Typing tool
|
|
|
|
|
|
Typing tool
|
Complete norovirus genomes
| MW305727 | GII.3 | |
|
|---|---|---|---|
| GII.P3 |
ORF1: 1..5077
ORF2: 5058..6704
ORF3: 6704..7468
LOCUS MW305727 7505 bp RNA linear VRL 06-JUL-2021
DEFINITION Norovirus GII isolate CHDC4090 nonstructural polyprotein (ORF1)
gene, partial cds; and VP1 (ORF2) and VP2 (ORF3) genes, complete
cds.
ACCESSION MW305727
VERSION MW305727.1
KEYWORDS .
SOURCE Norovirus GII
ORGANISM Norovirus GII
Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes;
Picornavirales; Caliciviridae; Norovirus; Norwalk virus.
REFERENCE 1 (bases 1 to 7505)
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JOURNAL Unpublished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 7505)
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..7505
/organism="Norovirus GII"
/mol_type="genomic RNA"
/isolate="CHDC4090"
/isolation_source="feces"
/host="Homo sapiens"
/db_xref="taxon:122929"
/country="USA"
/collection_date="14-Dec-1988"
/note="genotype: GII.3[GII.P3]"
gene <1..5077
/gene="ORF1"
CDS <1..5077
/gene="ORF1"
/codon_start=2
/product="nonstructural polyprotein"
/protein_id="QPJ59517.1"
/translation="VAGKNNNNDKEKSSSDSLFSNMTVTLKKALGARPKQPPPGETKQ
TQKPPRPPTPELVKRIPPPPPNGEDELKVVYRVGEGVSGLPDLTTVAQPDAQNTAYSV
PPLSQREVGEAKEPLPGSILEMWDGEIYHYGLYVEKGHILGVHKPPAAISLAKIELTP
LSLYWRVVYTPQYLIAPDTLKNLSGESFPYTAFDNNCYAFCCWVLDLNDSWLSRRMIQ
RTTGFFRPYQDWNRKPLPTMDEPKIKKAANAVLCALSSLFTRPIKDIIGKLKPMNILN
ILATCDWTFAGIVESLILLAELFGVFWTPPDVSAMIAPLLGDYEMQGPEDLAVELVPV
VMGGVGLVLGFTKEKIGKMLSSAASTLRACKDLGAYGLEILKLVMKWFFPKKEEANEL
AMVRAIEDAVLDLEAIENNHMTTLLKDKDSLATYMRTLDMEEEKARKLSTKSASPDIV
GTINALLARIAAARSLVHKAKEELSSRQRPVVVMISGRPGIGKTHLARELAKKIASTL
SGDQRIGLVPRNGVDHWDAYKGERVVLWDDYGMSNPIQDALRLQELADTCPLTLNCDR
IENKGKVFDSDAIIITTNLANPAPLDYVNFEACSRRIDFLVYADAPDIEKAKRDFPGQ
PDMWKDHYRPDFAHIKLQLAPQGGFDKNGNTPHGKGVVKSLTIGSLIARASGLLHERM
DEFELQGPNLPTFNFDRNKIAAFRQLAAENKYGMVDTLRVGNQLKSVKTMDELKQAIK
NITIKKCQIVYNGCTYTVESDGRGKVSVDKVQNATVQTNNELSGALHHLRSARIRYYV
KCFQEAVYSLLQIAGAAFVTSRIARRMNISSLWSKPPVEESDESEDKEGCPKPRDEDD
LTIDSKDIKVEGKKGKNKSGRGKKHTAFSSKGLSDEEYDEYKRIREERNGKYSIEEYL
QDRDRYYEELAIAKATEEDFCEEEEIKIRQRIFRPTRKQRKEERATLGLVTGSEIRKR
NPDDFKPKGKLWADDNRSVDYNERIDFEAPPSVWSRIVNFGTGWGFWVSPSLFITSTH
VIPKGITEAFGVPMNQIQIHKSGEFCRLRFPKPIRPDVSGMILEEGAPEGTVASILIK
RTTGELMPLAARMGTHATMKIQGRTVGGQMGMLLTGSNAKSMDLGTTPGDCGCPYIYK
RGNDFVVIGVHTAAARGGNTVICATQGSEGEATLEGGDNKGTYCGAPILGPGNAPKLS
TKTKFWRSSNAPLPPGTYEPAYLGGKDPRVKGGPSLQQVMRDQLKPFTEPRGKPPNPS
VLESAKKTIINVLEQVIDPPQKWSYAQACASLDKSTSSGHPHHVRKNEYWNGESFTGK
LADQASKANLMYEEGKHMPPVYTAALKDELVKTDKIYGKIKKRLLWGSDLSTMIRCAR
AFGGLMDELKANCITLPIRVGMNMNEDGPIIFEKHSRYRYHYDADYSRWDSTQQRAVL
AAALEIMVRFSAEPQLAQIVAEDLLAPSVVDVGDFKITINEGLPSGVPCTSQWNSIAH
WLLTLCALSEVTGLGPDIIQANSMCSFYGDDEIVSTDIKLDPEKLTAKLKEYGLKPTR
PDKTEGPLVISEDLNGLTFLRRTVTRDPAGWFGKLDQNSILRQLYWTRGPNHEDPSET
MIPHAQRPVQLMALLGESSLHGPSFYSKVSKLVISELKEGGMDFYVPRQESMFRWMRF
SDLSTWEGDRNLAPSFVNEDGVE"
mat_peptide <1..967
/gene="ORF1"
/product="p48"
mat_peptide 968..2065
/gene="ORF1"
/product="NTPase"
mat_peptide 2066..2602
/gene="ORF1"
/product="p22"
mat_peptide 2603..3001
/gene="ORF1"
/product="VPg"
mat_peptide 3002..3544
/gene="ORF1"
/product="Pro"
mat_peptide 3545..5074
/gene="ORF1"
/product="RdRp"
gene 5058..6704
/gene="ORF2"
CDS 5058..6704
/gene="ORF2"
/note="major capsid protein"
/codon_start=1
/product="VP1"
/protein_id="QPJ59518.1"
/translation="MKMASNDAAPSNDGAAGLVPEINNEAMALDPVAGAAIAAPLTGQ
QNIIDPWIMNNFVQAPGGEFTVSPRNSPGEVLLNLELGPEINPYLAHLARMYNGYAGG
FEVQVVLAGNAFTAGKVIFAAIPPNFPIDNLSAAQITMCPHVIVDVRQLEPINLPMPD
VRNNFFHYNQGSDSRLRLIAMLYTPLRANNSGDDVFTVSCRVLTRPSPDFSFNFLVPP
TVESKTKPFTLPILTISEMSNSRFPVPIDSLHTSPTENIVVQCQNGRVTLDGELMGTT
QLLPSQICAFKGTLTRSTNRVSDQADTATPRLFNYHWHIQLDNLNGTPYDPAEDIPAP
LGTPDFRGKVFGVASQRNPDSTTRAHEAKVDTTSGRFTPKLGSLEITTESNDFDSNQP
TKFTPVGIGVDNEVDFQQWSLPDYSGQLTHNMNLAPAVAPNFPGEQLLFFRSQLPSSG
GRSNGTLDCLVPQEWVQHFYQESAPAQTQVALVRYVNPDTGRVLFEAKLHKLGFMTIA
KNGDSPITVPPNGYFRFESWVNPFYTLAPMGTGNGRRRIQ"
gene 6704..7468
/gene="ORF3"
CDS 6704..7468
/gene="ORF3"
/note="minor structural protein; small basic protein"
/codon_start=1
/product="VP2"
/protein_id="QPJ59519.1"
/translation="MAGAFIAGLAGDMLTNTVGSLVNAGASVINQKVDFENNKYLQNA
SFNHDKEMLNAQIEATKRLQADMIAIKQGVLTAGGFSPTDAARGAINAPMTKVLDWSG
TRYWAPNATSTTSMSGGFTSQVVHRTAPNFGANQAPKFTPSSGSSVRSSSTQLTSLSS
HSSGSSRSSGSTVVSSLPSSSRTRDWVNQQNLNLEPHMPGSLRTAFVTPPSSTASSSD
TVSTVPKNVLDSWTSAFNTHRQPLFAHLRRRGESNA"
ORIGIN
1 cgttgctggc aaaaacaaca acaacgacaa ggaaaaatct tcaagtgaca gcttgttttc
61 taacatgact gttactttaa agaaagccct cggggcgcgg cctaaacaac cgcccccggg
121 agaaacaaaa caaacacaaa aaccaccaag accaccaaca cctgaattgg tgaaaagaat
181 acccccaccc ccacccaacg gcgaggatga actaaaggtg gtatacaggg tgggagaagg
241 tgtgtccggg ctgcccgact taacaaccgt ggcgcagcct gacgcacaaa acacagctta
301 tagtgtgccc ccacttagcc aaagagaggt aggcgaagct aaggaaccgc tacctggatc
361 cattctggaa atgtgggatg gtgagatcta ccactatggg ctgtacgttg agaaggggca
421 catacttggg gtgcataaac cacctgctgc aataagcctc gccaaaattg aattaacacc
481 actgtctctc tactggagag tggtttacac tccccagtac ttgatagccc cagacactct
541 gaagaacttg agtggagaat cattcccata cacggccttt gacaacaact gttacgcttt
601 ctgttgttgg gtcttagatc tcaatgactc ttggcttagc aggagaatga ttcaaaggac
661 aaccggcttc ttcaggccgt accaagattg gaatagaaaa cccctgccaa ccatggatga
721 gccaaaaatc aagaaggccg cgaatgctgt tctgtgcgct ctctcctcac tcttcactag
781 acccattaag gacattattg gaaagctcaa accaatgaac atcctcaata tattagcaac
841 ttgtgactgg acttttgcag gcatagtgga atcccttatt cttcttgctg aactctttgg
901 ggtgttctgg acacccccag atgtgtctgc aatgattgct cccttactcg gtgactacga
961 gatgcaaggc cccgaagacc tggccgtgga acttgtaccc gtggtaatgg gaggggtagg
1021 tttggtgttg ggattcacca aggagaagat cggcaagatg ctttcatcag ctgcatccac
1081 gcttagggcc tgcaaagatc taggagccta tggattggag atacttaaat tggtcatgaa
1141 gtggttcttc cctaagaaag aagaggctaa cgagttagcc atggtaaggg ccatcgagga
1201 tgcagtcctg gacttagagg caatagaaaa caaccacatg accactcttc tcaaggacaa
1261 agacagcctg gccacataca tgaggactct tgacatggag gaagagaaag caaggaaact
1321 gtccaccaaa tccgcatcac ctgacattgt gggcacaata aatgcattat tggcaaggat
1381 tgcagccgct aggtcactag tccacaaggc taaggaggag ctttcaagca gacagaggcc
1441 tgtcgtcgtg atgatatctg gcagaccagg catagggaag acccacctcg ccagagagct
1501 agccaagaaa attgcatcaa cactgtcggg cgaccaaagg attggactgg tgcctagaaa
1561 cggtgtagac cactgggatg cctacaaggg ggaaagagtg gtgctatggg atgactatgg
1621 catgagcaac cccatacagg atgcactgag acttcaagag ttggctgata cctgtcctct
1681 aactctaaac tgtgatagaa ttgaaaacaa gggaaaagtg tttgacagtg atgccataat
1741 cataacaacc aaccttgcaa acccagcacc gctggattat gtcaactttg aggcttgctc
1801 cagacgcata gacttcttag tgtatgcaga tgcacctgac attgagaaag ccaagcgtga
1861 cttccctggc caaccagata tgtggaaaga tcactacaga ccagactttg cacacatcaa
1921 acttcagcta gcaccacagg gaggttttga taagaatggc aacaccccac atggtaaagg
1981 tgtagtgaag tctctgacga ttgggtcatt gatcgccagg gcttctggct tgctccacga
2041 gagaatggat gaattcgagc tccaaggccc taacctacca accttcaatt tcgaccgcaa
2101 caagatcgcc gccttcaggc aattggcagc tgaaaacaaa tatggtatgg tagacacact
2161 gagggtcggt aatcaactga agagtgtcaa gaccatggat gagctcaaac aggctataaa
2221 gaatatcacc attaagaagt gccaaatagt gtacaatggg tgtacctaca cagtggagtc
2281 tgatggaaga ggcaaggttt cagttgacaa ggtgcaaaat gcaacagtcc aaactaataa
2341 tgagctttca ggagcgctgc accacttaag atctgcaaga ataagatatt atgtcaaatg
2401 tttccaggaa gctgtctatt ctttgctaca aatcgctggt gcggcctttg tcacctcacg
2461 cattgcgagg cgcatgaaca tctcaagcct ctggtcgaag ccacccgttg aagagagtga
2521 tgaatctgaa gacaaagaag ggtgccccaa gcccagagat gaagatgatc tcactatcga
2581 ttccaaggac atcaaagtgg aaggaaagaa aggcaagaac aagtccggcc gaggtaagaa
2641 acacacagcc ttctcatcta agggcctcag tgatgaagag tacgatgagt acaagagaat
2701 cagagaagaa aggaatggca aatactcaat agaggagtac ctccaagaca gggacaggta
2761 ctatgaagag cttgccattg ctaaggccac tgaagaggac ttctgtgaag aggaggagat
2821 caaaatccgt cagagaatct tccgccccac cagaaagcag cggaaagagg aaagggctac
2881 acttgggctc gtcacagggt cggagatcag aaagaggaat ccagatgact tcaaaccaaa
2941 agggaaattg tgggctgatg ataacaggag tgtggactac aatgagagga tagattttga
3001 agcgccccct agcgtttggt caaggatagt caactttggc acaggctggg gattctgggt
3061 ttctccaagt ctcttcataa cctcgacaca cgtgatacca aaaggaatca cggaggcatt
3121 tggggtgcct atgaaccaaa tccaaattca taaatcaggg gaattctgcc gcttacggtt
3181 tccaaaacca atcaggccag acgtaagtgg gatgattttg gaagagggtg cccctgaagg
3241 aactgttgcg tccatcctca tcaaaagaac aacaggggag ttgatgcctc ttgcagccag
3301 aatgggaacc cacgccacaa tgaaaatcca aggaagaacg gtgggtggcc agatgggcat
3361 gttactcacc ggttcaaatg ccaaaagcat ggacctaggc acaacaccag gtgactgtgg
3421 gtgcccctac atatacaaga ggggcaatga cttcgtggtc attggcgtgc acactgcagc
3481 agcacgtgga ggaaacacag ttatatgtgc cacacaagga agcgaaggtg aagccaccct
3541 tgagggaggt gacaacaagg gcacctattg tggagccccc attttaggac ctggcaatgc
3601 accaaaattg agcacaaaaa caaaattctg gaggtcttcc aacgcaccgc tcccgccagg
3661 cacctatgaa ccagcatacc tgggtgggaa agatccacgt gtgaagggtg gtccgtctct
3721 gcaacaggtc atgagagacc aacttaaacc tttcacagag cccagaggga aaccaccaaa
3781 cccaagtgtc ctagaatcag caaagaaaac tatcatcaat gttctagagc aggtcattga
3841 ccccccccag aagtggtcct atgcccaagc ttgtgcatcc cttgacaaat caacctccag
3901 tggacacccg caccacgttc ggaagaatga atactggaat ggtgaatcct tcacaggaaa
3961 acttgcagac caggcatcaa aagcaaatct catgtacgaa gaaggcaaac acatgccacc
4021 agtttacacc gcagcgctca aggacgagct ggtgaaaact gacaaaatct atggtaaaat
4081 taagaaaagg ctcctgtggg gttctgacct ctccaccatg attcgatgcg ccagagcatt
4141 tggtggcctc atggatgaac tcaaagcaaa ttgcatcaca cttcctatca gagttggcat
4201 gaacatgaat gaagatggtc ccataatatt tgagaaacat tccagatata gataccacta
4261 tgatgcagat tactcccgct gggattccac gcagcagcgg gcagtgttgg cagcagcact
4321 tgaaatcatg gtgagattct ctgctgaacc acagttagca caaatagtag ctgaagatct
4381 gctagcacca agtgtggttg atgtgggtga cttcaagatc accattaatg aaggcctacc
4441 ttctggtgtg ccttgcacct cacagtggaa ctccattgcc cactggttgc ttactctgtg
4501 tgccctttct gaagtgacag gactaggccc tgacatcata caagctaatt ccatgtgctc
4561 tttctatggt gatgatgaga ttgtgagcac tgacataaaa ttggacccag agaaactgac
4621 tgcaaaactc aaagagtacg gcctcaaacc cactcgcccc gacaaaaccg aagggccgct
4681 ggtaatcagt gaagacttga atggtttgac gttcctccgc cgaacggtca cccgtgaccc
4741 agcaggttgg tttggaaagc tggatcaaaa ttccatcctc aggcagctat actggacaag
4801 aggacccaac catgaagacc ccagtgaaac catgatacca catgcgcaga gacccgtgca
4861 gctcatggca ctgctgggag aatcctccct acatggaccc tcattttaca gcaaggttag
4921 caagctggtt atatctgaac ttaaggaggg aggaatggat ttttatgtgc ccagacaaga
4981 gtcaatgttc aggtggatga ggttctcaga tctaagcaca tgggagggcg atcgcaatct
5041 ggctcccagt tttgtgaatg aagatggcgt cgaatgacgc tgctccatct aatgatggtg
5101 ccgccggcct cgtcccagag atcaacaatg aggcaatggc gctagatcca gtggcgggtg
5161 cagctatagc agcacccctc actggccagc aaaatataat tgatccctgg attatgaata
5221 actttgtgca agcacctggt ggtgagttta cagtgtcacc taggaattcc cctggtgaag
5281 tgcttcttaa tttggaatta ggtccagaaa taaatcccta tttggctcat cttgctagaa
5341 tgtacaatgg ttatgcaggt gggtttgaag tgcaagtggt cctggctgga aatgcgttta
5401 cagcaggaaa ggttatcttt gcagctatac cccccaactt ccctattgat aatctgagcg
5461 cagcacagat cacaatgtgc ccgcatgtga ttgtggatgt caggcagttg gaaccaatca
5521 atcttccgat gcctgatgtt cgcaacaatt tctttcatta taatcaaggg tctgattcaa
5581 gattacgttt aattgcaatg ctgtatacac ctcttagggc aaataattct ggagatgatg
5641 ttttcactgt gtcttgtagg gtgttaacta ggcctagccc tgatttctca ttcaattttc
5701 ttgtcccacc cactgtggaa tcaaagacaa aaccttttac cctccccatt ttaaccatct
5761 ctgaaatgtc taattccagg tttccggtgc caattgactc tctacacacc agcccaactg
5821 agaatatcgt tgtccagtgc caaaatgggc gcgtcactct tgacggtgag ttaatgggca
5881 ccactcaact cttaccgagc caaatatgtg ctttcaaggg aacacttact agatcaacaa
5941 acagggtcag tgaccaagcc gacacagcaa cccccaggct atttaactat cattggcaca
6001 tacaattgga taatctaaat ggaaccccct acgaccctgc agaggacata ccagctcctt
6061 tgggtacacc agacttccgg ggcaaagtct ttggcgtagc cagccagaga aaccccgaca
6121 gcacaacaag ggcacatgaa gcaaaagtgg acacaacatc tggccgcttc accccaaaat
6181 tgggctccct agaaataacc actgaatcta atgactttga ctcaaaccag ccaacaaaat
6241 tcaccccagt tggcattgga gttgacaatg aggtagattt tcagcaatgg tccttacctg
6301 actattccgg tcagcttact cataacatga acttagcccc agctgtcgcc cccaattttc
6361 ctggtgaaca gcttcttttc ttccgatcac agctgccatc ttctggtggg cggtctaacg
6421 ggactctaga ctgcctggtc ccccaggaat gggttcaaca tttctatcaa gaatcagccc
6481 ccgcccaaac acaggtggcc ctggttaggt atgtcaaccc tgacactggt agagtgctat
6541 ttgaggccaa gctacacaaa ttgggtttta tgactatagc aaagaatggt gactccccaa
6601 taactgtccc tccaaatggg tattttagat ttgaatcttg ggttaacccc ttttacacac
6661 ttgcccccat gggaactgga aacgggcgta gaaggattca ataatggctg gagcctttat
6721 agcaggattg gctggtgaca tgctcacaaa cactgtggga tctttggtta atgcaggggc
6781 tagtgttatc aatcaaaaag ttgattttga aaataataaa tatttgcaaa atgcatcctt
6841 taatcatgat aaggaaatgt taaatgcaca aattgaggca acaaagaggc tgcaggctga
6901 catgattgct atcaagcaag gggtcttgac cgctggcggc ttttccccca ctgatgcagc
6961 acgtggggca attaatgccc caatgacaaa agttttggat tggagtggaa caaggtactg
7021 ggcaccaaac gccacctcca caacttcaat gtcaggtggc ttcacaagcc aagttgtgca
7081 cagaaccgca ccaaattttg gagcgaacca ggcccccaaa ttcacaccca gcagtgggtc
7141 ttcagtgaga tcaagctcaa cccaactcac tagcttgagc tcacactcat ccgggtcgtc
7201 ccgatctagc gggtctacgg ttgttagctc gttgccgtcc tctagtagga ctagggactg
7261 ggtcaatcaa cagaatctca atttggaacc acacatgcct ggatctctca ggacagcttt
7321 tgtcactcca ccatctagca cagcctctag ttcagacacg gtctcaaccg tgcccaaaaa
7381 tgttttggac tcctggacat ctgcgtttaa tacgcacaga cagccgctat ttgcacacct
7441 tcgtagaagg ggggagtcaa atgcttagtg aaaagattat tcctaaattt aatttagaat
7501 ctttt
//