George J. Xu., Comprehensive serological profiling of human populations using a synthetic human virome, Science 348, 6239 (2015)
We present VirScan, a high-throughput method to comprehensively analyze antiviral antibodies using immunoprecipitation and massively parallel DNA sequencing of a bacteriophage library displaying proteome-wide peptides from all human viruses. Although rates of specific virus exposure were heterogeneous across populations, antibody responses targeted strongly conserved “public epitopes” for each virus, suggesting that they may elicit highly similar antibodies.
Briefly, we used a programmable DNA microarray to synthesize 93,904 200-mer oligonucleotides, encoding 56-residue peptide tiles, with 28-residue overlaps, that together span the reference protein sequences (collapsed to 90% identity) of all viruses annotated to have human tropism in the UniProt database. This library includes peptides from 206 species of virus and over 1000 different strains. We cloned the library into a T7 bacteriophage display vector for screening.
To perform a screen, we incubate the library with a serum sample containing antibodies, recover the antibodies by using a mixture of protein A- and G-coated magnetic beads, and remove unbound phage particles by washing. Last we perform polymerase chain reaction (PCR) and massively parallel sequencing on the phage DNA to quantify enrichment of each library member resulting from antibody binding.
VirScan requires only 2 μg of immunoglobulin (<1 μl of serum) per sample.
We detected antibody responses to an average of 10 species of virus per sample.
We detected antibody responses to 62 of the 206 species of virus in our library in at least five individuals and 84 species in at least two individuals.
We found that, for a given protein, each sample generally only had strong responses against one to three immunodominant peptides.
Although sensitive and selective, VirScan has a few limitations, First it cannot detect epitopes that require post-translational modifications. Secondly, it cannot detect epitopes that involve discontinuous sequences on protein fragments greater than 56 residues. Third, VirScan is likely to be less specific compared with certain nucleic acid tests that discern highly related virus strains.