In a paper recently published in Viruses, Russian researchers reviewed the use of next-generation sequencing as a diagnostic as well as research tool in virology. According to their review, NGS is more precise at profiling pathogens than existing methods but it has not yet been widely accepted owing primarily to its high cost and the complexity of sample preparation and data analysis.
The COVID-19 pandemic has shed light on a variety of problems related to identifying and studying emerging pathogens. "There are, by various statistical estimations, over 320,000 various viruses infecting mammals," said Kamil Khafizov, senior author on the paper. "But up to date, less than 1% of this vast multitude has been studied."
Most viruses, including those that cause respiratory, digestive, and other diseases in humans, remain unresearched and thus almost undetectable, he added. The reason behind this is the narrow spectrum of viruses that the modern testing systems are designed to target.
In their paper, the team explores the shortcomings of the PCR method. They report that this essential technique for microorganism molecular testing fails to identify poorly explored viruses, which is one of the key problems in modern virology.
They hone in on next-generation sequencing (NGS) as the most promising method, but they acknowledged shortcomings including the high cost of equipment and reagents needed for running such tests and the lengthy sample preparation, sequencing, and data analysis processes. These limitations, combined with high lab personnel qualification requirements, prevent the method from being widely integrated in the mainstream clinical practice, they say. Nevertheless, the cost of the technology goes down with each year, while its speed, accuracy, and efficiency keep growing.
Khafizov noted that the coronavirus pandemic has demonstrated the importance of NGS methods for identifying new pathogens in clinical samples and studying the molecular mechanisms of virus transmission from animals to humans.