New Real-time PCR kit for the qualitative detection of RNA from genetic mutations in the S gene (P681R, L452R and E484Q) in positive SARS-CoV-2 respiratory samples.

Despite the slow evolutionary rate of SARS-CoV-2 relative to other RNA viruses, its massive and rapid transmission during the COVID-19 pandemic has enabled it to acquire significant genetic diversity since it first entered the human population. This led to the emergence of numerous variants, some of them recently being labeled “variants of concern” (VOC), due to their potential impact on transmission, morbidity/mortality, and the evasion of neutralization by antibodies elicited by infection, vaccination, or therapeutic application. However, the importance of variants (classification as variants of interest (VOI) or variants of concern (VOC)) may differ by location.

As of June 2021, more than 60 countries reported cases caused by a newly recognized variant, the lineage B.1.617 which was first detected in December 2020 in India. The emerging variant B.1.617 comprises distinct sublineages. The sublineage B.1.617.2 or Delta is associated with greater public health risk and is internationally recognized as VOC. B.1.617.2 is characterized by spike mutations T19R, G142D, Δ157-158, L452R, T478K, D614G, P681R, and D950N. The sublineage B.1.617.1 has been reclassified to a VOI (variant Kappa), and while it is still demonstrating increased transmissibility, global prevalence appears to be declining. B.1.617.1 is defined by the spike amino acid changes G142D, E154K, L452R, E484Q, D614G, P681R, and Q1071H. The impact on the immune escape capacity of B.1.617 sublineages is expected, owing to RBD mutations L452R, T478K, and E484Q and their combination with NTD mutations and deletions, particularly in the case of B.1.617.2.

In January 2021, the emergence of a novel variant in California carrying an L452R mutation in the RBD was reported. This variant (Epsilon) comprises two separate lineages B.1.427 and B.1.429, the first carrying two spike mutations (L452R, D614G) and the second carrying four (S13I, W152C, L452R, D614G). In California they reached prevalence of more than 50% as of February 2021 and they are recognized as VOC in the US and as VOI Epsilon by WHO. These lineages were shown to display moderate resistance to neutralization by convalescent sera and sera of vaccine recipients. The mechanism of RBD structural change due to L452R is offered in explanation of the reduced neutralization capacity of antibodies. The sub-lineage