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. 2021 Sep 29:2:286-290.
doi: 10.1109/OJEMB.2021.3116490. eCollection 2021.

RADx Variant Task Force Program for Assessing the Impact of Variants on SARS-CoV-2 Molecular and Antigen Tests

Richard Creager  1 , John Blackwood  2 , Thomas Pribyl  3 , Leda Bassit  4 , Anuradha Rao  4 , Morgan Greenleaf  4 , Filipp Frank  4 , Wilbur Lam  4   5 , Eric Ortlund  4 , Raymond Schinazi  4 , Alexander Greninger  6   7 , Mia Cirrincione  2 , Dale Gort  8 , Emily Kennedy  9 , Adam Samuta  2 , Megan Shaw  10 , Brian Walsh  11 , Eric Lai  12
Affiliations

RADx Variant Task Force Program for Assessing the Impact of Variants on SARS-CoV-2 Molecular and Antigen Tests

Richard Creager et al. IEEE Open J Eng Med Biol. .

Abstract

Goal: Monitoring the genetic diversity and emerging mutations of SARS-CoV-2 is crucial for understanding the evolution of the virus and assuring the performance of diagnostic tests, vaccines, and therapies against COVID-19. SARS-CoV-2 is still adapting to humans and, as illustrated by B.1.1.7 (Alpha) and B.1.617.2 (Delta), lineage dynamics are fluid, and strain prevalence may change radically in a matter of months. The National Institutes of Health's Rapid Acceleration of Diagnostics (RADxSM) initiative created a Variant Task Force to assess the impact of emerging SARS-CoV-2 variants on in vitro diagnostic testing. Working in tandem with clinical laboratories, the FDA, and the CDC, the Variant Task Force uses both in silico modeling and in vitro testing to determine the effect of SARS-CoV-2 mutations on diagnostic molecular and antigen tests. Here, we offer an overview of the approach and activities of the RADx Variant Task Force to ensure test performance against emerging SARS-CoV-2 lineages.

Keywords: COVID-19; SARS-CoV-2; in vitro diagnostics; mutations; variants of concern.

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Figures

Fig. 1.
Fig. 1.
ROSALIND Diagnostic Monitoring (DxM) system. ROSALIND DxM automatically imports sequences from U.S. and global databases. NAAT developers upload primer and probe sequences, and antigen test developers upload target epitopes. ROSALIND DxM automatically assesses each test design against all available sequences and assigns a severity (NAAT) or risk score (antigen tests) based on the potential impact of emerging SARS-CoV-2 variants on diagnostic performance. Results of in vitro testing are fed back into ROSALIND to improve scoring algorithms.
Fig. 2.
Fig. 2.
ROSALIND DxM incident detail. Example ROSALIND incident showing a mutation with a three base pair SNP in the middle of a primer resulting in a 11.8°C reduction in melting temperature and two amino acid changes.
Fig. 3.
Fig. 3.
Seven-day rolling average percent of S:D614G-positive sequences worldwide (left) and in the United States (right). Image courtesy of outbreak.info .
See this image and copyright information in PMC

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