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PostPosted: Sat Sep 13, 2014 7:31 am 
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The recent MMWR on enterovirus D68 cases in Kansas City, MO and Chicago, IL has focused attention on earlier outbreaks. The most recently released sequences are 5' LTR sequences from University of Texas Southwestern Medical Center. However, initial characterization sheets did not include the date or location of collected samples. The sheets were updated yesterday, to show that these sequences were collected in 2009 from cases in Texas.

Virtually all sequences were most closely related to 2010 sequences from Japan (clade C), and were distinct from the series of 2009 sequences from New York City (clade A).

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PostPosted: Sat Sep 13, 2014 7:39 am 
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LOCUS KJ748061 290 bp RNA linear VRL 12-SEP-2014
DEFINITION Enterovirus D68 isolate AK37 5' UTR.
ACCESSION KJ748061
VERSION KJ748061.1 GI:666685079
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 290)
AUTHORS Kaushik,A., Lee,W.M., Levitz,R. and Gill,M.A.
TITLE Spectrum of Disease and Type specific severity of Lower respiratory
Illness associated with Human Rhinovirus in Children
JOURNAL Unpublished
REFERENCE 2 (bases 1 to 290)
AUTHORS Kaushik,A., Lee,W.M., Levitz,R. and Gill,M.A.
TITLE Direct Submission
JOURNAL Submitted (26-APR-2014) Pediatrics and Immunology, University of
Texas Southwestern Medical Center, 5323, Harry Hines Boulevard,
Dallas, TX 75390, USA
COMMENT ##Assembly-Data-START##
Assembly Method :: DNASTAR v. 8
Sequencing Technology :: Sanger dideoxy sequencing
##Assembly-Data-END##
FEATURES Location/Qualifiers
source 1..290
/organism="Enterovirus D68"
/mol_type="genomic RNA"
/isolate="AK37"
/host="Homo sapiens"
/db_xref="taxon:42789"
/country="USA: Texas"
/collection_date="2009"
/note="genotype: EV68"
5'UTR <1..>290
ORIGIN
1 ccccggtgcg gttgtataaa ctgttcccac ggttgaaaac aacctatccg ttatccgcta
61 tagtacttcg agaaacctag tatcaccttt ggattgttga tgcgttgcgc tcagcacact
121 aacccgtgtg tagcttgggt cgatgagtct ggacacaccc cactggcgac agtggtccag
181 gctgcgttgg cggcctactc atggtgaaaa ccatgagacg ctaaacatga acaaggtgtg
241 aagagtctat tgagctacta tagagtcctc cggcccnnga ncgcggntaa

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PostPosted: Sat Sep 13, 2014 7:41 am 
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Select seq gb|KJ748080.1| Enterovirus D68 strain EV68 isolate AK56 5' UTR 509 509 100% 5e-141 100% KJ748080.1
Select seq gb|KJ748164.1| Enterovirus D68 strain EV68 isolate AK140 5' UTR 504 504 96% 2e-139 100% KJ748164.1
Select seq gb|KJ748134.1| Enterovirus D68 strain EV68 isolate AK110 5' UTR 504 504 96% 2e-139 100% KJ748134.1
Select seq gb|KJ748112.1| Enterovirus D68 strain EV68 isolate AK88 5' UTR 504 504 96% 2e-139 100% KJ748112.1
Select seq gb|KJ748077.1| Enterovirus D68 strain EV68 isolate AK53 5' UTR 504 504 96% 2e-139 100% KJ748077.1
Select seq gb|KJ748138.1| Enterovirus D68 strain EV68 isolate AK114 5' UTR 500 500 96% 3e-138 99% KJ748138.1
Select seq gb|KJ748113.1| Enterovirus D68 strain EV68 isolate AK89 5' UTR 500 500 96% 3e-138 99% KJ748113.1
Select seq dbj|AB601882.2| Human enterovirus 68 genomic RNA, complete genome, strain: JPOC10-290 499 499 96% 1e-137 99% AB601882.2
Select seq gb|KJ748061.1| Enterovirus D68 strain EV68 isolate AK37 5' UTR 497 497 95% 3e-137 100% KJ748061.1
Select seq gb|KJ748131.1| Enterovirus D68 strain EV68 isolate AK107 5' UTR 495 495 95% 1e-136 99% KJ748131.1
Select seq dbj|AB601883.2| Human enterovirus 68 genomic RNA, complete genome, strain: JPOC10-378 495 495 96% 1e-136 99% AB601883.2
Select seq gb|KJ748156.1| Enterovirus D68 strain EV68 isolate AK132 5' UTR 493 493 96% 4e-136 99% KJ748156.1
Select seq gb|KJ748106.1| Enterovirus D68 strain EV68 isolate AK82 5' UTR 493 493 96% 4e-136 99% KJ748106.1
Select seq gb|JX101831.1| Human enterovirus 68 strain ARI192 from USA polyprotein gene, 5' UTR and partial cds 491 491 96% 1e-135 99% JX101831.1
Select seq gb|JX310693.1| Human enterovirus 68 isolate 90905081 5' UTR 489 489 96% 5e-135 99% JX310693.1
Select seq gb|KM361524.1| Enterovirus sp. isolate CU171 polyprotein gene, partial cds 486 486 96% 6e-134 99% KM361524.1
Select seq gb|KM361523.1| Enterovirus sp. isolate CU134 polyprotein gene, partial cds 486 486 96% 6e-134 99% KM361523.1
Select seq gb|JQ755303.1| Human enterovirus 68 strain 4310600466 5' UTR 486 486 95% 6e-134 99% JQ755303.1
Select seq gb|JX310695.1| Human enterovirus 68 isolate 91006265 5' UTR 486 486 96% 6e-134 99% JX310695.1
Select seq gb|JX310692.1| Human enterovirus 68 isolate 91006756 5' UTR 486 486 96% 6e-134 99% JX310692.1
Select seq gb|JX310691.1| Human enterovirus 68 isolate 91003100 5' UTR 486 486 96% 6e-134 99% JX310691.1
Select seq gb|JX310688.1| Human enterovirus 68 isolate 91106975 5' UTR 486 486 96% 6e-134 99% JX310688.1
Select seq gb|JX310686.1| Human enterovirus 68 isolate 91110530 5' UTR 486 486 96% 6e-134 99% JX310686.1
Select seq gb|EF107098.1| Human enterovirus 68 isolate 37-99 from France, complete genome 486 486 96% 6e-134 99% EF107098.1
Select seq gb|AY426519.1| Human enterovirus 68 strain MD02-1 5' UTR 486 486 95% 6e-134 99% AY426519.1
Select seq gb|AY426518.1| Human enterovirus 68 strain MD02-2 5' UTR 486 486 95% 6e-134 99% AY426518.1
Select seq gb|JX101844.1| Human enterovirus 68 strain SA792 from South Africa polyprotein gene, 5' UTR and partial cds 482 482 96% 8e-133 99% JX101844.1
Select seq gb|JX101843.1| Human enterovirus 68 strain SA563 from South Africa polyprotein gene, 5' UTR and partial cds 482 482 96% 8e-133 99% JX101843.1
Select seq gb|JX101840.1| Human enterovirus 68 strain SA402 from South Africa polyprotein gene, 5' UTR and partial cds 482 482 96% 8e-133 99% JX101840.1
Select seq gb|JQ586205.1| Human enterovirus 68 strain 09-86 5' UTR 482 482 96% 8e-133 99% JQ586205.1
Select seq gb|JQ586204.1| Human enterovirus 68 strain 09-85 5' UTR 482 482 96% 8e-133 99% JQ586204.1
Select seq gb|KJ748132.1| Enterovirus D68 strain EV68 isolate AK108 5' UTR 480 480 96% 3e-132 98% KJ748132.1
Select seq gb|KF726085.1| Enterovirus D68 isolate BCH895A, complete genome 480 480 96% 3e-132 98% KF726085.1
Select seq gb|JQ755335.1| Human enterovirus 68 strain VR960 5' UTR 480 480 95% 3e-132 99% JQ755335.1
Select seq gb|JQ755317.1| Human enterovirus 68 strain 4310800806 5' UTR 480 480 95% 3e-132 99% JQ755317.1
Select seq gb|JQ755316.1| Human enterovirus 68 strain 4310800795 5' UTR 480 480 95% 3e-132 99% JQ755316.1
Select seq gb|AY426522.1| Human enterovirus 68 strain MN89 5' UTR 480 480 95% 3e-132 99% AY426522.1
Select seq gb|JX310694.1| Human enterovirus 68 isolate 91005416 5' UTR 479 479 95% 9e-132 99% JX310694.1
Select seq gb|JQ755325.1| Human enterovirus 68 strain 4311000721 5' UTR 477 477 95% 3e-131 99% JQ755325.1
Select seq gb|JX310690.1| Human enterovirus 68 isolate 91005422 5' UTR 477 477 95% 3e-131 99% JX310690.1
Select seq gb|JX310689.1| Human enterovirus 68 isolate 91013136 5' UTR 477 477 95% 3e-131 99% JX310689.1
Select seq gb|JX101845.1| Human enterovirus 68 strain SA1354 from South Africa polyprotein gene, 5' UTR and partial cds 477 477 96% 3e-131 98% JX101845.1
Select seq gb|JX101841.1| Human enterovirus 68 strain SA498 from South Africa polyprotein gene, 5' UTR and partial cds 477 477 96% 3e-131 98% JX101841.1
Select seq gb|AY426525.1| Human enterovirus 68 strain NY93 5' UTR 477 477 95% 3e-131 99% AY426525.1
Select seq gb|AY426524.1| Human enterovirus 68 strain MN98 5' UTR 477 477 95% 3e-131 99% AY426524.1
Select seq gb|AY426523.1| Human enterovirus 68 strain MD99 5' UTR 477 477 95% 3e-131 99% AY426523.1
Select seq gb|KJ748137.1| Enterovirus D68 strain EV68 isolate AK113 5' UTR 475 475 91% 1e-130 100% KJ748137.1
Select seq gb|JQ755306.1| Human enterovirus 68 strain 4310600545 5' UTR 473 473 92% 4e-130 99% JQ755306.1
Select seq gb|JX101842.1| Human enterovirus 68 strain SA551 from South Africa polyprotein gene, 5' UTR and partial cds 473 473 96% 4e-130 98% JX101842.1
Select seq gb|JX129471.1| Human enterovirus strain 68/Colombia/FLI5997/2010 polyprotein gene, partial cds 471 471 96% 1e-129 97% JX129471.1
Select seq gb|GU933069.1| Human rhinovirus 87 isolate VFC177 5' UTR 471 471 96% 1e-129 97% GU933069.1
Select seq gb|AY426517.1| Human enterovirus 68 strain WI00 5' UTR 471 471 95% 1e-129 98% AY426517.1
Select seq gb|AY426516.1| Human enterovirus 68 strain MO00 5' UTR 471 471 95% 1e-129 98% AY426516.1
Select seq gb|JX129479.1| Human enterovirus strain 68/Peru/FPU00294/2011 polyprotein gene, partial cds 468 468 96% 2e-128 97% JX129479.1
Select seq gb|JX129472.1| Human enterovirus strain 68/Colombia/FLI6044/2010 polyprotein gene, partial cds 468 468 96% 2e-128 97% JX129472.1
Select seq gb|JX129470.1| Human enterovirus strain 68/Colombia/FLI5994/2010 polyprotein gene, partial cds 468 468 96% 2e-128 97% JX129470.1
Select seq gb|JX101839.1| Human enterovirus 68 strain GA431 from Gambia polyprotein gene, 5' UTR and partial cds 468 468 96% 2e-128 97% JX101839.1
Select seq gb|JX101838.1| Human enterovirus 68 strain GA427 from Gambia polyprotein gene, 5' UTR and partial cds 468 468 96% 2e-128 97% JX101838.1
Select seq gb|JX101836.1| Human enterovirus 68 strain GA421 from Gambia polyprotein gene, 5' UTR and partial cds 468 468 96% 2e-128 97% JX101836.1
Select seq gb|JX101835.1| Human enterovirus 68 strain GA420 from Gambia polyprotein gene, 5' UTR and partial cds 468 468 96% 2e-128 97% JX101835.1
Select seq gb|GU933068.1| Human rhinovirus 87 isolate VFC176 5' UTR 468 468 96% 2e-128 97% GU933068.1
Select seq gb|AY426527.1| Human enterovirus 68 strain TX99 5' UTR 468 468 95% 2e-128 98% AY426527.1
Select seq gb|AY426526.1| Human enterovirus 68 strain TX03 5' UTR 468 468 95% 2e-128 98% AY426526.1
Select seq gb|JQ755305.1| Human enterovirus 68 strain 4310600517 5' UTR 466 466 90% 6e-128 99% JQ755305.1
Select seq gb|GU933077.1| Human rhinovirus 87 isolate VFC202 5' UTR 466 466 96% 6e-128 97% GU933077.1
Select seq gb|JX101837.1| Human enterovirus 68 strain GA424 from Gambia polyprotein gene, 5' UTR and partial cds 464 464 96% 2e-127 97% JX101837.1
Select seq gb|KM361525.1| Enterovirus sp. isolate CU70 polyprotein gene, partial cds 462 462 96% 7e-127 97% KM361525.1
Select seq gb|JQ755307.1| Human enterovirus 68 strain 4310700531 5' UTR 462 462 95% 7e-127 97% JQ755307.1
Select seq gb|JX070222.1| Human enterovirus 68 isolate NZ-2010-541, complete genome 462 462 96% 7e-127 97% JX070222.1
Select seq gb|JX101846.1| Human enterovirus 68 strain NYC403 from USA, complete genome 462 462 96% 7e-127 97% JX101846.1
Select seq gb|JQ755311.1| Human enterovirus 68 strain 4310800679 5' UTR 459 459 95% 9e-126 97% JQ755311.1
Select seq gb|JQ755314.1| Human enterovirus 68 strain 4310800724 5' UTR 459 459 95% 9e-126 97% JQ755314.1
Select seq gb|JQ755319.1| Human enterovirus 68 strain 4310800894 5' UTR 459 459 95% 9e-126 97% JQ755319.1
Select seq gb|JQ755310.1| Human enterovirus 68 strain 4310700615 5' UTR 459 459 95% 9e-126 97% JQ755310.1
Select seq gb|JX101834.1| Human enterovirus 68 strain SEN37 from Senegal polyprotein gene, 5' UTR and partial cds 459 459 96% 9e-126 97% JX101834.1
Select seq gb|JX101833.1| Human enterovirus 68 strain SEN30 from Senegal polyprotein gene, 5' UTR and partial cds 459 459 96% 9e-126 97% JX101833.1
Select seq gb|JX101830.1| Human enterovirus 68 strain NYC817 from USA polyprotein gene, 5' UTR and partial cds 459 459 96% 9e-126 97% JX101830.1
Select seq gb|JX101829.1| Human enterovirus 68 strain NYC567 from USA polyprotein gene, 5' UTR and partial cds 459 459 96% 9e-126 97% JX101829.1
Select seq gb|JX101827.1| Human enterovirus 68 strain NYC496 from USA polyprotein gene, 5' UTR and partial cds 459 459 96% 9e-126 97% JX101827.1
Select seq gb|JX101826.1| Human enterovirus 68 strain NYC465 from USA polyprotein gene, 5' UTR and partial cds 459 459 96% 9e-126 97% JX101826.1
Select seq gb|JX101823.1| Human enterovirus 68 strain NYC446 from USA polyprotein gene, 5' UTR and partial cds 459 459 96% 9e-126 97% JX101823.1
Select seq gb|JX101822.1| Human enterovirus 68 strain NYC442 from USA polyprotein gene, 5' UTR and partial cds 459 459 96% 9e-126 97% JX101822.1
Select seq gb|JX101821.1| Human enterovirus 68 strain NYC435 from USA polyprotein gene, 5' UTR and partial cds 459 459 96% 9e-126 97% JX101821.1
Select seq gb|JX101818.1| Human enterovirus 68 strain NYC399 from USA polyprotein gene, 5' UTR and partial cds 459 459 96% 9e-126 97% JX101818.1
Select seq gb|JX101817.1| Human enterovirus 68 strain NYC397 from USA polyprotein gene, 5' UTR and partial cds 459 459 96% 9e-126 97% JX101817.1
Select seq gb|JX101816.1| Human enterovirus 68 strain NYC394 from USA polyprotein gene, 5' UTR and partial cds 459 459 96% 9e-126 97% JX101816.1
Select seq gb|JX101815.1| Human enterovirus 68 strain NYC369 from USA polyprotein gene, 5' UTR and partial cds 459 459 96% 9e-126 97% JX101815.1
Select seq gb|JQ586214.1| Human enterovirus 68 strain 10-260 5' UTR 459 459 96% 9e-126 97% JQ586214.1
Select seq gb|JQ586211.1| Human enterovirus 68 strain 09-70 5' UTR 459 459 96% 9e-126 97% JQ586211.1
Select seq gb|JX101832.1| Human enterovirus 68 strain SEN3 from Senegal polyprotein gene, 5' UTR and partial cds 455 455 96% 1e-124 96% JX101832.1
Select seq gb|JX101820.1| Human enterovirus 68 strain NYC409 from USA polyprotein gene, 5' UTR and partial cds 455 455 96% 1e-124 96% JX101820.1
Select seq gb|JQ586218.1| Human enterovirus 68 strain 10-298 5' UTR 455 455 96% 1e-124 96% JQ586218.1
Select seq gb|JQ586215.1| Human enterovirus 68 strain 10-268 5' UTR 455 455 96% 1e-124 96% JQ586215.1
Select seq gb|JQ755333.1| Human enterovirus 68 strain VR568 5' UTR 453 453 95% 4e-124 97% JQ755333.1
Select seq gb|JQ755328.1| Human enterovirus 68 strain 4311000763 5' UTR 453 453 95% 4e-124 97% JQ755328.1
Select seq gb|JQ755329.1| Human enterovirus 68 strain 4311000771 5' UTR 453 453 95% 4e-124 97% JQ755329.1
Select seq gb|JQ755331.1| Human enterovirus 68 strain 4311000783 5' UTR 453 453 95% 4e-124 97% JQ755331.1
Select seq gb|JQ755322.1| Human enterovirus 68 strain 4311000675 5' UTR 453 453 95% 4e-124 97% JQ755322.1
Select seq gb|JQ755326.1| Human enterovirus 68 strain 4311000742 5' UTR 453 453 95% 4e-124 97% JQ755326.1
Select seq gb|JQ755324.1| Human enterovirus 68 strain 4311000687 5' UTR 453 453 95% 4e-124 97% JQ755324.1

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PostPosted: Sat Sep 13, 2014 7:50 am 
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Location: Pittsburgh, PA USA
LOCUS JX101820 566 bp RNA linear VRL 21-AUG-2012
DEFINITION Human enterovirus 68 strain NYC409 from USA polyprotein gene, 5'
UTR and partial cds.
ACCESSION JX101820
VERSION JX101820.1 GI:392358650
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 566)
AUTHORS Tokarz,R., Firth,C., Madhi,S.A., Howie,S.R., Wu,W., Sall,A.A.,
Haq,S., Briese,T. and Lipkin,W.I.
TITLE Worldwide emergence of multiple clades of enterovirus 68
JOURNAL J. Gen. Virol. 93 (PT 9), 1952-1958 (2012)
PUBMED 22694903
REFERENCE 2 (bases 1 to 566)
AUTHORS Tokarz,R., Firth,C., Madhi,S.A., Howie,S.R.C., Wu,W., Sall,A.A.,
Haq,S., Briese,T. and Lipkin,W.I.
TITLE Direct Submission
JOURNAL Submitted (22-MAY-2012) Center for Infection and Immunity, Columbia
University, 722 West 168th Street, New York, NY 10032, USA
FEATURES Location/Qualifiers
source 1..566
/organism="Enterovirus D68"
/mol_type="genomic RNA"
/strain="NYC409"
/isolation_source="nasal swab"
/host="Homo sapiens"
/db_xref="taxon:42789"
/country="USA"
/collection_date="Sep-2009"
5'UTR 1..527
CDS 528..>566
/codon_start=1
/product="polyprotein"
/protein_id="AFM73493.1"
/db_xref="GI:392358651"
/translation="MGAQVTRQQTGTH"
ORIGIN
1 cggtgcggtt gtatagactg tttccacggt tgaaaacaac ttatccgtta tccgctatag
61 tacttcgaga aacctagtat cacctttgga ttgtcgatgc gttgcgctca gcacactaac
121 ccgtgtgtag cttgggctga tgagtctgga cgtaccccac tggtgacagt ggtccaggct
181 gcgttggcgg cctactcatg gtgaaaacca tgagacgcta gacatgaaca aggtgtgaag
241 agtctattga gctactatag agtcctccgg cccctgaatg cggctaatct taaccatgga
301 gcaagtgctc acaagccagt gagttgcttg tcgtaacgcg caagtccgtg gcggaaccga
361 ctactttggg tgtccgtgtt tcacttttta cctttatgac tgcttatggt gacaatttaa
421 tattgttgcc atttagcttg tcaaattaat cgcgtgaaat cctaaatctt gtttatcaat
481 ttgtgtttgg atagcttcat ttgaaaattc taaactcatt cataaagatg ggagctcaag
541 ttactaggca gcaaactgga acccac

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PostPosted: Sat Sep 13, 2014 7:54 am 
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The US sample from Arizona came from a child with fever, cough and rhinitis, while 14 NYC samples came from patients between 14 and 47 years of age that were seen in outpatient clinics throughout the city from individuals presenting with respiratory illness.

http://vir.sgmjournals.org/content/93/Pt_9/1952.long

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PostPosted: Sat Sep 13, 2014 8:02 am 
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Posts: 56044
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niman wrote:
The US sample from Arizona came from a child with fever, cough and rhinitis, while 14 NYC samples came from patients between 14 and 47 years of age that were seen in outpatient clinics throughout the city from individuals presenting with respiratory illness.

http://vir.sgmjournals.org/content/93/Pt_9/1952.long

LOCUS JX101831 554 bp RNA linear VRL 21-AUG-2012
DEFINITION Human enterovirus 68 strain ARI192 from USA polyprotein gene, 5'
UTR and partial cds.
ACCESSION JX101831
VERSION JX101831.1 GI:392358672
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 554)
AUTHORS Tokarz,R., Firth,C., Madhi,S.A., Howie,S.R., Wu,W., Sall,A.A.,
Haq,S., Briese,T. and Lipkin,W.I.
TITLE Worldwide emergence of multiple clades of enterovirus 68
JOURNAL J. Gen. Virol. 93 (PT 9), 1952-1958 (2012)
PUBMED 22694903
REFERENCE 2 (bases 1 to 554)
AUTHORS Tokarz,R., Firth,C., Madhi,S.A., Howie,S.R.C., Wu,W., Sall,A.A.,
Haq,S., Briese,T. and Lipkin,W.I.
TITLE Direct Submission
JOURNAL Submitted (22-MAY-2012) Center for Infection and Immunity, Columbia
University, 722 West 168th Street, New York, NY 10032, USA
FEATURES Location/Qualifiers
source 1..554
/organism="Enterovirus D68"
/mol_type="genomic RNA"
/strain="ARI192"
/isolation_source="nasal swab"
/host="Homo sapiens"
/db_xref="taxon:42789"
/country="USA"
/collection_date="Oct-2009"
5'UTR 1..515
CDS 516..>554
/codon_start=1
/product="polyprotein"
/protein_id="AFM73504.1"
/db_xref="GI:392358673"
/translation="MGAQVTRQQTGTH"
ORIGIN
1 cggtgcggtt gtataaactg ttcccacggt tgaaaacaac ctatccgtta tccgctatag
61 tacttcgaga aacctagtat caccttcgga ttgttgatgc gttgcgctca gcacactaac
121 ccgtgtgtag cttgggtcga tgagtctgga cataccccac tggcgacagt ggtccaggct
181 gcgttggcgg cctactcatg gtgaaaacca tgagacgcta aacatgaaca aggtgtgaag
241 agtctattga gctactatag agtcctccgg cccctgaatg cggctaatct taaccatgga
301 gcaagtgctc acaagccagt gggttgcttg tcgtaatgcg caagtccgtg gcggaaccga
361 ctactttggg tgtccgtgtt tcacttttta cttttatgac tgcttatggt gacaatttga
421 tattgttacc atttagcttg tcaaatcaat tacaaaagac ctaaatctta tttatcaact
481 tgctttttga taacttcaat cagaaaattt taataatggg agctcaagtt accagacagc
541 aaaccggtac ccac

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PostPosted: Tue Sep 16, 2014 4:29 am 
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Joined: Wed Aug 19, 2009 10:42 am
Posts: 56044
Location: Pittsburgh, PA USA
niman wrote:
The recent MMWR on enterovirus D68 cases in Kansas City, MO and Chicago, IL has focused attention on earlier outbreaks. The most recently released sequences are 5' LTR sequences from University of Texas Southwestern Medical Center. However, initial characterization sheets did not include the date or location of collected samples. The sheets were updated yesterday, to show that these sequences were collected in 2009 from cases in Texas.

Virtually all sequences were most closely related to 2010 sequences from Japan (clade C), and were distinct from the series of 2009 sequences from New York City (clade A).

2700.6] Spectrum of Disease and Type-Specific Severity of Lower Respiratory Illness Associated With Human Rhinovirus (HRV) in Children

Ashlesha Kaushik, Wai-Ming Lee, Ruth Levitz, Margaret Trost, Carla Garcia, Michelle Gill. Pediatrics, UT Southwestern Medical Center, Dallas, TX; Biological Mimetics, Inc., Frederick, MD; Pediatrics, Children's Hospital Los Angeles, Los Angeles, CA; Pediatrics, Questcare Pediatrics, Dallas, TX; Immunology, UT Southwestern Medical Center, Dallas, TX.

BACKGROUND: Implementation of molecular testing has increased recognition of HRV and its association with lower respiratory illness (LRI) in children. Knowledge of HRV's role in the pathogenesis of asthma, bronchiolitis and pneumonia is evolving. The contribution of specific HRV serotypes to LRI disease severity is not well known.
OBJECTIVE: 1) Define LRI associated with HRV in children who had HRV detected by respiratory viral PCR (RVP) over a 1 yr period
2) Identify associations of HRV serotypes with LRI severity.
DESIGN/METHODS: All patients with HRV+ RVPs between 11/10/2008-11/09/2009 were included. RVPs were performed at the discretion of primary providers across all point-of-care sites (ED, clinics or inpatient wards). Samples were analyzed using the Multicode-PLx Respiratory Viral Panel (EraGen Biosciences). Retrospective chart review was conducted to obtain clinical and laboratory data and associated diagnoses. Molecular typing was performed on available respiratory samples collected throughout the study period.
RESULTS: Of the 7891 RVPs performed, 1992 (25%) were HRV+. Of these, 1718 (86%) had HRV alone. 922 (54%) were hospitalized and 176 (19%) received ICU care. The most common diagnoses in hospitalized HRV+ patients were asthma (23%), bronchiolitis (18%), and pneumonia (13%). When stratified by diagnoses in those who had received RVP testing, the association of HRV with asthma (48%), bronchiolitis (27%) and pneumonia (39%) was more pronounced.
Of 212 samples available from patients with LRI, 82% were typable: HRVA and HRVC (43% each) were most frequent, followed by Enterovirus (9%) and HRVB (3%). Among patients with pneumonia (n=41 samples typed), 63% were HRVA/B and 37% were HRVC (p= 0.147). HRV type-specific disease severity was also observed in the pneumonia group. HRV A/B+ patients with pneumonia had increased ICU admission rates (16 [57%] vs. 2 [13%]; p=0.004), greater supplemental oxygen needs (21[81%] vs. 6 [40%]; p=0.015) and longer hospitalizations (11 vs. 4.5 days, p<0.05) compared to pneumonia patients with HRVC. No HRV type-specific effects were observed among patients with asthma or bronchiolitis.
CONCLUSIONS: Our results indicate that asthma, pneumonia and bronchiolitis are the leading diagnoses in hospitalized HRV+ children. Our data also provide evidence that HRVA/B are associated with greater disease severity than HRVC in hospitalized children with pneumonia.
First Author is a Fellow in Training
E-PAS2014:2700.6

Session: Platform Session: Asthma (1:00 PM - 3:00 PM)
Date/Time: Sunday, May 4, 2014 - 2:15 PM
Room: West 220 - Vancouver Convention Centre
Course Code: 2700

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PostPosted: Mon Sep 22, 2014 9:56 am 
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Enterovirus D68 in the United States of America

Disease outbreak news
17 September 2014

On 10 September 2014, the United States of America informed the Pan American Health Organization/World Health Organization (PAHO/WHO) about an outbreak of severe respiratory illness associated with Enterovirus D68 (EV-D68). As of 16 September 2014, 130 laboratory-confirmed cases of EV-D68 have been reported in 12 US states – Alabama, Colorado, Illinois, Indiana, Iowa, Kansas, Kentucky, Louisiana, Missouri, New York, Oklahoma, and Pennsylvania. Investigations into suspected clusters in many other states are ongoing.

EV-D68 is identified using molecular techniques at a limited number of laboratories in the USA. Enterovirus infections, including EV-D68, are not nationally notifiable, but laboratory detections of enterovirus and parechovirus types are reported voluntarily to the National Enterovirus Surveillance System, which is managed by the US Centers for Disease Control and Prevention.

Currently, there are no available vaccines or specific treatments for EV-D68 and clinical care is supportive. Symptoms of EV-D68 may include fever, runny nose, sneezing, cough, and body and muscle aches. Individuals with pre-existing conditions, such as asthma or other respiratory diseases, may be especially prone to severe infections from EV-D68 and may experience difficulty breathing or have wheezing.

http://who.int/csr/don/17-september-201 ... ovirus/en/

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PostPosted: Mon Sep 22, 2014 9:59 am 
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States with Lab-confirmed Enterovirus D68
States with Confirmed EV-D68 Infections
From mid-August to September 19, 2014, a total of 160 people from 22 states were confirmed to have respiratory illness caused by EV-D68. The 22 states are Alabama, California, Colorado, Connecticut, Georgia, Illinois, Indiana, Iowa, Kansas, Kentucky, Louisiana, Michigan, Minnesota, Missouri, Montana, Nebraska, New Jersey, New York, Oklahoma, Pennsylvania, Virginia, and Washington. The cases of EV-D68 infection were confirmed by the CDC or state public health laboratories that notified CDC.
In the upcoming weeks, more states will have confirmed cases of EV-D68 infection.
The primary reason for increases in cases is that several states are investigating clusters of people with severe respiratory illness, and specimens are still being tested for EV-D68. It can take a while to test specimens and obtain lab results. That’s because the testing is complex and slower, and can only be done by CDC and a small number of state public health laboratories. As the backlog of specimens is processed, the number of states and confirmed cases will likely increase. These increases will not necessarily reflect changes in real time, or mean that the situation is getting worse.
Some of the increase will be from new EV-D68 infections since people are more likely to get infected with enteroviruses in the summer and fall. We are currently in the middle of the enterovirus season.
As investigations progress, we will have a better understanding of the trends for EV-D68 infections.

http://www.cdc.gov/non-polio-enteroviru ... tates.html

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