SARS-CoV-2 Variant Tracking

The Evolution of SARS-CoV-2

The emergence of novel variants such as Omicron or BA.2 Omicron was all but guaranteed when SARS-CoV-2 took hold and spread around the world.

RNA viruses replicate rapidly but imperfectly. Mutations naturally arise during this process, particularly during extended infection periods. Some genetic changes negatively impact the spread of the virus. Others are neutral. But sometimes, mutations emerge that confer an evolutionary advantage. In the right conditions, these new variants can quickly take hold and spread through the population. While we’re racing to develop vaccines and therapies, SARS-CoV-2 is in some ways also competing with itself.

Tracking, researching, and responding to variants is now an important part of our global health response to the COVID-19 pandemic. Understanding the implications of these different mutations (and their combined impact) is important on a number of levels. At the highest level, it allows public health officials to respond quickly to new threats, potentially limiting the variant’s spread and/or preparing for a surge in cases. Over time, COVID-19 vaccines may also need to be updated to address pervasive mutations. The sooner vaccine developers get that information, the sooner they can respond.

Seegene’s Novaplex™ SARS-CoV-2 Variants Assays are multiplex real-time PCR assays that detect and identify notable mutation sites in the crucial “spike protein” gene.

In March 2021, the World Health Organization (WHO) and the U.S. Centers for Disease Control and Prevention (CDC) introduced a new naming system for emerging SARS-CoV-2 mutations. Categorizations are based on the latest available evidence and may be updated as new data emerge. As a general philosophy, the bar for tracking “variants of interest” is low to maximize surveillance. Conversely, the threshold for a variant to be considered “high consequence” is rigorous. This ensures that resources are conserved for the highest priority threats. The three categories include:

  • Variants of interest: This applies to variants that have caused discrete clusters of infections (in the U.S. or overseas) with the potential to drive an increase or surge in cases. Some of the unique genetic changes may make the variant more contagious or able to escape immune detection. Therapeutics and tests may not be as effective against these strains.

  • Variants of concern: Scientific research and epidemiological analyses have shown these variants are likely to be more contagious and/or cause more severe disease. The genetic changes they have evolved may also reduce the effectiveness of therapeutics and vaccines. People who have previously had COVID-19 may be at risk of reinfection.

  • Variants of high consequence: These variants are proven to cause more severe disease and, in turn, increased likelihood of hospitalization, injury and death. Beyond a slight reduction in vaccine/therapeutic efficacy, variants of high consequence may entirely overcome medical interventions. As of March 2021, no variant had been labeled a variant of high consequence.

Engineering a Rapid Response

The most comprehensive technology for identifying SARS-CoV-2 mutations is genomic sequencing. While thorough, this cannot be performed at the scale needed to track a highly transmissible infectious disease. Despite being a technology pioneer, Science reports that the U.S. had only sequenced 0.36% of all confirmed cases as of February 2021. Genomic sequencing may also take weeks – sometimes months – to return results, limiting its value as a public health tool.

Agility and speed are critical when it comes to tracking and responding to viral variants. At Seegene, we’re applying a suite of specialized tools and technologies to serve our customers worldwide. This includes:

  • Proprietary bioinformatics (SG-Insilico™) to monitor newly emerging SARS-CoV-2 sequence information on a regular basis
  • Machine learning to rapidly process data and design new optimized diagnostic assays
  • World-class manufacturing and supply chain management to produce and deliver variant assays in a timely manner

For the foreseeable future, managing SARS-CoV-2 variants will be an ongoing challenge. Our ability to identify and adapt to these changes hinges on smart surveillance and real-time tracking of different mutations and their spread.

How do you know what to look for?

Conventional technology can be applied to the detection of a single variant – but not multiple variants. Seegene’s new multiplexed test can detect five different mutations in a single test tube, along with wild-type variants.   

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Learn more about Seegene SARS-CoV-2 Assays