Typing tool
|
|
|
|
|
|
Typing tool
|
Complete norovirus genomes
| MK762635 | GII.4 Sydney | |
|
|---|---|---|---|
| GII.P16 |
ORF1: 5..5104
ORF2: 5085..6707
ORF3: 6707..7513
LOCUS MK762635 7568 bp RNA linear VRL 13-APR-2019
DEFINITION Norovirus GII isolate Hu/US/2017/GII.P16-GII.4
Sydney/LosAngeles0190, complete genome.
ACCESSION MK762635
VERSION MK762635.1
KEYWORDS .
SOURCE Norovirus GII
ORGANISM Norovirus GII
Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes;
Picornavirales; Caliciviridae; Norovirus; Norwalk virus.
REFERENCE 1 (bases 1 to 7568)
AUTHORS Barclay,L., Cannon,J.L., Wikswo,M.E., Phillips,A., Browne,H.,
Montmayeur,A.M., Tatusov,R.L., Burke,R.M., Hall,A.J. and Vinje,J.
TITLE Emergence and characterization of multiple viruses associated with
a novel GII.P16 polymerase in the United States, 2015-2018
JOURNAL Unpublished
REFERENCE 2 (bases 1 to 7568)
AUTHORS Barclay,L., Cannon,J.L., Mundt,T., Montmayeur,A.M., Tatusov,R.L.,
Chhabra,P. and Vinje,J.
TITLE Direct Submission
JOURNAL Submitted (05-APR-2019) Division of Viral Diseases, Centers for
Disease Control and Prevention, 1600 Clifton Road NE, Atlanta, GA
30329, 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..7568
/organism="Norovirus GII"
/mol_type="genomic RNA"
/strain="LosAngeles0190"
/isolate="Hu/US/2017/GII.P16-GII.4 Sydney/LosAngeles0190"
/isolation_source="stool"
/host="Homo sapiens"
/db_xref="taxon:122929"
/country="USA"
/collection_date="19-Apr-2017"
/note="genotype: GII.P16-GII.4 Sydney"
gene 5..5104
/gene="ORF1"
CDS 5..5104
/gene="ORF1"
/codon_start=1
/product="nonstructural polyprotein"
/protein_id="QBX91132.1"
/translation="MKMASNDATVAVACNNNNDKEKSSGEGLFTNMSSTLKKALGARP
KQPAPRDEPQKPPRPPTPELVKRIPPPPPNGEEEEEPVIRYEVKSGISGLPELTTVPQ
PDVANTAFSVPPLSLRENREAKEPLTGAILEMWDGEIYHYGLYVEKGLVLGVHKPPAA
ISMARVELTPLSLYWRVVYTPQYLISPETLRRLNGEAFPYTAFDNNCYAFCCWVLDLN
DSWLSRRMVQRTTGFFRPYQEWNRKPLPTMDDSKIKKVANIFLCSLSTLFTRPIKDLI
GKIKPLNILNILATCDWTFAGIVESLILFAELFGVFWTPPDVSAMIAPLLGDYELQGP
EDLAVELVPVVMGGIGLVLGFTKEKIGKMLSSAASTLRACKDLGAYGLEILKLVMKWF
FPKKEEANELAMVRAIEDAVLDLEAIENNHMTTLLKDKDSLATYMKTLDMEEEKARRL
STKSASPDIVGTINALLARIAAARSLVHRAKEELSSRIRPVVVMISGKPGIGKTHLAR
EVARKVASTLTGDQRVGLIPRNGVDHWDAYKGERVVLWDDYGMSNPIHDALRIQELAD
TCPLTLNCDRIENKGKVFDSEVIIITTNLANPAPLDYVNFEACSRRIDFLVYAEAPEV
EKAKRDFPGQPDMWKDAFKPDFSHIKLQLAPQGGFDKNGNTPHGKGVMKTLTTGSLIA
RASGLLHERMDEFELQGPTITTFNFDRNRITAFRQLAAENKYGLMDTMKVGNQLKGVK
TMEELKQAIRNVTIKRCRIIYGGSTYDLESDGKGKVLVEKVKNTSVQTNNELAGALHH
LKHARIRYYVKCVQEAVYSIIQIAGAAFVTTRIARRMNIQELWSKPQLDQNESETKEE
TPKSEDDEFIISSKDIKEEGKKGKNKTGRGKKHTAFSSKGLSDEEYDEYKRIREERNG
KYSIEEYLQDRDRYYEELAIAKATEEDFCEEEEIKIRQRIFRPTRKQRKEERATLGLV
TGSEIRKRNPDDFKPKGKLWADDNRSVDYNEKLDFEAPPSIWSRIVSFGSGWGFWVSP
SLFITSTHVIPAGITEAFGVPIKQIQIHKSGEFCRFRFPKPIRPDVTGMILEEGAPEG
TVATVLIKRPTGELMPLAARMGTHATMKIQGRMVGGQMGMLLTGSNAKGMDLGTTPGD
CGCPYIYKRGNDYIVIGVHTAAARGGNTVICATQGSEGEATLEGGDGKGTYCGAPILG
PGGAPKLSTKTKFWRSSNTPLPPGTYEPAYLGGRDPRVKGGPSLQQVMRDQLKPFTEP
RGKPPRPSVLEAAKQTIINVLEQTLDPPQKWSYAQACASLDKTTSSGHPHHVRKNEFW
NGETFTGKLADQASKANLMFEEGKHMTPVYTAALKDELVKTEKIYGKIKKRLLWGSDL
STMIRCARSFGGLMDEMKAHCITLPVRVGMNMNEDGPIIFEKHSRYKYHYDADYSRWD
STQQRAVLAAALEIMVRFSAEPQLAQIVAEDLLAPSVVDVGDFKITINEGLPSGVPCT
SQWNSIAHWLLTLCALSEVTKLSPDIIQANSMFSFYGDDEIVSTDIKLDPEQLTAKLK
EYGLKPTRPDKTEGPLIISEDLNGLTFLRRTVTRDPAGWFGKLDQSSILRQMYWTRGP
NHEDPNETMIPHSQRPIQLMALLGEASLHGPSFYSKISKLVITELKEGGMDFYVPRQE
PMFRWMRFSDLSTWEGDRNLAPNFVNEDGVE"
mat_peptide 5..1000
/gene="ORF1"
/product="p48"
mat_peptide 1001..2098
/gene="ORF1"
/product="NTPase"
mat_peptide 2099..2629
/gene="ORF1"
/product="p22"
mat_peptide 2630..3028
/gene="ORF1"
/product="VPg"
mat_peptide 3029..3571
/gene="ORF1"
/product="Pro"
mat_peptide 3572..5101
/gene="ORF1"
/product="RdRp"
gene 5085..6707
/gene="ORF2"
CDS 5085..6707
/gene="ORF2"
/note="major capsid protein"
/codon_start=1
/product="VP1"
/protein_id="QBX91133.1"
/translation="MKMASSDANPSDGSAANLVPEVNNEVMALEPVVGAAIAAPVAGQ
QNVIDPWIRNNFVQAPGGEFTVSPRNAPGEILWSAPLGPDLNPYLSHLARMYNGYAGG
FEVQVILAGNAFTAGKIIFAAVPPNFPTEGLSPSQVTMFPHIIVDVRQLEPVLIPLPD
VRNNFYHYNQSNDSTIKLIAMLYTPLRANNAGDDVFTVSCRVLTRPSPDFDFIFLVPP
TVESRTKPFSVPVLTVEEMTNSRFPIPLEKLFTGPSSAFVVQPQNGRCTTDGVLLGTT
QLSPVNICTFRGDVTHITGSRNYTMNLASQNWNNYDPTEEIPAPLGTPDFVGKIQGML
TQTTRTDGSTRGHKATVYTGSADFAPKLGRVQFETDTDHDFEVNQNTKFTPVGVIQDG
STTHRNEPQQWVLPSYSGRNTHNVHLAPAVAPTFPGEQLLFFRSTMPGCSGYPNMDLD
CLLPQEWVQYFYQEAAPAQSDVALLRFVNPDTGRVLFECKLHKSGYVTVAHTGQHDLV
IPPNGYFRFDSWVNQFYTLAPMGNGTGRRRVV"
gene 6707..7513
/gene="ORF3"
CDS 6707..7513
/gene="ORF3"
/note="minor structural protein; small basic protein"
/codon_start=1
/product="VP2"
/protein_id="QBX91134.1"
/translation="MAGAFFAGLASDVLGSGLGSLINAGAGAINQKVEFENNRKLQQA
SFQFSSNLQQASFQHDKEMLQAQIEATKKLQQEMIKVKQAMLLEGGFSETDAARGAIN
APMTKALDWSGTRYWAPDARTTTYNAGRFSTPQPSGALPGRANLRDAVPARGPSNKSP
NSSTATSVYSNQTISTRLGSTAGSGTSVSSLPSTARTRSWVEDQSRNLSPFMRGAHNI
SFVTPPSSRSSSQGTVSTVPKEILDSWTGAFNTRRQPLFAHIRKRGESRV"
ORIGIN
1 gtgaatgaag atggcgtcta acgacgctac cgttgccgtt gcttgcaaca acaacaacga
61 caaggaaaaa tcttcaggtg aaggcttatt cacaaatatg tcttccacct taaagaaagc
121 cctcggggct aggcccaaac agcctgcccc gagagacgaa ccacaaaagc ccccaagacc
181 accaactccc gagttggtca agaggatacc ccctcctcca cctaatggcg aagaagaaga
241 agaaccagtc attaggtatg aggttaagag tgggatctct ggcctgcccg agctcacaac
301 agtcccccaa ccggacgtgg ccaacacagc attcagtgtt ccaccactga gcttgagaga
361 aaacagggag gccaaggaac cgctaacagg ggcaatatta gagatgtggg atggagagat
421 ataccactac ggcctgtacg tggagaaagg cttagtgttg ggtgtgcaca aaccacctgc
481 agccataagc atggcaagag tggagctgac accgctgtca ttgtactggc gtgtggtgta
541 cactccccaa tacctcatct cccctgaaac tctcaggagg ctcaacggag aggcattccc
601 ttacaccgcc ttcgacaaca actgctatgc cttttgctgc tgggtgttgg acctcaatga
661 ctcatggctt agcaggagga tggtgcaaag aacaacgggc ttcttcagac cttaccaaga
721 gtggaacaga aaacccctgc ccaccatgga tgactccaaa attaagaagg tagcaaatat
781 attcctatgt tcattgtcca cattattcac tagacccata aaagacctca taggaaaaat
841 taaaccatta aacatattga acatcctggc aacgtgtgac tggacgtttg ccggaatagt
901 ggagtctctg atattatttg ctgaactctt cggagttttc tggacacccc cagatgtgtc
961 tgctatgatc gctcccttac tcggggacta cgagttgcaa gggccagaag acctcgccgt
1021 tgaactcgta cctgtggtaa tgggagggat tggtttggtg ttgggattca ccaaagagaa
1081 aattggcaaa atgttgtcct cagcagcatc aacactcagg gcttgcaaag atcttggtgc
1141 ctatggctta gagatactca aattggtcat gaagtggttc ttcccaaaga aagaggaggc
1201 taatgagcta gccatggtga gggccataga ggatgccgta ctagatcttg aggcaataga
1261 aaataaccac atgacaaccc tgttgaaaga caaagacagc ttagcaacat acatgaaaac
1321 actggacatg gaggaggaga aagccagaag gttgtccaca aaatctgcat cccctgacat
1381 agttgggaca atcaacgctc tgctggctcg aatagcagcg gccaggtcat tagtccacag
1441 ggccaaggaa gagctatcta gcaggataag gccagtagtt gttatgatat ctggtaaacc
1501 aggaataggc aaaactcatc tggccaggga ggtggcaaga aaggtggcat ccactctcac
1561 aggggatcaa agagtcggac tcataccaag aaacggtgtg gaccattggg atgcatacaa
1621 aggtgagaga gtcgtgctgt gggacgacta tggcatgagt aaccccattc atgatgctct
1681 tcgcatacaa gaattggctg atacgtgtcc ccttacctta aattgtgaca gaattgaaaa
1741 taagggaaaa gtttttgaca gtgaagtcat aataattaca acaaaccttg ccaacccagc
1801 cccacttgat tatgtcaact ttgaggcctg ttccaggaga attgatttcc tggtgtacgc
1861 tgaggcacca gaagtggaaa aggcaaaacg ggactttcct ggtcagccag atatgtggaa
1921 ggacgccttc aagccggact tttcacacat caagctacag cttgcacctc agggcggctt
1981 tgacaagaat ggcaacaccc cacatgggaa aggagtgatg aagaccctca ctaccggttc
2041 tctgattgcc cgtgcatcag gcctactgca tgagaggatg gatgaatttg aactccaagg
2101 tcccacaatc accaccttca atttcgaccg gaatagaatc acagcattca gacaattggc
2161 tgcagaaaac aagtatggat tgatggatac catgaaagtt ggcaatcaac taaaaggagt
2221 gaaaaccatg gaagaactta aacaagcaat caggaatgtg accatcaaga ggtgccggat
2281 tatctacggt ggctccacgt atgaccttga atctgatggc aagggcaaag ttttggtgga
2341 aaaggtcaag aacacctctg tacagaccaa caacgagttg gccggggccc tgcaccatct
2401 caaacacgca cgaatcaggt actatgtaaa atgtgtgcaa gaagcagtct attccatcat
2461 acaaattgcc ggcgctgcgt ttgtcaccac gcgcattgca cgccgcatga acatacaaga
2521 actctggtcg aagccgcaat tagatcaaaa tgaatcagag actaaggaag agacccctaa
2581 gtcagaggat gacgagttca tcatatcttc taaggacatc aaggaggaag gaaagaaggg
2641 caaaaacaaa actggccgtg gcaagaaaca cactgcattc tccagcaagg gcttgagcga
2701 tgaggagtat gacgaataca agaggataag agaagagaga aatgggaagt actctataga
2761 ggaatatctt caagacagag acaggtacta tgaggagctc gccattgcca aggccacgga
2821 agaagacttc tgtgaagagg aggagatcaa aatccgtcag agaattttcc gtcccaccag
2881 gaaacaaagg aaggaagaga gggccacatt agggctagtg acaggttcag aaatcaggaa
2941 aagaaaccct gatgacttca aacccaaagg gaagctgtgg gctgatgaca acagaagtgt
3001 tgattacaat gagaaactgg attttgaggc ccccccaagc atatggtcta ggattgtgag
3061 ctttggttct ggctggggct tctgggtatc accaagcctg ttcataacat caactcatgt
3121 aatccccgct ggcataacag aagcatttgg agtccccatc aaacaaattc agatccacaa
3181 atcaggtgaa ttttgccgat tcagattccc aaaaccaatt agaccagatg tgacaggaat
3241 gatcttggaa gaaggtgcgc ctgaaggcac cgtggcaact gtgctcatca aacgccccac
3301 cggagagctc atgcctcttg cagccagaat gggaacacac gcaaccatga aaattcaagg
3361 ccgcatggtt ggcggacaga tgggtatgtt gctcactgga tcaaatgcta aaggaatgga
3421 tttgggaaca actcctggtg actgtggctg tccttacatc tataaaaggg gcaatgacta
3481 tatagtcatt ggggtgcaca ctgcagcagc ccgtggtgga aacaccgtta tctgtgccac
3541 acagggaagt gagggtgagg caactcttga gggtggagat ggcaaaggaa catactgtgg
3601 ggcacccatt ttaggccctg ggggtgcacc aaaattgagc accaaaacca aattttggag
3661 gtcatcgaac acgccccttc caccagggac atatgagcct gcctacctcg gtggccgtga
3721 cccgcgtgtt aagggtgggc cctccttgca gcaggtaatg agagaccagt tgaagccatt
3781 cactgaaccc aggggcaaac ctccaagacc aagtgtattg gaagcagcta aacagaccat
3841 tatcaatgtc ctcgaacaaa ccctggaccc tccacaaaaa tggtcatacg cacaggcgtg
3901 tgcctcactt gacaaaacca cctccagcgg gcacccccat cacgtccgaa agaatgaatt
3961 ctggaatggt gagaccttca ctggtaaatt ggcagaccaa gcatcaaaag caaacctaat
4021 gtttgaggaa gggaaacata tgacaccagt gtatacagca gcactcaagg acgagctagt
4081 caagactgag aaaatctatg gaaagatcaa gaagagactg ctctggggct ctgacttgtc
4141 caccatgatc cggtgcgcta ggtcatttgg tgggctcatg gacgagatga aggcacactg
4201 cataacactc ccagtacgag ttggcatgaa tatgaatgaa gatggcccaa taatatttga
4261 gaaacattcc agatacaaat atcactatga tgcagactac tctcgttggg attcaacaca
4321 acagagggca gtactagcag cagccttgga aatcatggtc agattctctg cagaaccaca
4381 attggcacaa atagtcgctg aggacctgct ggcccctagt gtagtagatg taggagactt
4441 taaaatcaca ataaatgaag ggctcccatc tggtgtgcca tgcacttccc aatggaactc
4501 catcgcacac tggctgctaa ctctctgtgc cttgtctgaa gtcaccaaac tgtcccctga
4561 cattatacaa gcaaattcca tgttctcatt ttacggtgat gacgagattg tcagcaccga
4621 cataaaattg gaccctgaac agttaaccgc caaattgaag gagtacggcc tgaaaccaac
4681 ccgcccagac aagaccgagg gacccctgat catcagtgaa gatttgaacg gactcacttt
4741 cctccgaagg acggtgactc gtgacccagc tggctggttt ggaaaactgg accaaagctc
4801 aattttgagg cagatgtact ggactagagg accaaatcat gaagatccca atgagacaat
4861 gataccccat tctcaaagac ccatacagct catggcactg cttggtgaag cctctctcca
4921 cggaccctct ttctacagta aaatcagtaa attggtcata actgaactca aagaaggtgg
4981 gatggacttt tacgtgccaa ggcaggaacc catgttcagg tggatgaggt tttctgactt
5041 gagcacgtgg gagggcgatc gcaatctggc tcccaatttt gtgaatgaag atggcgtcga
5101 gtgacgccaa cccatctgat gggtccgcag ccaacctcgt accagaggtc aacaatgagg
5161 ttatggcttt ggaacccgtt gttggtgccg ctattgcggc acctgtagcg ggccaacaaa
5221 atgtaattga cccctggatt agaaataatt ttgtacaagc ccctggtggg gagtttacag
5281 tatcccctag aaacgctcca ggtgaaatac tgtggagcgc gcccctaggc cctgacctaa
5341 atccctacct atcccatttg gccagaatgt acaatggtta tgcaggtggt tttgaagtgc
5401 aggtaattct cgcggggaac gcgttcaccg ccgggaagat catatttgca gcagtcccac
5461 caaattttcc aactgaaggc ttaagtccta gccaggtcac tatgttcccc catataatag
5521 tagatgttag acaattagaa cctgtgctga ttcccttacc cgatgtcagg aataatttct
5581 atcattacaa tcagtcaaat gactccacta ttaagttgat agcaatgttg tatacaccac
5641 ttagggctaa taatgctggg gatgatgttt tcacagtttc gtgccgagtt ctcacgagac
5701 catcccccga ttttgatttc atatttttag tgccacccac agttgaatca agaactaaac
5761 cattctctgt cccagtttta actgttgagg agatgaccaa ttcaagattc cccattcctt
5821 tggaaaagtt gttcacgggc cccagcagtg cctttgttgt tcaaccacaa aacggcaggt
5881 gcacaactga tggcgtgctc ctaggcacca cccaactgtc tcctgtcaac atctgcacct
5941 tcagagggga tgtcacccac atcacaggta gtcgcaacta cacaatgaac ttggcttctc
6001 aaaattggaa taactatgac ccaacagaag aaatcccagc ccctctagga actccagatt
6061 ttgtggggaa gattcaaggc atgctcaccc aaaccacaag gacagatggt tcaacacgtg
6121 gccacaaagc tacagtgtac actgggagcg ccgattttgc tccaaaactg ggtagagttc
6181 aatttgaaac tgacacagac catgattttg aagttaatca aaacacaaag ttcaccccag
6241 tcggtgtcat ccaagatggt agtaccaccc accgaaacga accccaacag tgggtgctcc
6301 caagttactc aggcagaaat actcacaatg tacatctggc ccccgctgta gcccccacct
6361 ttccaggtga gcaacttctc ttcttcagat ccaccatgcc cggatgcagc gggtacccca
6421 acatggattt ggactgtctg ctcccccagg aatgggtgca gtacttctat caagaggcag
6481 ccccagcaca atctgatgtg gctctgctaa gatttgtgaa tccagacact ggtagggttt
6541 tgtttgagtg caagcttcat aaatcaggct atgttacagt ggctcacact ggccaacatg
6601 atttggtcat tccccccaat ggttacttta ggtttgattc ctgggtcaac cagttctaca
6661 cgcttgcccc catgggaaat ggaacggggc gtagacgtgt agtataatgg ctggagcttt
6721 ctttgctgga ttggcatctg atgtccttgg ctctggactt ggttccctta tcaatgctgg
6781 ggctggggcc atcaaccaaa aagttgagtt tgaaaataac agaaaattgc aacaagcatc
6841 cttccaattt agcagcaatc tgcaacaggc ttcctttcaa catgataaag agatgctcca
6901 agcacaaatt gaggccacca aaaagctaca acaggaaatg ataaaagtta agcaggcaat
6961 gctcctagag ggtgggttct ctgagacaga tgcagcccgc ggggcaatta acgctcccat
7021 gacaaaagct ttggactgga gcgggactag gtactgggct cccgatgcta ggactacaac
7081 atacaatgca ggccgctttt ccacccctca accatcgggg gcactgccag gaagagctaa
7141 ccttagggat gctgtccctg ctcggggacc ctccaataaa tctcctaact cttctactgc
7201 cacctctgtg tactcaaatc aaaccatttc aacgagactt ggttctacag ctggttctgg
7261 aaccagtgtc tcgagcctcc cgtcaactgc aaggactagg agctgggttg aggatcaaag
7321 taggaatttg tcacctttca tgaggggggc ccacaacata tcatttgtca ccccaccatc
7381 tagcagatcc tctagccaag gcacagtctc aaccgtgcct aaagagattt tggactcctg
7441 gactggcgct ttcaacacgc gcaggcagcc tctcttcgct cacattcgta agcgagggga
7501 gtcacgggtg taatgtgaaa agacaaaact gattattttt cttttttctt tagtgtcttt
7561 taaaaaaa
//