Thermo Fisher Uses Next-Generation Sequencing to ID COVID Variants

Thermo Fisher Scientific recently launched the Ion AmpliSeq SARS-CoV-2 Insight Research Assay to improve surveillance and identification of new and known COVID-19 variants from samples with lower viral loads.

The Ion AmpliSeq SARS-CoV-2 Insight Research Assay improves local, regional, and national surveillance efforts to discover emerging COVID-19 variants. Specifically, it is able to sequence over 99 percent of the SARS-CoV-2 genome, covering all potential stereotypes. 

The panel leverages sensitive next-generation sequencing (NGS), allowing researchers to obtain epidemiological insights with rapid turn-around time, workflow automation, seamless informatics, and data uploading to public SARS-CoV-2 data repositories. 

"RNA viruses such as SARS-CoV-2 mutate at high rates in response to selective environmental pressures, requiring labs and vaccine developers to monitor mutations diligently," Andy Felton, vice president of clinical next generation sequencing at Thermo Fisher Scientific, said in the announcement. 

"Higher sensitivity next-generation sequencing assays are needed to identify mutations earlier in both symptomatic and asymptomatic individuals to help public health officials and labs globally track the spread of new and known variants for public health decisions and guidance locally,” Felton continued. 

Overall, the Ion AmpliSeq SARS-CoV-2 Insight Research Assay includes 237 amplicons specific to SARS-CoV-2, with the addition of variant-tolerant primers for emerging variants.

A Thermo Fisher Scientific spokesperson explained that the increased sensitivity of the panel will empower researchers to sequence the complete genome and discover new variants of sample tyles, including nasopharyngeal and shallow nasal swabs, and saliva. 

Josh Arant, chief operating officer at MAKO Medical Labs, explained that MAKO has been sequencing positive COVID-19 samples since the fall and recently formed a partnership with the CDC to boost national surveillance of known and emerging SARS-CoV-2 variants. 

Thermo Fisher Scientific’s new panel allows MAKO Medical Labs to quickly report valuable insights on SARS-CoV-2 variants to inform public health professionals across the country.

And Marco Loddo, PhD, BSc, co-founder and scientific director at Oncologica, explained that as one of the labs sequencing positive SARS-CoV-2 samples, they need precise sequencing technology that can help them understand which mutations are present in positive samples.

The Ion AmpliSeq SARS-CoV-2 offers fast improvement on the sensitivity for lower titer samples, Loddo explained, including samples from asymptomatic individuals. Therefore, the panel has been helpful for the discovery of emerging variants in the UK.

According to the CDC, attributes of a variant of concern include evidence that the variant is the cause of an increased proportion of cases or unique outbreak clusters, as well as limited prevalence or expansion in the US or other countries. 

Addition attributes of a variant of concern is evidence of impact on diagnostic, treatments or vaccines, evidence of increased transmissibility, and evidence of increased disease severity. 

Currently, B.1.1.7, B.1.351, P.1, B.1.427, and B.1.429 variants are circulating in the US and are classified as variants of concern.

The B.1.351 SARS-CoV-2 variant, first identified in the Republic of South Africa, has been detected in at least nine states in the US. In April, NIH initiated a Phase 1 clinical trial of Moderna’s variant-specific COVID-19 vaccine candidate, mRNA-1273.351.

Researchers will evaluate the safety and reactogenicity of mRNA-1273.351, as well as its ability to induce an immune response, in 210 healthy adult volunteers at four clinical research sites in the US. 

The trial will also enroll 150 volunteers aged 18 to 55 years who have not received any COVID-19 vaccine, have no known history of SARS-CoV-2 infection, and do not have health conditions that are associated with an increased risk of severe illness.

Volunteers in the trial will provide blood samples at specified times, which will be used to measure the immune response against circulating strains of SARS-CoV-2, including B.1.351.