Typing tool
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Typing tool
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Complete norovirus genomes
| KC409292 | GII.4 New Orleans | |
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| GII.P4 New Orleans |
ORF1: 3..5102
ORF2: 5083..6705
ORF3: 6705..7511
LOCUS KC409292 7511 bp ss-RNA linear VRL 13-MAR-2013
DEFINITION Norovirus Hu/GII/20357/2009/VNM, complete genome.
ACCESSION KC409292
VERSION KC409292.1
DBLINK BioProject: PRJNA70471
KEYWORDS .
SOURCE Norovirus Hu/GII/20357/2009/VNM
ORGANISM Norovirus Hu/GII/20357/2009/VNM
Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes;
Picornavirales; Caliciviridae; Norovirus; Norwalk virus.
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 :: 418.3x
Sequencing Technology :: Sanger; Illumina; 454
##Genome-Assembly-Data-END##
FEATURES Location/Qualifiers
source 1..7511
/organism="Norovirus Hu/GII/20357/2009/VNM"
/mol_type="genomic RNA"
/strain="Hu/GII/20357/2009/VNM"
/host="Homo sapiens; sex: F"
/db_xref="taxon:1291863"
/country="Viet Nam: Ho Chi Minh City"
/collection_date="29-Dec-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="AGE89594.1"
/translation="MKMASNDASAAAVANSNNDTAKSSSDGVLSSMAVTFKRALGARP
KQPPPREKPQRPPRPPTPELVKNIPPPPPNGEDEIVVSYSVKDGVSGLPDLSTVRQPE
ESNTAFSVPPLNQRENRDAKEPLTGTILEMWDGEIYHYGLYVDRGLVLGVHKPPAAIS
LARVELAPLSLYWRPVYTPQYLISPDTLKKLSGETFPYTAFDNNCYAFCCWVLDLNDS
WLSRRMIQRTTGFFRPYQDWNRKPLPTMDDSKIKKVANIFLCALSSLFTRPIKDIIGK
IRPLNILNILASCDWTFAGIVESLILLAELFGVFWTPPDVSAMIAPLLGDYELQGPED
LAVELVPVVMGGIGLVLGFTKEKIGKMLSSAASTLRACKDLGAYGLEILKLVMKWFFP
KKEEANELAIVRSIEDAVLDLEAIENNHMTTLLKDKDSLATYMRTLDLEEEKARKLST
KSASPDIVGTINALLARIAAARSLVHRAKEELSSRPRPVVLMISGRPGIGKTYLAREV
AKRIAASLTGDQRVGLIPRNGVDHWDAYKGERVVLWDDYGMSNPIHDALRLQELADTC
PLTLNCDRIENKGKVFDSDVIIITTNLANPAPLDYVNFEACSRRIDFLVYAEAPEVEK
AKRDFPGQPDMWKNAFSSDFSHIKLALAPQGGFDKNGNTPHGKGVMKTLTTGSLIARA
SGLLHERLDEFELQGPALTTFNFDRNKVLAFRQLAAENKYGLMDTMRVGKQLKDVRTM
PELKQALKNVSIKKCQLVYSGCTYILESDGKGNVKVDRIQSAAVQTNNELAGALHHLR
CARIRYYVKCVQEALYSIIQIAGAAFVTTRIAKRMNIQDLWSKPQVENTEETTSKDGC
PKPKDDEEFVISSDDIKAEGKKGKNKTGRGKKHTAFSSKGLSDEEYDEYKRIREERNG
KYSIEEYLQDRDKYYEEVAIARATEEDFCEEEEAKIRQRIFRPTRKQRKEERASLGLV
TGSEIRKRNPDDFKPKGKLWADDDRSVDYNEKLSFEAPPSIWSRIVNFGSGWGFWVSP
SLFITSTHVIPQGAKEFFGVPIKQIQVHKSGEFCRLRFPKPIRTDVTGMILEEGAPEG
TVVTLLIKRSTGELMPLAARMGTHATMKIQGRTVGGQMGMLLTGSNAKSMDLGTTPGD
CGCPYIYKRGNDYVVIGVHTAAARGGNTVICATQGSEGEATLEGGDNKGTYCGAPILG
PGSAPTLSTKTKFWRSSTASLPPGTYEPAYLGGKDPRVKGGPSLQQVMREQLKPFTEP
RGKPPKPSVLEAAKKTIINVLEQTIDPPEKWSFAQACASLDKTTSSGHPHHMRKNDCW
NGESFTGKLADQASKANLMFEEGKNMTPVYTAALKDELVKTDKIYGKIKKRLLWGSDL
ATMIRCARAFGGLMDELKAHCVTLPIRVGMNMNEDGPIIFERHSRYTYHYDADYSRWD
STQQRAVLAAALEIMVKFSPEPHLAQVVAEDLLSPSVVDVGDFTISINEGLPSGVPCT
SQWNSIAHWLLTLCALSEVTNLSPDTIQANSLFSFYGDDEIVSTDIKLDPEKLTAKLR
EYGLKPTRPDKTEGPLVISEDLNGLTFLRRTVTRDPAGWFGKLEQSSILRQMYWTRGP
NHGDPSETMIPHSQRPIQLMSLLGEAALHGPAFYSKISKLVIAELKEGGMDFYVPRQE
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="AGE89595.1"
/translation="MKMASSDANPSDGSTANLVPEVNNEVMALEPVVGAAIAAPVAGQ
QNVIDPWIRNNFVQAPGGEFTVSPRNAPGEILWSAPLGPDLNPYLSHLARMYNGYAGG
FEVQVILAGNAFTAGKIIFAAVPPNFPTEGLSPSQVTMFPHIIVDVRQLEPVLIPLPD
VRNNFYHYNQSNDPTIKLIAMLYTPLRANNAGDDVFTVSCRVLTRPSPDFDFIFLVPP
TVESRTKPFSVPVLTVEEMTNSRFPIPLEKLFTGPSSAFVVQPQNGRCTTDGVLLGTT
QLSPVNICTFRGDVTHIPGSRNYTMNLASQNWNSYDPTEEIPAPLGTPDFVGKIQGVL
TQTTRTNGSTRGHKATVYTGSADFSPKLGRVQFATDTDNDFETNQNTKFTPVGVIQDG
STTPRNEPQQWVLPSYSGRNIHNVHLAPAVAPTFPGEQLLFFRSTMPGCSGYPNMDLD
CLLPQEWVQYFYQEAAPAQSDVALLRFVNPDTGRVLFECKLHKSGYVTVAHTGQHDLV
IPPNGYFRFDSWVNQFYTLAPMGNGTGRRRAL"
gene 6705..7511
/gene="VP2"
CDS 6705..7511
/gene="VP2"
/note="minor capsid protein"
/codon_start=1
/product="capsid protein VP2"
/protein_id="AGE89596.1"
/translation="MAGAFFAGLASDVLGSGLGSLINAGAGAINQKVEFENNRKLQQA
SFQFSSNLQQASFQHDKEMLQAQIEATKKLQQEMMRVKQAMLLEGGFSETDAARGAIN
APMTKTLDWSGTRYWAPDARTTTYNAGRFSTPQPSGALPGRANLRATVPARGSSSTSS
NSSIATSVYSNQTTSTRLGSTAGSGTSVSSLPSTARTRSWVEDQNRNLSPFMRGAHNI
SFVTPPSSRSSSQGTVSTVPKEVLDSWTGAFNTRRQPLFAHIRKRGESRV"
ORIGIN
1 gaatgaagat ggcgtctaac gacgcttccg ctgccgctgt tgctaacagc aacaacgaca
61 ccgcaaaatc ttcaagtgac ggagtgcttt ctagcatggc tgtcactttt aaacgagccc
121 tcggggcgcg gcctaaacag cctcccccga gggaaaaacc acaaagaccc ccacgaccac
181 ctactccaga actggttaaa aatattcccc ctcccccacc caacggagag gatgaaatag
241 tggtttctta tagtgttaaa gatggtgttt ccggcttgcc tgacctttcc accgtcaggc
301 aaccggaaga atctaacacg gccttcagtg tccctccact caaccagagg gagaatagag
361 atgctaagga accacttact ggaacgattc tggaaatgtg ggacggggaa atctaccatt
421 atggcctgta tgtggatcga ggtcttgtac tgggtgtgca caaaccacca gctgccatca
481 gcctcgctag ggttgagcta gcaccactct ccttgtactg gagacctgtg tacactcctc
541 agtacctcat ctctccagac actctcaaga aattatccgg agaaacgttc ccctacacag
601 cctttgacaa caactgttat gccttttgct gctgggtcct ggacctaaat gactcgtggc
661 tgagcaggag aatgatccag agaacaactg gtttcttcag gccctaccaa gactggaata
721 ggaaacccct tcccactatg gatgactcca aaataaagaa ggtagctaac atattcctgt
781 gtgctctgtc ctcgctgttc accagaccca taaaagatat aatagggaag ataaggcctc
841 ttaacatcct caacatctta gcctcatgtg attggacttt tgcaggtata gtggagtccc
901 tgatactctt ggcagaactc tttggagttt tctggacacc cccagatgtg tctgcgatga
961 ttgccccctt acttggtgac tacgagctac aaggacctga ggaccttgca gttgagctcg
1021 tccccgtagt gatgggggga attggtttgg tgctaggatt caccaaagag aagattggga
1081 aaatgttgtc atctgctgcg tccaccttga gagcttgtaa agaccttggt gcatatgggc
1141 tagagatcct aaagttggtc atgaagtggt tcttcccgaa gaaggaagag gcaaatgagc
1201 tggctatagt gaggtctatc gaggatgcag tcctggatct cgaggcaatt gaaaacaacc
1261 atatgaccac cttgctcaaa gacaaagaca gtctggcaac ctatatgaga acacttgacc
1321 ttgaggagga gaaagccagg aaactctcaa ccaagtctgc ctcacccgac atcgtgggca
1381 caatcaacgc cctcctggcg agaatcgctg ccgcacgttc tctggtgcac cgagcgaagg
1441 aggagctttc cagcagacca agacctgtgg tgttgatgat atcaggcagg ccaggaatag
1501 ggaagacata cctcgctagg gaagtggcta agagaatcgc agcctccctt acaggagacc
1561 agcgtgtggg cctcatccca cgcaatggcg tcgaccattg ggatgcgtac aagggggaga
1621 gggtcgtcct atgggacgat tatggaatga gcaaccctat tcacgacgcc ctcaggctgc
1681 aagaactcgc tgacacttgc cccctcactc taaactgtga caggatcgaa aacaaaggaa
1741 aggtctttga cagcgacgtc atcattatca ccactaatct ggccaaccca gcgccactgg
1801 actatgtcaa ctttgaagca tgctcgaggc gcatcgactt cctcgtgtat gcagaagccc
1861 ctgaagtcga aaaggcgaag cgtgacttcc caggccagcc tgacatgtgg aagaacgctt
1921 tcagttctga tttctcacac ataaaactag cactggcccc acagggtggt ttcgacaaga
1981 acgggaacac cccacacgga aagggcgtta tgaagactct caccactggc tcccttattg
2041 cccgggcatc agggctactc catgagaggt tagatgaatt tgaactgcag ggcccagctc
2101 tcaccacctt caatttcgat cgcaataagg tgcttgcctt tagacagctt gctgctgaaa
2161 ataaatatgg attgatggac acaatgagag ttgggaaaca gctcaaggat gtcagaacca
2221 tgccagaact caaacaagca ctcaagaatg tctcaatcaa gaagtgccaa ttagtgtata
2281 gtggttgcac ctacatactt gagtctgatg gcaagggcaa tgtgaaagtc gacagaatcc
2341 aaagcgccgc cgtgcagacc aacaatgagc tggctggtgc cctgcaccat ttgaggtgcg
2401 ccagaatcag atactatgtc aagtgtgtcc aggaggccct gtattccatc attcaaatcg
2461 ctggggctgc atttgtcacc acgcgcattg ccaagcgcat gaacatacaa gacctatggt
2521 ccaagccaca agtggaaaac acagaggaga ctaccagcaa ggacgggtgc ccaaaaccta
2581 aggacgatga ggagtttgtc atttcatccg acgacatcaa agctgagggt aagaaaggga
2641 agaacaagac tggccgcggc aagaagcaca cagcattttc aagcaaaggc ctcagtgatg
2701 aagagtacga tgagtacaag aggattagag aagaaaggaa tggcaagtac tccatagaag
2761 agtaccttca ggacagggac aaatactatg aggaggtggc cattgccagg gcgactgagg
2821 aagacttctg tgaagaggag gaggccaaga tccggcaaag gatctttagg ccaacaagga
2881 aacaacgcaa ggaggaaaga gcctctctcg gtctggtcac aggctctgaa attaggaaaa
2941 gaaacccaga tgacttcaaa cccaaaggga aattgtgggc tgacgatgac aggagtgtag
3001 actacaatga gaaactcagt tttgaggccc caccaagcat ctggtcgaga atagtcaact
3061 ttggttcagg ctggggattt tgggtctccc ccagtctgtt cataacatca acccatgtca
3121 taccccaggg cgcaaaggag ttctttggag tccccatcaa acaaatacag gtacacaagt
3181 cgggcgagtt ctgtcgcttg agattcccaa aaccaatcag gactgatgtg acgggcatga
3241 tcttagaaga aggcgcacct gagggcaccg tggtcacact actcatcaaa aggtccactg
3301 gggaactcat gcccctagca gctaggatgg ggacccatgc gaccatgaag atccaagggc
3361 gcactgttgg aggccagatg ggcatgcttc tgacaggatc caacgccaag agcatggacc
3421 tgggtactac accaggtgat tgtggctgcc cctatatcta caagagaggt aatgactatg
3481 tggtcattgg ggtccacacg gctgccgcac gtggggggaa cactgtcata tgtgccaccc
3541 aggggagtga aggagaggct acacttgaag gtggtgacaa caaggggaca tactgtggtg
3601 caccaatcct aggcccaggg agtgccccaa cacttagcac caagaccaaa ttctggagat
3661 cgtccacagc atcactccca cctggcacct atgaaccagc ctatcttggt ggcaaggacc
3721 ctagggtcaa gggtggtcct tcactgcagc aagtcatgag ggaacagttg aagccattca
3781 cagagcccag gggcaagcca ccaaaaccaa gtgtattaga agctgccaag aagaccatca
3841 tcaatgtcct tgagcaaaca attgatccac ctgagaaatg gtcgttcgca caagcttgcg
3901 cgtcccttga caagaccact tccagtggtc atccgcacca catgcggaaa aacgactgct
3961 ggaacgggga gtccttcaca ggcaagctgg cagaccaggc ttccaaggcc aacctgatgt
4021 ttgaagaagg gaagaacatg accccagtct acacagctgc gctcaaggat gagttagtta
4081 aaactgacaa aatttatggt aagattaaga agaggcttct ctggggctcg gacttggcga
4141 ccatgatccg gtgtgctcga gcattcggag gcctaatgga tgaactcaaa gcacactgtg
4201 tcacacttcc tattagagtt ggcatgaata tgaatgagga tggccccatc atcttcgaga
4261 ggcattccag gtacacatat cactatgatg ctgattactc tcgatgggat tcaacacaac
4321 agagagccgt gttggcagca gctctagaaa tcatggttaa attctcccca gaaccacact
4381 tggctcaggt agtcgcggag gaccttcttt ctcctagcgt ggtggacgtg ggcgacttca
4441 caatatcaat caacgagggt cttccctctg gggtgccctg cacctcccaa tggaactcca
4501 tcgcccactg gcttctcact ctctgtgcgc tctctgaagt cacaaacctg tcccctgata
4561 ccatacaggc taactccctc ttctcttttt atggtgatga tgaaattgtt agcacagaca
4621 taaaattgga cccagaaaaa ttgacagcaa agctcagaga atatgggtta aaaccaaccc
4681 gccctgacaa aactgaagga ccccttgtca tctctgaaga cctgaatggc ctaactttcc
4741 tgcggagaac tgtgacccgc gacccagctg gttggtttgg aaaactggag cagagttcaa
4801 tactcaggca aatgtactgg actaggggtc ccaaccatgg agacccatct gaaacaatga
4861 ttccacactc ccaaagaccc atacaattga tgtccctact gggggaggcc gctctccacg
4921 gcccagcatt ttacagcaaa atcagcaaat tggtcattgc agagctaaaa gaaggtggca
4981 tggattttta cgtgcccaga caagagccaa tgttcagatg gatgagattc tcagatctga
5041 gcacgtggga gggcgatcgc aatctggctc ccagttttgt gaatgaagat ggcgtcgagt
5101 gacgccaacc catctgatgg gtccacagcc aaccttgtcc cagaggtcaa caatgaggtt
5161 atggctttgg agcccgtagt tggtgccgct attgcggcac ctgtagcggg ccaacaaaat
5221 gtaattgacc cctggattag aaacaatttt gtacaagccc ctggtggaga gtttacagta
5281 tcccctagaa acgctccagg tgaaatacta tggagcgcgc ccttaggccc tgatttgaat
5341 ccctaccttt cccatttggc cagaatgtac aatggttatg caggtggttt tgaagtgcag
5401 gtaatcctcg cggggaacgc gttcaccgcc gggaaaatca tatttgcagc agtcccacca
5461 aatttcccaa ctgaaggttt gagccccagc caggtcacta tgttccccca cataatagta
5521 gatgttaggc aattggaacc tgtgttgatt cccttacccg atgttaggaa taatttctac
5581 cattataatc aatcaaatga ccccaccatc aaattgatag caatgttgta cacaccactt
5641 agggctaata atgccgggga cgatgtcttc acagtttctt gtcgagttct cacgagacca
5701 tcccccgatt ttgatttcat atttttggtg ccacctacag tcgaatcaag aactaaacca
5761 ttctctgtcc cagttttaac tgttgaggag atgaccaatt caaggttccc cattcctttg
5821 gaaaagttgt tcacgggccc cagtagtgcc tttgttgttc aaccacaaaa cggcaggtgc
5881 acgactgatg gcgtgctcct aggtactacc caactgtctc ccgtcaacat ctgcaccttc
5941 agaggggatg tcacccatat tccaggcagt cgtaactaca caatgaattt ggcctcccaa
6001 aattggaaca gttacgatcc aacagaagaa atcccagccc ctctaggaac tccagatttc
6061 gtggggaaga ttcaaggtgt gctcacccaa accacaagga caaatggctc gacccgcggc
6121 cacaaagcta cagtgtacac tgggagcgcc gacttttctc caaaactggg tagagttcaa
6181 tttgccactg acacagacaa tgattttgaa actaaccaaa acacaaagtt caccccagtc
6241 ggtgttatcc aggatggtag taccaccccc cgaaatgaac cccaacaatg ggtgctccca
6301 agttactcag gcagaaacat tcacaatgtg cacctggccc ccgctgtagc ccccactttc
6361 ccgggcgagc agctcctctt cttcagatct actatgcccg gatgcagcgg gtaccccaac
6421 atggacttgg actgtctgct cccccaggaa tgggtgcagt atttctacca ggaggcagcc
6481 ccagcacaat ctgatgtggc tctgctaaga tttgtgaatc cggacacagg tagggttttg
6541 tttgagtgta agcttcataa atcaggctat gttacagtgg ctcacactgg ccaacatgat
6601 ttggttatcc cccccaatgg ttattttaga tttgattcct gggtcaacca gttctacaca
6661 cttgccccca tgggaaatgg gacggggcgc agacgtgcat tataatggct ggagctttct
6721 ttgctggatt ggcatctgac gtccttggct ctggacttgg ttccctaatc aatgctgggg
6781 ctggggccat caaccaaaaa gttgaatttg aaaataacag aaaattgcaa caagcttcct
6841 tccaatttag tagcaatcta caacaggctt cctttcaaca tgacaaagaa atgctccaag
6901 cacaaattga ggccaccaaa aagttgcaac aggaaatgat gagagttaaa caggcaatgc
6961 tcctagaggg tggattctct gagacagatg cagcccgtgg ggcaatcaac gcccccatga
7021 caaaaacttt ggactggagc gggacaaggt actgggctcc cgatgctagg actacaacat
7081 ataatgcagg ccgcttttcc accccccaac cctcgggggc actaccagga agagctaatc
7141 ttagggctac tgtccccgcc cggggttcct ccagcacgtc ctctaactct tctattgcta
7201 cttctgtgta ttcaaatcaa accacctcaa cgagacttgg ttctacagct ggttctggta
7261 ccagtgtctc gagcctcccg tcaactgcaa ggactaggag ctgggttgag gatcaaaata
7321 ggaatttgtc acctttcatg aggggggccc ataacatctc gtttgtcacc ccaccatcta
7381 gcagatcctc tagccaaggc acagtctcaa ccgtgcccaa agaagttttg gactcctgga
7441 ctggcgcttt caacacgcgc aggcagcctc tcttcgctca cattcgcaag cgaggggagt
7501 cacgggtgta a
//