The COVID-19 pandemic brought the term "Polymerase Chain Reaction testing" into the mainstream. The PCR method is a type of nucleic acid amplification test (NAAT) that detects a pathogen by finding and amplifying components of its genetic material, and it is widely used to detect SARS-CoV-2.
But these types of tests have a weakness: you have to know exactly what pathogen you're looking for. In a recent study, published in Scientific Reports, researchers from Lawrence Livermore National Laboratory (LLNL) and the California Department of Public Health identified other potentially harmful respiratory viruses in samples that tested negative in a standard, NAAT-based panel. The results suggest that a pathogen-agnostic approach is a crucial complement to tests like PCR.
"If a patient is infected with a life-threatening pathogen that is not covered by these tests, then this would cause a serious health risk," said LLNL scientist and author Crystal Jaing. "Pathogen-specific assays do not provide comprehensive coverage of a broad spectrum of pathogens, while pathogen-agnostic tests provide much more information."
To demonstrate the power of pathogen-agnostic testing, the authors examined samples with untargeted metagenomic sequencing. While PCR testing searches for and amplifies a specific DNA sequence, the untargeted approach reads all genetic material in the sample. That information is compared to an established database to identify what pathogens are present.
Most of the study's samples, obtained from a sentinel surveillance program to test patients with respiratory symptoms in counties throughout California, were negative for the 22 pathogens (including SARS-CoV-2) tested by the NAAT-based panel. But the team found that 5 percent of those negative results contained a different, previously undetected respiratory virus. They also identified bacterial or fungal species in a number of cases.
"Pathogen-agnostic tests provide the advantage that you don't have to know what pathogens are in a sample," said Jaing. "Using the agnostic approach, you can detect any or all pathogens in a sample with a single test."
However, metagenomic sequencing takes longer, costs more and requires more complex equipment than NAATs. The authors emphasize that it should not replace methods like PCR - it should complement them.
"NAAT can be used for routine tests because they are faster and cheaper. In the COVID-19 example, a standard NAAT will give us answers right away," said Jaing. "However, NAAT is not sufficient for surveillance of new and emerging pathogens and for future pandemic forecasting."
The researchers hope these findings will encourage public health entities to consider incorporating pathogen-agnostic approaches for detection and surveillance.
