Comprehensive serological profiling of human populations using a synthetic human virome

The collection of viruses found to infect humans can have profound effects on human health. In addition to directly causing acute or chronic illness, viral infection can alter host immunity in more subtle ways, leaving an indelible footprint on the immune system. This interplay between virome and host immunity has been implicated in the pathogenesis of complex diseases such as type 1 diabetes, inflammatory bowel disease, and asthma. Despite the growing appreciation for the importance of interactions between the virome and host, a comprehensive method to systematically characterize these interactions has yet to be developed.
 Current serological methods to detect viral infections are predominantly limited to testing one pathogen at a time and are therefore used primarily to address specific clinical hypotheses. A method that could simultaneously detect responses to all human viruses would allow hypothesis-free analysis to detect associations between past viral infections and particular diseases or population structures. Humoral responses to infection typically arise within 10 to 14 days of initial exposure and can persist over years or decades, thus providing a rich source of the history of pathogen encounters. In this work, we present VirScan, a high-throughput method that allows comprehensive analysis of antiviral antibodies in human sera. VirScan uses DNA microarray synthesis and bacteriophage display to create a uniform, synthetic representation of peptide epitopes comprising the human virome. Immunoprecipitation and high-throughput DNA sequencing reveal the peptides recognized by antibodies in the sample. The analysis requires less than 1 μl of blood.
 We screened sera from 569 human donors across four continents, assaying a total of over 108 antibody-peptide interactions for reactivity to 206 human viral species and >1000 strains. We found that VirScan’s performance in detecting known infections and distinguishing between exposures to related viruses is comparable to that of classical serum antibody tests for single viruses. We detected antibodies to an average of 10 viral species per person and 84 species in at least two individuals. Our approach maps antibody targets at 56–amino acid resolution, and our results nearly double the number of previously established viral B cell epitopes. Although rates of specific virus exposure varied depending on age, HIV status, and geographic location of the donor, we observed strong similarities in antibody responses across individuals. In particular, we found multiple instances of single peptides that were recurrently recognized by antibodies in the vast majority of donors. We performed tiling mutagenesis and found that these antibody responses targeted substantially conserved “public epitopes” for each virus, suggesting that antibodies with highly similar specificities, and possibly structures, are elicited across individuals.
VirScan is a method that enables human virome-wide exploration, at the epitope level, of immune responses in large numbers of individuals. We have demonstrated its effectiveness for determining viral exposure and characterizing viral B cell epitopes in high throughput and at high resolution. Our preliminary studies have revealed intriguing general properties of the human immune system, both at the individual and the population scale. VirScan may prove to be an important tool for uncovering the effect of host-virome interactions on human health and disease and could easily be expanded to include new viruses as they are discovered, as well as other human pathogens, such as bacteria, fungi, and protozoa.

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