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Qu, K.

Publications and source records attributed to Qu, K..

At least 19 recordsLinked to original sources

A lifespan-scale single-cell atlas defines an early-childhood immunometabolic transition linked to age-referenced immune states

Childhood represents a critical period with rapid metabolic and immune remodeling, during which perturbations may have lasting consequences for health. We integrated single-cell RNA sequencing (scRNA-seq) profiles of peripheral blood mononuclear cells (PBMCs) from 2,008 healthy individuals aged 0-100 years. Age-resolved modeling highlighted an early-childhood transition centered at age 6, characterized by coordinated remodeling of metabolism-related transcriptional programs, particularly in monocyte and B-lineage cells. Matched serum metabolomics and lipidomics in a pediatric subcohort detected a temporally concordant wave of metabolite and lipid changes around ages 6-8 and extensive metabolite/lipid-transcript associations, prominently involving steroid and phospholipid species. Building on these findings, we developed an immunometabolic transition score and age-specific reference chart, which were evaluated in an independent healthy cohort and applied to quantify deviations in pediatric immune disorders. These findings highlight a coordinated immunometabolic transition in early childhood and provide an age-referenced framework for distinguishing atypical immune-state variation from healthy age-associated variation.

immunology↗

Symptomatic human norovirus infection in zebrafish embryos uncovers neural infection and extracellular vesicle-mediated transmission dynamics

Human norovirus (hNoV) is the leading global cause of acute gastroenteritis, imposing a substantial health and economic burden worldwide. Progress in understanding hNoV pathogenesis has been hindered by the lack of tractable small-animal models that recapitulate symptomatic infection. Although zebrafish larvae support hNoV replication, infection remains asymptomatic, limiting their utility for studying disease mechanisms and host-pathogen interactions. In this study, we report that the zebrafish embryo infection model, in which microinjection of hNoV at the early cell stage, resulted in robust systemic viral replication accompanied by overt pathological manifestations, including pericardial and renal edema, yolk and cranial opacity, and mortality by 3 days post-infection. Disease severity displayed marked individual variability and correlated closely with viral burden. Integrated multi-omics analyses, including bulk transcriptomics, untargeted metabolomics, and single-cell RNA sequencing, demonstrated that embryonic infection elicits a stronger and more coordinated antiviral response than larval-stage infection, while enabling widespread viral dissemination across diverse cell lineages. Approximately two-thirds of infected cells were derived from the nervous system or neural crest lineages, providing a potential mechanistic basis for the neurological complications occasionally reported in hNoV-infected patients. Furthermore, we identified a developmental stage-dependent role for extracellular vesicle (EV)-associated hNoV transmission: free virions mediated more efficient infection and higher symptomatic incidence in immunologically immature embryos, whereas EV-associated virions exhibited enhanced infectivity in more immunocompetent larvae. Together, these findings establish the zebrafish embryo as a versatile and accessible in vivo platform for studying symptomatic hNoV infection, reveal host maturity-dependent viral transmission strategies, and provide new opportunities for mechanistic studies and high-throughput evaluation of antiviral and vaccine candidates. Author summaryHuman norovirus is the leading cause of stomach flu worldwide but studying it has been difficult because the lack of a simple, small-animal model that actually gets sick from the virus. While older zebrafish larvae can harbor the virus, they do not show symptoms. In this study, we successfully created a new model by injecting human norovirus into zebrafish embryos at their early cell stage. Unlike the older larvae, these embryos developed clear symptoms, including fluid buildup around the heart and kidneys, tissue cloudiness, and death within three days. Using advanced genetic and metabolic tracking, we discovered that the virus spreads widely throughout the embryos body, particularly targeting cells in the nervous system. This link might explain why human patients occasionally suffer from neurological symptoms. Additionally, our study revealed that the virus changes its transmission strategy based on the animals age: it travels freely to infect vulnerable embryos but hides inside lipid vesicles to infect older, more immune-developed larvae. Ultimately, these findings provide a practical, efficient animal model to better understand norovirus sickness and rapidly test new vaccines and treatments.

microbiology↗

NEO-AAV: an engineered extracellular vesicle-enveloped AAV platform for activation-coupled T cell transduction and CAR-T cell generation

Efficient delivery of genetic cargo to primary human T cells remains a critical barrier for cell-based immunotherapies. AAVs are widely used but limited by immune neutralization and poor T cell transduction efficiency. We present NEO-AAV, an engineered fusion protein (PH-ALG2-PKD12) that recruits AAV capsids into endogenous extracellular vesicles (EVs) via PI(4,5)P2-directed membrane targeting, multivalent PKD12-capsid clustering, and ALG2-mediated ESCRT machinery recruitment, yielding EV-enveloped particles with improved AAV loading compared with passive EV-AAV controls. NEO-AAV displayed enhanced resistance to an anti-AAV6 neutralizing antibody (ADK6), maintaining transduction at concentrations that neutralized naked AAV6 and outperformed passively formed EV-AAV6. Surface display of a CD7/CD3/CD28 tri-chimera enabled single-step activation and transduction of CD7 T cells within PBMCs, reaching [~]38% eGFP cells without exogenous pre-activation. As a proof-of-concept, NEO-AAV generated functional CAR-T cells from primary human PBMCs, exhibiting antigen-specific IFN-{gamma} release and cytotoxicity against CD19+ target cells. CAR expression peaked at day 5 and declined by day 15, consistent with episomal AAV kinetics, framing NEO-AAV as an activation-coupled delivery module rather than a durable solution. Together, NEO-AAV provides a programmable EV-enveloped AAV platform with improved immune shielding and single-step T cell transduction, offering a building block for immune cell engineering with in vivo potential.

bioengineering↗

An extracellular vesicle biogenesis-inspired engineering platform for efficient protein delivery and therapeutic base editing

Efficient and controllable delivery of genome-editing proteins remains a central challenge for therapeutic translation of gene-editing technologies. Extracellular vesicles (EVs) offer an attractive non-viral delivery modality due to their biocompatibility and large capacity for cytosolic cargo delivery. Yet, rational strategies to achieve controlled and programmable protein loading are still lacking. Here, we present NEO-TOP-EVs, an EV biogenesis-guided engineering platform that systematically integrates key features of three design principles inspired by vesicle formation: 1) PI(4,5)P2-mediated plasma membrane targeting, 2) ESCRT-dependent membrane scission, and 3) self-assembly-driven cargo clustering for enabling efficient encapsulation of genome-editing ribonucleoproteins. Together, the NEO design increased cargo incorporation and enhanced functional delivery of gene editing modalities under particle-normalized conditions. Using NEO-TOP-EVs, we achieve efficient delivery of Cas9 and adenine base editor ribonucleoproteins without nucleic acid templates. In an in vitro proof-of-concept, delivery of an adenine base editor targeting proprotein convertase subtilisin/kexin type 9 (PCSK9) induces efficient splice-site disruption, resulting in reduced PCSK9 expression and enhanced LDL receptor activity. Proof-of-concept in vivo experiments provide preliminary evidence of functional Cre protein delivery to the liver. Together, these findings establish NEO-TOP-EVs as a modular platform for protein-based genome editing, demonstrating how biogenesis-informed EV engineering yields functional protein delivery at levels relevant to therapeutic development.

bioengineering↗

Towards building a World Model to simulate perturbation-induced cellular dynamics by AlphaCell

Predicting cellular responses to perturbations is crucial for therapeutic discovery, yet experimental screening is severely constrained by the combinatorial vastness of biological space. While computational simulations offer a scalable alternative, current models are limited by the incomplete latent representation----mainly relying on highly variable genes in feature representation; the poor genome-wide reconstruction fidelity; and the ungeneralizable dynamic laws across diverse contexts. Consequently, they fail to mechanistically transfer learned dynamics to unseen cellular contexts. To address these systemic flaws, we introduce AlphaCell, a generative Virtual Cell World Model that unifies genome-wise representation with continuous state transition modeling. AlphaCell achieves three synergistic innovations: (1) Latent Manifold Rectification, processing the full protein-coding transcriptome to construct a differentiable Virtual Cell Space, effectively filtering noise while preserving intrinsic cellular topology; (2) Biological Reality Reconstruction, utilizing a massive, knowledge-rich decoder to translate abstract latent states back into high-fidelity, genome-wide expression profiles; and (3) Universal State Transition, applying Optimal Transport Conditional Flow Matching to model perturbations as continuous, deterministic vector fields. By abstracting perturbation mechanisms into generalized dynamic laws, AlphaCell makes robust prediction of perturbation responses in a compositional generalization scenario and enables zero-shot prediction of cellular dynamics in entirely unseen cellular contexts, providing a foundational engine for cellular-context-generalizable perturbation prediction and perturbation-induced cellular dynamics simulation.

bioinformatics↗

Unwinding of RNA G-quadruplexes induces mouse and human totipotency

Totipotent stem cells (TotiSCs) have significant application prospects in regenerative medicine and assisted reproductive technologies. The mRNAs of totipotency-related genes are rich in G-quadruplex (G4) structures, while the G4 density of pluripotency-related genes mRNAs is relatively low, suggesting a potential functional link between RNA G4s and the totipotent state. Nevertheless, how G4s are involved in the establishment or maintenance of mouse and human totipotency remains poorly understood. Here, we demonstrate that FC3, a small-molecule RNA G4 unwinder, enables efficient induction and maintenance of mouse and human TotiSCs (mG4TotiSCs and hG4TotiSCs). These FC3-induced TotiSCs closely recapitulate the molecular features of 2-cell-stage blastomeres via transcriptomic and epigenomic profiling. Functionally, both mG4TotiSCs and hG4TotiSCs exhibit totipotent capacity: they differentiate into embryonic and extraembryonic lineages in vitro and in chimeric embryos; moreover, they autonomously self-organize into blastocyst-like structures without exogenous signalling. Mechanistically, we identify that Gata2 mRNA, a G4-containing transcript, is essential for FC3-mediated reprogramming. Genetic disruption of Gata2 would abolish totipotency induction. Collectively, RNA G4 unwinding is a new regulatory axis governing totipotency acquisition and maintenance, providing insight into the functional interplay between nucleic acid secondary structures and cell fate plasticity.

cell biology↗

GuFi phages represent the most prevalent viral family-level clusters in the human gut microbiome

Despite being important ecological modulators of the gut microbiome, bacteriophage diversity and function remain under-characterized. We show that short-read metagenomic surveys can miss even globally highly prevalent viral family-level clusters (VFCs), that can be readily assembled and characterized with long-read metagenomic data from a relatively small cohort (n=109). While gut Bacteroidota phages have been the prevailing focus in the literature, we show that highly prevalent gut phage families frequently have Firmicutes hosts (termed GuFi phages), with broad host ranges verified using proximity-ligation (Hi-C) sequencing data. High-throughput sequencing of virus-like particles from fecal samples detected frequent enrichment of GuFi phages across samples, revealing their under-appreciated impact on the gut microbiome. We report the first in vitro induction and imaging of members of prevalent GuFi clades including the candidate orders Heliusvirales, Astravirales (VFC 2) and Suryavirales (VFC 4). Our findings underscore the importance of GuFi phages with broad host ranges in the gut microbiome, and the utility of long-read sequencing for viral discovery, paving the way for deeper insights into the role of bacteriophages in human health and disease.

microbiology↗

High-Quality Cell Capture Reveals Transcriptomic Changes After Single-Axon Injury of Mauthner Cells

In vivo single-cell capture methods based on micropipettes are essential for correlating morphological characteristics with transcriptomic profiling under physiological conditions. However, they often suffer from significant contamination of off-target cells. Consequently, we developed Hip-seq, which significantly reduces heavily contaminated cells, decreases contamination levels, improves cell reproducibility, and enhances data analysis accuracy compared to patch-seq. Using Hip-seq, we found that axon regeneration failure could be due to abnormal activation of translation and the circadian clock. Axon-regenerable central neurons reactivated axon development-related genes during regeneration. And one-to-one associated analysis helped identify pro-regenerative genes.

neuroscience↗

The conserved HIV-1 spacer peptide 2 triggers matrix lattice maturation

HIV-1 particles are released in an immature, non-infectious form. Proteolytic cleavage of the main structural polyprotein Gag into functional domains induces rearrangement into mature, infectious virions. In immature virus particles, the Gag membrane binding domain, MA, forms a hexameric protein lattice that undergoes structural transition upon cleavage into a distinct, mature MA lattice. The mechanism of MA lattice maturation is unknown. Here we show that released spacer peptide 2 (SP2), a conserved peptide of unknown function situated [~]300 residues downstream of MA, binds MA to induce structural maturation. By high-resolution in-virus structure determination of MA, we show that MA does not bind lipid into a side pocket as previously thought, but instead binds SP2 as an integral part of the protein-protein interfaces that stabilise the mature lattice. Analysis of Gag cleavage site mutants showed that SP2 release is required for MA maturation, and we demonstrate that SP2 is sufficient to induce maturation of purified MA on lipid layers in vitro. SP2-triggered MA maturation correlated with faster fusion of virus with target cells. Our results reveal a new, unexpected interaction between two HIV-1 components, provide a high-resolution structure of mature MA, establish the trigger of MA structural maturation, and assign function to the SP2 peptide.

microbiology↗

Comparative analysis of methodologies for detecting extrachromosomal circular DNA

Extrachromosomal circular DNA (eccDNA) is crucial in oncogene amplification, gene transcription regulation, and intratumor heterogeneity. While various analysis pipelines and experimental methods have been developed for eccDNA identification, their detection efficiencies have not been systematically assessed. To address this, we evaluated the performance of 7 analysis pipelines using three simulated datasets, in terms of accuracy, similarity, duplication rate, and computational resource consumption. We also compared the eccDNA detection efficiency of 7 experimental methods through twenty-one real sequencing datasets. Our results identified Circle-Map and CReSIL as the most effective pipelines for eccDNA detection through short-read and long-read sequencing data, respectively. Moreover, third-generation sequencing-based Circle-Seq showed superior efficiency in detecting copy number-amplified eccDNA over 10 kb in length. These results offer valuable insights for researchers in choosing the most suitable methods for eccDNA research.

cancer biology↗

Molecular dynamics simulations of HIV-1 matrix-membrane interactions at different stages of viral maturation

Although the structural rearrangement of the membrane-bound matrix (MA) protein trimers upon HIV-1 maturation has been reported, the consequences of MA maturation on the MA-lipid interactions are not well understood. Long-timescale molecular dynamics (MD) simulations of the MA multimeric assemblies of immature and mature virus particles with our realistic asymmetric membrane model have explored MA-lipid interactions and lateral organization of lipids around MA complexes. The number of stable MA-PS and MA-PIP2 interactions at the trimeric interface of the mature MA complex is observed to be greater compared to that of the immature MA complex. Our simulations identified an alternative PIP2 binding site in the immature MA complex where the multivalent headgroup of a PIP2 lipid with a greater negative charge binds to multiple basic amino acid residues such as, ARG3 residues of both the MA monomers at the trimeric interface, and HBR residues (LYS29, LYS31) of one of the MA monomers. Our enhanced sampling simulations have explored the conformational space of phospholipids at different binding sites of the trimeric interface of MA complexes. Unlike the immature MA complex, the 2 acyl tail of two PIP2 lipids at the trimeric interface of the mature MA complex is observed to sample stable binding pockets of MA consisting of helix4 residues. Together, our results provide molecular-level insights into the interactions of MA trimeric complexes with membrane and different lipid conformations at the specific binding sites of MA protein before and after viral maturation. SignificanceHIV-1 maturation facilitates the conversion of a newly formed immature virus particle to a mature infectious virion and initiates a new round of infection. The contributions of specific protein-lipid interactions in the HIV-1 assembly process are well recognized, however, the interactions of matrix protein lattice with the membrane before and after HIV-1 maturation are yet to be fully understood. Based on our simulated data, supported by prior experimental observations, the present study provides a molecular-level understanding of possible altered binding mode of PIP2 lipids after viral maturation. Identification of protein-lipid specific interactions, and lipid sorting data obtained from our long-time and large-scale atomistic MD simulations advance the understanding of the HIV-1 matrix and membrane maturation.

biophysics↗

Discovery of new deaminase functions by structure-based protein clustering

The elucidation of protein function and its exploitation in bioengineering have greatly contributed to the development of the life sciences. Existing protein mining efforts generally rely on amino acid sequences rather than protein structures due to technical difficulties in structural elucidation. We describe here for the use of AlphaFold2 to predict and subsequently cluster an entire protein family based on predicted structure similarities. We selected the deaminase family of proteins to analyze and through this approach identified many previously unknown deaminase properties. We applied these new deaminases to the development of new cytosine base editors with distinct features. Although we found many new double-stranded DNA deaminases from the DddA-like protein clade, we were surprised to find that most of the proteins in this family were not actually double-stranded DNA cytidine deaminases. From this protein clade, we engineered the smallest single-strand specific cytidine deaminase, which facilitates the first efficient cytosine base editor to be packaged into a single AAV vector. Importantly, we also profiled a deaminase from this clade that edits robustly in soybean plants, which previously suffered from poor editing by cytosine base editors. These newly discovered deaminases based on AI-assisted structural predictions greatly expand the utility of base editors for therapeutic and agricultural applications.

molecular biology↗

Structure of the NuA4 acetyltransferase complex bound to the nucleosome

DNA in eukaryotes wraps around the histone octamer to form nucleosomes1, the fundamental unit of chromatin. The N-termini of histone H4 interact with nearby nucleosomes, and play an important role in the formation of high order chromatin structure and heterochromatin silencing2-4. NuA4 in yeast and its homolog Tip60 complex in mammalian cells are the key enzymes that catalyze H4 acetylation, which in turn regulate chromatin packaging, and function in transcription activation and DNA repair5-10. Here we report the cryo-EM structure of NuA4 from Saccharomyces cerevisiae bound to the nucleosome. NuA4 comprises two major modules: the catalytic histone acetyltransferase (HAT) module and the transcription activator-binding TRA module. The nucleosome is mainly bound by the HAT module, and positioned close to a polybasic surface of the TRA module, which is important for the optimal activity of NuA4. The nucleosomal linker DNA carrying the upstream activation sequence is oriented towards the conserved, transcription-activator-binding surface of the Tra1 subunit, which suggests a potential mechanism of NuA4 to act as a transcription co-activator. The HAT module recognizes the disk face of the nucleosome through the H2A-H2B acidic patch and the nucleosomal DNA, projecting the catalytic pocket of Esa1 to the N-terminal tail of H4, supporting its function in selective acetylation of H4. Together, our findings illustrate how NuA4 is assembled, and provide mechanistic insights into nucleosome recognition and transcription coactivation by a histone acetyltransferase.

biophysics↗

FCHO controls AP2's critical endocytic roles through a PtdIns4,5P2 membrane-dependent switch

Clathrin-mediated endocytosis (CME) is the main mechanism by which mammalian cells control their cell surface proteome. Proper operation of the pivotal CME cargo-adaptor AP2 requires membrane-localised FCHO. Here, live-cell eTIRF-SIM shows that FCHO marks sites of clathrin- coated pit (CCP) initiation, which mature into uniform sized CCPs comprising a central patch of AP2 and clathrin corralled by an FCHO/Eps15 ring. We dissect the network of interactions between the FCHO interdomain-linker and AP2, which concentrates, orients, tethers and partially destabilizes closed AP2 at the plasma membrane. AP2s subsequent membrane deposition drives its opening, which triggers FCHO displacement through steric competition with PtdIns4,5P2, clathrin, cargo and CME accessory factors. FCHO can now relocate toward a CCPs outer edge to engage and activate further AP2s to drive CCP growth/maturation. 125 character summaryFCHO primes AP2 for CCV incorporation, a process that triggers FCHO release to enable activation/recruitment of further AP2s

cell biology↗

A Bayesian approach to single-particle electron cryo-tomography in RELION-4.0

We present a new approach for macromolecular structure determination from multiple particles in electron cryo-tomography (cryo-ET) data sets. Whereas existing subtomogram averaging approaches are based on 3D data models, we propose to optimise a regularised likelihood target that approximates a function of the 2D experimental images. In addition, analogous to Bayesian polishing and contrast transfer function (CTF) refinement in single-particle analysis, we describe approaches that exploit the increased signal-to-noise ratio in the averaged structure to optimise tilt series alignments, beam-induced motions of the particles throughout the tilt series acquisition, defoci of the individual particles, as well as higher-order optical aberrations of the microscope. Implementation of our approaches in the open-source software package RELION aims to facilitate their general use, in particular for those researchers who are already familiar with its single-particle analysis tools. We illustrate for three applications that our approaches allow structure determination from cryo-ET data to resolutions sufficient for de novo atomic modelling.

biophysics↗

Cell free extrachromosomal circular DNA is common in human urine

Cell free extrachromosomal circular DNA (eccDNA) is evolving as a potential biomarker in liquid biopsies for disease diagnosis. In this study, an optimized next generation sequencing-based Circle-Seq method was developed to investigate urinary cell free eccDNA (ucf-eccDNA) from 28 adult healthy volunteers (mean age = 28, 19 males/ 9 females). The genomic distributions and sequence compositions of ucf-eccDNAs were comprehensively characterized. Approximately 1.2 million unique ucf-eccDNAs are identified, covering 14.9% of the human genome. Comprehensive characterization of ucf-eccDNAs show that ucf-eccDNAs contain higher GC content than flanking genomic regions. Most eccDNAs are less than 1000 bp and present four pronounced peaks at 203, 361, 550 and 728 bp, indicating the association between eccDNAs and the numbers of intact nucleosomes. Analysis of genomic distribution of ucf-eccDNAs show that eccDNAs are found in all chromosomes but enriched in chromosomes i.e. chr.17, 19 and 20 with high density of protein-codding genes, CpG islands, SINE and simple repeat elements. Lastly, analysis of sequence motif signatures at eccDNA junction sites reveal that direct repeats (DRs) are commonly found, indicating a potential role of DRs in eccDNA biogenesis. This work underscores the deep sequencing analysis of ucf-eccDNAs and provides a valuable reference resource for exploring potential applications of ucf-eccDNA as diagnostic biomarkers of urogenital disorders in the future. Significance StatementExtrachromosomal circular DNA (eccDNA) is an important genetic element and a biomarker for disease diagnosis and treatment. In this study, we conduct a comprehensive characterization of urinary cell free eccDNA (ucf-eccDNA) in 28 heathy subjects. Over one million ucf-eccDNAs are identified. Ucf-eccDNAs are characterized as high GC content. The size of most ucf-eccDNAs is less than 1000 bp and enriched in four peaks resembling the size of single, double, triple, and quadruple nucleosomes. The genomic distribution of ucf-eccDNAs is enriched in generic regions, protein-coding genes, Alu, CpG islands, SINE and simple repeats. Sequence motif analysis of ucf-eccDNA junctions identified simple direct repeats (DRs) commonly presented in most eccDNAs, suggesting potential roles of DRs in eccDNA biogenesis.

genomics↗

The noncoding RNA PRANCR regulates splicing of Fibronectin-1 to control keratinocyte proliferation and migration

Most human genes undergo alternative splicing (AS), but the regulation and functional consequences of most splicing events remain unknown. Long noncoding RNAs (lncRNAs) have recently been discovered to have novel roles in the regulation of AS. Here we investigate whether PRANCR, a lncRNA recently identified to be essential for epidermis formation, functions by controlling AS of cell fate genes. Using transcriptome-wide analysis, we identified 238 exonic splicing events regulated by PRANCR. Among these is alternative splicing of an exon containing the extra domain A (EDA) in the gene fibronectin-1 (FN1). Expression of the FN1-EDA+ isoform is enriched in proliferating keratinocytes. We find that PRANCR regulates EDA inclusion by controlling expression of the serine/arginine-rich splicing factors (SRSFs) 1 and 7. Depletion of PRANCR or FN1-EDA resulted in decreased proliferation, increased CDKN1A/p21, and inhibition of keratinocyte migration. We find that these cellular phenotypes can be explained by reduced phosphorylation of focal adhesion kinase (FAK). Collectively, these results identify a lncRNA regulating skin function through alternative splicing of a cell fate gene.

cell biology↗

Structures and function of locked conformations of SARS-CoV-2 spike

The spike (S) protein of SARS-CoV-2 has been observed in three distinct pre-fusion conformations: locked, closed and open. Of these, the function of the locked conformation remains poorly understood. Here we engineered a SARS-CoV-2 S protein construct "S-R/x3" to arrest SARS-CoV-2 spikes in the locked conformation by a disulfide bond. Using this construct we determined high-resolution structures confirming that the x3 disulfide bond has the ability to stabilize the otherwise transient locked conformations. Structural analyses reveal that wild-type SARS-CoV-2 spike can adopt two distinct locked-1 and locked-2 conformations. For the D614G spike, based on which all variants of concern were evolved, only the locked-2 conformation was observed. Analysis of the structures suggests that rigidified domain D in the locked conformations interacts with the hinge to domain C and thereby restrains RBD movement. Structural change in domain D correlates with spike conformational change. We propose that the locked-1 and locked-2 conformations of S are present in the acidic high-lipid cellular compartments during virus assembly and egress. In this model, release of the virion into the neutral pH extracellular space would favour transition to the closed or open conformations. The dynamics of this transition can be altered by mutations that modulate domain D structure, as is the case for the D614G mutation, leading to changes in viral fitness. The S-R/x3 construct provides a tool for the further structural and functional characterization of the locked conformations of S, as well as how sequence changes might alter S assembly and regulation of receptor binding domain dynamics.

microbiology↗