Cellgenmedix’s highly sensitive COVID-19 delta variant /Variant of Interest RT-PCR test assay meets innovative app from Elevation studios in a new surveillance program

In a new project, Cellgenmedix and Elevation Studios teamed up to detect new SARS-CoV-2 variants. The partnership leveraged Cellgenmedix’s expertise in molecular studies and Elevation Studios’s software chops to make the first COVID_19 variant minisequencing/RNA microarray test-based app for tracking viral evolution.

Since COVID-19 was declared a pandemic more than one year ago, RT-PCR has been the go-to method for detecting SARS-CoV-2 infection because it offers high sensitivity for a relatively low cost. However, the continued emergence of variants like those originating from the UK (Alpha, B.1.1.7), South Africa (Beta, B.1.351), India (Delta, B.1.617.2.) and Brazil (Gamma, P.1) threatens to make diagnostic tests more prone to failure.

RT-PCR tests that form the backbone of the current global COVID-19 response rely on primer sequences that exactly match target SARS-CoV-2 sequences, which continue to change as the virus evolves.

Recognizing the potential issue with RT-PCR-based tests, Cellgenmedix and Elevation Studios came up with a joint solution: a RT-PCR/minisequencing/RNA microarray software platform capable of identifying the novel SARS-CoV-2 and any present or future novel variants coupled with a surveillance app that is a cross between Wikipedia and Citizen app.

 

strategy

Good Gene’s COVID strategy

Case numbers outpace surveillance efforts

Efforts to track the evolution of SARS-CoV-2 have lagged far behind case numbers, but are improving. At the time of writing, the US has hit its weekly goal of 7000 positive samples sequenced for seven straight weeks, accounting for around 11% of the weekly moving average case number.

Simply, detecting SARS-CoV-2 is cheap. But detecting SARS-CoV-2 variants? That’s much more expensive.

There are essentially four ways to detect SARS-CoV-2 variants. One uses “shotgun” metagenomics using Next Generation Sequencing (NGS) to sequence all the genetic material found in a clinical sample – viral and human. While comprehensive, the sequencing of the human genetic material is costly and unnecessary. It also requires that the sample is sequenced to a higher depth for accurate detection, given the viral genetic material is a very small proportion of the total sample.

There are 3 more targeted approaches to detect SARS-CoV-2 variants. PCR amplification to enrich for target sequences (SARS-CoV-2 genomes) that are then sequencing by “simple” sequencing is an option. And there are variant RT-PCR tests and hybridization capture probes as well as our DNA chip (microarray). The SNaPshot® Multiplex System is a primer extension-based method developed for the analysis of point mutations and single nucleotide polymorphisms. Through its multiplexing capability, up to 10 loci can be analyzed in a single reaction, regardless of their positions on the chromosome or the amount of separation from neighboring ‘hot spot’ loci.

While both targeted NGS sequencing approaches enable viral evolution tracking at lower depths of sequencing (and therefore lower cost), SNAPSHOT offers a clear advantage: SNAPSHOT can save time and money and is easy to use. This allows the assay to remain robust in the face of continual viral evolution.

Cellgenmedix’s VOC RT-PCR test and SNAPSHOT for SARS-CoV-2 variant testing has 8 probes targeting different regions of the viral genome, and has the capacity to detect all the variants of concern and interest in a very cost-effective format. Probes for each new loci is guaranteed to be developed within 2 weeks.

Cellgenmedix & Elevation Studios partner for the new SARS-CoV-2 Variant Assay
To devise robust hybrid capture reagents for targeted sequencing of SARS-CoV-2 genomes, Cellgenmedix and Elevation Studios played to their strengths: Cellgenmedix employed its molecular microbiology technology, and Elevation Studios on its software expertise. The targeted sequencing in addition to surveillance app approach developed by Cellgenmedix and Elevation Studios could bolster ongoing efforts to reduce the morbidity and mortality associated with COVID-19 by making it easier to discover and track newer and more dangerous variants. That said, better epidemiologic strategies are still needed and to encourage COVID-19 vacccination.

Combining minisequencing /chip/RT-PCR with Elevation Studios analysis software, we are developing ELEVATION app. We aim to elevate health care by building a platform in which HIPAA protected information of variant testing may be automatically and manually uploaded. We have built a platform in which people may exchange HIPAA compliant health information that are vital for COVID-19 control and new variants that come out. In practical use, it can aid in finding vaccination rates around you or variants that are around you that are vaccine / treatment resistant or that may not be detected by conventional testing methods. This could help you and your loved ones stay safe. This can offer insight into the progression of the COVID-19 pandemic.

In summary, despite over a year of research, we as a global community still have much to learn about control and surveillance of COVID-19 variants. The tools developed by Cellgenmedix and Elevation Studios will help facilitate this learning process and inform the global coronavirus response.