Typing tool
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Typing tool
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Complete norovirus genomes
| MK762565 | GII.13 | |
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| GII.P16 |
ORF1: 1..5073
ORF2: 5054..6682
ORF3: 6682..7413
LOCUS MK762565 7420 bp RNA linear VRL 13-APR-2019
DEFINITION Norovirus GII isolate Hu/US/2016/GII.P16-GII.13/CS0004
nonstructural polyprotein (ORF1) gene, partial cds; and VP1 (ORF2)
and VP2 (ORF3) genes, complete cds.
ACCESSION MK762565
VERSION MK762565.1
KEYWORDS .
SOURCE Norovirus GII
ORGANISM Norovirus GII
Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes;
Picornavirales; Caliciviridae; Norovirus; Norwalk virus.
REFERENCE 1 (bases 1 to 7420)
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JOURNAL Unpublished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 7420)
AUTHORS Barclay,L., Cannon,J.L., 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..7420
/organism="Norovirus GII"
/mol_type="genomic RNA"
/strain="CS0004"
/isolate="Hu/US/2016/GII.P16-GII.13/CS0004"
/isolation_source="stool"
/host="Homo sapiens"
/db_xref="taxon:122929"
/country="USA"
/collection_date="08-Jan-2016"
/note="genotype: GII.P16-GII.13"
gene <1..5073
/gene="ORF1"
CDS <1..5073
/gene="ORF1"
/codon_start=1
/product="nonstructural polyprotein"
/protein_id="QBX91022.1"
/translation="TVAVACNNNNDKEKSSGEGLFTNMSSTLKKALGARPKQPAPRDN
SQKPPRPPTPELVKRMPPPPPNGEEEEPVIRYEVKSGISGLPELTTVPQPDVANTAFS
VPPLSLRENREAKEPLTGAILEMWDGEIYHYGLYVEKGLVLGVHKPPAAISMAKVELT
PLSLYWRVVYTPQYLISPETLRRLNGEAFPYTAFDNNCYAFCCWVLDLNDSWLSRRMV
QRTTGFFRPYQEWNRKPLPTVDDSKIKKVANIFLCSLSSLFTRPIKDLMGKIKPLNIL
NILATCDWTFAGIVESLILLAELFGVFWTPPDVSAMIAPLLGDYELQGPEDLAVELVP
VVMGGIGLVLGFTKEKIGKMLSSAASTLRACKDLGAYGLEILKLVMKWFFPKKEEANE
LAMVRAIEDAVLDLEAIENNHMTTLLKDKDSLATYMKTLDMEEEKARRLSTKSASPDI
VGTINALLARIAAARSLVHRAKEELSSRIRPVVVMISGKPGIGKTHLAREVARKVAST
LTGDQRVGLIPRNGVDHWDAYKGERVVLWDDYGMSNPIHDALRIQELADTCPLTLNCD
RIENKGKVFDSEVIIITTNLANPAPLDYVNFEACSRRIDFLVYAEAPEVEKAKRDFPG
QPDMWKDAFKSDFSHIKLQLAPQGGFDKNGNTPHGKGVMKTLTTGSLIARASGLLHER
MDEFELQGPTVTTFNFDRNRIAAFRQLAAENKYGLVDTMRVGNQLKGVKTMEELKQAI
KNVTIKRCRIIYGGSTYDLESDGKGRVLVEKVKNTSVQTNNELAGALHHLKHARIRYY
VKCVQEAVYSIIQIAGAAFVTTRIVRRMNIQELWSKPPLDQNESEAKEEAPKSEDDEF
IISSKDIKEEGKKGKNKTGRGKKHTAFSSKGLSDEEYDEYKRIREERNGKYSIEEYLQ
DRDRYYEELAIAKATEEDFCEEEEIKIRQRIFRPTRKQRKEERVTLGLVTGSEIRKRN
PDDFKPKGKLWADDNRSVDYNEKLDFEAPPSIWSRIVSFGSGWGFWVSPSLFITSTHV
IPAGITEAFGVPIKQIQVHKSGEFCRLRFPKPIRSDVTGMILEEGAPEGTVATVLIKR
PTGELMPLAARMGTHATMKIQGRMVGGQMGMLLTGSNAKGMDLGTTPGDCGCPYIYKR
GNDYIVIGVHTAAARGGNTVICATQGSEGEATLEGGDDKGTYCGAPILGPGGAPKLST
KTKFWRSSNTPLPPGTYEPAYLGGRDPRVKGGPSLQQVMRDQLKPFTEPRGKPPRPSV
LEAAKQTIINVLEQTLDPPQKWTYAQACASLDKTTSSGHPHHVRKNEFWNGETFTGKL
ADQASKANLMFEEGKHMTPVYTAALKDELVKTDKVYGKIKKRLLWGSDLSTMIRCARS
FGGLMDEMKAHCITLPVRVGMNMNEDGPIIFEKHSRYKYHYDADYSRWDSTQQRAVLA
AALEIMVRFSAEPQLAQIVAEDLLAPSVVDVGDFKISINEGLPSGVPCTSQWNSIAHW
LLTLCALSEVTKLSPDIVQANSMFSFYGDDEIVSTDIKLDPEKLTTKLKEYGLKPTRP
DKTEGPLTISEDLNGLTFLRRTVTRDPAGWFGKLDQSSILRQMYWTRGPNHEDPNETM
IPHSQRPIQLMALLGEASLHGPSFYSKISKLVITELKEGGMDFYVPRQEPMFRWMRFS
DLSTWEGDRNLAPNFVNEDGVE"
mat_peptide <1..969
/gene="ORF1"
/product="p48"
mat_peptide 970..2067
/gene="ORF1"
/product="NTPase"
mat_peptide 2068..2598
/gene="ORF1"
/product="p22"
mat_peptide 2599..2997
/gene="ORF1"
/product="VPg"
mat_peptide 2998..3540
/gene="ORF1"
/product="Pro"
mat_peptide 3541..5070
/gene="ORF1"
/product="RdRp"
gene 5054..6682
/gene="ORF2"
CDS 5054..6682
/gene="ORF2"
/note="major capsid protein"
/codon_start=1
/product="VP1"
/protein_id="QBX91023.1"
/translation="MKMASNDAAPSNDGAASLVPEAINETMPLEPVAGASIAAPVAGQ
TNIIDPWIRTNFVQAPNGEFTVSPRNSPGEILLNLELGPDLNPYLAHLSRMYNGYAGG
VEVQVLLAGNAFTAGKILFAAIPPNFPVDMISPAQITMLPHLIVDVRTLEPIMIPLPD
VRNVFYHFNNQPQPRMRLVAMLYTPLRSNGSGDDVFTVSCRVLTRPTPDFEFIYLVPP
SVESKTKPFTLPILTISELTNSRFPIPIEQLYTAPNENNVVQCQNGRCTLDGELQGTT
QLLSSAVCSYRGRTVANSGDNWDQNLLQLTYPSGASYDPTDEVPAPLGTQDFSGLLYG
VLTQDNVSEGAGEAKNAKGVYISTTSGRFTPKIGTIGLHSITENVHPNQQSRFTPVGV
AQNENTPFQQWVLPHYAGALALNTNLAPAVAPTFPGEQLLFFRSRVPCVQGLQGQDAF
IDCLLPQEWVNHFYQEAAPSQADVALIRYVNPDTGRTLFEAKLHRSGFITVSHTGTYP
LVVPPNGHFRFDSWVNQFYSLAPMGTGNGRRRVQ"
gene 6682..7413
/gene="ORF3"
CDS 6682..7413
/gene="ORF3"
/note="minor structural protein; small basic protein"
/codon_start=1
/product="VP2"
/protein_id="QBX91024.1"
/translation="MAGAFIAGLAGDMLTSAVGSLTSAGANAINQKLNFDYNKQLQNA
SFQHDKEMLQAQIDATKKLQSEMIAIKHGVLTAGGFSPADAARGAVNAPMTRVLDWSG
TRYYAPNSVQTTSYSGQFTPSPVHRAQVKSPSNSSQRTAAPSSIRSLSTQSTSLGSTS
SGGSSTISSSSRTANWVQQQRALSPYMQGALQTAYVTPPSSRASSMSSVSTVPKGVLD
SWTPVFNTRRQPLFAHLRKRGESQV"
ORIGIN
1 accgttgccg ttgcttgcaa caacaacaac gacaaggaaa aatcttcagg tgaaggctta
61 ttcacaaaca tgtcttccac cttaaagaaa gccctcgggg cccggcccaa acagcctgcc
121 ccgagggaca actcacaaaa gcccccaaga ccgccaactc ccgagttggt taagaggatg
181 cctcctcccc caccaaacgg agaagaggaa gaaccagtca ttaggtatga ggttaagagt
241 ggaatctctg gcctgcccga gctcacaaca gtccctcaac cggatgtggc caacacggca
301 ttcagtgtcc caccgctgag cttgagagaa aacagggagg ccaaggaacc gctgacaggg
361 gcaatattag agatgtggga tggagagata taccactatg gcctgtacgt ggagaaaggc
421 ttagtgttgg gtgtgcacaa accacctgca gctataagca tggcaaaagt ggagctgacg
481 ccgttgtcat tgtactggcg tgtggtctac accccccaat acctcatctc ccctgaaact
541 ctcaggaggc tcaacggaga ggcattcccc tacactgctt ttgacaacaa ctgctatgcc
601 ttttgctgtt gggtattaga cctcaatgat tcatggctta gcaggaggat ggtgcaaaga
661 acaacaggct tcttcagacc ttaccaagag tggaatagaa aacccctgcc cactgtggat
721 gactccaaaa tcaagaaggt ggcaaacata ttcctgtgct cactgtcctc gttgttcacc
781 agacctataa aagacctcat gggaaaaatt aagccattaa acatcttgaa catcctggca
841 acgtgcgact ggacattcgc cggaatagtg gagtctctta tattacttgc tgaactcttt
901 ggagttttct ggacaccccc agatgtgtct gctatgatcg ctcctttact tggagactac
961 gagttgcaag gaccagaaga ccttgccgtt gagctcgtac ctgtagtgat gggagggatt
1021 ggtttggtgt tgggattcac caaagagaaa attggaaaga tgttgtcctc agcagcatca
1081 acgctcaggg cttgtaaaga tcttggtgcc tatggcttag agatactcaa actggtcatg
1141 aagtggttct tcccaaagaa agaagaggcc aatgagctag ccatggtgag agctatagag
1201 gatgctgtac tagatcttga ggcaatagaa aataatcaca tgacaactct gttgaaagac
1261 aaagacagcc tagcaaccta catgaaaaca ctagacatgg aggaggaaaa ggccagaaga
1321 ttgtccacaa aatctgcatc ccctgacata gttgggacga tcaacgccct gctggctcga
1381 atagcagcgg ctaggtcact agtccacagg gccaaggagg agttatctag caggataaga
1441 ccagtggttg ttatgatatc tggcaaacca gggataggca aaactcattt agccagggaa
1501 gtggcaagaa aggtggcatc cactctcaca ggggatcaaa gagtcgggct cataccgaga
1561 aacggtgtgg accattggga tgcatacaaa ggtgagagag tcgtgttgtg ggacgactat
1621 ggcatgagca accccattca tgatgctctg cgcatacaag aattggctga cacgtgtccc
1681 cttaccttaa attgtgacag aattgaaaat aagggaaaag tttttgacag tgaagtcata
1741 ataatcacaa caaaccttgc caatccagct ccacttgatt atgttaactt tgaggcctgt
1801 tccaggagaa ttgacttcct ggtgtacgcc gaggcaccag aagtagaaaa ggcaaaacga
1861 gactttcctg gtcaaccgga tatgtggaag gacgccttca agtcggactt ttcacatatc
1921 aagctgcaac ttgcacctca gggcggcttt gacaagaatg gcaacacccc acatgggaaa
1981 ggagtgatga agaccctcac caccggttca ctgatcgccc gtgcatcagg cttactgcat
2041 gagaggatgg atgaatttga actccaaggc cccacagtca ccacctttaa ttttgaccgg
2101 aacagaatcg ctgcattcag acaattggct gcagaaaaca agtatggatt ggtggacacc
2161 atgagagttg gcaatcaatt aaaaggggtg aaaaccatgg aagaactcaa acaagcaatc
2221 aagaatgtga ccatcaagag gtgccggatc atctacggcg gctccacgta tgaccttgaa
2281 tctgatggta agggcagagt tctggtggaa aaggtcaaaa acacctctgt acagaccaac
2341 aacgagttgg ccggggccct gcatcacctc aaacatgccc gaatcaggta ctatgtcaaa
2401 tgtgtgcaag aagcagtcta ctctattata caaatcgccg gcgctgcgtt tgtcaccaca
2461 cgcatagtac gccgcatgaa catacaagag ctttggtcga agccaccatt agatcaaaat
2521 gaatcagagg ctaaggaaga ggcccccaag tcagaagatg acgagttcat catatcttct
2581 aaagacatca aggaggaagg aaagaagggc aaaaacaaaa ctggccgtgg caagaaacac
2641 actgcattct ctagcaaggg cttgagcgat gaagagtacg atgagtacaa gaggataaga
2701 gaagagagaa atgggaagta ctctatagag gagtatcttc aagacagaga caggtactat
2761 gaggaactcg ccatcgccaa ggccacggaa gaagacttct gtgaggagga ggagatcaaa
2821 atccgtcaga ggatcttccg tcccaccagg aagcaaagga aggaagagag ggtcacacta
2881 gggctagtaa ctggttcaga aatcagaaaa agaaaccctg atgacttcaa acctaaaggg
2941 aaactgtggg ctgatgacaa cagaagtgtt gactacaatg agaaactgga ctttgaggcc
3001 cccccaagca tatggtctag gattgtgagt tttggttctg gttggggttt ctgggtgtca
3061 ccaagcctgt tcataacatc aactcacgta atccctgcag gcataacaga ggcatttggt
3121 gtccccatca aacaaatcca ggtccacaaa tcaggtgaat tttgccggct cagattccca
3181 aaaccaatta gatcagatgt gacaggaatg atcttggaag aaggtgcgcc tgagggcacc
3241 gtggcaaccg tgctcatcaa acgacctacc ggagagctca tgccccttgc agccagaatg
3301 ggaacacacg caaccatgaa aattcagggc cgcatggttg gcggacagat gggtatgttg
3361 ctcactggtt caaatgctaa aggaatggat ttaggaacaa ctcctggtga ttgtggctgt
3421 ccctacatct acaagagggg caatgactat atagtcattg gggtgcacac agcagcagcc
3481 cgtggtggaa acaccgtcat ctgtgccaca cagggaagtg agggtgaggc aacccttgag
3541 ggtggagatg acaaaggaac atactgtggg gcacccattc taggccccgg gggggcacca
3601 aaattgagca ccaaaaccaa gttttggagg tcatcgaaca cgcctcttcc accagggacg
3661 tatgagcctg cctacctcgg tggccgtgac ccgcgtgtta agggtgggcc ctccttgcag
3721 caggtaatga gagaccagtt gaagccattc accgagccca ggggtaaacc tccaagacca
3781 agtgtgttgg aagcagccaa acaaaccatc atcaacgtcc tcgaacaaac tctggaccct
3841 ccacaaaaat ggacatacgc acaggcgtgt gcttcacttg acaaaaccac ctccagcggg
3901 cacccccacc atgtccggaa gaatgaattc tggaatggtg agaccttcac tggtaaattg
3961 gcagaccaag catcaaaagc aaacttaatg tttgaggaag ggaaacacat gacaccagtg
4021 tatacagcag ccctcaagga tgagctggtc aagactgaca aagtctatgg aaagatcaag
4081 aagagactgc tctggggctc tgacttatcc accatgatcc ggtgcgccag gtcctttggt
4141 gggctcatgg atgagatgaa agcgcactgc ataacactcc cagtccgagt aggcatgaac
4201 atgaatgaag atggtccaat aatatttgag aagcactcca gatacaagta tcactatgat
4261 gcagattact cccgctggga ttcaacacaa cagagggcag tgctagcagc agccttggag
4321 atcatggtca ggttctctgc agagccacaa ttggcacaaa tagtcgctga ggatctgctg
4381 gcccccagtg tggtagatgt aggagacttt aaaatttcaa taaatgaagg gctcccctct
4441 ggtgtaccat gcacttctca atggaactcc atcgcacact ggctgctaac cctctgcgcc
4501 ttgtctgaag tcaccaaact gtcccctgac attgtacagg caaactccat gttctcattt
4561 tacggtgatg acgagattgt cagcaccgat ataaaattgg accctgaaaa gttgaccacc
4621 aaattgaagg agtacggcct gaaaccaact cgcccagaca aaaccgaggg acccctgacc
4681 atcagtgagg atttgaacgg actcactttc ctccggagaa cggtgactcg tgacccagct
4741 ggctggtttg gaaaattgga ccaaagctca atattgaggc agatgtactg gactagagga
4801 ccgaatcatg aagaccccaa cgagacaatg ataccccact ctcaaagacc catacagctc
4861 atggcactgc ttggtgaggc ctcccttcac ggaccctctt tctacagtaa aattagtaag
4921 ttggttataa ctgaactcaa agaaggtggg atggattttt acgtgccaag gcaggaaccc
4981 atgttcaggt ggatgaggtt ttctgacttg agcacgtggg agggcgatcg caatctggct
5041 cccaattttg tgaatgaaga tggcgtcgaa tgacgccgct ccatcgaatg atggtgcagc
5101 tagtctcgta ccagaggcca ttaatgagac tatgccattg gaacccgttg ctggcgcatc
5161 tattgctgcc ccagtggcgg gacaaactaa tataattgac ccctggataa gaacaaattt
5221 tgtgcaagcc cctaatggag agttcacagt gtcaccgaga aattcccctg gagagattct
5281 attaaattta gagttaggac cagatttgaa tccttatctg gcccatctgt caaggatgta
5341 caatggatat gctggaggtg ttgaggtgca agtgcttctt gctgggaatg cgttcacagc
5401 aggaaagata ttatttgcag caatcccacc caactttcct gtagatatga ttagcccagc
5461 tcaaattact atgcttcccc atttgattgt agatgttagg acattggaac ctattatgat
5521 acccttacca gatgttagga atgtgttcta tcattttaat aatcaacccc aacctaggat
5581 gagattagtg gctatgctct ataccccatt gagatctaat ggttcaggag atgatgtctt
5641 tactgtgtct tgtagagtgt tgaccaggcc aacccctgat tttgaattca tttacctagt
5701 gcctccctct gtagagtcca aaactaaacc attcacactt ccaatattga ccatttctga
5761 attaaccaac tcccggtttc ccatcccaat tgagcaactg tacacggccc caaatgagaa
5821 taatgttgta cagtgtcaaa atggaaggtg caccttggat ggagagcttc agggcaccac
5881 ccagctgcta tcaagtgcag tttgctctta caggggtagg actgtggcta acagtgggga
5941 caattgggac cagaatttgc tccagttgac ctacccaagc ggtgcaagct atgaccccac
6001 tgatgaagta ccagcaccct tgggcaccca ggattttagt gggttgttgt atggggtgtt
6061 aacccaagac aatgtaagtg agggtgcagg ggaggccaaa aatgctaagg gagtatacat
6121 atccaccacc agtggaagat tcaccccaaa aattggaaca attggattgc attcaataac
6181 tgaaaatgtg caccccaatc agcaatcacg gttcacaccc gttggagttg ctcaaaatga
6241 aaataccccc ttccagcaat gggttctacc acactacgca ggtgctctcg ctctaaacac
6301 caatttggca cccgctgttg ccccgacttt ccctggcgag caattactgt tcttcaggtc
6361 ccgtgttcca tgtgttcaag gtctgcaggg gcaggatgct ttcatagact gtctcctacc
6421 tcaagagtgg gtgaaccatt tttatcaaga ggctgctccc tcccaagcag acgttgccct
6481 catcaggtat gtcaaccctg atactggtcg cacgctgttt gaggccaaat tgcacaggtc
6541 aggtttcatt actgtgtcac acactggcac ctaccccctt gtggtccccc caaatggtca
6601 tttcaggttt gattcttggg ttaaccaatt ctactcactc gcccccatgg gaactggcaa
6661 tgggcgtaga agagttcaat aatggcagga gcatttatag ctggtctagc cggtgacatg
6721 ctgacttctg ctgttggttc actgacctct gcaggagcca atgctatcaa tcagaaattg
6781 aattttgatt acaataaaca actccaaaat gcatcctttc aacatgataa ggaaatgttg
6841 caggcccaaa ttgatgctac gaagaagctc caatcagaaa tgattgcaat taagcatggg
6901 gttttgaccg cgggcggctt ttccccagct gatgcagcca gaggggcagt caacgcccca
6961 atgactcgag tgttggattg gtcagggaca cgctactacg ccccaaattc tgtgcaaacc
7021 accagttatt ccgggcaatt caccccctcg ccagtccatc gggcgcaggt gaagtcccct
7081 tccaattcat ctcagcggac tgcagctcca agcagtatcc gcagcctgtc aacccaatca
7141 acttctttag gctccacctc ctcaggggga tcttctacaa tctcctctag ttcgaggaca
7201 gcaaactggg tgcaacaaca aagggccctt agcccgtaca tgcagggagc cctgcagacg
7261 gcatacgtca caccgccgtc tagtagggct tccagtatga gctctgtctc aacagtgccc
7321 aaaggggttt tggactcctg gacacctgtg tttaacacac gcaggcagcc gctgtttgca
7381 cacctcagga agagggggga gtcacaggtt tagtgaaaag
//