Blog based on Dark Daily Webinar: “Emerging SARS-CoV-2 Mutations: Impact on Thermo Fisher Scientific Assay Performance“
The World Health Organization (WHO) has classified four SARS-CoV-2 strains as “variants of concern.” These variants include the B.1.1.7 strain first detected in the United Kingdom, the B.1.351 strain first detected in South Africa, the P.1 strain first detected in Brazil and, most recently, the B.1.617 SARS-CoV-2 variant first detected in India.
So what is a variant of concern? And what do these variants mean as guidelines continue to loosen and people around the world begin traveling, attending events and going back to work and school again?
In a recent webinar for Dark Daily, Manoj Gandhi, M.D., Ph.D., Thermo Fisher’s senior director of medical affairs, Genetic Sciences, joined Peter De Hoff, Ph.D., and Shashank Sathe from the University of California San Diego, along with Karthik Gangavarapu from Scripps Research, for a panel discussion on how variants emerge and implications for treatments, vaccines and ongoing testing.
Understanding Mutations, Variants and Variants of Concern
During the panel, before Dr. Gandhi addressed any specific variants he spent some time breaking down commonly used COVID-19 terminology.
- A mutation is a single error that is introduced into the genome as it undergoes replication. Errors may include a single nucleotide change or a deletion of a set of nucleotides.
- A variant is a viral genome that contains a particular set of mutations.
- A variant of concern, or VOC, is a variant that has some biological significance, such as an increase in transmissibility or virulence.
- A variant of interest, or VOI, is when the virus has undergone a change with suspected implications.
Since new strains began emerging in late 2020, a few concerning variants with shared common features have become dominant. “This concept is called convergent evolution,” said Dr. Gandhi during the webinar. “We see that this is a phenomenon that is not just happening locally in specific countries, but this has now been observed pretty much across the world.” Dr. Gandhi explained that while some variants may be transported due to travel, the same mutation can also occur de novo in completely different locations.
“Why are we seeing these variants? Well, viruses mutate, and especially RNA viruses like coronaviruses are more prone to undergoing mutation,” explained Dr. Gandhi. As the human body mounts an immune response there is selective pressure on the virus to mutate at higher rates. These mutations might offer the virus an advantage for it to spread rapidly throughout the population and increase human-to-human transmission.
Mutations may also be associated with higher viral loads in an infected patient that can increase disease severity and potentially lead to worse outcomes. “Some of these mutations might offer a mechanism for the virus such that the virus is able to become more resistant to treatment, such as antibody therapies, or worse they are able to escape vaccine immunity,” said Dr. Gandhi. “And last but not the least, some of the mutations in these variants…may impact the way that diagnostic tests are able to detect the presence of the virus.”
Keeping Up with Emerging Variants
To ensure its assays can continue to identify SARS-CoV-2 even as it mutates, Thermo Fisher monitors public databases and evaluates its assays’ performance for emerging variants, variants of concern and variants of interest. As Dr. Gandhi explained, the TaqPath assays offer labs confidence in their performance as they have been designed specifically on three fundamental principles: genomic conservation, specificity and redundancy.
Genomic conservation means Thermo Fisher’s assays are designed to look at areas of the viral genome that are less likely to mutate even as the virus evolves. Specificity means the assays are designed to only detect regions that are unique to the SARS-CoV-2 virus, not other viruses or microorganisms. And lastly, redundancy means they are designed with built-in backups. With the TaqPath assays’ three-target design, if one of the targets is affected by a mutation there are two other targets to fall back on that are still functional for the assay to perform as it was intended.
Already, the redundancy of Thermo Fisher’s TaqPath assays has proven essential. With the B.1.1.7 strain, one particular mutation produces a phenomenon known as the S gene dropout, or failure to detect the S gene. Because of the assays’ multi-target design, however, not only are they still able to identify the virus, they can actually be used as surveillance tools to help detect emerging variants.
To hear how labs are continuing to keep pace with the emergence of SARS-CoV-2 variants, watch the on-demand webinar.
To learn more about Thermo Fisher Scientific’s COVID-19 Testing Solutions, please visit thermofisher.com/covid19.