Typing tool
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Typing tool
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Complete norovirus genomes
| OP205527 | GII.4 Sydney | |
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| GII.P4 New Orleans |
ORF1: 1..5100
ORF2: 5081..6703
ORF3: 6703..7506
LOCUS OP205527 7506 bp RNA linear VRL 21-JUN-2023
DEFINITION Norovirus GII isolate RIVM-NOV-2016-0039_R01-01 nonstructural
polyprotein (ORF1), VP1 (ORF2), and VP2 (ORF3) genes, complete cds.
ACCESSION OP205527
VERSION OP205527.1
KEYWORDS .
SOURCE Norovirus GII
ORGANISM Norovirus GII
Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes;
Picornavirales; Caliciviridae; Norovirus; Norwalk virus.
REFERENCE 1 (bases 1 to 7506)
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JOURNAL Unpublished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 7506)
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..7506
/organism="Norovirus GII"
/mol_type="genomic RNA"
/isolate="RIVM-NOV-2016-0039_R01-01"
/isolation_source="Human feces"
/host="Homo sapiens"
/db_xref="taxon:122929"
/country="Netherlands"
/collection_date="2016-01-25"
/note="genotype: GII.4 Sydney[P4 New Orleans]"
gene 1..5100
/gene="ORF1"
CDS 1..5100
/gene="ORF1"
/codon_start=1
/product="nonstructural polyprotein"
/protein_id="UUV60882.1"
/translation="MKMASNDASAAAVANSNDDTAKSSSDGVLSSMAVTFKRALGARP
KQPPPREKSQRPPRPPTPELVKNIPPPPPNGEDEIVVSYSVKDGVSGLPDLSTVRQPE
ESNTAFSVPPLNQRENRDAKEPLTGTILEMWDGEIYHYGLYVERGLVLGVHKPPAAIS
LAKVELAPLSLYWRPVYTPQYLISPDTLKKLSGETFPYTAFDNNCYAFCCWVLDLNDS
WLSRRMIQRTTGFFRPYQDWNRKPLPTMDDSKIKKVANIFLCALSSLFTRPIKDIIGK
IRPLNILNILASCDWTFAGIVESLILLAELFGVFWTPPDVSAMIAPLLGDYELQGPED
LAVELVPVVMGGIGLVLGFTKEKIGKMLSSAASTLRACKDLGAYGLEILKLVMKWFFP
KKEEANELAIVRSIEDAVLDLEAIENNHMTTLLKDKDSLATYMRTLDLEEEKARKLST
KSASPDIVGTINALLARIAAARSLVHRAKEELSSRPRPVVLMISGRPGIGKTHLAREV
AKRIAASLTGDQRVGLIPRNGVDHWDAYKGERVVLWDDYGMSNPIHDALRLQELADTC
PLTLNCDRIENKGKVFDSDVIIITTNLANPAPLDYVNFEACSRRVDFLVYAEAPDVEK
AKRDFPGQPDMWKNAFSSDFSHIKLALAPQGGFDKNGNTPHGKGVMKTLTTGSLIARA
SGLLHERLDEFELQGPALTTFNFDRNKVLAFRQLAAENKYGLMDTMRVGKQLKDVKTM
PELKQALKNVSIKKCQIVYSGCTYMLESDGKGNVKVDRIQSAAVQTNNELAGALHHLR
CARIRYYVKCVQEALYSIIQIAGAAFVTTRIAKRMNIQDLWSKPQVENTEETTSKDGC
PKPKDDEEFVISSDDIKTEGKKGKNKTGRGKKHTAFSSKGLSDEEYDEYKRIREERNG
KYSIEEYLQDRDKYYEEVAIARATEEDFCEEEEAKIRQRIFRPTRKQRKEERVSLGLV
TGSEIRKRNPDDFKPKGKLWADDDRSVDYNEKLSFEAPPSIWSRIVNFGSGWGFWVSP
SLFITSTHVIPQGAKEFFGVPIKQIQVHKSGEFCRLRFPKPIRTDVTGMILEEGAPEG
TVVTLLIKRSTGELMPLAARMGTHATMKIQGRTVGGQMGMLLTGSNAKSMDLGTTPGD
CGCPYIYKRGNDYVVIGVHTAAARGGNTVICATQGSEGEATLEGGDNKGTYCGAPILG
PGSAPTLSTKTKFWRSSTASLPPGTYEPAYLGGKDPRVKGGPSLQQVMREQLKPFTEP
RGKPPKPSVLEAAKKTIINVLEQTIDPPEKWSFAQACASLDKTTSSGHPHHMRKNDCW
NGESFTGKLADQASKANLMFEEGKNMTPVYTAALKDELVKTDKIYGKIKKRLLWGSDL
ATMIRCARAFGGLMDELKAHCVTLPIRVGMNMNEDGPIIFERHSRYTYHYDADYSRWD
STQQRAVLAAALEIMVKFSPEPHLAQVVAEDLLSPSVVDVGDFTISINEGLPSGVPCT
SQWNSIAHWLLTLCALSEVTNLSPDTIQANSLFSFYGDDEIVSTDIKLDPEKLTAKLR
EYGLKPTRPDKTEGPLVISEDLNGLTFLRRTVTRDPAGWFGKLEQSSILRQMYWTRGP
NHGDPSETMIPHSQRPIQLMSLLGEAALHGPAFYSKISKLVIAELKEGGMDFYVPRQE
PMFRWMRFSDLSTWEGDRNLAPSFVNEDGVE"
mat_peptide 1..990
/gene="ORF1"
/product="p48"
mat_peptide 991..2088
/gene="ORF1"
/product="NTPase"
mat_peptide 2089..2625
/gene="ORF1"
/product="p22"
mat_peptide 2626..3024
/gene="ORF1"
/product="VPg"
mat_peptide 3025..3567
/gene="ORF1"
/product="Pro"
mat_peptide 3568..5097
/gene="ORF1"
/product="RdRp"
gene 5081..6703
/gene="ORF2"
CDS 5081..6703
/gene="ORF2"
/note="major capsid protein"
/codon_start=1
/product="VP1"
/protein_id="UUV60883.1"
/translation="MKMASSDANPSDGSAANLVPEVNNEVMALEPVVGAAIAAPVAGQ
QNVIDPWIRNNFVQAPGGEFTVSPRNAPGEILWSAPLGPDLNPYLSHLARMYNGYAGG
FEVQVILAGNAFTAGKVIFAAVPPNFPTEGLSPSQVTMFPHIVVDVRQLEPVLIPLPD
VRNNFYHYNQSNDPTIKLIAMLYTPLRANNAGDDVFTVSCRVLTRPSPDFDFIFLVPP
TVESRAKPFSVPVLTVEEMTNSRFPIPLEKLFTGPSSAFVVQPQNGRCTTDGVLLGTT
QLSPVNICTFRGDVTHITGSRNYTMNLASQNWNNYDPTEEIPAPLGAPDFVGKIQGML
TQTTRADGSTRGHKATVYTGSADFAPKLGRVQFETDTDHDFEANQNTKFTPVGVIQDG
STTHRNEPQQWVLPSYSGRNTHNVHLAPAVAPTFPGEQLLFFRSTMPGCSGYPNMDLD
CLLPQEWVQYFYQEAAPAQSDVALLRFVNPDTGRVLFECKLHKSGYVTVAHTGQHDLV
IPPNGYFRFDSWVNQFYTLAPMGNGAGRRRAV"
gene 6703..7506
/gene="ORF3"
CDS 6703..7506
/gene="ORF3"
/note="minor structural protein; small basic protein"
/codon_start=1
/product="VP2"
/protein_id="UUV60884.1"
/translation="MAGAFFAGLASDVLGSGLGSLINAGAGAINQKVEFENNRKLQQA
SFQFSSNLQQASFQHDKEMLQAQIEATKKLQQEMMKVKQAMLLEGGFSETDAARGAIN
APMTKALDWSGTRYWAPDARTTTYNAGRFSTPQPSGALPGRANLRDAVPARGSSSKSY
SSTATSVYSNQTTSTRLGSTAGSGTSVSSLPSTARTRSWVEDQSRNLSPFMRGAHNIS
FVTPPSSRSSSQGTVSTVPKEVLDSWTGAFNTRRQPLFAHIRKRGESRV"
ORIGIN
1 atgaagatgg cgtctaacga cgcttccgct gccgctgttg ctaacagcaa cgacgacacc
61 gcaaaatctt caagtgacgg agtgctttct agcatggctg tcacttttaa acgagccctc
121 ggggcgcggc ctaaacagcc tcccccgagg gaaaaatcac aaagaccccc acgaccaccc
181 acaccagaac tggttaaaaa tattcccccc cccccaccca acggagagga tgaaatagtg
241 gtttcttata gtgtcaaaga tggtgtttct ggcttgcctg acctttccac cgtcaggcag
301 ccggaagaat ccaacacggc cttcagtgtc cctccactca atcagaggga gaatagagat
361 gctaaggaac cactcactgg aacaattctg gaaatgtggg acggggaaat ctaccattat
421 ggcctgtatg tggagcgagg tcttgtgcta ggcgtgcaca aaccgccagc tgccatcagc
481 ctcgctaagg ttgagttagc accactctcc ttgtactgga gacctgtgta cactcctcag
541 tacctcatct ctccagacac tctcaagaaa ttgtccggag aaacgttccc ctacacagcc
601 tttgacaaca actgctatgc cttttgttgc tgggtcctgg acctaaatga ctcgtggctg
661 agcaggagaa tgatccagag aacaactggt ttcttcaggc cctaccaaga ctggaatagg
721 aaaccccttc ccactatgga tgactccaaa ataaagaagg tggctaacat atttctgtgt
781 gctttgtcct cgctattcac caggcccata aaagatataa tagggaagat aaggcctctt
841 aacatcctca acatcttagc ctcatgtgat tggacctttg cgggcatagt ggagtccctg
901 atactcttgg cagaactctt tggagttttc tggacacccc cagatgtgtc tgcgatgatt
961 gcccccttac ttggtgacta cgagctacaa ggacctgagg accttgcagt ggagctcgtc
1021 cccgtggtga tggggggaat tggtttggtg ctaggattca ccaaagagaa gattgggaaa
1081 atgttgtcat cagctgcgtc caccttaaga gcttgcaaag accttggtgc atatgggcta
1141 gagatcctaa agttagtcat gaagtggttc ttcccgaaga aggaggaggc aaatgagctg
1201 gctatagtga ggtccatcga ggatgcagtc ctggatctcg aagcaattga aaacaatcat
1261 atgaccacct tgcttaaaga caaagacagt ctggcaacct acatgagaac acttgacctt
1321 gaagaggaga aagccaggaa actctcaacc aaatctgcct cacccgacat cgtgggcaca
1381 atcaacgccc tcctggcgag aatcgctgcc gcacgttctc tagtgcatcg agcgaaggag
1441 gagctctcca gcagaccaag acctgtagtg ttgatgatat caggcaggcc aggaataggg
1501 aagacccacc tcgctaggga agtggctaag agaatcgcag cctcccttac aggagaccaa
1561 cgtgttggtc tcatcccacg caatggcgtc gaccattggg atgcgtacaa gggggagagg
1621 gtcgtcctat gggacgatta tggaatgagc aaccctattc acgatgccct caggctgcaa
1681 gaactcgctg acacttgccc cctcactctg aactgtgaca ggattgaaaa taaaggaaag
1741 gtctttgaca gcgatgtcat cattatcacc accaatctgg ccaacccagc cccactggac
1801 tatgtcaact ttgaagcatg ctcgaggcgc gttgacttcc tcgtgtatgc agaagcccct
1861 gatgtcgaaa aggcgaagcg tgacttccca ggccagcctg acatgtggaa gaacgctttc
1921 agttctgatt tctcacacat aaaactagca ctggccccac agggtggttt cgacaagaac
1981 gggaacaccc cacacggaaa gggcgtcatg aagactctca ccactggctc ccttattgcc
2041 cgggcatcag ggctactcca tgagaggtta gatgaatttg aactgcaggg cccagctctc
2101 accaccttca atttcgatcg caataaagtg cttgccttta gacagcttgc tgctgaaaat
2161 aaatatggat tgatggatac aatgagggtt gggaaacagc tcaaggatgt caaaaccatg
2221 ccagaactca aacaagcact caagaatgtc tcaatcaaga agtgtcaaat agtgtatagt
2281 ggttgcacct acatgcttga gtctgatggc aagggcaatg tgaaagttga caggatccaa
2341 agcgccgccg tgcagaccaa caatgagctg gctggtgccc tgcaccactt gaggtgcgcc
2401 agaatcagat actatgtcaa gtgtgtccag gaagccctgt actccatcat tcaaattgct
2461 ggggctgcat ttgtcaccac gcgcattgcc aagcgcatga acatacaaga cctatggtcc
2521 aagccacaag tggaaaacac agaggagact accagcaagg acgggtgccc aaaacctaag
2581 gatgatgagg agtttgtcat ttcatccgac gacatcaaaa ctgagggcaa gaaagggaag
2641 aacaagactg gccgtggcaa gaagcacaca gcattttcaa gcaaaggcct cagtgatgaa
2701 gagtacgatg aatacaagag gatcagagaa gaaaggaatg gcaagtactc tatagaagag
2761 taccttcagg acagggacaa atactatgaa gaggtggcca ttgccagagc gactgaggaa
2821 gacttctgtg aagaggagga agccaagatc cgacaaagga tctttaggcc aacaaggaaa
2881 caacgcaagg aggaaagagt ctctctcggt ttggtcacag gttctgaaat taggaaaaga
2941 aacccagatg acttcaaacc caaggggaaa ttgtgggctg acgatgacag gagtgtggac
3001 tacaatgaga aactcagttt tgaggccccg ccaagcattt ggtcaagaat agtcaacttt
3061 ggttcaggct ggggattctg ggtctccccc agcttgttca taacatcaac ccatgttata
3121 ccccagggcg caaaggagtt ctttggagtc cccatcaaac aaatacaggt acacaagtca
3181 ggcgagttct gtcgcttgag attccctaaa ccaattagga ctgatgtgac gggcatgatc
3241 ttagaagaag gcgcacctga gggcaccgtg gttacactac tcatcaaaag gtccactggg
3301 gaacttatgc ccctagcagc taggatgggg acccatgcga ccatgaagat ccaagggcgc
3361 actgttgggg gccagatggg catgcttctg acaggatcca acgccaagag tatggacctg
3421 ggtaccacac caggtgattg tggttgcccc tacatctaca agagaggtaa tgactatgtg
3481 gtcattggag tccacacggc tgccgcacgt ggggggaaca ctgtcatatg tgccacccag
3541 gggagtgaag gagaggctac acttgagggt ggtgacaaca aggggacata ctgtggtgca
3601 ccaatcctag gcccagggag tgccccaaca cttagcacca agaccaaatt ctggaggtcg
3661 tccacagcat cgctcccacc tggcacctat gaaccagcct atcttggtgg caaggaccct
3721 agagtcaagg gtggcccttc actgcagcaa gtcatgaggg aacagttgaa accattcaca
3781 gagcccaggg gtaagccacc aaagccaagt gtgttagaag ctgccaagaa aaccatcatt
3841 aatgtccttg agcaaacaat tgatccacct gagaaatggt cgttcgcaca agcttgcgcg
3901 tctcttgaca agaccacttc cagtggtcat ccgcaccaca tgcggaaaaa cgactgctgg
3961 aacggggagt ccttcacagg caagctggca gaccaggctt ctaaggccaa cctgatgttt
4021 gaagaaggga agaacatgac cccagtctac acagctgcgc tcaaggatga gttagttaaa
4081 actgacaaaa tttatggtaa gatcaagaag aggcttcttt ggggctcgga cttggcgacc
4141 atgatccggt gtgctcgagc attcggaggc ctaatggatg aactcaaagc gcactgtgtc
4201 acacttccca tcagagttgg catgaatatg aatgaggatg gccccatcat cttcgagagg
4261 cattccaggt acacgtacca ctatgatgct gattactctc gatgggattc aacacaacag
4321 agggccgtgt tggcagcagc tctagaaatc atggtaaaat tctccccaga accacatttg
4381 gctcaggtag ttgctgaaga ccttctttct cctagcgtgg tggacgtggg cgacttcaca
4441 atatcaatca acgagggtct tccctctggg gtgccttgca cctcccaatg gaactccatc
4501 gcccactggc ttctcactct ctgtgcgctc tccgaagtca caaacctgtc tcctgatacc
4561 atacaggcta attctctctt ctctttttat ggtgatgatg aaattgttag cacagacata
4621 aaattggacc cagagaagtt gacagcaaag ctcagagaat atgggttaaa gccaacccgc
4681 cctgacaaaa ctgaaggacc ccttgtcatc tctgaagacc tgaatggcct aactttcctg
4741 cggaggactg tgacccgcga cccagctggt tggtttggaa aactggagca gagttcaata
4801 ctcaggcaaa tgtactggac taggggtccc aaccatggag acccatctga aacaatgatt
4861 ccacactccc aaagacccat acaattgatg tccctactgg gggaggccgc tctccacggc
4921 ccagcgtttt acagtaaaat cagcaaattg gtcattgcag agctaaaaga aggtggtatg
4981 gatttttacg tgcccagaca agagccaatg ttcagatgga tgagattctc agacctgagc
5041 acgtgggagg gcgatcgcaa tctggctccc agttttgtga atgaagatgg cgtcgagtga
5101 cgccaaccca tctgatgggt ccgcagccaa cctcgtccca gaggtcaaca atgaggttat
5161 ggctctggag cccgttgttg gtgccgccat tgcggcacct gtagcgggcc aacaaaatgt
5221 aattgacccc tggattagaa acaatttcgt acaagcccct ggtggagagt ttacagtgtc
5281 ccccagaaac gctccaggtg aaatactatg gagcgcgccc ttaggccctg atttaaatcc
5341 ctacctatcc catttggcca gaatgtataa tggttatgca ggtggttttg aagtgcaggt
5401 aattctcgcg gggaacgcgt tcaccgccgg gaaggtcata tttgcagcag tcccaccaaa
5461 tttcccaact gaaggcctta gccccagcca ggtcactatg ttcccccata tagtagtaga
5521 tgttaggcaa ctagaacctg tgttgattcc cttacccgat gttaggaata atttctatca
5581 ttacaaccaa tcaaatgacc ccaccattaa gttgatagca atgttgtaca caccacttag
5641 ggctaataat gctggggacg atgtcttcac agtttcttgc cgagttctca cgagaccatc
5701 ccccgatttt gatttcatat ttctagtgcc acccacagtt gagtctagag ctaaaccatt
5761 ctctgtccca gttttaactg ttgaggagat gaccaattca agattcccca ttcctctgga
5821 aaagttgttc acgggtccca gcagtgcctt tgttgttcaa ccacaaaacg gtagatgcac
5881 gactgatggc gtgctcctag gcactaccca attgtctcct gtcaacatct gcaccttcag
5941 aggggatgtc acccacatta caggtagtcg taactacaca atgaatttgg cttctcaaaa
6001 ttggaacaat tatgacccaa cagaagaaat cccagcccct ctaggagctc cagattttgt
6061 ggggaagatt caaggcatgc tcacccaaac cacacgggca gatggctcaa cacgcggcca
6121 caaagctacg gtgtacactg ggagcgccga ctttgctcca aaactgggca gagttcaatt
6181 tgaaactgac acagaccatg attttgaagc taaccaaaac acaaagttca ccccagtcgg
6241 tgtcatccaa gatggcagca ccacccaccg aaatgaaccc caacagtggg tgctcccaag
6301 ttactcaggc agaaatactc ataatgttca tctggccccc gctgtagccc ctacttttcc
6361 gggtgagcaa cttctcttct ttaggtccac tatgcccgga tgtagcgggt accccaacat
6421 ggatttggac tgcctgctcc cccaggaatg ggtgcagtac ttctaccaag aggcagcccc
6481 agcacaatct gatgtggctc tgctaagatt tgtgaatcca gacacaggta gggttttgtt
6541 tgagtgtaaa cttcataaat caggctatgt tacagtggct cacactggcc aacatgattt
6601 ggttatcccc cccaatggtt attttaggtt tgattcctgg gtcaaccagt tctacacgct
6661 tgcccccatg ggaaatggag cggggcgtag acgtgcagta taatggctgg agctttcttt
6721 gctggattag catctgatgt ccttggctct ggacttggtt cccttatcaa tgctggggct
6781 ggggccatca accaaaaagt tgagtttgaa aataacagaa aattgcaaca agcatccttc
6841 caatttagca gtaatctaca acaggcttcc tttcaacatg acaaagaaat gctccaagca
6901 caaattgagg ccaccaaaaa gctacaacag gaaatgatga aagttaagca ggcaatgctc
6961 ctagagggtg ggttctctga gacagatgcg gcccgcgggg caatcaacgc ccccatgaca
7021 aaagctttgg actggagcgg gacaaggtac tgggctcctg atgctaggac tacaacatac
7081 aatgcaggcc gcttttccac ccctcaacca tcgggggcac tgccaggaag agctaatctt
7141 agggatgctg tccctgctcg gggttcctct agtaaatctt actcttctac tgctacttct
7201 gtgtactcaa atcaaaccac ttcaacgaga cttggttcta cagcaggttc tggtaccagt
7261 gtctcgagtc tcccgtcaac tgcaaggact aggagctggg ttgaggatca aagtaggaat
7321 ttgtctcctt tcatgagggg ggcccacaac atatcgtttg tcaccccacc atctagcaga
7381 tcctctagcc aaggcacagt ctcaaccgtg cctaaagagg ttttggactc ctggactggc
7441 gctttcaaca cgcgcaggca gcctctcttc gctcacattc gtaaacgagg ggagtcacgg
7501 gtgtaa
//