By N. Mueller

A year and a half into the SARS coronavirus (SARS-CoV-2) pandemic and we are still playing catchup. Just as COVID testing ramped up, the UK, South African (S.A.), and Brazilian (Bz) variants appeared. Now we hear about an Indian variant, aka the Delta variant. The ever-evolving COVID-19 landscape has us searching for easy and adaptable detection methods to track Mother Nature’s changes to the virus.
Starting out in the COVID-19 pandemic, we heard about antigen, antibody, and molecular assays for detecting coronavirus. We were told that antibody tests detected past infection and likely immunity but only were beneficial weeks after infection. In contrast, antigen tests detected viral proteins indicating current infection, but sensitivity concerns remained. We adapted to molecular testing for the sensitivity we needed with reasonable turnaround times and associated costs. After setting up these assays and validating them, reports of molecular dropout of some targets occurred, which were the beginnings of the emerging Alpha variant (UK strain). Molecular reagent companies scrambled and developed new RNA target sequences for continued COVID detection as well as options for differentiating emerging variants.

What causes COVID-19 Variants?

Variants of the COVID virus occur as random mutations in the viral RNA genome. As infected cells each produce thousands of new viral particles, errors are likely to occur during replication. While many newly made viruses are exact copies of the virus that first infected the cell, others may contain one or more random mutations throughout the RNA genome. However, unless a mutation improves growth rate or gives increased fitness, it will not become a dominant variant. Thus, we have seen the alpha variant (UK strain) with improved growth and the beta variant (S.A. strain) with immune evasion infect more people and spread faster resulting in their increased prevalence in samples tested. Now the Delta variant is emerging with even faster growth rates than its predecessors.

How to track and predict variant infection rates?

Currently, COVID-19 variant testing is done in one of two ways at the molecular level. The first way variant testing is performed is by Next-Generation Sequencing (NGS). Here positive COVID-19 samples are sent to a lab with sophisticated equipment that collects RNA sequences and uses software to determine the viral genome and changes to it. This method is sensitive, but it is time (24-48 hours), cost, and labor-intensive. Additionally, this method detects all old and new variants at once. In contrast, the second method for COVID variant detection uses qPCR diagnostic assays. Here, samples positive for COVID-19 are assayed for specific mutations in known variants. These detection methods take about 2 hours, use standard qPCR equipment, and cost only a few dollars each. However, unlike NGS, qPCR does not detect old or novel variants that are not specifically probed for in the assay. Therefore, a mixture of NGS and qPCR methods for COVID variant diagnostics should be used to monitor trends in currently circulating strains and the detection of new variants that may become variants of interest (VOI) or variants of concern (VOC). In combination, these COVID-19 variant detection methods will indicate the prevalence of current variants and the occurrence of new ones.

How can Seegene Technologies help your lab?

Seegene is at the forefront of helping labs identify both COVID-19 and its variants to best understand how the virus is moving through their region. Our FDA Emergency Use authorized (FDA EUA) Allplex™ 2019-nCoV assay detects multiple targets (E gene, N gene, RdRP) within SARS-CoV-2 and is ideal for initial screening of COVID-19 in diagnostic, epidemiological, research, and other settings. For those seeking further identification of COVID variants, Seegene offers Research Use Only (RUO) qPCR assays that detect specific mutations in the U.K. (Alpha), S.A. (Beta), Brazilian (Gamma), and Indian (Delta) variants.  Our patented technologies combined with machine learning allow for rapid development, validation, and deployment of new variant detection assays as needed.  

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