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Novel Method for Rapid Detection of COVID-19 Omicron Variant and Future Emerging Variants
Qixin Leng1,2, A James Mixson1
1Department of Pathology, University of Maryland School of Medicine, 685 West Baltimore St., Baltimore, Maryland 20201, USA.
Insights
Two new, cost-effective qPCR methods can rapidly detect the Omicron variant and its sublineages, aiding global surveillance of SARS-CoV-2 variants. These molecular tools offer a faster alternative to sequencing for tracking COVID-19 evolution.
Area of Science:
- Molecular Biology
- Virology
- Epidemiology
Background:
- The COVID-19 pandemic has caused millions of deaths globally, driven by evolving SARS-CoV-2 variants like Alpha, Delta, and Omicron.
- Monitoring the emergence and spread of new variants is crucial for public health response.
- Traditional sequencing methods for variant tracking are slow and costly.
Purpose of the Study:
- To develop rapid, sensitive, specific, and economical molecular assays for identifying SARS-CoV-2 variants.
- To differentiate the Omicron variant from other major SARS-CoV-2 strains.
- To establish methods adaptable for tracking future variants of concern.
Main Methods:
- Development of two quantitative polymerase chain reaction (qPCR) assays.
- Assay 1: Targets a specific base mutation characteristic of the Omicron variant.
- Assay 2: Utilizes primers designed for a unique deletion-insertion region in Omicron, adaptable for sublineages like BA.2.
Main Results:
- Both qPCR methods demonstrated high sensitivity and specificity in distinguishing Omicron from other variants.
- The developed assays provide a faster and more economical alternative to genomic sequencing for variant surveillance.
- The primer-based method is adaptable for detecting novel mutations, including deletions and insertions.
Conclusions:
- The novel qPCR assays offer efficient tools for real-time monitoring of SARS-CoV-2 variant prevalence.
- These methods can significantly enhance global surveillance of COVID-19 variants, including Omicron and its sublineages.
- The adaptability of these assays supports preparedness for future viral evolution and emergence of new variants.
Abstract:
Over six million people have died worldwide as a result of SARS-CoV-19 (Covid-19). Several major and minor variant waves of Covid-19 including the Alpha (B.1.1.7), Delta (B.1.617.2), and the Omicron (B.1.1.529) have infected patients in the last two years. These individual variants have been associated with different infectivity and death rates, and it is anticipated that other variants of significance will occur. As a result, the emergence and frequency of the different Covid-19 variants at various locations in the world are critically important to monitor. To date, sequencing of these variants has been the primary method to track the prevalence of the different variants, but this approach is relatively slow and expensive. In contrast, we have developed two qPCR methods that are sensitive, specific, and economical which can distinguish the Omicron variant from the other variants. The first qPCR method detects a specific base mutation in Omicron enabling improved amplification. The second method is based on designing a primer specific for the region in which a deletion and an insertion have occurred in the Omicron variant. While the first approach can be readily adapted to identify other variants with point mutations, the second method can identify emerging deletion/insertion mutations such as BA.2, a subvariant of the Omicron.
