Typing tool
|
|
|
|
|
|
Typing tool
|
Complete norovirus genomes
| MW305543 | GII.4 Den Haag | |
|
|---|---|---|---|
| GII.P4 Den Haag |
ORF1: 1..5069
ORF2: 5050..6672
ORF3: 6672..7478
LOCUS MW305543 7510 bp RNA linear VRL 06-JUL-2021
DEFINITION Norovirus GII isolate PNV004566 nonstructural polyprotein (ORF1)
gene, partial cds; and VP1 (ORF2) and VP2 (ORF3) genes, complete
cds.
ACCESSION MW305543
VERSION MW305543.1
KEYWORDS .
SOURCE Norovirus GII
ORGANISM Norovirus GII
Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes;
Picornavirales; Caliciviridae; Norovirus; Norwalk virus.
REFERENCE 1 (bases 1 to 7510)
AUTHORS Tohma,K., Lepore,C.J., Martinez,M., Degiuseppe,J.I., Khamrin,P.,
Saito,M., Mayta,H., Nwaba,A., Ford-Siltz,L.A., Galeano,M.E.,
Zimic,M., Stupka,J.A., Gilman,R.H., Maneekarn,N., Ushijima,H.,
Green,K.Y. and Parra,G.I.
TITLE Genome-wide analyses of human noroviruses reveal coexistence of
viral populations evolving under recombination constraints
JOURNAL Unpublished
REFERENCE 2 (bases 1 to 7510)
AUTHORS Tohma,K., Lepore,C.J., Martinez,M., Degiuseppe,J.I., Khamrin,P.,
Saito,M., Mayta,H., Nwaba,A., Ford-Siltz,L.A., Galeano,M.E.,
Zimic,M., Stupka,J.A., Gilman,R.H., Maneekarn,N., Ushijima,H.,
Green,K.Y. and Parra,G.I.
TITLE Direct Submission
JOURNAL Submitted (23-NOV-2020) CBER/OVRR/DVP/LHV, U.S. Food and Drug
Administration, 10903 New Hampshire Avenue, Silver Spring, MD
20993, USA
COMMENT ##Assembly-Data-START##
Assembly Method :: High-performance Integrated Virtual
Environment (HIVE) v. 2
Sequencing Technology :: Illumina
##Assembly-Data-END##
FEATURES Location/Qualifiers
source 1..7510
/organism="Norovirus GII"
/mol_type="genomic RNA"
/isolate="PNV004566"
/isolation_source="feces"
/host="Homo sapiens"
/db_xref="taxon:122929"
/country="Peru"
/collection_date="08-Mar-2008"
/note="genotype: GII.4[GII.P4]"
gene <1..5069
/gene="ORF1"
CDS <1..5069
/gene="ORF1"
/codon_start=3
/product="nonstructural polyprotein"
/protein_id="QPJ58965.1"
/translation="AVVNNNNDTAKPSSDKMFSNMAVTLKRALGARPKQPPPREIPQR
PPRPPTPELVKKIPPPPPNGEDEVVVSYSAKDGVSGLPELSTVRQPEETNTAFSVPPL
NQRENRDAKEPLTGTILEMWDGEIYHYGLYVERGLVLGVHKPPAAISLAKVELTPLSL
FWRPVYTPQYLISPDTLKKLHGETFPYTAFDNNCYAFCCWVLDLNDSWLSRRMIQRTT
GFFRPYQDWNRKPLPTMDDSKLKKVANIFLCTLSSLFTRPIKDIIGKLRPLNIINILA
SCDWTFAGIVESLILLAELFGVFWTPPDVSAMIAPLLGDFELQGPEDLVVELVPVVMG
GIGLVLGFTKEKIGKMLSSAASTLRACKDLGAYGLEILKLVMKWFFPKKEEANELAMV
RSIEDAVLDLEAIENNHMTTLLKDKDSLATYMRTLDLEEEKARKLSTKSASPDIVGTI
NALLARIAAARSLVHRAKEELSSRLRPVVLMISGRPGIGKTHLAREVAKRIAASLTGD
QRVGLIPRNGVDHWDAYKGERVVLWDDYGMSNPIHDALRLQELADTCPLTLNCDRIEN
KGKVFDSDVIIITTNLANPAPLDYVNFEACSRRIDFLVYAEAPEVEKAKRDFPGQPDM
WKNAFRPDFSHIKLALAPQGGFDKNGNTPHGKGVMKTLTTGSLIARASGLLHERLDEF
ELQGPALTTFNFDRNKVLAFRQLAAENKYGLMDTMKVGRQLKDVKTMPELKQALKNIS
IKKCQIVYSGCTYTLESDGKGNVKVDRVQSTSVQTNNELAGALHHLRCARIRYYVKCV
QEALYSIIQIAGAAFVTTRIIKRVNIQDLWSKPQVENTEEATNKDGCPKPKDDEEFVI
SSDDIKTEGKKGKNKTGRGKKHTAFSSKGLSDEEYDEYKRIREERNGKYSIEEYLQDR
DKYYEEVAIARATEEDFCEEEEAKIRQRIFRPTRKQRKEERASLGLVTGSEIRKRNPE
DFKPKGKLWADDDRSVDYNEKLSFEAPPSIWSRIVNFGSGWGFWVSPSLFITSTHVIP
QGAKEFFGVPIKQIQIHKSGEFCRLRFPKPIRTDVTGMILEEGAPEGTVVTLLIKRST
GELMPLAARMGTHATMKIQGRTVGGQMGMLLTGSNAKSMDLGTTPGDCGCPYIYKRGN
DYVVIGVHTAAARGGNTVICATQGGEGEATLEGGDSKGTYCGAPILGPGSAPKLSTKT
KFWRSSTAPLPPGTYEPAYLGGKDPRVKGGPSLQQVMRDQLKPFTEPRGKPPKPSVLE
AAKKTIINVLEQTIDPPEKWSFSQACASLDKTTSSGHPHHMRKNDCWNGESFTGKLAD
QASKANLMFEEGKNMTPVYTGALKDELVKTDKIYGKIKKRLLWGSDLATMIRCARAFG
GLMDELKAHCVTLPIRVGMNMNEDGPIIFEKHSRYRYHYDADYSRWDSTQQRAVLAAA
LEIMVKFSSEPHLAQVVAEDLLSPSVVDVGDFTISINEGLPSGVPCTSQWNSIAHWLL
TLCALSEITNLSPDIIQANSLFSFYGDDEIVSTDIKLDPEKLTAKLKEYGLKPTRPDK
TEGPLVISEDLDGLTFLRRTVTRDPAGWFGKLEQSSILRQMYWTRGPNHEDPSESMIP
HSQRPIQLMSLLGEAALHGPTFYSKISKLVIAELKEGGMDFYVPRQEPMFRWMRFSDL
STWEGDRNLAPSFVNEDGVE"
mat_peptide <1..959
/gene="ORF1"
/product="p48"
mat_peptide 960..2057
/gene="ORF1"
/product="NTPase"
mat_peptide 2058..2594
/gene="ORF1"
/product="p22"
mat_peptide 2595..2993
/gene="ORF1"
/product="VPg"
mat_peptide 2994..3536
/gene="ORF1"
/product="Pro"
mat_peptide 3537..5066
/gene="ORF1"
/product="RdRp"
gene 5050..6672
/gene="ORF2"
CDS 5050..6672
/gene="ORF2"
/note="major capsid protein"
/codon_start=1
/product="VP1"
/protein_id="QPJ58966.1"
/translation="MKMASNDANPSDGSAANLVPEVNNEVMALEPVVGAAIAAPVAGQ
QNVIDPWIRNNFVQAPGGEFTVSPRNAPGEILWSAPLGPDLNPYLSHLARMYNGYAGG
FEVQVILAGNAFTAGKIIFAAVPPNFPTEGLSPSQVTMFPHIIVDVRQLEPVLIPLPD
VRNNFYHYNQSNDSTIKLIAMLYTPLRANNAGDDVFTVSCRVLTRPSPDFDFIFLVPP
TVESRTKPFTVPILTVEEMTNSRFPIPLEKLFTGPSGAFVVQPQNGRCTTDGVLLGTT
QLSPVNICTFRGDVTHIAGSRNYTMNLASLNWNNYDPTEEIPAPLGTPDFVGKIQGVL
TQTTKGNGSTRGHKATVYTGSAPFTPKLGSVQFETDTENDFETHQNTKFTPVGVIQDG
STTHRNEPQQWVLPSYSGRDVHNVHLAPAVAPTFPGEQLLFFRSTMPGCSGYPNMDLD
CLLPQEWVQYFYQEAAPAQSDVALLRFVNPDTGRVLFECKLHKSGYVTVAHTGQHDLV
IPPNGYFRFDSWVNQFYTLAPMGNGTGRRRAL"
gene 6672..7478
/gene="ORF3"
CDS 6672..7478
/gene="ORF3"
/note="minor structural protein; small basic protein"
/codon_start=1
/product="VP2"
/protein_id="QPJ58967.1"
/translation="MAGAFFAGLASDVLGTGLGSLINAGAGAINQKIDFENNRKLQQA
SFQFSSNLQQASFQHDKEMLLAQIEATKKLQQEMMKVKQAMLLEGGFSETDAARGAIN
APMTKALDWSGTRYWAPDARTTTYNAGRFSTPQPSGTLPGRINPRTSTPARGSSSTSS
NASIATSIYSNQTVSTRLGSTAGSGTNVSSLPSTARTRSWVEDQNRNLSPFMRGAHNI
SFVTPPSSRSSSQGTVSTVPKGVLDSWTGAFNTRRQPLFAHIRRRGESRV"
ORIGIN
1 ccgctgttgt taacaacaac aacgacaccg caaaaccttc aagtgacaaa atgttttcta
61 acatggctgt cactcttaaa cgagccctcg gggcgcggcc taaacagccc cccccgaggg
121 aaataccaca aagaccccca cgaccaccca ctccagaact ggtcaaaaag atccctcctc
181 ccccgcccaa cggagaggat gaagtagtgg tttcttatag cgccaaagat ggcgtttccg
241 gtttgcctga gctttccacc gtcaggcaac cggaagaaac caacacggcc ttcagtgtcc
301 ccccactcaa ccagagagag aatagagatg ctaaggaacc actgacagga acaattctgg
361 aaatgtggga tggagaaatc taccattatg gcctgtatgt tgagcgaggt cttgtgctgg
421 gtgtgcacaa accaccagct gccattagcc tcgccaaggt cgaactaaca ccactctcct
481 tgttctggag acctgtgtac actcctcagt acctcatctc tccagacact ctcaagaaat
541 tacacggaga aacatttccc tacacagcct ttgacaacaa ttgctatgcc ttttgttgct
601 gggtcctgga tctaaacgac tcgtggctga gtaggagaat gatccagaga acaactggct
661 tcttcagacc ctaccaagac tggaatagga aacccctccc cactatggat gattccaaat
721 taaagaaggt agctaacata ttcctgtgca ctctgtcttc gctattcacc agacccataa
781 aagacataat aggaaagtta aggcctctca acatcatcaa catcctggct tcatgtgatt
841 ggactttcgc aggcatagtg gagtccttga tactcttggc agagctcttt ggagtcttct
901 ggacaccccc agatgtgtct gcgatgattg cccccttact cggtgatttc gagctacaag
961 gacctgagga ccttgtagtg gagctcgtcc ctgtagtaat ggggggaatt ggtttggtgc
1021 taggattcac caaagagaag attggaaaaa tgttgtcatc tgctgcatcc accttgaggg
1081 cttgtaaaga tcttggtgca tatgggctag agatcctaaa gttagtcatg aagtggttct
1141 tcccgaagaa agaggaagca aacgaactgg ctatggtgag atccatcgag gatgcagtac
1201 tggaccttga ggcaattgaa aacaaccaca tgaccacctt gctcaaagac aaagacagcc
1261 tggcaaccta catgagaacc cttgacctcg aggaagagaa ggccagaaaa ctctcaacca
1321 agtctgcttc acctgacatc gtgggtacaa tcaacgccct tctggcgaga atcgccgctg
1381 cacgctccct ggtgcaccga gcaaaggagg agctttccag cagactaaga cctgtagtct
1441 tgatgatatc aggcagacca gggataggga agacccacct tgctagggaa gtggctaaga
1501 gaatcgcagc ctccctcaca ggagaccagc gtgtaggcct catcccacgc aatggcgtcg
1561 atcactggga tgcgtacaag ggggagaggg tcgtcctatg ggacgactat ggaatgagca
1621 atcccatcca cgacgccctc aggctgcaag aactcgctga cacttgcccc ctcactctaa
1681 attgtgacag gattgagaat aaaggaaagg tctttgacag cgatgtcatc attatcacta
1741 ctaatctggc caacccagca ccactggact atgtcaactt tgaagcgtgc tcgaggcgca
1801 tcgattttct cgtgtatgca gaagcccctg aggtcgaaaa ggcgaagcgt gacttcccgg
1861 gccaacctga catgtggaaa aacgctttta ggcctgattt ctcacacata aaattggcac
1921 tggctccaca aggtggcttt gataagaacg ggaacacccc acacgggaag ggcgtcatga
1981 agactctcac cactggctcc ctcattgccc gggcatcagg gctgctccat gagagattgg
2041 atgagtttga actacagggc ccagctctta ccaccttcaa ctttgaccgc aacaaagtgc
2101 ttgccttcag gcagcttgct gctgaaaaca aatatgggtt gatggacaca atgaaagttg
2161 ggaggcagct caaggatgtc aaaaccatgc cagaactcaa acaagcactc aagaatatct
2221 caatcaagaa gtgtcagatt gtgtatagtg gttgcaccta cacacttgag tctgatggta
2281 agggcaatgt gaaagttgac agagttcaga gcacctccgt acagaccaac aatgagctgg
2341 ctggcgccct gcatcatcta aggtgcgcca gaatcaggta ctatgtcaag tgtgtccagg
2401 aggccctgta ttctatcatc cagattgctg gggctgcatt tgtcaccacg cgcatcatca
2461 agcgtgtgaa cattcaagac ctatggtcca agccacaagt ggaaaacaca gaggaggcta
2521 ccaacaagga cgggtgccca aaacccaaag atgatgagga gttcgtcatt tcatctgacg
2581 acattaaaac tgagggtaag aaagggaaga acaagactgg ccgtggcaag aagcacacag
2641 ccttctcaag taaaggtctc agtgatgaag agtatgatga gtacaagaga attagagagg
2701 aaaggaatgg caagtactcc atagaagagt acctacagga cagggacaaa tactatgagg
2761 aggtggccat tgccagggcg accgaggaag acttctgtga agaggaggag gccaagatcc
2821 ggcaaaggat cttcagacca acaaggaaac aacgcaagga agaaagagct tctctcggtt
2881 tagttacagg ttctgaaatt aggaaaagaa acccagaaga cttcaagccc aaggggaagc
2941 tatgggctga cgatgacaga agcgtggact acaatgagaa acttagtttt gaggccccac
3001 caagcatctg gtcaaggata gtcaactttg gctcaggttg gggcttctgg gtctccccta
3061 gcctgttcat aacatcaacc cacgtcatac cccagggcgc aaaggagttc ttcggagtcc
3121 ccatcaaaca aattcagata cacaaatcag gcgaattctg tcgcttgagg ttcccaaaac
3181 caatcagaac tgatgtgact ggcatgatct tggaagaagg tgcgcccgaa ggcaccgtgg
3241 tcacactact catcaaaagg tctactggag aactcatgcc cctagcagct agaatgggga
3301 cccatgcaac catgaaaatt caagggcgca ctgttggagg tcagatgggc atgcttctga
3361 caggatccaa cgccaaaagc atggatctag gcaccacacc aggtgactgc ggctgtccct
3421 acatctacaa gagaggaaat gactatgtgg tcattggagt ccacacagct gccgctcgtg
3481 ggggaaacac tgtcatatgc gccacccagg ggggtgaggg ggaagctaca cttgaaggtg
3541 gtgacagtaa gggaacatac tgtggtgcac caatcctagg cccagggagt gccccaaaac
3601 ttagcaccaa aaccaaattc tggagatcat ccacagcacc actcccacct ggcacctacg
3661 aaccagccta ccttggtggc aaggacccca gagtcaaggg cggcccctcg ttgcagcaag
3721 tcatgaggga ccagctgaaa ccatttacag agcccagggg taagccacca aagccaagtg
3781 tgttagaagc tgccaagaaa accatcatca atgtccttga acaaacaatt gacccacctg
3841 agaagtggtc gttctcgcaa gcttgcgcgt cccttgacaa gaccacttct agcggccatc
3901 cgcaccacat gcggaaaaac gactgctgga acggggaatc cttcacaggc aagctggcag
3961 accaggcttc caaggccaac ctgatgtttg aagaagggaa gaacatgacc ccagtttaca
4021 caggtgcact taaggatgaa ttagtcaaaa ctgacaaaat ttatggtaag atcaagaaga
4081 ggcttctctg gggctcggat ttagcaacca tgatccggtg tgctcgagca ttcggaggcc
4141 taatggatga actcaaagca cactgtgtca cacttcccat cagagttggt atgaatatga
4201 atgaggatgg ccccatcatc ttcgagaagc attccaggta cagataccac tatgatgctg
4261 attactctcg gtgggattca acacaacaga gagccgtgct ggcagcagct ctagaaatca
4321 tggttaaatt ctcctcagaa ccacatttgg ctcaggtagt cgcagaagac cttctttctc
4381 ctagcgtggt ggatgtgggt gactttacaa tatcaatcaa cgagggtctt ccctctgggg
4441 tgccctgcac ctcccaatgg aactccatcg cccactggct tctcactctc tgtgcactat
4501 ccgaaatcac aaatttgtcc ccagatatca tacaggctaa ctctctcttc tccttctatg
4561 gtgatgatga aattgttagc acagacataa aattagaccc agaaaagttg acagcaaagc
4621 ttaaggaata tgggttgaaa ccaacccgcc ctgataaaac tgaaggacct cttgttattt
4681 ctgaagactt agatggtttg actttcctgc ggagaactgt gacccgcgac ccagctggtt
4741 ggtttggaaa actggagcag agttcaatac tcaggcaaat gtactggact aggggcccca
4801 accatgaaga tccatctgaa tcaatgattc cacactctca aagacccata caattgatgt
4861 ccctactggg agaggccgca cttcacggcc caacattcta cagtaaaatc agcaaattag
4921 tcattgcaga gctaaaagaa ggtggtatgg atttttacgt gcccaggcaa gagccaatgt
4981 tcagatggat gagattctcg gatctgagca cgtgggaggg cgatcgcaat ctggctccca
5041 gttttgtgaa tgaagatggc gtcgaatgac gccaacccat ctgatgggtc cgcagccaac
5101 ctcgtcccag aggtcaacaa tgaggttatg gctttggagc ccgttgtcgg tgccgctatt
5161 gcggcgcctg tagcgggcca acaaaatgta attgacccct ggattagaaa taattttgta
5221 caagcccctg gtggagagtt cacagtatcc cctagaaacg ctccaggtga aatactatgg
5281 agcgcgccct taggccctga tctgaacccc tacctatccc atttggctag aatgtataat
5341 ggttacgcag gtggttttga agtgcaggtg atcctcgcgg ggaacgcgtt caccgccgga
5401 aaaattatat ttgcagcagt cccaccaaat ttcccaactg aaggcttgag tcctagccag
5461 gtcactatgt tcccccacat aatagtagat gttaggcaat tggaacctgt gttgatcccc
5521 ttacctgatg ttaggaataa cttctatcat tataatcagt caaatgattc taccattaaa
5581 ttgatagcaa tgctgtatac accacttagg gctaataatg ctggggacga tgtcttcaca
5641 gtctcttgtc gagtcctcac gaggccatcc cctgattttg attttatatt tttggtgcca
5701 cctacagttg agtcaagaac taaaccattt actgtcccaa tcctaactgt tgaagagatg
5761 accaattcaa gattccccat tcctttggaa aagttgttca cgggtcccag cggtgccttt
5821 gttgttcaac cacaaaatgg caggtgcacg actgatggcg tgctcttagg caccacccaa
5881 ctgtctcctg tcaacatctg caccttcaga ggggatgtca cccacattgc aggttctcgt
5941 aattacacaa tgaatttggc ttctctaaat tggaacaatt atgacccaac agaagaaatt
6001 ccagcccctc taggaactcc agatttcgtg ggaaagatcc aaggtgtgct cactcaaacc
6061 acaaagggaa atggctcgac ccgtggccat aaagctacag tttacactgg gagtgccccc
6121 tttactccaa agctgggcag tgttcaattc gaaactgata cagaaaatga ttttgaaact
6181 caccaaaaca caaaattcac cccagtcggt gtcatccagg atggtagcac cacccaccga
6241 aatgaacccc aacaatgggt gctcccaagt tattcaggta gagatgtcca taatgtacac
6301 ctagcccctg ctgtagcccc cacttttccg ggtgaacaac ttcttttctt caggtccact
6361 atgcccggat gcagcgggta tcccaacatg gatttggatt gcctactccc ccaggagtgg
6421 gtgcagtact tctaccaaga ggcagctcca gcacaatctg atgtggctct attgagattt
6481 gtgaatccag acacgggtag ggtcctgttt gagtgcaaac ttcataaatc aggctatgtc
6541 acagtggctc acaccggcca gcatgatttg gtcatccccc ccaatggcta ttttaggttt
6601 gattcctggg ttaatcaatt ctacacactt gcccccatgg gaaatggaac ggggcgcagg
6661 cgtgctttat aatggctgga gctttctttg ctggattggc atctgatgtt cttggcactg
6721 gacttggttc cctaatcaat gctggggctg gggctatcaa ccaaaagatt gattttgaaa
6781 ataacagaaa actgcaacaa gcttccttcc agtttagcag taatctacaa caggcttcct
6841 ttcaacatga taaagagatg ctcctagcac aaattgaggc cactaaaaag ttgcaacagg
6901 aaatgatgaa agtcaaacag gcaatgctct tagaaggtgg attctctgaa acagatgcag
6961 cccgtggggc aatcaatgcc cccatgacaa aggctttgga ctggagcgga acaaggtact
7021 gggcccctga tgctaggact acgacgtaca atgcaggccg cttttccacc cctcaacctt
7081 cggggacact gccaggaaga atcaatccca ggacttccac ccccgctcgg ggctcctcca
7141 gcacatcttc taatgcttct attgctactt ctatatattc aaatcaaact gtttcaacga
7201 gacttggttc tacagctggt tctggcacca atgtctcgag tctcccgtca actgcaagaa
7261 ctaggagttg ggttgaggat caaaacagga atttgtcacc tttcatgagg ggggctcaca
7321 atatatcgtt tgtcacccca ccatctagca gatcctctag ccaaggcaca gtctcaaccg
7381 tgcctaaagg agttttggac tcctggactg gcgctttcaa cacgcgcagg cagcctctct
7441 tcgctcacat tcgtaggcga ggggagtcac gggtgtaatg tgaaaagaca aaattgatta
7501 tctttctttt
//