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Breakthrough early detection of Omicron BA.2 in wastewater achieved with hpPCR


13 apr. 2022

Breakthrough early detection of Omicron BA.2 in wastewater achieved with hpPCR

APLEX Bio announces it has demonstrated superior performance of multiplexed COVID variant detection in wastewater, including the generally difficult to detect variant BA.2, using its next-generation hpPCR technology. In a study where samples were tracing back to the end of 2021, results showed that BA.2 could be detected at least one week and up to three weeks earlier compared to next-generation sequencing (NGS) analysis. The study also demonstrated how APLEX Bio’s hpPCR enables ultra-sensitivite analysis while retaining specificity with a cost-effective and rapid workflow going from sample to result within 3 hours.

STOCKHOLM – APLEX Bio, developer of a next-generation hyperplexed PCR platform (hpPCR), announces it has demonstrated superior performance of wastewater detection using its platform.

PCR based methods in general have limitations over NGS in terms of specificity, which is the reason why the BA.2 variant has been difficult to detect using PCR analysis. This variant is similar to the early Delta variant except for a few point nucleotide substitutions. Thus, NGS is better suited for detecting such variants over PCR based methods. PCR based tests also have the limitation of multiplexity over NGS, which keeps the number of variants or pathogens that can be detected low.

NGS on the other hand has limitations when it comes to sensitivity and cost, which is why the method is sub-optimal for tracing emerging variants of concern, especially when such variants are present at low levels. Therefore, the two methods are usually combined, where qPCR is used to detect and quantify the presence of a pathogen and additional NGS is performed to do variant profiling.

APLEX Bio has now shown that single-copy sensitivity surpassing qPCR and multiplexity/specificityfor which NGS is resorted to, can be achieved in a single cost-effective and rapid nucleic acid test by using its hyperplexed hpPCR platform.

In a study in collaboration with Swedish Environmental Epidemiology Center (SEEC), a Pandemic Preparedness Laboratory initative within SciLifeLab, samples containing down to less than 10 copies of viral genome per microliter were analysed in retrospect as part of a timeline tracing back to the end of 2021. The results showed that BA.2 could be detected at least one week and up to three weeks earlier with hpPCR compared to NGS. In addition, hpPCR can provide results within 3 hours, compared to several days for a typical NGS pipeline. The study also demonstrated the hyperplexing capabilities of hpPCR as a proof-of-concept where BA.2 was detected simultaneously with BA.1, Delta and the conserved N1 gene.

“With hpPCR, we will be able to detect more than 100 markers in the same sample without compromising sensitivity or specificity”, says Umear Naseem, CEO and founder.

“We chose to work with wastewater samples because they are challenging for multiple reasons. Wastewater is a naturally pooled source of sample that contains a plethora of highly diluted pathogens and other biomarkers from humans, as well as unwanted and uncontrolled components including inhibitors that make analysis difficult. This puts high demands on analysis concerning sensitivity and specificity, and by demonstrating state-of-the-art performance in these samples we could show the great potential hpPCR holds in addressing many molecular diagnostic challenges” continues Umear Naseem.

Performance of SARS-CoV-2 variant detection in wastewater using NGS and Aplex Bio’s hpPCR. Early detection of Omicron BA.2 could be achieved with zero cross reactivity towards the Delta variant. The results are the average output from wastewater samples collected weekly in Kalmar, Umeå, Uppsala and Örebro.

“We are excited about the results provided by APLEX technology. Sensitivity and simultaneous variant/pathogen detection is very important for wastewater analysis and we see great potential for this based on the pilot data we have gotten“ commented the collaborators Anna Székely and Maja Malmberg from SEEC, who also mentioned the potential of APLEX Bio’s technology in a blog post recently.

About APLEX Bio

APLEX Bio is a Swedish start-up founded in 2020 developing and commercializing a next-generation hyperplexed molecular detection technology for analysis of massive numbers of biomarkers both in-vitro and in-situ. The technology enables applications from research to mass-scale in-vitro diagnostics (IVD) and precision diagnostics. APLEX Bio is based in Stockholm at the Karolinska Institute (KI) campus and is part of KI Innovations.


Umear Naseem, CEO and Founder, APLEX Bio

Maja Malmberg, Researcher at SEEC and Swedish University of Agricultural Sciences

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