Typing tool
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Typing tool
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Complete norovirus genomes
| MK073888 | GII.4 Sydney | |
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| GII.P16 |
ORF1: 1..5076
ORF2: 5057..6679
ORF3: 6679..7485
LOCUS MK073888 7506 bp RNA linear VRL 07-FEB-2019
DEFINITION Norovirus GII.4 isolate Hu/USA/2016/GII.P16-GII.4
Sydney/Roscommon-0105 nonstructural polyprotein (ORF1) gene,
partial cds; and VP1 (ORF2) and VP2 (ORF3) genes, complete cds.
ACCESSION MK073888
VERSION MK073888.1
DBLINK BioProject: PRJNA322324
KEYWORDS .
SOURCE Norovirus GII.4
ORGANISM Norovirus GII.4
Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes;
Picornavirales; Caliciviridae; Norovirus; Norwalk virus.
REFERENCE 1 (bases 1 to 7506)
AUTHORS Soehnlen,M., Riner,D., Mosher,L., Vavricka,V., Castro,C.J.,
Marine,R. and Rodeman,K.
TITLE Direct Submission
JOURNAL Submitted (19-OCT-2018) Polio and Picornavirus Laboratory Branch,
Centers for Disease Control and Prevention, 1600 Clifton Rd. NE,
Atlanta, GA 30329, USA
COMMENT ##Assembly-Data-START##
Assembly Method :: SPAdes v. 3.9
Sequencing Technology :: Illumina
##Assembly-Data-END##
FEATURES Location/Qualifiers
source 1..7506
/organism="Norovirus GII.4"
/mol_type="genomic RNA"
/isolate="Hu/USA/2016/GII.P16-GII.4 Sydney/Roscommon-0105"
/isolation_source="stool"
/host="Homo sapiens"
/db_xref="taxon:489821"
/country="USA: MI, Roscommon County, Roscommon"
/collection_date="10-Apr-2016"
/note="genotype: GII.P16-GII.4"
gene <1..5076
/gene="ORF1"
CDS <1..5076
/gene="ORF1"
/codon_start=1
/product="nonstructural polyprotein"
/protein_id="AZJ17750.1"
/translation="TVAVACNNNNDKEKSSGEGLFTNMSSTLKKALGARPKQPAPRDE
PQKPPRPPTPELVKRIPPPPPNGEGEEEPVIRYEVKSGISGLPELTTVPQPDVANTAF
SVPPLSLRENREAKEPLTGAILEMWDGEIYHYGLYVEKGLVLGVHKPPAAISMARVEL
TPLSLYWRVVYTPQYLISPETLRRLNGEAFPYTAFDNNCYAFCCWVLDLNDSWLSRRM
VQRTTGFFRPYQEWNRKPLPTMDDSKIKKVANIFLCSLSTLFTRPIKDLIGKIKPLNI
LNILATCDWTFAGIVESLILLAELFGVFWTPPDVSAMIAPLLGDYELQGPEDLAVELV
PVVMGGIGLVLGFTKEKIGKMLSSAASTLRACKDLGAYGLEILKLVMKWFFPKKEEAN
ELAMVRAIEDAVLDLEAIENNHMTTLLKDKDSLATYMKTLDMEEEKARRLSTKSASPD
IVGTINALLARIAAARSLVHRAKEELSSRIRPVVVMISGKPGIGKTHLAREVARKVAS
TLTGDQRVGLIPRNGVDHWDAYKGERVVLWDDYGMSNPIHDALRIQELADTCPLTLNC
DRIENKGKVFDSEVIIITTNLANPAPLDYVNFEACSRRIDFLVYAEAPEVEKAKRDFP
GQPDMWKDAFKPDFSHIKLQLAPQGGFDKNGNTPHGKGVMKTLTTGSLIARASGLLHE
RMDEFELQGPTITTFNFDRNRITAFRQLAAENKYGLVDTMKVGNQLKGVKTMEELKQA
IRNVTIKRCRIIYGGSTYDLESDGKGKVLVEKVKNTSVQTNNELAGALHHLKHARIRY
YVKCVQEAVYSIIQIAGAAFVTTRIARRMNIQELWSKPQLDQNESETKEEAPKSEDDE
FIISSKDIKEEGKKGKNKTGRGKKHTAFSSKGLSDEEYDEYKRIREERNGKYSIEEYL
QDRDRYYEELAIAKATEEDFCEEEEIKIRQRIFRPTRKQRKEERATLGLVTGSEIRKR
NPDDFKPKGKLWADDNRSVDYNEKLDFEAPPSIWSRIVSFGSGWGFWVSPSLFITSTH
VIPAGITEAFGVPIKQIQIHKSGEFCRFRFPKPIRPDVTGMILEEGAPEGTVATVLIK
RPTGELMPLAARMGTHATMKIQGRMVGGQMGMLLTGSNAKGMDLGTTPGDCGCPYIYK
RGNDYIAIGVHTAAARGGNTVICATQGSEGEATLEGGDDKGTYCGAPILGPGGAPKLS
TKTKFWRSSNTPLPPGTYEPAYLGGRDPRVKGGPSLQQVMRDQLKPFTEPRGKPPRPS
VLEAAKQTIINVLEQTLDPPQKWTYAQACASLDKTTSSGHPHHVRKNEFWNGETFSGK
LADQASKANLMFEEGKHMTPVYTAALKDELVKTEKIYGKIKKRLLWGSDLSTMIRCAR
SFGGLMDEMKAHCISLPVRVGMNMNEDGPIIFEKHSRYKYHYDADYSRWDSTQQRAVL
AAALEIMVRFSAEPQLAQIVAEDLLAPSVVDVGDFKITINEGLPSGVPCTSQWNSIAH
WLLTLCALSEVTKLSPDIIQANSMFSFYGDDEIVSTDIKLDPEQLTAKLKEYGLKPTR
PDKTEGPLIISEDLNGLTFLRRTVTRDPAGWFGKLDQSSILRQMYWTRGPNHEDPNET
MIPHSQRPIQLMALLGEASLHGPSFYSRISKLVITELKEGGMDFYVPRQEPMFRWMRF
SDLSTWEGDRNLAPNFVNEDGVE"
mat_peptide <1..972
/gene="ORF1"
/product="p48"
mat_peptide 973..2070
/gene="ORF1"
/product="NTPase"
mat_peptide 2071..2601
/gene="ORF1"
/product="p22"
mat_peptide 2602..3000
/gene="ORF1"
/product="VPg"
mat_peptide 3001..3543
/gene="ORF1"
/product="Pro"
mat_peptide 3544..5073
/gene="ORF1"
/product="RdRp"
gene 5057..6679
/gene="ORF2"
CDS 5057..6679
/gene="ORF2"
/note="major capsid protein"
/codon_start=1
/product="VP1"
/protein_id="AZJ17751.1"
/translation="MKMASSDANPSDGSAANLVPEVNNEVMALEPVVGAAIAAPVAGQ
QNVIDPWIRNNFVQAPGGEFTVSPRNAPGEILWSAPLGPDLNPYLSHLARMYNGYAGG
FEVQVILAGNAFTAGKVIFAAVPPNFPTEGLSPSQVTMFPHIVVDVRQLEPVLIPLPD
VRNNFYHYNQSNDSTIKLIAMLYTPLRANNAGDDVFTVSCRVLTRPSPDFDFIFLVPP
TVESRTKPFSVPVLTVEEMTNSRFPIPLEKLFTGPSSAFVVQPQNGRCTTDGVLLGTT
QLSPVNICTFRGDVTHITGSRNYTMNLASQNWNNYDPTEEIPAPLGTPDFVGKIQGVL
TQTTRTDGSTRGHKATVYTGSADFAPKLGRVQFETDTDHDFEANQNTKFTPVGVIQDG
STTHRNEPQQWMLPSYSGRNTHNVHLAPAVAPTFPGEQLLFFRSTLPGCSGYPNMDLD
CLLPQEWVQYFYQEAAPAQSDVALLRFVNPDTGRVLFECKLHKSGYVTVAHTGQHDLV
IPPNGYFRFDSWVNQFYTLAPMGNGTGRRRVV"
gene 6679..7485
/gene="ORF3"
CDS 6679..7485
/gene="ORF3"
/note="minor structural protein; small basic protein"
/codon_start=1
/product="VP2"
/protein_id="AZJ17752.1"
/translation="MAGAFFAGLASDVLGSGLGSLINAGAGAINQKVEFENNRKLQQA
SFQFSSNLQQASFQHDKEMLQAQIEATKKLQQEMMKVKQAMLLEGGFSETDAARGAIN
APMTKALDWSGTRYWAPDARTTTYNAGRFSTPQPSGALPGRANLRDAVPARGPSNKSS
NSSTATSVYSNQTISTRLGSTAGSGTSVSSLPPTARTRSWVEDQNRNLSPFMRGAHNI
SFVTPPSSRSSSQGTVSTVPKEILDSWTGAFNTRRQPLFAHIRKRGESRV"
ORIGIN
1 accgttgccg ttgcttgcaa caacaacaac gacaaggaaa aatcttcagg tgaaggctta
61 ttcacaaata tgtcttccac cctaaagaaa gccctcgggg ctaggcccaa acagcctgcc
121 ccgagagacg aaccacaaaa gcccccaaga ccaccaactc ccgagttggt caagaggata
181 ccccctcctc cacctaatgg cgaaggagaa gaagaaccag tcattaggta tgaggttaag
241 agtgggatct ctggcctgcc cgagctcaca acagtccccc aaccggacgt ggccaacaca
301 gcattcagtg ttccaccact gagcttgaga gaaaacaggg aggccaagga accgctaaca
361 ggggcaatat tagagatgtg ggatggagag atataccact atggcctgta cgtggagaaa
421 ggcttagtgt tgggtgtgca caaaccacct gcagccataa gcatggcaag agtggagctg
481 acgccgctgt cattgtactg gcgtgtggtg tacactcccc aatacctcat ctcccctgaa
541 actctcagga ggctcaacgg agaggcgttc ccttacaccg ccttcgacaa caactgctat
601 gccttttgct gctgggtgtt agacctcaat gactcatggc ttagcaggag gatggtgcaa
661 agaacaacgg gcttcttcag accttaccaa gagtggaaca gaaagcccct gcctaccatg
721 gatgactcca aaattaagaa ggtagcaaat atattcctat gttcattgtc cacattattc
781 accagaccca taaaagacct cataggaaaa attaaaccat taaacatatt gaacatcctg
841 gcaacgtgtg actggacgtt tgccggaata gtggagtctc tgatattact tgctgaactc
901 ttcggagttt tctggacgcc cccagatgtg tctgctatga tcgctccctt actcggggac
961 tacgagttgc aagggccaga agacctcgcc gttgaactcg tacctgtggt aatgggaggg
1021 attggtttgg tgttgggatt caccaaagag aaaattggca aaatgttgtc ctcagcagca
1081 tcaacactca gggcttgcaa agatcttggt gcctatggtt tagagatact caaattggtc
1141 atgaagtggt tcttcccaaa gaaagaggag gccaatgagc tagccatggt gagggccata
1201 gaggatgccg tactagatct tgaggcaata gaaaataacc acatgacaac cctgttgaaa
1261 gacaaagaca gcttagcaac atacatgaaa acactggaca tggaggagga gaaagccaga
1321 aggttgtcca caaaatctgc atcccctgac atagttggga caatcaacgc cctgctggct
1381 cgaatagcag cggccaggtc attagtccac agggccaagg aagagctatc tagcaggata
1441 agaccagtag ttgttatgat atctggcaaa ccaggaatag gcaaaactca tctggccagg
1501 gaggtggcaa gaaaggtggc atccactctc acaggggacc aacgagtcgg actcatacca
1561 agaaacggtg tggaccattg ggatgcatac aaaggtgaga gagtcgtgct gtgggacgac
1621 tatggcatga gtaaccccat tcatgatgct cttcgcatac aagaattggc tgatacgtgt
1681 ccccttacct taaattgtga cagaattgaa aataagggaa aagttttcga cagtgaagtc
1741 ataataatta caacaaacct tgccaatcca gccccacttg attatgtcaa ctttgaggcc
1801 tgttccagga gaattgattt cctggtgtac gctgaggcac cagaagtaga aaaggcaaaa
1861 cgggactttc ctggtcagcc agatatgtgg aaggacgcct tcaagccgga cttttcacac
1921 atcaagctac agcttgcacc tcagggcggc tttgacaaga atggcaacac cccacatggg
1981 aaaggagtga tgaagaccct cactaccggt tctctgattg cccgtgcatc aggcctactg
2041 catgagagga tggatgaatt cgaactccaa ggtcccacaa tcaccacctt caatttcgac
2101 cggaacagaa tcacagcatt cagacaattg gctgcagaaa acaagtatgg attggtggat
2161 accatgaaag ttggcaatca actaaaagga gtgaaaacca tggaagaact caaacaagca
2221 atcagaaatg tgaccatcaa gaggtgccgg atcatctacg gtggctccac gtatgacctt
2281 gaatctgatg gcaagggcaa agttttggtg gaaaaggtca agaacacctc tgtacagacc
2341 aacaacgagt tggccggggc cctgcaccat ctcaaacacg cccgaatcag gtactatgtc
2401 aaatgtgtgc aagaagcagt ctattccatc atacaaattg ccggcgctgc gtttgtcacc
2461 acgcgcattg cacgccgcat gaacatacaa gaactctggt cgaagccaca attagatcaa
2521 aatgaatcag agactaagga agaggccccc aagtcagaag atgacgagtt catcatatct
2581 tctaaggaca tcaaggagga aggaaagaag ggcaaaaaca aaactggccg tggcaagaaa
2641 cacactgcat tctccagcaa gggcttgagc gatgaggagt atgacgagta caagaggata
2701 agagaagaga gaaatgggaa gtactctata gaggagtatc ttcaagacag agacaggtac
2761 tatgaggagc tcgccattgc caaggccacg gaagaagact tctgtgaaga ggaggagatt
2821 aaaatccgtc agagaatttt ccgtcccacc aggaaacaaa gaaaggaaga gagggccaca
2881 ttaggactgg taacaggttc agaaatcaga aaaagaaacc ctgatgactt caaacccaaa
2941 gggaagctgt gggccgatga caacagaagt gttgactata atgagaaact ggactttgag
3001 gcccccccaa gcatatggtc taggattgtg agctttggtt ctggctgggg cttctgggta
3061 tcaccaagcc tgttcataac atcaactcat gtaatccccg caggcataac agaagcattt
3121 ggagtcccca tcaagcaaat tcagatccac aaatcaggtg aattttgccg attcagattc
3181 ccaaaaccaa ttagaccaga cgtgacagga atgatcttgg aagaaggtgc gcctgaaggc
3241 accgtggcaa ctgtgctcat caaacgcccc accggagagc tcatgcctct tgcagccaga
3301 atgggaacac acgcaaccat gaaaattcaa ggccgcatgg ttggcggaca gatgggtatg
3361 ttgctcactg gatcaaatgc taaaggaatg gatttgggaa caactcctgg tgactgtggc
3421 tgtccttaca tctacaaaag gggcaatgac tatatagcca ttggggtgca cactgcagca
3481 gcccgtggtg gaaacaccgt catctgtgcc acacagggaa gtgagggtga ggcaactctt
3541 gagggtggag atgacaaagg aacatactgt ggggcaccca ttctaggccc tgggggtgca
3601 ccaaagttga gcaccaaaac caaattttgg aggtcatcga acacgcccct tccaccaggg
3661 acatatgagc ctgcctacct cggtggccgt gatccgcgtg ttaagggtgg gccctccttg
3721 cagcaggtaa tgagagacca gttgaagcca ttcactgaac ccaggggcaa acctccgaga
3781 ccaagtgtat tggaagcagc caaacaaacc attatcaatg tcctcgaaca aaccctggac
3841 cctccacaaa aatggacata cgcacaggcg tgtgcctcac ttgacaaaac cacttccagc
3901 gggcatcccc atcacgtccg aaagaatgaa ttctggaatg gtgagacctt cagcggcaaa
3961 ttggcagacc aagcatcaaa agcaaaccta atgtttgagg aagggaaaca catgacacca
4021 gtgtatacag cagcactcaa ggacgagcta gtcaagactg agaaaatcta tggaaagatc
4081 aagaagagac tgctctgggg ctctgacttg tccaccatga tccggtgcgc taggtcattt
4141 ggtgggctca tggacgagat gaaggcacac tgcatatcac tcccagtacg agttggcatg
4201 aatatgaatg aagatggccc aataatattt gagaaacatt ccagatacaa ataccactat
4261 gatgcagact actctcgttg ggattcaaca caacagaggg cagtactagc agcagccttg
4321 gaaatcatgg tcagattctc tgcagaacca caattggcac aaatagtcgc tgaggatctg
4381 ctggccccta gcgtagtaga tgtaggagac tttaaaatca caataaatga agggctccca
4441 tctggtgtgc catgcacttc tcaatggaac tccatcgcac actggctgct aactctctgt
4501 gccttgtctg aagtcaccaa actgtcccct gacattatac aagcaaattc catgttctca
4561 ttttacggtg atgacgagat tgtcagcacc gacataaaat tggaccctga acagttaacc
4621 gccaagttga aggagtacgg cctgaaacca acccgcccag acaagaccga gggacccctg
4681 atcatcagtg aagatttgaa cggactcact ttcctccgaa ggacggtgac tcgtgaccca
4741 gctggctggt ttggaaaact ggaccaaagt tcaattttga ggcagatgta ctggactaga
4801 ggaccaaatc atgaagatcc caatgagaca atgatacccc attctcaaag acccatacag
4861 ctcatggcac tgcttggtga agcctctctt cacggaccct ctttctacag tagaatcagt
4921 aaattggtca taactgaact caaagaaggt gggatggact tttacgtgcc aaggcaggaa
4981 cccatgttca ggtggatgag gttttctgac ttgagcacgt gggagggcga tcgcaatctg
5041 gctcccaatt ttgtgaatga agatggcgtc gagtgacgcc aacccatctg atgggtccgc
5101 agccaacctc gtaccagagg tcaacaatga ggttatggct ttggagcccg ttgttggtgc
5161 cgctattgcg gcacctgtag cgggccaaca aaatgtaatt gacccctgga ttagaaataa
5221 ttttgtacaa gcccctggtg gggagtttac agtatccccc agaaacgctc caggtgaaat
5281 actatggagc gcgcccctag gccctgacct aaatccctac ctatcccatt tggccagaat
5341 gtacaatggt tatgcaggtg gttttgaagt gcaggtaatt ctcgcgggga acgcgttcac
5401 cgccgggaag gtcatatttg cagcagtccc accaaatttt ccaactgaag gcttaagtcc
5461 tagccaggtc actatgttcc cccatatagt agtagatgtt agacaattag aacctgtgct
5521 gattccctta cccgatgtta ggaataattt ctatcattac aatcagtcaa atgactccac
5581 tatcaaattg atagcaatgt tgtatacacc acttagggct aataatgctg gggatgatgt
5641 tttcacagtt tcgtgccgag ttctcacgag accatccccc gattttgatt ttatattttt
5701 agtgccaccc acagttgagt caagaactaa accattctct gtcccagttt taactgttga
5761 ggagatgacc aattcaagat tccccatccc tttggaaaag ttgttcacag gccccagcag
5821 tgcctttgtt gttcaaccac aaaacggcag gtgcacaact gatggcgtgc tcctaggcac
5881 cacccaactt tctcctgtca acatctgcac cttcagaggg gatgtcaccc acatcacagg
5941 tagtcgcaac tacacaatga atttggcttc tcaaaattgg aacaactatg acccaacaga
6001 agaaatccca gcccctctag gaactccaga ttttgtgggg aagattcaag gtgtgctcac
6061 ccaaaccaca aggacagatg gttcaacacg cggccacaaa gctacagtgt acactgggag
6121 cgccgacttt gctccaaaac tgggtagagt tcaatttgaa actgacacag accatgattt
6181 tgaagctaac caaaacacaa agttcacccc agtcggtgtc atccaagatg gtagcaccac
6241 ccatcgaaac gaaccccaac agtggatgct cccaagttac tcaggcagaa atactcacaa
6301 tgtacatctg gcccccgctg tagcccccac ctttccgggt gagcaacttc tcttcttcag
6361 atccaccttg cccggatgca gcgggtaccc caacatggat ttggactgtc tgctccccca
6421 ggaatgggtg cagtacttct accaagaggc agccccagca caatctgatg tggctctgct
6481 aagatttgtg aatccagaca caggtagggt tttgtttgag tgcaagcttc acaaatcagg
6541 ctatgttaca gtggctcaca ctggccaaca tgatttggtt atccccccca atggctactt
6601 taggtttgat tcctgggtca accagttcta tacgcttgcc cccatgggaa atggaacggg
6661 gcgtagacgt gtagtataat ggctggagct ttctttgctg gattggcatc tgatgtcctt
6721 ggctctggac ttggttccct tatcaatgct ggggctgggg ccatcaacca aaaagttgag
6781 tttgaaaata acagaaaatt gcaacaagca tccttccaat ttagcagcaa tctgcaacag
6841 gcttcctttc aacatgataa agagatgctc caagcacaaa ttgaggccac caaaaagcta
6901 caacaggaaa tgatgaaagt taagcaggca atgctcctag agggtgggtt ctctgagaca
6961 gatgcagccc gcggggcaat taacgccccc atgacaaaag ctttggactg gagcgggaca
7021 aggtactggg ctcccgatgc taggactaca acatacaatg caggccgctt ttccacccct
7081 caaccatcgg gagcactgcc aggaagagct aatcttaggg atgctgtccc tgctcgggga
7141 ccctccaaca aatcttctaa ctcttctact gctacctctg tgtattcaaa tcaaactatt
7201 tcaacgagac ttggttctac agctggttct ggaaccagtg tctcgagcct cccgccaact
7261 gcaaggacta ggagctgggt tgaggatcaa aataggaatt tgtcaccttt catgaggggg
7321 gcccacaaca tatcatttgt caccccacca tctagcagat cctctagcca aggcacagtc
7381 tcaaccgtgc ctaaagagat tttggactcc tggactggcg ctttcaacac gcgcaggcag
7441 cctctcttcg ctcacattcg taagcgaggg gagtcacggg tgtaatgtga aaagacaaaa
7501 ttgatt
//