Typing tool
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Typing tool
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Complete norovirus genomes
| OP205545 | GII.2 | |
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| GII.P16 |
ORF1: 1..5099
ORF2: 5080..6708
ORF3: 6708..7487
LOCUS OP205545 7487 bp RNA linear VRL 21-JUN-2023
DEFINITION Norovirus GII isolate RIVM-NOV-2018-0306_R02-24 nonstructural
polyprotein (ORF1) gene, partial cds; and VP1 (ORF2) and VP2 (ORF3)
genes, complete cds.
ACCESSION OP205545
VERSION OP205545.1
KEYWORDS .
SOURCE Norovirus GII
ORGANISM Norovirus GII
Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes;
Picornavirales; Caliciviridae; Norovirus; Norwalk virus.
REFERENCE 1 (bases 1 to 7487)
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JOURNAL Unpublished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 7487)
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..7487
/organism="Norovirus GII"
/mol_type="genomic RNA"
/isolate="RIVM-NOV-2018-0306_R02-24"
/isolation_source="Human feces"
/host="Homo sapiens"
/db_xref="taxon:122929"
/country="Netherlands"
/collection_date="2018-07-03"
/note="genotype: GII.2[P16]"
gene <1..5099
/gene="ORF1"
CDS <1..5099
/gene="ORF1"
/codon_start=3
/product="nonstructural polyprotein"
/protein_id="UUV60936.1"
/translation="KMASNDATVAVACNNTNDKEKSSGEGLFTNMSSTLKKALGARPK
QPAPRDKPQKPPRPPTPELVKRIPPPPPNGEEEEEPVIRYEVKSGISGLPELTTVPQP
DVANTAFSVPPLSLRENREAKEPLTGAILEMWDGEIYHYGLYVEKGLVLGVHKPPAAI
SMARVELTPLSLYWRVVYTPQYLISPETLRRLNGEAFPYTAFDNNCYAFCCWVLDLND
SWLSRRMIQRTTGFFRPYQEWNRKPLPTMDDSKIKKVANVFLCSLSTLFTRPIKDLIG
KIKPLNILNILATCDWTFAGIVESLILLAELFGVFWTPPDVSAMIAPLLGDYELQGPE
DLAVELVPVVMGGIGLVLGFTKEKIGKMLSSAASTLRACKDLGAYGLEILKLVMKWFF
PKKEEANELAMVRAIEDAVLDLEAIENNHMTTLLKDKDSLATYMKTLDMEEEKARRLS
TKSASPDIVGTINALLARIAAARSLVHRAKEELSSRIRPVVVMLSGKPGIGKTHLARE
VARKVASTLTGDQRVGLIPRNGVDHWDAYKGERVVLWDDYGMSNPIHDALRIQELADT
CPLTLNCDRIENKGKVFDSEVIIITTNLANPAPLDYVNFEACSRRIDFLVYAEAPEVE
KAKRDFPGQPDMWKDAFKPDFSHIKLQLAPQGGFDKNGNTPHGKGVMKTLTTGSLIAR
ASGLLHERMDEFELQGPTITTFNFDRNRITAFRQLAAENKYGLVDTMKVGNQLKGVKT
MEELKQAIRNVTIKRCQIIYGGSTYDLESDGKGKVLVEKVKNTSVQTNNELAGALHHL
KHARIRYYVKCVQEAVYSIIQIAGAAFVTTRIARRMNIQELWSKPQLDQNESETKEEA
PKSEDDEFIISSKDIKEEGKKGKNKTGRGKKHTAFSSKGLSDEEYDEYKRIREERNGK
YSIEEYLQDRDRYYEELAIAKATEEDFCEEEEIKIRQRIFRPTRKQRKEERATLGLVT
GSEIRKRNPDDFKPKGKLWADDNRSVDYNEKLDFEAPPSIWSRIVSFGSGWGFWVSPS
LFITSTHVIPAGITEAFGVPIKQIQIHKSGEFCRFRFPKPIRPDVTGMILEEGAPEGT
VATVLIKRPTGELMPLAARMGTHATMKIQGRMVGGQMGMLLTGSNAKGMDLGTTPGDC
GCPYIYKRGNDYIVIGVHTAAARGGNTVICATQGSEGEATLEGGDDKGTYCGAPILGP
GGAPKLSTKTKFWRSSNTPLPPGTYEPAYLGGRDPRVKGGPSLQQVMRDQLKPFTEPR
GKPPRPSVLEAAKQTIINVLEQTLDPPQKWTYAQACASLDKTTSSGHPHHVRKNEFWN
GETFTGKLADQASKANLMFEEGKHMTPVYTAALKDELVKTEKIYGKIKKRLLWGSDLS
TMIRCARSFGGLMDEMKAHCISLPVRVGMNMNEDGPIIFEKHSRYKYHYDADYSRWDS
TQQRAVLAAALEIMVRFSAEPQLAQIVAEDLLAPSVVDVGDFKITINEGLPSGVPCTS
QWNSIAHWLLTLCALSEVTKLSPDIIQANSMFSFYGDDEIVSTDIKLDPEQLTAKLKE
YGLKPTRPDKTEGPLIISEDLNGLTFLRRTVTRDPAGWFGKLDQSSILRQMYWTRGPN
HEDPNETMIPHSQRPIQLMALLGEASLHGPSFYSKISKLVITELKEGGMDFYVPRQEP
MFRWMRFSDLSTWEGDRNLAPNFVNEDGVE"
mat_peptide <1..995
/gene="ORF1"
/product="p48"
mat_peptide 996..2093
/gene="ORF1"
/product="NTPase"
mat_peptide 2094..2624
/gene="ORF1"
/product="p22"
mat_peptide 2625..3023
/gene="ORF1"
/product="VPg"
mat_peptide 3024..3566
/gene="ORF1"
/product="Pro"
mat_peptide 3567..5096
/gene="ORF1"
/product="RdRp"
gene 5080..6708
/gene="ORF2"
CDS 5080..6708
/gene="ORF2"
/note="major capsid protein"
/codon_start=1
/product="VP1"
/protein_id="UUV60937.1"
/translation="MKMASNDAAPSTDGAAGLVPESNNEVMALEPVAGAALAAPVTGQ
TNIIDPWIRANFVQAPNGEFTVSPRNAPGEVLLNLELGPELNPYLAHLARMYNGYAGG
MEVQVMLAGNAFTAGKLVFAAVPPHFPVENLSPQQITMFPHVIIDVRTLEPVLLPLPD
VRNNFFHYNQKDDPKMRIVAMLYTPLRSNGSGDDVFTVSCRVLTRPSPDFDFTYLVPP
TVESKTKPFTLPILTLGELSNSRFPVSIDQMYTSPNETISVQCQNGRCTLDGELQGTT
QLQVSGICAFKGEVTAHLHDNDHLYNVTITNLNGSPFDPSEDIPAPLGVPDFQGRVFG
IISQRDKHNSPGHNEPANRGHDAVVPTYTAQYTPKLGQIQIGTWQTDDLTVNQPVKFT
PVGLNDTEHFNQWVVPRYAGALNLNTNLAPSVAPVFPGERLLFFRSYIPLKGGYGNPA
IDCLLPQEWVQHFYQEAAPSMSEVALVRYINPDTGRALFEAKLHRAGFMTVSSNTSAP
VVVPANGYFRFDSWVNQFYSLAPMGTGNGRRRVQ"
gene 6708..7487
/gene="ORF3"
CDS 6708..7487
/gene="ORF3"
/note="minor structural protein; small basic protein"
/codon_start=1
/product="VP2"
/protein_id="UUV60938.1"
/translation="MAGAFVAGLAGDVLSNGFSSLINAGANAINQRAEFDFNQKLQQN
SFNHDKEMLQAQIQATKQLQADMMAIKQGVLTAGGFSPADAARGAVNAPMTQALDWNG
TRYWAPNSMRTTSYSGKFTSTAPVRQADFQHTQSRPSSGSSVSSFATQSSRPTLTTTT
GSSYGTASSNSTRSTSLSQSTVSRATSRTGEWVRDQNRSLEPYMHGALQTAFVTPPSS
RASDGTVSTVPKGVLDSWTPAFNTRRQPLFAHLRKRGESQA"
ORIGIN
1 tgaagatggc gtctaacgac gctaccgttg ccgttgcttg caacaacacc aacgacaaag
61 aaaaatcttc aggtgaaggc ttattcacaa atatgtcttc caccttaaag aaagccctcg
121 gggctaggcc caaacagcct gccccgagag acaaaccaca aaagccccca agaccaccaa
181 ctcccgagtt ggtcaagagg ataccccccc ctccacctaa cggcgaagaa gaagaagaac
241 cagtcattag gtatgaggtc aagagtggaa tctctggcct gcccgagctc acaacagtcc
301 cccaaccgga cgtggccaac acagcattca gtgttccacc actgagcttg agagaaaaca
361 gggaggccaa ggagccgcta acaggggcaa tattagagat gtgggatgga gagatatacc
421 actatggcct gtacgtggag aaaggcttag tgttgggtgt gcacaaacca cctgcagcca
481 taagcatggc aagagtggag ctgacgccgt tgtcattgta ctggcgtgtg gtgtacactc
541 cccaatacct catctcccct gaaaccctca ggaggctcaa cggagaggca ttcccttaca
601 ccgcctttga caacaactgc tatgcctttt gctgctgggt gttagacctc aatgactcat
661 ggcttagcag gaggatgata caaagaacaa cgggcttctt cagaccttac caagagtgga
721 acagaaaacc cctgcctacc atggatgact ccaaaattaa gaaggtagca aatgtattcc
781 tatgttcatt gtccacatta ttcaccagac ccataaaaga cctcatagga aaaattaaac
841 cattgaacat attgaatatc ctggcaacgt gtgactggac ttttgccgga atagtggagt
901 ctctgatatt acttgctgaa ctcttcggag ttttctggac acccccagat gtgtctgcta
961 tgatcgctcc cttactcggg gactacgagt tgcaagggcc agaagacctc gccgttgaac
1021 tcgtgcctgt ggtaatgggg gggattggtt tggtgttagg attcaccaaa gagaaaattg
1081 gcaaaatgtt gtcctcagca gcatcaacac ttagggcttg caaagatctt ggtgcctatg
1141 gcttagagat actcaaattg gtcatgaagt ggttcttccc aaagaaagag gaggccaatg
1201 agctagctat ggtgagggcc atagaggatg ctgtattaga ccttgaggca atagaaaata
1261 accacatgac aaccctgttg aaagacaaag acagcttagc aacatacatg aaaacactgg
1321 acatggagga ggagaaagcc aggaggttgt ccacaaaatc tgcatcccct gacatagttg
1381 ggacaatcaa cgccctgctg gctcgaatag cagcggccag gtcattagtc cacagggcca
1441 aggaagagct atctagtagg ataaggccag tagttgttat gttatctggc aagccaggaa
1501 taggcaaaac tcatctggcc agggaggtgg caagaaaggt ggcatccact ctcacaggag
1561 atcaaagagt cggactcata ccacgaaacg gtgtggacca ttgggatgca tacaaaggtg
1621 agagagtcgt gctgtgggac gactatggca tgagtaaccc tattcatgat gctcttcgca
1681 tacaagaatt ggctgatacg tgtcccctta ccttaaattg tgacagaatt gaaaataagg
1741 gaaaagtttt tgacagtgaa gtcataataa ttacaacaaa ccttgccaat ccagccccac
1801 ttgattatgt caactttgag gcctgttcca ggagaattga tttcctggtg tacgctgagg
1861 caccagaagt agaaaaggca aaacgggact ttcctggtca gccagatatg tggaaggacg
1921 ccttcaagcc ggacttttca cacatcaagc tacagcttgc accccagggc ggctttgaca
1981 agaatggcaa caccccacat gggaaaggag tgatgaagac cctcactacc ggttctctga
2041 ttgcccgtgc atcaggccta ctgcatgaga ggatggatga atttgaactc caaggcccca
2101 caatcaccac ctttaatttc gaccgaaaca gaatcacggc attcagacaa ttggctgcag
2161 aaaacaagta tggattggtg gataccatga aagttggcaa tcaattaaaa ggagtgaaaa
2221 ccatggaaga actcaaacaa gcaatcagga atgtgaccat caagaggtgc cagatcatct
2281 acggtggttc cacgtatgac cttgaatctg atggcaaggg caaagttttg gtggaaaagg
2341 tcaagaacac ctctgtacag accaataacg agttggctgg ggccctgcac catctcaaac
2401 atgcccgaat caggtactat gtcaaatgtg tgcaagaagc agtctattct atcatacaaa
2461 ttgccggcgc tgcgtttgtc accacgcgca tcgcacgccg catgaacata caagaactct
2521 ggtcgaagcc acaactagat caaaatgaat cagagactaa ggaagaggcc cccaagtcag
2581 aagatgacga gttcatcata tcttctaagg acatcaagga ggaaggaaag aagggcaaaa
2641 acaaaactgg ccgtggcaag aaacacactg cattctccag caagggcttg agcgatgagg
2701 agtatgacga gtacaagagg ataagagaag agagaaatgg gaagtactct atagaggagt
2761 atcttcaaga cagagacagg tactatgagg agctcgccat tgccaaggcc acggaagaag
2821 acttctgtga agaggaggag atcaaaatcc gtcagagaat tttccgtccc accaggaaac
2881 aaagaaagga agagagggcc acattagggc tagtaacagg ttcagaaatc agaaaaagaa
2941 accctgatga cttcaaaccc aaagggaagc tgtgggccga tgacaacagg agtgttgact
3001 acaatgagaa actggacttt gaggcccccc caagcatatg gtctaggatt gtgagctttg
3061 gctctggctg gggcttctgg gtgtcaccaa gccttttcat aacatcaact catgtaatcc
3121 ccgcaggcat aacagaagca tttggagtcc ccatcaaaca aattcagatc cacaaatcag
3181 gcgaattttg ccgattcaga ttcccaaaac caattagacc agatgtgaca ggaatgatct
3241 tggaagaagg tgcgcctgag ggcaccgtgg caactgtgct catcaaacgc cccaccggag
3301 agctcatgcc tcttgcagcc agaatgggaa cacacgcaac catgaaaatt caaggccgca
3361 tggttggcgg acagatgggt atgttgctca ctggatcaaa tgctaaagga atggacttgg
3421 gaacaactcc tggtgactgt ggctgtcctt acatctataa aaggggcaat gactatatag
3481 tcattggggt gcacactgca gcagcccgtg gtggaaacac tgtcatctgt gccacacagg
3541 gaagtgaggg tgaggcaact cttgagggtg gagatgacaa aggaacatac tgtggggcac
3601 ccattctagg ccctgggggt gcaccaaaat tgagcaccaa aaccaaattt tggaggtcat
3661 cgaacacgcc ccttccacca gggacatatg agcctgccta cctcggtggc cgtgatccgc
3721 gtgttaaggg tgggccttcc ctgcagcagg tgatgagaga ccagttgaag ccattcactg
3781 aacccagggg caaacctcca agaccaagtg tattggaagc agccaaacaa accatcatca
3841 atgtcctcga acaaaccctg gaccctccac aaaaatggac atacgcacag gcgtgcgcct
3901 cacttgacaa aaccacctcc agcgggcacc cccatcacgt ccgaaagaat gaattctgga
3961 atggtgagac cttcactggt aaactggcag accaagcatc aaaagcaaac ctaatgtttg
4021 aggaagggaa acacatgaca ccagtgtaca cagcagcact caaggacgag ctagtcaaga
4081 ctgagaaaat ttatggaaag atcaagaaga gactgctctg gggctctgac ttgtccacca
4141 tgatccggtg cgctaggtca tttggtgggc ttatggacga gatgaaggca cactgcatat
4201 cactcccagt ccgagttggc atgaatatga atgaagatgg cccaataata tttgagaaac
4261 attccagata caaatatcac tatgatgcag actactctcg ttgggattca acacaacaga
4321 gggcagttct agcagcagcc ttggaaatca tggtcagatt ttctgcagaa ccacaattgg
4381 cacaaatagt cgctgaggat ctgctggccc ctagtgtagt agatgtagga gactttaaaa
4441 tcacaataaa tgaagggctc ccttctggtg tgccatgcac ttctcaatgg aactccatcg
4501 cacactggct gctaactctc tgtgccttgt ctgaagtcac caaactatcc cctgacatta
4561 tacaggcaaa ttccatgttc tcattttacg gtgatgacga gattgtcagt accgacataa
4621 aattggaccc tgaacagtta accgccaaat tgaaggagta cggcctgaaa ccaacccgcc
4681 cagacaaaac cgagggaccc ctgattatca gtgaagattt gaacggtctc actttcctcc
4741 gaaggacggt gactcgtgac ccagctggct ggtttggaaa actggaccaa agctcaattt
4801 tgaggcagat gtactggact agaggaccaa atcatgaaga ccccaatgag acaatgatac
4861 cccattccca aagacccata cagctcatgg cactgcttgg tgaagcctct cttcacggac
4921 cctctttcta cagtaaaatc agtaaattgg tcataactga actcaaagaa ggtgggatgg
4981 acttttacgt gccaaggcag gaacccatgt tcaggtggat gaggttttct gacttgagca
5041 cgtgggaggg cgatcgcaat ctggctccca attttgtgaa tgaagatggc gtcgaatgac
5101 gccgctccat ctactgatgg tgcagccggc ctcgtgccag aaagtaacaa tgaggtcatg
5161 gctcttgaac ccgtggctgg tgccgccttg gcagccccgg tcaccggtca aacaaatatt
5221 atagaccctt ggattagagc aaattttgtc caggccccca atggtgaatt tacagtctct
5281 ccccgaaatg cccctggtga agtgctactg aatctagagt tgggtccaga attaaatcct
5341 tatctggcac atttagcaag aatgtacaat gggtatgccg gtgggatgga ggtgcaggtc
5401 atgttggctg ggaacgcgtt cacagccggc aagttggtct tcgccgccgt gccaccccac
5461 ttcccggttg aaaaccttag tccacagcaa atcaccatgt tccctcatgt gatcatagat
5521 gtgagaacct tggaacctgt tttattacca ctccctgatg ttaggaataa cttcttccat
5581 tataaccaga aagatgatcc caagatgaga attgtggcta tgctttatac ccccctcagg
5641 tctaatggtt caggtgatga tgtgtttaca gtctcctgta gagtgttgac tagaccttcc
5701 cctgactttg acttcacata cctggtgcca ccaacagtgg agtctaaaac aaagccattc
5761 accctcccaa tcctcacact tggggaactt tccaattcta ggttcccagt gtccatagac
5821 cagatgtaca ccagccctaa tgaaactata tcagtgcagt gtcaaaatgg taggtgcaca
5881 ctggacgggg agcttcaagg gacaacacaa ctccaagtca gtggcatttg tgctttcaaa
5941 ggtgaagtga ccgcccactt gcatgacaat gatcacctat ataatgtcac catcacaaac
6001 ttgaatgggt ccccttttga tccctccgag gatatccctg cccctttggg tgtgcctgac
6061 ttccagggaa gggtttttgg tatcatctcc caaagagata aacacaatag tcctgggcat
6121 aatgaaccag caaacagggg acacgacgct gtggtcccta cttacacagc acagtacact
6181 ccaaaacttg gacaaattca aattggcaca tggcaaactg acgaccttac agtcaaccaa
6241 ccagtcaaat tcaccccagt tggactcaat gacactgaac actttaacca atgggtggtc
6301 cctaggtatg ctggtgccct aaacctcaat acaaaccttg ccccttctgt tgctccagta
6361 tttccaggag agcgcctgct cttcttcaga tcatacattc ccctcaaggg cggttatgga
6421 aacccagcca ttgattgcct actaccacaa gagtgggtgc agcacttcta tcaggaagca
6481 gccccttcaa tgagtgaggt ggccctcgtc agatacatca acccggacac tggtcgggca
6541 ctgtttgagg ccaagctcca cagagctggt ttcatgacag tctcgagcaa caccagtgcc
6601 ccggtggttg tgcctgccaa cgggtacttc agatttgatt cttgggtgaa ccaattttat
6661 tctctcgccc ccatgggaac tgggaatggg cgtagaaggg ttcaataatg gctggagctt
6721 ttgtagctgg tcttgcaggg gacgtgctca gcaatgggtt tagttcatta atcaatgcag
6781 gtgctaatgc aataaatcag agggcagaat ttgattttaa tcaaaaattg cagcaaaatt
6841 cttttaatca tgataaggag atgttgcagg ctcagattca ggcaactaag cagctgcagg
6901 cagacatgat ggctataaaa caaggggtct tgaccgctgg cggcttttcc cctgctgatg
6961 cagccagagg tgctgtgaac gcgcccatga cacaggcgct ggattggaat ggcacaaggt
7021 attgggcacc aaactccatg aggaccacat cttattctgg aaaattcaca tcaaccgccc
7081 cagtgaggca ggctgacttc cagcacaccc aaagccggcc ttcgagtggc tcctctgtgt
7141 cttcctttgc cactcagtct tcaaggccaa ctctgaccac aaccactggt tcctcatatg
7201 gcacagcctc atcaaattca actcgcagca caagcctctc ccaatcaacg gtctccagag
7261 ctacatctag gactggtgag tgggttagag atcaaaatag aagtttggaa ccctacatgc
7321 atggtgcctt acagacagcc tttgtcaccc caccttccag cagggcgtct gacgggacag
7381 tctcaaccgt ccctaaaggt gttttggact cctggacacc tgcgtttaac acccgcaggc
7441 agccgctttt tgcacacctc cgtaagaggg gggagtcaca agcttag
//