RT’s Three Key Takeaways:
- PCR Assessments Require Recognized Targets: Whereas Polymerase Chain Response assessments are extensively used to detect pathogens reminiscent of SARS-CoV-2, they will solely determine organisms that the take a look at is particularly designed to detect.
- Pathogen-Agnostic Sequencing Finds Hidden Infections: A research in Scientific Studies by researchers at Lawrence Livermore Nationwide Laboratory and the California Division of Public Well being used untargeted metagenomic sequencing to detect beforehand missed respiratory viruses in about 5% of samples that had examined damaging on commonplace NAAT panels.
- Complementary Software for Future Surveillance: Though metagenomic sequencing is slower and costlier than routine PCR testing, researchers say pathogen-agnostic approaches might play a key position in figuring out rising pathogens and strengthening pandemic preparedness when used alongside conventional diagnostic assessments.
The COVID-19 pandemic introduced the time period “Polymerase Chain Response testing” into the mainstream. The PCR technique is a sort of nucleic acid amplification take a look at (NAAT) that detects a pathogen by discovering and amplifying elements of its genetic materials, and it’s extensively used to detect SARS-CoV-2.
However all these assessments have a weak spot: it’s a must to know precisely what pathogen you’re in search of. In a latest research, printed in Scientific Studies, researchers from Lawrence Livermore Nationwide Laboratory (LLNL) and the California Division of Public Well being recognized different doubtlessly dangerous respiratory viruses in samples that examined damaging in a regular, NAAT-based panel. The outcomes counsel {that a} pathogen-agnostic method is a vital complement to assessments like PCR.
“If a affected person is contaminated with a life-threatening pathogen that’s not coated by these assessments, then this may trigger a severe well being threat,” stated LLNL scientist and writer Crystal Jaing. “Pathogen-specific assays don’t present complete protection of a broad spectrum of pathogens, whereas pathogen-agnostic assessments present rather more data.”
To exhibit the ability of pathogen-agnostic testing, the authors examined samples with untargeted metagenomic sequencing. Whereas PCR testing searches for and amplifies a particular DNA sequence, the untargeted method reads all genetic materials within the pattern. That data is in comparison with a longtime database to determine what pathogens are current.
A lot of the research’s samples, obtained from a sentinel surveillance program to check sufferers with respiratory signs in counties all through California, had been damaging for the 22 pathogens (together with SARS-CoV-2) examined by the NAAT-based panel. However the workforce discovered that 5 p.c of these damaging outcomes contained a distinct, beforehand undetected respiratory virus. Additionally they recognized bacterial or fungal species in a variety of instances.
“Pathogen-agnostic assessments present the benefit that you just don’t must know what pathogens are in a pattern,” stated Jaing. “Utilizing the agnostic method, you’ll be able to detect all or any pathogens in a pattern with a single take a look at.”
Nonetheless, metagenomic sequencing takes longer, prices extra and requires extra advanced gear than NAATs. The authors emphasize that it shouldn’t change strategies like PCR — it ought to complement them.
“NAAT can be utilized for routine assessments as a result of they’re sooner and cheaper. Within the COVID-19 instance, a regular NAAT will give us solutions straight away,” stated Jaing. “Nonetheless, NAAT is just not adequate for surveillance of recent and rising pathogens and for future pandemic forecasting.”
The researchers hope these findings will encourage public well being entities to think about incorporating pathogen-agnostic approaches for detection and surveillance.
