Featured Research

from universities, journals, and other organizations

Creating standards for sequencing viral genomes: Army leads collaborative effort

Date:
June 25, 2014
Source:
US Army Medical Research Institute of Infectious Diseases
Summary:
A set of standards aimed at developing a common 'language' among investigators working to sequence viral genomes and characterize viral stocks has been proposed by scientists at the US Army Medical Research Institute of Infectious Diseases. while there is a great deal of viral genome sequencing taking place, "there is currently no unifying framework, no common vocabulary about how 'finished' a particular viral genome is," said the paper's first author.

Scientists at the U.S. Army Medical Research Institute of Infectious Diseases (USAMRIID) have proposed a set of standards aimed at developing a common "language" among investigators working to sequence viral genomes and characterize viral stocks.

Related Articles


According to USAMRIID senior author Gustavo Palacios, Ph.D., the proposed system, published as an editorial in the journal mBio, is the result of a collaborative effort involving scientists from many of the world's leading institutions. Contributors include the Broad Institute, the J. Craig Venter Institute, Los Alamos National Laboratory, the National Institute of Allergy and Infectious Diseases, the University of Maryland, and Johns Hopkins University.

"One of our main accomplishments was to sit everyone at the same table and agree to something meaningful," he explained.

The genome is the genetic material of an organism, which is encoded either in DNA or, for many types of viruses, in RNA, according to the authors. The genome includes both the genes and the non-coding "sequences" of the DNA or RNA, which contain the information necessary for the virus to replicate and transmit. Determining the sequence, therefore, yields useful information that can be applied in any number of medical and scientific disciplines.

"Thanks to high-throughput sequencing technologies, genome sequencing has become a common component in nearly all aspects of viral research, including molecular epidemiology, drug and vaccine development, surveillance and diagnostics," said Palacios. "Thus, we are currently experiencing an explosion in both the number of available genome sequences and the number of institutions producing such data."

However, while there is a great deal of viral genome sequencing taking place, "there is currently no unifying framework, no common vocabulary about how 'finished' a particular viral genome is," said the paper's first author, Jason Ladner, Ph.D., of USAMRIID. The level of finishing determines a genome's suitability for various downstream applications, including the design of diagnostics, reverse genetics systems and countermeasure development.

The team hopes to fill that void by outlining five "standard" categories that encompass all stages of viral genome finishing, and defining the categories using simple criteria that apply regardless of the technology used for sequencing.

"Because technology may phase out quickly, we wanted the standards to be 'agnostic' -- meaning they're not tied to a particular platform -- so they can continue to be relevant over time," Ladner explained.

He and Palacios credit the group's ability to form a consensus around these genome standard categories, which will provide a framework that can be used across all fields of research involving viruses. In addition, the standards could be utilized by public sequence repositories and by federal agencies that approve and regulate products related to viruses, including diagnostics, vaccines and therapeutics.


Story Source:

The above story is based on materials provided by US Army Medical Research Institute of Infectious Diseases. Note: Materials may be edited for content and length.


Journal Reference:

  1. J. T. Ladner, B. Beitzel, P. S. G. Chain, M. G. Davenport, E. Donaldson, M. Frieman, J. Kugelman, J. H. Kuhn, J. O'Rear, P. C. Sabeti, D. E. Wentworth, M. R. Wiley, G.-Y. Yu, S. Sozhamannan, C. Bradburne, G. Palacios. Standards for Sequencing Viral Genomes in the Era of High-Throughput Sequencing. mBio, 2014; 5 (3): e01360-14 DOI: 10.1128/mBio.01360-14

Cite This Page:

US Army Medical Research Institute of Infectious Diseases. "Creating standards for sequencing viral genomes: Army leads collaborative effort." ScienceDaily. ScienceDaily, 25 June 2014. <www.sciencedaily.com/releases/2014/06/140625132548.htm>.
US Army Medical Research Institute of Infectious Diseases. (2014, June 25). Creating standards for sequencing viral genomes: Army leads collaborative effort. ScienceDaily. Retrieved November 23, 2014 from www.sciencedaily.com/releases/2014/06/140625132548.htm
US Army Medical Research Institute of Infectious Diseases. "Creating standards for sequencing viral genomes: Army leads collaborative effort." ScienceDaily. www.sciencedaily.com/releases/2014/06/140625132548.htm (accessed November 23, 2014).

Share This


More From ScienceDaily



More Plants & Animals News

Sunday, November 23, 2014

Featured Research

from universities, journals, and other organizations


Featured Videos

from AP, Reuters, AFP, and other news services

Ebola-Hit Sierra Leone's Late Cocoa Leaves Bitter Taste

Ebola-Hit Sierra Leone's Late Cocoa Leaves Bitter Taste

AFP (Nov. 23, 2014) The arable district of Kenema in Sierra Leone -- at the centre of the Ebola outbreak in May -- has been under quarantine for three months as the cocoa harvest comes in. Duration: 01:32 Video provided by AFP
Powered by NewsLook.com
Anglerfish Rarely Seen In Its Habitat Will Haunt You

Anglerfish Rarely Seen In Its Habitat Will Haunt You

Newsy (Nov. 22, 2014) For the first time Monterey Bay Aquarium recorded a video of the elusive, creepy and rarely seen anglerfish. Video provided by Newsy
Powered by NewsLook.com
Birds Around the World Take Flight

Birds Around the World Take Flight

Reuters - Light News Video Online (Nov. 22, 2014) An imperial eagle equipped with a camera spreads its wings over London. It's just one of the many birds making headlines in this week's "animal roundup". Jillian Kitchener reports. Video provided by Reuters
Powered by NewsLook.com
Could Your Genes Be The Reason You're Single?

Could Your Genes Be The Reason You're Single?

Newsy (Nov. 21, 2014) Researchers in Beijing discovered a gene called 5-HTA1, and carriers are reportedly 20 percent more likely to be single. Video provided by Newsy
Powered by NewsLook.com

Search ScienceDaily

Number of stories in archives: 140,361

Find with keyword(s):
Enter a keyword or phrase to search ScienceDaily for related topics and research stories.

Save/Print:
Share:

Breaking News:

Strange & Offbeat Stories


Plants & Animals

Earth & Climate

Fossils & Ruins

In Other News

... from NewsDaily.com

Science News

Health News

Environment News

Technology News



Save/Print:
Share:

Free Subscriptions


Get the latest science news with ScienceDaily's free email newsletters, updated daily and weekly. Or view hourly updated newsfeeds in your RSS reader:

Get Social & Mobile


Keep up to date with the latest news from ScienceDaily via social networks and mobile apps:

Have Feedback?


Tell us what you think of ScienceDaily -- we welcome both positive and negative comments. Have any problems using the site? Questions?
Mobile: iPhone Android Web
Follow: Facebook Twitter Google+
Subscribe: RSS Feeds Email Newsletters
Latest Headlines Health & Medicine Mind & Brain Space & Time Matter & Energy Computers & Math Plants & Animals Earth & Climate Fossils & Ruins