New bacteriophage-based assay gives a person’s whole viral infection history in a drop of blood.


New technology developed by Howard Hughes Medical Institute (HHMI) and Brigham and Women’s Hospital researchers makes it possible to test for current and past infections with any known human virus by analyzing a single drop of a person’s blood. The method, called VirScan, is an efficient alternative to existing diagnostics that test for specific viruses one at a time.  The team state that with VirScan, scientists can run a single test to determine which viruses have infected an individual, rather than limiting their analysis to particular viruses. That unbiased approach could uncover unexpected factors affecting individual patients’ health, and also expands opportunities to analyze and compare viral infections in large populations. The comprehensive analysis can be performed for about $25 per blood sample.  The opensource study is published in the journal Science.

The researchers state that they have developed a screening methodology to basically look back in time in people’s [blood] sera and see what viruses they have experienced. They go on to add that instead of testing for one individual virus at a time, which is labor intensive, the medical team can assay all of these at once.  The current study used VirScan to screen the blood of 569 people in the United States, South Africa, Thailand, and Peru.

VirScan works by screening the blood for antibodies against any of the 206 species of viruses known to infect humans, explain the team. The immune system ramps up production of pathogen-specific antibodies when it encounters a virus for the first time, and it can continue to produce those antibodies for years or decades after it clears an infection. That means VirScan not only identifies viral infections that the immune system is actively fighting, but also provides a history of an individual’s past infections.

To develop the new test, the researchers synthesized more than 93,000 short pieces of DNA encoding different segments of viral proteins. They introduced those pieces of DNA into bacteria-infecting viruses called bacteriophage. Each bacteriophage manufactured one of the protein segments, known as a peptide, and displayed the peptide on its surface. As a group, the bacteriophage displayed all of the protein sequences found in the more than 1,000 known strains of human viruses.

Previous studies show that antibodies in the blood find their viral targets by recognizing unique features known as epitopes that are embedded in proteins on the virus surface. To perform the VirScan analysis in the current study, all of the peptide-displaying bacteriophage are allowed to mingle with a blood sample. Antiviral antibodies in the blood find and bind to their target epitopes within the displayed peptides. The researchers then retrieve the antibodies and wash away everything except for the few bacteriophage that cling to them. By sequencing the DNA of those bacteriophage, they can identify which viral protein pieces were grabbed onto by antibodies in the blood sample. That tells the team which viruses a person’s immune system has previously encountered, either through infection or through vaccination. The researchers estimates it would take about 2-3 days to process 100 samples, assuming sequencing is working optimally. They are optimistic the speed of the assay will increase with further development.

To test the method, the current study used it to analyze blood samples from patients known to be infected with particular viruses, including HIV and hepatitis C.  The results showed that the VirScan was within a sensitivity range of 95 to 100 percent for those, and the specificity was good, with test giving no false-positive results for people who were negative. That gave the team the confidence that the VirScan could detect other viruses.

The team then used VirScan to analyze the antibodies in 569 people from four countries, examining about 100 million potential antibody/epitope interactions. They found that on average, each person had antibodies to ten different species of viruses. As expected, antibodies against certain viruses were common among adults but not in children, suggesting that children had not yet been exposed to those viruses. Individuals residing South Africa, Peru, and Thailand, tended to have antibodies against more viruses than people in the United States. The researchers also found that people infected with HIV had antibodies against many more viruses than did people without HIV.

The team was surprised to find that antibody responses against specific viruses were surprisingly similar between individuals, with different people’s antibodies recognizing identical amino acids in the viral peptides.  They state that in this paper alone they have identified more antibody/peptide interactions to viral proteins than had been identified in the previous history of all viral exploration. The surprising reproducibility of those interactions allowed the team to refine their analysis and improve the sensitivity of VirScan, and they state that the method will continue to improve as they analyze more samples. They go on to add that their findings on viral epitopes may also have important implications for vaccine design.

The researchers surmise that the approach they have developed is not limited to antiviral antibodies with the lab also using it to look for antibodies that attack a body’s own tissue in certain autoimmune diseases that are associated with cancer. A similar approach could also be used to screen for antibodies against other types of pathogens, conclude the team.

Source:  Howard Hughes Medical Institute

 

Systematic viral epitope scanning (VirScan). This method allows comprehensive analysis of antiviral antibodies in human sera. VirScan combines 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 color of each cell in the heatmap depicts the relative number of antigenic epitopes detected for a virus (rows) in each sample (columns). Credit: Figure from the print summary of Xu et al 2015.  Comprehensive serological profiling of human populations using a synthetic human virome.

Systematic viral epitope scanning (VirScan). This method allows comprehensive analysis of antiviral antibodies in human sera. VirScan combines 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 color of each cell in the heatmap depicts the relative number of antigenic epitopes detected for a virus (rows) in each sample (columns). Credit: Figure from the print summary of Xu et al 2015. Comprehensive serological profiling of human populations using a synthetic human virome.

 

One comment

  • Outstanding!

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