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The Human Virome
Scientists propose plan to sequence, catalog, and track human viruses
  
By Kate Dalke


Featured Article.

Viruses are on the move. SARS. West Nile. Monkeypox. The list of new infectious diseases is growing, and those are just the viruses that occur naturally. The threat of biological terrorism using Ebola or smallpox is equally frightening.



Clearly, it's time to develop a sophisticated global system to catalog viruses and detect emerging diseases throughout the world.

One such system, now being proposed, would routinely screen human blood to identify every human virus and monitor any new viruses that may appear in humans. The viral genomes would be collected in a database called the “human virome.”

The proposal goes something like this: Scientists would collect blood from hospitals and labs weekly. Then they would extract viruses from it and sequence the viral genomes. Once a database of viruses is constructed, researchers could use it to screen for new viruses as they appear in the population.

Having a database of genome sequences could speed the characterization of emerging viruses. For instance, genomic information about coronaviruses, collected over many years, helped researchers identify the SARS genome in a matter of weeks.

“We want to know what’s actually ‘going around,’ and that is something that nobody knows,” says Norman Anderson of the Viral Defense Foundation in Kensington, Maryland, who is leading the project along with his son, N. Leigh Anderson of the Plasma Proteome Institute in Washington, D.C.

Together with John L. Gerin of Georgetown University Medical Center in Rockville, Maryland, the Andersons have drafted a proposal for a surveillance system, which they call Project Global Screen. It will be published in the July issue of the U.S. Centers for Disease Control and Prevention’s journal Emerging and Infectious Diseases.

What makes this broad and ambitious proposal possible, the authors say, is today’s sequencing technology and capacity for large-scale projects. Sequencing genomes is now routine, so it’s reasonable to expect that we can decode the genomes of every virus in our bodies.


“We want to know what’s actually ‘going around’”

Viral genomes are much smaller than bacterial or human genomes, and so far, fewer sequences are needed to put together their genomes.

“Sequencing is the most solid and detailed way to characterize a pathogen,” says Maria Salvato of the Institute of Human Virology at the University of Maryland Biotechnology Institute in Baltimore, who is working on a diagnostic tool for viruses.

Inspiration for Anderson’s project comes from the effort to sequence large communities of viruses from the ocean, done by marine biologists at San Diego State University in California.

The potential for scientists to take an unknown environment, like seawater or blood, and sequence the genomes of the microbes or viruses is not so far-fetched anymore. Scientists are sequencing all kinds of communities, from the bacteria in your gut to microbes in your dental plaque.


K-II ultracentrifuge could be used to isolate viruses from blood.

Anderson’s proposal is still in the early stages, and the researchers have not projected the costs or secured funding. Many details remain “confidential for the time being,” says Norman Anderson. He and his son have 35 patents pending in the U.S. Patent Office that are related to the proposal.

They estimate that the surveillance system could be up and running in less than a year.

But the list of challenges seems endless. Contained laboratories, with robot workers, might have to be designed to extract the potentially dangerous viruses. Viral RNA would have to be transcribed to DNA for sequencing, which is still very difficult to do.

Identifying the source of viruses requires efficient tracking. In addition, scientists have to decipher whether a virus is actually harmful or not.

Both Andersons and Gerin say these obstacles could be overcome. Gerin suggests first setting up small demonstrations for the proposed plan to test whether the approach would work.

“Ignorance is not bliss,” says Gerin. “Just because we don’t know what viruses are out there, doesn’t mean they’re not dangerous.”

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Anderson, N. G. et al. Global screening for human viral pathogens. Emerging and Infectious Diseases 9 (July 2003).
 
Breitbart, M. et al. Genomic analysis of uncultured marine viral communities. Proceedings of the National Academy of Sciences USA 99, 14250-14255 (October 29, 2002).
 

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