As some health departments reduce the frequency of COVID-19 reporting and testing rates continue to decline, experts warn we may not have an accurate picture of current infection rates. Even more alarming, as Boston Children’s Hospital Chief Innovation Officer John Brownstein, Ph.D., recently cautioned in an interview with ABC News, “an undercount of cases undermines the legitimacy of public health reporting and may mask any early indications of a surge, especially in unvaccinated populations.”
While COVID-19 reporting has dropped off to some extent, global case counts still show the virus is surging in parts of the world.  Even in regions like the U.S. where the pandemic is under some control, there are pockets where cases per week are starting to creep back up. These numbers indicate remaining need for vigilance and caution, particularly as new strains continue to circulate.
Public health officials are urging people to get vaccinated, if they are not already, and to continue testing. “The pandemic isn’t over yet,” the Utah Department of Health warned in a recent statement reminding residents of the importance of testing. “In fact, now that new variants are circulating and some are even more transmissible, finding out if you’re positive and isolating can prevent you from exposing others.”
At the World Microbe Forum in June, experts discussed the need for ongoing SARS-CoV-2 surveillance and the importance of global and national strategies to monitor new coronavirus strains along with more localized efforts to track variants in the community.
“We recommend a two-pronged approach for surveillance,” Andy Felton, Ph.D, vice president of clinical next generation sequencing at Thermo Fisher, shared during his presentation at the event. At the global or national level, it is important to sequence a random sampling of positives. “Typically, what the W.H.O. and other public health entities recommend is 5-10% of samples,” he noted. As new strains continue to emerge, highly sensitive next-generation sequencing (NGS) is critical. Some sequencing technology only looks at 50% of the virus’s genome, potentially leaving blind spots in surveillance efforts. Thermo Fisher’s Ion Ampliseq SARS-CoV-2 Insight Research Assay sequences more than 99% of the SARS-CoV-2 genome, providing increased resilience to new mutations. The highly sensitive assay also enables sequencing of a variety of sample types, including nasopharyngeal, shallow nose swabs and saliva, with lower viral loads.
At the local level, Felton emphasized the importance of a decentralized approach where samples are sequenced at or near the point of origin so public health officials can identify any emerging variants ahead of a potential outbreak. Rapid, cost-effective SARS-CoV-2 surveillance can also help local public health officials make real-time, data-driven decisions on business openings, access to recreational sites, and in-person learning. Felton described two options for local labs to track and quickly intersect any variants on the ground. Labs may choose to sequence all positive samples using a rapid NGS platform such as the Ion Torrent Genexus System or they may opt to genotype all positive samples and then use sequencing as a reflex test for any samples with defined mutation profiles.
For labs that opt to reflex to NGS, Sanger sequencing or PCR are quick, cost-effective methods to screen samples and flag those that may require further study. Sanger sequencing by capillary electrophoresis looks at targeted areas of interest in the virus’s genome, predominantly the S gene, as most variants seem to affect the spike protein. As an alternative, newly available PCR assays can be used to determine the presence of mutations associated with specific viral strains. The advantage of PCR for rapid genotyping is that labs can use existing instrumentation already in place for COVID-19 molecular diagnostic testing cost-effectively and with rapid turnaround times, even for large-scale testing.
“As more variants started to emerge globally, we needed to develop a test capable of discriminating between different circulating variants, so we designed a convenient and customized RT-PCR solution that can be used as a surveillance tool,” Jelena Feenstra, senior manager of global scientific communications for genetic sciences at Thermo Fisher, shared during her presentation the event. Feenstra highlighted how the same mutations tend to emerge in many variants, and how Thermo Fisher designed the TaqMan SARS-CoV-2 Mutation Panel* with a menu of 22 verified RT-PCR assays to detect known variants of concern circulating in the population. The panel is customizable so researchers can adapt quickly as additional mutations and variants emerge.
“With each month the pandemic has lasted, we have seen a more and more complex picture,” Feenstra said of the variants circulating the globe. She described how new variants may be more transmissible and can even carry increased risk of resistance to antibody treatments or vaccines. Changes in the viral genome can impact public health policies, how the illness spreads in the population, impact of treatment options, and vaccine development and efficacy. In this evolving landscape, global and localized surveillance remain critical to detect and monitor COVID-19 mutations.
For more information on emerging mutations and variants, please visit thermofisher.com/covid19mutations
And, for more information on Thermo Fisher’s COVID-19 surveillance solutions, please visit thermofisher.com/covid19surveillance
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