Typing tool
|
|
|
|
|
|
Typing tool
|
Complete norovirus genomes
| MK616560 | GII.12 | |
|
|---|---|---|---|
| GII.P16 |
ORF1: 1..5037
ORF2: 5018..6625
ORF3: 6625..7404
LOCUS MK616560 7439 bp RNA linear VRL 17-MAR-2019
DEFINITION Norovirus GII isolate CA-RGDS-1019 nonstructural polyprotein (ORF1)
gene, partial cds; and VP1 (ORF2) and VP2 (ORF3) genes, complete
cds.
ACCESSION MK616560
VERSION MK616560.1
KEYWORDS .
SOURCE Norovirus GII
ORGANISM Norovirus GII
Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes;
Picornavirales; Caliciviridae; Norovirus; Norovirus norwalkense.
REFERENCE 1 (bases 1 to 7439)
AUTHORS Pan,C.-Y., Huynh,T., Castro,C.J., Ng,T.F., Marine,R.L. and
Wadford,D.A.
TITLE Norovirus GII.P16-GII.12 genomes from gastroenteritis outbreaks,
California, 2018
JOURNAL Unpublished
REFERENCE 2 (bases 1 to 7439)
AUTHORS Pan,C.-Y., Huynh,T., Castro,C.J., Ng,T.F., Marine,R.L. and
Wadford,D.A.
TITLE Direct Submission
JOURNAL Submitted (11-MAR-2019) Viral and Rickettsial Disease Laboratory,
California Department of Public Health, 850 Marina Bay Parkway,
Richmond, CA 94804, USA
COMMENT ##Assembly-Data-START##
Assembly Method :: Geneious v. R10; SPAdes v. 3.6
Sequencing Technology :: Illumina
##Assembly-Data-END##
FEATURES Location/Qualifiers
source 1..7439
/organism="Norovirus GII"
/mol_type="genomic RNA"
/isolate="CA-RGDS-1019"
/isolation_source="stool"
/host="Homo sapiens"
/db_xref="taxon:122929"
/geo_loc_name="USA: CA"
/collection_date="Aug-2018"
/note="genotype: GII.P16-GII.12"
gene <1..5037
/gene="ORF1"
CDS <1..5037
/gene="ORF1"
/codon_start=1
/product="nonstructural polyprotein"
/protein_id="QBL14287.1"
/translation="KSSGEGLFTNMSSTLKKALGARPKQPAPRDKPQKPPRPPTPELV
KRIPPPPPNGEEEEEPVIRYEVKSGVSGLPELTTVPQPDVANTAFSVPPLSLRENREA
KEPLTGAILEMWDGEIYHYGLYVEKGLVLGVHKPPAAISMAKVELTPLSLYWRVVYTP
QYLISPETLRRLNGEAFPYTAFDNNCYAFCCWVLDLNDSWFSRRMVQRTTGFFRPYQE
WNRKPLPTMDDSKIKKVANIFLCSLSTLFTRPIKDLIGKIKPLNILNILATCDWTFAG
IVESLILLAELFGVFWTPPDVSAMIAPLLGDYELQGPEDLAVELVPVVMGGIGLVLGF
TKEKIGRMLSSAASTLRACKDLGAYGLEILKLVMKWFFPKKEEANELAMVRAIEDAVL
DLEAIENNHMTTLLKDKDSLATYMKTLDMEEEKARRLSTKSASPDIVGTINALLARIA
AARSLVHRAKEELSSRIRPVVVMISGKPGIGKTHLAREVARKVASTLTGDQRVGLIPR
NGVDHWDAYKGERVVLWDDYGMSNPIHDALRIQELADTCPLTLNCDRIENKGKVFDSE
VIIITTNLANPAPLDYVNFEACSRRIDFLVYAEAPDVEKAKRDFPGQPDMWKDAFKSD
FSHIKLQLAPQGGFDKNGNTPHGKGVMKTLTTGSLIARASGLLHERMDEFELQGPTIT
TFNFDRNRITAFRQLAAENKYGLVDTMKVGNQLKGVKTMEELKQAIRNVTIKRCRIIY
GGSTYDLESDGKGKVLVEKVKNASVQTNNELAGALHHLKHARIRYYVKCVQEAVYSII
QIAGAAFVTTRIARRMNIQELWSKPQLDQNESETKEEAPKPEDDEFVISCKDIKEEGK
KGKNKTGRGKKHTAFSSKGLSDEEYDEYKRIREERNGKYSIEEYLQDRDRYYEELAIA
KATEEDFCEEEEIKIRQRIFRPTRKQRKEERATLGLVTGSEIRKRNPDDFKPKGKLWA
DDNRSVDYNEKLDFEAPPSIWSRIVSFGSGWGFWVSPSLFITSTHVIPTGITEAFGVP
IKQVQIHKSGEFCRFRFPKPIRPDVTGMILEEGAPEGTVATVLIKRPTGELMPLAARM
GTHATMKIQGRMVGGQMGMLLTGSNAKGMDLGTTPGDCGCPYIYKRGNDYIVIGVHTA
AARGGNTVICATQGSEGEATLEGGDDKGTYCGAPILGPGGAPKLSTKTKFWRSSNTPL
PPGTYEPAYLGGRDPRVKGGPSLQQVMRDQLKPFTEPRGKPPRPSVLEAAKQTIINVL
EQTLDPPQKWTYAQACASLDKTTSSGHPYHVRKNEFWNGETFTGKLADQASKANLMFE
EGKHMTPVYTAALKDELVKTEKIYGKIKKRLLWGSDLSTMIRCARSFGGLMDEMKAHC
ISLPVRVGMNMNEDGPIIFEKHSRYKYHYDADYSRWDSTQQRAVLAAALEIMVRFSAE
PQLAQIVAEDLLAPSVVDVGDFKITINEGLPSGVPCTSQWNSIAHWLLTLCALSEVTK
LSPDIIQANSMFSFYGDDEIVSTDIKLDPEQLTAKLKEYGLKPTRPDKTEGPLIISED
LNGLTFLRRTVTRDPAGWFGKLDQSSILRQMYWTRGPNHEDPNETMIPHSQRPIQLMA
LLGEASLHGPSFYSKISKLVITELKEGGMDFYVPRQEPMFRWMRFSDLSTWEGDRNLA
PNFVNEDGVE"
mat_peptide <1..933
/gene="ORF1"
/product="p48"
mat_peptide 934..2031
/gene="ORF1"
/product="NTPase"
mat_peptide 2032..2562
/gene="ORF1"
/product="p22"
mat_peptide 2563..2961
/gene="ORF1"
/product="VPg"
mat_peptide 2962..3504
/gene="ORF1"
/product="Pro"
mat_peptide 3505..5034
/gene="ORF1"
/product="RdRp"
gene 5018..6625
/gene="ORF2"
CDS 5018..6625
/gene="ORF2"
/note="major capsid protein"
/codon_start=1
/product="VP1"
/protein_id="QBL14288.1"
/translation="MKMASNDAVPSNDGAAGLVPEVNNETMALEPVAGASIAAPLTGQ
NNVIDPWIRLNFVQAPNGEFTVSPRNSPGEVLLNLELGPELNPYLAHLSRMYNGYAGG
VEVQVLLAGNAFTAGKLVFAAVPPHFPLENISPGQITMFPHVIIDVRTLEPVLLPLPD
VRNNFFHYNQQNEPRMRLVAMLYTPLRSNGSGDDVFTVSCRVLTRPSPDFDFNYLVPP
TVESKTKPFTLPVLTIGELTNSRFPVPIDELYTSPNESLVVQPQNGRCALDGELQGTT
QLLPTAICSFRGRINQKVSGENHVWNMQVTNINGTPFDPTEDVPAPLGTPDFSGKLFG
VLSQRDHDNACRSHDAVIATDSTKFTPKLGAVQIGTWEQDDVHINQPTKFTPVGLFEN
EGFNQWTLPNYSGALTLNMGLAPPVAPTFPGEQILFFRSHIPLKGGVADPVIDCLLPQ
EWIQHLYQESAPSQTDVALIRFTNPDTGRVLFEAKLHRSGYITVANTGSRPIVVPANG
YFRFDSWVNQFYSLAPMGTGNGRRRMQ"
gene 6625..7404
/gene="ORF3"
CDS 6625..7404
/gene="ORF3"
/note="minor structural protein; small basic protein"
/codon_start=1
/product="VP2"
/protein_id="QBL14289.1"
/translation="MAGAFIAGLAGDIVTNSIGSLVNAGANAINQKVDFENNKQLQQA
SFNHDKEMLQAQIQATKQLQADMIAIRQGVLTAGGFSPTDAARGAVNAPMTQVLDWNG
TRHWAPGAAKTTAFSGGFTSASHARTVDLTKKTSATPAPMPVSRPSSIASTVSTRSTL
ISGSSDSPSSARSSSSVSSQPTSSSSRTSEWVRSQNRALEPYMNGALRTAYVTPPSSR
ASSNGTVSTVPKEVLDSWSSAFNTHRQPLFAHLRRRGESQA"
ORIGIN
1 aaatcttcag gtgaaggctt attcacaaat atgtcttcca ccttaaagaa agccctcggg
61 gctaggccca aacagcctgc cccgagagac aaaccacaaa agcccccaag accaccaact
121 cccgagttgg tcaagaggat accccctcct ccacctaacg gcgaagaaga agaagaacca
181 gtcattaggt atgaggttaa gagtggggtc tctggcctgc ccgagctcac aacagtcccc
241 caaccggacg tggccaacac agcattcagt gttccaccac tgagcttgag agaaaacagg
301 gaagccaagg aaccgctgac aggggcaata ttagagatgt gggatggaga gatataccac
361 tacggcctgt acgtggagaa aggcttagtg ttgggtgtac acaaaccacc tgcagccata
421 agcatggcaa aagtggagct gacgccgctg tcattgtatt ggcgtgtggt gtacactccc
481 caatacctca tctcccctga aactctcagg aggctcaacg gagaggcatt cccttacacc
541 gcctttgaca acaactgcta tgccttttgc tgctgggtat tagacctcaa tgactcatgg
601 tttagcagga gaatggtgca aagaacaacg ggcttcttca gaccttacca agagtggaac
661 agaaaacccc tgcctaccat ggacgactcc aaaattaaga aggtagcaaa tatattccta
721 tgttcattgt ccacattgtt cactagaccc ataaaagacc tcataggaaa aattaaacca
781 ttaaacatat tgaatatcct ggcaacgtgt gactggacgt ttgccggaat agtggagtct
841 ctaatactac ttgctgaact cttcggagtt ttctggacac ccccagatgt gtctgctatg
901 atcgctccct tacttgggga ttacgagttg caagggccag aagacctcgc cgtcgaactc
961 gtacctgtgg tgatgggtgg gattggtttg gtgttgggat tcaccaaaga gaaaattggc
1021 agaatgttgt cctcggcagc atcaacactc agggcttgca aagaccttgg tgcctatggc
1081 ttagagatac tcaaattagt catgaagtgg ttcttcccaa agaaagagga ggccaatgag
1141 ctagccatgg tgagggccat agaggacgct gtactagatc ttgaggcaat agaaaataac
1201 cacatgacaa ccctgttgaa agacaaagac agcttagcaa catacatgaa aacactggac
1261 atggaggagg agaaagccag aaggttgtcc acaaaatctg catcccctga catagttggg
1321 acaatcaacg ccctgctggc tcgaatagca gcggccaggt cattagtcca cagggccaag
1381 gaagagctat ctagcaggat cagaccagta gttgttatga tatctggcaa accaggaata
1441 ggcaaaactc atctggccag ggaagtggca agaaaggtgg catccactct cacaggggat
1501 caaagagtcg gactcatacc aagaaacggt gtggaccatt gggatgcata caaaggtgag
1561 agagtcgtgc tgtgggacga ctatggcatg agtaacccca ttcatgatgc tcttcgcata
1621 caagaattgg ctgatacgtg tcccctcacc ttaaattgtg acagaattga aaataaagga
1681 aaagtttttg acagtgaagt cataataatc acaacaaacc ttgccaatcc agccccgctt
1741 gattatgtca actttgaggc ctgttccagg agaattgatt tcctggtgta cgctgaggca
1801 ccagatgtgg aaaaggcaaa acgggacttt cctggtcagc cagatatgtg gaaggacgcc
1861 ttcaaatcgg acttttcaca catcaagcta cagcttgcac ctcagggcgg ctttgacaaa
1921 aacggcaaca ccccacatgg gaaaggggtg atgaagaccc tcactaccgg ttctttgatt
1981 gcccgtgcat caggcctact gcatgagagg atggatgaat ttgaactcca aggtcctaca
2041 atcaccacct tcaatttcga ccggaacaga atcacagcat tcagacaatt ggctgcagaa
2101 aacaagtatg gactggtgga caccatgaaa gtcggcaatc aattaaaagg agtgaaaacc
2161 atggaagagc tcaaacaagc aatcaggaat gtgaccatca agaggtgccg gatcatctac
2221 ggtggctcca catatgacct tgaatctgat ggcaagggca aagttttggt ggaaaaggtc
2281 aagaacgcct ctgtacagac caacaacgag ttggccgggg ccctgcacca tctcaaacac
2341 gcccgaatca ggtactatgt caagtgtgtg caagaagcag tctattctat catacaaatt
2401 gccggcgctg cgtttgtcac cacgcgcatt gcacgccgca tgaacataca agaactctgg
2461 tcgaagccac aattggatca aaatgaatca gagactaagg aagaggcccc caagccagaa
2521 gatgacgagt tcgtcatatc ttgtaaggac atcaaggagg aaggaaagaa gggcaaaaat
2581 aaaactggcc gtggcaagaa acacactgca ttctccagca agggcttgag cgatgaggag
2641 tatgacgagt acaagaggat aagagaagag agaaatggga agtactctat agaggaatac
2701 cttcaagaca gagacaggta ctatgaagaa ctcgccattg ccaaggccac ggaagaagac
2761 ttctgtgaag aggaggagat aaaaatccgt cagagaattt tccgtcctac caggaaacaa
2821 aggaaggaag agagggccac attagggcta gtaacaggtt cagaaatcag aaaaagaaat
2881 cctgatgact tcaaacccaa agggaagctg tgggccgatg acaacagaag tgttgactac
2941 aatgagaagc tggattttga ggccccccca agcatatggt ctaggattgt gagctttggt
3001 tctggctggg gcttctgggt atcaccaagc ctgttcataa catcaactca tgtaatcccc
3061 acaggcataa cagaagcgtt tggagtcccc atcaaacaag ttcaaatcca caaatcaggt
3121 gaattttgcc gattcagatt cccaaagcca attagaccag atgtgacagg aatgatcttg
3181 gaagaaggtg cgcctgaggg caccgtggca actgtgctca tcaaacgccc caccggagag
3241 ctcatgcctc ttgcagccag aatgggaaca cacgcaacca tgaaaattca aggccgcatg
3301 gttggcggac agatgggcat gttgctcact ggatcaaatg ctaaaggaat ggatttggga
3361 acaactcctg gagactgtgg ctgtccttac atctataaaa ggggcaatga ctatatagtc
3421 attggggtgc acactgcagc agcccgtggt ggaaacaccg tcatctgtgc cacacaggga
3481 agtgagggtg aggcaactct tgagggtgga gatgacaaag gaacatattg tggggcaccc
3541 atcctaggcc ctgggggtgc accaaaattg agcaccaaaa ccaaattttg gaggtcatcg
3601 aacacgcccc ttccaccagg gacatatgag cctgcctacc tcggcggtcg tgacccgcgt
3661 gttaagggtg ggccctcctt gcagcaggta atgagagacc agttgaagcc attcactgaa
3721 cccaggggca aacctccaag accaagtgta ttggaagcag ccaaacaaac catcatcaat
3781 gtcctcgagc aaaccctgga ccctccacaa aaatggacat acgcacaggc gtgtgcctca
3841 cttgacaaaa caacctctag cggtcacccc tatcacgttc gaaagaatga attctggaat
3901 ggtgagacct tcactggtaa attggcagac caagcatcaa aagcaaacct aatgtttgag
3961 gaagggaaac acatgacacc agtgtataca gcagcactca aggacgagct agtcaagact
4021 gagaaaatct atggaaaaat caagaagaga ctgctctggg gctctgattt gtccaccatg
4081 atccggtgtg ctaggtcatt tggtgggctc atggacgaga tgaaggcaca ctgcatatca
4141 ctcccagtcc gagttggcat gaatatgaat gaagatggcc caataatatt tgagaaacat
4201 tctagataca aatatcacta tgatgcagac tactctcgtt gggattcaac acaacagagg
4261 gcagtactgg cagcagcctt ggaaatcatg gtcagattct ctgcagaacc acaattggca
4321 caaatagtcg ctgaggacct actggcccct agtgtagtag atgtaggaga ctttaaaatc
4381 acaataaatg aggggctccc ctctggtgtg ccatgcactt ctcaatggaa ctccatcgca
4441 cactggttgc taactctctg tgccttgtct gaagtcacta agctgtcacc tgacattata
4501 caggcaaatt ccatgttctc attttacggt gatgacgaga ttgtcagcac cgacataaaa
4561 ttggaccccg aacagttaac cgccaaattg aaggagtacg gtctaaaacc aacccgccca
4621 gacaaaaccg agggacccct gatcatcagt gaagatttga acggactcac tttcctccga
4681 aggacggtga ctcgtgaccc agctggctgg tttggaaaac tggaccaaag ctcaattttg
4741 aggcagatgt actggactag aggaccaaat catgaagacc ccaatgagac aatgataccc
4801 cattctcaaa ggcccataca gctcatggca ctgcttggtg aagcctctct tcacggaccc
4861 tctttctaca gtaaaatcag taaattggtc ataactgaac tcaaagaagg tgggatggac
4921 ttttacgtgc caaggcagga acccatgttc aggtggatga ggttttctga cctgagcacg
4981 tgggagggcg atcgcaatct ggctcccaat tttgtgaatg aagatggcgt cgaatgacgc
5041 cgttccatct aatgatggtg cagccggtct cgtaccagag gtcaacaatg agaccatggc
5101 acttgaaccg gtggctgggg cttcgatagc cgccccactc accggccaaa ataatgttat
5161 agacccctgg attagattaa attttgtgca ggcccctaat ggagagttta cagtctcacc
5221 ccgcaactcg cctggggaag tcctactcaa tttggaatta ggtcccgaat tgaatccata
5281 tttggcacac ctttctagaa tgtataatgg ttatgcaggt ggagttgagg tacaagtgct
5341 actggctggg aacgcgttca cggctggaaa attggtattt gctgcagttc cccctcattt
5401 tccattagag aatataagcc ctggtcaaat aaccatgttc cctcatgtaa ttattgatgt
5461 taggactttg gaaccagttt tattgcctct accagatgtc agaaataact tcttccatta
5521 caaccagcaa aatgagccga ggatgaggct tgttgcaatg ctttataccc ctcttagatc
5581 taatggttct ggtgatgatg tgttcaccgt ctcctgtagg gtgctcactc gaccctctcc
5641 tgattttgat tttaattatt tggtgccccc aacagttgaa tctaaaacaa aaccattcac
5701 actccctgtc ttgaccattg gggagttaac caattccagg ttccctgtgc ccatagatga
5761 actctacact agccccaatg agagtttggt ggttcaaccc cagaatggga ggtgcgcgct
5821 ggatggggag ttgcagggca ccacccagct ccttcccacg gcgatttgct cgttcagggg
5881 tcggatcaat cagaaagtga gtggagagaa tcatgtttgg aacatgcaag tcaccaacat
5941 taacggaacc ccttttgatc caacagagga tgttccagcc cctctgggca cgccagactt
6001 ttctggcaag ctctttggtg tcctaagcca gagggaccat gataatgcct gcaggagtca
6061 tgatgcagtg attgcaactg attctaccaa atttacccca aaattgggtg ctgtacaaat
6121 tggcacatgg gaacaagatg atgtacacat caaccaaccc accaagttta ctccagttgg
6181 attgtttgag aatgaaggtt ttaatcaatg gacacttcct aattattctg gagctttaac
6241 actcaatatg gggttggccc cccctgtggc ccccacattc cctggtgagc aaattctctt
6301 cttcaggtcc cacattcccc ttaaaggagg tgttgcagac ccagttattg attgtcttct
6361 accccaagag tggatccagc acctttatca ggagtcagcc ccttcacaaa cagatgtggc
6421 actgattaga ttcacaaatc cagacacagg gcgtgtccta tttgaagcaa aattgcacag
6481 gagtggttac atcacagtgg ccaacactgg tagcagacca attgtggtgc cagctaatgg
6541 ttatttcagg tttgactctt gggttaatca gttttactct cttgccccca tgggaactgg
6601 gaatgggcgc agaaggatgc agtaatggct ggagctttca tagcagggct tgccggtgac
6661 atagtcacca acagcattgg ctcactcgtg aacgctgggg ccaatgcaat aaaccagaaa
6721 gtagactttg aaaacaacaa gcaactacaa caggcatctt ttaaccatga caaagagatg
6781 ttgcaagctc aaattcaggc caccaaacaa ctacaggctg atatgattgc gatcagacaa
6841 ggggtgttga ccgcaggcgg cttctcccct actgatgcag caagaggtgc agtcaacgcg
6901 cccatgactc aagtcttgga ttggaatggg accagacatt gggcccccgg agccgcgaaa
6961 acaactgctt tctccggtgg gtttaccagt gcctctcatg ccaggaccgt tgacctgacc
7021 aagaagacat cagccacacc agcccctatg cctgtttcta ggcccagttc tattgcttcc
7081 actgtttcta ctcgctctac tttgattagt gggtcctctg attctccttc ttcagctagg
7141 agctcttcta gtgtttcttc ccaacccact tcctcatcct cccgaactag tgagtgggta
7201 cgcagtcaaa atagggcgct ggagccttat atgaatgggg cgctgcgtac agcctacgtg
7261 acgcctccat ccagtagggc ttctagcaat ggcacagtct caaccgtgcc aaaagaggtt
7321 ttggactcct ggtcgtctgc gtttaataca cacagacagc cgctgtttgc tcatctccgt
7381 cggagagggg agtcacaagc ttagtgaaaa gatggtcttt tctttctttc ctttgaaaa
//