Daily Archives: October 30, 2014

Researchers at Washington University School of Medicine in St. Louis have sequenced the genome of enterovirus D68 sampled from patients treated at St. Louis Children's Hospital. Nationwide, the virus has spread rapidly in recent months and caused severe respiratory illness in young children, with some patients requiring hospitalization.

"Having the DNA sequence of this virus enables additional research," said senior author Gregory A. Storch, MD, the Ruth L. Siteman Professor of Pediatrics. "It can be used to create better diagnostic tests. It also may help us understand why this epidemic seems to be producing severe and unusual disease, and why it's spreading more extensively than in the past."

The work appears Oct. 28 in Emerging Infectious Diseases. The investigators published the DNA sequences in GenBank, an open-access database maintained by the National Institutes of Health (NIH).

The new sequencing data, produced by The Genome Institute at Washington University, includes one complete genome sequence and eight partial sequences taken from patient samples. Further, scientists at the Centers for Disease Control and Prevention (CDC) contributed to GenBank seven complete or partial sequences of enterovirus D68 sampled in the Midwest.

Storch said routine laboratory tests can't identify specific enterovirus strains. Most hospitals and clinics only can perform tests to determine if a patient has a virus that fits broadly into the enterovirus/rhinovirus category. In the new study, Storch and his colleagues analyzed 14 patient samples testing positive for enterovirus/rhinovirus. Of those, nine were identified as enterovirus D68 using specialized laboratory techniques developed at Washington University and St. Louis Children's Hospital. The remaining five samples were other respiratory viruses.

While many children may contract enterovirus D68 and never know it because symptoms are mild, others may require hospitalization to support their breathing. Children with a history of breathing disorders such as asthma are at higher risk of severe disease.

In this study, seven of the nine patients with the D68 strain had severe disease that required admission to the pediatric intensive care unit. The remaining two had moderate symptoms resulting in general hospital admission. Of the five patients with other viruses, three were classified with severe disease. The only two patients discharged home with mild disease did not have the D68 strain.

"There is currently no specific treatment and no vaccine for this virus," said Storch, who treats patients at St. Louis Children's Hospital. "But having the DNA sequence available helps work toward both of those goals."

The data also allow comparisons between strains circulating in different parts of the country.

"The CDC has published some additional genomes from Missouri, Illinois and Kentucky," said first author Kristine M. Wylie, PhD, research instructor in pediatrics. "The Missouri genomes, including ours, are all very similar, but the Illinois and Kentucky genomes are different from the Missouri types, suggesting there are some distinct strains circulating in the U.S. right now."

Originally posted here:
Genome sequenced of enterovirus D68 circulating in St. Louis

Local researchers have new clues about a rare respiratory virus that caused a national outbreak and filled childrens hospital beds in August and September.

Researchers at the Genome Institute at Washington University mapped the genetic code of enterovirus D68 samples taken from nine children treated at St. Louis Childrens Hospital. Their work, along with about six other genome sequences of the virus from around the country, will be used to study the makeup of the virus with a goal of developing a better diagnostic test, treatments and potentially a vaccine.

Knowing the whole genome sequence is a very important starting point for research, said Dr. Gregory Storch, a professor of pediatrics who co-wrote a paper on their work in the journal Emerging Infectious Diseases. The next thing is that it could be helpful to us in designing better diagnostic tests, and further down the road, it can be very useful for people trying to develop new treatments.

The virus surprised disease investigators when it started showing up in children in Missouri and Illinois in August. Now 47 states have reported illnesses, according to the Centers for Disease Control and Prevention. The virus can cause severe symptoms, including coughing, wheezing and fever, especially in children with asthma. In rare cases, neurological symptoms have included paralysis linked to the virus, which is related to polio.

Respiratory viruses are seen every summer and fall, but the enterovirus D68 caused more serious, widespread illnesses and raised questions about its pathology.

Something has changed about the virus or the way it fits into the community, Storch said. It seems to be emerging as a cause of widespread respiratory disease. We dont know what the future holds, but we may see future outbreaks.

Since August, more than 1,100 confirmed enterovirus D68 cases have been confirmed in the country and eight deaths in children who tested positive for the virus.

But thousands more are probably sickened by the virus, including as many as 1,500 children treated at St. Louis Childrens Hospital for respiratory illness this year. Most of the cases did not receive comprehensive testing that would determine the strain. Storch said the genome sequencing could point to an easier way to diagnose the virus.

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Researchers dive deep into rare enterovirus

PUBLIC RELEASE DATE:

29-Oct-2014

Contact: Press Office huwen@genomics.cn BGI Shenzhen

October 27, 2014 Cambridge, MA and Hebei, China BGI Tech and Hebei Agricultural University jointly announced the complete, high quality sequencing of the Jujube genome. Jujube is the most economically important member of the Rhamnaceae family, and the Jujube genome is particularly difficult to sequence due the high level of heterozygosity and other complicating factors. It is the first time that a genome in the Rhamnaceae (Buckthorn) family has been sequenced. This study has been recently published in Nature Communications.

Jujube is a major commercial fruit with up to 30 million acres under cultivation close to that of apple and citrus and China accounts for 99% of the 6 million tons of dried fruit produced annually. Jujube has a much higher vitamin C content than other well-known vitamin C-rich fruits such as orange and kiwi fruit, and also high levels of nucleotides, polysaccharides and other important functional components. Furthermore, the jujube tree is highly resistant to salinity and drought, and grows well in sandy, alkaline and arid areas. Therefor, decoding the genome of the jujube tree will have great implications to exploit those important traits.

The Jujube genome has the highest degree of heterozygosity (1.9%) of plants sequenced to date using next generation sequencing (NGS). In addition, the very high density of simple sequence repeats and low GC content make the Jujube genome particularly challenging for whole genome sequencing and assembly. By using a combination of BAC-to-BAC sequencing and PCR-free whole genome sequencing, the researchers were able to successfully complete the high quality de novo sequencing of 98.6% of the estimated Jujube genome, identifying 32,808 genes.

"This study has accelerated the functional genomics research of the Jujube tree, and will facilitate the genetic improvement and selective breeding of Buckthorn fruit trees", said Professor Mengjun Liu, head of the research team, for Hebei Agricultural Unviersity. "This research not only shows the expertise of the team and the power of sequencing technology, but we also expect its future applications in bring more value and benefits in healthy food production."

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About Agricultural University of Hebei

Founded in 1902, Agricultural University of Hebei (AUH) is one of the main universities of Hebei province. Its five campuses are located in the cities of Baoding, Qinhuangdao, Huanghua and Dingzhou, covering the areas of more than 1.9 million square meters. Since 1989, the university has won 6 national awards and 163 provincial awards for its excellence in teaching and research, making it the top ranked university among all Chinese provincial universities, for ten years in a row. AUH has also ranked among the top 10 agricultural universities in China for decades.

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BGI Tech and Hebei Agricultural University complete the genome sequencing of the jujube tree