Typing tool
|
|
|
|
|
|
Typing tool
|
Complete norovirus genomes
| PQ304632 | GII.17 | |
|
|---|---|---|---|
| GII.P31 |
ORF1: 6..5105
ORF2: 5086..6708
ORF3: 6708..7487
LOCUS PQ304632 7508 bp RNA linear VRL 17-OCT-2024
DEFINITION Norovirus GII isolate Hu/GII.17[P31]/SanMateo0237/2022/USA
nonstructural polyprotein (ORF1), VP1 (ORF2), and VP2 (ORF3) genes,
complete cds.
ACCESSION PQ304632
VERSION PQ304632.1
KEYWORDS .
SOURCE Norovirus GII
ORGANISM Norovirus GII
Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes;
Picornavirales; Caliciviridae; Norovirus; Norovirus norwalkense.
REFERENCE 1 (bases 1 to 7508)
AUTHORS Chhabra,P., Wong,S., Niendorf,S., Lederer,I., Vennema,H., Faber,M.,
Nisavanh,A., Jacobsen,S., Williams,R., Colgan,A., Yandle,Z.,
Garvey,P., Al-Hello,H., Ambert-Balay,K., Barclay,L., de Graaf,M.,
Celma,C., Breuer,J., Vinje,J. and Douglas,A.
TITLE Increased circulation of GII.17 noroviruses, six European countries
and the United States, 2023 to 2024
JOURNAL Euro Surveill 29 (39) (2024)
REMARK DOI: 10.2807/1560-7917.ES.2024.29.39.2400625
REFERENCE 2 (bases 1 to 7508)
AUTHORS Pan,C.-Y., Barclay,L., Montmayeur,A.M., Vinje,J. and Chhabra,P.
TITLE Direct Submission
JOURNAL Submitted (10-SEP-2024) 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 :: Sanger dideoxy sequencing; Illumina
##Assembly-Data-END##
FEATURES Location/Qualifiers
source 1..7508
/organism="Norovirus GII"
/mol_type="genomic RNA"
/isolate="Hu/GII.17[P31]/SanMateo0237/2022/USA"
/isolation_source="stool"
/host="Homo sapiens"
/db_xref="taxon:122929"
/geo_loc_name="USA"
/collection_date="12-Oct-2022"
/note="genotype: GII.17[P31]"
gene 6..5105
/gene="ORF1"
CDS 6..5105
/gene="ORF1"
/codon_start=1
/product="nonstructural polyprotein"
/protein_id="XGK29418.1"
/translation="MKMASNDASAAAAANSNNDTVKSSSDGVLSSMAVTFKRALGARP
KQPPPKEIPPRPPRPPTPELVKKIPPPPPNGEDEPVVSYSAKDGVSGLPELTTVRQPD
EVNTAFSVPPLNQRENRDAKEPLTGTIIEMWDGEIYHYGLYVERGLILGVHKPPAAIS
LAKVELTPLSLFWRPVYTPQYLISPDTLRRLHGESFPYTAFDNNCYAFCCWVLDLNDS
WLSRRMIQRTTGFFRPYQEWNRKPLPTMDDSKLKKVANIFLCTLSSLFTRPIKDIIGK
LKPLNILNILATCDWTFAGVVESMILLAELFGVFWTPPDVSAMIAPLLGDYELQGPED
LAVELVPVVMGGIGLVLGFTKEKIGKMLSSAASTLRACKDLGAYGLEILKLVIKWFFP
KKEEENELAMVRSIEDAVLDLEAIENNHLTTLLKDKDSLATYMRTLDLEEEKARKLST
KSASPDIVGTINALLARIAAARSLVHRAKEELSSRLRPVVVMISGKPGIGKTHLAREL
AKKIAASLTGDQRVGLIPRNGVDHWDAYKGERVVLWDDYGMSNPIHDALRLQELADTC
PLTLNCDRIENKGKVFDSDAIIITTNLANPAPLDYVNFEACSRRIDFLVYAEAPEVER
AKRDFPGQPDMWKNAFSPDFSHIKLSLAPQGGFDKNGNTPHGKGVMKTLTTGSLIARA
SGLLHERLDEYELQGPALTTFNFDRNKILAFRQLAAENKYGLMDTMRVGKQLKDVKTM
PDLKQALKNVAIRKCQIVYGGSTYTLEADGKGSVKIDKVQSAAVQTNNEIAGALHHLR
CARIRYYVKCVQEALYSIIQIAGAAFVTTRIAKRMNIQNLWSKPQVEDTEETASKDGC
PKPKEDEEFVVSSDDIKTEGKKGKNKSGRGKKHTAFSSKGLSDEEYDEYKRIREERNG
KYSIEEYLQDRDKYYEEVAIARATEEDFCEEEEAKIRQRIFRPTRKQRKEERVSLGLV
TGSEIRKRNPDDFKPKGKLWADDDRSVDYNEKLNFEAPPSIWSRIVNFGSGWGFWVSP
SLFITSTHVIPQGAKEFFGVSIKQIQIHKSGEFCRLRFPKPIRTDVTGMILEEGAPEG
TVATLLIKRPTGELMPLAARMGTHATMKIQGRTVGGQMGMLLTGSNAKSMDLGTTPGD
CGCPYIYKRGNDYVVIGVHTAAARGGNTVICATQGSEGEATLEGGDNKGTYCGAPILG
PGSAPKLSTKTKFWRSSTTPLPPGTYEPAYLGGKDPRVRGGPSLQQVMRDQLKPFTEP
RGKPPRPNVLEAAKKTIINVLEQTIDPPQKWSFSQACASLDKTTSSGHPHHMRKNDCW
NGESFTGRLADQASKANLMFEEGKNMTPVYTGALKDELVKTDKIYGKIKKRLLWGSDL
ATMIRCARAFGGLMDELKAHCVTLPVRVGMNMNEDGPIIFEKHSRYKYHYDADYSRWD
STQQRDVLAAALEIMVKFSPEPHLAQVVAEDLLSPSVMDVGDFQISISEGLPSGVPCT
SQWNSIAHWLLTLCALSEVTDLSPDIIQANSLFSFYGDDEIVSTDIKLDPEKLTAKLK
EYGLKPTRPDKTEGPLVISEDLDGLTFLRRTVTRDPAGWFGKLEQSSILRQMYWTRGP
NHEDPSETMIPHSQRPIQLMSLLGEAALHGPAFYSKISKLVIAELKEGGMDFYVPRQE
PMFRWMRFSDLSTWEGDRNLAPSFVNEDGVE"
mat_peptide 6..995
/gene="ORF1"
/product="p48"
mat_peptide 996..2093
/gene="ORF1"
/product="NTPase"
mat_peptide 2094..2630
/gene="ORF1"
/product="p22"
mat_peptide 2631..3029
/gene="ORF1"
/product="VPg"
mat_peptide 3030..3572
/gene="ORF1"
/product="Pro"
mat_peptide 3573..5102
/gene="ORF1"
/product="RdRp"
gene 5086..6708
/gene="ORF2"
CDS 5086..6708
/gene="ORF2"
/note="major capsid protein"
/codon_start=1
/product="VP1"
/protein_id="XGK29419.1"
/translation="MKMASNDAAPSNDGATGLVPEINNETLPLEPVAGAAIAAPVTGQ
NNIIDPWIRTNFVQAPNGEFTVSPRNSPGEILLNLELGPDLNPYLAHLSRMYNGYAGG
VEVQVLLAGNAFTAGKILFAAVPPNFPVEFLSPAQITMLPHLIVDVRTLEPIMIPLPD
VRNTFFHYNNQPANRMRLVAMLYTPLRSNGSGDDVFTVSCRVLTRPTPDFEFTYLVPP
SVESKTKPFSLPILTISELTNSRFPVPVDSLFTAQNNNLNVQCQNGRCTLDGELQGTT
QLQPSGICAFRGKITADVRPNHDDRWHMQLTNLNGTPFDPTEDVPAPLGTPDFTGLLF
GVASQRNVQPNPNTTRAHEAVISTTSSQFVPKLGSINFGSTSEDFIVGQPTKFTPVGI
KIEDGHAFDQWTLPRYSGHLTLNMNLAPPVAPNFPGEQLLFFRSNVPCAGGISDGVID
CLLPQEWIQHFYQESAPSQSDVALIRYVNPDTGRTLFEAKLHRTGYITVAHSGDYPLV
VPSNGYFRFDSWVNQFYSLAPMGTGNGRRRVQ"
gene 6708..7487
/gene="ORF3"
CDS 6708..7487
/gene="ORF3"
/note="minor structural protein; small basic protein"
/codon_start=1
/product="VP2"
/protein_id="XGK29420.1"
/translation="MAGAFIAGLAGDMLTNTVGSLANAGANAITQKIDFENNKQLQSA
SFQHDKDMLQAQVAATKQLQADMIAIKQGILTAGGFSPTDAARGAVGAPMTKVLDWSG
TRYWAPNSTKTTGYSGQFTSAPVHIPTKMIQPTPVKRTQPLSSSSGSVYSLSTQSTAL
TKPSSGSSSVSSASTQSTKLSSVSSMDRTANWVNQQRNLSPFMSGALNISHVTPPSSR
ASSSGTVSTVPKEVLDSWTPAFNTRRQPLFAHLRVRGESRV"
ORIGIN
1 tgtgaatgaa gatggcgtct aacgacgctt ccgctgccgc tgctgccaac agcaacaacg
61 acaccgtaaa atcttcaagt gacggtgtgc tctctagcat ggctgtcact tttaaacggg
121 ccctcggggc gcggcctaaa cagccgcccc cgaaggaaat accacctaga cccccacggc
181 cacccacacc agagttggtc aaaaagatcc ctcctccccc acccaacgga gaggatgaac
241 cagtggtttc ctatagcgcc aaagatggtg tttccgggct gcctgagctc accactgtca
301 gacaaccgga tgaagttaac acggcgttca gtgttccccc gctcaaccaa agggagaaca
361 gggacgccaa ggaaccatta actggaacaa ttattgagat gtgggacgga gaaatctacc
421 attacggcct gtacgtggaa cgaggtctta tacttggtgt gcataagcca ccggcggcca
481 tcagccttgc caaagtcgag ctaacaccac tctctctgtt ctggagacct gtatacacac
541 cccagtacct catctctcca gacactctca ggagactaca tggggagtca ttcccctaca
601 ctgcatttga taacaattgc tatgccttct gttgttgggt attagaccta aacgactcat
661 ggctaagcag gagaatgatt cagagaacaa caggtttctt cagaccatac caggaatgga
721 acaggaaacc cctccccact atggatgatt ccaaattgaa gaaggtggcc aacatattct
781 tgtgtacttt gtcttcacta ttcactaggc ccattaagga cataatagga aagcttaaac
841 ctcttaacat ccttaatatt ctggctacat gtgattggac cttcgcaggc gtagtggaat
901 ccatgatact cttggcagag ctctttggag ttttctggac acccccagat gtgtctgcga
961 tgatcgcccc cttactagga gactatgaac tgcaaggacc tgaggacctt gcagtagaac
1021 tggtcccagt ggtaatgggg gggataggtt tggtgctagg atttaccaaa gagaaaattg
1081 gaaagatgct atcatccgct gcatctactt tgagagcttg taaagacctt ggtgcatacg
1141 gactggaaat tttaaaatta gtcataaaat ggttcttccc aaagaaagag gaagaaaatg
1201 agttagctat ggtgagatcc atcgaggatg cagtgttaga cctcgaagca attgaaaaca
1261 atcacttgac caccctgctc aaagataaag acagcttggc aacctacatg agaacccttg
1321 accttgagga ggagaaagct agaaaactct caaccaaatc tgcttcaccc gatattgtgg
1381 gcacaatcaa cgcccttctg gcaagaatcg ctgccgcacg ctccctagtg catcgggcga
1441 aagaagagct ctccagcagg ctgagacctg tcgttgtgat gatatcaggg aaaccaggga
1501 taggaaaaac tcaccttgcc agggagttgg ccaagaagat cgcagcctcc ctcacagggg
1561 accagcgtgt gggtcttatc ccgcgcaatg gtgttgacca ctgggacgca tacaagggtg
1621 aaagagtggt cctatgggat gactatggaa tgagcaaccc catccatgac gccctcagat
1681 tgcaggaact tgctgacact tgccccctca cgctaaattg tgacagaatt gagaacaaag
1741 ggaaagtctt tgacagtgat gccataatta tcaccaccaa tctggccaac ccagcaccac
1801 tggactatgt caacttcgaa gcgtgctcga ggcgcattga cttcctcgtg tacgcagaag
1861 ctccagaggt agaaagggca aagcgcgact tcccaggtca acctgacatg tggaagaacg
1921 ctttcagtcc tgacttctca cacataaaac tgtcattggc tccacagggt ggttttgaca
1981 agaacggcaa caccccgcat ggaaaaggtg tcatgaaaac cctcaccact ggttccctca
2041 tcgcccgagc atcagggcta ctccatgaga gactagatga atatgaattg caaggcccag
2101 ccctcaccac tttcaacttt gatcgcaaca agatacttgc ttttagacag cttgctgctg
2161 aaaacaagta tgggctgatg gatacaatga gagttggaaa acagctcaag gatgtcaaga
2221 ctatgccaga cctcaaacaa gcactcaaga atgtcgcgat caggaagtgc cagatagtgt
2281 acggtggtag cacctacaca cttgaggccg atggtaaggg tagtgtaaaa attgataaag
2341 tgcaaagtgc tgctgtacaa actaacaatg aaatagctgg cgccctacac cacctaaggt
2401 gtgccagaat cagatactat gttaagtgtg tccaggaggc attgtattcc atcattcaaa
2461 tcgctggggc tgcattcgtc accacgcgca tcgctaagcg catgaacata cagaatctct
2521 ggtccaagcc acaggtggaa gacacagaag agacggccag caaagatggt tgcccaaaac
2581 ccaaagaaga tgaagagttt gttgtttcat ccgacgacat caaaactgaa ggcaagaaag
2641 ggaagaacaa gtctggtcgt ggcaagaagc acacagcctt ctcaagtaaa gggctcagtg
2701 atgaggagta cgacgagtac aagagaatca gagaagaaag gaatggcaag tattccatag
2761 aagagtacct acaggataga gacaagtact atgaggaggt ggctattgcc agggcaaccg
2821 aagaagactt ctgtgaagaa gaagaggcca aaatccggca gagaattttc agaccaacaa
2881 ggaaacaacg caaagaagag agggtctctc tcggcttggt cacaggttct gaaatcagaa
2941 agagaaaccc agacgacttt aagcccaagg gaaagctgtg ggctgatgat gacagaagtg
3001 ttgactacaa tgaaaaactc aactttgagg ccccgccaag catctggtcg cggatagtca
3061 actttggttc aggttggggt ttctgggtct cccccagtct gttcataaca tcaacccatg
3121 tcatacccca gggtgcaaaa gagttcttcg gagtctctat caaacaaatc cagatacaca
3181 aatcaggtga attctgtcga ttgagattcc caaaaccaat caggactgat gtgacgggca
3241 tgattctaga agaaggtgcg cccgaaggaa ccgtggccac actgctcatc aagagaccaa
3301 ctggagaact catgcctctg gcagccagaa tgggaaccca tgcaaccatg aagattcaag
3361 ggcgcacagt tggaggacaa atgggtatgc tcctgacagg atccaacgcc aagagcatgg
3421 acctaggcac aacaccaggt gactgcggct gtccctacat ctacaagaga gggaatgact
3481 acgtggtcat aggggtccac acggccgctg cccgtggagg aaacactgtc atatgtgcca
3541 cccaggggag tgagggagaa gccacacttg aaggaggtga taacaaagga acatactgtg
3601 gtgcaccaat cttgggccca gggagtgctc caaagctcag caccaaaact aaattttgga
3661 ggtcatccac aacaccactc ccgcctggca cctacgaacc agcctacctc ggtggaaaag
3721 atcccagagt cagaggtggc ccttcattgc aacaagttat gagggaccag ctaaagccat
3781 tcacagaacc cagaggcaaa ccaccaagac caaatgtgtt ggaagctgcc aagaaaacca
3841 tcatcaacgt tcttgagcaa acaattgacc caccacaaaa atggtcattc tcgcaagctt
3901 gcgcatccct tgacaaaacc acctccagcg gccatccgca ccatatgcgg aagaacgatt
3961 gctggaatgg ggaatccttc acaggaagat tggcagatca ggcctccaag gccaacctaa
4021 tgtttgaaga gggaaagaac atgactccag tctacacggg tgcacttaaa gatgaattgg
4081 taaagactga caaaatttat ggtaagatca agaagaggct tctttggggc tcagacctgg
4141 cgaccatgat acggtgcgcc cgagcttttg gaggtcttat ggatgaactt aaggcacact
4201 gtgtcactct tcctgtcaga gttggtatga acatgaatga ggatggcccc attatctttg
4261 agaaacactc cagatataaa tatcactatg atgctgatta ttcccggtgg gactcgacac
4321 aacaaaggga tgtgctggca gcagcactag aaatcatggt caaattctct ccagaaccac
4381 acttggctca ggtagttgca gaagacctcc tctctcctag tgtaatggat gtaggtgact
4441 ttcaaatatc aataagtgag gggctcccct ctggggtgcc ttgcacctcc cagtggaact
4501 ccatcgccca ctggcttctc actctttgtg cactctctga agtcacggac ctgtcccctg
4561 atatcattca ggccaactcc cttttctcct tctatggtga tgatgagatt gtgagcacgg
4621 acataaagtt ggacccagag aagctgacag caaaactcaa ggagtacggg ctgaaaccaa
4681 cccgtcccga caaaactgaa ggaccccttg ttatctctga agatctggat ggcctgacat
4741 tcctccggag gactgtgacc cgtgacccag ctggttggtt tggaaaattg gaacaaagct
4801 caattctcag gcaaatgtac tggactaggg gtcccaatca tgaagaccca tctgaaacaa
4861 tgataccaca ctcccaaaga cccatacaat tgatgtcctt gctgggcgag gctgcactcc
4921 acggcccagc attttacagc aaaattagta aattggttat tgcagagttg aaggaaggtg
4981 gtatggattt ttacgtgcct agacaagagc caatgttcag atggatgagg ttctcagatc
5041 tgagcacgtg ggagggcgat cgcaatctgg ctcccagttt tgtgaatgaa gatggcgtcg
5101 aatgacgccg ctccatctaa tgatggtgcc acgggcctcg tcccagagat caacaacgag
5161 acccttcctt tggaaccggt agcgggtgca gctattgccg cgcctgttac tggccaaaat
5221 aatataattg atccctggat tagaacaaat tttgtacaag cacccaatgg ggagttcaca
5281 gtctcaccca gaaactctcc tggagaaatt cttctaaatt tggaattggg tcctgattta
5341 aatccatatc tggcacattt atctagaatg tataatgggt atgctggtgg cgtagaagtc
5401 caagtcctcc ttgcagggaa tgcgttcact gcaggaaaga ttctcttcgc tgccgttcca
5461 ccaaatttcc cagttgaatt cttgagtcct gcgcaaatca ccatgttgcc acacttaata
5521 gttgatgtta gaacccttga acccatcatg ataccactcc ctgatgtcag gaacaccttc
5581 tttcattaca ataatcaacc tgccaatcgt atgcgattgg tagccatgtt gtataccccc
5641 ctgagatcta atggttctgg tgatgatgtt ttcacagtgt catgtagagt gctaactaga
5701 cccaccccag attttgagtt tacatatttg gtcccccctt cggtagagtc taagactaaa
5761 cccttttctc tgcccatact gaccatctct gaattgacca attcaagatt tcctgtaccg
5821 gtggattcat tattcacagc ccaaaacaat aatcttaatg ttcaatgtca aaatggtcgc
5881 tgcacattag atggtgagtt gcagggaacc actcagttgc aaccatcagg catctgcgcc
5941 ttcagaggca aaataacggc agatgtacgt ccaaaccacg atgacagatg gcatatgcaa
6001 ctgacaaatc tcaatggaac ccccttcgac ccaacagagg atgtgccagc tccactgggc
6061 accccagatt ttacaggcct tctcttcgga gtggcgagcc aaagaaatgt ccaacccaac
6121 ccaaacacca ccagggcaca tgaagccgtg atatccacaa ccagttcaca gtttgtgcca
6181 aaattaggat caattaactt tggtagcaca agtgaagatt tcattgtggg ccagcccaca
6241 aaattcacac cagttggcat caagattgag gacggacatg catttgatca gtggacccta
6301 cccaggtact caggccattt aactctcaat atgaaccttg ccccacctgt tgccccaaat
6361 ttccctggtg aacaactact cttctttagg tcaaatgtcc cctgtgccgg cggcattagt
6421 gatggtgtca tcgactgcct gctgcctcag gagtggatac agcactttta ccaggagtct
6481 gctccctccc agtccgatgt ggccctgatc agatacgtca accccgacac gggccgcaca
6541 cttttcgagg cgaaactcca tagaacaggc tatatcactg ttgctcattc aggtgattac
6601 ccccttgttg tcccctccaa tggatacttt agatttgatt cttgggtgaa tcaattttat
6661 tcacttgccc ccatgggaac tgggaatggg cgcaggcggg tgcagtaatg gcaggagctt
6721 tcatagcagg tctagcaggt gacatgctca ccaacacagt tggctcactg gcgaacgccg
6781 gggccaatgc catcactcaa aagatagact ttgaaaacaa caaacagctc caatctgcct
6841 ccttccaaca tgacaaagac atgctccaag cacaagtggc tgccaccaag cagttacagg
6901 ctgacatgat cgccatcaag caggggatac tgaccgcggg cggcttttcc cctactgatg
6961 cggcgagagg agcagtgggt gcacccatga ccaaagtcct cgactggtct ggtactcgtt
7021 actgggctcc aaattccacg aagacaacag gttattcagg gcagttcaca tcagcaccag
7081 tgcacatacc cacaaaaatg attcagccta ctcctgttaa aaggactcaa cctctttctt
7141 cctcttcagg tagtgtctat agtctttcaa cacagagcac tgccttgacc aagccttctt
7201 caggctcttc ttctgtttct tctgcttcta cacaatctac aaaattgagt tcagtttctt
7261 caatggatag aacagcaaat tgggtaaatc agcaaagaaa cctcagcccc ttcatgagtg
7321 gtgcactcaa catatctcat gtaacacctc catcgagcag ggcttcgagt tcggggacag
7381 tctcaactgt acccaaagaa gttttggact cctggacacc tgcattcaac acacgcaggc
7441 agccgctctt cgcacacctc agagtgaggg gggagtcacg tgtttagtga aaagaattaa
7501 ctagtttt
//