Typing tool
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Typing tool
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Complete norovirus genomes
| OP205554 | GII.13 | |
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| GII.P16 |
ORF1: 1..5082
ORF2: 5063..6691
ORF3: 6691..7422
LOCUS OP205554 7422 bp RNA linear VRL 21-JUN-2023
DEFINITION Norovirus GII isolate RIVM-NOV-2018-0381_R03-09 nonstructural
polyprotein (ORF1) gene, partial cds; and VP1 (ORF2) and VP2 (ORF3)
genes, complete cds.
ACCESSION OP205554
VERSION OP205554.1
KEYWORDS .
SOURCE Norovirus GII
ORGANISM Norovirus GII
Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes;
Picornavirales; Caliciviridae; Norovirus; Norwalk virus.
REFERENCE 1 (bases 1 to 7422)
AUTHORS Schmitz,D., Zwagemaker,F., van der Veer,B., Vennema,H., Bosch,T.,
Laros,J.F., Koopmans,M.P., de Graaf,M. and Kroneman,A.
TITLE Shotgun whole genome sequencing for gastroenteritis surveillance
using Norovirus as a model
JOURNAL Unpublished
REFERENCE 2 (bases 1 to 7422)
AUTHORS Schmitz,D., Zwagemaker,F., van der Veer,B., Vennema,H., Bosch,T.,
Laros,J.F., Koopmans,M.P., de Graaf,M. and Kroneman,A.
TITLE Direct Submission
JOURNAL Submitted (05-AUG-2022) Center for Infectious Diseases,
Rijksinstituut voor Volksgezondheid en Milieu, Antonie van
Leeuwenhoeklaan 9, Bilthoven, Utrecht 3721 MA, Netherlands
COMMENT ##Assembly-Data-START##
Assembly Method :: SPAdes v. v3.11.0
Sequencing Technology :: Illumina
##Assembly-Data-END##
FEATURES Location/Qualifiers
source 1..7422
/organism="Norovirus GII"
/mol_type="genomic RNA"
/isolate="RIVM-NOV-2018-0381_R03-09"
/isolation_source="Human feces"
/host="Homo sapiens"
/db_xref="taxon:122929"
/country="Netherlands"
/collection_date="2018-10-03"
/note="genotype: GII.13[P16]"
gene <1..5082
/gene="ORF1"
CDS <1..5082
/gene="ORF1"
/codon_start=1
/product="nonstructural polyprotein"
/protein_id="UUV60963.1"
/translation="DATVAVACNNNNDKEKSSGEGLFTNMSSTLKKALGARPKQPAPR
DKPQKPPRPPTPELIKRIPSPPPNGEEEEEPVIRYEVKSGISGLPELTTVPQPDVANT
AFSVPPLSLRENREAKEPLTGAILEMWDGEIYHYGLYVEKGLVLGVHKPPAAVSMARV
ELTPLSLYWRVVYTPQYLISPETLRRLNGEAFPYTAFDNNCYAFCCWVLDLNDSWLSR
RMVQRTTGFFRPYQEWNRKPLPTMDDSKIKKVANIFLCSLSTFFTRPIKDLIGKIKPL
NILNILATCDWTFAGIVESLILLAELFGVFWTPPDVSAMIAPLLGDYELQGPEDLAVE
LVPVVMGGIGLVLGFTKEKIGKMLSSAASTLRACKDLGAYGLEILKLVMKWFFPKKEE
ANELAMVRAIEDAVLDLEAIENNHMTTLLKDKDSLATYMKTLDMEEEKARRLSTKSAS
PDIVGTINALLARIAAARSLVHRAKEELSSRIRPVVVMISGKPGIGKTHLAREVARKV
ASTLTGDQRVGLIPRNGVDHWDAYKGERVVLWDDYGMSNPIHDALRIQELADTCPLTL
NCDRIENKGKVFDSEVIIITTNLANPAPLDYVNFEACSRRIDFLVYADAPEVEKAKRD
FPGQPDMWKDAFKPDFSHIKLQLAPQGGFDKNGNTPHGKGVMKTLTTGSLIARASGLL
HERMDEFELQGPTITTFNFDRNRITAFRQLAAENKYGLVDTMRVGNQLKGVKTMEELK
QAIRNVTIKRCRIIYGGSTYDLESDGKGKVLVEKVKNTSVQTNNELAGALHHLKHARI
RYYVKCVQETVYSIIQIAGAAFVTTRIARRMNIQELWSKPQLDQNESETKEEAPKSGD
DEFIISSKDFKEEGKKGKNKTGRGKKHTAFSSKGLSDEEYDEYKRIREERNGKYSIEE
YLQDRDRYYEELAIAKATEEDFCEEEEIKIRQRIFRPTRKQRKEERATLGLVTGSEIR
KRNPDDFKPKGKLWADDNRSVDYNEKLDFEAPPSIWSRIVSFGSGWGFWVSPSLFITS
THVIPAGITEAFGVPIKQIQIHKSGEFCRFRFPKPIRPDVTGMILEEGAPEGTVATVL
IKRPTGELMPLAARMGTHATMKIQGRMVGGQMGMLLTGSNAKGMDLGTTPGDCGCPYI
YKRGNDYIVIGVHTAAARGGNTVICATQGSEGEATLEGGDDKGTYCGAPILGPGGAPK
LSTKTKFWRSSNTPLPPGTYEPAYLGGRDPRVKGGPSLQQVMRDQLKPFTEPRGKPPR
PSVLEAAKQTIINVLEQTLDPPQKWTYAQACASLDKTTSSGHPYHVRKNEFWNGETFT
GKLADQASKANLMFEEGKHMTPVYTAALKDELVKTEKIYGKIKKRLLWGSDLSTMIRC
ARSFGGLMDEMKAHCISLPVRVGMNMNEDGPIIFEKHSRYKYHYDADYSRWDSTQQRA
VLAAALEIMVRFSAEPQLAQIVAEDLLAPSVVDVGDFKITINEGLPSGVPCTSQWNSI
AHWLLTLCALSEVTKLSPDIIQANSMFSFYGDDEIVSTDIKLDPEQLTAKLKEYGLKP
TRPDKTEGPLIISEDLNGITFLRRTVTRDPAGWFGKLDQSSILRQMYWTRGPNHEDPN
ETMIPHSQRPIQLMALLGEASLHGPSFYSKISKLVITELKEGGMDFYVPRQEPMFRWM
RFSDLSTWEGDRNLAPNFVNEDGVE"
mat_peptide <1..978
/gene="ORF1"
/product="p48"
mat_peptide 979..2076
/gene="ORF1"
/product="NTPase"
mat_peptide 2077..2607
/gene="ORF1"
/product="p22"
mat_peptide 2608..3006
/gene="ORF1"
/product="VPg"
mat_peptide 3007..3549
/gene="ORF1"
/product="Pro"
mat_peptide 3550..5079
/gene="ORF1"
/product="RdRp"
gene 5063..6691
/gene="ORF2"
CDS 5063..6691
/gene="ORF2"
/note="major capsid protein"
/codon_start=1
/product="VP1"
/protein_id="UUV60964.1"
/translation="MKMASNDAAPSNDGAASLVPEAINETMPLEPVAGASIAAPVAGQ
TNIIDPWIRTNFVQAPNGEFTVSPRNSPGEILLNLELGPDLNPYLAHLSRMYNGYAGG
VEVQVLLAGNAFTAGKILFAAIPPNFPVDMISPAQITMLPHLIVDVRTLEPIMIPLPD
VRNVFYHFNNQPQPRMRLVAMLYTPLRSNGSGDDVFTVSCRVLTRPTPDFEFIYLVPP
SVESKTKPFTLPILTISELTNSRFPIPIEQLYTAPNENNVVQCQNGRCTLDGELQGTT
QLLSSAVCSYRGRTMANSGDNWDQNLLQLTYPSGASYDPTDEVPAPLGTQDFSGILYG
VLTQDNVSEGTGEAKNAKGVYISTTSGRFTPKIGTIGLHSITENVHPNQQSRFTPVGV
AQNENTPFQQWVLPHYAGALALNTNLAPAVAPTFPGEQLLFFRSRVPCVQGLRGQDAF
IDCLLPQEWVNHFYQEAAPSQADVALIRYVNPDTGRTLFEAKLHRSGFITVSHTGTYP
LVVPPNGHFRFDSWVNQFYSLAPMGTGNGRRRVQ"
gene 6691..7422
/gene="ORF3"
CDS 6691..7422
/gene="ORF3"
/note="minor structural protein; small basic protein"
/codon_start=1
/product="VP2"
/protein_id="UUV60965.1"
/translation="MAGAFIAGLAGDMLTSAVGSLTSAGANAINQKLNFDYNKQLQNA
SFQHDKEMLQAQIDATKKLQSEMIAIKHGVLTAGGFSPADAARGAVNAPMTRVLDWSG
TRYYAPSSVQTTSYSGQFTPSPVHRAQVKSPSNSSQRTAAPSSIRSLSTQSTSLGSTS
SGGSSTASSSSRTADWVQQQRALSPYMHGALQTAYVTPPSSRASSVSSVSTVPKGVLD
SWTPVFNTHRQPLFAHLRKRGESQA"
ORIGIN
1 gacgctaccg ttgccgttgc ttgcaacaac aacaacgaca aagaaaaatc ttcaggtgaa
61 ggcttattca caaatatgtc ttccacctta aagaaagccc tcggggctag gcccaaacag
121 cctgccccga gagataaacc acaaaagccc ccaaggccac caactcccga gttgatcaag
181 aggataccct ctcctccacc taatggtgaa gaagaagaag aaccagtcat taggtatgag
241 gttaagagtg ggatctctgg cctgcccgag ctcacaacag tcccccaacc ggacgtggcc
301 aacacagcat tcagtgttcc accactgagc ttgagagaaa acagggaggc caaggaaccg
361 ctaacagggg caatattaga gatgtgggat ggagagatat accactatgg cctgtacgtg
421 gagaaaggct tagtgttggg tgtgcacaaa ccacctgcag ccgtaagcat ggcaagagtg
481 gagctgacgc cgctgtcatt gtactggcgt gtggtgtaca ctccccaata cctcatctcc
541 cctgaaactc tcaggagact caacggagag gcattccctt acaccgcctt tgacaataac
601 tgctatgcct tttgctgctg ggtgttagac ctcaatgact catggcttag caggaggatg
661 gtgcaaagaa caacgggctt cttcagacct tatcaagagt ggaacagaaa acccctgccc
721 accatggatg actccaaaat taagaaggta gcaaacatat tcctatgttc attgtccaca
781 tttttcacca gacccataaa agacctcata ggaaaaatta aaccattaaa catattgaat
841 atcctggcaa cgtgtgactg gacctttgcc ggaatagtgg agtctctgat attgcttgct
901 gaactcttcg gagttttctg gacaccccca gatgtgtctg ctatgatcgc tcccttactc
961 ggggactacg agttgcaagg gccagaagac ctcgccgttg aactcgtacc tgtggtaatg
1021 ggggggattg gtttggtgtt gggattcacc aaagagaaaa ttggcaaaat gttgtcctca
1081 gcagcatcaa cactcagggc ttgcaaagat cttggtgcct atggcttaga gatactcaaa
1141 ttggtcatga agtggttctt cccaaagaaa gaggaggcca atgagttagc catggtgagg
1201 gctatagagg atgctgtact agatcttgag gcaatagaaa ataaccacat gacaaccctg
1261 ttgaaagaca aagacagctt ggcaacatac atgaaaacac tggacatgga ggaggagaaa
1321 gccaggaggt tgtccacaaa atctgcatcc cctgacatag ttgggacaat caacgccctg
1381 ctggctcgaa tagcagcggc caggtcatta gtccataggg ccaaggaaga gctatctagc
1441 aggataagac cagtagttgt catgatatct ggcaaaccag gaataggcaa aactcatctg
1501 gccagggagg tggcaaggaa ggtggcgtcc actctcacag gggatcaaag agtcggactc
1561 ataccaagaa acggtgtgga ccattgggat gcatacaaag gtgagagagt cgtgctgtgg
1621 gatgactatg gcatgagtaa ccctatacat gatgcccttc gcatacaaga attggctgac
1681 acgtgtcccc ttaccttaaa ttgtgacaga attgagaaca agggaaaggt ttttgacagt
1741 gaggtcataa taattacgac aaaccttgcc aatccagccc cacttgatta tgttaatttt
1801 gaggcctgtt ccaggagaat tgatttcctg gtgtacgctg atgcaccaga agtagaaaag
1861 gcaaaacggg actttcctgg tcagccagat atgtggaagg acgccttcaa gccggacttt
1921 tcacacatca agctacagct tgcaccccag ggcggctttg ataagaatgg caacacccca
1981 catgggaaag gagtgatgaa gaccctcact accggttctc tgattgcccg tgcatcaggc
2041 ctactgcatg agaggatgga tgaatttgaa ctccaaggtc ctacaatcac caccttcaat
2101 ttcgaccgga acagaatcac agcattcaga caattggctg cagaaaacaa gtatggattg
2161 gtggatacca tgagggttgg caatcaacta aaaggagtga aaaccatgga ggaacttaaa
2221 caggcaatca ggaatgtgac catcaagagg tgccggatca tctacggtgg ctccacgtat
2281 gaccttgaat ctgatggcaa gggcaaagtt ttggtggaaa aggtcaagaa cacctctgta
2341 cagaccaaca acgagttggc tggggccctg caccatctca aacatgcccg aatcaggtat
2401 tatgtcaaat gtgtgcaaga aacagtctat tccatcatac aaattgccgg cgctgcgttc
2461 gtcaccacgc gcattgcacg ccgcatgaac atacaagaac tctggtcgaa gccacaatta
2521 gatcaaaatg aatcagagac taaggaagag gcccccaagt caggagatga cgagttcatc
2581 atatcttcta aggacttcaa ggaggaagga aagaagggca aaaacaaaac tggccgtggc
2641 aagaaacaca ctgcattctc cagcaagggc ttgagcgatg aggagtatga cgagtacaag
2701 aggataagag aagagagaaa tgggaagtac tccatagagg agtatcttca agacagagac
2761 aggtactatg aggagctcgc cattgccaag gccacggaag aagacttctg tgaagaggag
2821 gagatcaaaa tccgtcagag aattttccgt cccaccagga aacaaagaaa ggaagagagg
2881 gccacattag ggctagtaac aggttcagaa atcagaaaaa gaaaccctga tgacttcaaa
2941 cccaaaggga agctgtgggc cgatgacaac aggagcgttg actacaatga gaaactggac
3001 tttgaggccc ccccaagcat atggtctagg attgtgagct ttggttccgg ctggggcttc
3061 tgggtgtcac caagcctttt tataacgtca actcatgtaa tccccgcagg cataacagaa
3121 gcatttggag tccccatcaa acaaattcag atccacaaat caggtgaatt ttgccgattc
3181 agattcccaa aaccaattag accagatgtg acagggatga tcttggaaga aggtgcgcct
3241 gagggcaccg tggcaactgt gctcatcaaa cgccccaccg gagagctcat gcctcttgca
3301 gccagaatgg gaacacacgc aaccatgaaa attcaaggcc gcatggttgg tggacagatg
3361 ggtatgttgc tcactggatc aaatgctaaa ggaatggatt tgggaacaac tcctggtgac
3421 tgtggctgtc cttacatcta taaaaggggc aatgactata tagtcattgg ggtgcacact
3481 gcagcagccc gtggtggaaa caccgtcatc tgtgccacac agggaagtga gggtgaggca
3541 actcttgagg gtggggatga caaaggaaca tactgtgggg cacccattct aggccctggg
3601 ggtgcaccaa aattgagcac caaaaccaaa ttttggaggt catcgaacac gccccttcca
3661 ccagggacgt atgaacctgc ctacctcggt ggccgtgatc cgcgtgttaa gggtgggccc
3721 tccctgcagc aggtaatgag agaccagttg aagccattca ctgaacccag gggcaaacct
3781 ccaagaccaa gtgtattgga agcagccaaa caaaccatca tcaatgtcct cgaacaaacc
3841 ctggaccctc cacaaaaatg gacatacgca caggcgtgtg cctcacttga caaaaccacc
3901 tccagcgggc atccctatca cgtccgaaag aatgaattct ggaatggtga gaccttcact
3961 ggtaaattgg cagaccaagc atcaaaagca aacctaatgt ttgaggaagg gaaacacatg
4021 acaccagtat acacagcagc actcaaggac gagctagtca agactgagaa aatctatgga
4081 aagatcaaga agagactgct ctggggctct gacttgtcca ccatgatccg gtgcgctagg
4141 tcatttggtg ggctcatgga cgaaatgaag gcacactgca tatcactccc agtccgagtt
4201 ggcatgaata tgaatgaaga tggcccaata atatttgaga aacattccag atacaaatat
4261 cactatgatg cagactactc gcgttgggat tcaacacaac agagggcagt actagcagca
4321 gccttggaaa ttatggtcag attctctgca gaaccacaat tggcacaaat agtcgctgag
4381 gatctgctgg cccctagtgt ggtggatgta ggagacttta aaattacaat aaatgaaggg
4441 ctcccctctg gtgtgccatg cacttctcaa tggaactcca tcgcacactg gctgctaact
4501 ctctgtgcct tgtctgaagt caccaaactg tcccctgaca ttatacaggc aaattccatg
4561 ttctcatttt acggtgatga cgagattgtc agcaccgaca taaaattgga ccctgaacag
4621 ttaaccgcca aattgaagga gtacggcctg aaaccaaccc gcccagacaa aaccgaggga
4681 cccctgatta tcagtgaaga tttgaacgga atcactttcc tccgaaggac agtgactcgt
4741 gacccagctg gctggtttgg aaaactggac caaagctcaa ttttgagaca gatgtactgg
4801 actagaggac caaatcatga agaccctaat gagacaatga taccccattc tcaaagaccc
4861 atacagctca tggcactgct tggtgaagcc tctcttcacg gaccctcttt ctacagtaaa
4921 atcagtaaat tggtcataac tgagctcaaa gaaggtggga tggactttta cgtgccaagg
4981 caggaaccca tgttcaggtg gatgaggttt tctgacttga gcacgtggga gggcgatcgc
5041 aatctggctc ccaattttgt gaatgaagat ggcgtcgaat gacgccgctc catcgaatga
5101 tggtgcagct agtctcgtac cagaggccat taatgagact atgccattgg aacccgttgc
5161 tggcgcatct attgctgccc cagtggcggg gcaaactaac ataattgacc cctggataag
5221 aacaaatttt gtgcaagccc ctaatggaga atttacagta tcacccagaa attcccctgg
5281 agagatccta ttaaatttag agttgggacc agatttgaat ccttatttgg cccatctatc
5341 aaggatgtat aatggatatg ctggaggtgt tgaggtgcaa gtacttcttg ctgggaacgc
5401 gttcacagcg ggaaagatat tatttgcagc aatcccaccc aactttcctg tagatatgat
5461 tagtccagct caaattacta tgcttcctca tttaattgta gatgttagga cattggaacc
5521 tattatgata cccttacctg atgttaggaa tgtgttctac cattttaata atcaacccca
5581 acctaggatg agattagtgg ctatgctcta taccccattg agatctaatg gttcaggaga
5641 tgatgttttc actgtgtctt gtagagtgtt gaccaggcca acccctgatt ttgaattcat
5701 ttacctggtg cctccctctg tagagtccaa aactaaacca ttcacactac caatattgac
5761 catttctgaa ctaaccaact cccggtttcc catcccaatt gagcaactgt acacggcccc
5821 aaatgaaaat aatgttgtgc agtgtcaaaa tggaaggtgc accttggatg gagagcttca
5881 gggcaccacc cagctgctat caagtgcagt ttgctcttac aggggcagga ctatggctaa
5941 cagtggggac aattgggacc agaatttgct ccagttgacc tacccaagtg gtgcaagcta
6001 tgaccccact gatgaagtac cagcaccatt gggcacccaa gatttcagtg ggatattgta
6061 tggggtgtta actcaagata atgtaagtga gggtacaggg gaggccaaaa atgctaaggg
6121 agtgtacata tccaccacta gtggaagatt caccccaaaa attgggacaa ttggattgca
6181 ttcaataact gaaaatgtgc accccaatca gcaatcacgg ttcacccccg ttggggtcgc
6241 tcagaatgaa aacaccccct ttcaacaatg ggttctacca cactacgcag gtgctcttgc
6301 tctaaacacc aatttggcac ctgctgttgc cccgactttc cctggcgagc aattgctgtt
6361 cttcaggtcc cgtgttccat gtgttcaagg tctgcggggg caggatgctt tcatagactg
6421 tctcctacct caagagtggg tgaaccactt ttatcaagag gctgctccct cccaagcaga
6481 cgtcgccctc atcaggtatg tcaaccctga tactggtcgc acgctgtttg aggccaaatt
6541 gcataggtca ggtttcatta ctgtatcaca cactggcacc taccctcttg tggtcccccc
6601 gaatggtcat ttcaggtttg attcttgggt taaccaattc tactcactcg cccccatggg
6661 aactggcaat gggcgcagaa gagttcaata atggcaggag catttatagc tggtttagcc
6721 ggtgacatgc tgacttctgc tgttggttca ctgacctctg caggagccaa cgccatcaat
6781 cagaaactga attttgatta taataaacaa ctccaaaatg catcctttca acatgataag
6841 gaaatgttgc aggcccaaat tgatgctaca aagaagctcc aatcagaaat gattgcaatc
6901 aagcatgggg ttttgaccgc gggcggcttt tccccagctg atgcagccag aggggcagtc
6961 aacgctccaa tgactcgagt gttggattgg tcagggacac gctactacgc tccaagttct
7021 gtgcaaacta ccagttattc tgggcaattc accccctcgc cagtccatcg ggcgcaggtg
7081 aagtcccctt ccaattcatc ccagcggact gcagctccaa gcagtatccg cagcctgtca
7141 acccagtcaa cttctttagg ctccacctcc tcaggggggt cctctacagc ctcctctagt
7201 tcgaggacag cagattgggt gcaacaacaa agggctctta gcccgtacat gcatggagcc
7261 ctgcagacgg catacgtcac accgccgtct agtagggctt ctagtgtgag ctctgtctca
7321 acagtgccca aaggggtttt ggactcctgg acacctgtgt ttaacacaca caggcagccg
7381 ctgtttgcac acctcaggaa gaggggggag tcacaggctt ag
//