Modeling a Pandemic in a Tube

New tool provides a framework to identify human genetic determinants of infectious disease outcomes 

As the COVID-19 pandemic has made clear, viruses affect different people differently. Some people get dangerously, even fatally, sick while others infected with the same virus barely feel a thing. With influenza most people experience some illness, but about one in five show no symptoms, while one in 50 require hospitalizations, and one in 500 die from the virus. 

Multiple factors can contribute to disease severity, but researchers at Duke are getting some new answers from our genomes. Typically, researchers search for clues to genetic susceptibility to any disease by using genome-wide association studies to look at the millions of genetic differences among people. Such studies use thousands — or, in the case of COVID-19 susceptibility — even millions of subjects.  

Dennis Ko
Dennis Ko, MD, PhD

Dennis Ko, MD, PhD, associate professor in molecular genetics and microbiology, and colleagues wanted to develop a faster method that would not require a pathogen to become widespread before such genetic differences affecting susceptibility could be discovered. They developed scHi-HOST (pronounced “sky-host”), or single cell High throughput Human in vitrO Susceptibility Testing. Findings were published in Cell Genomics on November 9th. 

scHi-HOST uses single cell RNA-sequencing to genetically identify individual cell lines from multiple populations, including those of European, African, and Asian origin. Dozens of cell lines are pooled together and receive a single exposure to a strain of influenza. Differences seen with viral infection in the real world, such as different circulating viral strains, amount of exposure, and access to medical care, are eliminated with this model pandemic-in-a-tube approach. Once the cells are infected, researchers can begin to see how the cells respond to the virus and how well the virus replicates in cells from different people. 

Benjamin Schott
Benjamin Schott

“By using single cell RNA sequencing,” Benjamin Schott, graduate student in the lab of Dennis Ko and co-lead author, said, “we can assign each cell back to the cell line of origin and look at the genetic variants associated with flu burden.” 

They were able to identify a single base pair in the genome that has a large effect on how infected cells become. This variant, called rs27895, interrupts how the ERAP1 protein functions. One of the roles of ERAP1 is to cut many types of proteins into smaller peptides that the immune system recognizes. The rs27895 variant is predicted to affect ERAP1 binding to its target peptides. By affecting part of that process, or perhaps some other mysterious function of ERAP1, the rs27895 variation leads to a higher viral burden. 

Once rs27895 was identified in cell lines, the Ko lab used data collected by a collaboration between the teams of Chris Woods, MD, professor of medicine, and Chris Chiu from Imperial College London from a flu challenge in which healthy participants were infected with influenza to see how their immune systems responded.  

The Ko lab genotyped the participants from the flu challenge and found that people with the rs27895 variant became sicker and had a higher viral load when infected by the flu, validating their data from the cellular screens.  

“Our cellular approach translates to humans,” Schott said, “which points to the utility of the approach we developed to identify genes, proteins, and cellular pathways that are relevant to infection in humans.” 

Because scHi-HOST works quickly, the team believes it can be scaled to investigate viruses other than influenza. The Ko lab has already grown the cell lines, mixed them together, and stored them in liquid nitrogen.  

“Then when we want to do a screen,” Ko said, “we can thaw one tube of cell lines and infect them all at once.” The tool can be optimized for whatever virus they want and enables them to investigate any human genetic difference that may protect or make a person more susceptible to that virus. 

For example, a plethora of viruses exist in animal reservoirs that haven’t jumped to humans — yet, as we saw with the SARS-CoV-2 virus, those viruses have the potential to wreak havoc if they ever do make that jump.  

“If one of those viral strains emerges,” Schott said, “we could quickly test in our cell lines to see if there are big differences in susceptibility to infection and if there are human genetic variants associated with that susceptibility.” This could lead to finding drug targets that could help fight off or prevent the infection, maybe even before it reaches pandemic levels. 

This work is just beginning, but ultimately, the team hopes scHi-HOST will be used to help assess genetic susceptibility and resistance to a host of viruses and bacteria that pose emerging threats to humans.