Researchers from UC San Francisco and the Chan Zuckerberg Biohub (CZ Biohub) have developed a new approach for COVID-19 testing that detects a distinct pattern of immune gene expression in infected individuals. This type of test could be used as a check against possible errors generated by the standard tests that directly detect the SARS-CoV-2 virus, the scientists said.
In addition, the gene expression patterns seen in COVID-19 patients in the study indicate that, unlike other respiratory viruses, SARS-CoV-2 may suppress immune reactions in the early stages of infection, setting the stage for the virus to spread before patients develop symptoms.
The immune response to respiratory infections is largely responsible for symptoms like fever, nasal congestion and cough, which might typically encourage someone to isolate from others and seek testing. Because people with COVID-19 are most infectious early in their disease course, this suppressed immune response in COVID-19’s first stages makes it more likely that individuals will infect others before they realize they are sick.
The leaders of the new study, published online in Nature Communications on Nov. 17, 2020, say that although the new testing approach analyzes completely different molecules – from the person infected, rather than from the virus that infects the person – it can be implemented using the same PCR technology on the same nasal swab samples. It could be used as a standalone test, or even combined into the same testing panels used in standard PCR tests to detect the virus. Combining the technologies could lessen the chances of false negative or false positive results, the researchers said.
“Without even having to detect the virus itself, these tests to measure changes in the expression of immune-related genes can determine whether or not someone has COVID-19,” said co-senior study author Chaz Langelier, MD, PhD, assistant professor in the Division of Infectious Diseases in the UCSF Department of Medicine, who led the research with Amy Kistler, PhD, of CZ Biohub.
The UCSF scientists created three proof-of-concept versions of the new test – one based on readouts of gene activity from three key genes, one based on readouts from 10 genes, and one based on 27 genes. The tests independently detected COVID-19 infection in clinically confirmed cases, increasing in sensitivity with the number of genes included.Original Source