In silico analysis – Sequences containing lineage-defining mutations were obtained from GISAID for in silico analysis by customized application of the NextClade tool () to compare individual assay target sequences for Abbott ID NOW COVID-19, m2000 RealTi me SARS-CoV-2, Alinity m SARS-CoV-2, and Alinity m Resp-4-Plex molecular assays the BinaxNOW COVID-19 Ag Card and Panbio COVID-19 Ag Rapid Test Device and the ARCHITECT/Alinity i SARS-CoV-2 IgG and AdviseDx IgM assays, Panbio COVID-19 IgG assay, and ARCHITECT/Alinity i AdviseDx SARS-CoV-2 IgG II assay. With diagnostic tests designed to target viral regions that are expected to be well conserved, continued evaluation of those assumptions by sequence analysis and specimen testing is critical to ensure that diagnostic tests continue to keep pace with viral evolution throughout the SARS-CoV-2 pandemic. While spike gene mutations are key hallmarks of VOC/VOI lineages, the presence of additional mutations throughout other regions of the genome warrant further examination for potential impact on diagnostic assay performance. Additional lineages have been identified as variants of interest (VOI) or under the ‘monitoring’ category by the World Health Organization (WHO) due to the presence of identical or similar mutations present in VOCs and increasing prevalence. Similarly, the B.1.617.2 lineage first identified in India has been shown to be less susceptible to neutralizing antibodies and is linked to the highest transmissibility increases worldwide, likely due to the presence of L452R and P681R mutations in the spike protein. The P.1 variant contains similar mutations in the spike gene as the B.1.1.7 and B.1.351 variants, suggesting a convergence of SARS-CoV-2 spike mutations that may increase transmissibility and risk of re-infection. The P.1 variant was first reported in Japan as a branch of the B.1.128 lineage, but was subsequently traced back to Brazil. The B.1.351 lineage was first identified in South Africa and has since spread globally, with several reports indicating that this variant can escape neutralizing antibodies. The B.1.1.7 lineage was first identified in the United Kingdom and carries spike mutations that have been linked to increased transmissibility, including N501Y. To meet this challenge, the Abbott Global Surveillance program has been tracking the sequences of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) variants that have emerged throughout the pandemic, including variant of concern (VOC) lineages that have spread globally: B.1.1.7 (alpha), B.1.351 (beta), P.1 (gamma), and B.1.617.2 (delta). While assay design can mitigate the impact of viral diversity, assay performance must be continually monitored through variant testing and molecular surveillance. As viruses continue to evolve, diagnostic tests must keep pace to ensure accurate detection of all circulating variants.

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