Enya Qing

Yes a personal favorite of papers! It confirmed with structure many of our conclusions (without structure), less about the exact location of the fusion peptide, but more about the sequence of appearance of the fusion intermediate steps!

Hey if you are at #ASV2025 this year feel free to stop by to chat! I won’t get to say much at my Flash Talk (below), but will have tons of time pacing by my poster (P24-94) that same evening! 😁😁😁

lol but honestly Ryan thanks for all your work, stringing different findings together to reveal holistic insights! 🫡🫡🫡

Antibody escape drives emergence of diverse spike haplotypes resembling variants of concern in persistent SARS-CoV-2 infections Evolution of SARS-CoV-2 in long-term persistent infections is hypothesised to be a major source of variants of concern (VOC). However, the linkage of intra-host variants into haplotypes that reflect v...

New preprint from Luke Snell from GSTT, Suzanne Pickering in my lab and Rui Galao, my colleague at KCL.

Here we examine in detail the evolution of the SARS CoV-2 spike in persistent infections, and essentially catch a potential variant in the act of developing. 1/n

www.biorxiv.org/content/10.1...

The final version of our paper on #SARSCoV2 Spike H655Y vs. Stem-helix Antibody! I really recommend reading our reader-friendly🫡Discussion section, where we explained in detail the implications of our findings on CoV entry, antibody neutralization, and viral evolution!

In SARS-2 evolution, amino acid (AA) mutations get the lion’s share of attention—& rightfully so, as noncoding & synonymous nucleotide muts—which cause no AA change‚ are mostly inconsequential. But there are many exceptions, including a possible new one I find intriguing. 1/32

We thank #everyone (lol) involved, for we could not have done it without these efforts, and this includes you as well, anonymous reviewers!

Top: The S "extended intermediate" - stabilizing H655Y also widens the effective window for neutralization by stem-helix antibodies. Bottom: It is likely the case that, S only fully exposes its stem-helix antibody epitopes while in the "extended intermediate" conformation. Fully exposed epitopes then facilitates the maximum number of stem-helix antibody binding, which is likely a requirement for efficient viral neutralization.

What about stem-helix antibody mechanism? Because H655Y-stabilized S “extended intermediate” also prolonged the effective time window of stem-helix antibodies, their binding epitopes must only be fully exposed in this S conformation, and required for effective neutralization! 9/9

SARS-CoV-2 with a slower fusing S (i.e. H655Y) may enable more viruses move to the main cell body of human nasal epithelial cells. Cell entry at the cell body may be more likely result in productive infections than if entry happens on the cilia.

How could a SLOWER entry benefit SARS-CoV-2? The key may be on the ciliated nasal epithelial cells, where slowing could enable more viral entry on not the cilia but the cell body for more productive infections. The same delay can show up in cell cultures as “endosomal entry”. 8/9

In conclusion, S cap must still be present for S “extended intermediate” formation, where H655Y affects its durability. While H655Y delays #SARSCoV2 entry kinetics at a late stage, Omicron BA.1 compensates likely by acquiring a higher binding affinity for receptor hACE2. 7/9

Top: H655Y widens the effective window for HR2 to neutralize S, suggesting that H655Y stabilizes the "extended intermediate" S structure. Bottom: While H655Y does slow down the process of membrane fusion (left), the overall viral entry time of Omicron is comparable to ancestor virus because of a higher-affinity receptor binding domain (S1B) (right).

Mechanistically, H655Y stabilized the “extended intermediate” S, prolonging the time HR2 peptides can bind to its transiently exposed S epitope, actually delaying the total time needed for entry. Interestingly, tighter hACE2-binding BA.1 S1B (RBD) compensated for this delay. 6/9

H655Y sensitizes SARS-CoV-2 S for neutralization by HR2 peptides, which only binds to a late-stage, transient S conformation called "extended intermediate".

because H655 is part of the S cap believed to be shed early on, hence should not affect S functions past S2’ activation. Contrary to this belief, H655Y sensitized S for HR2 peptides, a conformation-specific inhibitor for the downstream “extended intermediate” S structure. 5/9

H655Y does not affect stem-helix antibodies binding to S in its prefusion conformation.

H655 is more than 5 nm away from the stem-helix antibody binding site, making it unlikely to be directly affecting antibody binding. We confirmed this using a newly developed virion binding system. So, H655Y must be affecting a late entry step, but this shouldn’t make sense, 4/9

Pan-Omicron mutation H655Y sensitizes SARS-CoV-2 S for neutralization by stem-helix antibodies.

Hoping for insights, we next looked for natural adaptations that affected stem-helix antibody neutralization. Paradoxical to strong antibody selections for S adaptations, Omicron BA.1 S had become more sensitive to these antibodies, and it traced to, surprise surprise, H655Y! 3/9

Stem-helix antibodies do not affect S2' proteolytic activation.

…by ACCIDENT! We were testing stem-helix antibodies, cool because they cross-neutralize βCoVs by binding to not the variable receptor-binding S cap, but the conserved S stalk. We first saw that they also didn’t affect S2’ proteolytic activation, a crucial step for #coronavirus entry. 2/9

SARS-CoV-2 Omicron variations reveal mechanisms controlling cell entry dynamics and antibody neutralization Author summary Most adaptive mutations endowing SARS-CoV-2 with increased human transmissibility and infectivity alter viral spike (S) protein structure and function. Orchestrated structural transitio...

New paper from us! 🤩Remember #Omicron S:H655Y mutation that shifted #SARSCoV2 to endosomal entry in cell lines? H655Y lost favor because endosomal entry was not observed in primary nasal cells or animals. Here we found the actual mechanism of H655Y… 1/9
doi.org/10.1371/jour...

Cannot agree more! 😁

Haha thanks! I’m still new on this platform…😅

Sialoglycan binding triggers spike opening in a human coronavirus - Nature Binding of a sialoglycan-based primary receptor by the spike protein of the common cold human coronavirus HKU1 triggers conformational changes to a state that would allow binding to a second receptor ...

Our latest #virology research is now online at Nature 🎉

Using #cryoEM and MD simulations, we show how a sugar-based receptor can trigger opening of a coronavirus spike protein through an allosteric mechanism 🍬

www.nature.com/articles/s41...