Typing tool
|
|
|
|
|
|
Typing tool
|
Complete norovirus genomes
| MW305723 | GII.4 Sydney | |
|
|---|---|---|---|
| GII.P16 |
ORF1: 1..5069
ORF2: 5050..6672
ORF3: 6672..7478
LOCUS MW305723 7520 bp RNA linear VRL 06-JUL-2021
DEFINITION Norovirus GII isolate CMH-N010-18 nonstructural polyprotein (ORF1)
gene, partial cds; and VP1 (ORF2) and VP2 (ORF3) genes, complete
cds.
ACCESSION MW305723
VERSION MW305723.1
KEYWORDS .
SOURCE Norovirus GII
ORGANISM Norovirus GII
Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes;
Picornavirales; Caliciviridae; Norovirus; Norwalk virus.
REFERENCE 1 (bases 1 to 7520)
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JOURNAL Unpublished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 7520)
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..7520
/organism="Norovirus GII"
/mol_type="genomic RNA"
/isolate="CMH-N010-18"
/isolation_source="feces"
/host="Homo sapiens"
/db_xref="taxon:122929"
/country="Thailand"
/collection_date="18-Jan-2018"
/note="genotype: GII.4[GII.P16]"
gene <1..5069
/gene="ORF1"
CDS <1..5069
/gene="ORF1"
/codon_start=3
/product="nonstructural polyprotein"
/protein_id="QPJ59505.1"
/translation="VACNNNNDKEKPSGEGLFTNMSSTLKKALGARPKQPAPRGEPQK
PPRPPTPELVKRIPPPPPNGEEEEEPVIRYEVKSGISGLPELTTVPQPDVANTAFSVP
PLSLRENRDAKEPLTGAILEMWDGEIYHYGLYVEKGLVLGVHKPPAAVSMARVELTPL
SLYWRVVYTPQYLISPETLRRLNGEAFPYTAFDNNCYAFCCWVLDLNDSWLSRRMVQR
TTGFFRPYQEWNRKPLPTMDDSKIKKVANIFLCSLSTLFTRPIKDLIGKIKPLNILNI
LATCDWTFAGIVESLILLAELFGVFWTPPDVSAMIAPLLGDYELQGPEDLAVELVPVV
MGGIGLVLGFTKEKIGKMLSSAASTLRACKDLGAYGLEILKLVMKWFFPKKEEANELA
MVRAIEDAVLDLEAIENNHMTTLLKDKDSLATYMKTLDMEEEKARRLSTKSASPDIVG
TINALLARIAAARSLVHRAKEELSSRIRPVVVMISGKPGIGKTHLAREVARKVASTLT
GDQRVGLIPRNGVDHWDAYKGERVVLWDDYGMSNPIHDALRIQELADTCPLTLNCDRI
ENKGKVFDSEVIIITTNLANPAPLDYVNFEACSRRIDFLVYAEAPEVEKAKRDFPGQP
DMWKDAFKPDFSHIKLQLAPQGGFDKNGNTPHGKGVMKTLTTGSLIARASGLLHERMD
EFELQGPTITTFNFDRNRITAFRQLAAENKYGLVDTMKVGNQLKGVKTMEELKQAIRN
VTIKRCRIIYGGSTYDLESDGKGKVLVEKVKNTSVQTNNELAGALHHLKHARIRYYVK
CVQEAVYSIIQIAGAAFVTTRIARRMNIQELWSKPQLDQNESEAKEEAPKSEDDEFII
SSKDIKEEGKKGKNKTGRGKKHTAFSSKGLSDEEYDEYKRIREERNGKYSIEEYLQDR
DRYYEELAIAKATEEDFCEEEEIKIRQRIFRPTRKQRKEERATLGLVTGSEIRKRNPD
DFKPKGKLWADDNRSVDYNEKLDFEAPPSIWSRIVSFGSGWGFWVSPSLFITSTHVIP
AGITEAFGVPIKQIQIHKSGEFCRFRFPKPIRPDVTGMILEEGAPEGTVATVLIKRPT
GELMPLAARMGTHATMKIQGRMVGGQMGMLLTGSNAKGMDLGTTPGDCGCPYIYKRGN
DYIVIGVHTAAARGGNTVICATQGSEGEATLEGGDDKGTYCGAPILGPGGAPKLSTKT
KFWRSSNTPLPPGTYEPAYLGGRDPRVKGGPSLQQVMRDQLKPFTEPRGKPPRPSVLE
AAKQTIINVLEQTLDPPQKWTYAQACASLDKTTSSGHPHHVRKNEFWNGDTFTGKLAD
QASKANLMFEEGKHMTPVYTAALKDELVKTEKIYGKIKKRLLWGSDLSTMIRCARSFG
GLMDEMKAHCISLPVRVGMNMNEDGPIIFEKHSRYKYHYDADYSRWDSTQQRAVLAAA
LEIMVRFSAEPQLAQIVAEDLLAPSVVDVGDFKITINEGLPSGVPCTSQWNSIAHWLL
TLCALSEVTKLSPDIIQANSMFSFYGDDEIVSTDIKLDPEQLTAKLKEYGLKPTRPDK
TEGPLIISEDLNGLTFLRRTVARDPAGWFGKLDQSSILRQMYWTRGPNHEDPNETMIP
HSQRPIQLMALLGEASLHGPSFYSRISKLVITELKEGGMDFYVPRQEPMFRWMRFSDL
STWEGDRNLAPNFVNEDGVE"
mat_peptide <1..965
/gene="ORF1"
/product="p48"
mat_peptide 966..2063
/gene="ORF1"
/product="NTPase"
mat_peptide 2064..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="QPJ59506.1"
/translation="MKMASSDANPSDGSAANLVPEVNNEVMALEPVVGAAIAAPVAGQ
QNVIDPWIRNNFVQAPGGEFTVSPRNAPGEILWSAPLGPDLNPYLSHLARMYNGYAGG
FEVQVILAGNAFTAGKIIFAAVPPNFPTEGLSPSQVTMFPHIIVDVRQLEPVLIPLPD
VRNNFYHYNQSNDSTIKLIAMLYTPLRANNAGDDVFTVSCRVLTRPSPDFDFIFLVPP
TVESRTKPFSVPVLTVEEMTNSRFPIPLEKLFTGPSSAFVVQPQNGRCTTDGVLLGTT
QLSPVNICTFRGDVTHITGSRNYTMNLASQNWNNYDPTEEIPAPLGTPDFVGKIQGML
TQTTRTDGSTRGHKATVYTGSADFAPKLGRVQFETDTDHDFEANQNTKFTPVGVIQDG
STTHRNEPQQWVLPSYSGRNTHNVHLAPAVAPTFPGEQLLFFRSTMPGCSGYPNMDLD
CLLPQEWVQYFYQEAAPAQSDVALLRFVNPDTGRVLFECKLHKSGYVTVAHTGQHDLV
IPPNGYFRFDSWVNQFYTLAPMGNGAGRRRVV"
gene 6672..7478
/gene="ORF3"
CDS 6672..7478
/gene="ORF3"
/note="minor structural protein; small basic protein"
/codon_start=1
/product="VP2"
/protein_id="QPJ59507.1"
/translation="MAGAFFAGLASDVLGSGLGSLISAGAGAINQKVEFENNRKLQQA
SFQFSSNLQQASFQHDKEMLQAQIEATKKLQQEMMKVKQAMLLEGGFSETDAARGAIN
APMTKALDWSGTRYWAPDARITTYNAGHFSTPQPSRVLPGRANLGDAAPARGPSNKSS
NSSTVTSVYSNQTISTRLGPTAGSGTSVSSLPSTARTRSWVEDQNRNLSPFMRGAHNI
SFVTPPSSRSSSQGTVSTVPKEILDSWTGAFNTRRQPLFAHIRKRGESRV"
ORIGIN
1 ccgttgcttg taacaacaac aacgacaagg aaaaaccttc aggtgaaggc ttattcacaa
61 atatgtcttc caccttaaag aaagccctcg gggctaggcc caaacagcct gccccgagag
121 gcgaaccaca aaagccccca agaccaccaa ctcccgagtt ggtcaagagg ataccccctc
181 ctccacctaa tggcgaagaa gaagaagaac cagtcattag gtatgaggtt aagagtggga
241 tctctggcct gcccgagctc acaacagtcc cccaaccgga cgtggccaac acagcattca
301 gtgttccacc actgagcttg agagaaaaca gggatgccaa ggaaccgctt acaggggcaa
361 tattagagat gtgggacgga gagatatacc actatggcct gtacgtggag aaaggcttag
421 tgttgggtgt gcacaaacca cctgcagccg taagcatggc aagagtggag ctgacgccgc
481 tgtcattgta ctggcgtgtg gtgtacactc cccaatacct catctcccct gaaactctca
541 ggaggctcaa cggagaggcg ttcccttaca ccgccttcga caacaactgc tatgcctttt
601 gctgctgggt gttagacctc aatgactcat ggcttagcag gaggatggtg caaagaacaa
661 cgggcttctt cagaccttac caagagtgga acagaaaacc cctgcccacc atggatgact
721 ccaaaataaa gaaggtagca aatatattcc tatgttcatt gtccacatta ttcaccagac
781 ccataaaaga cctcatagga aaaattaaac cactaaacat attgaacatc ctggcaacgt
841 gtgactggac gtttgccgga atagtggagt ctctgatact acttgctgaa ctcttcggag
901 ttttctggac acccccagat gtgtctgcta tgatcgctcc cttactcggg gactacgagt
961 tgcaagggcc agaagacctc gccgttgaac tcgtacctgt ggtaatggga gggattggtt
1021 tggtgttggg attcaccaaa gagaaaattg gcaaaatgtt gtcttcagca gcatcaacac
1081 tcagggcttg caaagatctt ggtgcctatg gtttagagat actcaaattg gtcatgaagt
1141 ggttcttccc aaagaaagag gaggccaatg agctagccat ggtgagggcc atagaggatg
1201 ccgtactaga tcttgaggca atagaaaata accacatgac aaccctgttg aaagacaaag
1261 acagcttagc aacatacatg aaaacactgg acatggagga ggagaaagcc agaaggttgt
1321 ccacaaaatc tgcatcccct gacatagttg ggacaatcaa cgccctgctg gctcgaatag
1381 cggcagccag gtcattagtc cacagggcca aggaagagct atctagcagg ataagaccag
1441 tagttgttat gatatctggc aaaccaggaa taggcaaaac tcatctggcc agggaggtgg
1501 caagaaaggt agcatccact ctcacagggg atcaaagagt cggactcata ccaagaaacg
1561 gtgtggacca ttgggatgca tacaaaggtg agagagtcgt gctgtgggac gactatggca
1621 tgagtaaccc tattcatgat gctcttcgca tacaagaatt ggctgatacg tgtcccctta
1681 ccttaaattg tgacagaatt gaaaataagg gaaaagtgtt tgacagtgaa gtcataataa
1741 tcacaacaaa ccttgccaac ccagccccac ttgattatgt caactttgag gcctgttcca
1801 ggagaattga tttcctggtg tacgctgagg caccagaagt agaaaaggca aaacgggatt
1861 ttcctggtca accagatatg tggaaggacg ccttcaagcc ggacttttca catatcaagc
1921 tacagcttgc acctcagggc ggctttgaca agaatggcaa caccccacat ggaaaagggg
1981 tgatgaagac cctcactacc ggttctctga ttgcccgtgc gtcaggccta ctgcatgaga
2041 ggatggatga atttgaactc caaggtccca caatcaccac cttcaatttc gaccggaaca
2101 gaatcacagc attcagacaa ttggctgcag aaaacaagta tggattggtg gacaccatga
2161 aagttggcaa tcaactaaaa ggagtgaaaa ccatggaaga actcaaacaa gcaatcagga
2221 atgtgaccat caagaggtgc cggatcatct acggtggttc cacgtatgac cttgaatctg
2281 atggcaaggg caaagttttg gtggaaaagg tcaagaacac ctctgtacag accaacaacg
2341 agttagccgg ggccctgcac cacctcaaac acgcccgaat caggtactat gtcaaatgtg
2401 tgcaagaagc agtctactcc atcatacaaa ttgccggcgc tgcgtttgtc accacgcgca
2461 ttgcacgccg catgaacata caagaactct ggtcgaagcc acaattagat caaaatgaat
2521 cagaggctaa ggaagaggcc cccaagtcag aggatgacga gtttatcata tcttctaagg
2581 acatcaagga ggaaggaaag aagggcaaaa acaaaactgg ccgtggcaag aaacacactg
2641 cattctccag caagggcttg agcgatgagg agtatgacga gtacaagagg ataagagaag
2701 agagaaatgg gaagtactct atagaggagt atctacaaga cagagacagg tactatgagg
2761 agctcgccat tgccaaggcc acggaagaag acttctgtga agaggaggag atcaaaatcc
2821 gtcagagaat tttccgtccc accaggaaac aaagaaagga agagagggcc acattagggc
2881 tggtaacagg ttcagaaatc agaaaaagaa accccgatga cttcaaaccc aaagggaagc
2941 tgtgggccga tgacaacaga agtgttgact acaatgagaa actggatttt gaggcccccc
3001 caagcatatg gtctaggatt gtgagctttg gttctggctg gggcttctgg gtatcaccaa
3061 gcctgttcat aacatcaact catgtaatcc ccgcaggcat aacagaagca tttggagtcc
3121 ccatcaagca aattcagatc cacaaatcag gtgaattttg ccgattcaga ttcccaaaac
3181 caattagacc agatgtgaca gggatgatct tggaagaagg tgcgcctgaa ggcaccgtgg
3241 caactgtgct catcaaacgc cctaccggag agctcatgcc tcttgcagcc agaatgggaa
3301 cacacgcaac catgaaaatt caaggccgca tggttggcgg acagatgggt atgttgctca
3361 ctggatcaaa tgctaaagga atggatctgg gaacaactcc tggtgactgt ggctgtcctt
3421 acatctataa aaggggcaat gactatatag tcatcggggt gcacactgca gcagcccgtg
3481 gtggaaacac cgtcatctgt gccacacagg gaagtgaggg tgaggcaact cttgagggtg
3541 gagatgacaa aggaacatac tgtggggcac ccattttagg ccctgggggt gcaccaaaat
3601 tgagcaccaa aaccaaattt tggaggtcat cgaacacgcc ccttccacca gggacatatg
3661 agcctgccta cctcggtggc cgtgatccgc gtgttaaggg tgggccctcc ttgcagcagg
3721 taatgagaga ccagttgaag ccattcactg aacccagggg caaacctcca agaccaagtg
3781 tattggaagc agccaaacaa accattatca atgttctcga acaaaccctg gaccctccac
3841 aaaaatggac atacgcacag gcgtgtgcct cacttgacaa aaccacctcc agcgggcatc
3901 cccatcacgt ccgaaagaat gaattctgga atggtgatac cttcactggt aagttggcag
3961 accaagcatc aaaagcaaac ctaatgtttg aggaagggaa acacatgaca ccagtgtata
4021 cagcagcact caaggacgag ctagttaaga ctgagaaaat ctatggaaag atcaagaaga
4081 gactgctctg gggctctgac ttgtccacca tgatccggtg cgctaggtca tttggtgggc
4141 tcatggacga gatgaaggca cactgcatat cactcccagt acgagttggc atgaatatga
4201 atgaagatgg cccaataata tttgagaaac attccaggta caaataccac tatgatgcag
4261 actactctcg ttgggattca acacagcaaa gggcagtact tgcagcagcc ttggaaatca
4321 tggtcagatt ctctgcagaa ccacaattgg cacaaatagt cgctgaggat ctactggccc
4381 ctagtgtagt agatgtagga gactttaaaa ttacaataaa tgaaggactc ccatctggtg
4441 tgccatgcac ttctcaatgg aactccatcg cacactggct gctaactctc tgtgccttgt
4501 ctgaagtcac caaactgtcc cctgacatta tacaagcaaa ttccatgttc tcattttacg
4561 gtgatgacga gattgtcagc accgacataa aattggatcc tgaacagtta accgccaagt
4621 tgaaggagta cggcctgaaa ccaacccgcc cagacaagac cgagggaccc ctgatcatca
4681 gtgaagattt gaacggactc actttcctcc gaaggacggt ggctcgagac ccagctggct
4741 ggtttggaaa actggatcaa agttcaattt tgaggcagat gtactggact agaggaccaa
4801 atcatgaaga ccccaatgag acaatgatac cccattctca aagacccata cagctcatgg
4861 cactgcttgg tgaagcctct cttcacgggc cctctttcta tagtagaatc agtaaattgg
4921 tcataactga actcaaagaa ggagggatgg acttttacgt gccaaggcag gaacccatgt
4981 tcaggtggat gaggttttct gacttgagca cgtgggaggg cgatcgcaat ctggctccca
5041 attttgtgaa tgaagatggc gtcgagtgac gccaacccat ctgatgggtc cgcagccaac
5101 ctcgtaccag aggtcaacaa tgaggttatg gctttggagc ccgttgttgg tgccgctatt
5161 gcggcacctg tagcgggcca acaaaatgta attgacccct ggattagaaa taattttgta
5221 caagcccctg gtggggagtt tacagtgtcc cctagaaacg ctccaggtga aatactatgg
5281 agcgcgcccc taggccctga cctaaatccc tacctatccc atttggccag aatgtacaat
5341 ggttatgcag gtggttttga agtgcaggta attctcgcgg ggaacgcgtt caccgccggg
5401 aagattatat ttgcagcagt tccaccaaac tttccaactg aaggcttaag tcctagccag
5461 gtcactatgt tcccccatat aatagtagat gttagacaat tagaacctgt gctgattccc
5521 ttacccgatg ttaggaataa cttctatcat tataatcagt caaatgattc cactattaag
5581 ttgatagcaa tgttgtatac accacttagg gctaataatg ctggagatga tgttttcaca
5641 gtttcgtgcc gagttctcac gagaccatcc cccgattttg atttcatatt tttagtgcca
5701 cccacagttg agtcaagaac taaaccattc tctgtcccag ttttaactgt tgaggagatg
5761 accaattcaa gattccccat ccctttggaa aagttgttca caggccctag cagtgccttt
5821 gttgttcagc cacaaaacgg caggtgcaca actgatggcg tgctcctagg caccacccaa
5881 ctttctcctg tcaacatctg caccttcaga ggggatgtca cccacatcac aggtagtcgc
5941 aactacacaa tgaatttggc ttctcaaaac tggaacaact atgacccaac agaagaaatc
6001 ccagcccctc taggaactcc agattttgta gggaagattc aaggcatgct cacccaaacc
6061 acaaggacag acggttcaac acgcggccac aaagctacag tgtacactgg gagcgccgac
6121 tttgctccaa aactgggtag agtccaattt gaaactgaca cagaccatga ttttgaagct
6181 aatcaaaaca caaagttcac cccagtcggt gtcatccaag atggtagcac cacccaccga
6241 aacgaacccc aacagtgggt gctcccaagt tactcaggca gaaatactca caatgtacat
6301 ttggcccccg ctgtagcccc cacctttccg ggtgagcaac ttctcttttt cagatccacc
6361 atgcccggat gcagcgggta ccccaacatg gatttggact gtctgctccc ccaggaatgg
6421 gtgcagtact tctaccaaga ggcagcccca gcacaatctg atgtggctct gctaagattt
6481 gtgaatccag acacaggtag ggttttgttt gagtgcaagc ttcataaatc aggctatgtt
6541 acagtggctc acactggcca acatgatttg gttatccccc ccaatggtta ctttaggttt
6601 gattcctggg tcaaccagtt ctacacgctt gcccccatgg gaaatggagc ggggcgtaga
6661 cgtgtagtat aatggctgga gctttctttg ctgggttggc atctgatgtc cttggctctg
6721 gacttggttc ccttatcagt gctggggctg gggccatcaa ccaaaaagtt gaatttgaaa
6781 ataacagaaa attgcaacaa gcatcctttc aatttagcag caatctgcaa caggcttcct
6841 ttcaacatga taaagagatg ctccaagcac aaattgaggc caccaaaaag ctacaacagg
6901 aaatgatgaa agttaagcag gcaatgctct tagagggtgg gttctccgag acagatgcag
6961 cccgcggggc aattaacgcc cccatgacaa aagctttgga ctggagcggg acaaggtact
7021 gggctccaga tgctaggatt acaacataca atgcaggcca cttttccacc cctcaaccat
7081 cgagggtgct gccaggaaga gctaatcttg gggatgctgc ccctgctcgg ggaccctcca
7141 ataaatcttc taactcttcc actgttacct ctgtgtactc aaatcaaact atttcaacga
7201 gacttggtcc tacagctggt tctggaacca gtgtctcgag cctcccgtca actgcaagga
7261 ctaggagctg ggttgaggat caaaatagga atttgtcacc tttcatgagg ggggcccaca
7321 acatatcatt tgtcacccca ccatctagca gatcctctag ccaaggcaca gtctcaaccg
7381 tgcctaaaga gattttggac tcctggactg gcgctttcaa cacgcgcagg cagcctctct
7441 tcgctcacat tcgtaagcga ggggagtcac gggtgtaatg tgaaaagaca aaactgatta
7501 tttttctttt tcttttcttt
//