Typing tool
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Typing tool
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Complete norovirus genomes
| OP205542 | GII.2 | |
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| GII.P16 |
ORF1: 1..5099
ORF2: 5080..6708
ORF3: 6708..7487
LOCUS OP205542 7487 bp RNA linear VRL 21-JUN-2023
DEFINITION Norovirus GII isolate RIVM-NOV-2018-0049_R02-21 nonstructural
polyprotein (ORF1) gene, partial cds; and VP1 (ORF2) and VP2 (ORF3)
genes, complete cds.
ACCESSION OP205542
VERSION OP205542.1
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JOURNAL Unpublished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-2018-0049_R02-21"
/isolation_source="Human feces"
/host="Homo sapiens"
/db_xref="taxon:122929"
/country="Netherlands"
/collection_date="2018-01-11"
/note="genotype: GII.2[P16]"
gene <1..5099
/gene="ORF1"
CDS <1..5099
/gene="ORF1"
/codon_start=3
/product="nonstructural polyprotein"
/protein_id="UUV60927.1"
/translation="KMASNDATVAVACNDNNDKEKSSGEGLFTNMSSTLKKALGARPK
QPAPRDKPQKPPRPPTPELVKRIPPPPPNGEEEEEPVIRYEVKSGISGLPELTTVPQP
DVANTAFSVPPLSLRENREAKEPLTGAILEMWDGEIYHYGLYVEKGLVLGVHKPPAAI
SMARVELTPLSLYWRVVYTPQYLISPETLRRLNGEAFPYTAFDNNCYAFCCWVLDLND
SWLSRRMVQRTTGFFRPYQEWNRKPLPTMDDSKIKKVANIFLCSLSTLFTRPIKDLIG
KIKPLNILNILATCDWTFAGIVESLILLAELFGVFWTPPDVSAMIAPLLGDYELQGPE
DLAVELVPVVMGGIGLVLGFTKEKIGKMLSSAASTLRACKDLGAYGLEILKLVMKWFF
PKKEEANELAMVRAIEDAVLDLEAIENNHMTTLLKDKDSLATYMKTLDMEEEKARRLS
TKSASPDIVGTINALLARIAAARSLVHRAKEELSSRMRPVVVMISGKPGIGKTHLARE
VARKVASTLTGDQRVGLIPRNGVDHWDAYKGERVVLWDDYGMSNPIHDALRIQELADT
CPLTLNCDRIENKGKVFDSEVIIITTNLANPAPLDYVNFEACSRRIDFLVYAEAPEVE
KAKRDFPGQPDMWKDAFKSDFSHIKLQLAPQGGFDKNGNTPHGKGVMKTLTTGSLIAR
ASGLLHERMDEFELQGPTITTFNFDRNRITAFRQLAAENKYGLVDTMKVGNQLKGVKT
MEELKQAIRNVTIKRCQIIYGGSTYDLESDGKGKVLVEKVKNTSVQTNNELAGALHHL
KHARIRYYVKCVQEAVYSIIQIAGAAFVTTRIARRMNIQELWSKPQLDQNESETKEEA
PKSEDDEFIISSKDIKEEGKKGKNKTGRGKKHTAFSSKGLSDEEYDEYKRIREERNGK
YSIEEYLQDRDRYYEELAIAKATEEDFCEEEEIKIRQRIFRPTRKQRKEERATLGLVT
GSEIRKRNPDDFKPKGKLWADDNRSVDYNEKLDFEAPPSIWSRIVSFGSGWGFWVSPS
LFITSTHVIPAGITEAFGVPTKQIQIHKSGEFCRFRFPKPIRPDVTGMILEEGAPEGT
VATVLIKRPTGELMPLAARMGTHATMKIQGRMVGGQMGMLLTGSNAKGMDLGTTPGDC
GCPYIYKRGNDYVVIGVHTAAARGGNTVICATQGSEGEATLEGGDDKGTYCGAPILGP
GGAPKLSTKTKFWRSSNTPLPPGTYEPAYLGGRDPRVKGGPSLQQVMRDQLKPFTEPR
GKPPRPSVLEAAKQTIINVLEQTLDPPQKWTYAQACASLDKTTSSGHPHHVRKNEFWN
GETFTGKLADQASKANLMFEEGKHMTPVYTAALKDELVKTEKIYGRIKKRLLWGSDLS
TMIRCARSFGGLMDEMKAHCISLPVRVGMNMNEDGPIIFEKHSRYKYHYDADYSRWDS
TQQRAVLATALEIMVRFSAEPQLAQIVAEDLLAPSVVDVGDFKITINEGLPSGVPCTS
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="UUV60928.1"
/translation="MKMASNDAAPSTDGAAGLVPESNNEVMALEPVAGAALAAPVTGQ
TNIIDPWIRANFVQAPNGEFTVSPRNAPGEVLLNLELGPELNPYLAHLARMYNGYAGG
MEVQVMLAGNAFTAGKLVFAAVPPHFPVENLSPQQITMFPHVIIDVRTLEPVLLPLPD
VRNNFFHYNQKDDPKMRIVAMLYTPLRSNGSGDDVFTVSCRVLTRPSPDFDFTYLVPP
TVESKTKPFTLPILTLGELSNSRFPVSIDQMYTSPNEIISVQCQNGRCTLDGELQGTT
QLQVSGICAFKGEVTAHLHDNDHLYNVTITNLNGSPFDPSEDIPAPLGVPDFQGRVFG
IISQRDKHNSPGHNEPANRGHDAVVPTYTAQYTPKLGQVQIGTWQTDDLTVNQPVKFT
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="UUV60929.1"
/translation="MAGAFVAGLAGDVLSNGLSSLINAGANAINQRAEFDFNQKLQQN
SFNHDKEMLQAQIQATKQLQADMMAIKQGVLTAGGFSPADAARGAVNAPMTQALDWNG
TRYWAPNSMRTTSYSGKFTSTAPVRQADFQHTQSRPSSGSSVSSFATQSSRPTLTTTT
GSSHGTASSNSTRSTSLSQSTVSRATSRTGEWVRDQNRNLEPYMHGALQTAFVTPPSS
RASDGTVSTVPKGVLDSWTPAFNTRRQPLFAHLRKRGESQA"
ORIGIN
1 tgaagatggc gtctaacgac gctaccgttg ccgttgcttg caacgacaac aacgacaaag
61 aaaaatcttc aggtgaaggc ttattcacaa acatgtcttc caccttaaag aaagccctcg
121 gggctaggcc caaacagcct gccccgagag acaaaccaca aaagccccca agaccaccaa
181 ctcccgaatt ggtcaagagg ataccccctc ctccacctaa tggcgaagaa gaagaagaac
241 cagtcattag gtatgaggtt aagagtggga tctctggcct gcccgagctc acaacagtcc
301 cccaaccgga cgtggccaat 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 gaggatggta caaagaacaa cgggcttctt cagaccttac caagagtgga
721 acagaaaacc cctgcctacc atggatgact ccaaaataaa gaaggtagca aatatattcc
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 gccgttgagc
1021 tcgtacctgt ggtaatgggg gggattggtt tggtgttggg attcaccaaa gagaaaattg
1081 gcaaaatgtt gtcctcagca gcatcaacac tcagggcttg caaagatctt ggtgcctatg
1141 gcttagagat actcaaattg gtcatgaagt ggttcttccc aaagaaagag gaggccaatg
1201 agctagctat ggtgagggcc atagaggatg cagtactaga ccttgaggca atagaaaata
1261 accacatgac aaccctgttg aaagacaaag acagcttagc aacatacatg aaaacactgg
1321 acatggagga ggagaaagcc aggaggttgt ccacaaaatc tgcatcccct gacatagttg
1381 ggacaatcaa cgccctgctg gctcgaatag cagcggctag gtcattagtc cacagggcca
1441 aagaagagct atctagcagg atgaggccag tagttgttat gatatctggc aaaccaggaa
1501 taggcaaaac tcatctggcc agggaggtgg caagaaaagt ggcatccact ctcacagggg
1561 atcaaagagt cggactcata ccacgaaacg gtgtggacca ttgggatgca tacaaaggtg
1621 agagagtcgt gctgtgggac gactatggca tgagtaaccc tattcatgat gctcttcgca
1681 tacaagaatt ggctgatacg tgtcccctta ccttaaattg tgacagaatc gaaaataaag
1741 gaaaagtttt tgacagtgaa gtcataataa ttacaacaaa ccttgccaat ccagccccac
1801 ttgattatgt caactttgag gcctgttcca ggaggattga tttcctggtg tacgctgagg
1861 caccagaagt agaaaaggca aaacgggact ttcctggtca gccagatatg tggaaggacg
1921 ctttcaagtc ggacttttca cacatcaagc tacagcttgc accccaaggc ggctttgaca
1981 agaatggcaa caccccacat gggaaaggag tgatgaagac cctcactacc ggttctctga
2041 ttgcccgtgc atcaggccta ctgcatgaga ggatggatga atttgaactc caaggtccca
2101 caatcaccac cttcaatttc gaccggaaca gaatcacggc attcagacaa ttggctgcag
2161 aaaacaagta tgggttggtg gataccatga aagttggcaa tcaattaaaa ggagtgaaaa
2221 ccatggaaga actcaaacaa gcaatcagga atgtgaccat caagaggtgc cagatcatct
2281 acggtggttc cacgtatgac cttgaatctg acggcaaggg caaagttttg gtggaaaagg
2341 tcaagaacac ctctgtacag accaataacg agttggctgg ggctctgcac catctcaaac
2401 atgcccgaat caggtactat gtcaaatgtg tgcaagaagc agtctattcc atcatacaaa
2461 ttgccggcgc tgcgtttgtc accacgcgca ttgcacgccg catgaacata caagaactct
2521 ggtcgaagcc acaactagat caaaatgaat cagagactaa ggaagaggcc cccaagtcag
2581 aagatgacga gttcattata tcttctaagg acatcaagga ggaaggaaag aagggcaaaa
2641 acaaaactgg ccgtggcaag aagcacactg cattctccag caagggcttg agcgatgagg
2701 agtatgacga gtacaagagg ataagagaag agagaaacgg 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 gttctggctg gggcttctgg gtgtcaccaa gccttttcat aacatcaact catgtaatcc
3121 ccgcaggtat aacagaagca tttggagtcc ccaccaaaca 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 tgccaaaggg atggacttag
3421 gaacaactcc tggtgattgt ggctgtcctt acatctacaa aaggggcaat gactatgtag
3481 tcattggggt gcacactgca gcagcccgtg gtggaaacac tgtcatctgt gccacacagg
3541 gaagtgaggg tgaggcaact cttgagggtg gagatgacaa aggaacatac tgtggggcac
3601 ccattctagg ccctgggggt gcaccaaaat tgagcaccaa aaccaaattt tggagatcat
3661 caaacacgcc ccttccacca gggacatatg agcctgccta cctcggtggc cgcgatccgc
3721 gtgttaaggg tgggccttcc ctgcagcagg taatgagaga ccagttgaag ccattcactg
3781 aacccagggg caaacctcca agaccaagtg tattggaagc agccaaacaa accatcatca
3841 atgtcctcga acaaaccctg gaccctccac aaaaatggac atacgcacag gcgtgtgcct
3901 cacttgacaa aaccacctcc agcgggcacc cccatcacgt ccgaaagaat gaattctgga
3961 atggtgagac cttcactggc aaactggcag accaagcatc aaaagcaaac ctaatgtttg
4021 aggaagggaa acacatgaca ccagtgtaca cagcagcact caaggacgag ctagtcaaga
4081 ctgagaaaat ctatggaagg 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 gggcagtact agcaacagcc ttggaaatca tggtcagatt ctctgcagaa ccacaattgg
4381 cacaaatagt cgctgaggat ctgctggccc ctagtgtagt agatgtagga gactttaaaa
4441 ttacaataaa tgaagggctt ccttctggtg tgccatgcac ttctcaatgg aactccatcg
4501 cacactggct gctaactctc tgtgccttgt ctgaagtcac caaactgtcc cctgatatca
4561 tacaggcaaa ctccatgttc tcattttacg gtgatgacga gattgtcagc accgacataa
4621 aattggaccc tgaacagtta accgccaaat tgaaggagta cggcctaaaa ccaacccgcc
4681 cagacaaaac cgagggaccc ctgattatca gtgaagattt gaatggtctc actttcctcc
4741 gaaggacggt gactcgtgac ccagctggct ggtttggaaa actggaccaa agctcaattt
4801 tgaggcagat gtactggact agaggaccaa atcatgaaga ccccaacgag acaatgatac
4861 cccattctca aagacccata cagctcatgg cactgcttgg tgaagcctct cttcacggac
4921 cctctttcta cagtaaaatc agtaaattgg tcataactga actcaaagaa ggtgggatgg
4981 acttttacgt gccaaggcag gaacccatgt tcaggtggat gaggttttct gacttgagca
5041 cgtgggaggg cgatcgcaat ctggctccca atttcgtgaa tgaagatggc gtcgaatgac
5101 gccgctccat ctactgatgg tgcagccggc ctcgtgccag aaagtaacaa tgaggtcatg
5161 gctcttgaac ccgtggctgg tgccgccttg gcagccccgg tcaccggtca aacaaatatt
5221 atagaccctt ggattagagc aaattttgtc caggccccca atggtgaatt tacagtctct
5281 ccccgaaacg cccctggtga agtgctactg aatctagagt tgggtccaga attaaatcct
5341 tatctggcac atttagcaag aatgtacaat gggtatgccg gtgggatgga ggtgcaggtc
5401 atgttggctg ggaacgcgtt cacagccggc aagttggtct tcgccgccgt gccaccccac
5461 ttcccggttg aaaaccttag cccacagcaa ataaccatgt tccctcatgt gatcatagat
5521 gtgagaaccc tggaacctgt tttgttacca 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 tgaaattata tcagtgcagt gtcaaaatgg taggtgcaca
5881 ctggacgggg agctccaagg gacaacacaa ctccaagtca gtggcatttg tgctttcaaa
5941 ggtgaagtga ccgcccactt gcatgacaat gatcacctat ataatgtcac catcacaaac
6001 ttgaatgggt ccccttttga tccctctgag gatatccctg cccctctggg tgtgcctgac
6061 ttccagggaa gggtttttgg tatcatctcc caaagagata aacacaatag tcctgggcat
6121 aatgaaccag caaacagggg acacgacgct gtggtcccta cttacacagc acagtacact
6181 ccaaaacttg gacaagttca aattggcaca tggcaaactg acgaccttac agtcaaccaa
6241 ccagttaaat tcaccccagt tggactcaat gacactgaac acttcaacca atgggtggtc
6301 cctaggtatg ctggtgccct aaacctcaat acaaaccttg ccccttctgt tgctccagta
6361 ttcccaggag agcgcctgct cttcttcaga tcatacattc ccctcaaggg cggttatgga
6421 aacccagcca ttgattgcct actaccacaa gagtgggtgc aacacttcta tcaagaagca
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 gcaatgggct tagttcatta atcaatgcag
6781 gtgctaatgc aataaatcag agggcagaat ttgattttaa tcagaaattg cagcaaaatt
6841 cttttaatca tgataaggag atgttgcagg ctcagattca ggcaactaag cagctgcagg
6901 cagacatgat ggctataaaa caaggggtct tgaccgctgg cggtttttcc 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 tcctcacatg
7201 gcacagcctc atcaaattca actcgcagca caagcctctc ccaatcaacg gtctccagag
7261 ctacatctag gactggtgag tgggttagag atcaaaatag aaatttggaa ccctacatgc
7321 atggtgcctt acagacagcc tttgtcaccc caccttccag cagggcatct gacgggacag
7381 tctcgaccgt ccctaaaggt gttttggact cctggacacc tgcgtttaac acccgcaggc
7441 agccgctttt tgcacacctc cgtaagaggg gggagtcaca agcttag
//