Typing tool
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Typing tool
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Complete norovirus genomes
| KC409282 | GII.4 Den Haag | |
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| GII.P4 Den Haag |
ORF1: 3..5102
ORF2: 5083..6705
ORF3: 6705..7511
LOCUS KC409282 7511 bp ss-RNA linear VRL 13-MAR-2013
DEFINITION Norovirus Hu/GII/20230/2009/VNM, complete genome.
ACCESSION KC409282
VERSION KC409282.1
DBLINK BioProject: PRJNA70471
KEYWORDS .
SOURCE Norovirus Hu/GII/20230/2009/VNM
ORGANISM Norovirus Hu/GII/20230/2009/VNM
Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes;
Picornavirales; Caliciviridae; Norovirus; Norovirus norwalkense.
REFERENCE 1 (bases 1 to 7511)
AUTHORS Madupu,R., Halpin,R.A., Ransier,A., Fedorova,N., Tsitrin,T.,
McLellan,M., Stockwell,T., Amedeo,P., Appalla,L., Bishop,B.,
Edworthy,P., Gupta,N., Hoover,J., Katzel,D., Li,K., Schobel,S.,
Shrivastava,S., Thovarai,V., Wang,S., My,P.V., Campbell,J.,
Farrar,J., Vinh,H., Hoang,N.V., Wentworth,D.E. and Baker,S.
TITLE Direct Submission
JOURNAL Submitted (17-DEC-2012) J. Craig Venter Institute, 9704 Medical
Center Drive, Rockville, MD 20850, USA
COMMENT This work was supported by the National Institute of Allergy and
Infectious Diseases (NIAID), Genome Sequencing Centers for
Infectious Diseases (GSCID) program.
The genome sequence was generated using overlapping PCR amplicons
spanning the genome. The amplicons were pooled by sample and then
barcoded and sequenced using Next Generation Sequencing platforms.
The consensus sequences of the internal PCR primer hybridization
sites were manually verified using reads from amplicons that
spanned across the sites.
Genome sequence lacks part of non-coding region.
##Genome-Assembly-Data-START##
Current Finishing Status :: Finished
Assembly Method :: clc_ref_assemble_long v. 3.22.55705
Genome Coverage :: 298.1x
Sequencing Technology :: Illumina; 454
##Genome-Assembly-Data-END##
FEATURES Location/Qualifiers
source 1..7511
/organism="Norovirus Hu/GII/20230/2009/VNM"
/mol_type="genomic RNA"
/strain="Hu/GII/20230/2009/VNM"
/host="Homo sapiens; sex: M"
/db_xref="taxon:1291853"
/geo_loc_name="Viet Nam: Ho Chi Minh City"
/collection_date="27-Oct-2009"
/PCR_primers="fwd_name: Ampl_1_Forward, fwd_seq:
gtgaatgawgatggcgt, rev_name: Ampl_1_Reverse, rev_seq:
ttggttgagagyttyctg"
/PCR_primers="fwd_name: Ampl_2_Forward, fwd_seq:
ccgcaaaatcttcaagtg, rev_name: Ampl_2_Reverse, rev_seq:
cwacaggtcttggtctgctrga"
/PCR_primers="fwd_name: Ampl_3_Forward, fwd_seq:
tcaaccaartctgcttcacctg, rev_name: Ampl_3_Reverse, rev_seq:
ratcctttgccggatcttgg"
/PCR_primers="fwd_name: Ampl_4_Forward, fwd_seq:
ggcaagaagcacacagcctt, rev_name: Ampl_4_Reverse, rev_seq:
crrctctytgttgtgttgaatccc"
/PCR_primers="fwd_name: Ampl_5_Forward, fwd_seq:
tggyaagatcaagaagaggc, rev_name: Ampl_5_Reverse, rev_seq:
acaacaaargcacygctrgg"
/PCR_primers="fwd_name: Ampl_6_Forward, fwd_seq:
gagrccrtccccygattttg, rev_name: Ampl_6_Reverse, rev_seq:
atcaatyttgtcttttcaca"
/note="genotype: II"
gene 3..5102
/gene="POL"
CDS 3..5102
/gene="POL"
/note="genome polyprotein"
/codon_start=1
/product="nonstructural polyprotein"
/protein_id="AGE89564.1"
/translation="MKMASNDASAAAVANSNNDTAKSSSDKMFSNMAVTFRRALGARP
KQPPPREIPQRPPRPPTPELVKKIPPPPPNGEDEAVVSYSAKDGVSGLPELSTVRQPE
ETNTAFSVPPLNQRENRDAKEPLTGTILEMWDGEIYHYGLYVERGLVLGVHKPPAAIS
LAKVELTPLSLFWRPVYTPQYLISPDTLKKLHGETFPYTAFDNNCYAFCCWVLDLNDS
WLSRRMIQRTTGFFRPYQDWNRKPLPTMDDSKLKKVANIFLCALSSLFTRPIKDIIGK
LRPLNIINILASCDWTFAGIVESLILLAELFGVFWTPPDVSAMIAPLLGDFELQGPED
LVVELVPVVMGGIGLVLGFTKEKIGKMLSSAASTLRACKDLGAYGLEILKLVMKWFFP
KKEEANELAMVRSIEDAVLDLEAIENNHMTTLLKDKDSLATYMRTLDLEEEKARKLST
KSASPDIVGTINALLARIAAARSLVHRAKEELSSRPRPVVLMISGRPGIGKTHLAREV
AKRIAASLTGDQRVGLIPRNGVDHWDAYKGERVVLWDDYGMSNPIHDALRLQELADTC
PLTLNCDRIENKGKVFDSDVIIITTNLANPAPLDYVNFEACSRRIDFLVYAEAPEVEK
AKRDFPGQPDMWKNAFSSDFSHIKLALAPQGGFDKNGNTPHGKGVMKTLTTGSLIARA
SGLLHERLDEFELQGPALTTFNFDRNKVLAFRQLAAENKYGLIDTMKVGKQLKEVKTM
PELKQALKNISIKKCQIVYSGCTYTLESDGKGNVKVDRIQSTSVQTNNELAGALHHLR
CARIRYYVKCVQEALYSIIQIAGAAFVTTRIIKRVNIQDLWSKPQVENTEEATNKDGC
PKPKDDEEFVISSDDIKTEGKKGKNKTGRGKKHTAFSSKGLSDEEYDEYKRIREERNG
RYSIEEYLQDRDKYYEEVAIARATEEDFCEEEEAKIRQRIFRPTRKQRKEERASLGLV
TGSEIRKRNPDDFKPKGKLWADDDRSVDYNEKLSFEAPPSIWSRIVNFGSGWGFWVSP
SLFITSTHVIPQGAKEFFGVPIKQIQVHKSGEFCRLRFPKPIRTDVTGMILEEGAPEG
TVVTLLIKRSTGELMPLAARMGTHATMKIQGRTVGGQMGMLLTGSNAKSMDLGTTPGD
CGCPYIYKRGNDYVVIGVHTAAARGGNTVICATQGGEGEATLEGGDSKGTYCGAPILG
PGSAPKLSTKTKFWRSSTAPLPPGTYEPAYLGGKDPRVKGGPSLQQVMRDQLKPFTEP
RGKPPKPSVLEAAKKTIINVLEQTIDPPEKWSFAQACASLDKTTSSGHPHHVRKNDCW
NGESFTGKLADQASKANLMFEEGKNMTPVYTGALKDELVKTDKIYGKIKKRLLWGSDL
ATMIRCARAFGGLMDELKAHCVTLPIRVGMNMNEDGPIIFEKHSRYRYHYDADYSRWD
STQQRAVLAAALEIMVKFSSEPHLAQVVAEDLLSPSVVDVGDFTISINEGLPSGVPCT
SQWNSIAHWLLTLCALSEVTNLSPDIIQANSLFSFYGDDEIVSTDIKLDPEKLTAKLR
EYGLKPTRPDKTEGPLVISEDLDGLTFLRRTVTRDPAGWFGKLEQSSILRQMYWTRGP
NHEDPSESMIPHSQRPIQLMSLLGEAALHGPTFYSKISKLVIAELKEGGMDFYVPRQE
PMFRWMRFSDLSTWEGDRNLAPSFVNEDGVE"
mat_peptide 3..992
/gene="POL"
/product="protein p48"
mat_peptide 993..2090
/gene="POL"
/product="NTPase"
/note="p41"
mat_peptide 2091..2627
/gene="POL"
/product="protein p22"
mat_peptide 2628..3026
/gene="POL"
/product="viral genome-linked protein"
/note="VPg"
mat_peptide 3027..3569
/gene="POL"
/product="3C-like protease"
/note="3CLpro; calcivirin"
mat_peptide 3570..5099
/gene="POL"
/product="RNA-directed RNA polymerase"
gene 5083..6705
/gene="VP1"
CDS 5083..6705
/gene="VP1"
/codon_start=1
/product="capsid protein VP1"
/protein_id="AGE89565.1"
/translation="MKMASNDANPSDGSAANLVPEVSNEVMALEPVVGAAIAAPVAGQ
QNVIDPWIRNNFVQAPGGEFTVSPRNAPGEILWSAPLGPDLNPYLSHLARMYNGYAGG
FEVQVILAGNAFTAGKIIFAAVPPNFPTEGLSPSQVTMFPHIIVDVRQLEPVLIPLPD
VRNNFYHYNQTNDSTIKLIAMLYTPLRANNAGEDVFTVSCRVLTRPSPDFDFIFLVPP
TVESRTKPFTVPILTVEEMTNSRFPIPLEKLFTGPSGAFVVQPQNGRCTTDGVLLGTT
QLSPVNICTFRGDVTHIAGSRNYTMNLASLNWNNYDPTEETPAPLGTPDFVGKIQGVL
TQTTKGDGSTRGHKATVYTGSAPFTPKLGSVQFSTDTENDFETHQNTKFTPVGVIQDG
GTTHRNEPQQWVLPSYSGRDVHNVHLAPAVAPTFPGEQLLFFRSTMPGCSGYPNMDLD
CLLPQEWVQHFYQEAAPAQSDVALLRFVNPDTGRVLFECKLHKSGYVTVAHTGQHDLV
IPPNGYFRFDSWVNQFYTLAPMGNGTGRRRAL"
gene 6705..7511
/gene="VP2"
CDS 6705..7511
/gene="VP2"
/note="minor capsid protein"
/codon_start=1
/product="capsid protein VP2"
/protein_id="AGE89566.1"
/translation="MAGAFFAGLASDVLSSGLGSLINAGAGAINQKIDFENNRKLQQA
SFQFSSNLQQASFQHDKEMLQAQIEATKKLQQEMMKVKQAMLLEGGFSETDAARGAIN
APMTKVLDWSGTRYWAPDARTTTYNAGRFSTPQPSGTLPGRINPRIPTPARGSSSTSS
NASTATSIYSNQTVSTRLGSTAGSGTNVSSLPSTARTRSWVEDQNRNLSPFMRGAHNI
SFVTPPSSRSSSQGTVSTVPKEVLDSWTGAFNTRRQPLFAHIRRRGESRV"
ORIGIN
1 gaatgaagat ggcgtctaac gacgcttccg ctgccgctgt tgctaacagc aacaacgaca
61 ccgcaaaatc ttcaagtgac aaaatgtttt ctaacatggc tgtcactttt agacgagccc
121 tcggggcgcg gcctaaacag ccccccccga gggaaatacc acaaagaccc ccacgaccac
181 ctaccccaga actggtcaaa aagatccccc ctcccccgcc caacggagag gatgaagcag
241 tggtttctta tagtgccaaa gatggcgttt ccggtttacc tgagctttcc accgtcaggc
301 aaccggaaga aaccaatacg gccttcagtg tccctccact caaccagagg gagaatagag
361 atgctaagga accactgact ggaacaattc tggaaatgtg ggatggagaa atctaccatt
421 acggcctgta tgttgagcga ggtcttgtgc tgggtgtgca caaaccacca gctgccataa
481 gcctcgccaa ggtcgaacta acaccactct ccttgttctg gagacctgtg tacacccccc
541 agtacctcat ctctccagac accctcaaga aattgcacgg agaaacgttt ccctacacag
601 cctttgacaa caattgctat gccttttgtt gttgggtcct ggatctaaat gactcgtggc
661 tgagtaggag aatgatccag agaacaactg gcttcttcag accctaccaa gactggaata
721 ggaaacccct ccccactatg gatgattcca aattaaagaa ggtagctaac atattcctgt
781 gcgccctgtc ttcgctattc accaggccca taaaagacat aataggaaag ctaagacctc
841 tcaacatcat taacatcctg gcttcatgtg attggacttt cgcaggcata gtggagtctt
901 tgatactctt ggcagagctc tttggagtct tctggacacc cccagatgtg tctgcgatga
961 ttgccccctt actcggtgat ttcgagttac aaggacctga ggaccttgta gtagagctcg
1021 tccctgtagt aatgggggga attggtttgg tgctgggatt caccaaagag aagattggga
1081 aaatgttgtc atctgctgca tccaccttga gagcttgtaa agatcttggt gcatatgggc
1141 tagagatcct aaagttagtc atgaagtggt tcttcccgaa gaaagaggag gcaaatgaac
1201 tggctatggt gagatccatc gaggatgcag tactggacct tgaggcaatt gaaaacaacc
1261 atatgaccac cttgctcaaa gacaaagaca gcctagcaac ctacatgagg acccttgacc
1321 tcgaggaaga gaaagccaga aaactctcaa ccaagtctgc ttcacctgac atcgtgggta
1381 caatcaacgc ccttctggcg agaatcgctg ctgcacgctc cctggtgcac cgagcgaagg
1441 aggagctttc cagcagacca aggcctgtag tcttgatgat atcaggcaga ccagggatag
1501 gaaaaaccca ccttgctagg gaagtggcta agagaatcgc agcctccctc acaggagacc
1561 agcgtgtagg cctcatccca cgcaatggcg tcgatcactg ggatgcgtac aagggggaga
1621 gggtcgtcct atgggacgac tatggaatga gcaaccccat tcacgacgcc cttaggctgc
1681 aagaactcgc tgacacttgc ccccttactc taaattgtga caggattgag aacaaaggaa
1741 aggtctttga cagcgatgtc atcattatca ccactaatct ggccaaccca gcaccactgg
1801 actatgtcaa ctttgaagcg tgctcgaggc gcatcgattt cctcgtgtat gcagaagccc
1861 ccgaggtcga aaaggcgaag cgtgacttcc cgggccaacc tgacatgtgg aaaaacgctt
1921 ttagttctga tttctcacac ataaaattgg cactggctcc acaaggtggc tttgataaga
1981 acgggaacac cccacacggg aagggcgtca tgaagactct caccactggc tccctcattg
2041 cccgggcatc agggctgctc catgagagat tggatgagtt tgaactacag ggcccagctc
2101 ttaccacctt caactttgac cgcaacaaag tgcttgcctt cagacagctt gcagctgaaa
2161 acaaatatgg gttgatagac acaatgaaag ttgggaagca gctcaaggaa gtcaaaacca
2221 tgccagaact taaacaagca ctcaaaaaca tctcaatcaa gaagtgccag attgtgtata
2281 gtggttgcac ctacacactt gagtctgatg gcaagggcaa tgtgaaagtt gacagaatcc
2341 agagcacctc cgtacagacc aacaatgagc ttgctggcgc cctgcatcat ctgaggtgcg
2401 ccagaatcag gtactatgtc aagtgtgtcc aggaggccct gtattctatc atccagattg
2461 ctggggccgc atttgtcacc acgcgcatta tcaagcgtgt gaacattcaa gacttatggt
2521 ccaagccaca agtggaaaac acagaggagg ccaccaacaa ggacgggtgc ccaaaaccca
2581 aagatgatga ggagttcgtc atttcatctg acgacattaa aactgagggt aagaaaggga
2641 agaacaagac tggccgtggc aagaagcata cagccttttc aagtaaaggt ctcagtgatg
2701 aggagtatga tgagtacaag agaattagag aggaaaggaa tggcaggtat tccatagaag
2761 agtaccttca ggacagggac aaatactatg aggaggtggc cattgccagg gcgaccgagg
2821 aagacttctg tgaagaggag gaggccaaga tccggcaaag gatctttaga ccaacaagga
2881 aacaacgcaa ggaagaaaga gcttctctcg gtttagtcac aggttctgag attaggaaaa
2941 gaaacccaga tgacttcaag cctaagggaa aactgtgggc tgacgatgac agaagtgtgg
3001 actacaatga gaaactcagt tttgaggccc caccaagtat ctggtcaagg atagtcaact
3061 ttggttcagg ttggggcttc tgggtctccc ctagcctgtt cataacatca acccacgtca
3121 taccccaggg cgcaaaggag ttctttggag ttcccatcaa acaaattcag gtacacaagt
3181 caggcgaatt ttgtcgcttg aggttcccaa aaccaatcag gactgacgtg actggcatga
3241 tcttggaaga aggtgcgccc gaaggcaccg tggtcacact actcatcaaa aggtctactg
3301 gagaactcat gcccctagca gctagaatgg ggacccatgc aaccatgaaa attcaagggc
3361 gcaccgttgg gggacagatg ggcatgcttc tgacaggatc caacgccaaa agcatggatc
3421 taggcaccac accaggtgat tgcggctgtc cctacatcta caagagagga aatgactatg
3481 tggtcattgg agttcatacg gctgccgctc gtgggggaaa cactgtcata tgtgccaccc
3541 aggggggcga gggggaagct acacttgaag gtggtgacag taagggaaca tactgtggtg
3601 caccaatcct aggcccaggg agtgccccaa aacttagcac caaaaccaaa ttctggagat
3661 catccacagc accactccca cctggcacct atgaaccagc ataccttggt ggcaaggacc
3721 ccagagtcaa gggtggccct tcgttgcagc aagtcatgag ggaccagctg aaaccattta
3781 cagagcccag gggtaagcca ccaaagccaa gtgtgttaga agctgccaag aaaaccatca
3841 tcaatgtcct tgaacaaaca attgacccac ctgagaagtg gtcgttcgca caagcttgcg
3901 cctcccttga caagaccact tctagcggcc atccgcacca cgtgcggaaa aacgactgct
3961 ggaatgggga gtccttcaca ggcaagctgg cagaccaggc ctctaaggct aacctgatgt
4021 ttgaagaagg gaagaacatg accccagtct acacaggtgc acttaaggat gaattagtca
4081 aaactgacaa aatttatggt aagatcaaga agaggcttct ctggggctcg gatttagcaa
4141 ccatgatccg gtgtgctcga gcattcggag gcctaatgga tgaacttaaa gcacactgtg
4201 tcacacttcc tattagagtt ggtatgaata tgaatgagga tggccccatc atcttcgaga
4261 agcattccag gtacagatac cactatgatg ctgattactc tcggtgggat tcaacacaac
4321 agagagccgt gctggcagct gctctagaaa tcatggttaa attctcctca gaaccacatt
4381 tggctcaggt agtcgcagaa gatcttcttt cccctagcgt ggtggatgtg ggtgacttca
4441 caatatcaat caacgagggc cttccctctg gggtgccctg cacctcccaa tggaactcca
4501 tcgcccactg gcttctcact ctttgtgcac tctccgaagt cacaaatttg tccccagaca
4561 tcatacaggc taattctctc ttctccttct atggtgatga tgaaattgtt agtacagaca
4621 taaaattgga cccagagaag ttgacagcaa agcttaggga atatgggttg aaaccaaccc
4681 gccctgacaa aactgaagga cctctcgtta tttctgaaga cttagatggt ttgactttcc
4741 tgcggagaac tgtgacccgc gacccagctg gttggtttgg aaaactggag cagagctcaa
4801 tactcaggca aatgtactgg actaggggcc ccaaccatga agatccatct gaatcaatga
4861 ttccacactc tcaaagaccc atacaattga tgtccttact gggagaggcc gcactccacg
4921 gcccaacatt ctacagtaaa atcagcaaat tagtcattgc agagctaaaa gaaggtggta
4981 tggattttta cgtgcccagg caagagccaa tgttcagatg gatgagattc tcagatctga
5041 gcacgtggga gggcgatcgc aatctggctc ccagttttgt gaatgaagat ggcgtcgaat
5101 gacgccaacc catctgatgg gtccgcagcc aacctcgtcc cagaggtcag caatgaggtt
5161 atggctttgg agcccgttgt cggtgccgct attgcggcgc ctgtagcggg ccaacaaaat
5221 gtaattgacc cctggattag aaacaatttt gtacaagccc ctggtggaga gttcacagta
5281 tcccctagaa acgctccagg tgaaatacta tggagcgcgc ccttaggccc tgatctgaat
5341 ccctacctat cccatttggc cagaatgtat aatggttatg caggtggttt tgaagtgcag
5401 gtgatcctcg cggggaacgc gttcaccgcc ggaaaaatta tatttgcagc agtcccacca
5461 aattttccaa ctgaaggcct gagtcccagc caggtcacta tgttccccca cataatagta
5521 gatgttaggc aattggaacc tgtgttgatc cccttacctg atgttaggaa taacttctat
5581 cattataatc aaacaaatga ttctaccatt aaattgatag caatgctgta tacaccactt
5641 agggccaata atgctgggga agatgtcttc acagtctctt gtcgagtcct cactaggccg
5701 tcccctgatt ttgattttat atttttggtg ccacccacag ttgagtcaag aactaaacca
5761 tttactgtcc caatcttaac cgttgaagaa atgaccaact caagattccc cattcctttg
5821 gaaaagttgt tcacgggtcc cagcggtgcc tttgttgtcc aaccacaaaa tggcaggtgc
5881 acgactgatg gcgtgctctt aggcaccacc caactgtctc ctgtcaacat ctgcaccttc
5941 agaggggatg tcacccacat tgcaggttct cgtaattaca caatgaattt ggcatctcta
6001 aattggaaca attatgaccc aacagaagaa actccagccc ctctgggaac tccagatttc
6061 gtgggaaaga tccaaggtgt gctcactcaa accacaaaag gagatggctc gacccgtggc
6121 cataaagcta cagtttacac tgggagtgcc ccctttactc caaagctggg cagtgttcaa
6181 ttcagtactg acacagaaaa tgattttgaa actcaccaaa acacaaaatt caccccagtc
6241 ggtgtcatcc aggatggtgg caccacccac cgaaatgaac cccaacaatg ggtgctccca
6301 agttattcag gtagagatgt tcacaatgta cacctagccc ctgctgtggc ccccactttt
6361 ccgggtgaac aacttctttt cttcaggtcc actatgcccg gatgcagcgg gtatcccaac
6421 atggatttgg attgcctact cccccaggag tgggtgcagc acttctacca agaggcagct
6481 ccagcacaat ctgatgtggc tctattgaga tttgtgaatc cagacacggg tagggtcctg
6541 tttgagtgca aacttcataa atcaggctat gtcacagtgg ctcacaccgg tcagcatgat
6601 ttggtcatcc cccccaatgg ctattttagg tttgattcct gggttaacca gttctacacg
6661 cttgccccca tgggaaacgg aacggggcgt aggcgcgcct tataatggct ggagctttct
6721 ttgctggatt ggcatctgat gtccttagct ctggacttgg ttccttaatc aatgctgggg
6781 ctggggccat caaccaaaag attgattttg aaaataatag aaaattgcag caagcttcct
6841 tccagtttag cagtaatcta caacaggctt cctttcaaca cgataaagag atgctccaag
6901 cacaaattga ggccactaaa aagttgcaac aggagatgat gaaagtcaaa caggcaatgc
6961 tcctagaagg tggattctct gaaacagatg cagcccgtgg ggcaatcaat gcccccatga
7021 caaaggtttt ggactggagc ggaacaaggt actgggcccc tgatgctagg accacaacat
7081 acaatgcagg ccgcttttcc acccctcaac cttcggggac gctgccagga agaatcaatc
7141 ccaggattcc tacccccgct cggggctcct ccagcacatc ttctaatgct tctactgcta
7201 cttctatata ttcaaatcaa actgtttcaa cgagacttgg ttctacagct ggttctggta
7261 ccaatgtctc gagtctcccg tcaactgcaa ggactaggag ctgggttgag gatcaaaaca
7321 gaaatttgtc acctttcatg aggggggctc ataacatatc gtttgtcacc ccaccatcta
7381 gcagatcctc tagccaaggc acagtctcaa ccgtgcctaa agaagttttg gactcctgga
7441 ctggcgcttt caacacgcgc aggcagcctc tcttcgctca cattcgtagg cgaggggagt
7501 cacgggtgta a
//