BREAKING! Harvard Led Study Uncovers How Delta Variant's Spike Mutations Causes Cell Membrane Fusion And Evades Immunity
A new study led by researchers from Harvard’s Boston Children’s Hospital, Harvard Institutes of Medicine, Brigham and Women’s Hospital, Ragon Institute of MGH-MIT, and Harvard Medical School along with support from Codex BioSolutions, Inc-Maryland and Georgetown University School of Medicine-Washington has uncovered the mechanisms by which the Delta variant’s spike mutations causes cell membrane fusion and evades immunity.
The Delta variant of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has outcompeted previously prevalent variants and become a dominant strain worldwide.
The study team in the findings, report the structure, function and antigenicity of its full-length spike (S) trimer in comparison with those of other variants, including Gamma, Kappa, and previously characterized Alpha and Beta.
The study found that the Delta spike proteins can fuse membranes more efficiently at low levels of cellular receptor ACE2 and its pseudotyped viruses infect target cells substantially faster than all other variants tested, possibly accounting for its heightened transmissibility. Mutations of each variant rearrange the antigenic surface of the N-terminal domain of the S protein in a unique way, but only cause local changes in the receptor-binding domain, consistent with greater resistance particular to neutralizing antibodies. These results advance the molecular understanding of distinct properties of these viruses and may guide intervention strategies.
The study findings were published on a preprint server and are currently being peer reviewed. https://www.biorxiv.org/content/10.1101/2021.08.17.456689v1
The study findings show how the Delta variant of the novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) achieved higher transmissibility and resistance to neutralization.
The ongoing COVID-19) pandemic was triggered by the emergence of the SARS-CoV-2 coronavirus. Despite advances in its management, new variants keep emerging, often showing partial resistance to pre-existing antibodies elicited by vaccines or natural infection.
The variant that is current wreaking havoc globally ie the Delta variant B.1.617.2
is a variant of the virus that emerged first in India but has rapidly spread and become dominant over the course of a few months. It is a variant of concern (VOC) because it has twice the transmissibility potential of the reference Wuhan strain.
Initial research suggests that it has a shorter incubation period, while the viral load is a thousand times greater compared to that achieved by earlier lineages. It has caused breakthrough infections after full vaccination. This makes it important to understand the underlying mechanisms that make it so different so that appropriate intervention strategies can be developed. https://www.medrxiv.org/content/10.1101/2021.07.07.21260122v1
Basically the virus spike is a surface envelope glycoprotein that mediates the attachment and entry of the virus into the host cell. Found in nature as a trimer, it binds to the viral receptor angiotensin-converting enzyme 2 (ACE2).
It should be noted that the spike has two domains, the S1 and S2, which mediates receptor engagement and membrane fusion, respectively. Cleavage into these two fragments is with the help of a host furin-like protease. Receptor binding is followed by spike cleavage via the host enzyme TMPRSS2, or cathepsins B and L. This causes the S1 domain to fall away, while S2 undergoes a cascade of events that causes the virus to fuse to the cell membrane and adjacent cell membranes to fuse together.These promote viral entry into the cell as well as propagation of the infection to neighboring cells via syncytia formation.
Importantly the S1 domain has an NTD (N-terminal domain), RBD (receptor-binding domain), and two CTDs (C-terminal domains), all surrounding a bundle of helices that comprises the prefusion S2 domain. The RBDs may be in the ‘up’ or ‘down’ conformation, when it is accessible for receptor binding or not, respectively. It is this movement at the RBD prevents the host immune response from targeting this functionally important site on the virus.
The study team found that the Delta spike fuses the membranes of adjacent cells more efficiently, increasing over time. When replicated using a pseudovirus with an engineered spike that promotes incorporation into viral particles, the Delta variant was observed to infect the cells much faster than any other variant, over one hour.
It was found that all variants reached their maximum level of infection over eight hours. Comparing the Gamma, Kappa and Delta spike variants, the study team found the prefusion spike trimer made up <40% of the whole, for the Gamma spike, with inefficient spike cleavage by furin.
However, in contrast, the Delta variant formed a single prefusion spike peak, indicating that it is very stable in the cleaved S1/S2 complex state, similar to the G614 and beta spike variants.
The team also found that receptor binding was stronger for the Gamma spike relative to G614 because of the K417T, E484K and N501Y mutations in the RBD.
The Delta variant however had an intermediate affinity, perhaps because receptor binding causes the S1 subunit to dissociate, especially with dimeric ACE2. However, spike dissociation from the receptor was comparable for all three variants.
The study findings also showed that the G614 trimer bound to antibodies in convalescent plasma directed against the spike protein, either the NTD or the RBD, but the Gamma mutant did not bind to the RBD antibodies and one of the NTD antibodies. For the other NTD antibody, it had reduced affinity.
In the case of the Delta variant, it was found that it did not bind the NTD antibodies, but retained binding to the others. Binding affinity was related to the neutralization capacity for almost all antibodies. The mutations affected sensitivity to antibody-mediated neutralization for the Gamma variant more than the Delta.
The detailed cryo-electron microscopic structures of the spike trimers were examined, showing no major structural changes have occurred in the different variants compared to the G614 parent. The Delta trimer is the most stable among the spike variants, while the Gamma prefusion trimeric spike tends to dissociate.
However when the Delta spike trimer was superposed onto the G614 parent trimer in the closed RBD conformation, focusing on the S2 region, the differences were most apparent in the NTD, with its three mutations and one two-residue deletion.
Also when the NTDs are aligned, the loop between residues 143-154 is seen to take on a different shape. This makes it face away from the virus membrane.
Surprisingly, the mutations simultaneously reshape the N-terminal segment and another loop between residues 173-187. This changes the shape of the antigen at the NTD-1 group of epitopes in the NTD.
The team said that such changes help explain why NTD-1 antibodies fail to bind and neutralize the Delta variant as efficiently. Meanwhile, the two Delta RBD mutations L452R and T478K fail to cause structural changes and are not on the ACE2 interface. They do not make up part of a neutralizing epitope either, as they do not alter either binding or neutralization.
Also it was suggested that another mutation ie the S2 D950N mutation, may change the local electrostatic state.
Researchers have been seeking explanations for the increased transmissibility of the Delta variant over the Alpha VOC, itself much more infectious than the Wuhan strain.
The team says that it is possible that the viral replication process for the Delta variant is itself the subject of unique mutations that speed up genomic replication.
Also many other steps are also key to assembling viral particles. However, to explain how the viral load in the infected cell is a thousand times higher for this variant. While ACE2 binding by this variant is comparable to that of earlier variants, and spike cleavage remains similar, the current study reveals two other factors that may contribute to its unusual speed of transmission and propagation.
One factor is the increased fusion efficiency with high Delta spike expression on the cell surface even when the ACE2 levels are low, compared to any other variant. Secondly, the fusion step is optimized to allow entry into the cell even at low ACE2 levels.
The study team says that this optimization may explain why the Delta variant can transmit upon relatively brief exposure and infect many more host cells rapidly, leading to a short incubation period and greater viral load during the infection.”
More detailed studies will be required to confirm this, using authentic viruses rather than the spike trimer or RBD construct used in this experiment.
It should be also note that structural changes appear inadequate to explain the increased fusogenicity. The D950N mutation, found only in the Delta variant, removes one negative charge from each of the protomers in the trimeric spike. Its location near a possible control unit of the spike protein may destabilize the prefusion S2 subunit by electrostatic mechanisms.
However such loss of stability cannot be too great, as it could cause the spike trimer to change its conformation too soon and thus become inactive before membrane fusion occurs.
Interestingly although the RBD conserves its structure and function among all variants, with mutations occurring at only a few specific sites, the NTD seems to allow rearrangement of its surface loops, central Beta-strands and a few N-linked glycans while retaining infectivity but evading the host immune response.
The key findings from this study are that therapeutic antibodies should avoid targeting the NTD as it is easily able to evade them. New-generation vaccines will depend on such studies of structure, antigenicity and function to choose the most effective antigens that elicit antibodies against the most highly conserved epitopes.
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