Typing tool
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Typing tool
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Complete norovirus genomes
| OR262325 | GII.4 San Francisco | |
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| GII.P31 |
ORF1: 5..5104
ORF2: 5085..6710
ORF3: 6710..7516
LOCUS OR262325 7567 bp RNA linear VRL 11-DEC-2023
DEFINITION Norovirus GII isolate Hu/GII.4 San
Francisco[P31]/SanFrancisco0131/2017/USA, complete genome.
ACCESSION OR262325
VERSION OR262325.1
KEYWORDS .
SOURCE Norovirus GII
ORGANISM Norovirus GII
Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes;
Picornavirales; Caliciviridae; Norovirus; Norwalk virus.
REFERENCE 1 (bases 1 to 7567)
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 7567)
AUTHORS Pan,C.-Y., Huynh,T., Barclay,L., Cannon,J.L., Montmayeur,A.M.,
Xu,R., Vinje,J. and Chhabra,P.
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 :: Geneious v. v. 11.1.2; SPAdes v. v. 3.6
Sequencing Technology :: Illumina
##Assembly-Data-END##
FEATURES Location/Qualifiers
source 1..7567
/organism="Norovirus GII"
/mol_type="genomic RNA"
/isolate="Hu/GII.4 San
Francisco[P31]/SanFrancisco0131/2017/USA"
/isolation_source="stool"
/host="Homo sapiens"
/db_xref="taxon:122929"
/country="USA"
/collection_date="30-Jul-2017"
/note="genotype: GII.4 San Francisco[P31]"
gene 5..5104
/gene="ORF1"
CDS 5..5104
/gene="ORF1"
/codon_start=1
/product="nonstructural polyprotein"
/protein_id="WKD81248.1"
/translation="MKMASNDASAAAAANSNNDIEKSSSDGVFSNMAVTFKRALGARP
KQPPPKEIPPRPPRPPTPELVKRIPPPPPNGEDELVVSYSAKDGVSGLPELTTVSQPE
ENNTAFSVPPLNQRENRDAKEPLTGTIIEMWDGEIYHYGLYVERGLILGVHKPPAAIS
LAKVELTPLSLFWRPVYTPQYLISPDTLKRLHGESFPYTAFDNNCYAFCCWVLDLNDS
WLSRRMIQRTTGFFRPYQEWNRKPLPTMDDSKLKKVANIFLCTLSSLFTRPIKDIIGK
LKPLNILNILATCDWTFPGIVESLILLAELFGVFWTPPDVSAMIAPLLGDYELQGPED
LAVELVPVVMGGIGLVLGFTKEKIGKMLSSAASTLRACKDLGAYGLEILKLVMKWFFP
KKEEANELAMVRSIEDAVLDLEAIENNHMTTLLKDKDSLATYMRTLDLEEEKARKLST
KSASPDIVGTINSLLARIAAARSLVHRAKEELSSRPRPVVVMISGKPGIGKTHLAREL
AKKIAASLTGDQRVGLIPRNGVDHWDAYKGERVVLWDDYGMSNPIHDALRLQELADTC
PLTLNCDRIENKGKVFDSDAIIITTNLANPAPLDYVNFEACSRRIDFLVYAEAPGVEK
AKHDFPGQPDMWKNAFSPDFSHIKLALAPQGGFDKNGNTPHGKGVMKTLTTGSLIARA
SGLLHERLDEYELQGPALTTFNFDRNKILAFRQLAAENKYGLMDTMRVGKQLKDVKTM
PDLKQALKNIAIKKCQIVYNGSTYTLEADGKGSVKVDKVQSATVQTNNELAGALHHLR
CARIRYYVKCVQEALYSIIQIAGAAFVTTRIAKRMNIQNLWSKPQVEDTEETTNKDGC
PKPKDDEEFVVSSDDIKTEGKKGKNKSGRGKKHTAFSSKGLSDEEYDEYKRIREERNG
KYSIEEYLQDRDKCYEEVAIARATEEDFCEEEEAKIRQRIFRPTRKQRKEERTSLGLV
TGSEIRKRNPEDFKPKGKLWADDDRSVDYNEKLNFEAPPSIWSRIVNFGSGWGFWVSP
SLFITSTHVIPQGAKEFFGVPIKQIQIHKSGEFCRLRFPKPIRTDVTGMILEEGAPEG
TVATLLIKRPTGELMPLAARMGTHATMKIQGRTVGGQMGMLLTGSNAKSMDLGTTPGD
CGCPYIYKRGNDYVVIGVHTAAARGGNTVICATQGSEGEATLEGGDNKGTYCGAPILG
PGSAPKLSTKTKFWRSSTTPLPPGTYEPAYLGGKDPRVKGGPSLQQVMRDQLKPFTEP
RGKPPRPNVLEAAKKTVINVLEQTIDPPQKWSFAQACASLDKTTSSGHPHHMRKNDCW
NGESFTGKLADQASKANLMFEEGKNMTPVYTGALKDELVKTDKIYGKIKKRLLWGSDL
ATMIRCARAFGGLMDELKAHCVTLPVRVGMNMNEDGPIIFEKHSRYKYHYDADYSRWD
STQQRDVLAAALEIMVKFSPEPHLAQIVAEDLLSPSVMDVGDFQISISEGLPSGVPCT
SQWNSIAHWLLTLCALSEVTDLSPDIIQANSLFSFYGDDEIVSTDIKLDPEKLTAKLK
EYGLKPTRPDKTEGPLVISEDLDGLTFLRRTVTRDPAGWFGKLEQSSILRQMYWTRGP
NHEDPSETMIPHSQRPIQLMSLLGEAALHGPAFYSKISKLVIAELKEGGMDFYVPRQE
PMFRWMRFSDLSTWEGDRNLAPSFVNEDGVE"
mat_peptide 5..994
/gene="ORF1"
/product="p48"
mat_peptide 995..2092
/gene="ORF1"
/product="NTPase"
mat_peptide 2093..2629
/gene="ORF1"
/product="p22"
mat_peptide 2630..3028
/gene="ORF1"
/product="VPg"
mat_peptide 3029..3571
/gene="ORF1"
/product="Pro"
mat_peptide 3572..5101
/gene="ORF1"
/product="RdRp"
gene 5085..6710
/gene="ORF2"
CDS 5085..6710
/gene="ORF2"
/note="major capsid protein"
/codon_start=1
/product="VP1"
/protein_id="WKD81249.1"
/translation="MKMASSDANPSDGSAANLVPEVNNEVMALEPVVGAAIAAPVAGQ
QNVIDPWIRNNFVQAPGGEFTVSPRNAPGEILWSAPLGPDLNPYLSHLARMYNGYAGG
FEVQVILAGNAFTAGKIIFAAVPPNFPTEGLSPSQVTMFPHIIVDVRQLEPVLIPLPD
VRNNFYHYNQSNDPTIKLIAMLYTPLRANNAGDDVFTVSCRVLTRPSPDFDFIFLVPP
TVESRTKPFSVPILTVEEMTNSRFPIPLEKLFTGPSSTFVVQPQNGRCTTDGVLLGTT
QLSPVNICTFRGSVTQTATGSHNYTMNLASQNWNSYDPTEEIPAPLGTPDFVGKIRGM
LTQTTRGNGSTRGHTATVYTGSNDFAPKLGRVQFETDTNNDFETNQNTKFTPVGVIQN
GDTAHRNEPQQWVLPSYSGRNTHNVHLAPAVAPTFPGEQLLFFRSTLPGCSGYPNMDL
DCLLPQEWVQYFYQEAAPAQSEVALLRFVNPDTGRVLFECKLHKSGYVTVAHTGQHDL
VIPPNGYFRFDSWVNQFYTLAPMGNGTGRRRAL"
gene 6710..7516
/gene="ORF3"
CDS 6710..7516
/gene="ORF3"
/note="minor structural protein; small basic protein"
/codon_start=1
/product="VP2"
/protein_id="WKD81250.1"
/translation="MAGAFFAGLASDVLGSGLGSLVNAGAGTINQKIEFENNRKLQQA
SFQFSSNLQQASFQHDKEMLQAQIEATKKLQQEMMKVKQAVLLEGGFSETDAARGAIN
APMTKALDWSGTRYWAPDARTTTYNAGRFSTPQPSGVLPGRANLRNAVPARGSSSTPS
NSSIATSVYSNQTASTRLGSTAGSGTSVSSLPSTARTRSWVEDQNRNLSPFMRGAHDI
SFVTPPSSRSSSQGTVSTVPKEVLDSWTGAFNTHRQPLFAHIRKRGESRV"
ORIGIN
1 gtgaatgaag atggcgtcta acgacgcttc cgctgccgct gctgctaaca gcaacaacga
61 catcgaaaaa tcttcaagtg acggtgtgtt ttctaacatg gctgtcactt ttaagcgggc
121 cctcggggcg cggcctaaac agccgccccc gaaggaaata ccgcccagac ccccacgacc
181 acccacacca gagttggtta aaaggatccc acctccccca cccaacgggg aggatgaact
241 agtggtttct tacagcgcca aagacggcgt ttccggattg cctgagctca ccaccgtcag
301 ccaaccggaa gaaaacaaca cggcgttcag tgttcccccg ctcaatcaaa gggagaacag
361 ggacgctaag gaaccactaa ctgggacaat cattgagatg tgggatggag aaatctacca
421 ttacggcctg tacgtggaac gaggccttat acttggtgtg cataagccac cggcagccat
481 cagtcttgcc aaggttgagc taacaccact ctctttgttc tggagacctg tgtatacccc
541 ccagtacctc atctctccag acactcttaa gagactacat ggagagtcat tcccctacac
601 cgcatttgac aacaattgct acgccttctg ctgttgggtg ttagacctaa acgactcatg
661 gctaagtagg agaatgattc agaggacaac aggtttcttc agaccatacc aagaatggaa
721 caggaaaccc ctccccacta tggatgactc caaattgaag aaggtagcca acatattctt
781 gtgcaccttg tcttcactat tcaccagacc cattaaggac ataataggga aattgaaacc
841 tcttaacatc ctcaatattc tggccacatg tgattggact ttcccaggca tagtggaatc
901 cctaatactc ttggcagaac tctttggagt tttctggaca cccccagacg tgtctgcgat
961 gatcgccccc ttactaggtg attatgaact gcaaggacct gaggaccttg cagtagaact
1021 ggtcccagtg gtgatggggg ggataggttt ggtgctagga ttcaccaaag agaaaattgg
1081 aaagatgctg tcgtccgctg catccacctt gagagcttgc aaagaccttg gggcatacgg
1141 gcttgaaatt ttgaaactag tcatgaagtg gttcttccca aagaaagagg aagcaaatga
1201 actggccatg gtgagatcca tcgaggacgc agtgctagac ctcgaggcaa ttgaaaacaa
1261 ccacatgacc accctgctca aagacaaaga cagcttggca acctacatga gaacccttga
1321 ccttgaggag gagaaagcca gaaaactctc aactaaatcc gcttcacctg atattgtggg
1381 cacaatcaac tctcttctgg cacgaatcgc cgctgcacgc tccctagtgc atcgggcgaa
1441 agaggagctc tccagcaggc cgagacctgt tgtcgtgatg atatcgggaa aaccagggat
1501 agggaaaact caccttgcca gggagttggc caagaagatc gcagcctccc tcacagggga
1561 ccagcgtgtg ggtttgatcc cacgcaacgg cgtcgaccac tgggacgcat acaagggtga
1621 aagagttgtc ctatgggacg actatgggat gagcaacccc atacacgatg ccctcaggtt
1681 gcaggaactt gctgacactt gccccctcac actaaattgt gacaggattg agaacaaagg
1741 aaaagtcttt gatagtgatg ccataattat taccaccaat ctggccaacc cagcaccact
1801 ggattatgtc aattttgaag cgtgttcgag gcgcattgac ttcctcgtgt acgcggaagc
1861 tcctggggtg gagaaggcaa aacacgactt cccaggccaa cctgacatgt ggaagaacgc
1921 tttcagccct gatttctcac acataaaact ggcattggct ccacagggtg gttttgacaa
1981 gaacggcaac accccgcatg gaaaaggtgt catgaagacc ctcaccactg gctccctcat
2041 cgcccgagca tcagggttac tccatgagag gctagatgaa tatgaattac aaggcccagc
2101 cctcaccact ttcaactttg accgcaacaa gatacttgct tttagacagc tcgctgctga
2161 gaacaagtat ggtctaatgg acacaatgag agttggaaaa cagctcaagg atgtcaagac
2221 tatgccagac cttaaacaag cactcaagaa tatcgcgatc aagaagtgcc agatagtgta
2281 caatggtagc acctacacac ttgaggccga cggcaagggt agtgtgaaag ttgacaaagt
2341 gcaaagtgcc accgtgcaaa ccaacaatga actagccggc gccctgcacc acctaaggtg
2401 cgccagaatc aggtattatg ttaagtgtgt ccaggaggca ctgtattcca tcatccaaat
2461 cgctggggct gcatttgtca ccacgcgcat cgccaagcgc atgaatatac aaaatctctg
2521 gtccaagcca caggtggaag acacagaaga gacgaccaac aaagatggtt gcccaaaacc
2581 caaagatgat gaagagttcg tcgtttcatc cgacgacatc aaaactgagg gcaagaaagg
2641 gaagaacaag tccggccgtg gcaagaagca cacagccttc tcaagcaaag ggctcagtga
2701 tgaagagtac gatgagtaca aaagaattag agaagagagg aatggtaagt actccataga
2761 ggagtacctc caggacagag acaagtgcta tgaggaagtg gctattgcca gggcaactga
2821 agaggacttc tgtgaagaag aagaggccaa aatccggcag agaattttca gaccaacaag
2881 gaaacaacgt aaagaagaga ggacctctct aggcttggtc acaggctcag aaatcaggaa
2941 gagaaaccca gaagacttca aacccaaggg aaagctgtgg gctgatgatg acagaagtgt
3001 tgactacaac gagaagctca actttgaggc cccaccaagc atctggtcgc ggatagtcaa
3061 ctttggttca ggttggggtt tctgggtctc tcccagtctg tttataacat caacccatgt
3121 cataccccaa ggtgcaaaag agttcttcgg agtccccatc aaacaaatcc agatacacaa
3181 atcaggtgaa ttctgtcgat tgagattccc aaaaccaatc agaactgatg tgacgggcat
3241 gattctggaa gaaggtgcgc cagaagggac cgtggccaca ctgctcatca agagaccaac
3301 tggagaactc atgcctttgg cagccagaat gggaacccat gcaaccatga agattcaggg
3361 gcgcacggtt ggaggacaaa tgggtatgct cttgacagga tccaacgcca agagtatgga
3421 cttgggcaca acaccaggcg actgtggctg tccctacatc tacaaaagag ggaatgacta
3481 cgtggttata ggagtccata cagccgctgc ccgtggagga aacactgtca tctgcgccac
3541 ccagggtagt gaaggagaag ccacacttga aggaggtgac aacaaaggaa cgtactgtgg
3601 tgcaccaatt ttgggcccag ggagtgctcc gaaactcagc accaaaacta agttttggag
3661 atcatccaca acgccactcc caccaggcac ctacgaacca gcctacctcg gtggcaagga
3721 ccccagagtc aaaggtggcc cttcattgca acaagttatg agggaccagc taaaaccatt
3781 cacagaaccc agaggcaaac cgccaagacc aaatgtgttg gaagctgcca agaaaaccgt
3841 cattaatgtt cttgagcaaa caattgaccc accccaaaaa tggtcattcg cgcaagcttg
3901 cgcatccctt gacaaaacca cctccagcgg acatccgcac cacatgcgga aaaacgactg
3961 ctggaatggg gagtccttca caggaaaatt ggcagatcag gcctctaagg ccaacctaat
4021 gtttgaagag ggaaagaaca tgactccagt ttacacaggt gcacttaaag atgaattagt
4081 gaagactgac aaaatttatg gtaagatcaa gaagaggctc ctgtggggct cggacctggc
4141 gaccatgata cggtgcgccc gggctttcgg aggccttatg gatgaactca aggcacattg
4201 tgtcaccctt cctgtcagag ttggtatgaa tatgaatgaa gatggtccca taatctttga
4261 gaagcactcc agatataaat accattatga tgctgattac tccaggtggg actcaacaca
4321 acaaagggat gtgttagcag cagcactaga aatcatggtt aagttctctc cagaaccaca
4381 cttggcccag atagttgcag aagacctcct ttcccctagt gtaatggacg tgggcgactt
4441 ccaaatatca ataagtgaag ggctcccctc cggggtacct tgcacctccc agtggaattc
4501 catcgcccac tggctcctca ccctttgtgc actctctgaa gtcacggacc tgtcccctga
4561 catcattcag gccaactccc ttttctcctt ctatggtgat gatgagattg tgagtacaga
4621 cataaagttg gacccagaga agctgacggc aaaactcaag gagtacgggc tgaagccaac
4681 ccgcccagac aaaactgaag gaccccttgt catctctgaa gatctggatg gcctgacatt
4741 cctccggagg actgtgaccc gtgacccagc tggctggttt gggaaattgg aacaaagttc
4801 aattctcagg caaatgtact ggaccagggg tcccaaccat gaagatccat ctgaaacaat
4861 gataccacac tcccaaagac ccatacaatt gatgtccttg ctgggcgagg ctgcactcca
4921 cggcccagca ttttacagca aaattagcaa attggtcatt gcagaattga aggaaggtgg
4981 catggatttt tacgtgccca gacaagaacc aatgttcaga tggatgagat tctcagatct
5041 gagcacgtgg gagggcgatc gcaatctggc tcccagtttt gtgaatgaag atggcgtcga
5101 gtgacgccaa cccatctgat gggtccgcag ccaacctcgt cccagaggtc aacaatgagg
5161 ttatggctct ggagcccgtt gttggtgccg ctattgcggc gcctgtagcg ggccaacaaa
5221 atgtaattga cccctggatt agaaataatt ttgtgcaagc ccctggtgga gagtttacag
5281 tatcccctag aaacgctcca ggtgaaatac tatggagcgc gcccttaggc cctgatctaa
5341 atccctacct atcccatttg gccagaatgt ataatggtta tgcaggtggt tttgaagtgc
5401 aggtaatcct tgcggggaac gcgttcaccg ccggaaagat catatttgca gcagtcccac
5461 caaattttcc aactgaaggc ttgagcccca gccaggtcac tatgttcccc catataatag
5521 tagatgttag acaactggaa cctgtgttga ttcccttacc cgatgttagg aacaatttct
5581 atcactataa ccaatcaaat gaccccacca ttaaattgat agcaatgttg tatacaccac
5641 ttagggctaa caatgctggg gatgatgtct tcacggtttc ttgccgagtc ctcacgagac
5701 catcccctga ttttgatttc atattcttag tgccacccac agttgagtca agaactaaac
5761 cattctctgt cccaatttta actgttgagg agatgactaa ttcaagattc cccattcctt
5821 tggaaaagtt gttcacaggt cccagcagta cctttgttgt tcaaccacaa aatggcaggt
5881 gcacaactga tggcgtgctc ctaggtacca cccaattgtc tcctgtcaac atctgcacct
5941 tcagagggag tgtcacccaa acagcgacag gtagtcataa ctacacaatg aatttggctt
6001 cccaaaattg gaacagttat gatccaacag aagaaatccc agcccctcta ggaactccag
6061 acttcgtagg gaaaattcga ggtatgctca cccaaaccac aaggggaaat ggctcaacac
6121 gcggccacac agccacagtg tatactggga gcaacgactt tgctccaaaa ctgggtaggg
6181 ttcaatttga aactgacaca aacaacgatt ttgaaactaa ccaaaacaca aagttcaccc
6241 cggtcggcgt catccagaat ggtgacactg cccaccgaaa tgaaccccaa caatgggtgc
6301 tcccaagtta ttcaggcaga aatactcata atgtgcacct ggcccccgct gtagccccca
6361 cttttccggg cgagcaactc ttattcttca gatctacctt gcccggatgt agcgggtacc
6421 ccaacatgga tttggattgt ctgctccccc aggaatgggt gcagtacttc tatcaagagg
6481 cagccccagc acaatctgaa gtggctctgt taaggtttgt gaatccagac acaggtaggg
6541 ttttgtttga gtgtaagctc cacaaatcgg gctatgtcac agtggctcac actggccaac
6601 atgatttggt tatccccccc aatggttatt tcagatttga ttcctgggtc aaccaattct
6661 acacgcttgc ccccatggga aatggaacgg ggcgtagacg tgcattataa tggctggagc
6721 tttctttgct ggattggcat ctgatgtcct tggctctgga cttggttccc tggtcaacgc
6781 tggggctggg accatcaacc aaaagattga atttgaaaat aacagaaaat tgcaacaagc
6841 ttccttccaa tttagtagca acctacaaca ggcttccttt caacacgaca aagagatgct
6901 ccaagcacaa attgaggcca ccaaaaagct gcaacaggaa atgatgaaag ttaagcaggc
6961 agtgctccta gagggtgggt tctctgagac agatgcagcc cgcggtgcaa tcaacgcccc
7021 tatgacaaag gctttggatt ggagcggtac aaggtattgg gcccccgatg ctagaactac
7081 aacatacaat gcaggccgct tctccacccc ccaaccatcg ggggtactgc caggaagagc
7141 taatctcagg aatgctgtcc ccgctcgggg ttcctccagc acaccttcca attcctctat
7201 tgctacttct gtgtactcaa atcaaactgc ttcaacgaga cttggttcta cagctggttc
7261 tgggaccagt gtctcgagcc tcccgtcaac tgcaaggact aggagctggg ttgaggatca
7321 aaataggaat ctgtcgcctt tcatgagggg ggcccacgac atatcgtttg tcaccccacc
7381 atctagcaga tcctctagcc aaggcacagt ctcaaccgtg cctaaagaag ttttggactc
7441 ctggactggt gctttcaaca cgcacaggca gcctctcttc gctcacattc gtaagcgagg
7501 ggagtcacgg gtgtaatgtg aaaagacaaa attgattatc tttcttttct ttagtgtctt
7561 ttaaaaa
//