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.
According to USAMRIID senior author Gustavo Palacios, Ph.D., the
proposed system, published last week 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.
According to the authors, DTRA and the Interagency Filovirus Animal
Non-Clinical Group (FANG) already have begun to incorporate these
standards into their planning and evaluation procedures. The FANG is
involved in medical countermeasure development for the filoviruses,
Ebola and Marburg, with the ultimate goal of moving these products into
the FDA approval process.
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