MRIGlobal improves the health and safety of people everywhere by addressing some of the world’s greatest threats and complex biological, chemical, and engineering challenges. Founded in 1944 as an independent, non-profit organization, MRIGlobal provides customized research and development services to health and defense-focused organizations in need of innovative and multidisciplinary solutions. This includes expertise in clinical research support, infectious disease and biological threat agent detection, global biological engagement, in vitro diagnostics, and laboratory management and operations. To learn more, visit mriglobal.org.
Biomeme® and MRIGlobal have a long history of working together to achieve decentralized lab solutions for providing comprehensive detection, diagnostics, and bio surveillance of emerging infectious diseases in low-resource, high-need locations.
MRIGlobal Validates Rapid, Accessible, and Portable SARS-CoV-2 Genotyping Panel using Biomeme’s Franklin® Platform
A recent publication pre-print*, Development, testing, and validation of a SARS-CoV-2 multiplex panel for detection of the five major variants of concern on a portable PCR platform, explores the recent collaboration between Biomeme and MRIGlobal on the process of creating a SARS-CoV-2 multiplex variant panel that can be used in almost any setting.
Genetic variants of SARS-CoV-2 have been emerging and circulating around the world throughout the COVID-19 pandemic. All viruses mutate and change, and SARS-CoV-2 is no different. The emergence of variants has created a need for increased genomic surveillance to monitor transmissibility, severity of disease, reduced effectiveness of treatment, and increase of hospitalizations in relation to the SARS-CoV-2 virus.
Based on the study data, these panels could be valuable tools to fill variant testing needs and serve as a screening test to inform selection/prioritization of samples for whole genome sequencing.
There are several distinct advantages to using SARS-CoV-2 variant genotyping assays as a screening tool.
- PCR is extremely less complex, cheaper, and faster compared to sequencing, meaning a PCR panel could be a better alternative for rapid identification and tracking of variants in comparison to sequencing every sample.
- A genotyping PCR panel could be very useful in resource-limited settings, since sequencing is not done at the same level in all locations/countries, and many laboratories do not have the infrastructure or expertise to perform sequencing.
- Obtaining whole genome sequence data from clinical samples is very much dependent on viral load; reported PCR Cq cutoffs for obtaining full-length genome sequences range from approximately 25-33. A PCR panel could fill this gap by providing genotype information for numerous samples that cannot be sequenced due to low viral load as reflected by high Cq values.
- A variant PCR panel can be used as an efficient and cost-effective screening assay to prioritize samples for sequencing, conserve resources, and minimize over/under-sampling of certain lineages for sequencing.
- Mutation-specific PCR amplification can be a more precise option than a proxy based on assay failure, such as the well-known S gene target failure (SGTF). Unlike SGTF, in which negative results are used as a proxy to indicate presence of variants like Alpha and Omicron BA.1, this variant PCR panel comprises specific assays that amplify only the mutant template and not the wild type. So variant detection is based on a positive PCR amplification of the presence of a variant in the sample.
- During the pandemic, multiple ‘discrete’ waves of variants emerged; hence, unique variant panels can be very useful to detect variants with no ambiguity when there are multiple variants in the community; the same is true for mixed infections.
- Wastewater testing is a good predictor of the impending community prevalence, in fact, a few days to a week in advance of community prevalence. But sequencing wastewater samples to monitor the spread of genotypes is problematic/difficult due to sample quality and the presence of many different strains/genotypes in the same sample, potentially at low titer, so a PCR panel that can detect variant markers would be ideal for wastewater monitoring.
Understanding the underlying variant of a SARS-CoV-2 infection in a timely manner can affect recommended treatments and provide important public health data to researchers. The rapid identification of prevalent variants without having to wait days to weeks for sequence data is an invaluable tool in the global, enduring fight against SARS-CoV-2.
This publication has also been featured in GenomeWeb. GenomeWeb is an independent online news organization the serves the global community of scientists, technology professionals, and executives who use and develop the latest advanced tools in molecular biology research and molecular diagnostics. Read the full article on GenomeWeb (Subscription Required.)
*Before formal publication in a scholarly journal, scientific and medical articles are traditionally certified by “peer review.” In this process, the journal’s editors take advice from various experts—called “referees”—who have assessed the paper and may identify weaknesses in its assumptions, methods, and conclusions. Typically, a journal will only publish an article once the editors are satisfied that the authors have addressed referees’ concerns and that the data presented support the conclusions drawn in the paper.
Because this process can be lengthy, authors use the medRxiv service to make their manuscripts available as “preprints” before certification by peer review, allowing other scientists to see, discuss, and comment on the findings immediately