These differences may reflect variation in the strains endemic in each region

These differences may reflect variation in the strains endemic in each region. Introduction The collection of viruses found to infect humans (the human virome) can have profound effects on human health (1). In addition to directly causing acute or chronic illness, viral infection can also alter host immunity in more subtle ways, leaving an indelible footprint on the immune system (2). For A2AR-agonist-1 example, latent herpesvirus infection has been shown to confer symbiotic protection against bacterial infection in mice through prolonged production of interferon- and systemic activation of macrophages (3). This interplay between virome and host immunity has also been implicated in the pathogenesis of complex diseases such as type 1 diabetes, inflammatory bowel disease, and asthma (4). A2AR-agonist-1 Despite this 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 (5). Viral infections can be detected by serological- or nucleic acid-based methods (6). However, nucleic acid tests fail in cases where viruses have already Rabbit Polyclonal to OR10A7 been cleared after causing or initiating tissue damage and can miss viruses of low abundance or viruses not normally present in the sampled fluid or surface. In contrast, humoral responses to infection typically arise within two weeks of initial exposure and can persist over years or decades (7). Tests detecting antiviral antibodies in peripheral blood can therefore identify ongoing and cleared infections. However, current serological methods are predominantly limited to testing one virus at a time and are therefore only employed to address specific clinical hypotheses. Scaling serological analyses to encompass the complete human virome poses significant technical challenges, but would be of great value for better understanding host-virus interactions, and would overcome many of the limitations associated with current clinical technologies. In this work, we present VirScan, a programmable, high-throughput method to comprehensively analyze antiviral antibodies using immunoprecipitation and massively parallel DNA sequencing of a bacteriophage library displaying proteome-wide coverage of peptides from all human viruses. Results The VirScan Platform VirScan utilizes the Phage Immunoprecipitation sequencing (PhIP-seq) technology previously developed in our laboratory (8). 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 (Fig. 1A.a and 1A.b) (9). This library includes peptides from 206 species of virus and over 1,000 different strains. We cloned the library into a T7 bacteriophage display vector for screening (Fig. 1A.c). Open in a separate window Fig. 1 General VirScan analysis of the human virome. (A) Construction of the virome peptide library and VirScan screening procedure. (known positives. Specificity is the percentage of samples negative for the virus by VirScan out of all known negatives. < 0.05, Fig. 2B). These results are consistent with prior studies indicating higher risk of these co-infections in HIV positive patients (20C22). Patients with HIV may engage in activities that put them A2AR-agonist-1 at higher risk for exposure to these viruses. Alternatively, these viruses may increase the risk of HIV infection. HIV infection may reduce the immune systems ability to control reactivation of normally dormant resident viruses or to prevent opportunistic infections from taking hold and triggering a strong adaptive immune response. Finally, we compared the evidence of viral exposure between samples taken from adult HIV-negative donors residing in countries from four different continents (the United States, Peru, Thailand, and South Africa). In general, donors outside the United States had higher frequencies of seropositivity (Fig. 2CCE). For example, cytomegalovirus antibodies were found in significantly higher frequencies in samples from Peru, Thailand, and South Africa. Other viruses, such as Kaposis sarcoma-associated herpesvirus and HSV1 were detected more frequently in donors from Peru and South.