Typing tool
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Typing tool
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Complete norovirus genomes
| OP205539 | GII.4 Sydney | |
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| GII.P4 New Orleans |
ORF1: 1..5099
ORF2: 5080..6702
ORF3: 6702..7508
LOCUS OP205539 7508 bp RNA linear VRL 21-JUN-2023
DEFINITION Norovirus GII isolate RIVM-NOV-2016-0188_R02-14 nonstructural
polyprotein (ORF1) gene, partial cds; and VP1 (ORF2) and VP2 (ORF3)
genes, complete cds.
ACCESSION OP205539
VERSION OP205539.1
KEYWORDS .
SOURCE Norovirus GII
ORGANISM Norovirus GII
Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes;
Picornavirales; Caliciviridae; Norovirus; Norwalk virus.
REFERENCE 1 (bases 1 to 7508)
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JOURNAL Unpublished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 7508)
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..7508
/organism="Norovirus GII"
/mol_type="genomic RNA"
/isolate="RIVM-NOV-2016-0188_R02-14"
/isolation_source="Human feces"
/host="Homo sapiens"
/db_xref="taxon:122929"
/country="Netherlands"
/collection_date="2016-03-30"
/note="genotype: GII.4 Sydney[P4 New Orleans]"
gene <1..5099
/gene="ORF1"
CDS <1..5099
/gene="ORF1"
/codon_start=3
/product="nonstructural polyprotein"
/protein_id="UUV60918.1"
/translation="KMASNDASAAAVANSNDDTAKSSSDGVLSSMAVTFKRALGARPK
QPPPREKSQRPPRPPTPELVKNIPPPPPNGEDEIVVSYSVKDGVSGLPDLSTVRQPEE
SNTAFSVPPLNQRENRDAKEPLTGTILEMWDGEIYHYGLYVERGLVLGVHKPPAAISL
AKVELAPLSLYWRPVYTPQYLISPDTLKKLSGETFPYTAFDNNCYAFCCWVLDLNDSW
LSRRMIQRTTGFFRPYQDWNRKPLPTMDDSKIKKVANIFLCALSSLFTRPIKDIIGKI
RPLNILNILASCDWTFAGIVESLILLAELFGVFWTPPDVSAMIAPLLGDYELQGPEDL
AVELVPVVMGGIGLVLGFTKEKIGKMLSSAASTLRACKDLGAYGLEILKLVMKWFFPK
KEEANELAIVRSIEDAVLDLEAIENNHMTTLLKDKDSLAAYMRTLDLEEEKARKLSTK
SASPDIVGTINALLARIAAARSLVHRAKEELSSRPRPVVLMISGRPGIGKTHLAREVA
KRIAASLTGDQRVGLIPRNGVDHWDAYKGERVVLWDDYGMSNPIHDALRLQELADTCP
LTLNCDRIENKGKVFDSDVIIITTNLANPAPLDYVNFEACSRRIDFLVYAEAPDVEKA
KRDFPGQPDMWKNAFSSDFSHIRLALAPQGGFDKNGNTPHGKGVMKTLTTGSLIARAS
GLLHERLDEFELQGPALTTFNFDRNKVLAFRQLAAENKYGLMDTMRVGKQLKDVKTMP
GLKQALKNVSIKRCQIVYSGCTYMLESDGKGNVKVDRIQSTAVQTNNELAGALHHLRC
ARIRYYVKCVQEALYSIIQIAGAAFVTTRIAKRMNIQDLWSKPQVENTEETTSKDGCP
KPKDDEEFVISSDDIKTEGKKGKNKTGRGKKHTAFSSKGLSDEEYDEYKRIREERNGK
YSIEEYLQDRDKYYEEVAIARATEEDFCEEEEAKIRQRIFRPTRKQRKEERVSLGLVT
GSEIRKRNPDDFKPKGKLWADDDRSVDYNEKLSFEAPPSIWSRIVNFGSGWGFWVSPS
LFITSTHVIPQGAKEFFGVPIKQIQVHKSGEFCRLRFPKPIRTDVTGMILEEGAPEGT
VVTLLIKRSTGELMPLAARMGTHATMKIQGRTVGGQMGMLLTGSNAKSMDLGTTPGDC
GCPYIYKRGNDYVVIGVHTAAARGGNTVICATQGSEGEATLEGGDNKGTYCGAPILGP
GSAPTLSTKTKFWRSSTASLPPGTYEPAYLGGKDPRVKGGPSLQQVMREQLKPFTEPR
GKPPKPSVLEAAKKTIINVLEQTIDPPEKWSFAQACASLDKTTSSGHPHHMRKNDCWN
GESFTGKLADQASKANLMFEEGKNMTPVYTAALKDELVKTDKIYGKIKKRLLWGSDLA
TMIRCARAFGGLMDELKAHCVTLPIRVGMNMNEDGPIIFERHSRYTYHYDADYSRWDS
TQQRAVLAAALEIMVKFSPEPHLAQVVAEDLLSPSVVDVGDFTISINEGLPSGVPCTS
QWNSIAHWLLTLCALSEVTNLSPDTIQANSLFSFYGDDEIVSTDIKLDPEKLTAKLRE
YGLKPTRPDKTEGPLVISEDLNGLTFLRRTVTRDPAGWFGKLEQSSILRQMYWTRGPN
HGDPSETMIPHSQRPIQLMSLLGEAALHGPAFYSKISKLVIAELKEGGMDFYVPRQEP
MFRWMRFSDLSTWEGDRNLAPSFVNEDGVE"
mat_peptide <1..989
/gene="ORF1"
/product="p48"
mat_peptide 990..2087
/gene="ORF1"
/product="NTPase"
mat_peptide 2088..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..6702
/gene="ORF2"
CDS 5080..6702
/gene="ORF2"
/note="major capsid protein"
/codon_start=1
/product="VP1"
/protein_id="UUV60919.1"
/translation="MKMASSDANPSDGSAANLVPEVNNEVMALEPVVGAAIAAPVAGQ
QNVIDPWIRNNFVQAPGGEFTVSPRNAPGEILWSAPLGPDLNPYLSHLARMYNGYAGG
FEVQVILAGNAFTAGKVIFAAVPPNFPTEGLSPSQVTMFPHIVVDVRQLEPVLIPLPD
VRNNFYHYNQSNDPTIKLIAMLYTPLRANNAGDDVFTVSCRVLTRPSPDFDFIFLVPP
TVESRTKPFSVPVLTVEEMTNSRFPIPLEKLFTGPSSAFVVQPQNGRCTTDGVLLGTT
QLSPVNICTFRGDVTHITGSRNYTMNLASQNWNNYDPTEEIPAPLGAPDFVGKIQGML
TQTTRANGSTRGHKATVYTGSADFAPKLGRVQFETDTDHDFEANQNTKFTPVGVIQDG
STTHRNEPQQWVLPSYSGRNTHNVHLAPAVAPTFPGEQLLFFRSTMPGCSGYPNMDLD
CLLPQEWVQYFYQEAAPAQSDVALLRFVNPDTGRVLFECKLHKSGYVTVAHTGQHDLV
IPPNGYFRFDSWVNQFYTLAPMGNGAGRRRVV"
gene 6702..7508
/gene="ORF3"
CDS 6702..7508
/gene="ORF3"
/note="minor structural protein; small basic protein"
/codon_start=1
/product="VP2"
/protein_id="UUV60920.1"
/translation="MAGAFFAGLASDVLGSGLGSLINAGAGAINQKVEFENNRKLQQA
SFQFSSNLQQASFQHDKEMLQAQIEATKKLQQEMMKVKQAMLLEGGFSETDAARGAIN
APMTKTLDWSGTRYWAPDARTTTYNAGRFSTPQPSGALPGRANLRDAVPARGSSSKSF
NSSTATSVYSNQTTSTRLGSTAGSGTSVSSLPSTARTRSWVEDQSRNLSPFMRGAHNI
SFVTPPSSRSSSQGTVSTVPKEVLDSWTGAFNTRRQPLFAHIRKRGESRA"
ORIGIN
1 tgaagatggc gtctaacgac gcttccgctg ccgctgttgc taacagcaac gacgacaccg
61 caaaatcttc aagtgacgga gtgctttcta gcatggctgt cacttttaaa cgagccctcg
121 gggcgcggcc taaacagcct cccccgaggg aaaaatcaca aagaccccca cgaccaccca
181 caccagaact ggttaaaaat attccccccc ccccacccaa cggagaggat gaaatagtgg
241 tttcttatag tgtcaaagat ggtgtttccg gcttgcctga cctttccacc gtcaggcagc
301 cggaagaatc caacacggcc ttcagtgtcc ctccactcaa tcagagggag aatagagatg
361 ctaaagaacc actcactgga acaattctgg aaatgtggga cggggaaatc taccattatg
421 gcctgtatgt ggagcgaggt cttgtactag gcgtgcacaa accgccagct gccatcagcc
481 tcgccaaggt tgagttagca ccactctcct tgtactggag acctgtgtac actcctcagt
541 acctcatctc tccagacact ctcaagaaat tgtccggaga aacgttcccc tacacagcct
601 ttgacaacaa ctgctatgcc ttttgttgct gggtcctgga cctaaatgac tcgtggctga
661 gcaggagaat gatccagaga acaactggtt tcttcaggcc ctaccaagat tggaatagga
721 aaccccttcc cactatggat gactccaaaa taaagaaggt ggctaacata tttctgtgtg
781 ctctgtcctc gctattcacc aggcccataa aagatataat agggaagata aggcctctta
841 acatcctcaa catcttagcc tcatgtgatt ggacctttgc gggcatagtg gagtccctga
901 tactcttggc agaactcttt ggagttttct ggacaccccc agatgtgtct gcgatgattg
961 cccccttact tggtgactac gagctacaag gacctgagga ccttgcagtg gagctcgtcc
1021 ccgtggtgat ggggggaatt ggtttggtgc taggattcac caaagagaag attgggaaaa
1081 tgttgtcatc agctgcgtcc accttaagag cttgcaaaga ccttggtgca tatgggctag
1141 agatcctaaa gttagtcatg aagtggttct tcccgaagaa ggaggaggca aatgagctgg
1201 ctatagtgag gtccatcgag gatgcagtcc tggatctcga agcaattgaa aacaatcata
1261 tgaccacctt gcttaaagac aaagacagtc tggcagccta catgagaaca cttgaccttg
1321 aagaggagaa agccaggaaa ctctcaacta aatctgcctc acccgacatc gtgggcacaa
1381 tcaacgccct cctggcgaga atcgctgccg cacgttctct agtgcatcga gcgaaggagg
1441 agctttccag cagaccaaga cctgtggtgt tgatgatatc aggcaggcca ggaataggga
1501 agacccacct cgctagggaa gtggctaaga gaatcgcagc ctcccttaca ggagaccaac
1561 gtgttggtct catcccacgc aatggcgttg accattggga tgcgtacaag ggggagaggg
1621 tcgtcctatg ggacgattat ggaatgagca accctattca cgatgccctc aggctgcaag
1681 aactcgctga cacttgcccc ctcactctga actgtgacag gattgaaaat aaaggaaagg
1741 tctttgacag cgatgtcatc attatcacca ccaatctggc caacccagcc ccactggact
1801 atgtcaactt tgaagcatgc tcgaggcgca ttgacttcct cgtgtatgca gaagcccctg
1861 atgtcgaaaa ggcgaagcgt gacttcccag gccagcctga catgtggaag aacgctttca
1921 gttctgattt ctcacacata agactagcac tggccccaca gggtggtttc gacaagaacg
1981 ggaacacccc acacggaaag ggcgtcatga agactctcac cactggctcc cttattgccc
2041 gggcatcagg gctactccat gagaggttag atgaatttga actgcaaggc ccagctctca
2101 ccaccttcaa tttcgatcgc aataaagtgc ttgcctttag acagcttgct gctgaaaata
2161 aatatggatt gatggataca atgagggttg ggaaacagct caaggatgtc aaaaccatgc
2221 caggactcaa acaagcactc aagaatgtct caatcaagag gtgtcaaata gtgtatagtg
2281 gttgcaccta catgctcgag tctgatggca agggcaatgt gaaagttgac aggatccaaa
2341 gcaccgccgt gcagaccaac aatgagctgg ctggtgccct gcaccacttg aggtgcgcca
2401 gaatcagata ctatgtcaag tgtgtccagg aagccctgta ctccatcatt caaattgctg
2461 gggctgcatt tgtcaccacg cgcattgcca agcgcatgaa catacaagac ctatggtcca
2521 agccacaagt ggaaaacaca gaggagacta ccagcaagga cgggtgccca aaacctaagg
2581 atgatgagga gtttgtcatt tcatccgacg acatcaaaac tgagggcaag aaagggaaga
2641 acaagactgg ccgtggcaag aagcacacag cattttcaag caaaggcctc agtgatgaag
2701 agtacgatga atacaagagg atcagagaag aaaggaatgg caagtactct atagaagagt
2761 accttcagga cagggacaaa tactatgaag aggtggccat tgccagagcg actgaggaag
2821 acttctgtga agaggaggaa gccaagatcc gacaaaggat ctttaggcca acaaggaaac
2881 aacgcaagga ggaaagagtc tctctcggtt tggtcacagg ttctgaaatt aggaaaagaa
2941 acccagatga cttcaaaccc aaggggaaat tgtgggctga cgatgacagg agtgtggact
3001 acaatgagaa actcagtttt gaggccccgc caagcatttg gtcaagaata gtcaactttg
3061 gttcaggctg gggattctgg gtctccccca gcttgttcat aacatcaacc catgttatac
3121 cccagggcgc aaaggagttc tttggagttc ccatcaaaca gatacaggta cacaagtcag
3181 gcgagttctg tcgcttgaga ttccctaaac caattaggac tgatgtgacg ggcatgatct
3241 tagaagaagg cgcacctgag ggcaccgtgg ttacactact catcaaaagg tccactgggg
3301 aacttatgcc cctagcagct aggatgggga cccatgcgac catgaagatc caagggcgca
3361 ctgttggggg ccagatgggc atgcttctga caggatccaa cgccaagagt atggacctgg
3421 gtaccacacc aggtgattgt ggttgcccct acatctacaa gagaggtaat gactatgtgg
3481 tcattggagt ccacacggct gccgcacgtg gggggaacac tgtcatatgt gccacccagg
3541 ggagtgaagg agaggccaca cttgagggtg gtgacaacaa ggggacatac tgtggtgcac
3601 caatcctagg cccagggagt gccccaacac ttagcaccaa gaccaaattc tggaggtcgt
3661 ccacagcatc gctcccacct ggcacttatg aaccagccta tcttggtggc aaggacccta
3721 gagtcaaggg tggcccttca ttgcagcaag tcatgaggga acagttgaaa ccattcacag
3781 agcccagggg taagccacca aagccaagtg tgttagaagc tgccaagaaa accatcatta
3841 atgtccttga gcaaacaatt gatccacctg agaaatggtc gttcgcacaa gcttgcgcgt
3901 ctcttgacaa gaccacttcc agtggtcatc cgcaccacat gcggaaaaac gactgctgga
3961 acggggagtc cttcacaggc aagctggcag accaggcttc taaggccaac ctgatgtttg
4021 aagaagggaa gaacatgacc ccagtctaca cagctgcgct caaggatgag ttggttaaaa
4081 ctgacaaaat ttatggtaag atcaagaaga ggcttctttg gggctcggac ttggcgacca
4141 tgatccggtg tgctcgagca ttcggaggcc taatggatga actcaaagcg cactgtgtca
4201 cacttcccat tagagttggc atgaatatga atgaggatgg ccccatcatc ttcgagaggc
4261 attccaggta cacgtaccat tatgatgctg attactctcg atgggattca acacaacaga
4321 gagccgtgtt ggcagcagct ctagaaatca tggtaaaatt ctccccagaa ccacatttgg
4381 ctcaggtagt tgctgaagac cttctttctc ctagcgtggt ggacgtgggc gacttcacaa
4441 tatcaatcaa cgagggtctt ccctctgggg tgccttgcac ctcccaatgg aactccatcg
4501 cccactggct tctcactctc tgtgcgctct ccgaagtcac aaacctgtct cctgatacca
4561 tacaggctaa ttctctcttc tctttttatg gtgatgatga aattgttagc acagacataa
4621 aattggaccc agagaaattg acagcaaagc tcagagaata tgggttaaag ccaacccgcc
4681 ctgacaaaac tgaaggaccc cttgtcatct ctgaagacct gaatggccta actttcctgc
4741 ggaggactgt gacccgcgac ccagctggtt ggtttggaaa actggagcag agttcaatac
4801 tcaggcaaat gtactggact aggggtccca accatggaga cccatctgaa acaatgattc
4861 cacactccca aagacccata caattgatgt ccctactggg ggaggccgct ctccacggcc
4921 cagcatttta cagtaaaatc agcaaattgg tcattgcaga gctaaaagaa ggtggtatgg
4981 atttttacgt gcccagacaa gagccaatgt tcagatggat gagattctca gatctgagca
5041 cgtgggaggg cgatcgcaat ctggctccca gttttgtgaa tgaagatggc gtcgagtgac
5101 gccaacccat ctgatgggtc cgcagccaac ctcgtcccag aggtcaacaa tgaggttatg
5161 gctctggagc ccgttgttgg tgccgccatt gcggcacctg tagcgggcca acaaaatgta
5221 attgacccct ggattagaaa caattttgta caagcccctg gtggagagtt tacagtgtcc
5281 cccagaaacg ctccaggtga aatactatgg agcgcgccct taggccctga tttaaatccc
5341 tacctatccc atttggccag aatgtataat ggttatgcag gtggttttga agtgcaggta
5401 attctcgcgg ggaacgcgtt caccgccggg aaggtcatat ttgcagcagt cccaccaaat
5461 ttcccaactg aaggcttgag ccccagccag gtcactatgt tcccccacat agtagtagat
5521 gttaggcaac tagaacctgt gttgattccc ttacccgatg ttaggaataa tttctatcat
5581 tacaaccaat caaatgaccc caccattaag ttgatagcaa tgttgtacac accacttagg
5641 gctaataatg ctggggacga tgtcttcaca gtttcttgcc gagttctcac gagaccatcc
5701 cccgattttg atttcatatt tctagtgcca cccacagttg agtctagaac taaaccattc
5761 tctgtcccag ttttaactgt tgaggagatg accaattcaa gattccccat tcctctggaa
5821 aagttgttca cgggtcccag cagtgccttt gttgttcaac cacaaaacgg tagatgcacg
5881 actgatggcg tgctcctagg caccacccaa ttgtctcctg tcaacatctg caccttcaga
5941 ggggatgtca cccacattac aggtagtcgt aactacacaa tgaacttggc ttctcaaaat
6001 tggaacaatt atgacccaac agaagaaatc ccagcccctc taggagctcc agattttgtg
6061 gggaagattc aaggcatgct cacccaaacc acaagggcaa atggctcaac acgcggccac
6121 aaagctacgg tgtacactgg gagcgccgat tttgctccaa aactgggcag agttcaattt
6181 gaaactgaca cagaccatga ttttgaagct aaccaaaaca caaagttcac cccagtcggt
6241 gtcatccaag atggcagcac cacccaccga aatgaacccc aacagtgggt gctcccaagt
6301 tactcaggca gaaatactca taatgttcat ctggcccccg ctgtagcccc cacttttccg
6361 ggtgagcaac ttctcttctt taggtccact atgcccggat gtagcgggta ccccaacatg
6421 gatttggact gtctgctccc ccaggaatgg gtacagtact tctaccaaga ggcagcccca
6481 gcacaatctg atgtggctct gctaagattt gtgaatccag acacaggtag ggttttgttt
6541 gagtgtaaac ttcataaatc aggctatgtt acagtggctc acactggcca acatgatttg
6601 gttattcccc ccaatggtta ttttaggttt gattcctggg tcaaccagtt ctacacgctt
6661 gcccccatgg gaaatggagc ggggcgtaga cgtgtagtat aatggctgga gctttctttg
6721 ctggattagc atctgatgtc cttggctctg gacttggttc ccttatcaat gctggggctg
6781 gggccatcaa ccaaaaagtt gagtttgaaa ataacagaaa attgcaacaa gcatccttcc
6841 aatttagcag taatctacaa caggcttcct ttcaacatga caaagaaatg ctccaagcac
6901 aaattgaggc caccaaaaag ctacaacagg aaatgatgaa agttaagcag gcaatgctcc
6961 tagagggtgg gttctctgag acagatgcag cccgcggggc aatcaacgcc cccatgacaa
7021 aaactttgga ctggagcggg acaaggtact gggctcctga tgctaggact acaacataca
7081 atgcaggccg cttttccacc cctcaaccat cgggggcact gccaggaaga gctaatctta
7141 gggatgctgt ccctgctcgg ggttcctcta gtaaatcttt taactcttct actgctactt
7201 ctgtgtactc aaatcaaacc acttcaacga gacttggttc tacagctggt tctggcacca
7261 gtgtctcgag tctcccgtca actgcaagga ctaggagctg ggttgaggat caaagtagga
7321 atttgtctcc tttcatgagg ggggcccaca acatatcgtt tgtcacccca ccatctagca
7381 gatcctctag ccaaggcaca gtctcaaccg tgcctaaaga ggttttggac tcctggactg
7441 gcgctttcaa cacgcgcagg cagcctctct tcgctcacat tcgtaaacga ggggagtcac
7501 gggcgtaa
//