The primary goal is to know if the virus is changing in ways that would affect current medical treatments.
The U.S. Food and Drug Administration (FDA) issued an emergency use authorization (EUA) for the use of genomic sequencing in COVID-19 that will both significantly improve the level of research into COVID-19, as well as holding real promise for the ongoing treatment of the coronavirus.
The FDA authorized the Illumina COVIDSeq Test for the qualitative detection of SARS-CoV-2 RNA from respiratory specimens collected from individuals suspected of COVID-19 by medical response teams, or by their healthcare provider. In the fight against coronavirus, using next-generation sequencing tools means that the test can generate information about the genomic sequence of the virus present in a sample.
In a recent interview, Dr. Phil Febbo, chief medical officer of Illumina, explained that diagnostic testing helps medical professionals manage patients, while surveillance is required to manage whole populations. Diagnostic testing, he explained, provides yes/no answers for individual patients. Dr. Febbo contrasted diagnostics with surveillance testing, where the goal is to inform public health professionals to track the path of a pandemic, understand transmission routes, and determine viral evolution. The most important goal is to know if the virus is changing in ways that would affect current medical treatments.
The EUA means that medical professionals can use the COVIDSeq test to produce information about the genomic sequence of the virus, as recognized as present in a sample obtained in research or from a patient. The FDA uses the EUA to fast track the availability of medicine or treatment programs in a time of emergency.
Dr. Stephen Hahn, MD, the Commissioner of the FDA, explored the promise this new set of testing tools offers medical professionals in response to COVID-19. “Throughout the COVID-19 pandemic, we have seen the ingenuity that results from the FDA working in partnership with the private sector. Genetic sequencing information will help us monitor if and how the virus mutates, which will be crucial to our efforts to continue to learn and fight this virus,” said Dr. Hahn, M.D.
Understanding why sequencing matters
Sequencing is necessary to track the transmission route of the virus globally, monitoring exposure to the most established cluster. More aggressive measures are warranted to contain the spread of the virus.
In finding the best therapeutics, sequencing can determine how quickly the virus is adapting as it spreads. It appears that SARS-CoV-2 achieves two mutations per month as it spreads. This information allows public health officials to identify how likely the virus is to avoid detection from established PCR assays and become resistant to therapies.
Sequencing identifies targets for therapies. Knowing the viral genome is essential to understanding therapeutic efficacy from small molecule therapeutics targeting specific viral proteins to vaccines directed against viral antigens.
Sequencing-based surveillance is required to understand the role of co-infection. COVID-19 can range from asymptomatic to fatal. Respiratory pathogens can often cause progressive disease by lowering host immunity and fostering a co-infection that results in more severe and life-threatening diseases.