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

March 22, 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 to review new mutations and to determine if these variants affect the performance of 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 table below summarizes SARS-CoV-2 variant strains identified to date and the impact, if any, on the ePlex RP2 Panel based on bioinformatic analysis.^1-5

• This list will be updated as new strain 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 and mutations that are 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.

Analysis of more than 150,500 complete genome sequences of SARS-CoV-2 submitted to GISAID between February 1, 2021 and March 10, 2021 identified only 3 sequences in this dataset predicted to be missed by both of the N gene assays resulting in a combined inclusivity of the 2 N gene assays on the ePlex RP2 Panel of 99.99%.

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

1. Centers for Disease Control and Prevention. Emerging SARS-CoV-2 Variants. https://www.cdc.gov/coronavirus/2019-ncov/more/science-and-research/scientific-brief-emerging-variants.html (accessed March 2021)
2. Centers for Disease Control and Prevention. SARS-CoV-2 Variant classifications and definitions. https://www.cdc.gov/coronavirus/2019-ncov/cases-updates/variant-surveillance/variant-info.html (accessed March 2021)
3. Public Health England. Variants: distribution of cases data. https://www.gov.uk/government/publications/covid-19-variants-genomically-confirmed-case-numbers/variants-distribution-of-cases-data (date accessed March 2021)
4. European Centre for Disease Prevention and Control. January 21, 2021. Risk Related to Spread of New SARS-CoV-2 Variants of Concern in the EU/EEA- first update.
5. Tu, H. et al. (2021) Distinct patterns of emergence of SARS-CoV-2 spike variants including N501Y in clinical samples in Columbus Ohio. bioRxiv 2021.01.12.426407; doi: https://doi.org/10.1101/2021.01.12.426407