Typing tool
|
|
|
|
|
|
Typing tool
|
Complete norovirus genomes
| MK764018 | GII.4 Sydney | |
|
|---|---|---|---|
| GII.P16 |
ORF1: 1..4997
ORF2: 4978..6600
ORF3: 6600..7406
LOCUS MK764018 7413 bp RNA linear VRL 13-APR-2019
DEFINITION Norovirus GII isolate Hu/US/2016/GII.P16-GII.4 Sydney/Stafford0184
nonstructural polyprotein (ORF1) gene, partial cds; and VP1 (ORF2)
and VP2 (ORF3) genes, complete cds.
ACCESSION MK764018
VERSION MK764018.1
KEYWORDS .
SOURCE Norovirus GII
ORGANISM Norovirus GII
Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes;
Picornavirales; Caliciviridae; Norovirus; Norovirus norwalkense.
REFERENCE 1 (bases 1 to 7413)
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JOURNAL Unpublished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 7413)
AUTHORS Barclay,L., Cannon,J.L., Dickinson,M.K., 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..7413
/organism="Norovirus GII"
/mol_type="genomic RNA"
/strain="Stafford0184"
/isolate="Hu/US/2016/GII.P16-GII.4 Sydney/Stafford0184"
/isolation_source="stool"
/host="Homo sapiens"
/db_xref="taxon:122929"
/geo_loc_name="USA"
/collection_date="11-Jan-2016"
/note="genotype: GII.P16-GII.4 Sydney"
gene <1..4997
/gene="ORF1"
CDS <1..4997
/gene="ORF1"
/codon_start=3
/product="nonstructural polyprotein"
/protein_id="QBX92733.1"
/translation="LKKALGARPKQPAPRGGPQKPPRPPTPELVKRIPPPPPNGEEEE
EPVIRYEVKSGISGLPELTTVPQPDVANTAFSVPPLSLRENREAKEPLTGAILEMWDG
EIYHYGLYVEKGLVLGVHKPPAAISMARVELTPLSLYWRVVYTPQYLISPETLRRLNG
EAFPYTAFDNNCYAFCCWVLDLNDSWLSRRMVQRTTGFFRPYQEWNRKPLPTMDDSKI
KKVANIFLCSLSTLFTRPIKDLIGKIKPLNILNILATCDWTFAGIVESLILLAELFGV
FWTPPDVSAMIAPLLGDYELQGPEDLAVELVPVVMGGIGLVLGFTKEKIGKMLSSAAS
TLRACKDLGAYGLEILKLVMKWFFPKKEEANELAMVRAIEDAVLDLEAIENNHMTTLL
KDKDSLATYMKTLDMEEEKARRLSTKSASPDIVGTINALLARIAAARSLVHRAKEELS
SRIRPVVVMISGKPGIGKTHLAREVARKVASTLTGDQRVGLIPRNGVDHWDAYKGERV
VLWDDYGMSNPIHDALRIQELADTCPLTLNCDRIENKGKVFDSEVIIITTNLANPAPL
DYVNFEACSRRIDFLVYAEAPEVEKAKRDFPGQPDMWKDAFKPDFSHIKLQLAPQGGF
DKNGNTPHGKGVMKTLTTGSLIARASGLLHERMDEFELQGPTITTFNFDRNRITAFRQ
LAAENKYGLVDTMKVGNQLKGVKTMEELKQAIRNVTIKRCRIIYGGSTYDLESDGKGK
VLVEKVKNISVQTNNELAGALHHLKHARIRYYVKCVQEVVYSIIQIAGAAFVTTRIAR
RMNIQELWSKPQLDQNESETKEEAPKSEDDEFIISSKDIKEEGKKGKNKTGRGKKHTA
FSSKGLSDEEYDEYKRIREERNGKYSIEEYLQDRDRYYEELAIAKATEEDFCEEEEIK
IRQRIFRPTRKQRKEERATLGLVTGSEIRKRNPDDFKPKGKLWADDNRSVDYNEKLDF
EAPPSIWSRIVSFGSGWGFWVSPSLFITSTHVIPAGITEAFGVPIKQIQIHKSGEFCR
FRFPKPIRPDVTGMILEEGAPEGTVATVLIKRPTGELMPLAARMGTHATMKIQGRMVG
GQMGMLLTGSNAKGMDLGTTPGDCGCPYIYKRGNDYIVIGVHTAAARGGNTVICATQG
SEGEATLEGGDDKGTYCGAPILGPGGAPKLSTKTKFWRSSNTPLPPGTYEPAYLGGRD
PRVKGGPSLQQVMRDQLKPFTEPRGKPPRPSVLEAAKQTIINVLEQTLDPPQKWTYAQ
ACASLDKTTSSGHPYHVRKNEFWNGETFTGKLADQASKANLMFEEGKHMTPVYTAALK
DELVKTEKIYGKIKKRLLWGSDLSTMIRCARSFGGLMDEMKAHCISLPVRVGMNMNED
GPIIFEKHSRYKYHYDADYSRWDSTQQRAVLAAALEIMVRFSAEPQLAQIVAEDLLAP
SVVDVGDFKITINEGLPSGVPCTSQWNSIAHWLLTLCALSEVTKLSPDIIQAHSMFSF
YGDDEIVSTDIKLDPEQLTAKLKEYGLKPTRPDKTEGPLIISEDLNGLTFLRRTVTRD
PAGWFGKLDQSSILRQMYWTRGPNHEDPNETMIPHSQRPIQLMALLGEASLHGPSFYS
KISKLVITELKEGGMDFYVPRQEPMFRWMRFSDLSTWEGDRNLAPNFVNEDGVE"
mat_peptide <1..893
/gene="ORF1"
/product="p48"
mat_peptide 894..1991
/gene="ORF1"
/product="NTPase"
mat_peptide 1992..2522
/gene="ORF1"
/product="p22"
mat_peptide 2523..2921
/gene="ORF1"
/product="VPg"
mat_peptide 2922..3464
/gene="ORF1"
/product="Pro"
mat_peptide 3465..4994
/gene="ORF1"
/product="RdRp"
gene 4978..6600
/gene="ORF2"
CDS 4978..6600
/gene="ORF2"
/note="major capsid protein"
/codon_start=1
/product="VP1"
/protein_id="QBX92734.1"
/translation="MKMASSDANPSDGSAANLVPEVNNEVMALEPVVGAAIAAPVAGQ
QNVIDPWIRNNFVQAPGGEFTVSPRNAPGEILWSAPLGPDLNPYLSHLARMYNGYAGG
FEVQVILAGNAFTAGKIIFAAVPPNFPTEGLSPSQVTMFPHIIVDVRQLEPVLIPLPD
VRNNFYHYNQSNDSTIKLIAMLYTPLRANNAGDDVFTVSCRVLTRPSPDFDFIFLVPP
TVESRTKPFSVPVLTVEEMTNSRFPIPLEKLFTGPSSAFVVQPQNGRCTTDGVLLGTT
QLSPVNICTFRGDVTHITGSRNYTMNLASQNWNNYDPTEETPAPLGAPDFVGKIQGML
TQTTRTDGSTRGHKATVYTGSADFAPKLGRVQFETDTDHDFEANQNTKFTPVGVIQDG
STTHRNEPQQWVLPSYSGRNTHNVHLAPAVAPTFPGEQLLFFRSTMPGCSGYPNMDLD
CLLPQEWVQYFYQEAAPAQSDVALLRFVNPDTGRVLFECKLHKSGYVTVAHTGQHDLV
IPPNGYFRFDSWVNQFYTLAPMGNGTGRRRVV"
gene 6600..7406
/gene="ORF3"
CDS 6600..7406
/gene="ORF3"
/note="minor structural protein; small basic protein"
/codon_start=1
/product="VP2"
/protein_id="QBX92735.1"
/translation="MAGAFFAGLASDVLGSGLGSLINAGAGAINQKVEFENNRKLQQA
SFQFSSNLQQASFQHDKEMLQAQIEATKKLQQELMKVKQAMLLEGGFSETDAARGAIN
APMTKALDWSGTRYWAPDARTTTYNAGRFSTPQPSGTLPGRANLRDAVPARGPSNKSS
NSSTATSVYSNQTISTRLGSTAGSGTSVSSLPSTARTRSWVEDQSRNLSPFMRGAHNI
SFVTPPSSRSSSQGTVSTVPKEILDSWTGAFNTRRQPLFAHIRKRGESRV"
ORIGIN
1 ccttaaagaa agccctcggg gctaggccca aacagcctgc cccgagaggc ggaccacaaa
61 agcccccaag accaccaact cccgagttgg tcaagaggat accccctcct ccacctaatg
121 gcgaagaaga agaagaacca gtcattaggt atgaggttaa gagtgggatc tctggcctgc
181 ccgagctcac aacagtcccc caaccggacg tggccaacac agcattcagt gttccaccac
241 tgagcttgag agaaaacagg gaggccaagg aaccgctaac aggggcaata ttagagatgt
301 gggatggaga gatataccac tatggccttt acgtggagaa aggcttagtg ttgggtgtgc
361 acaaaccacc tgcagccata agcatggcaa gagtggagct gacgccgctg tcattgtact
421 ggcgtgtggt gtacactccc caatacctca tctcccctga aactctcagg aggctcaacg
481 gagaggcgtt cccctacacc gcctttgaca acaactgcta tgccttttgc tgctgggtgt
541 tagacctcaa tgactcatgg cttagcagga ggatggtgca aagaacaacg ggcttcttca
601 gaccttacca agagtggaac agaaaacccc tgcctaccat ggatgactcc aaaattaaga
661 aggtagcaaa tatattccta tgttcattgt ccacattatt caccagaccc ataaaagacc
721 tcataggaaa aattaaacca ttaaacatat tgaacatcct ggcaacgtgt gactggacgt
781 ttgccggaat agtggagtct ctgatattac ttgctgaact cttcggagtt ttctggacac
841 ccccagatgt gtctgctatg atcgctccct tactcgggga ctacgagttg caagggccag
901 aagacctcgc cgttgaactc gtacctgtgg taatgggagg gattggtttg gtgttgggat
961 tcaccaaaga gaaaattggc aaaatgttgt cctcagcagc atcaacactc agggcttgca
1021 aagatcttgg tgcctatggc ttagagatac tcaaattggt catgaagtgg ttcttcccaa
1081 agaaagagga ggccaatgag ctagccatgg tgagggccat agaggatgcc gtactagatc
1141 ttgaggcaat agaaaataat cacatgacaa ccctgttgaa agacaaagac agcttagcaa
1201 catacatgaa aacgctggac atggaggagg agaaagccag aaggttgtcc acaaagtctg
1261 catcccctga catagttggg acaatcaacg ccctgctggc tcgaatagca gcggccaggt
1321 cattagtcca cagggccaag gaagagctat ctagcaggat aagaccagta gttgttatga
1381 tatctggcaa accaggaata ggcaaaactc atctggccag ggaggtggca agaaaggtgg
1441 catccactct cacaggggat caaagagtcg gactcatacc aagaaacggt gtggaccatt
1501 gggatgcata caaaggtgag agagtcgtgc tgtgggacga ctatggcatg agtaacccca
1561 ttcatgatgc tcttcgcata caagaattgg ctgatacgtg tccccttacc ttaaattgtg
1621 acagaattga aaataaggga aaagtttttg acagcgaagt cataataatt acaacaaacc
1681 ttgccaatcc agccccactt gattatgtca actttgaggc ctgttccagg agaattgatt
1741 tcctggtgta cgctgaggca ccagaagtag aaaaggcaaa acgggacttt cctggtcagc
1801 cagatatgtg gaaggacgcc ttcaagccgg acttttcaca catcaagcta cagcttgcac
1861 ctcagggcgg ctttgacaag aatggcaaca ccccacatgg gaaaggagtg atgaagaccc
1921 tcactaccgg ttctctgatt gcccgtgcat caggcctact gcacgagagg atggatgaat
1981 ttgaactcca aggtcccaca atcaccacct tcaatttcga ccggaacaga atcacagcat
2041 tcagacagtt ggctgcagaa aacaagtatg gattggtgga taccatgaaa gttggcaatc
2101 aactaaaagg agtgaaaact atggaagaac tcaaacaagc aatcaggaat gtgaccatca
2161 agaggtgccg gatcatctac ggtggctcca cgtatgacct tgaatctgat ggcaagggca
2221 aagttttggt ggaaaaggtc aagaacatct ctgtacagac caacaacgag ttggccgggg
2281 ccctgcacca tctcaaacac gcccgaatca ggtactatgt caaatgtgtg caagaagtag
2341 tctattccat catacaaatt gccggcgctg cgtttgtcac cacgcgcatt gcacgccgca
2401 tgaacataca agaactctgg tcgaagccac aattagatca aaatgaatca gagactaagg
2461 aagaggcccc caagtcagaa gatgacgagt tcatcatatc ttctaaggac atcaaggagg
2521 aaggaaagaa gggcaaaaac aaaactggcc gtggcaagaa acacactgca ttctccagca
2581 agggcttgag cgatgaggag tatgacgagt acaagaggat aagagaagag agaaatggga
2641 agtactctat agaggagtat cttcaagaca gagacaggta ctatgaggag ctcgccattg
2701 ccaaggccac ggaagaagac ttctgtgaag aggaggagat caaaatccgt cagagaattt
2761 tccgtcccac caggaaacaa agaaaggaag agagggccac attagggcta gtaacaggtt
2821 cagaaatcag aaaaagaaac cctgatgact tcaaacccaa agggaagctg tgggccgatg
2881 acaacagaag tgttgactac aatgagaaac tggactttga ggccccccca agcatatggt
2941 ctaggattgt gagctttggt tctggctggg gcttctgggt atcaccaagc ctgttcataa
3001 catcaactca tgtaatcccc gcaggcataa cagaagcatt tggagtcccc atcaaacaaa
3061 ttcagatcca caaatcaggt gaattttgcc gattcagatt cccaaaacca attagaccag
3121 atgtgacagg aatgatcttg gaagaaggtg cgcctgaagg caccgtggca actgtgctca
3181 tcaaacgccc caccggagag ctcatgcctc ttgcagccag aatgggaaca cacgcaacca
3241 tgaaaattca aggccgcatg gttggcggac agatgggtat gttgctcact ggatcaaatg
3301 ctaaaggaat ggatttggga acaactcctg gtgactgcgg ctgtccttac atctataaaa
3361 ggggcaatga ctatatagtc attggggtgc acactgcagc agcccgtggt ggaaacaccg
3421 tcatctgtgc cacacaggga agtgagggtg aggcaactct tgagggtgga gatgacaaag
3481 gaacatactg tggggcaccc attctaggcc ctgggggtgc accaaaattg agcaccaaaa
3541 ccaaattttg gaggtcatcg aacacgcccc ttccaccagg gacatatgag cctgcctacc
3601 tcggtggccg tgatccgcgt gttaagggtg ggccctcctt gcagcaggta atgagagacc
3661 agttgaagcc attcactgaa cccaggggca aacctccaag accaagtgta ttggaagcag
3721 ccaaacaaac cattatcaat gtcctcgaac aaaccctgga ccctccacaa aaatggacat
3781 acgcacaggc gtgtgcctca cttgacaaaa ccacctccag cgggcatccc tatcacgtcc
3841 gaaagaatga attctggaat ggtgagacct tcactggtaa attggcagac caagcatcaa
3901 aagcaaacct aatgtttgag gaagggaaac acatgacacc agtgtataca gcagcactca
3961 aggacgagct agtcaagact gagaaaatct atggaaagat caagaagaga ctgctctggg
4021 gctctgactt gtccaccatg atccggtgcg ctaggtcatt tggtgggctc atggacgaga
4081 tgaaggcaca ctgcatatca ctcccagtac gagttggcat gaatatgaat gaagatggcc
4141 caataatatt tgagaaacat tccagataca aataccacta tgatgcagac tactctcgtt
4201 gggattcaac acaacagagg gcagtactag cagcagcctt agaaatcatg gtcagattct
4261 ctgcagaacc acaactggca caaatagtcg ctgaggatct gctggcccct agtgtagtag
4321 atgtagggga ctttaaaatc acaataaatg aagggctccc atctggtgtg ccatgcactt
4381 ctcaatggaa ctccatcgca cactggctgc taaccctctg tgccttgtct gaagtcacca
4441 aactgtcccc tgacattata caagcacatt ccatgttctc attttacggt gatgacgaga
4501 ttgtcagcac cgacataaaa ttggaccctg aacagttaac cgccaaattg aaggagtacg
4561 gcctgaaacc aacccgccca gacaagaccg agggacccct aatcatcagt gaagatttga
4621 acggactcac tttcctccga aggacggtga ctcgtgaccc agctggctgg tttggaaaac
4681 tggaccaaag ctcaattttg aggcaaatgt actggactag aggaccaaat catgaagacc
4741 ccaatgagac aatgataccc cattctcaaa gacccataca gctcatggca ctgcttggtg
4801 aagcctctct tcacggaccc tctttctaca gtaaaatcag taaattggtc ataactgaac
4861 tcaaagaagg tgggatggac ttttacgtgc caaggcagga acccatgttc aggtggatga
4921 ggttttctga cttgagcacg tgggagggcg atcgcaatct ggctcccaat tttgtgaatg
4981 aagatggcgt cgagtgacgc caacccatct gatgggtccg cagccaacct cgtaccagag
5041 gtcaacaatg aggttatggc tttggagccc gttgttggtg ccgctattgc ggcacctgta
5101 gcgggccaac aaaatgtaat tgacccctgg attagaaata attttgtaca agcccctggt
5161 ggggaattta cagtatcccc tagaaacgct ccaggtgaaa tactatggag cgcgccccta
5221 ggccctgacc taaatcccta cctatcccat ttggccagaa tgtacaatgg ttatgcaggt
5281 ggttttgaag tgcaggtaat tctcgcgggg aacgcgttca ccgccgggaa gatcatattt
5341 gcagcagtcc caccaaattt tccaactgaa ggcttaagcc ctagccaggt cactatgttc
5401 ccccatataa tagtagatgt tagacaatta gaacctgtgc tgattccctt acccgatgtc
5461 aggaataatt tttatcatta caatcagtca aatgactcca ctattaagtt gatagcaatg
5521 ttgtatacac cacttagggc taataatgct ggggatgatg ttttcacagt ttcgtgccga
5581 gttctcacga gaccatcccc cgattttgat ttcatatttc tagtgccacc cacagttgag
5641 tcaagaacca aaccattctc tgtcccagtt ttaactgttg aggagatgac caattcaaga
5701 ttccccattc ctttggaaaa gttgttcacg ggccccagca gtgcctttgt tgttcaacca
5761 caaaacggca ggtgcacaac tgatggcgtg ctcctaggca ccacccaact gtctcctgtc
5821 aacatctgca ccttcagagg ggatgtcacc cacatcacag gtagtcgcaa ctacacaatg
5881 aatttggctt ctcaaaattg gaacaactat gacccaacag aagaaacccc agcccctcta
5941 ggagccccag attttgtggg gaagattcaa ggcatgctca cccagaccac aagaacagat
6001 ggttcaacac gcggtcacaa agctacggtg tacactggga gcgccgactt tgctccaaaa
6061 ctgggtagag ttcaatttga aactgacaca gaccatgatt ttgaagctaa tcaaaacaca
6121 aagttcaccc cagtcggtgt catccaagat ggtagcacca cccaccgaaa cgaaccccaa
6181 cagtgggtgc tcccaagtta ctcaggcaga aatactcaca atgtacatct ggcccccgct
6241 gtagccccca cctttccggg tgaacaactt ctcttcttca gatccaccat gcccggatgt
6301 agcgggtacc ccaacatgga tttggactgt ctgctccccc aggaatgggt gcagtacttc
6361 taccaagagg cagccccagc acaatctgat gtggctctgc taagatttgt gaatccagac
6421 acaggtaggg ttttgtttga gtgcaagctt cacaaatcag gctatgttac agtggctcac
6481 actggccaac acgatttggt tatccccccc aatggttact ttaggtttga ttcctgggtc
6541 aaccagttct acacgcttgc ccccatggga aatggaacgg ggcgtagacg tgtagtataa
6601 tggctggagc tttctttgct ggattggcat ctgatgtcct tggctctgga cttggttccc
6661 ttatcaatgc tggggctggg gccatcaacc aaaaagttga gtttgaaaat aacagaaaat
6721 tgcaacaagc atccttccaa tttagcagca atctgcaaca ggcttccttt caacatgata
6781 aagagatgct ccaagcacaa attgaggcca ccaaaaagct acaacaggaa ctgatgaaag
6841 ttaagcaggc aatgctccta gagggtgggt tctctgagac agatgcagcc cgcggggcaa
6901 ttaacgcccc catgacaaaa gctttggact ggagcgggac aaggtactgg gctcccgatg
6961 ctaggactac aacatacaat gcaggccgct tttccacccc tcaaccatcg gggacactgc
7021 caggaagagc taatcttagg gatgctgtcc ctgctcgggg accctctaat aaatcttcta
7081 actcttctac tgccacctct gtgtactcaa atcaaactat ttcaacgaga cttggttcta
7141 cagctggttc tggaaccagt gtctcgagcc tcccgtcaac tgcaaggact aggagctggg
7201 ttgaggatca aagtaggaat ttgtcacctt tcatgagggg ggctcacaac atatcatttg
7261 tcaccccacc atctagcaga tcctctagcc aaggcacagt ctcaaccgtg cctaaagaga
7321 ttttggactc ctggactggc gctttcaaca cgcgcaggca gcctctcttc gctcacattc
7381 gtaagcgagg ggagtcacgg gtgtaatgtg aaa
//