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PostPosted: Mon Nov 10, 2014 11:10 am 
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Location: Pittsburgh, PA USA
2014 enterovirus D68 sequences from California and Colorado match 2013 California acute flaccid paralysis sequences, which are also circulating in Missouri.

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PostPosted: Mon Nov 10, 2014 11:19 am 
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Location: Pittsburgh, PA USA
UCSF Title of 2014 seqs from CA and CO
Genomic Analysis Uncovers a Novel Circulating Enterovirus D68 Strain in Association with Cases of Acute Flaccid Paralysis from 2012-2014

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PostPosted: Mon Nov 10, 2014 11:29 am 
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Location: Pittsburgh, PA USA
LOCUS KP100793 7265 bp RNA linear VRL 07-NOV-2014
DEFINITION Enterovirus D68 strain US/CO/14-94 polyprotein gene, complete cds.
ACCESSION KP100793
VERSION KP100793.1 GI:705382647
KEYWORDS .
SOURCE Enterovirus D68 (EV-D68)
ORGANISM Enterovirus D68
Viruses; ssRNA positive-strand viruses, no DNA stage;
Picornavirales; Picornaviridae; Enterovirus; Enterovirus D.
REFERENCE 1 (bases 1 to 7265)
AUTHORS Greninger,A.L., Naccache,S.N., Yu,G., Messacar,K., Somasekar,S.,
Dominguez,S. and Chiu,C.Y.
TITLE Genomic Analysis Uncovers a Novel Circulating Enterovirus D68
Strain in Association with Cases of Acute Flaccid Paralysis from
2012-2014
JOURNAL Unpublished
REFERENCE 2 (bases 1 to 7265)
AUTHORS Greninger,A.L., Naccache,S.N., Yu,G., Messacar,K., Somasekar,S.,
Dominguez,S. and Chiu,C.Y.
TITLE Direct Submission
JOURNAL Submitted (07-NOV-2014) Laboratory Medicine, UCSF, 185 Berry St,
San Francisco, CA 94107, USA
COMMENT ##Assembly-Data-START##
Assembly Method :: Geneious v. v8.0.2
Sequencing Technology :: Illumina; Sanger dideoxy sequencing
##Assembly-Data-END##
FEATURES Location/Qualifiers
source 1..7265
/organism="Enterovirus D68"
/mol_type="genomic RNA"
/strain="US/CO/14-94"
/serotype="EV-D68"
/isolation_source="nasopharyngeal swab"
/host="Homo sapiens"
/db_xref="taxon:42789"
/country="USA"
/collection_date="Sep-2014"
5'UTR 1..698
CDS 699..7265
/codon_start=1
/product="polyprotein"
/protein_id="AIW58909.1"
/db_xref="GI:705382648"
/translation="MGAQVTRQQTGTHENANIATNGSHITYNQINFYKDSYAASASKQ
DFSQDPSKFTEPVVEGLKAGAPVLKSPSAEACGYSDRVLQLKLGNSAIVTQEAANYCC
AYGEWPNYLPDHEAVAIDKPTQPETATDRFYTLKSVKWETGSTGWWWKLPDALNNIGM
FGQNVQHHYLYRSGFLIHVQCNATKFHQGALLVVAIPEHQRGAHNTNTSPGFDDIMKG
EEGGTFNHPYVLDDGTSLACATIFPHQWINLRTNNSATIVLPWMNAAPMDFPLRHNQW
TLAIIPVVPLGTRTTSSMVPITVSIAPMCCEFNGLRHAITQGVPTYLLPGSGQFLTTD
DHSSAPALPCFNPTPEMHIPGQVRNMLEVVQVESMMEINNTESAVGMERLKVDISALT
DVDQLLFNIPLDIQLDGPLRNTLVGNISRYYTHWSGSLEMTFMFCGSFMATGKLILCY
TPPGGSCPTTRETAMLGTHIVWDFGLQSSVTLIIPWISGSHYRMFNNDAKSTNANVGY
VTCFMQTNLIVPSESSDTCSLIGFIAAKDDFSLRLMRDSPDIGQLDHLHAAEAAYQIE
SIIKTATDTVKSEINAELGVVPSLNAVETGATSNTEPEEAIQTRTVINQHGVSETLVE
NFLSRAALVSKRSFEYKDHTSSAAQADKNFFKWTINTRSFVQLRRKLELFTYLRFDAE
ITILTTVAVNGSSNNTYVGLPDLTLQAMFVPTGALTPEKQDSFHWQSGSNASVFFKIS
DPPARITIPFMCINSAYSVFYDGFAGFEKNGLYGINPADTIGNLCVRIVNEHQPVGFT
VTVRVYMKPKHIKAWAPRPPRTLPYMSIANANYKGKERAPNALSAIIGNRDSVKTMPH
NIVNTGPGFGGVFVGSFKIINYHLATAEERQSAIYVDWQSDVLVTPIAAHGRHQIARC
KCNTGVYYCRHKNRSYPICFEGPGIQWIEQNEYYPARYQTNVLLAVGPAEAGDCGGLL
VCPHGVIGLLTAGGGGIVAFTDIRNLLWLDTDAMEQGITDYIQNLGNAFGAGFTETIS
NKAKEVQDMLIGESSLLEKLLKALIKIISALVIVIRNSEDLVTVTATLALLGCHDSPW
SYLKQKVCSYLGIPYVPRQGESWLKKFTEACNALRGLDWLSQKIDKFINWLKTKILPE
AREKYEFVQRLKQLPVIENQVSTIEHSCPTTEQQQALFNNVQYYSHYCRKYAPLYAVE
AKRVVALEKKINNYIQFKSKSRIEPVCLIIHGSPGTGKSVASNLIARAITEKLGGDIY
SLPPDPKYFDGYKQQTVVLMDDLMQNPDGNDISMFCQMVSTVDFIPPMASLEEKGTLY
TSPFLIATTNAGSIHAPTVSDSKALSRRFKFDVDIEVTDSYKDSNKLDMSRAVEMCKP
DGCAPTNYKRCCPLICGKAIQFRDRRTNARSTIDMLVTDIIKEYRTRNSTQDKLEALF
QGPPQFKEIKISVTPDTPAPDAINDLLRSVDSQEVRDYCQKKGWIVVHPSNELIVEKH
ISRAFITLQAIATFVSIAGVVYVIYKLFAGIQGPYTGIPNPKPKVPSLRTAKVQGPGF
DFAQAIMKKNTVIARTEKGEFTMLGVYDRVAVIPTHASVGETIYINDVETKVLDACAL
RDLTDTNLEITIVKLDRNQKFRDIRHFLPRYEDDYNDAVLSVHTSKFPNMYIPVGQVT
NYGFLNLGGTPTHRILMYNFPTRAGQCGGVVTTTGKVIGIHVGGNGAQGFAAMLLHSY
FTDTQGEIVSSEKSGVCINAPAKTKLQPSVFHQVFEGSKEPAVLNPKDPRLKTDFEEA
IFSKYTGNKIMLMDEYMEEAVDHYVGCLEPLDISVDPIPLESAMYGMDGLEALDLTTS
AGFPYLLQGKKKRDIFNRHTRDTSEMTKMLEKYGVDLPFVTFVKDELRSKEKVEKGKS
RLIEASSLNDSVAMRVAFGNLYATFHNNPGTATGSAVGCDPDIFWSKIPILLDGEIFA
FDYTGYDASLSPVWFACLKKVLIKLGYTHQTSFIDYLCHSVHLYKDKKYIVNGGMPSG
SSGTSIFNTMINNIIIRTLLIRVYKGIDLDQFKMIAYGDDVIASYPHKIDPGLLAEAG
KQYGLVMTPADKGTSFIDTNWENVTFLKRYFRADDQYPFLIHPVMPMKEIHESIRWTK
DPRNTQDHVRSLCYLAWHNGEEAYNEFCRKIRSVPVGRALTLPAYSSLRRKWLDSF"
mat_peptide 699..905
/product="VP4 peptide"
mat_peptide 906..1649
/product="VP2 peptide"
mat_peptide 1650..2354
/product="VP3 peptide"
mat_peptide 2355..3281
/product="VP1 peptide"
mat_peptide 3282..3722
/product="2A peptide"
mat_peptide 3723..4019
/product="2B peptide"
mat_peptide 4020..5009
/product="2C peptide"
mat_peptide 5010..5276
/product="3A peptide"
mat_peptide 5277..5342
/product="3B peptide"
mat_peptide 5343..5891
/product="3C peptide"
mat_peptide 5892..7262
/product="3D product"
ORIGIN
1 ttaaaacagc cttggggttg ttcccactcc aagggcccac gtggcggcta gtactctggt
61 acttcggtac ctttgtacgc ctgttttatc tcccttccca atgtaactta gaagttctta
121 aatcaatgct caataggtgg ggcgcaaacc agcgctctca tgagcaagca ctcctgtctc
181 cccggtgagg ttgtataaac tgttcccacg gttgaaaaca acctatccgt tatccgctat
241 agtacttcga gaaacctagt accacctttg gattgttgac gcgttgcgct cagcacacta
301 acccgtgtgt agcttgggtc gatgagtctg gacatacctc actggcgaca gtggtccagg
361 ctgcgttggc ggcctactca tggtgaaagc catgagacgc tagacatgaa caaggtgtga
421 agagtctatt gagctactat agagtcctcc ggcccctgaa tgcggctaat cctaaccatg
481 gagcaagtgc tcacaggcca gtgagttgct tgtcgtaatg cgcaagtccg tggcggaacc
541 gactactttg ggtgtccgtg tttcactttt tacttttatg actgcttatg gtgacaattt
601 tatattgtta ccatttagct tgtcaaatca attgcaaaag atcctaactc ttatttatca
661 acttgcatct cgataactct aatttgaaaa ttttaacaat gggagctcag gttactagac
721 aacaaactgg cactcatgaa aatgccaaca ttgccacaaa tggatctcat atcacataca
781 atcagataaa cttttacaag gatagttatg cggcttcagc cagcaagcag gatttttcac
841 aagacccatc aaaattcact gaaccagtag tggaaggttt aaaagcaggg gcgccagttt
901 tgaaatctcc tagtgctgag gcatgtggct acagtgatag agtattacag ctcaaattag
961 gaaactcagc tattgtcacc caggaagcag cgaactactg ctgcgcttat ggtgaatggc
1021 ccaattactt accagaccat gaagcagtag ccattgataa acctacacaa ccagaaactg
1081 ctacagatag attctacact ttgaaatcag tcaaatggga aactggaagc acaggatggt
1141 ggtggaaatt acccgatgca ctaaataata taggcatgtt tggacagaat gtacagcatc
1201 actacctata tagatctggt ttcttgattc atgtgcagtg taatgccaca aaattccatc
1261 aaggtgcctt attagtggta gcaattccag aacatcagag gggagcgcac aacaccaaca
1321 ctagcccagg gtttgatgat ataatgaaag gtgaagaagg agggaccttc aatcatccat
1381 atgtccttga tgatggaaca tcattggctt gtgcgacgat atttccacat cagtggataa
1441 atctgagaac caacaattca gcaacaattg ttcttccctg gatgaatgct gctccaatgg
1501 atttcccact cagacataat cagtggacgc tagcaataat accagtggtg ccattaggca
1561 cgcgtacaac atcaagtatg gtcccaataa cagtttcaat cgctccaatg tgttgtgagt
1621 ttaatggact tagacacgcc attactcaag gtgtcccaac atacctttta ccaggctcgg
1681 gacaattcct aacaactgat gatcatagct ctgcaccagc tctcccgtgt ttcaacccaa
1741 ctccagaaat gcatatccca gggcaggtcc gtaacatgct agaagtggtc caagtggaat
1801 caatgatgga gattaataac acagaaagtg cagttggcat ggagcgtctt aaggttgata
1861 tatcagcatt gacagatgtc gatcaattgt tattcaacat tccactggac atacagttgg
1921 atgggccact tagaaacact ttagtaggaa acatatctag atattacact cattggtctg
1981 gatccctaga aatgacgttt atgttttgtg gcagcttcat ggcaacggga aaattaatcc
2041 tgtgctatac tcctccaggt ggatcatgcc cgacaaccag agagaccgcc atgttaggta
2101 cacatattgt ttgggatttt ggattacaat ctagtgtaac cctgataata ccttggatta
2161 gtggatccca ctacaggatg tttaataatg atgctaagtc aactaatgcc aacgttggct
2221 atgtcacttg ttttatgcag accaatctga tagtccccag tgaatcctct gacacgtgtt
2281 ctttgatagg gttcatagca gcaaaagatg atttctccct cagattaatg agagacagcc
2341 ctgacattgg acaactagac catttacatg cagcagaggc agcctaccag atcgagagca
2401 tcatcaaaac agcaactgac actgtgaaaa gtgagattaa tgctgaactt ggtgtggtcc
2461 ctagcttaaa tgcagttgaa acaggtgcaa cttctaacac tgaaccagaa gaagccatac
2521 aaactcgcac agtgataaat cagcacggtg tatccgagac tctagtggag aattttctca
2581 gtagagcagc tttggtatca aagagaagtt ttgaatacaa agatcatact tcgtctgcag
2641 cacaagcaga caagaacttt ttcaaatgga caattaacac cagatccttt gtacagttaa
2701 gaagaaaatt agaattattc acatacctta gatttgatgc tgagatcact atactcacaa
2761 ctgtagcagt gaatggtagt agtaataata catacgtggg tcttcctgac ttgacacttc
2821 aagcaatgtt tgtgcccact ggtgctctta ccccagaaaa gcaggactca ttccactggc
2881 agtcaggcag taatgctagt gtattcttta aaatctctga ccccccagcc agaataacca
2941 taccttttat gtgcattaac tcagcatact cagtttttta tgatggcttt gccggatttg
3001 agaaaaacgg tctgtatgga ataaatccag ctgatactat tggtaactta tgtgttagaa
3061 tagtgaatga acaccaacca gttggtttca cagtgaccgt tagggtttac atgaagccta
3121 aacacataaa agcatgggca ccacgaccac cacgaactct gccatatatg agtattgcaa
3181 atgcaaatta caaaggtaaa gaaagagcac caaatgcgct cagtgctata attggcaata
3241 gagacagtgt caaaaccatg cctcataata tagtgaacac tggtccaggc ttcggaggag
3301 tttttgtagg gtctttcaaa ataatcaact atcacttggc cactgcagaa gagagacagt
3361 cagctatcta tgtggattgg caatcagacg tcttggttac ccccattgct gctcatggaa
3421 ggcaccaaat agcaagatgc aagtgcaaca caggggttta ctattgtagg cacaaaaaca
3481 gaagttaccc gatttgcttt gaaggcccag ggattcaatg gattgaacaa aatgaatatt
3541 acccagcaag gtaccagacc aatgtacttt tggcagttgg tcctgcggaa gcaggagatt
3601 gcggtggttt actagtttgt ccacatgggg taatcggtct tcttacagca ggagggggtg
3661 gaattgtagc tttcactgat atcaggaatt tgctatggtt agatactgat gctatggaac
3721 aaggcattac tgattatatt caaaatcttg gtaatgcctt tggagcagga tttacagaaa
3781 caatctctaa taaagccaag gaagtgcaag atatgctaat tggagagagt tcactattag
3841 aaaaattgtt aaaagctcta atcaaaatca tatcagcatt agtaattgta atcagaaact
3901 cagaagattt agtcacagtc acagccacac tagcattgtt gggatgccat gattcaccat
3961 ggagctactt gaaacagaag gtatgttcat acttaggtat tccttatgta cctagacagg
4021 gtgaatcgtg gctcaagaag ttcacagagg catgcaatgc tcttagaggt ctggattggc
4081 tatcgcaaaa gatagataaa ttcatcaact ggcttaaaac caaaatatta ccagaagcta
4141 gggagaaata tgaatttgtg caaaggctca aacagttacc ggtgatagaa aaccaagtta
4201 gtacaatcga gcatagctgc ccaacaacag aacaacaaca ggccttattc aacaacgtcc
4261 aatactattc acactactgt agaaagtacg caccacttta cgcagtggaa gcaaagaggg
4321 tagtagctct tgaaaagaaa ataaacaact acatccagtt caagtccaaa tctcgcattg
4381 aaccggtttg tttaataata catggctctc caggaactgg caagtcagtg gcttcaaatt
4441 taattgccag ggctatcaca gagaaattgg ggggggacat ttattccttg cctccagacc
4501 ctaaatattt tgatggatac aaacagcaaa cagtggtcct catggatgat ttaatgcaaa
4561 atccagatgg gaatgacata tctatgttct gccaaatggt ctccactgta gatttcatac
4621 ccccaatggc tagtttggag gaaaaaggaa ctctatacac cagtccattt ttaatagcta
4681 ctaccaatgc tggctcaata catgcaccaa ctgtatcaga ctcaaaggct ttgtcacgca
4741 gatttaaatt tgacgtggac attgaagtca cagattcata caaggactca aataaattgg
4801 atatgtcaag ggcagtcgag atgtgcaaac cagacggctg tgcccccacc aattacaaaa
4861 gatgctgccc attgatctgt ggaaaggcta tccaattcag agatcgcaga actaatgcaa
4921 gatccactat tgatatgcta gtaaccgata ttataaagga atatagaacc agaaacagta
4981 cacaggataa gctggaagct ctgtttcagg ggcctccaca gtttaaagag atcaaaattt
5041 cagtcacccc agatacacca gctcctgatg ctataaatga ccttcttagg tcagtggatt
5101 ctcaagaagt tagggattat tgccaaaaga aaggatggat tgtagtacac ccatcaaatg
5161 agctaatagt agaaaaacac attagtagag cttttattac tctacaagcc attgccacct
5221 ttgtatcaat agctggtgta gtttatgtta tatacaaact ttttgctggc attcagggtc
5281 catacacagg aatccccaat cctaaaccta aagtaccctc tctcagaaca gctaaagtgc
5341 aaggaccagg gttcgatttt gcacaagcca taatgaagaa aaataccgtc attgcaagga
5401 ctgaaaaggg tgagttcacc atgctgggtg tatatgatag ggtagcggtc atccccacac
5461 acgcatctgt tggagaaacc atttacatta atgatgtaga gactaaagtt ttagatgcgt
5521 gtgcacttag agacttgact gatacaaact tagagataac catagtcaaa ttagaccgta
5581 accaaaaatt tagagatatc agacattttc tgcccagata tgaggatgat tacaatgacg
5641 ctgtgcttag cgtacataca tcaaaattcc caaatatgta tatcccagtt ggacaagtca
5701 ccaattatgg cttcttgaac ctaggtggta caccgacgca ccgcatttta atgtataact
5761 tcccaacaag agctggccag tgtggtggtg tggtgacaac tacaggtaag gtgataggaa
5821 tacatgtagg tggaaatgga gctcaaggat ttgcagcaat gctactacac tcttacttta
5881 ccgatacaca aggtgagata gttagtagtg aaaagagtgg ggtgtgcatt aacgcaccgg
5941 caaagactaa actccaaccc agtgttttcc atcaagtttt tgaaggttca aaggaaccag
6001 cagttctcaa tccaaaagat cctaggctta aaacagattt cgaggaggcc attttctcaa
6061 agtacacagg taacaaaatc atgttaatgg atgagtacat ggaagaggca gtggatcatt
6121 atgtggggtg tttagaacca ttagacatca gtgtggatcc catacccctg gaaagtgcca
6181 tgtatggaat ggatggcctt gaggcattag acttaactac cagtgcagga ttcccttact
6241 tactacaagg gaagaagaaa agggatatat ttaatagaca tactagagac accagtgaaa
6301 tgacaaaaat gttagagaaa tatggagttg acctaccttt tgtaaccttt gtaaaagatg
6361 agcttagatc aaaagaaaaa gttgaaaaag ggaaatcacg cctgattgag gccagttcct
6421 tgaatgactc agttgctatg agagttgcct ttggaaacct ttacgccaca tttcacaaca
6481 atccaggtac agcaactggt agtgcagttg gttgtgatcc agatatattt tggtcaaaaa
6541 tccctatttt gttagatgga gaaatctttg cttttgacta cactggttat gatgctagtt
6601 tgtcaccagt gtggtttgcc tgtttaaaga aagttctaat taagttaggt tacacacatc
6661 aaacgtcttt tatagattat ttgtgtcatt cagtacattt atataaggac aaaaagtaca
6721 tagttaatgg tggaatgccc tctggttctt caggcaccag catattcaac actatgatca
6781 acaatataat cataagaact ttattaatta gggtttacaa aggcatagac ctggaccagt
6841 tcaaaatgat tgcctatggg gatgatgtta ttgctagcta cccacataag attgatccag
6901 gtttgctggc agaagcaggc aaacagtatg gattagtaat gacaccagca gacaaaggaa
6961 ccagttttat tgacacaaat tgggaaaatg tgactttctt aaaaagatat ttcagagcag
7021 atgatcaata cccctttctc atacatccag tgatgccaat gaaagagata catgaatcta
7081 ttagatggac taaagatccc agaaacacac aggatcatgt taggtctttg tgctacctcg
7141 catggcataa tggagaggag gcttataatg aattttgcag aaaaatcaga agtgtgcctg
7201 tgggaagagc attgacacta cctgcatact ctagtcttag acggaaatgg ttagattcgt
7261 tctag

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PostPosted: Mon Nov 10, 2014 11:30 am 
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Joined: Wed Aug 19, 2009 10:42 am
Posts: 56044
Location: Pittsburgh, PA USA
Select seq gb|KP100793.1| Enterovirus D68 strain US/CO/14-94 polyprotein gene, complete cds 612 612 100% 9e-172 100% KP100793.1
Select seq gb|KM892502.1| Enterovirus D68 isolate CA/AFP/v14T04344 VP1 capsid protein gene, partial cds 612 612 100% 9e-172 100% KM892502.1
Select seq gb|KM851228.1| Enterovirus D68 strain US/MO/14-18950, partial genome 612 612 100% 9e-172 100% KM851228.1
Select seq gb|KM851226.1| Enterovirus D68 strain US/MO/14-18948, partial genome 612 612 100% 9e-172 100% KM851226.1
Select seq gb|KP100796.1| Enterovirus D68 strain US/CA/14-6100 polyprotein gene, partial cds 607 607 100% 4e-170 99% KP100796.1
Select seq gb|KP100795.1| Enterovirus D68 strain US/CA/14-6103SIB polyprotein gene, complete cds 607 607 100% 4e-170 99% KP100795.1
Select seq gb|KP100792.1| Enterovirus D68 strain US/CA/14-6092 polyprotein gene, partial cds 607 607 100% 4e-170 99% KP100792.1
Select seq gb|KM975347.1| Enterovirus D68 strain 4311400698_NL14 capsid protein VP1 gene, partial cds 607 607 100% 4e-170 99% KM975347.1
Select seq gb|KM881710.1| Enterovirus D68 strain EV-D68_STL_2014_12 polyprotein gene, complete cds 603 603 100% 5e-169 99% KM881710.1
Select seq gb|KM851227.1| Enterovirus D68 strain US/MO/14-18949, partial genome 603 603 100% 5e-169 99% KM851227.1
Select seq gb|KM851225.1| Enterovirus D68 strain US/MO/14-18947, partial genome 598 598 100% 2e-167 99% KM851225.1
Select seq gb|KM975343.1| Enterovirus D68 strain 4311300117_NL13 capsid protein VP1 gene, partial cds 594 594 100% 3e-166 99% KM975343.1
Select seq gb|KC763162.1| Human enterovirus 68 strain ITA/20528/12 VP1 gene, partial cds 589 589 100% 1e-164 99% KC763162.1
Select seq gb|JQ924865.1| Human enterovirus isolate CQ-5584 VP1 gene, partial cds 589 589 100% 1e-164 99% JQ924865.1
Select seq gb|KP100794.1| Enterovirus D68 strain US/CO/14-60 polyprotein gene, complete cds 585 585 100% 1e-163 98% KP100794.1
Select seq gb|JX898785.1| Human enterovirus 68 isolate CQ5585 VP1 gene, partial cds 585 585 100% 1e-163 98% JX898785.1
Select seq gb|JQ411807.1| Human enterovirus D isolate TH_CU124 VP1 gene, partial cds 585 585 100% 1e-163 98% JQ411807.1
Select seq gb|JQ924867.1| Human enterovirus isolate CQ-5759 VP1 gene, partial cds 585 585 100% 1e-163 98% JQ924867.1
Select seq gb|KM361524.1| Enterovirus sp. isolate CU171 polyprotein gene, partial cds 580 580 100% 6e-162 98% KM361524.1
Select seq gb|KM361523.1| Enterovirus sp. isolate CU134 polyprotein gene, partial cds 580 580 100% 6e-162 98% KM361523.1
Select seq gb|JQ411803.1| Human enterovirus D isolate TH_CU134 VP1 gene, partial cds 580 580 100% 6e-162 98% JQ411803.1
Select seq gb|JQ411804.1| Human enterovirus D isolate TH_CU101 VP1 gene, partial cds 580 580 100% 6e-162 98% JQ411804.1
Select seq gb|KM975338.1| Enterovirus D68 strain 4311200780_NL12 capsid protein VP1 gene, partial cds 576 576 100% 7e-161 98% KM975338.1
Select seq gb|KM892499.1| Enterovirus D68 isolate CA/AFP/v12T00346, partial genome 576 576 100% 7e-161 98% KM892499.1
Select seq gb|KM892498.1| Enterovirus D68 isolate CA/AFP/v12T04950 VP1 capsid protein gene, partial cds 576 576 100% 7e-161 98% KM892498.1
Select seq gb|JQ924866.1| Human enterovirus isolate CQ-5735 VP1 gene, partial cds 571 571 100% 3e-159 97% JQ924866.1
Select seq gb|KM892501.1| Enterovirus D68 isolate CA/AFP/11-1767, complete genome 567 567 100% 4e-158 97% KM892501.1
Select seq dbj|AB817708.1| Human enterovirus 68 VP1 gene for capsid protein VP1, partial cds, note: Hospital study number: TTa-08-Ph597_VP1 553 553 100% 8e-154 96% AB817708.1
Select seq gb|JF830048.1| Human enterovirus 68 strain 4310901880 capsid VP1 gene, partial cds 553 553 100% 8e-154 96% JF830048.1
Select seq gb|JF896311.1| Human enterovirus 68 isolate EV68_NL_200912598 VP1 protein gene, partial cds 553 553 100% 8e-154 96% JF896311.1
Select seq gb|KJ556327.1| Enterovirus D68 isolate CSP329 VP1 gene, partial cds 549 549 100% 9e-153 96% KJ556327.1
Select seq dbj|AB817709.1| Human enterovirus 68 VP1 gene for capsid protein VP1, partial cds, note: Hospital study number: TTa-08-Ph608_VP1 549 549 100% 9e-153 96% AB817709.1
Select seq dbj|AB817706.1| Human enterovirus 68 VP1 gene for capsid protein VP1, partial cds, note: Hospital study number: TTa-08-Ph560_VP1 549 549 100% 9e-153 96% AB817706.1
Select seq dbj|AB817705.1| Human enterovirus 68 VP1 gene for capsid protein VP1, partial cds, note: Hospital study number: TTa-08-Ph519_VP1 549 549 100% 9e-153 96% AB817705.1
Select seq dbj|AB817704.1| Human enterovirus 68 VP1 gene for capsid protein VP1, partial cds, note: Hospital study number: TTa-08-Ph513_VP1 549 549 100% 9e-153 96% AB817704.1
Select seq dbj|AB817702.1| Human enterovirus 68 VP1 gene for capsid protein VP1, partial cds, note: Hospital study number: TTa-08-Ph343_VP1 549 549 100% 9e-153 96% AB817702.1
Select seq gb|JQ586222.1| Human enterovirus 68, VP1, partial sequence, 09-85 549 549 100% 9e-153 96% JQ586222.1
Select seq gb|JF830047.1| Human enterovirus 68 strain 4310901514 capsid VP1 gene, partial cds 549 549 100% 9e-153 96% JF830047.1
Select seq gb|JF830045.1| Human enterovirus 68 strain 4310900947 capsid VP1 gene, partial cds 549 549 100% 9e-153 96% JF830045.1
Select seq dbj|AB614409.1| Human enterovirus 68 gene for polyprotein, VP1 protein region, strain: 1975-Yamagata-2010 549 549 100% 9e-153 96% AB614409.1
Select seq dbj|AB902837.1| Enterovirus D68 gene for polyprotein, partial cds, strain: EV68/Okinawa/174/2010 547 547 99% 3e-152 96% AB902837.1
Select seq gb|KM975350.1| Enterovirus D68 strain 4311400743_NL14 capsid protein VP1 gene, partial cds 544 544 100% 4e-151 96% KM975350.1
Select seq dbj|AB817716.1| Human enterovirus 68 VP1 gene for capsid protein VP1, partial cds, note: Hospital study number: TTa-11-Ph395_VP1 544 544 100% 4e-151 96% AB817716.1
Select seq dbj|AB817711.1| Human enterovirus 68 VP1 gene for capsid protein VP1, partial cds, note: Hospital study number: TTa-11-Ph245_VP1 544 544 100% 4e-151 96% AB817711.1
Select seq gb|JQ586223.1| Human enterovirus 68, VP1, partial sequence, 09-86 544 544 100% 4e-151 96% JQ586223.1
Select seq gb|JF830049.1| Human enterovirus 68 strain 4310902042 capsid VP1 gene, partial cds 544 544 100% 4e-151 96% JF830049.1
Select seq gb|JF896310.1| Human enterovirus 68 isolate EV68_NL_200914918 VP1 protein gene, partial cds 544 544 100% 4e-151 96% JF896310.1
Select seq gb|JF896302.1| Human enterovirus 68 isolate EV68_NL_201013557 VP1 protein gene, partial cds 544 544 100% 4e-151 96% JF896302.1
Select seq gb|JF896303.1| Human enterovirus 68 isolate EV68_NL_201012467 VP1 protein gene, partial cds 544 544 100% 4e-151 96% JF896303.1
Select seq dbj|AB614430.1| Human enterovirus 68 gene for polyprotein, VP1 protein region, strain: 2082-Yamagata-2010 544 544 100% 4e-151 96% AB614430.1
Select seq dbj|AB614431.1| Human enterovirus 68 gene for polyprotein, VP1 protein region, strain: 2145-Yamagata-2010 544 544 100% 4e-151 96% AB614431.1
Select seq dbj|AB614427.1| Human enterovirus 68 gene for polyprotein, VP1 protein region, strain: 2035-Yamagata-2010 544 544 100% 4e-151 96% AB614427.1
Select seq gb|JQ586224.1| Human enterovirus 68, VP1, partial sequence, 09-115 542 542 99% 1e-150 96% JQ586224.1
Select seq gb|KM975346.1| Enterovirus D68 strain 4311400668_NL14 capsid protein VP1 gene, partial cds 540 540 100% 5e-150 95% KM975346.1
Select seq gb|KM975345.1| Enterovirus D68 strain 4311301187_NL13 capsid protein VP1 gene, partial cds 540 540 100% 5e-150 95% KM975345.1
Select seq gb|KM975330.1| Enterovirus D68 strain 3101400307_NL14 capsid protein VP1 gene, partial cds 540 540 100% 5e-150 95% KM975330.1
Select seq dbj|AB861414.1| Enterovirus D68 VP1 gene for VP1 polyprotein, partial cds, isolate: TTa-11-Ph344_VP1 540 540 100% 5e-150 95% AB861414.1
Select seq dbj|AB817715.1| Human enterovirus 68 VP1 gene for capsid protein VP1, partial cds, note: Hospital study number: TTa-11-Ph344_VP1 540 540 100% 5e-150 95% AB817715.1
Select seq dbj|AB817713.1| Human enterovirus 68 VP1 gene for capsid protein VP1, partial cds, note: Hospital study number: TTa-11-Ph269_VP1 540 540 100% 5e-150 95% AB817713.1
Select seq dbj|AB817703.1| Human enterovirus 68 VP1 gene for capsid protein VP1, partial cds, note: Hospital study number: TTa-08-Ph451_VP1 540 540 100% 5e-150 95% AB817703.1
Select seq gb|KC763167.1| Human enterovirus 68 strain ITA/23695/12 VP1 gene, partial cds 540 540 100% 5e-150 95% KC763167.1
Select seq gb|JQ586226.1| Human enterovirus 68, VP1, partial sequence, 09-398 540 540 100% 5e-150 95% JQ586226.1
Select seq gb|JF896308.1| Human enterovirus 68 isolate EV68_NL_200913563 VP1 protein gene, partial cds 540 540 100% 5e-150 95% JF896308.1
Select seq gb|JF896309.1| Human enterovirus 68 isolate EV68_NL_200914986 VP1 protein gene, partial cds 540 540 100% 5e-150 95% JF896309.1
Select seq gb|JF896307.1| Human enterovirus 68 isolate EV68_NL_201012867 VP1 protein gene, partial cds 540 540 100% 5e-150 95% JF896307.1
Select seq gb|JF896305.1| Human enterovirus 68 isolate EV68_NL_201014073 VP1 protein gene, partial cds 540 540 100% 5e-150 95% JF896305.1
Select seq dbj|AB614437.1| Human enterovirus 68 gene for polyprotein, VP1 protein region, strain: 2161-Yamagata-2010 540 540 100% 5e-150 95% AB614437.1
Select seq dbj|AB614433.1| Human enterovirus 68 gene for polyprotein, VP1 protein region, strain: 2086-Yamagata-2010 540 540 100% 5e-150 95% AB614433.1
Select seq gb|KM975334.1| Enterovirus D68 strain 3101400542_NL14 capsid protein VP1 gene, partial cds 535 535 100% 2e-148 95% KM975334.1
Select seq gb|KM975333.1| Enterovirus D68 strain 3101400474_NL14 capsid protein VP1 gene, partial cds 535 535 100% 2e-148 95% KM975333.1
Select seq gb|KM975332.1| Enterovirus D68 strain 3101400473_NL14 capsid protein VP1 gene, partial cds 535 535 100% 2e-148 95% KM975332.1
Select seq gb|KM975331.1| Enterovirus D68 strain 3101400309_NL14 capsid protein VP1 gene, partial cds 535 535 100% 2e-148 95% KM975331.1
Select seq gb|KM975329.1| Enterovirus D68 strain 3101400018_NL14 capsid protein VP1 gene, partial cds 535 535 100% 2e-148 95% KM975329.1
Select seq gb|KM975326.1| Enterovirus D68 strain 3101200440_NL12 capsid protein VP1 gene, partial cds 535 535 100% 2e-148 95% KM975326.1
Select seq gb|KM851230.1| Enterovirus D68 strain US/IL/14-18952, partial genome 535 535 100% 2e-148 95% KM851230.1
Select seq gb|KM851229.1| Enterovirus D68 strain US/KY/14-18951, partial genome 535 535 100% 2e-148 95% KM851229.1
Select seq gb|KF254924.1| Enterovirus D68 isolate SO9406 VP1 gene, partial cds 535 535 100% 2e-148 95% KF254924.1
Select seq gb|KF254922.1| Enterovirus D68 isolate SO9288 VP1 gene, partial cds 535 535 100% 2e-148 95% KF254922.1
Select seq gb|KF254920.1| Enterovirus D68 isolate SO9277 VP1 gene, partial cds 535 535 100% 2e-148 95% KF254920.1
Select seq gb|KF254919.1| Enterovirus D68 isolate SO9320 VP1 gene, partial cds 535 535 100% 2e-148 95% KF254919.1
Select seq gb|KF254918.1| Enterovirus D68 isolate SO9493 VP1 gene, partial cds 535 535 100% 2e-148 95% KF254918.1
Select seq gb|KF254917.1| Enterovirus D68 isolate SO9336 VP1 gene, partial cds 535 535 100% 2e-148 95% KF254917.1
Select seq gb|KJ472886.1| Enterovirus D68 isolate HEV196011 VP1 gene, partial cds 535 535 100% 2e-148 95% KJ472886.1
Select seq dbj|AB817712.1| Human enterovirus 68 VP1 gene for capsid protein VP1, partial cds, note: Hospital study number: TTa-11-Ph257_VP1 535 535 100% 2e-148 95% AB817712.1
Select seq gb|KC763164.1| Human enterovirus 68 strain ITA/22516/12 VP1 gene, partial cds 535 535 100% 2e-148 95% KC763164.1
Select seq gb|JQ586221.1| Human enterovirus 68, VP1, partial sequence, 09-56 535 535 100% 2e-148 95% JQ586221.1
Select seq gb|JF896306.1| Human enterovirus 68 isolate EV68_NL_201013230 VP1 protein gene, partial cds 535 535 100% 2e-148 95% JF896306.1
Select seq gb|KF254923.1| Enterovirus D68 isolate SO9306 VP1 gene, partial cds 531 531 100% 3e-147 95% KF254923.1
Select seq gb|KF254921.1| Enterovirus D68 isolate SO9411 VP1 gene, partial cds 531 531 100% 3e-147 95% KF254921.1
Select seq gb|KC763169.1| Human enterovirus 68 strain ITA/24518/12 VP1 gene, partial cds 531 531 100% 3e-147 95% KC763169.1
Select seq gb|JF896304.1| Human enterovirus 68 isolate EV68_NL_201011595 VP1 protein gene, partial cds 531 531 100% 3e-147 95% JF896304.1
Select seq gb|KM975342.1| Enterovirus D68 strain 4311201039_NL12 capsid protein VP1 gene, partial cds 526 526 100% 1e-145 94% KM975342.1
Select seq gb|KM975328.1| Enterovirus D68 strain 3101300356_NL13 capsid protein VP1 gene, partial cds 526 526 100% 1e-145 94% KM975328.1
Select seq gb|KM975327.1| Enterovirus D68 strain 3101200566_NL12 capsid protein VP1 gene, partial cds 526 526 100% 1e-145 94% KM975327.1
Select seq gb|KF254913.1| Enterovirus D68 isolate ID72 VP1 gene, partial cds 526 526 100% 1e-145 94% KF254913.1
Select seq emb|LN626610.1| Human enterovirus partial 1D gene for polyprotein, VP1 region, isolate CF267090_FRA14 517 517 100% 6e-143 94% LN626610.1
Select seq gb|JX101800.1| Human enterovirus 68 strain SA792 from South Africa VP1 gene, partial cds 513 513 100% 7e-142 94% JX101800.1
Select seq gb|JX101799.1| Human enterovirus 68 strain SA563 from South Africa VP1 gene, partial cds 508 508 100% 3e-140 93% JX101799.1
Select seq gb|JF830021.1| Human enterovirus 68 strain 3000000227 capsid VP1 gene, partial cds 508 508 100% 3e-140 93% JF830021.1
Select seq gb|JF830020.1| Human enterovirus 68 strain 3009903700 capsid VP1 gene, partial cds 508 508 100% 3e-140 93% JF830020.1

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PostPosted: Mon Nov 10, 2014 12:10 pm 
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Location: Pittsburgh, PA USA
Thread on polio-like D68

viewtopic.php?f=5&t=12916

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PostPosted: Mon Dec 08, 2014 12:58 pm 
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Joined: Wed Aug 19, 2009 10:42 am
Posts: 56044
Location: Pittsburgh, PA USA
Thread on 7 CDC sequences
viewtopic.php?f=5&t=13066

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