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More 2014 CO and CA Enterovirus D68 Flaccid Paralysis Seqs
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Author:  niman [ Sun Nov 30, 2014 1:22 pm ]
Post subject:  More 2014 CO and CA Enterovirus D68 Flaccid Paralysis Seqs

UCSF has released additional 2014 CO and CA Enterovirus D68 novel sub-clade seqs linked to acute flaccid paralysis.

Author:  niman [ Sun Nov 30, 2014 1:38 pm ]
Post subject:  Re: More 2014 CO and CA Enterovirus D68 Flaccid Paralysis Se

Enterovirus D68 strain US/CA/14-R2 polyprotein gene, partial cds
1,395 bp linear RNA
Accession: KP126908.1 GI: 721772256
GenBank FASTA Graphics
Select item 721772273
2.
Enterovirus D68 strain US/CA/14-R1 polyprotein gene, partial cds
1,481 bp linear RNA
Accession: KP126909.1 GI: 721772273
GenBank FASTA Graphics
Select item 721772290
3.
Enterovirus D68 strain US/CA/14-6067 polyprotein gene, partial cds
1,416 bp linear RNA
Accession: KP126910.1 GI: 721772290
GenBank FASTA Graphics
Select item 721772306
4.
Enterovirus D68 strain US/CO/14-94 polyprotein gene, complete cds
7,265 bp linear RNA
Accession: KP126911.1 GI: 721772306
GenBank FASTA Graphics
Select item 721772321
5.
Enterovirus D68 strain US/CO/14-86 polyprotein gene, partial cds
1,423 bp linear RNA
Accession: KP126912.1 GI: 721772321
GenBank FASTA Graphics

Author:  niman [ Sun Nov 30, 2014 2:02 pm ]
Post subject:  Re: More 2014 CO and CA Enterovirus D68 Flaccid Paralysis Se

Select seq gb|KP126908.1| Enterovirus D68 strain US/CA/14-R2 polyprotein gene, partial cds 2516 2516 100% 0.0 100% KP126908.1
Select seq gb|KP100792.1| Enterovirus D68 strain US/CA/14-6092 polyprotein gene, partial cds 2453 2453 100% 0.0 99% KP100792.1
Select seq gb|KM851228.1| Enterovirus D68 strain US/MO/14-18950, partial genome 2453 2453 100% 0.0 99% KM851228.1
Select seq gb|KP126909.1| Enterovirus D68 strain US/CA/14-R1 polyprotein gene, partial cds 2448 2448 100% 0.0 99% KP126909.1
Select seq gb|KP100793.1| Enterovirus D68 strain US/CO/14-94 polyprotein gene, complete cds 2448 2448 100% 0.0 99% KP100793.1
Select seq gb|KP100796.1| Enterovirus D68 strain US/CA/14-6100 polyprotein gene, partial cds 2444 2444 100% 0.0 99% KP100796.1
Select seq gb|KP100795.1| Enterovirus D68 strain US/CA/14-6103SIB polyprotein gene, complete cds 2444 2444 100% 0.0 99% KP100795.1
Select seq gb|KM851227.1| Enterovirus D68 strain US/MO/14-18949, partial genome 2444 2444 100% 0.0 99% KM851227.1
Select seq gb|KP126910.1| Enterovirus D68 strain US/CA/14-6067 polyprotein gene, partial cds 2439 2439 100% 0.0 99% KP126910.1
Select seq gb|KM851226.1| Enterovirus D68 strain US/MO/14-18948, partial genome 2439 2439 100% 0.0 99% KM851226.1
Select seq gb|KM851225.1| Enterovirus D68 strain US/MO/14-18947, partial genome 2435 2435 100% 0.0 99% KM851225.1
Select seq gb|KM881710.1| Enterovirus D68 strain EV-D68_STL_2014_12 polyprotein gene, complete cds 2426 2426 100% 0.0 99% KM881710.1
Select seq gb|KP126912.1| Enterovirus D68 strain US/CO/14-86 polyprotein gene, partial cds 2415 2415 99% 0.0 98% KP126912.1
Select seq gb|KM892499.1| Enterovirus D68 isolate CA/AFP/v12T00346, partial genome 2397 2397 99% 0.0 98% KM892499.1
Select seq gb|KP100794.1| Enterovirus D68 strain US/CO/14-60 polyprotein gene, complete cds 2394 2394 100% 0.0 98% KP100794.1
Select seq gb|KM361523.1| Enterovirus sp. isolate CU134 polyprotein gene, partial cds 2361 2361 99% 0.0 98% KM361523.1
Select seq gb|KM361524.1| Enterovirus sp. isolate CU171 polyprotein gene, partial cds 2356 2356 99% 0.0 97% KM361524.1
Select seq gb|KM892501.1| Enterovirus D68 isolate CA/AFP/11-1767, complete genome 2352 2352 99% 0.0 97% KM892501.1
Select seq gb|KM851229.1| Enterovirus D68 strain US/KY/14-18951, partial genome 2154 2154 99% 0.0 94% KM851229.1
Select seq gb|KM851230.1| Enterovirus D68 strain US/IL/14-18952, partial genome 2145 2145 99% 0.0 94% KM851230.1
Select seq dbj|AB601885.1| Human enterovirus 68 gene for polyprotein, complete cds, strain: JPOC10-404 1995 1995 99% 0.0 92% AB601885.1
Select seq gb|EF107098.1| Human enterovirus 68 isolate 37-99 from France, complete genome 1974 1974 99% 0.0 91% EF107098.1
Select seq dbj|AB601883.2| Human enterovirus 68 genomic RNA, complete genome, strain: JPOC10-378 1968 1968 99% 0.0 91% AB601883.2
Select seq dbj|AB601882.2| Human enterovirus 68 genomic RNA, complete genome, strain: JPOC10-290 1959 1959 99% 0.0 91% AB601882.2
Select seq dbj|AB601884.1| Human enterovirus 68 gene for polyprotein, complete cds, strain: JPOC10-396 1959 1959 99% 0.0 91% AB601884.1
Select seq gb|JX101846.1| Human enterovirus 68 strain NYC403 from USA, complete genome 1831 1831 99% 0.0 89% JX101846.1
Select seq gb|KM361525.1| Enterovirus sp. isolate CU70 polyprotein gene, partial cds 1828 1828 99% 0.0 89% KM361525.1
Select seq gb|KF726085.1| Enterovirus D68 isolate BCH895A, complete genome 1811 1811 99% 0.0 89% KF726085.1
Select seq gb|KM892500.1| Enterovirus D68 isolate CA/RESP/10-786, complete genome 1795 1795 99% 0.0 89% KM892500.1
Select seq gb|JX070222.1| Human enterovirus 68 isolate NZ-2010-541, complete genome 1795 1795 99% 0.0 89% JX070222.1
Select seq gb|KM851231.1| Enterovirus D68 strain US/KY/14-18953, complete genome 1772 1772 99% 0.0 88% KM851231.1
Select seq gb|AY426531.1| Human enterovirus 68 strain Fermon, complete genome 1678 1678 99% 0.0 87% AY426531.1
Select seq gb|KM892502.1| Enterovirus D68 isolate CA/AFP/v14T04344 VP1 capsid protein gene, partial cds 1622 1622 66% 0.0 99% KM892502.1
Select seq gb|KM892498.1| Enterovirus D68 isolate CA/AFP/v12T04950 VP1 capsid protein gene, partial cds 1570 1570 66% 0.0 98% KM892498.1
Select seq gb|KC763162.1| Human enterovirus 68 strain ITA/20528/12 VP1 gene, partial cds 1570 1570 65% 0.0 98% KC763162.1
Select seq dbj|AB614427.1| Human enterovirus 68 gene for polyprotein, VP1 protein region, strain: 2035-Yamagata-2010 1472 1472 66% 0.0 95% AB614427.1
Select seq dbj|AB614430.1| Human enterovirus 68 gene for polyprotein, VP1 protein region, strain: 2082-Yamagata-2010 1463 1463 66% 0.0 95% AB614430.1
Select seq dbj|AB614431.1| Human enterovirus 68 gene for polyprotein, VP1 protein region, strain: 2145-Yamagata-2010 1463 1463 66% 0.0 95% AB614431.1
Select seq dbj|AB614409.1| Human enterovirus 68 gene for polyprotein, VP1 protein region, strain: 1975-Yamagata-2010 1463 1463 66% 0.0 95% AB614409.1
Select seq dbj|AB861414.1| Enterovirus D68 VP1 gene for VP1 polyprotein, partial cds, isolate: TTa-11-Ph344_VP1 1458 1458 66% 0.0 95% AB861414.1
Select seq dbj|AB614433.1| Human enterovirus 68 gene for polyprotein, VP1 protein region, strain: 2086-Yamagata-2010 1458 1458 66% 0.0 95% AB614433.1
Select seq dbj|AB614437.1| Human enterovirus 68 gene for polyprotein, VP1 protein region, strain: 2161-Yamagata-2010 1454 1454 66% 0.0 95% AB614437.1
Select seq gb|KC763167.1| Human enterovirus 68 strain ITA/23695/12 VP1 gene, partial cds 1442 1442 65% 0.0 95% KC763167.1
Select seq gb|KC763164.1| Human enterovirus 68 strain ITA/22516/12 VP1 gene, partial cds 1424 1424 65% 0.0 94% KC763164.1
Select seq gb|KC763169.1| Human enterovirus 68 strain ITA/24518/12 VP1 gene, partial cds 1415 1415 65% 0.0 94% KC763169.1
Select seq gb|JX101799.1| Human enterovirus 68 strain SA563 from South Africa VP1 gene, partial cds 1413 1413 66% 0.0 94% JX101799.1
Select seq gb|AY426493.1| Human enterovirus 68 strain MO00 polyprotein gene, partial cds 1409 1409 66% 0.0 94% AY426493.1
Select seq gb|AY426494.1| Human enterovirus 68 strain WI00 polyprotein gene, partial cds 1400 1400 66% 0.0 94% AY426494.1
Select seq gb|JX101795.1| Human enterovirus 68 strain SA402 from South Africa VP1 gene, partial cds 1395 1395 66% 0.0 93% JX101795.1
Select seq gb|AY426495.1| Human enterovirus 68 strain TX02-1 polyprotein gene, partial cds 1391 1391 66% 0.0 93% AY426495.1
Select seq gb|KJ472886.1| Enterovirus D68 isolate HEV196011 VP1 gene, partial cds 1370 1370 64% 0.0 94% KJ472886.1
Select seq gb|AY426491.1| Human enterovirus 68 strain MD02-1 polyprotein gene, partial cds 1364 1364 66% 0.0 93% AY426491.1
Select seq gb|AY426492.1| Human enterovirus 68 strain MD02-2 polyprotein gene, partial cds 1359 1359 66% 0.0 93% AY426492.1
Select seq gb|AY426496.1| Human enterovirus 68 strain TX02-2 polyprotein gene, partial cds 1357 1357 66% 0.0 93% AY426496.1
Select seq dbj|AB667894.1| Human enterovirus 68 VP1 gene for polyprotein, partial cds, strain: 2251-Yamagata-2005 1346 1346 66% 0.0 92% AB667894.1
Select seq gb|JX101800.1| Human enterovirus 68 strain SA792 from South Africa VP1 gene, partial cds 1337 1337 62% 0.0 94% JX101800.1
Select seq dbj|AB667893.1| Human enterovirus 68 VP1 gene for polyprotein, partial cds, strain: 2218-Yamagata-2005 1337 1337 65% 0.0 92% AB667893.1
Select seq dbj|AB667891.1| Human enterovirus 68 VP1 gene for polyprotein, partial cds, strain: 2062-Yamagata-2005 1337 1337 66% 0.0 92% AB667891.1
Select seq gb|KC763157.1| Human enterovirus 68 strain ITA/18641/08 VP1 gene, partial cds 1333 1333 65% 0.0 92% KC763157.1
Select seq dbj|AB667895.1| Human enterovirus 68 VP1 gene for polyprotein, partial cds, strain: 1703-Yamagata-2007 1332 1332 66% 0.0 92% AB667895.1
Select seq dbj|AB667892.1| Human enterovirus 68 VP1 gene for polyprotein, partial cds, strain: 2124-Yamagata-2005 1332 1332 66% 0.0 92% AB667892.1
Select seq gb|KC763172.1| Human enterovirus 68 strain ITA/26868/08 VP1 gene, partial cds 1324 1324 65% 0.0 92% KC763172.1
Select seq gb|KM892497.1| Enterovirus D68 isolate CA/RESP/09-871 VP1 capsid protein gene, partial cds 1323 1323 66% 0.0 92% KM892497.1
Select seq emb|LN626610.1| Human enterovirus partial 1D gene for polyprotein, VP1 region, isolate CF267090_FRA14 1321 1321 61% 0.0 94% LN626610.1
Select seq gb|JX101797.1| Human enterovirus 68 strain SA551 from South Africa VP1 gene, partial cds 1319 1319 66% 0.0 92% JX101797.1
Select seq gb|JX101796.1| Human enterovirus 68 strain SA498 from South Africa VP1 gene, partial cds 1319 1319 66% 0.0 92% JX101796.1
Select seq dbj|AB614436.1| Human enterovirus 68 gene for polyprotein, VP1 protein region, strain: 2146-Yamagata-2010 1319 1319 66% 0.0 92% AB614436.1
Select seq dbj|AB614424.1| Human enterovirus 68 gene for polyprotein, VP1 protein region, strain: 2015-Yamagata-2010 1319 1319 66% 0.0 92% AB614424.1
Select seq dbj|AB614434.1| Human enterovirus 68 gene for polyprotein, VP1 protein region, strain: 2101-Yamagata-2010 1319 1319 66% 0.0 92% AB614434.1
Select seq dbj|AB614435.1| Human enterovirus 68 gene for polyprotein, VP1 protein region, strain: 2116-Yamagata-2010 1319 1319 66% 0.0 92% AB614435.1
Select seq gb|AY426497.1| Human enterovirus 68 strain MN98 polyprotein gene, partial cds 1319 1319 66% 0.0 92% AY426497.1
Select seq gb|KC763158.1| Human enterovirus 68 strain ITA/19179/08 VP1 gene, partial cds 1315 1315 65% 0.0 92% KC763158.1
Select seq dbj|AB601880.1| Human enterovirus 68 gene for polyprotein, partial cds, VP1 protein region, strain: JPOC10-616 1314 1314 66% 0.0 91% AB601880.1
Select seq dbj|AB614438.1| Human enterovirus 68 gene for polyprotein, VP1 protein region, strain: 2166-Yamagata-2010 1314 1314 66% 0.0 91% AB614438.1
Select seq dbj|AB614411.1| Human enterovirus 68 gene for polyprotein, VP1 protein region, strain: 1980-Yamagata-2010 1314 1314 66% 0.0 91% AB614411.1
Select seq dbj|AB614412.1| Human enterovirus 68 gene for polyprotein, VP1 protein region, strain: 1981-Yamagata-2010 1314 1314 66% 0.0 91% AB614412.1
Select seq gb|KC763173.1| Human enterovirus 68 strain ITA/27708/08 VP1 gene, partial cds 1312 1312 65% 0.0 92% KC763173.1
Select seq dbj|AB601881.1| Human enterovirus 68 gene for polyprotein, partial cds, VP1 protein region, strain: JPOC10-618 1310 1310 66% 0.0 91% AB601881.1
Select seq dbj|AB601873.1| Human enterovirus 68 gene for polyprotein, partial cds, VP1 protein region, strain: JPOC10-373 1310 1310 66% 0.0 91% AB601873.1
Select seq dbj|AB601874.1| Human enterovirus 68 gene for polyprotein, partial cds, VP1 protein region, strain: JPOC10-402 1310 1310 66% 0.0 91% AB601874.1
Select seq dbj|AB601878.1| Human enterovirus 68 gene for polyprotein, partial cds, VP1 protein region, strain: JPOC10-471 1310 1310 66% 0.0 91% AB601878.1
Select seq dbj|AB601872.1| Human enterovirus 68 gene for polyprotein, partial cds, VP1 protein region, strain: JPOC10-200 1310 1310 66% 0.0 91% AB601872.1
Select seq dbj|AB614426.1| Human enterovirus 68 gene for polyprotein, VP1 protein region, strain: 2032-Yamagata-2010 1310 1310 66% 0.0 91% AB614426.1
Select seq dbj|AB614425.1| Human enterovirus 68 gene for polyprotein, VP1 protein region, strain: 2016-Yamagata-2010 1310 1310 66% 0.0 91% AB614425.1
Select seq dbj|AB614423.1| Human enterovirus 68 gene for polyprotein, VP1 protein region, strain: 2011-Yamagata-2010 1310 1310 66% 0.0 91% AB614423.1
Select seq dbj|AB614410.1| Human enterovirus 68 gene for polyprotein, VP1 protein region, strain: 1976-Yamagata-2010 1310 1310 66% 0.0 91% AB614410.1
Select seq dbj|AB614408.1| Human enterovirus 68 gene for polyprotein, VP1 protein region, strain: 1946-Yamagata-2010 1310 1310 66% 0.0 91% AB614408.1
Select seq dbj|AB614406.1| Human enterovirus 68 gene for polyprotein, VP1 protein region, strain: 1939-Yamagata-2010 1310 1310 66% 0.0 91% AB614406.1
Select seq dbj|AB614407.1| Human enterovirus 68 gene for polyprotein, VP1 protein region, strain: 2013-Yamagata-2010 1310 1310 66% 0.0 91% AB614407.1
Select seq gb|AY426499.1| Human enterovirus 68 strain MD99 polyprotein gene, partial cds 1310 1310 66% 0.0 91% AY426499.1
Select seq gb|KC763168.1| Human enterovirus 68 strain ITA/24281/08 VP1 gene, partial cds 1306 1306 65% 0.0 92% KC763168.1
Select seq gb|KC763160.1| Human enterovirus 68 strain ITA/19962/08 VP1 gene, partial cds 1306 1306 65% 0.0 92% KC763160.1
Select seq dbj|AB601877.1| Human enterovirus 68 gene for polyprotein, partial cds, VP1 protein region, strain: JPOC10-445 1306 1306 66% 0.0 91% AB601877.1
Select seq gb|JX101798.1| Human enterovirus 68 strain SA553 from South Africa VP1 gene, partial cds 1305 1305 66% 0.0 91% JX101798.1
Select seq dbj|AB601875.1| Human enterovirus 68 gene for polyprotein, partial cds, VP1 protein region, strain: JPOC10-412 1305 1305 66% 0.0 91% AB601875.1
Select seq dbj|AB601879.1| Human enterovirus 68 gene for polyprotein, partial cds, VP1 protein region, strain: JPOC10-573 1305 1305 66% 0.0 91% AB601879.1
Select seq dbj|AB614429.1| Human enterovirus 68 gene for polyprotein, VP1 protein region, strain: 2052-Yamagata-2010 1305 1305 66% 0.0 91% AB614429.1
Select seq gb|JX101786.1| Human enterovirus 68 strain ARI192 from USA VP1 gene, partial cds 1301 1301 66% 0.0 91% JX101786.1
Select seq dbj|AB614439.1| Human enterovirus 68 gene for polyprotein, VP1 protein region, strain: 2167-Yamagata-2010 1301 1301 66% 0.0 91% AB614439.1
Select seq dbj|AB614428.1| Human enterovirus 68 gene for polyprotein, VP1 protein region, strain: 2037-Yamagata-2010 1301 1301 66% 0.0 91% AB614428.1

Author:  niman [ Wed Dec 03, 2014 4:02 am ]
Post subject:  Re: More 2014 CO and CA Enterovirus D68 Flaccid Paralysis Se

CDC: Link between polio-like illness and EV-D68 looks likely
Filed Under: Enterovirus; Misc Emerging Topics
Robert Roos | News Editor | CIDRAP News | Dec 02, 2014

With the recent outbreaks of enterovirus D68 (EV-D68) respiratory infections and mysterious polio-like illnesses in US children fading, it seems increasingly likely that the two are related, says an expert with the Centers for Disease Control and Prevention (CDC).

The CDC has reported 1,121 EV-D68 cases in 47 states since August, a number that has not increased since Nov 20, with nearly all cases in children. Meanwhile, the total for the unexplained polio-like cases, involving sudden onset of weakness in one or more limbs, reached 90 on Nov 28, which was 2 more than a week earlier. Two reported cases were still being verified.

James J. Sejvar, MD, a neuroepidemiologist with the CDC, said the latest known onset of a case of the polio-like illness occurred about 3 weeks ago. "We're continuing our surveillance and trying to identify new cases, but the good news is that it does appear that new cases have kind of ceased at this point," he told CIDRAP News.

Change in terminology
The CDC now refers to the condition as acute flaccid myelitis (AFM) in children. Earlier the agency generally referred to it as unexplained neurologic illness with limb weakness in children.

"It's an illness with acute onset that basically results in flaccid weakness of the limbs, sometimes with cranial nerve involvement, and it is a myelitis, an inflammation of the spinal cord," Sejvar explained.

He said some earlier CDC statements referred to the condition as "anterior myelitis," which is often used to describe polio. "But in many of the cases we've seen, the inflammation or infection is not limited to the anterior portion of the spinal cord; it's in fact the whole central portion of the spinal cord, so we dropped the 'anterior' part."

Telling observations
Sejvar said the CDC is not ready to state flatly that the AFM cases were caused by EV-D68, but several observations are "pretty convincing."

A little less than half of the 90 children who met the AFM case definition had evidence of EV-D68 infection at nonsterile sites, such as in nasal or stool samples, he said. "There are reasons that a child may actually have been infected with EV-68 but not tested positive," he added. "That has to do with the timing of the collection of the specimen in relation to onset of illness and the way the specimen is handled. It's entirely possible that even more children with this illness have had EV-68 infection than we're currently ascertaining."

Sejvar noted that the first cluster of AFM cases was seen in Colorado in August and September (officials said 4 of 10 case-patients there tested positive for EV-D68), and more cases were later found in other states. "It's notable that this clustering or outbreak of acute flaccid myelitis occurred against the backdrop of this large national outbreak of EV-68 respiratory infection among children," he said.

In addition, the number of new EV-D68 cases started dropping sharply in early October, and the incidence of new AFM cases started declining about the same time, Sejvar observed.

"When you put all these pieces together, it kind of makes a compelling argument that there's some relationship between EV-68 and the occurrence of the acute flaccid myelitis cases," he said.

Still looking for proof
But experts aren't ready to declare that the AFM cases were caused by EV-D68, because the link is mainly a temporal association at this point, Sejvar added. "We haven't isolated the virus from the nervous system of these children that are suffering from acute flaccid myelitis, which would be far more convincing biologically that the virus is getting into the nervous system and causing this neurologic damage."

To further investigate the link, the agency is continuing to test patients' cerebrospinal fluid samples to see if the virus is in the spinal cord or the nerve system, he said. Also there are plans to launch a nationwide case-control study to find out if children who have AFM are more likely to have antibodies against EV-D68 than children who don't have the condition.

Disease manifestations persist
Sejvar also said he and his colleagues will be assessing how the patients fare over the long haul. He said the children in Colorado have been followed most closely, and some have had varying degrees of improvement in limb strength, but in most of them the weakness has persisted.

The patients will be followed for 1 or 2 years, he said, adding, "If this behaves like other illnesses of this type, unfortunately the likelihood is that most of these children are going to be left with permanent neurologic and functional disability."

The CDC has said that EV-D68 infection was found in 12 patients who died, but it has not commented on the virus's role in the deaths, saying that determination is made by state and local officials. In October, New Jersey officials said EV-D68 contributed to the death of a 4-year-old boy who died in his sleep.

The virus was uncommon until recently. It typically causes only cold-like symptoms, but some children experience a severe respiratory illness.

See also:

CDC update on investigation of AFM cases

CDC information on EV-D68

Related Oct 10 CIDRAP News story

Related Oct 3 CIDRAP News story

http://www.cidrap.umn.edu/news-perspect ... oks-likely

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