Detection of variant SARS-CoV-2 strains on the ePlex^® RP2 Panel^*

August 3, 2021

Genetic surveillance of SARS-CoV-2 strains circulating globally has identified multiple variants containing one or more mutations that can potentially impact detection by nucleic acid-based testing methods. These variants can also impact behavior of the virus, such as making a virus more or less transmissible or capable of causing more severe illness. Health organizations around the world are closely monitoring the circulation of these known variants and are also working to identify any additional variants that arise.

The ePlex Respiratory Pathogen Panel 2 (RP2 Panel) targets 2 unique regions of the N (nucleoprotein) gene. The GenMark bioinformatics team performs regular sequence analysis of available SARS-CoV-2 strains in GISAID database to monitor for mutations in the N gene regions targeted by the ePlex RP2 Panel SARS-CoV-2 assays. Mutations in other regions of the genome, such as the spike protein or envelope protein, have no impact on the performance of the SARS-CoV-2 assays on the ePlex RP2 Panel.

The bioinformatic assessment includes expected performance of both the N1 and N2 SARS-CoV-2 assays for any mutation located within the gene regions targeted by the two assays. Predicted inclusivity is provided for each of the N1 and N2 assays, as well as the overall inclusivity of both the N1 and N2 assays combined.

Since October 2020, bioinformatics analysis of over 2,448,000 sequences predicts overall inclusivity of the two N gene assays on the ePlex RP2 Panel of 99.99% and has identified only 50 sequences (0.002%) that have mutations within both the N1 and N2 gene regions targeted by the ePlex RP2 Panel and may not be detected based on this assessment.

The table below summarizes known SARS-CoV-2 variant strains and the impact, if any, on the ePlex RP2 Panel based on bioinformatic analysis.

•  This list will be updated as new information becomes available.
• This list is not intended to be a comprehensive list of all variants or mutations identified; it includes the most prevalent variants in circulation believed to be clinically significant.
• For the most up to date information on specific mutations identified in each strain and prevalence, please refer to your regional health authorities.

*For use under the Emergency Use Authorization (EUA) only. For in vitro diagnostic use.

1 Analysis of Alpha (B.1.1.7) based on assessment of >62,500 sequences in GISAID as of February 10, 2021.
2 Analysis of Beta (B.1.351) based on assessment of ~1,200 sequences in GISAID as of February 10, 2021.
3 Analysis of Gamma (P.1) and Zeta (P.2) based on assessment of >400 sequences in GISAID as of February 10, 2021.
4 Analysis of Kappa (B.1.617.1) and Delta (B.1.617.2) based on assessment of >4,500 sequences in GISAID as of May 12, 2021.
5 Analysis of Epsilon (B.1.427/B.1.429) based on assessment of ~8,700 sequences submitted to GISAID between February 1, 2021 and March 10, 2020.
6 Analysis of Eta (B.1.525) based on assessment of ~500 sequences submitted to GISAID between February 1, 2021 and March 10, 2020.
7 Analysis of Theta (P.3) based on assessment of >100 sequences in GISAID as of April 13, 2021.
8 Analysis of Iota (B.1.526) based on assessment of >2,000 sequences submitted to GIASAID between February 1, 2021 and March 10, 2020.
9 Analysis of Lambda C.37 based on assessment of ~3,400 sequences in GISAID as of July 23, 2021.
10 Analysis of A.23.1 with E484K based on assessment of >40 sequences in GISAID as of February 8, 2021.
11 Analysis of B.1.616 based on assessment of 23 sequences in GISAID as of April 13, 2021.
12 Analysis of A.27 based on assessment of 288 sequences in GISAID as of April 13, 2021.