Typing tool
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Typing tool
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Complete norovirus genomes
| KY947548 | GII.13 | |
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| GII.P16 |
ORF1: 4..5100
ORF2: 5081..6709
ORF3: 6709..7440
LOCUS KY947548 7457 bp ss-RNA linear VRL 18-MAY-2017
DEFINITION Norovirus GII strain Hu/USA/2015/GII.P16-GII.13/Carlsbad 4246
polyprotein, VP1, and VP2 genes, complete cds.
ACCESSION KY947548
VERSION KY947548.1
KEYWORDS .
SOURCE Norovirus GII
ORGANISM Norovirus GII
Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes;
Picornavirales; Caliciviridae; Norovirus; Norwalk virus.
REFERENCE 1 (bases 1 to 7457)
AUTHORS Cannon,J.L., Barclay,L., Collins,N.R., Wikswo,M.E., Castro,C.J.,
Magana,L.C., Gregoricus,N., Marine,R.L., Chhabra,P. and Vinje,J.
TITLE Genetic and Epidemiologic Trends of Norovirus Outbreaks in the US
Demonstrated Emergence of Novel GII.4 Recombinant Viruses,
2013-2016
JOURNAL J. Clin. Microbiol. (2017) In press
PUBMED 28490488
REMARK Publication Status: Available-Online prior to print
REFERENCE 2 (bases 1 to 7457)
AUTHORS Cannon,J.L., Barclay,L., Collins,N.R., Chhabra,P., Wikswo,M.E.,
Castro,C.J., Magana,L.C., Gregoricus,N. and Vinje,J.
TITLE Direct Submission
JOURNAL Submitted (14-APR-2017) Viral Gastroenteritis Branch/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. 8
Sequencing Technology :: Illumina
##Assembly-Data-END##
FEATURES Location/Qualifiers
source 1..7457
/organism="Norovirus GII"
/mol_type="genomic RNA"
/strain="Hu/USA/2015/GII.P16-GII.13/Carlsbad 4246"
/isolation_source="stool"
/host="Homo sapiens"
/db_xref="taxon:122929"
/country="USA"
/collection_date="03-Jan-2016"
/note="genotype: GII.P16-GII.13"
5'UTR 1..3
CDS 4..5100
/note="nonstructural protein; ORF1"
/codon_start=1
/product="polyprotein"
/protein_id="ARR95960.1"
/translation="MKMASNDATVAVACNNNNDKEKSSGEGLFTNMSSTLKKALGARP
KQPAPRDNSQKPPRPPTPELVKRMPPPPPNGEEEEPVIRYEVKSGISGLPELTTVPQP
DVANTAFSVPPLSLRENREAKEPLTGAILEMWDGEIYHYGLYVEKGLVLGVHKPPAAI
SMAKVELTPLSLYWRVVYTPQYLISPETLRRLNGEAFPYTAFDNNCYAFCCWVLDLND
SWLSRRMVQRTTGFFRPYQEWNRKPLPTMDDSKIKKVANIFLCSLSTLFTRPIKDLMG
KIKPLNILNILATCDWTFAGIVESLILLAELFGVFWTPPDVSAMIAPLLGDYELQGPE
DLAVELVPVVMGGIGLVLGFTKEKIGKMLSSAASTLRACKDLGAYGLEILKLVMKWFF
PKKEEANELAMVRAIEDAVLDLEAIENNHMTTLLKDKDSLATYMKTLDMEEEKARRLS
TKSASPDIVGTINALLARIAAARSLVHRAKEELSSRIRPVVVMISGKPGIGKTHLARE
VARKVASTLTGDQRVGLIPRNGVDHWDAYKGERVVLWDDYGMSNPIHDALRIQELADT
CPLTLNCDRIENKGKVFDSEVIIITTNLANPAPLDYVNFEACSRRIDFLVYAEAPEVE
KAKRDFPGQPDMWKDAFKSDFSHIKLQLAPQGGFDKNGNTPHGKGVMKTLTTGSLIAR
ASGLLHERMDEFELQGPTVTTFNFDRNRIAAFRQLAAENKYGLVDTMRVGNQLKGVKT
MEELKQAIKNVTIKRCRIIYGGSTYDLESDGKGRVLVEKVKNTSVQTNNELAGALHHL
KHARIRYYVKCVQETVYSIIQIAGAAFVTTRIVRRMNIQELWSKPPLDQIESETKEEA
PKLEDDEFIISSKDIKEEGKKGKNKTGRGKKHTAFSSKGLSDEEYDEYKRIREERNGK
YSIEEYLQDRDRYYEELAIAKATEEDFCEEEEIKIRQRIFRPTRKQRKEERATLGLVT
GSEIRKRNPDDFKPKGKLWADDNRSVDYNEKLDFEAPPSIWSRIVSFGSGWGFWVSPS
LFITSTHVIPAGITEAFGVPIKQIQVHKSGEFCRFRFPKPIRSDVTGMILEEGAPEGT
VATVLIKRPTGELMPLAARMGTHATMKIQGRMVGGQMGMLLTGSNAKGMDLGTTPGDC
GCPYIYKRGNDYIVIGVHTAAARGGNTVICATQGSEGEATLEGGDDKGTYCGAPILGP
GGAPKLSTKTKFWRSSNTPLPPGTYEPAYLGGRDPRVKGGPSLQQVMRDQLKPFTEPR
GKPPRPSVLEAAKQTIINVLEQTLDPPQKWTYAQACASLDKTTSSGHPHHVRKNEFWN
GETFTGKLADQASKANLMFEEGKHMTPVYTAALKDELVKTDKVYGKIKKRLLWGSDLS
TMIRCARSFGGLMDEMKAHCISLPVRVGMNMNEDGPIIFEKHSRYKYHYDADYSRWDS
TQQRAVLAAALEIMVRFSAEPQLAQIVAEDLLAPSVVDVGDFKISINEGLPSGVPCTS
QWNSIAHWLLTLCALSEVTKLSPDIVQANSMFSFYGDDEIVSTDIKLDPEKLTTKLKE
YGLKPTRPDKTEGPLIISEDLNGLTFLRRTVTRDPAGWFGKLDQSSILRQMYWTRGPN
HEDPNETMIPHSQRPIQLMALLGEASLHGPSFYSKISKLVITELKEGGMDFYVPRQEP
MFRWMRFSDLSTWEGDRNLAPNFVNEDGVE"
CDS 5081..6709
/note="major capsid protein; ORF2"
/codon_start=1
/product="VP1"
/protein_id="ARR95961.1"
/translation="MKMASNDAAPSNDGAASLVPEAINETMPLEPVAGASIAAPVAGQ
TNIIDPWIRTNFVQAPNGEFTVSPRNSPGEILLNLELGPDLNPYLAHLSRMYNGYAGG
VEVQVLLAGNAFTAGKILFAAIPPNFPVDMISPAQITMLPHLIVDVRTLEPIMIPLPD
VRNVFYHFNNQPQPRMRLVAMLYTPLRSNGSGDDVFTVSCRVLTRPTPDFEFIYLVPP
SVESKTKPFTLPILTISELTNSRFPIPIEQLYTAPNENNVVQCQNGRCTLDGELQGTT
QLLSSAVCSYRGRTVANSGDNWDQNLLQLTYPSGASYDPTDEVPAPLGTQDFSGILYG
VLTQDNVSEGTGEAKNAKGVYISTTSGRFTPKIGTIGLHSITENVHPNQQSRFTPVGV
AQNENTPFQQWVLPHYAGALALNTNLAPAVAPTFPGEQLLFFRSRVPCVQGLRGQDAF
IDCLLPQEWVNHFYQEAAPSQADVALIRYVNPDTGRTLFEAKLHRSGFITVSHTGTYP
LVVPPNGHFRFDSWVNQFYSLAPMGTGNGRRRVQ"
CDS 6709..7440
/note="minor structural protein; ORF3"
/codon_start=1
/product="VP2"
/protein_id="ARR95962.1"
/translation="MAGAFIAGLAGDMLTSAVGSLTSAGANAINQKLNFDYNKQLQNA
SFQHDKEMLQAQIDATKKLQSEMIAIKHGVLTAGGFSPADAARGAVNAPMTRVLDWSG
TRYYAPNSVQTTSYSGQFTPSPVHRAQVKSPSNSSQRTAAPSSIRSLSTQSTSLGSTS
SGGSSTISSSSRTADWVQQQRALSPYMQGALQTAYVTPPSSRASSVSSVSTVPKGVLD
SWTPVFNTRRQPLFAHLRKRGESQA"
3'UTR 7441..7457
ORIGIN
1 tgaatgaaga tggcgtctaa cgacgctacc gttgccgttg cttgcaacaa caacaacgac
61 aaggaaaaat cttcaggtga aggcttattc acaaacatgt cttccacctt aaagaaagcc
121 ctcggggccc ggcccaaaca gcctgccccg agggacaact cacaaaagcc cccgagacca
181 ccaactcccg agttggttaa gaggatgccc cctcccccac ctaacggaga agaagaagaa
241 ccagtcatta ggtatgaggt taagagtgga atctctggcc tgcccgagct cacaacagtc
301 cctcaaccgg atgtggccaa cacggcattc agtgtcccac cgctgagctt gagagaaaac
361 agggaggcca aggaaccgct gacaggggca atattagaga tgtgggatgg agagatatac
421 cactatggcc tgtacgtgga gaaaggctta gtgttgggtg tgcacaaacc acctgcagct
481 ataagcatgg caaaagtgga gctgacgccg ttgtcattgt actggcgtgt ggtctacacc
541 ccccaatacc tcatctcccc tgaaactctc aggaggctca acggagaggc attcccttac
601 actgcctttg acaacaactg ctatgccttt tgctgttggg tattagacct caatgactca
661 tggcttagca ggaggatggt gcaaagaaca acaggcttct tcagacctta ccaagagtgg
721 aacagaaaac ccctgcccac tatggatgac tccaaaatca agaaggtggc aaacatattc
781 ctgtgctcat tgtccacgtt gttcaccaga cctataaaag acctcatggg aaaaattaag
841 ccattaaaca tcttgaacat cctggcaacg tgtgactgga cattcgccgg aatagtggag
901 tctcttatat tacttgctga actctttgga gttttctgga cacccccaga tgtgtctgct
961 atgatcgctc ctttacttgg agactacgag ttgcaggggc cagaagacct tgccgttgag
1021 ctcgtacctg tagtaatggg agggattggt ttggtgttgg gattcaccaa agagaaaatt
1081 ggaaaaatgt tgtcctcagc agcatcaacg ctcagggctt gtaaagatct tggtgcctat
1141 ggcttagaga tactcaaact ggtcatgaag tggttcttcc caaagaaaga agaggccaat
1201 gagctagcca tggtgagagc tatagaggat gctgtactgg atcttgaggc aatagaaaat
1261 aatcacatga caactttgtt gaaagacaaa gacagcctag caacctacat gaaaacacta
1321 gacatggagg aggaaaaggc cagaagattg tccacaaaat ctgcatcccc tgacatagtt
1381 gggacgatca acgccctgct ggctcgaata gcagcggcta ggtcactagt ccacagggcc
1441 aaggaggagt tgtctagcag gataagacca gtggttgtta tgatatctgg taagccaggg
1501 ataggcaaaa ctcatttggc cagggaagtg gcaagaaagg tggcatccac tctcacaggg
1561 gatcaaagag tcgggctcat accgagaaac ggtgtggacc attgggatgc atacaaaggt
1621 gagagagtcg tgctgtggga cgactatggc atgagcaacc ccattcatga tgctctgcgc
1681 atacaagaat tggctgacac gtgtcccctt accttaaatt gtgacagaat tgaaaataag
1741 ggaaaagttt ttgacagtga agtcataata atcacaacaa acctcgccaa tccagctcca
1801 cttgattatg ttaactttga ggcctgttcc aggagaattg acttcctggt gtacgccgag
1861 gcaccagaag tagaaaaggc aaaacgagat tttcctggtc aaccagatat gtggaaggac
1921 gccttcaagt cggacttttc acacatcaag ctgcaacttg cacctcaggg cggctttgac
1981 aagaatggca acaccccaca tggaaaagga gtgatgaaga ccctcaccac cggctccctg
2041 atcgcccgtg catcaggctt actgcatgag aggatggatg aatttgaact ccaaggcccc
2101 acagtcacca ccttcaattt tgaccggaac agaatcgctg cattcagaca attggctgca
2161 gaaaacaagt atggattggt ggacaccatg agagttggca atcaattaaa aggggtgaaa
2221 accatggaag aactcaaaca agcaatcaag aatgtgacca tcaagaggtg ccggatcatc
2281 tacggcggct ccacgtatga ccttgaatct gacggtaagg gcagagttct ggtggaaaag
2341 gtcaagaaca cctccgtaca gaccaacaac gaattggccg gagccctgca tcacctcaaa
2401 catgcccgaa tcaggtacta tgtcaaatgt gtgcaagaaa cagtctactc tattatacaa
2461 atcgccggcg ctgcgtttgt caccacacgc atagtacgcc gcatgaacat acaagagctt
2521 tggtcgaagc caccattaga tcaaattgaa tcagagacca aggaagaggc ccccaagtta
2581 gaagatgacg agttcatcat atcttctaag gacatcaagg aggaaggaaa gaagggcaaa
2641 aacaaaactg gccgtggcaa gaaacatact gcattctcta gcaagggctt gagcgatgag
2701 gagtacgacg agtacaagag gataagagaa gagagaaatg ggaagtactc tatagaggag
2761 tatcttcaag acagagacag gtactatgag gaactcgcca tcgccaaggc cacggaagaa
2821 gacttctgtg aggaggagga gatcaaaatc cgtcagagga tcttccgtcc caccaggaag
2881 caaaggaagg aagagagggc cacactaggg ctagtaactg gttcagaaat cagaaaaaga
2941 aaccctgatg actttaaacc taaagggaaa ctgtgggctg atgacaacag aagtgttgac
3001 tacaatgaga aactggactt tgaggccccc ccaagcatat ggtctaggat tgtgagtttt
3061 ggttctggtt ggggcttctg ggtgtcacca agcctgttca taacatcaac tcacgtaatc
3121 cctgcaggca taacagaggc atttggagtc cccatcaagc aaatccaggt ccacaaatca
3181 ggtgaatttt gccggttcag attcccaaaa ccaattagat cagatgtgac aggaatgatc
3241 ttggaagaag gtgcgcctga gggcaccgtg gcaaccgtgc ttatcaaacg ccctaccgga
3301 gagctcatgc cccttgcggc cagaatggga acacacgcaa ccatgaaaat tcagggccgc
3361 atggttggcg gacagatggg tatgttgctc actggttcaa atgctaaagg aatggatttg
3421 ggaacaactc ctggtgattg tggctgtccc tacatctaca aaaggggcaa tgactatata
3481 gtcattgggg tgcacacagc agcagcccgt ggtggaaaca ccgtcatctg tgccacacag
3541 ggaagtgagg gtgaggcaac ccttgagggt ggagatgaca aaggaacata ttgtggggca
3601 cccattctag gccccggggg ggcaccaaaa ttgagcacca aaaccaaatt ttggaggtca
3661 tcgaacacgc ctcttccacc agggacgtat gagcctgcct acctcggtgg ccgtgacccg
3721 cgtgttaagg gtgggccctc cttgcagcag gtaatgagag accagttgaa gccattcacc
3781 gagcccaggg gtaaacctcc aagaccaagt gtgttggaag cagccaaaca aaccatcatc
3841 aatgtcctcg aacaaaccct ggaccctcca caaaaatgga catacgcaca ggcgtgtgct
3901 tcacttgaca aaaccacctc cagcgggcac ccccaccacg tccgaaagaa tgaattctgg
3961 aatggtgaga ccttcactgg taaattggca gaccaagcat caaaagcaaa tctaatgttt
4021 gaggaaggga aacatatgac accagtgtat acagcagccc tcaaggatga gctggtcaag
4081 actgacaaag tctatggaaa gatcaagaag agactgctct ggggctctga cttgtccacc
4141 atgatccggt gcgccaggtc ctttggtggg ctcatggatg agatgaaagc acactgcata
4201 tcactcccag tccgagttgg catgaacatg aatgaagatg gtccaataat atttgagaag
4261 cactccagat acaagtatca ctatgatgca gactactccc gctgggattc aacacaacag
4321 agggcagtac tagcagcagc cttggagatc atggtcaggt tctctgcaga gccacaattg
4381 gcacaaatag tcgctgagga tctgctggcc cccagtgtgg tagatgtagg agactttaaa
4441 atttcaataa atgaagggct cccctctggt gtaccatgca cttctcaatg gaattccatc
4501 gcacactggc tgctaaccct ctgcgccttg tctgaagtca ccaaactgtc ccccgacatt
4561 gtacaggcaa actccatgtt ctcattttac ggtgatgacg agattgtcag caccgatata
4621 aaattggacc ctgaaaagtt aaccaccaaa ttgaaggagt acggcctgaa accaactcgc
4681 ccagacaaaa ccgagggacc cctgatcatc agtgaggatt tgaacggact cactttcctc
4741 cggagaacgg tgactcgtga cccagctggc tggtttggaa aattggacca aagctcaata
4801 ttgaggcaga tgtactggac tagaggacca aatcatgaag accccaacga gacaatgata
4861 ccccactctc aaagacccat acagctcatg gcactgcttg gtgaggcctc ccttcacgga
4921 ccctctttct acagcaaaat tagtaagttg gtcataactg aactcaaaga aggtgggatg
4981 gatttttacg tgccaaggca ggaacccatg ttcaggtgga tgaggttttc tgacttgagc
5041 acgtgggagg gcgatcgcaa tctggctccc aattttgtga atgaagatgg cgtcgaatga
5101 cgccgctcca tcgaatgatg gtgcagctag tctcgtacca gaggccatta atgagactat
5161 gccattggaa cccgttgctg gcgcatctat tgctgcccca gtggcgggac aaactaacat
5221 aattgacccc tggataagaa caaattttgt gcaagcccct aatggagagt tcacagtatc
5281 accgagaaat tcccctggag agattctatt aaatttagag ttaggaccag atttgaatcc
5341 ttatttggcc catctgtcaa ggatgtacaa tggatatgcc ggaggtgttg aggtgcaagt
5401 gcttcttgct gggaacgcgt tcacagcagg aaagatatta tttgcagcaa tcccacccaa
5461 ctttcctgta gatatgatta gcccagctca aattactatg cttccccatt tgattgtaga
5521 tgttaggaca ttggaaccta ttatgatacc cttaccagat gtcaggaatg tgttctatca
5581 ttttaataat caaccccaac ctaggatgag attagtggct atgctctata ccccattgag
5641 atctaatggt tcaggagatg atgtctttac tgtgtcttgt agagtgttga ctaggccaac
5701 ccctgacttt gaatttattt acctagtgcc tccctctgta gagtccaaaa ctaaaccatt
5761 cacacttcca atattgacca tttctgaact aaccaactcc cggtttccca tcccaattga
5821 gcaactgtat acggccccaa atgagaataa tgttgtacag tgtcaaaatg gaaggtgcac
5881 cttggatgga gagcttcagg gcaccaccca gctgctatca agtgcagttt gctcttacag
5941 gggtaggact gtggctaaca gtggggacaa ttgggaccag aatctgctcc agctgaccta
6001 cccaagcggt gcaagctatg accccactga tgaagtacca gcacccttgg gcacccagga
6061 tttcagtggg atattgtatg gggtgttaac ccaagacaat gtaagtgagg gtacagggga
6121 ggccaaaaat gctaagggag tatacatatc caccaccagt ggaagattca ccccaaaaat
6181 tgggacaatt ggattgcatt caataactga aaatgtgcac cccaatcagc aatcacggtt
6241 cacccccgtt ggagtcgctc agaatgaaaa cacccccttc cagcaatggg ttctaccaca
6301 ctacgcaggt gctctcgctc taaacaccaa tttggcacct gctgttgccc cgactttccc
6361 tggcgagcaa ttactgttct tcaggtcccg tgtcccatgt gttcaaggtc tgcgggggca
6421 ggatgctttc atagattgtc tcctacctca agagtgggtg aaccattttt atcaagaggc
6481 tgctccctcc caagcagacg ttgctctcat caggtatgtc aaccctgaca ctggtcgcac
6541 gctgtttgag gccaaattgc acaggtcagg tttcattact gtgtcacaca ctggtaccta
6601 cccccttgtg gtccccccaa atggtcattt caggtttgat tcttgggtta accaattcta
6661 ctcactcgcc cccatgggaa ctggcaatgg gcgcagaaga gttcaataat ggcaggagca
6721 tttatagctg gtctagccgg tgacatgctg acttctgctg ttggttcgct gacctctgca
6781 ggagccaatg ccatcaatca gaaattgaat tttgattaca ataaacaact ccaaaacgca
6841 tcctttcaac atgacaagga aatgttgcag gcccaaattg atgctacgaa gaagctccaa
6901 tcagaaatga ttgcaattaa gcatggggtt ttgaccgcgg gcggcttttc cccagctgat
6961 gcagccagag gggcagtcaa cgccccaatg actcgagtgt tggattggtc agggacacgc
7021 tattacgctc caaattctgt gcaaaccacc agttattctg ggcaattcac cccctcgcca
7081 gtccatcggg cgcaggtgaa gtccccttcc aattcatctc agcggactgc agctccaagc
7141 agtatccgca gcctgtcaac ccaatcaact tctttaggct ccacctcctc aggggggtcc
7201 tctacaatct cctctagttc gaggacagca gactgggtgc aacaacaaag ggctcttagc
7261 ccgtacatgc agggagccct gcagacggca tacgtcacac cgccgtctag tagggcttcc
7321 agtgtgagct ctgtctcaac agtgcccaaa ggggttttgg actcctggac acctgtgttt
7381 aacacacgca ggcagccgct gtttgcacac ctcaggaaga ggggggagtc acaggcttag
7441 tgaaaaggat aatcaac
//