New Assay Defines an Individual’s Total Virus Burden

An advanced bacteriophage-based microarray assay allows the simultaneous identification of all the viruses comprising an individual’s virome from a sample of less than one microliter of blood.


Image: Some of the hundreds of viruses that make up the human virome (Photo courtesy of the European Molecular Biology Laboratory).

In addition to directly causing acute or chronic illness, viral infections can alter host immunity and have a long-lasting effect on the immune system. This interplay between virome—an individual’s total viral burden from previous and current infections and vaccinations—and host immunity has been implicated in the pathogenesis of complex diseases such as type I diabetes, inflammatory bowel disease, and asthma.

Current serological methods to detect viral infections are predominantly limited to testing one pathogen at a time and are therefore used primarily to diagnose specific diseases. Investigators at Harvard Medical School (Boston, MA, USA) developed a method to simultaneously detect responses to all human viruses in order to establish associations between past viral infections and particular diseases or population structures.

The new assay method, VirScan, is a high-throughput technique that allows comprehensive analysis of antiviral antibodies in human sera. The technique is based on a library of bacteriophages that carry DNA fragments specific for more than 93,000 different segments of viral proteins. The bacteriophages produce distinct surface peptides that bind to anti-viral antibodies in the patient’s blood. Immunoprecipitation and high-throughput DNA sequencing reveal the peptides recognized by antibodies in the sample. The analysis requires less than one microliter of blood, and currently requires two to three days to process 100 samples.

The investigators screened sera from 569 human donors from the United States, South Africa, Thailand, and Peru, assaying a total of over 108 antibody-peptide interactions for reactivity to 206 human viral species and more than 1000 strains. They found that VirScan’s performance in detecting known infections and distinguishing between exposures to related viruses was comparable to that of classical serum antibody tests for single viruses. They detected antibodies to an average of 10 viral species per person and 84 species in at least two individuals. This approach mapped antibody targets at 56–amino acid resolution, and the results nearly doubled the number of previously established viral B-cell epitopes.

Senior author Dr. Stephen Elledge, professor of genetics at Harvard Medical School, said, “We have developed a screening methodology to basically look back in time in people’s [blood] sera and see what viruses they have experienced. Instead of testing for one individual virus at a time, which is labor intensive, we can assay all of these at once. It is one-stop shopping, and it turns out that it works really well. We were in the sensitivity range of 95% to 100% for those, and the specificity was good—we did not falsely identify people who were negative. That gave us confidence that we could detect other viruses, and when we did see them we would know they were real. In this paper alone we identified more antibody/peptide interactions to viral proteins than had been identified in the previous history of all viral exploration.”

The study was published in the June 5, 2015, issue of the journal Science.