A new sequencing panel developed by researchers at Augusta University and the University of Georgia and Illumina can accurately scan for a panel of 41 respiratory viruses including SARS-CoV-2.
The team hopes this will allow fast identification and treatment of patients with different respiratory infections, improve epidemic and pandemic surveillance and also identify those with co-infections with more than one respiratory pathogen.
“We are concerned that because most of us are no longer wearing masks or social distancing and have mostly resumed our normal schedules that one consequence will be more coinfections,” says Ravindra Kolhe, a senior researcher and clinician at the Medical College of Georgia at Augusta University, who led the study.
“Another immediate public health deficit pertaining to other respiratory viruses is already of major concern since co-circulating respiratory viruses other than SARS-CoV-2 largely remained undocumented for nearly the entire year of 2020,” write Kolhe and co-authors in the journal Viruses.
Working with Illumina, the researchers developed a high-throughput next-generation sequencing (NGS) respiratory viral panel capable of detecting 41 different viruses. These included various types of coronaviruses and influenza viruses, as well as different types of respiratory syncytial virus, enterovirus, parainfluenza virus, and bocavirus, among others.
The team tested the panel on 533 samples taken from people in the state of Georgia with known viral infection status and found it to be 94% accurate. Positive percentage agreement (sensitivity) and negative percentage agreement (specificity) for the panel were 96% and 86%, respectively, meaning false negatives were low for the test.
Although PCR testing is accurate at detecting a single virus such as SARS-CoV-2 in a sample, it only searches for small segments of the viral genome and does not contain as much information as the sequencing panel. Searching for multiple viruses in one sample is also much more complex.
Kolhe and team say this kind of sequencing panel is needed to help guide treatment of patients admitted to hospital with COVID-19, as many patients (as many as 1 in 5) have co-infections with other viruses that can make them sicker.
They also emphasize that the tool can also help track the spread and evolution of SARS-CoV-2 and monitor other viruses of concern to warn of future epidemic or pandemic threats, especially combined with an online model called Nextstrain, which contains ‘real-time’ information on pathogen evolution including emerging strains of SARS-CoV-2 and is routinely used by the CDC to predict flu virus distribution for the upcoming season.
“This study demonstrates that genomic epidemiology is essential in predicting disease transmission and pattern of transmission and that it has the potential to recognize the imminent resurgence of a regional outbreak,” write the authors.
“Given the challenges associated with establishing such a surveillance program, it is essential to develop and maintain the infrastructure for such analysis for future pandemics.”
The panel developed for this study can now be accessed by researchers through Illumina.