Coronavirus spherules are supported by a novel triple-layer protein lattice

Phillips, P. M.; Wells, J.; Mathew, N.; Doyle, N.; Keep, S.; Majumder, P.; Gilchrist, J. B.; Hawes, P. C.; Grimes, J.; Harkiolaki, M.; Clare, D. K.; Maier, H. J.

doi:10.64898/2026.10.09.757900

bioRxiv · 10.64898/2026.10.09.757900

Coronavirus spherules are supported by a novel triple-layer protein lattice

Phillips, P. M.·Wells, J.·Mathew, N.·Doyle, N.·Keep, S.·Majumder, P.·Gilchrist, J. B.·Hawes, P. C.·Grimes, J.·Harkiolaki, M.·Clare, D. K.·Maier, H. J.

View original source ↗Export metadata ↓

Abstract

Coronaviruses (CoVs) cause significant disease in humans and animals, with a track-record of cross-species transmission. Despite their global significance, available control strategies are limited, especially for emerging CoVs. A deeper fundamental understanding of the virus life cycle is essential to underpin development of control measures. A critical step of the CoV life cycle is the rearrangement of host cell membranes into replication organelles (ROs). This is conserved across all CoVs and ROs comprise double membrane vesicles (DMVs), the site of viral RNA synthesis, and double membrane spherules. CoV spherules are complex structures requiring both positive and negative curvature of paired membranes so are predicted to have a high energy cost to maintain. To date they have an entirely unknown function. Interestingly, although always present, abundance of spherules in CoV infected cells varies with Betacoronavirus Middle East Respiratory Syndrome coronavirus, Gammacoronavirus infectious bronchitis virus (IBV) and porcine deltacoronavirus in particular producing a considerable number. Here, using cryo-bioimaging we identified for the first time that CoV spherules are embedded with a complex and organised triple-layered protein lattice and that spherules always contain a cargo that appears arranged as a shell inside the vesicle. In addition, we confirmed the presence of a double membrane spanning molecular pore in Gammacoronavirus DMVs and further identified a population of potential DMV formation intermediates. Together, this work provides a foundation for understanding a fundamental yet unresolved aspect of coronavirus replication.

Explore related subjects

microbiology Preprint

Keep this discovery

Explore connections, maps & timelines

BibTeX RIS

Phillips, P. M., Wells, J., Mathew, N., Doyle, N., Keep, S., Majumder, P., Gilchrist, J. B., Hawes, P. C., Grimes, J., Harkiolaki, M., Clare, D. K., Maier, H. J.. 2026-10-09. Coronavirus spherules are supported by a novel triple-layer protein lattice. https://doi.org/10.64898/2026.10.09.757900

Cite the original work for its findings. Save a collection to share your selection of sources.

KEEP EXPLORING

Related preprints

bioRxiv2026

Effects of Alternating Polarity Frequency on the Assembly of Electro-Methanogenic Microbial Communities

Electro-methanogenesis can enhance methane production and has attracted extensive interest, but the current strategies for building electro-methanogenic microbial communities suffer from several limitations. Alternating polarity has been shown as a new strategy to build electro-methanogenic communities, but the impact of alternation frequency on community assembly remains to be understood. In this study, the impact was evaluated using bioelectrochemical systems amended with granular activated carbon, and the working-electrode potential was alternated between +0.4 and -0.4 V vs. SHE at six frequencies ranging from 0.5 to 12 days. Among the tested conditions, 4-d alternation led to the best overall performance, producing approximately 250 L/L/kg cumulative biogas, 96% methane content, and a 45% methane yield, while preserving a stable and reproducible community structure. The community contained two Methanobacterium populations, two putatively electroactive Geobacter populations, and one putatively electroactive Pseudomonas population, together with diverse fermentative and syntrophic bacteria. Transcript-based analyses revealed clear frequency- and potential-dependent shifts in the activity of these functional groups. Redundancy analysis associated the Methanobacterium formicicum-related population with cathodic current and methane production, whereas the Geobacter sulfurreducens-related population was linked to anodic current and methane production. Bayesian and local-similarity networks further connected methanogen dynamics with specific electroactive, fermentative, and syntrophic partners. Collectively, these results establish alternating polarity frequency as a critical parameter for building robust communities capable of high-rate, high-quality methane production.

microbiology↗

bioRxiv2026

Benchmarking Microbiome Methods for Improved Metagenomic Sequencing of Lower Respiratory Tract Samples

Bronchoalveolar lavage is a common diagnostic strategy used to sample immune cells and microbiota of the lower respiratory tract. Metagenomic sequencing of raw bronchoalveolar lavage fluid reveals a low biomass microbial community often obscured by abundant host DNA. Here, we set out to determine an optimal strategy to robustly purify microbial DNA in excess of human DNA using a combinatorial lysis, host-depletion, DNA extraction approach. We identify strategies that improve metagenomic sequencing success that are commensurate with purification challenges that reduce signal from respiratory microbiota. Finally, we present a general framework to further improve microbial sequencing of lower respiratory tract samples in a robust and reproducible manner.

microbiology↗

bioRxiv2026

Shared genomic features of oral bacterial habitat specialization

The oral microbiome exhibits spatial organization, with related bacteria occupying different surfaces despite continual dispersal between habitats. Whether this ecological partitioning is accompanied by genomic functions that recur across evolutionarily divergent lineages remains unclear. Here we compared plaque- and mucosa-associated bacteria representing 47 human microbial taxa, 13 genera and six phyla, using 1,121 reference genome assemblies and habitat-affinity estimates assembled from six oral microbiome abundance summaries. Across 13 genera, a genus-balanced screen of 13,917 nonredundant genomic profiles prioritised 14 exploratory annotations with nominal associations in the same direction before and after adjustment for genome composition with none passing genome-wide family-wise error correction. Proteins carrying recurrent domains belonged to multiple sequence clusters. Closely spaced, divergently oriented HxlR-SnoaL_2 gene pairs occurred in 66 genomes associated with plaque biofilms across four genera, although overall HxlR-SnoaL_2 linkage was not significantly associated with plaque preference. Using source-family-balanced habitat scores, nested cross-validation with entire genera held out supported prediction of habitat preference (macro-average within-genus AUC, 0.821; empirical P = 0.010). Predictive performance was lower after adjustment for genome size, GC content and coding-sequence number (AUC, 0.776; empirical P = 0.059). These findings reveal partial recurrence of habitat-associated genomic annotations amid lineage-dependent protein repertoires and genetic arrangements. They provide a comparative framework for distinguishing broadly shared ecological genomic signatures from alternative, potentially lineage-specific routes to oral habitat specialization.

microbiology↗