Typing tool
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Typing tool
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Complete norovirus genomes
| KC409311 | GII.4 New Orleans | |
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| GII.P4 Hunter |
ORF1: 1..5100
ORF2: 5081..6703
ORF3: 6703..7509
LOCUS KC409311 7512 bp ss-RNA linear VRL 13-MAR-2013
DEFINITION Norovirus Hu/GII/30199/2009/VNM, complete genome.
ACCESSION KC409311
VERSION KC409311.1
DBLINK BioProject: PRJNA70471
KEYWORDS .
SOURCE Norovirus Hu/GII/30199/2009/VNM
ORGANISM Norovirus Hu/GII/30199/2009/VNM
Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes;
Picornavirales; Caliciviridae; Norovirus; Norwalk virus.
REFERENCE 1 (bases 1 to 7512)
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 :: 671.8x
Sequencing Technology :: Illumina; 454
##Genome-Assembly-Data-END##
FEATURES Location/Qualifiers
source 1..7512
/organism="Norovirus Hu/GII/30199/2009/VNM"
/mol_type="genomic RNA"
/strain="Hu/GII/30199/2009/VNM"
/host="Homo sapiens; sex: F"
/db_xref="taxon:1291882"
/country="Viet Nam: Ho Chi Minh City"
/collection_date="25-Sep-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 1..5100
/gene="POL"
CDS 1..5100
/gene="POL"
/note="genome polyprotein"
/codon_start=1
/product="nonstructural polyprotein"
/protein_id="AGE89651.1"
/translation="MKMASNDASAAAVANSNNDTAKSSSDGVLSSMAVTFKRALGARP
KQPPPREIPQRPPRPPTPELIKNIPPPPPNGEDDIVVSYNVKDGVSGLPDLSTVRQPE
ESNTAFSVPPLNQRENRDAKEPLTGTILEMWDGEIYHYGLYVERGLVLGVHKPPAAIS
LARVELTPLSLYWRPVYTPQYLISPDALKKLHGETFPYTAFDNNCYAFCCWVLDLNDS
WLSRRMIQRTTGFFRPYQDWNRKPLPTMDDSKLKKVANIFLCALSSLFTRPIKDLIGK
LRPLNILNILASCDWTFAGIVESLILLAELFGVFWTPPDVSAMIAPLLGDYELQGPED
LAVELVPVVMGGIGLVLGFTKEKIGKMLSSAASTLRACKDLGAYGLEILKLVMKWFFP
KKEEANELAIVRSIEDAVLDLEAIENNHMTTLLKDKDSLATYMRTLDLEEEKARKLST
KSASPDIVGTINALLARIAAARSLVHRAKEELSSRPRPVVLMISGRPGIGKTHLAREV
AKRIAASLTGDQRVGLVPRNGVDHWDAYKGERVVLWDDYGMSNPIHDALRLQELADTC
PLTLNCDRIENKGKVFDSDVIIITTNLANPAPLDYVNFEACSRRIDFLVYAEAPEVEK
AKRDFPGQPDMWKNAFSSDFSHIKLTLAPQGGFDKNGNTPHGKGVMKTLTTGSLIARA
SGLLHERLDEFELQGPTLTTFNFDRNKVLAFRQLAAENKYGLMDTMKVGRQLKDVRTM
PELKQALKNTSIKKCQIVYSGSTYTLESDGKGNVKVDRVQSTSVQTNNELAGALHHLR
CARIRYYVRCVQEALYSIIQIAGAAFVTTRIVKRMNIQNLWSKPQVENTEETTSKDGC
PKPKDDEEFVISSDDIKTEGKKGKNKTGRGKKHTAFSSKGLSDEEYDEYKRIREERNG
KYSIEEYLQDRDKYYEEVAIARATEEDFCEEEEAKIRQRIFRPTRKQRKEERASLGLV
TGSEIRKRNPDDFKPKGKLWADDDRSVDYNEKLSFEAPPSIWSRIVSFGSGWGFWVSP
SLFITSTHVIPQGAKEFFGVPIKQIQVHKSGEFCRLRFPKPIRTDVTGMILEEGAPEG
TVVTLLIKRPTGELMPLAARMGTHATMKIQGRTVGGQMGMLLTGSNAKSMDLGTTPGD
CGCPYIYKRGNDYVVIGVHTAAARGGNTVICATQGSEGEATLEGGDNKGTYCGAPILG
PGSAPKLSTKTKFWRSSTAPLPPGTYEPAYLGGKDPRVKGGPSLQQVMRDQLKPFTEP
RGKPPKPSVLEAAKKTIINVLEQTIDPPEKWSFAQACASLDKTTSSGHPHHMRKNDCW
NGESFTDKLADQASKANLMFEEGKNMTPVYTAALKDELVKTDKIYGKIKKRLLWGSDL
ATMIRCARAFGGLMDELKAHCVTLPIRVGMNMNEDGPIIFERHSRYTYHYDADYSRWD
STQQRAVLAAALEIMVKFSPEPHLAQVVAEDLLSPSVVDVGDFTISINEGLPSGVPCT
SQWNSIAHWLLTLCALSEVTNLSPDTIQANSLFSFYGDDEIVSTDIKLDPEKLTAKLR
EYGLKPTRPDKTEGPLVISEDLNGLTFLRRTVTRDPAGWFGKLEQSSILRQMYWTRGS
NHEDPSETMIPHSQRPIQLMSLLGEAALHGPAFYSKISKLVIAELKEGGMDFYVPRQE
PMFRWMRFSDLSTWEGDRNLAPSFVNEDGVE"
mat_peptide 1..990
/gene="POL"
/product="protein p48"
mat_peptide 991..2088
/gene="POL"
/product="NTPase"
/note="p41"
mat_peptide 2089..2625
/gene="POL"
/product="protein p22"
mat_peptide 2626..3024
/gene="POL"
/product="viral genome-linked protein"
/note="VPg"
mat_peptide 3025..3567
/gene="POL"
/product="3C-like protease"
/note="3CLpro; calcivirin"
mat_peptide 3568..5097
/gene="POL"
/product="RNA-directed RNA polymerase"
gene 5081..6703
/gene="VP1"
CDS 5081..6703
/gene="VP1"
/codon_start=1
/product="capsid protein VP1"
/protein_id="AGE89652.1"
/translation="MKMASSDANPSDGSTANLVPEVNNEVMALEPVVGAAIAAPVAGQ
QNVIDPWIRNNFVQAPGGEFTVSPRNAPGEILWSAPLGPDLNPYLSHLARMYNGYAGG
FEVQVVLAGNAFTAGKIIFAAVPPNFPTEGLSPSQVTMFPHMIVDVRQLEPVLIPLPD
VRNNFYHYNQSNDPTIKLIAMLYTPLRANNAGDDVFTVSCRVLTRPSPDFDFIFLVPP
TVESRTKPFSVPILTVEEMTNSRFPIPLEKLFTGPSSAFVVQPQNGRCTTDGVLLGTT
QLSPVNICTFRGDVTHITGSHNYTMNLATQNWNSYDPTEEIPAPLGTPDFVGKIQGVL
TQTTRADGSTRGHKATVYTGSADFAPKLGRVQFATDTNNDLGANQNTKFTPVGVIQDG
GTAHRNEPQQWVLPSYSGRNSHNVHLAPAVAPTFPGEQLLFFRSTMPGCSGYPNMDLD
CLLPQEWVQYFYQEAAPAQSDVALLRFVNPDTGRVLFECKLHKSGYVTVAHTGQHDLV
IPPNGYFRFDSWVNQFYTLAPMGNGTGRRRAL"
gene 6703..7509
/gene="VP2"
CDS 6703..7509
/gene="VP2"
/note="minor capsid protein"
/codon_start=1
/product="capsid protein VP2"
/protein_id="AGE89653.1"
/translation="MAGAFFAGLASDVLGSGLGSLINAGAGAINQKVEFENNRKLQQA
SFQFSSNLQQASFQHDKEMLQAQIEATKKLQQEMMRVKQAMLLEGGFSETDAARGAIN
APMTKALDWSGTRYWAPDARTTTYNAGHFSTPQSSGALPGRANLRAAVPARGSSSTSS
NSSTATSVYSNQTISTRLGSTAGSGTSVSSLPSTARTRSWVEDQNRNLSPFMRGAHNI
SFVTPPSSRPSSQGTVSTVPKEVLDSWTGAFNTRRQPLFAHIRKRGESRA"
ORIGIN
1 atgaagatgg cgtctaacga cgcttccgct gccgctgttg ctaacagcaa caacgacacc
61 gcaaaatctt caagtgacgg agtgctttct agcatggctg tcactttcaa acgagccctc
121 ggggcgcggc ctaaacagcc tcccccgagg gaaataccac aaagaccccc acgaccaccc
181 actccagaac tgattaaaaa catcccccct cccccaccca acggagagga tgacatagtg
241 gtctcttata atgttaaaga tggtgtctct ggtttgcctg atctttccac cgtcaggcaa
301 ccagaagaat ccaacacggc cttcagtgtc cctccactca atcagaggga gaatagagat
361 gctaaggagc cactgactgg aacaattctg gaaatgtggg atggagaaat ctaccattat
421 ggcctgtatg tagagcgagg tcttgttcta ggtgtgcaca aaccaccagc tgccatcagc
481 ctcgctaggg tcgaactaac accactttcc ttgtactgga gacctgtgta tactccccag
541 tacctcatct ctccagacgc cctcaagaaa ctacacggag agacgttccc ctacacagcc
601 tttgacaaca actgctatgc cttttgttgt tgggtcctgg acctaaacga ctcgtggctg
661 agtaggagaa tgatccagag aacaactggc ttcttcagac cctaccaaga ttggaatagg
721 aaacccctcc ccactatgga tgactccaag ttaaaaaagg tagctaacat attcctgtgt
781 gcactgtctt cgctattcac caggcctata aaagatttaa tagggaagct aaggcccctt
841 aacatcctca atatcttggc ctcatgtgat tggacttttg caggcatagt ggagtccttg
901 atactcttgg cagaactctt cggagttttc tggacacccc cagatgtgtc tgcgatgatt
961 gcccccttac tcggtgatta cgagctacaa ggacctgagg accttgcagt agagctcgtc
1021 cctgtagtga tggggggaat tggtctggtg ctaggattca ccaaagagaa gattgggaaa
1081 atgttgtcat ctgctgcatc caccttgaga gcttgtaaag atcttggtgc gtatgggcta
1141 gagatcctga agttggtcat gaagtggttc ttcccgaaga aagaagaagc aaatgaactg
1201 gctatagtga gatccatcga ggatgcagtc ctggatctcg aggcaattga aaacaaccat
1261 atgaccacct tgctcaaaga caaagacagt ctggcaacct acatgagaac ccttgacctt
1321 gaggaggaga aagccaggaa actctcaacc aagtctgctt cacctgacat tgtgggcaca
1381 atcaacgccc ttctagcgag aatcgctgct gcacgttctc tggtgcatcg agcgaaggag
1441 gaactttcta gcagaccaag accggtggtg ttgatgatat caggcagacc aggaataggg
1501 aagacccacc ttgctaggga agtggccaag agaatcgcag cctcccttac aggagaccag
1561 cgtgtaggcc tcgtcccacg caatggcgtc gaccattggg atgcgtacaa gggggagagg
1621 gtcgttctgt gggacgacta tggaatgagc aatcccatcc acgatgccct cagattgcaa
1681 gaactcgctg acacttgtcc cctcacccta aactgtgaca ggattgagaa caaaggaaag
1741 gtctttgaca gcgatgtcat cattatcacc actaatctgg ctaacccagc accactggac
1801 tacgtcaact ttgaagcatg ctcgaggcgc atcgacttcc tcgtgtatgc agaagcccct
1861 gaggtcgaaa aggcgaagcg tgacttccca ggccaacccg acatgtggaa gaacgccttc
1921 agttctgatt tctcacacat aaagctaaca ttggctccac agggtggttt cgacaagaac
1981 gggaacaccc cacacgggaa gggcgtcatg aagactctca ccaccggctc ccttattgcc
2041 cgggcatcag ggctacttca tgagaggcta gatgaatttg aactacaggg cccaactctc
2101 accaccttca actttgatcg caataaagtg cttgccttta gacaacttgc tgctgaaaac
2161 aaatatgggt tgatggatac aatgaaagtt gggaggcagc tcaaggatgt cagaacaatg
2221 ccagagctca agcaagcact caagaatact tcgatcaaga agtgccagat agtgtatagt
2281 ggcagcacct acacacttga gtctgatggc aagggcaatg tgaaagttga cagagttcaa
2341 agcacctccg tgcagaccaa caatgagctg gctggcgccc tacaccatct aaggtgcgcc
2401 agaataagat actatgtcag gtgtgtccag gaggccctgt attccattat ccagattgct
2461 ggggctgcgt ttgtcaccac gcgcatcgtc aagcgcatga acatacaaaa cttatggtct
2521 aagccacaag tggaaaacac agaggagact accagcaagg acgggtgtcc aaaacccaaa
2581 gatgatgaag agttcgtcat ttcatccgac gacatcaaaa ctgagggcaa gaaagggaaa
2641 aacaagactg gtcgcggcaa gaaacacaca gccttctcaa gcaaaggtct cagtgatgaa
2701 gagtacgatg aatacaagag gattagagaa gaaaggaacg gtaagtactc tatagaagag
2761 taccttcagg acagggacaa atactatgag gaggtggcca ttgccagggc gactgaggaa
2821 gacttctgtg aagaggagga ggccaagatc cggcaaagga tcttcaggcc aacaaggaaa
2881 caacgcaagg aggaaagagc ttctctcggt ttagttacag gttctgaaat taggaaaaga
2941 aatccagatg atttcaaacc caaggggaaa ctgtgggctg acgatgacag aagtgtggac
3001 tacaatgaga aactcagttt tgaagcccca ccaagcatct ggtcgagaat agtcagcttt
3061 ggttcaggtt gggggttctg ggtctccccc agtttgttca taacatcaac ccatgtcata
3121 ccccagggag caaaggagtt ctttggagtc cccatcaaac aaattcaggt acacaagtca
3181 ggcgaattct gtcgcttgag attcccaaaa ccaatcagga ctgatgtgac gggcatgatc
3241 ttagaagaag gtgcacccga gggcaccgtg gtcacactac tcatcaaaag gcccactgga
3301 gagctcatgc ccttagcagc taggatgggg acccatgcaa ccatgaaaat ccaaggacgc
3361 actgttggag gccagatggg catgcttctg acaggatcca acgccaaaag catggatctg
3421 ggtactacac caggtgattg tggctgtccc tacatctaca agagaggaaa tgactatgtg
3481 gtcattggag tccacacggc tgccgctcgc gggggcaaca ctgtcatatg tgccacccag
3541 gggagtgagg gagaggctac acttgaaggt ggtgacaata aagggacata ctgtggtgca
3601 ccaatcctag gcccagggag tgccccaaaa cttagcacca agaccaaatt ctggagatcg
3661 tccacagcac cactcccacc tggcacttat gaaccagcct atcttggtgg caaggacccc
3721 agagtcaagg gtggcccttc actgcagcag gtcatgaggg accagttgaa gccattcaca
3781 gagcccaggg gcaagccacc aaagccaagt gtgttggaag ctgctaagaa aaccatcatc
3841 aatgtccttg aacaaacaat tgatccacct gagaaatggt cgttcgcaca agcttgcgcg
3901 tcccttgaca agaccacctc cagtggccat ccgcatcaca tgcggaaaaa cgactgctgg
3961 aacggggagt ccttcacaga caagctggca gaccaggctt ccaaggctaa cctgatgttt
4021 gaagaaggga agaacatgac gccagtctat acagctgcgc ttaaggacga attagttaaa
4081 actgacaaaa tttatggcaa gatcaagaag aggcttctct ggggttcgga tttggcgacc
4141 atgatccggt gtgctcgagc attcggaggt ctaatggacg aactcaaagc gcactgtgtc
4201 acacttccca ttagagttgg tatgaatatg aatgaggatg gccccatcat cttcgagagg
4261 cactctaggt acacatacca ctatgatgct gattactctc gatgggattc aacacaacag
4321 agagccgtgc tggcagcagc tctagaaatc atggttaagt tctccccaga accacatttg
4381 gcccaggtag tcgcagaaga ccttctttct cctagcgtgg tggacgtggg tgacttcaca
4441 atatcaatta acgagggtct tccctctggg gtgccctgca cctcccaatg gaactccatc
4501 gcccactggc tcctcaccct ctgtgcgctc tctgaagtta caaatttgtc tcctgacacc
4561 atacaagcta attccctctt ctctttttat ggtgatgatg aaattgttag cacagacata
4621 aaattggacc cagaaaagtt gacagcaaag ctcagggaat atgggttaaa gccaacccgc
4681 cccgacaaaa ctgaaggacc ccttgtcatc tctgaagact tgaatggcct gactttcctg
4741 cggagaactg taacccgcga cccagctggt tggtttggga aactggagca gagttcaata
4801 cttaggcaaa tgtactggac taggggttcc aaccatgaag acccatctga aacaatgatt
4861 ccacactccc aaagacccat acaactgatg tccctactgg gggaggccgc actccacggc
4921 ccagcattct acagcaaaat cagcaagtta gtcattgcag agctaaaaga aggtggcatg
4981 gatttttacg tgcccagaca agagccgatg ttcagatgga tgagattctc agatctgagc
5041 acgtgggagg gcgatcgcaa tctggctccc agttttgtga atgaagatgg cgtcgagtga
5101 cgccaaccca tctgatgggt ccacagccaa cctcgtccca gaggtcaaca atgaggttat
5161 ggctttggag cccgttgttg gtgccgccat tgcggcacct gtagcgggcc aacaaaatgt
5221 aattgacccc tggattagaa acaattttgt acaagcccct ggtggagagt tcacagtatc
5281 ccctagaaac gctccaggtg aaatactatg gagcgcgccc ttaggccctg atttgaaccc
5341 ctacctttcc catttggcca gaatgtacaa tggttatgca ggtggttttg aagtgcaggt
5401 agtcctcgcg gggaacgcgt tcaccgccgg aaaaattata tttgcagcag tcccaccaaa
5461 tttcccaact gaaggcttga gccccagcca ggtcaccatg ttcccccaca tgatagtaga
5521 tgttaggcaa ttggaacctg tgttgatccc cctacccgat gttaggaata atttctatca
5581 ctataaccaa tcaaatgacc ccaccatcaa attgatagca atgttgtata caccacttag
5641 ggccaataat gctggggacg atgtcttcac agtctcttgt cgggttctca cgaggccatc
5701 ccccgatttt gatttcatat ttttagtacc acccacagtt gagtcaagaa ctaaaccatt
5761 ctctgtccca attttaactg ttgaggagat gaccaattca agattcccca ttcctttgga
5821 aaagctgttc acgggtccca gcagtgcctt tgttgttcaa ccacaaaacg gcaggtgcac
5881 gactgatggc gtgctcctag gtaccaccca actgtctcct gtcaacatct gcactttcag
5941 aggggatgtc acccatatta caggtagtca taactacaca atgaatttgg ctactcaaaa
6001 ttggaacagt tatgacccaa cagaagaaat cccagcccct ctgggaactc cagatttcgt
6061 ggggaagatt caaggtgtgc tcacccaaac cacaagggca gatggctcga cccgcggcca
6121 caaagccaca gtgtacactg ggagcgccga ttttgctcca aaactgggta gagttcaatt
6181 tgccactgac acaaacaatg atcttggtgc caaccaaaac acaaagttca ccccagtcgg
6241 tgtcatccag gatggtggca ctgcccaccg aaatgaaccc caacaatggg tgctcccaag
6301 ttactcaggc agaaatagtc ataatgtgca cctggccccc gctgtagccc ccacttttcc
6361 gggtgagcaa cttctcttct ttagatccac tatgcccgga tgcagcgggt accccaacat
6421 ggatttggac tgtctgctcc cccaggaatg ggtgcagtat ttctatcaag aggcagcccc
6481 agcacaatct gatgtggctc tgctaagatt tgtgaatcca gacacaggta gggttttgtt
6541 tgagtgtaag cttcataaat caggctatgt tactgtggct cacactggcc aacatgattt
6601 ggttatcccc cccaatggtt attttagatt tgattcctgg gtcaaccagt tctacacact
6661 tgcccccatg ggaaatggaa cggggcgtag acgtgcgtta taatggctgg agctttcttt
6721 gctggattgg catctgacgt cctgggctcc ggacttggtt ctctgatcaa tgccggggct
6781 ggggccatca accaaaaagt tgaatttgaa aataacagaa aattgcaaca agcttccttc
6841 caatttagca gcaatctaca acaggcttcc tttcagcatg ataaagagat gctccaagca
6901 caaattgagg ccaccaaaaa gttgcaacag gaaatgatga gagttaaaca ggcaatgctc
6961 ctagagggtg gattctctga gacagatgca gcccgtgggg caattaacgc ccccatgaca
7021 aaggctttgg actggagtgg gacaaggtac tgggctcccg atgctaggac tacaacatac
7081 aatgcaggcc acttttccac ccctcaatcc tcgggggcac tgccagggag agctaacctt
7141 agggctgctg tccctgctcg aggctcctct agcacatctt ctaactcttc tactgctact
7201 tctgtgtact caaatcaaac tatttcaacg agacttggtt ctacagctgg ttctggtacc
7261 agtgtctcga gcctcccgtc aactgcaagg actaggagct gggttgagga tcaaaatagg
7321 aatttgtcac ctttcatgag gggggcccac aacatatcgt ttgtcacccc accatctagc
7381 agaccctcta gccaaggcac agtctcaacc gtgcccaaag aagttttgga ctcctggact
7441 ggcgctttca atacgcgcag gcagcctctc ttcgctcaca ttcgtaaacg aggggagtca
7501 cgggcgtaat gt
//