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Exposing the Human Virome Vikram Sheel Kumar1* and Molly Webster2

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Exposing the Human Virome Vikram Sheel Kumar1* and Molly Webster2 Technology Corner Exposing the Human Virome Vikram Sheel Kumar1* and Molly Webster2 As medicine advances, we have come to realize that viral “They created a cus- infections early in life can still be playing out in our body tom phage display library decades later, long after the primary infection has ended. that contains virtually all New research has indicated that viral infections can precip- potential antigens from Downloaded from https://academic.oup.com/clinchem/article/61/10/1311/5611579 by guest on 23 September 2021 itate the onset of a diverse array of long-term illnesses, from viruses that are known to Alzheimer disease to chronic fatigue syndrome and type 1 infect humans,” says diabetes mellitus (1). With that in mind, clinicians are in- Mosammaparast. “Se- terested in understanding more about viral exposures and rum antibodies from an how viral infections affect the body over the longterm. individual are then com- “Technologies exist for rapid identification of diverse bined with the library, bacteria,” says Dr. Nima Mosammaparast, Assistant Profes- immunoprecipitated, and sor of Pathology and Immunology at Washington Univer- the phage are sequenced sity School of Medicine, who cites as an example MALDI- Nima Mosammaparast using next-generation TOF mass spectrometry. However, he says, such rapid technology.” identification “is not the case for viral diagnostics.” The genius in their Viral diagnostics search the body for only 1 hypoth- work could be the appli- esized virus at a time, or screen for only limited panels. cation of 30-year-old That is, until now. technology (phage dis- Researchers at Harvard Medical School, under the play) in an environment guidance of Dr. Steve Elledge, Professor of Genetics and in which playing with Medicine, have brought together “an ingenious combi- DNA has never been nation of different technologies: DNA microarray, phage cheaper. “To test for 200 display, and high-throughput sequencing,” says Mosam- viral species, it is neces- maparast, to assess the entire viral infection history of an sary to have specific an- organism—including current viral infections the im- tigens from all 200 spe- mune system is processing—using just a single drop of cies,” writes Xu in an blood. By all accounts, the tool, known as VirScan, has email to Clinical Chem- the potential to change our understanding of disease and George Xu help us develop new medical interventions, as well as istry. “We took advan- better see how disease moves through populations. tage of the precipitous drop in the price of DNA syn- thesis and sequencing to cost-effectively make all of How Does It Work? the viral antigens and assay for their interaction with antibodies.” There are 206 virus species known to infect humans. Today, For the system, the investigators created a virome pep- when a patient is tested for viral infection, a clinician makes tide library with Ͼ93000 peptides. The DNA sequences an educated guess about what viruses that patient may have, encoding these peptides were each cloned into a bacterio- and then has to run an individual diagnostic test to screen phage. A bacteriophage displays on its surface the peptide for each possibility. With VirScan, the clinician can take a sin- encoded in its genome. When human serum is added, anti- gle drop of blood and scan, at once, for all 206 of those virus Ͼ viral antibodies interact with the bacteriophage and bind to species and their variants, 1000 strains in all. The tool is “a target peptides. What is left after washing are antibodies and high-throughput method that allows comprehensive analy- the bacteriophage to which they bind. The bacteriophage, sis of antiviral antibodies from human sera,” writes lead au- once sequenced, provides the genotype of the viral proteins thor and graduate student George Xu in a recent report to which an antibody reacted (Fig. 1). about the innovation in Science (2). The most significant observation comes from a scan of 569 donors from 4 continents and indicates that despite heterogeneity in viral exposures across 1 Boston Children’s Hospital, Boston, MA; 2 Science writer and producer, Brooklyn, NY. populations, the antiviral antibodies elicited are very * Address correspondence to this author at: Boston Children’s Hospital, 390 Commonwealth similar (2). As Xu writes to Clinical Chemistry, “the Ave, Apt 605, Boston, MA 02215; Fax 617-899-8944; e-mail [email protected]. Received July 13, 2015; accepted July 17, 2015. same portion of a viral antigen is targeted by the anti- © 2015 American Association for Clinical Chemistry bodies by the vast majority of people. We believe this Clinical Chemistry 61:10 (2015) 1311 Technology Corner Downloaded from https://academic.oup.com/clinchem/article/61/10/1311/5611579 by guest on 23 September 2021 Fig. 1. Systematic viral epitope scanning (VirScan). This method allows comprehensive analysis of antiviral antibodies in human sera. VirScan combines DNA microarray synthesis and bacterio- phage 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 color of each cell in the heat map depicts the relative number of antigenic epitopes detected for a virus (rows) in each sample (columns). Reproduced with permission from Xu et al. (2). remarkable similarity may be due to inherent biases in immune system, but may also produce virus with new the immune system.” host tropism. I envision a VirScan 2.0 that includes a broader phage display library that allows us to detect What Are Its Applications? viruses not thought to infect humans, which may permit more rapid identification of novel, emerging viral “There are often infectious disease cases, such as myocar- pathogens.” ditis, where the differential diagnosis includes a broad Xu adds that as new viruses known to infect humans range of viral pathogens, and casting a wide net may be emerge, as long as their genome is sequenced, VirScan necessary,” says Mosammaparast. “Having a tool such as can account for them. VirScan allows us to take a ‘hypothesis-free’ approach to And what about applications in the clinical labora- these more difficult cases.” tory? Says Mosammaparast, “While this technology But more than that, the authors believe that VirScan won’t be adopted right away in the clinical lab, it suggests can be used to correlate viral infection with chronic dis- that the widespread use of high-throughput sequencing ease status. “There are clinical hypotheses that certain for microbiological diagnostics is not far away.” chronic diseases are initially triggered by viral infection, but the identity of the virus has not been determined,” says Xu. “Using VirScan, we can assay hundreds of pa- Author Contributions: All authors confirmed they have contributed to the tient samples to discover viruses that could trigger an intellectual content of this paper and have met the following 3 requirements: (a) aberrant immune response.” significant contributions to the conception and design, acquisition of data, or As the platform assays the entire proteome of each analysis and interpretation of data; (b) drafting or revising the article for intel- virus, in 56-residue fragments, it has the potential to be lectual content; and (c) final approval of the published article. used in the discovery of novel viral antigens for drug Authors’ Disclosures or Potential Conflicts of Interest: No authors development.Or, according to Xu, other applications declared any potential conflicts of interest. could be epidemiological, “such as measuring what frac- tion of a population is infected or for monitoring vaccine References coverage.” Mosammaparast expects the platform will evolve to 1. O’Connor SM, TaylorCE, Hughes JM. Emerging infectious determinants of chronic dis- eases. Emerg Infect Dis 2006;12:1051–7. accommodate this usage.“VirScan 1.0 tested antigens 2. Xu GJ, Kula T, Xu Q, Li MZ, Vernon SD, Ndung’u T, et al. Viral immunology. Comprehen- from viruses known to infect humans,” he says. “We sive serological profiling of human populations using a synthetic human virome. Sci- know, however, that certain viruses, such as influenza, ence. 2015;348:aaa0698. rapidly evolve by rearranging gene segments when 2 or more viruses coinfect the same host cell. This not only DOI: 10.1373/clinchem.2015.246462 allows the generation of novel virus that can evade the 1312 Clinical Chemistry 61:10 (2015).
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