By Deborah Borfitz
November 17, 2021 | Labs around the country with next-generation sequencing capabilities have begun using a respiratory virus panel that simultaneously tests for SARS-CoV-2 and 40 other potentially co-occurring respiratory viruses, including four cold-causing coronaviruses, both types of respiratory syncytial viruses (RSV), and more than a dozen influenza viruses. The target population currently are elderly nursing home residents and immunocompromised patients in hospital intensive care units with suspected coinfection, according to Ravindra Kolhe, M.D., Ph.D., director of the Georgia Esoteric and Molecular Laboratory at the Medical College of Georgia at Augusta University.
Kolhe was part of the research team that confirmed the validity of Illumina’s Respiratory Virus Oligo Panel on 483 samples (471 nasopharyngeal swabs and 12 saliva) taken from patients across three regions of Georgia, as detailed in an article recently published in Viruses (DOI: 10.3390/v13102063). In terms of delivering consistent results relative to the gold standard RT-PCR assay, “it worked every single time,” he says.
The decision about what the new test should cover, beyond SARS-CoV-2, was reached by “literature-based consensus” on the most common viruses found in upper respiratory tract infections in recent years and the capacity of the Illumina sequencing platform, Kolhe adds. For the study, the sequencing data was used to create an epidemiology model for Georgia identifying the original B strain of SARS-CoV-2 as the dominant one circulating in the state at the timeframe (May through August 2020) that patient samples were taken.
Sequencing detected not only clinically critical variants but benign changes in the larger, conserved region of the SARS-CoV-2 virus providing a sort of genomic stamp of where it came from, he explains. Any time there was “people movement,” such as a football game, researchers could monitor those alterations to predict the zip codes where the virus would show up next.
The coinfection rate in the study population was low (0.8%) as a reflection of strict mask mandates, social distancing recommendations, and widespread school closures, notes Kolhe. But with restrictions loosening and more large gatherings again happening, communicable viruses—most significantly seasonal flu, now most people have received their COVID shot—are much likelier to deliver a one-two punch.
Respiratory viruses commonly occur in pairs, Kolhe says. Stanford University reported in late March 2020 that about one in five people with COVID-19 were also infected with other respiratory viruses. One in 10 diagnosed with a common respiratory virus also were co-infected with SARS-CoV-2.
“Going forward there is one test we can do that will help us identify… coinfections and their sequences,” says Kolhe. Understanding the causative agent would certainly help doctors make more informed treatment-related decisions.
But the test will be reserved for the trickier cases, largely because it requires sequencing capacity and expertise, says Kolhe. For COVID-19, it is also too slow and costly relative to qualitative (yes/no) PCR-based testing for routine use.
“This particular test takes three to five days [to produce results] because it will not only tell you if you have SARS-CoV-2 [as well as the flu or RSV] but the sequence of the virus so we can identify the variant,” Kolhe says. It is done primarily by large commercial labs with virus-sequencing capacity and tertiary institutes such as Augusta University Medical Center.
The public health department in every state has created channels for sequencing data to get into a central repository, which the Centers for Disease Control and Prevention can access. All public health departments, and many academic centers, are now using Illumina’s respiratory virus panel or something similar, he adds.
Viruses of greatest interest depend on the population in question since susceptibility and severity of illness are often age dependent, Kolhe says. But the flu virus is most studied because it returns every year—and can be serious for anyone.
“I know flu-based research doesn’t seem very glamorous, but it has saved millions of lives,” he says, noting that scientists at Augusta University worked on the new respiratory virus panel collaboratively with colleagues at the University of Georgia’s premier influenza research facility. “We’re fortunate to be able to replicate their model [so quickly] for SARS-CoV-2.”
Variant Forecasting
Predicting which SARS-CoV-2 variants will be circulating in the future could help inform the development of booster shots, much as the sequences of influenza viruses have been used for the last few decades to forecast the strains that next season’s flu vaccines should cover, says Kolhe. The intent here is to create research protocols for COVID-19 that would similarly run like a “well-oiled machine,” and creation of the respiratory virus panel is a first step in that direction.
SARS-CoV-2 will at some point leave center stage and be “grandfathered into the family of upper respiratory tract infections,” Kolhe says, but it is for now responsible for the bulk of virus-associated morbidity and mortality. Sequencing the entire virus reveals biologically important variants [e.g., Delta] as well as how cases may be connected—and if one iteration of a virus experiences more of the same changes with each person it infects.
By monitoring these changes, molecular epidemiologists can also see how the virus moves and behaves. Sequences of SARS-CoV-2 get uploaded to the open-source platform Nextstrain, making it possible to watch the virus as it evolves in different parts of the country and the world, says Kolhe. Coupled with human movement data and vaccination rates, that would provide public health officials with a picture of disease transmission patterns as well as forewarning of pandemic-related surges.
Various labs are already submitting sequencing data—some just for the COVID-19 or flu and others from coinfections using the new respiratory virus panel—to the Nextstrain database. The U.K. has been particularly proactive about SARS-CoV-2 sequencing, Kolhe notes. Early in the pandemic, the government set up a national program (COVID-19 Genomics UK Consortium) that is now sequencing close to 15% of all identified cases in the country.