Case Study: COVID-19 Variant Surveillance as Part of the NIH RADx Program

Case Study:
COVID-19 Variant Surveillance as Part of the NIH RADx Program

March 21, 2023

Challenge:

Public health organizations have been employing a range of techniques to detect and characterize new mutations of the SARS-CoV2 virus. This valuable information is used to update all stakeholders on any new variants that could potentially be highly transmissible or increase the risk of severe illness. Furthermore, close attention has been paid to specific variants of concern that exhibit unusual patterns of infection.

The Variant Task Force as part of the National Institutes of Health (NIH) Rapid Acceleration of Diagnostics (RADx®) Tech program was formed to track infection rates and patterns. The primary objective of the Variant Task Force was to accelerate the development, commercialization, and deployment of testing technologies that were effective for monitoring emerging new SARS-CoV2 variants before virome sequencing data became available in diverse geographic regions.

A feasible and efficient way to identify and monitor SARS-CoV2 variants as the virus mutates within the US population was needed. This capability would allow public health officials to strategize and focus on preventative and treatment measures as quickly as possible, as new variants infect the population, thus establishing robust public health responses.

Approach:

To monitor the rapidly occurring COVID-19 variants, the NIH selected partners capable of sourcing samples from diverse geographic locations, such as Ovation and its Ovation Research Network (ORN). Many labs in the ORN were specifically established to handle the influx of molecular diagnostic testing during the pandemic, making them an excellent fit for the project. Additionally, the Ovation data provides a diverse array of patients from various racial and ethnic backgrounds, which is also critical for effective surveillance.

“Ovation’s data were instrumental in accessing COVID variant genotyping in order to monitor mutations and changes in variant prevalence quickly. This also allowed us to provide a comprehensive picture of the nationwide distribution of the virus as it mutates in real time.” – Eric Lai, Managing Partner for Pharma-Dx on the NIH RADx Tech Project

Ovation utilized quantitative real-time PCR (qPCR) to monitor up to four different COVID-19 genotypes at a time, enabling detection of the virus at low concentrations in samples. In addition, Ovation collected structured data such as state-level location, date of collection, and date of assay. The results of these assays were contributed to the Rosalind Tracker, a free public dashboard that reports regional positivity rates and percentage of each variant in circulation. These results were also compared to other public data sources, including the GISAID and CDC databases. This approach has demonstrated the efficacy and speed of genotyping as part of the surveillance framework.

Results:

Through the program, mutations were detected and assays were designed and quickly deployed to participating labs, sometimes as often as every 2 weeks. In February 2023, the NIH published their learnings from their response to COVID in Science, emphasizing the importance of including recent variants in testing protocols and streamlining diagnostic testing. Ovation is proud to have contributed to the rapid response efforts in the global pandemic of COVID-19

Resources:

You can find our COVID dataset on AWS Data Exchange

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