Intrinsic D614G and P681R/H mutations in SARS-CoV-2 VoCs Alpha, Delta, Omicron and viruses with D614G plus key signature mutations in spike protein alters fusogenicity and infectivity

Abstract

The SARS-CoV-2 virus has been rapidly evolving over the time and the genetic variation has led to the generation of Variants of Concerns (VoC), which have shown increased fitness. These VoC viruses contain the key mutations in the spike protein which have allowed better survival and evasion of host defense mechanisms. The D614G mutation in the spike domain is found in the majority of VoC; additionally, the P681R/H mutation at the S1/S2 furin cleavage site junction is also found to be highly conserved in major VoCs; Alpha, Delta, Omicron, and its’ current variants. The impact of these genetic alterations of the SARS-CoV-2 VoCs on the host cell entry, transmissibility, and infectivity has not been clearly identified. In our study, Delta and D614G + P681R synthetic double mutant pseudoviruses showed a significant increase in the cell entry, cell-to-cell fusion and infectivity. In contrast, the Omicron and P681H synthetic single mutant pseudoviruses showed TMPRSS2 independent cell entry, less fusion and infectivity as compared to Delta and D614G + P681R double mutants. Addition of exogenous trypsin further enhanced fusion in Delta viruses as compared to Omicron. Furthermore, Delta viruses showed susceptibility to both E64d and Camostat mesylate inhibitors suggesting, that the Delta virus could exploit both endosomal and TMPRSS2 dependent entry pathways as compared to the Omicron virus. Taken together, these results indicate that the D614G and P681R/H mutations in the spike protein are pivotal which might be favoring the VoC replication in different host compartments, and thus allowing a balance of mutation vs selection for better long-term adaptation.

In vitrocomparison of SARS-CoV-2 variants

“…Omicron and WT viral titers in the supernatants of Calu3/hACE2 cells were significantly higher than delta. Cell lysates of Calu3/hACE2 have shown higher viral titers for delta compared to omicron (33), suggesting altered viral release of delta from Calu3/hACE2. Similarly, in A549, no CPE was observed at day 5 post-infection for all three variants, with minimal viral release observed for WT and omicron (Fig.…”

A Nomogram for Predicting Delayed Viral Shedding in Non-Severe SARS-CoV-2 Omicron Infection

“…In this work, we found that individuals over the age of 68 are at an increased risk for extended viral shedding of the SARS-CoV-2 Omicron strain, which might be attributed to age-related changes in the immune system, such as decreased production of type I interferon, which in turn leads to an imbalance between M1 and M2 macrophages and impair natural killer cell activity, resulting in reduced virus clearance. 28 According to an in vitro study, the Omicron virus can efficiently replicate to high titers in Angiotensin-converting enzyme 2 (ACE2) receptor-overexpressed cell lines, 29 and the upregulation of ACE2 receptors in respiratory tract of elderly people may allow for more rapid virus replication. 30 , 31 Furthermore, older individuals may have a lower tolerance for increased inflammation and pro-inflammatory cytokine production, which can result in cytokine storms.…”

Blood-brain barrier function in response to SARS-CoV-2 and its spike protein

“…For example, the D614G and P681R/H mutations in the S-protein increase the transmission and infectivity of the virus due to the increased affinity of the S1 subunit to the ACE receptor [84]. Remarkably, certain VOCs with a higher virulence can eliminate from circulation less pathogenic variants.…”