SARS-CoV-2 variants’-Alpha, Delta, and Omicron D614G and P681R/H mutations impact virus entry, fusion, and infectivity

Abstract SARS-CoV-2 variants acquire mutations to survive within the host and evade immunity. In addition to harboring D614G mutation in spike domain, P681R/H mutation at the junction of the S1/S2 furin cleavage site, is found to be the key mutation in variants of concerns (VoC); Alpha, Delta, and Omicron (B.1.1.519). The impact of these acquired mutations on entry, transmissibility, and infectivity of SARS-CoV2 VoC is not clearly identified. Here, using the spike-based pseudovirus, Delta and D614G+P681R synthetic mutants showed a significant increase in the pseudovirus entry, fusion, and infectivity. In contrast, Omicron spike-based pseudovirus and a synthetic P681H mutant showed preferential hACE2-mediated virus entry over TMPRSS2, less fusion, and highly susceptible to Cathepsin L inhibitor. Taken together, these results indicate while the Delta variant utilizes both ACE2 and TMPRSS2 mediated entry, thus causing systemic infection; Omicron has favored growth in ACE2 expressed cells thus mainly replicating in the upper respiratory tract.