDSKLKKVANIFLCTLSSLFTRPIKDIIGKLKPLNI
LNILATCDWTFPGIVESLILLAELFGVFWTPPDVSAMIAPLLGDYELQGPEDLAVELV
PVVMGGIGLVLGFTKEKIGKMLSSAASTLRACKDLGAYGLEILKLVMKWFFPKKEEAN
ELAMVRSIEDAVLDLEAIENNHMTTLLKDKDSLATYMRTLDLEEEKARKLSTKSASPD
IVGTINALLARIAAARSLVHRAKEELSSRLRPVVVMISGKPGIGKTHLARELAKKIAA
SLTGDQRVGLIPRNGVDHWDAYKGERVVLWDDYGMSNPIHDALRLQELADTCPLTLNC
DRIENKGKVFDSDAIIITTNLANPAPLDYVNFEACSRRIDFLVYAEAPGVEKAKHDFP
GQPDMWKNAFSSDFSHIKLALAPQGGFDKNGNTPHGKGVMKTLTTGSLIARASGLLHE
RLDEYELQGPALTTFNFDRNKVLAFRQLAAENKYGLMDTMRVGKQLKDVKTMSDLKQA
LKNVSIKKCQIVYNGGTYTLEADGKGSVKVDKVQSATVQTNNELAGALHHLRCARIRY
YVKCVQEALYSIIQIAGAAFVTTRIAKRMNIQNLWSKPQVEDTEETTNKDGCPKPKED
EEFVVSSDDIKTEGKKGKNKSGRGKKHTAFSSKGLSDEEYDEYKRIREERNGKYSIEE
YLQDRDKYYEEVAIARATEEDFCEEEEAKIRQRIFRPTRKQRKEERASLGLVTGSEIR
KRNPEDFKPKGKLWADDDRSVDYNEKLNFEAPPSIWSRIVNFGSGWGFWVSPSLFITS
THVIPQGANEFFGVPIKQIQIHKSGEFCRLRFPKPIRTDVTGMILEEGAPEGTVATLL
IKRPTGELMPLAARMGTHATMRIQGRTVGGQMGMLLTGSNAKSMDLGTTPGDCGCPYI
YKRGNDYVVIGVHTAAARGGNTVICATQGSEGEATLEGGDNKGTYCGAPILGPGSAPK
LSTKTKFWRSSTTPLPPGTYEPAYLGGKDPRVKGGPSLQQVMRDQLKPFTEPRGKPPR
PSVLEAAKKTIINVLEQTIDPPQKWSFAQACASLDKTTSSGHPHHMRKNDCWNGESFT
GKLADQASKANLMFEEGKNMTPVYTGALKDELVKTDKIYGKIKKRLLWGSDLATMIRC
ARAFGGLMDELKAHCVTLPVRVGMNMNEDGPIIFEKHSRYKYHYDADYSRWDSTQQRD
VLAAALEIMVKFSPEPHLAQIVAEDLLSPSVMDVGDFQILISEGLPSGVPCTSQWNSI
AHWLLTLCALSEVTDLSPDIIQANSLFSFYGDDEIVSTDIKLDPEKLTAKLKEYGLKP
TRPDKTEGPLVISEDLDGLTFLRRTVTRDPAGWFGKLEQSSILRQMYWTRGPNHEDPS
ETMIPHSQRPIQLMSLLGEAALHGPSFYSKISKLVIAELKEGGMDFYVPRQEPMFRWM
RFSDLSTWEGDRNLAPSFVNEDGVE"
mat_peptide <1..973
/gene="ORF1"
/product="p48"
mat_peptide 974..2071
/gene="ORF1"
/product="NTPase"
mat_peptide 2072..2608
/gene="ORF1"
/product="p22"
mat_peptide 2609..3007
/gene="ORF1"
/product="VPg"
mat_peptide 3008..3550
/gene="ORF1"
/product="Pro"
mat_peptide 3551..5080
/gene="ORF1"
/product="RdRp"
gene 5064..6689
/gene="ORF2"
CDS 5064..6689
/gene="ORF2"
/note="major capsid protein"
/codon_start=1
/product="VP1"
/protein_id="WKD81252.1"
/translation="MKMASSDANPSDGSAANLVPEVNNEVMALEPVVGAAIAAPVAGQ
QNVIDPWIRNNFVQAPGGEFTVSPRNAPGEILWSAPLGPDLNPYLSHLARMYNGYAGG
FEVQVILAGNAFTAGKIIFAAVPPNFPTEGLSPSQVTMFPHIIVDVRQLEPVLIPLPD
VRNNFYHYNQSNDPTIKLIAMLYTPLRANNAGDDVFTVSCRVLTRPSPDFDFIFLVPP
TVESRTKPFSVPILTVEEMTNSRFPIPLEKLFTGPSSTFVVQPQNGRCTTDGVLLGTT
QLSPVNICTFRGSVTQTATGSHNYTMNLASQNWNSYDPTEDIPAPLGTPDFVGKIQGV
LTQTTRGDGSTRGHKATLYTGSNDFTPKLGRVQFETDTNHDFEANQNTKFTPVGVIQN
GDTAHRNEPQQWVLPSYSGRNTHNVHLAPVVAPTFPGEQLLFFRSTLPGCSGYPNMDL
DCLLPQEWVQYFYQEAAPAQSEVALLRFVNPDTGRVLFECKLHKSGYVTVAHTGQHDL
VIPPNGYFRFDSWVNQFYTLAPMGNGTGRRRAL"
gene 6689..7495
/gene="ORF3"
CDS 6689..7495
/gene="ORF3"
/note="minor structural protein; small basic protein"
/codon_start=1
/product="VP2"
/protein_id="WKD81253.1"
/translation="MAGAFFAGLASDVLGSGLGSLINAGAGAINQKIEFENNRKLQQA
SFQFSSNLQQASFQHDKEMLQAQIEATKKLQQEMMKVKQAVLLEGGFSETDAARGAIN
APMTKALDWSGTRYWAPDARTTTYNAGRFSTPQPSGALPGRANFRNAAPARGSSSTPS
NSSIATSVYSNQTASTRLGSTAGSGTSVSSPPSTARTRSWVEDQNRNLSPFMRGAHNI
SFVTPPSSRSSSQGTVSTVPKEVLDSWTGAFNTHRQPLFAHIRRRGESRV"
ORIGIN
1 cgacgcttcc gctgccgctg ctgctaacag caacaacgac atcgaaaaat cttcaagtga
61 cggtgtgttt tctaacatgg ctgtcacttt taagcgggcc ctcggggcgc ggcccaaaca
121 gccgcccccg aaggaaatac cacccagacc cccacgacca cccacaccag agttggccaa
181 aaagatccca cctcccccac ccaatgggga ggatgaacta gtggtttctt acagcgccaa
241 aggcggcgtt tccggattgc ctgagctcac caccgtcagc caaccagaag aaaacaacac
301 ggcgttcagt gttcccccgc tcaatcaaag ggagaatagg gacgctaagg aaccactaac
361 tggaacgatc attgagatgt gggatgggga aatctatcat tacggcctgt acgtagaacg
421 aggccttata cttggtgtgc acaagccacc ggcagccatc agccttgcca aagttgagct
481 agcaccactc tctctgttct ggagacctgt gtataccccc cagtacctca tctctccaga
541 cactcttaag agactacatg gagagttatt cccctacacc gcatttgaca acaactgcta
601 cgccttctgc tgttgggtgt tagacctaaa cgactcatgg ttaagtagga gaatgattca
661 gagaacaaca ggtttcttca ggccatgcca agagtggaac aggaaacccc tccccactat
721 ggatgactcc aaattgaaga aggtagccaa catattcttg tgcactttgt cttcactatt
781 caccaggccc attaaggaca taataggaaa attgaaacct ctcaacatcc tcaatattct
841 ggccacatgt gattggacct tcccaggcat agtggaatcc ctgatactct tggcagaact
901 ctttggagtt ttctggacac ccccagatgt gtctgcgatg atcgccccct tactaggtga
961 ttatgaactg caagggcctg aggaccttgc agtagaactg gtcccagtgg taatgggggg
1021 gataggtttg gtgctaggat tcaccaaaga gaaaattgga aagatgctgt cgtccgctgc
1081 atccaccttg agagcttgca aagaccttgg tgcatacgga ctggaaattt tgaaactagt
1141 catgaagtgg ttctttccaa agaaagagga agcaaatgaa ctggctatgg tgagatccat
1201 cgaggacgca gtgctagacc tcgaggcaat cgaaaacaac catatgacca ccctgctcaa
1261 ggacaaagac agcttggcaa cctacatgag aacccttgac cttgaggagg agaaagccag
1321 aaaactctca accaagtccg cttcacctga tattgtgggc acaatcaacg ctcttctggc
1381 acgaatcgcc gctgcacgct ccctagtgca tcgggcgaaa gaggagctct ccagcaggct
1441 gagacctgtt gttgtgatga tatcgggaaa accagggata gggaaaactc accttgccag
1501 ggagttggcc aaaaagatcg cagcctccct cacaggggac cagcgtgtgg gtttgatccc
1561 acgcaacggc gtcgaccact gggatgcata caagggtgaa agagttgtcc tttgggacga
1621 ctatgggatg agtaacccca tacacgatgc cctcaggttg caggaacttg ctgacacttg
1681 ccccctcaca ctaaattgtg ataggattga gaacaaagga aaagtctttg atagcgatgc
1741 cataattatt accaccaatc tggccaaccc agcaccactg gattatgtca attttgaagc
1801 gtgttcgagg cgcattgact tcctcgtgta cgcggaagct cctggggtgg agaaggcaaa
1861 acacgacttc ccaggccaac ctgacatgtg gaagaacgct ttcagctctg acttctcaca
1921 cataaaactg gcattggctc cacagggtgg ttttgacaag aacggtaaca ccccgcatgg
1981 aaaaggtgtc atgaagaccc tcaccactgg ctctctcatc gcccgagcat cagggttact
2041 ccacgagagg ctagatgaat atgaattaca aggccctgcc ctcaccactt tcaactttga
2101 ccgcaataag gtacttgctt ttaggcagct cgctgctgaa aacaagtatg gtctaatgga
2161 cacaatgaga gttggaaaac agctcaagga tgtcaaaact atgtcagacc ttaaacaagc
2221 actcaagaat gtttcgatca agaaatgcca gatagtgtac aatggtggca cctacacact
2281 tgaagccgac ggcaagggta gtgtgaaagt tgacaaggtg caaagtgcca ccgtgcaaac
2341 caacaatgaa ctagccggcg ccctgcacca cctaaggtgc gccagaatta ggtattatgt
2401 caagtgtgtc caggaggcgc tgtactccat catccaaatc gctggggctg cgtttgtcac
2461 cacgcgcatc gccaagcgca tgaatataca aaatctctgg tccaagccac aggtggaaga
2521 cacagaagag acaaccaaca aagatggttg cccaaaaccc aaagaggatg aagagttcgt
2581 cgtttcatcc gacgacatta aaactgaggg caagaaaggg aagaacaagt ccggccgtgg
2641 caagaagcac acagccttct caagtaaagg gctcagtgat gaagagtacg atgagtacaa
2701 gagaattaga gaagagagga atggtaagta ctccattgag gagtacctcc aggacagaga
2761 caaatactat gaggaagtgg ccattgccag ggcaactgaa gaggacttct gtgaagaaga
2821 agaggccaaa atccggcaga gaatcttcag gccaacaagg aaacaacgta aagaagagag
2881 ggcctctcta ggcttggtca caggctcaga aatcaggaag agaaacccag aagacttcaa
2941 acccaaggga aagctgtggg ctgatgatga cagaagtgtt gactacaacg agaagctcaa
3001 ctttgaggcc ccaccaagca tctggtcgcg gatagtcaac tttggttcag gttggggttt
3061 ctgggtctcc cccagtctgt ttataacgtc aacccatgtc ataccccaag gtgcaaacga
3121 gttcttcgga gtccccatca aacaaatcca gatacacaaa tcaggtgaat tctgccgact
3181 gagattccca aaaccaatca gaactgatgt gacgggcatg attctggaag aaggtgcgcc
3241 agaaggaacc gtggccacac tgctcatcaa gagaccaact ggagagctca tgcctttggc
3301 agccagaatg ggaacccatg caaccatgag gattcagggg cgcacggttg gaggacaaat
3361 gggtatgctc ttgacaggat ccaacgccaa gagtatggac ttgggcacaa cgccaggcga
3421 ctgtggctgt ccctacatct acaaaagagg gaacgactac gtggttatag gagtccatac
3481 agccgctgcc cgtggaggga acactgtcat ctgcgccacc cagggtagtg aaggagaagc
3541 cacacttgaa ggaggtgaca ataaaggaac gtactgtggt gcaccaattt tgggcccagg
3601 gagtgctccg aaactcagta ctaaaaccaa gttttggaga tcatccacaa cgccactccc
3661 accaggcacc tacgaaccag cctacctcgg tggcaaggac cccagagtca aaggtggccc
3721 ttcattgcaa caagttatga gggaccaact aaaaccattc acagaaccca gaggcaaacc
3781 gccaagacca agtgtgttgg aagctgccaa gaaaaccatc attaatgtcc ttgagcaaac
3841 aattgaccca ccccaaaaat ggtcgttcgc gcaagcttgc gcatcccttg acaaaaccac
3901 ctccagcggc catccgcatc acatgcggaa aaacgactgc tggaatgggg aatcctttac
3961 aggaaaattg gcagatcagg cctccaaggc caacctaatg tttgaagagg gtaagaacat
4021 gactccagtc tacacaggtg cgcttaaaga tgaattagtg aagactgaca agatttatgg
4081 taagatcaag aagaggctcc tgtggggctc ggacctggcg accatgatac ggtgcgcccg
4141 ggctttcggg ggccttatgg atgaactcaa ggcacattgt gtcacccttc ctgtcagagt
4201 tggtatgaac atgaatgaag atggccccat aatctttgag aagcactcca gatataagta
4261 tcattatgat gctgattact ccaggtggga ctcgacacaa caaagggatg tgctagcagc
4321 agcactagaa atcatggtta agttttctcc agaaccacac ttggcccaga tagttgcaga
4381 agacctcctt tcccctagtg taatggatgt gggtgacttc cagatattaa taagtgaagg
4441 actcccctct ggagtacctt gcacctccca gtggaactcc atcgcccact ggctcctcac
4501 cctttgtgca ctctctgaag tcacggacct gtcccctgac atcattcagg ccaactccct
4561 tttctccttc tatggtgatg atgagattgt gagtacagac ataaagttgg acccagagaa
4621 gctgacggca aaactcaagg agtacgggct gaagccaacc cgccccgaca aaactgaagg
4681 accccttgtc atctctgaag atctggatgg cctgacattc ctccggagga ctgtgacccg
4741 tgacccagct ggctggtttg gaaaattgga acaaagttcg attctcaggc aaatgtactg
4801 gaccaggggt cccaaccatg aagacccatc tgaaacaatg ataccacact cccaaaggcc
4861 catacaattg atgtccttgc taggcgaggc tgcactccac ggcccatcat tttacagcaa
4921 aattagcaaa ttggtcattg cagaattgaa ggaaggtggc atggattttt acgtgcccag
4981 acaagagcca atgttcagat ggatgagatt ctcagatctg agcacgtggg agggcgatcg
5041 caatctggct cccagttttg tgaatgaaga tggcgtcgag tgacgccaac ccatctgatg
5101 ggtccgcagc caacctcgtc ccagaggtca acaatgaggt tatggctctg gagcccgttg
5161 ttggtgccgc tattgcggcg cctgtagcgg gccaacaaaa tgtgattgac ccctggatta
5221 gaaataattt tgtgcaagcc cctggtggag agtttacagt atcccctaga aacgctccag
5281 gtgaaatact atggagcgca cccttaggcc ctgatctaaa cccctaccta tcccatttgg
5341 ctagaatgta taatggttat gcaggtggtt ttgaagtgca ggtaattctt gcggggaatg
5401 cgttcaccgc cggaaagatc atatttgcag cagtcccacc aaatttccca actgaaggct
5461 tgagcccaag ccaggtcact atgttccccc atataatagt agatgttaga caactggagc
5521 ctgtgttgat ccccttaccc gatgttagga ataatttcta tcactataac caatcaaatg
5581 accccaccat taagttgata gcaatgttgt atacaccact tagggctaat aatgctgggg
5641 atgatgtctt cacggtttct tgccgagtcc tcacgagacc atcccctgat tttgatttca
5701 tattcttagt accacccaca gttgaatcaa gaactaaacc attctctgtc ccaattttaa
5761 ctgttgagga gatgactaat tcaagattcc ccattccttt ggaaaaattg ttcacaggtc
5821 ccagcagtac ctttgttgtt caaccacaga atggtaggtg tacgactgat ggcgtgctcc
5881 taggtaccac ccaattgtca cctgtcaaca tctgcacctt cagagggagt gtcacccaaa
5941 cagcgacagg tagtcataac tacacaatga atctggcttc ccaaaattgg aacagttatg
6001 atccaacaga agacatccca gcccctctag gaactccaga tttcgtaggg aagattcaag
6061 gtgtgctcac ccagaccaca agaggagatg gctcaacacg cggccacaaa gccacattgt
6121 atactgggag caacgatttc actccaaaac tgggtagggt ccaatttgaa actgacacaa
6181 accacgattt tgaggccaac caaaacacaa agttcactcc ggtcggcgtc atccagaacg
6241 gagacactgc ccaccgaaat gaacctcaac aatgggtgct cccaagttat tcaggcagaa
6301 acactcataa tgtgcatctg gcccccgttg tagctcccac ttttccgggc gagcagctcc
6361 tcttcttcag atctaccttg cctggatgca gcgggtatcc caacatggat ttggattgtc
6421 tactccccca ggaatgggtg cagtacttct atcaagaggc agccccagca caatctgaag
6481 tggctctgtt gaggtttgtg aatccagaca caggtagggt tttgtttgag tgtaagctcc
6541 acaaatcggg ctatgtcaca gtggcccaca ctggccaaca tgatttggtt atccccccca
6601 atggttattt cagatttgat tcctgggtca accaattcta cacgcttgcc cccatgggaa
6661 atggaacggg gcgcagacgt gcattataat ggctggagct ttctttgctg gattggcatc
6721 tgatgtcctt ggctctggac ttggttccct gatcaacgct ggggctgggg ccatcaatca
6781 aaagattgaa tttgaaaaca acagaaaatt gcaacaagct tcattccaat ttagtagcaa
6841 cctacaacag gcttcctttc aacatgacaa agagatgctc caagcacaaa ttgaggccac
6901 caaaaagctg caacaggaaa tgatgaaagt taagcaggca gtgctcctag agggtgggtt
6961 ttctgagaca gatgcagccc gcggagcaat caacgcccct atgacaaaag ctttggactg
7021 gagcggtaca aggtattggg cacccgatgc taggactaca acatacaatg caggccgctt
7081 ctctaccccc caaccatcgg gggcactgcc aggaagagct aacttcagga atgctgcccc
7141 cgctcggggt tcctctagta caccctccaa ttcctctatt gctacttctg tgtactcaaa
7201 tcaaactgct tcaacgagac ttggttctac agccggttct gggaccagtg tctcgagccc
7261 cccgtcaact gcaaggacta ggagctgggt tgaggatcaa aacaggaatc tgtcgccttt
7321 catgaggggg gcccacaaca tatcgtttgt caccccacca tctagcagat cctctagcca
7381 aggcacagtc tcaaccgtgc ctaaagaagt tttggactcc tggactggtg ctttcaacac
7441 gcacaggcag cctctcttcg ctcacattcg taggcgaggg gagtcacggg tgtaatgtga
7501 aaagacaaaa ttgattatct ttcttttctt tagtgtcttt t
//