Sarbecoviruses, the subgenus of coronaviruses that includes SARS-CoV and SARS-CoV-2, attach to their host cells through the receptor-binding domain, or RBD, of the Spike protein. This domain grips the angiotensin-converting enzyme 2 receptor, ACE2, on the surface of host cells, and it is also the principal target of neutralising antibodies. That dual role creates an intimate link between host range and antigenicity: the same molecular surface that determines which species’ receptors a virus can engage also determines how well antibodies raised against one virus recognise another. The research team, led by scientists at The Pirbright Institute together with collaborators including researchers at King’s College London, set out to map that relationship systematically across a diverse collection of bat sarbecoviruses.

The experimental strategy combined three complementary approaches. First, the researchers used binding assays to test whether the Spike proteins of different sarbecoviruses could attach to ACE2 proteins from a wide panel of mammalian species. Second, they used pseudotype-entry assays, in which harmless lentiviral particles are decorated with each coronavirus Spike protein, to test whether receptor binding actually translates into cell entry. Third, they measured how sera from SARS-CoV-2 convalescent individuals and monoclonal antibodies from vaccinated people who had experienced breakthrough infections neutralised the different viruses. By running the same viruses through all three assays, the team could directly correlate receptor usage with antigenic behaviour.

The results revealed a striking pattern. Sarbecoviruses in clade 1, the group that contains SARS-CoV-2 itself and the BANAL viruses isolated from bats in Laos, tended to be generalists. Their Spike proteins could productively engage ACE2 receptors from many different bat species, indicating that they are not finely tuned to a single host. In contrast, viruses from clade 3, exemplified by RhGB07, and clade 5, exemplified by Rc-o319, behaved as specialists, using a much narrower range of ACE2 receptors. Rc-o319, which was previously known to be unable to use human ACE2 efficiently, fits this specialist profile, whereas the BANAL viruses, which can use human ACE2, sit firmly in the generalist camp alongside SARS-CoV-2.

To understand the structural basis of this specialism, the team solved a novel structure of the RhGB07 Spike protein. The structure allowed them to identify specific residues within the RBD that are associated with the restricted receptor usage of this clade 3 virus. These residues presumably shape the receptor-binding interface in ways that favour particular bat ACE2 variants while excluding others. Such structural insights are valuable because they point to the molecular features that distinguish viruses capable of flexible receptor engagement from those locked into narrow host ranges, and they may help predict the properties of newly discovered sarbecoviruses from sequence data alone.

When the researchers extended their receptor panel beyond bats to include more diverse mammalian ACE2 proteins, the generalist phenotype largely held. Clade 1 viruses could bind and enter cells expressing ACE2 from humans, non-human primates, livestock, and rodents, as well as from species considered potential intermediate reservoir hosts, such as civets, raccoon dogs, and pangolins. This is significant because intermediate hosts are thought to have played a role in previous coronavirus spillovers, including the emergence of SARS-CoV in 2002. A virus that can already use the receptors of many species faces fewer barriers on the path from bat to human. The specialist viruses, by contrast, showed wider phenotypic diversity across this expanded panel, with RhGB07 exhibiting a more idiosyncratic pattern of receptor usage that did not simply mirror its bat-host profile.

The study also examined how SARS-CoV-2’s ongoing evolution in humans has changed its receptor preferences. Comparing variants that have emerged during the pandemic, the researchers found an expanding and, in some cases, shifting pattern of generalism, particularly for Omicron and its many sub-lineages. Omicron’s Spike has accumulated numerous mutations in the RBD, and these changes appear to have broadened or reconfigured the range of ACE2 molecules the virus can engage. This observation underscores that receptor usage is not a fixed property of a virus but a dynamic trait that can evolve under immune pressure and changing transmission landscapes, with potential consequences for which animal species might serve as new reservoirs for human-derived variants.

The antigenic side of the analysis produced equally important findings. When convalescent sera from people who had recovered from COVID-19 were tested against the panel of bat sarbecoviruses, clade 1 viruses, being phylogenetically closest to SARS-CoV-2, were antigenically the most similar. There was robust evidence for cross-neutralisation of these viruses, meaning that immunity generated against SARS-CoV-2 offers meaningful protection against its closest bat relatives. Importantly, however, the team also found evidence for limited cross-neutralisation across the entire subgenus, suggesting that even the more distantly related specialist viruses are not completely invisible to immunity primed by SARS-CoV-2 infection. This graded pattern of cross-reactivity maps closely onto the phylogenetic and receptor-usage relationships the researchers had established.

Using monoclonal antibodies derived from COVID-19 vaccinees who subsequently experienced breakthrough infections, the researchers were able to pinpoint which classes of antibody epitopes are responsible for the broader neutralisation observed across the sarbecovirus panel. Because antibodies recognise specific structural features of the RBD, identifying the epitope classes that mediate cross-neutralisation provides a rational basis for designing vaccines and therapeutics with deliberately broad coverage. Antibodies directed against more conserved features of the receptor-binding interface, rather than those specific to SARS-CoV-2’s particular configuration, appear to underpin the wider neutralising activity.

Taken together, the study delivers a unifying message: generalist ACE2 usage, phylogenetic proximity to SARS-CoV-2, and antigenic similarity travel together. A bat sarbecovirus that can flexibly use receptors from many mammalian species is likely to be a close relative of SARS-CoV-2 and likely to be partially neutralised by existing human immunity. This constellation of traits offers surveillance teams a practical framework for triage. When a new sarbecovirus is discovered, characterising its receptor-binding breadth through binding and pseudotype assays could provide an early, laboratory-based assessment of both its zoonotic potential and the degree to which current vaccines and antibodies might protect against it. As bat habitats are disturbed and human-wildlife interfaces expand, such tools for distinguishing the generalists from the specialists among the thousands of circulating bat coronaviruses could prove essential for anticipating, and perhaps preventing, the next spillover.

Subject of Research: ACE2 receptor usage breadth as a predictor of host range and antigenic relatedness across bat sarbecoviruses

Article Title: Breadth of ACE2 receptor usage predicts host range and antigenic relatedness across bat sarbecoviruses

Article References: Thakur, N., Newman, J., Ni, D., Seow, J., Hay, A. L., Lee, Y., Upadhyay, A., Ekundayo, B. E., Hammond, J. A., Peacock, T. P., Lau, K., Doores, K. J., & Bailey, D. (2026). Breadth of ACE2 receptor usage predicts host range and antigenic relatedness across bat sarbecoviruses. PLOS Biology, 24(10), e3003944. https://doi.org/10.1371/journal.pbio.3003944

Image Credits: AI Generated

DOI: 10.1371/journal.pbio.3003944

Keywords: sarbecoviruses, ACE2, SARS-CoV-2, host range, receptor-binding domain, antigenicity, cross-neutralisation, bat coronaviruses, zoonotic spillover, Omicron, monoclonal antibodies, pseudotype assays

The story began with a reanalysis of fungal DNA sequencing data from 291 Arabidopsis root samples collected at 18 sites across Europe. From more than 26 million sequenced reads targeting the fungal internal transcribed spacer region, the researchers identified 338 fungal sequence variants present in roots. Only five of these were reproducibly detected in more than 80 percent of the samples, defining a tiny multispecies core mycobiota. Among these five, one variant stood out: it was detected in 98 percent of root samples, and when the team cross-referenced it against 488 cultured fungal isolates from four of the sampling sites, 18 percent of those isolates matched it perfectly. The organism behind this ubiquitous signature was Plectosphaerella cucumerina.

To understand how widespread this fungus really is, the researchers queried the GlobalFungi database, a global repository of fungal occurrence data from environmental sequencing studies. Plectosphaerella sequences appeared in soil, mosses, topsoil, rhizosphere and root samples distributed across the planet, and the plants associated with these detections spanned a phylogenetically diverse array of monocot and dicot hosts. Among the five most prevalent root-associated fungal variants, Plectosphaerella showed the strongest enrichment at the soil–root interface, confirming that it is not merely a soil dweller but an active root colonizer with a host range that cuts across the plant tree of life.

With the ecological stage set, the team assembled a collection of 72 Plectosphaerella strains isolated from plants as diverse as mosses, grasses and flowering dicots, gathered from multiple continents. Using PacBio long-read sequencing, they generated high-quality genome assemblies ranging from 35.5 to 40.5 million base pairs. A phylogeny built from 5,466 single-copy genes revealed two subspecies and a small outgroup, with a burst of transposable elements in one subspecies. Yet the most important result was what the genomes did not show: when the researchers tested whether the host plant from which each strain had been isolated explained variation in the fungi’s repertoires of carbohydrate-active enzymes, proteases and candidate effectors, it did not. Fungal phylogeny accounted for roughly half of the variance in these gene families, but host identity had no detectable effect. The fungus, in other words, carries no signature of specialization on particular plants.

Functional assays reinforced this picture of a generalist. Most isolates, regardless of their host of origin, were detrimental to Arabidopsis seedlings grown in sterile culture, and two Arabidopsis-derived strains retained their harmful effects across 12 geographically diverse Arabidopsis accessions. All 72 isolates consumed carbon sources with nearly identical profiles, showing a particular aptitude for plant cell wall-derived monosaccharides. The modest genetic variation among strains therefore seemed unlikely to explain the fungus’s remarkable environmental and host flexibility on its own, pointing the investigators toward gene regulation rather than gene content as the decisive factor.

To test this, the researchers performed controlled recolonization experiments in which germ-free Arabidopsis, tomato and barley seedlings were inoculated with a single fungal strain originally isolated from Arabidopsis roots. The results were strikingly host-dependent. The fungus significantly reduced a combined index of plant survival and growth by 19.5 percent in Arabidopsis and 10.7 percent in tomato, both dicots, but had no measurable effect on barley, a monocot. Quantitative PCR showed that the fungus colonized the roots of all three species, including barley, but confocal microscopy revealed a crucial difference: in Arabidopsis, fungal hyphae penetrated deep into the peridermal and cortical cell layers, establishing extensive endophytic growth throughout the root system. In tomato, invasion was confined largely to the epidermal layer. In barley, hyphae clustered around root hairs but never entered the root interior, suggesting that the monocot’s immune system or structural barriers halt the fungus at the surface.

The transcriptomic explanation for this host specificity emerged when the team sequenced fungal gene expression inside the roots of all three plants. Of 3,399 fungal genes significantly regulated during root colonization compared with growth on inert membranes, most responded in a host-specific manner, revealing remarkable transcriptional plasticity. Genes involved in catabolism were disproportionately represented among the upregulated sets, and genes encoding carbohydrate-active enzymes, the molecular tools fungi use to dismantle plant cell walls, were strongly overrepresented among induced genes in every host condition. Crucially, the specific enzymes activated mirrored the cell wall chemistry of each host. In the pectin-rich walls of the two dicots, the fungus induced pectin-degrading enzymes; in barley, whose walls are dominated by xylans and mixed-linkage glucans, it switched on xylan-degrading enzymes instead. The fungus, it appears, reads the chemical composition of its host’s walls and tailors its enzymatic arsenal accordingly.

One gene rose above all others in this analysis: a single-copy gene encoding a secreted enzyme from glycoside hydrolase family 64, a candidate β-1,3-glucanase whose expression was induced more than 100-fold inside roots regardless of host species. Structural prediction placed it close to a biochemically characterized β-1,3-glucanase from a soil bacterium, an enzyme with strict specificity for β-1,3-linked glucose chains. These linkages occur in plant callose and mixed-linkage glucans, but they are also the principal immunogenic components of fungal cell walls, meaning the enzyme could serve the fungus in two ways: dismantling host defenses or masking its own wall from immune detection. When the researchers deleted the gene using CRISPR-Cas9 genome editing, confirmed by whole-genome resequencing to be a clean single insertion, the consequences were dramatic. Pathogenicity on Arabidopsis and tomato dropped by 62 to 77 percent, and root colonization fell by 18 to 24 percent, while growth in artificial media and colonization of barley were unaffected. The enzyme, in short, is a specific determinant of infection in the hosts the fungus can actually invade.

The evolutionary reach of this mechanism became apparent when the team surveyed 2,534 fungal genomes. GH64 genes are significantly enriched in plant saprotrophs, pathogens and endophytes, and multiple species in the destructive genus Colletotrichum carry a single copy. Deleting the orthologous gene in Colletotrichum incanum, a root pathogen from a different fungal family that diverged from Plectosphaerella long ago, reduced fungal load in Arabidopsis roots by 68.5 percent and increased plant shoot weight by 10 percent. Notably, the gene was dispensable for infection of Nicotiana benthamiana, consistent with its low expression in that host’s roots. Two independently evolved pathogens thus rely on the same enzyme family to infect the same host, demonstrating that host-induced carbohydrate-active enzymes can couple fungal virulence with multihost compatibility. Because core root fungi are normally held in check by bacterial commensals and plant immune metabolites in nature, the authors suggest that disease emerges when these restraints fail. The GH64 enzyme and its relatives now stand out as promising targets for protecting crops against broad-host-range root pathogens, and the study more broadly reframes fungal host range not as a fixed genomic property but as a dynamic regulatory capacity, unlocked one enzyme at a time by the chemical cues of whatever root the fungus encounters.

Subject of Research: Carbohydrate-active enzymes enabling multihost root infection by the fungus Plectosphaerella cucumerina

Article Title: Carbohydrate-active enzymes from a core root mycobiota member enable infection of multiple plant hosts

Article References: Raja-Kumar, R.-S., Mesny, F., Basak, A. K., Newfeld, J., Chesneau, G., Entila, F., Lee, T., Rigerte, L., Carvajal Acevedo, S., Hüttel, B., Crous, P. W., Maciá-Vicente, J. G., Stewart, H., Ryan, M., Fakhoury, A. M., Sacristán, S., Aitouguinane, M., Batisson, I., Dumontet, S., … Hacquard, S. (2026). Carbohydrate-active enzymes from a core root mycobiota member enable infection of multiple plant hosts. Nature Microbiology. https://doi.org/10.1038/s41564-026-02492-3

Image Credits: AI Generated

DOI: 10.1038/s41564-026-02492-3

Keywords: Plectosphaerella cucumerina, root microbiome, CAZymes, GH64, β-1,3-glucanase, plant pathology, Arabidopsis thaliana, Colletotrichum incanum, fungal genomics, cell wall degradation, host range, CRISPR gene editing

Previous metagenomic surveys of human breast milk had revealed an abundance of viral genetic material, much of it phage DNA, hinting that these viruses might be active participants in the early-life microbiome. But metagenomics alone cannot distinguish between free-floating DNA fragments, prophage genomes quietly embedded in bacterial chromosomes, and fully formed virions capable of infection. Demonstrating the presence of actual phage particles requires a different approach: culturing a susceptible bacterial host and showing that something in the milk sample can lyse it, producing the clear plaques on a bacterial lawn that have been the calling card of phage hunters for more than a century.

That is precisely what the team, led by Steven De Soir of UCLouvain and the Queen Astrid Military Hospital in Brussels, together with colleagues at KU Leuven, the University of Minho, and Monash University, set out to do. Working with breast milk samples collected from a lactating donor under written informed consent, the researchers succeeded in isolating six distinct bacteriophages capable of infecting P. aeruginosa, along with a co-occurring strain of the bacterium itself. The identification of the Pseudomonas isolates was carried out with the support of the microbiology laboratory of the Cliniques universitaires Saint-Luc in Brussels, ensuring that the host bacterium recovered from the milk was unambiguously characterized.

The genomic characterization of the six phages revealed a striking diversity. Four of the isolates proved to be strictly lytic, meaning they replicate inside and destroy their bacterial hosts rather than integrating into the host genome. The remaining two were temperate phages, the kind that can choose between a lytic cycle and a lysogenic lifestyle in which their genome becomes a quiet passenger within the bacterium. Across the six isolates, the genomes spanned multiple genera, indicating that a single sample of human breast milk can harbor phages drawn from several branches of the viral tree of life, all targeting the same bacterial species.

Among the four lytic phages, three showed highly similar host ranges and produced comparable plaque morphologies, suggesting they may be closely related despite being recovered as separate isolates. This kind of redundancy is a familiar feature of phage ecology, where dominant viral lineages can appear repeatedly within a single ecological niche. Whether these three represent genuinely distinct entities or variants of a locally dominant phage is one of the questions the study leaves open for future work, but their coexistence in the same sample underscores how concentrated phage activity against a single host species can be within this body fluid.

Host-range profiling, the standard method for determining which bacteria a given phage can infect and kill, showed that the newly isolated phages display broad activity against P. aeruginosa. Critically, that activity included the co-occurring P. aeruginosa strain recovered from the very same milk sample. This observation is significant because it demonstrates that the phages and their bacterial host were not merely passive co-travelers; the viruses were capable of infecting the bacterium found alongside them, raising the possibility of active phage-host dynamics unfolding within the milk itself.

Perhaps the most intriguing laboratory finding concerns synergy. The researchers observed synergistic interactions between pairs of lytic phages, as well as between lytic phages and one of the temperate isolates. In practical terms, synergy means that combinations of phages can suppress bacterial growth more effectively than the sum of their individual effects, a property that underpins the design of phage cocktails in therapeutic applications. That such interactions should be detectable among phages recovered from breast milk suggests that the viral community in this fluid is not a random assortment but potentially a functionally coordinated ensemble shaped by coevolution with its bacterial targets.

The implications extend in two directions. The first concerns neonatal biology. P. aeruginosa is an opportunistic pathogen of considerable clinical importance, notorious for its antibiotic resistance and its role in hospital-acquired infections, particularly in immunocompromised patients and those with cystic fibrosis. Yet Pseudomonas species are also documented members of the early-life microbiome, and the presence of both the bacterium and its phages in breast milk raises the possibility that infants ingest a miniature predator-prey system with every feed. Such a system could influence which bacterial strains colonize the infant gut, modulate bacterial population sizes, and even shape the developing immune system’s encounter with microbial antigens. The authors note that these findings elicit questions toward phage-host dynamics in human breast milk and highlight implications for neonatal microbial colonization and immune modulation.

The second direction concerns phage therapy and biotechnology. Phages active against P. aeruginosa are of intense interest because of the pathogen’s inclusion on lists of priority antibiotic-resistant bacteria. Discovering that novel, genetically characterized lytic phages with broad host ranges can be recovered from an unexpected and easily accessible human source adds to the growing catalog of candidate therapeutic agents. The Belgian research community involved in this study, including the Laboratory for Molecular and Cellular Technology at the Queen Astrid Military Hospital, has a long-standing track record in phage therapy research, and the isolation methods demonstrated here could inform future searches for phages in other human-associated niches. The work was supported by Innoviris, the Brussels regional research funder, and by the Belgian FRS-FNRS, with fellowship support for early-career researchers.

There are, of course, important caveats. The study reports findings from breast milk of a single lactating woman, so the prevalence of active Pseudomonas phages in breast milk across the broader population remains unknown. It is also not yet clear whether the phages and the bacterium were produced locally within the mammary gland, transported there from elsewhere in the maternal body, or introduced through environmental contact. The entero-mammary pathway, by which maternal gut immune cells and microbes are thought to traffic to the breast, offers one plausible route, but confirming the origin of these phages will require further study. What the work establishes beyond doubt is that functional phage particles targeting a clinically significant pathogen exist in human breast milk, transforming what was once a metagenomic hint into a demonstrable biological reality. As researchers begin to probe the dynamics between these viruses, their bacterial hosts, and the infant recipients of both, breast milk may prove to be one of the most accessible windows into the hidden ecology of the human virome.

Subject of Research: Isolation of active Pseudomonas aeruginosa bacteriophages and their bacterial host from human breast milk

Article Title: Isolation of active Pseudomonas aeruginosa bacteriophages and of their host from human breast milk

Article References: De Soir, S., Sáez Moreno, D., Wagemans, J., Glorieux, A., Lavigne, R., Pirnay, J.-P., Merabishvilli, M., Barr, J. J., Van Bambeke, F., & De Vos, D. (2026). Isolation of active Pseudomonas aeruginosa bacteriophages and of their host from human breast milk. npj Viruses. https://doi.org/10.1038/s44298-026-00235-z

Image Credits: AI Generated

DOI: 10.1038/s44298-026-00235-z

Keywords: bacteriophages, Pseudomonas aeruginosa, human breast milk, virome, neonatal microbiome, phage therapy, lytic phages, temperate phages, host range, phage-host dynamics, microbiome development, antibiotic resistance

The discovery began not in a hospital ward but in an environmental survey. The team was assessing bacteria in a wetland that is home to a camp of grey-headed flying foxes, Pteropus poliocephalus, large fruit bats whose roosts make the surrounding waters a rich and underexplored microbial habitat. From those waters the researchers isolated a strain of Klebsiella pneumoniae, designated sequence type ST4919, and with it the phage that preys upon it. That phage, christened Ptero in a nod to the flying foxes, became the founding member of a new family of minimalist viruses.

Klebsiella pneumoniae is a pathogen of considerable clinical concern. It is a leading cause of hospital-acquired infections, including pneumonia, bloodstream infections, and urinary tract infections, and its growing resistance to last-line antibiotics has made it a priority target for alternative therapies. Because many drug-resistant bacteria circulate through the environment, moving between farms, gardens, waterways, and human communities, environmental surveillance serves a dual purpose: it maps the spread of dangerous strains and can uncover natural predators, the bacteriophages, that keep those populations in check.

What sets Ptero and its relatives apart is their minimized architecture. Comparative genomics revealed that the thirteen related phages characterized in the study carry substantially reduced gene sets compared with many of their contractile-tailed cousins. Rather than being a limitation, this simplicity proved to be a scientific asset. When a biological machine has fewer parts, each remaining component becomes easier to assign a function, and the Monash team exploited this by combining structural analysis of the phage virions with biochemical analysis of purified phage proteins.

Contractile phages, members of the broader class that includes the well-studied T4 phage, infect bacteria using a sophisticated injection apparatus. At the tip of the tail sits the baseplate, a multiprotein hub that senses the host cell surface and triggers a dramatic conformational change. That change drives the tail sheath to contract, driving an inner tube through the bacterial cell envelope so that the phage genome can be delivered into the host cytoplasm. In complex phages, the baseplate involves dozens of proteins whose interdependencies are difficult to untangle. The minimalist phages, by contrast, appear to retain only the essential core elements of this device.

By studying Ptero’s simplified version of this machinery, the researchers were able to define what constitutes the irreducible baseplate of a contractile phage. The analysis also brought two virion-associated enzymes into focus. Each phage particle carries two such enzymes, which the study indicates are deployed to kill specific Klebsiella hosts, most plausibly by degrading components of the bacterial cell surface to facilitate attachment and entry. Enzymes of this kind are of particular interest in phage therapy and biotechnology because they can act on the bacterial cell wall independently of the infection cycle itself.

One of the most striking implications of the study concerns host range. The thirteen related phages have evolved to infect diverse bacteria with distinct surface features. Bacterial surfaces vary enormously between species and strains, decorated with different polysaccharides, outer membrane proteins, and other appendages that phages typically use as recognition cues. A phage family that maintains a minimal infection apparatus while accommodating this diversity suggests that the core elements of the baseplate are more versatile than previously appreciated, with host specificity likely tuned by a small number of variable components.

The methodological approach underpinning the work drew on multiple platforms at Monash University. Structural analysis of the virions was performed using cryo-electron microscopy at the Monash Ramaciotti Cryo Electron Microscopy Facility, allowing the researchers to visualize the architecture of the phage particles at near-atomic resolution. Proteomic and biochemical characterization of purified phage proteins was carried out at the Monash Proteomics and Metabolomics Platform, with support from Bioplatforms Australia through the National Collaborative Research Infrastructure Strategy. The study was led by Alex Hall, Hansel Adriel, Yan Li, Pok Man Leung, and colleagues, with senior authors Fasséli Coulibaly and Trevor Lithgow coordinating the structural and microbiological arms of the project.

The broader context of the research is the global crisis of antimicrobial resistance, which is driven by the spread of drug-resistant bacteria through human communities. As conventional antibiotics lose effectiveness, phage therapy has attracted renewed attention as a means of treating infections caused by multidrug-resistant organisms. Recent years have seen a surge of studies isolating and engineering phages against Klebsiella pneumoniae, including efforts to expand host ranges through experimental evolution and to develop synthetic phages with broader coverage of resistant clinical isolates. Fundamental work such as this, which dissects the minimal machinery of infection, provides the mechanistic foundation on which such applied efforts depend.

The minimalist phages also carry lessons for evolutionary biology. Genome reduction is a recurring theme in virology, as viruses shed genes that their hosts or co-infecting viruses can supply. Yet a contractile phage cannot dispense with the machinery needed to pierce a bacterial cell envelope, one of the more demanding mechanical tasks in biology. The fact that Ptero and its relatives accomplish this with a pared-down toolkit indicates that the essential functions of host recognition, cell wall dissolution, and membrane penetration can be achieved with a remarkably small complement of proteins. For phage biologists, these thirteen viruses now serve as a reference scaffold for understanding how the more elaborate baseplates of complex phages are assembled from and built upon this core. For the growing community working to turn phages into therapeutic agents, they offer a simplified platform in which the determinants of host specificity can be mapped, engineered, and ultimately redeployed against the drug-resistant bacteria that continue to emerge from natural environments.

Subject of Research: Minimalist bacteriophages typified by phage Ptero and their infection machinery in Klebsiella pneumoniae

Article Title: A family of minimalist bacteriophages, typified by phage Ptero, have evolved to infect diverse bacteria with distinct surface features

Article References: Hall, A., Adriel, H., Li, Y., Leung, P. M., Lee, H.-C., Schittenhelm, R. B., Dunstan, R. A., Coulibaly, F., & Lithgow, T. (2026). A family of minimalist bacteriophages, typified by phage Ptero, have evolved to infect diverse bacteria with distinct surface features. npj Viruses. https://doi.org/10.1038/s44298-026-00240-2

Image Credits: AI Generated

DOI: 10.1038/s44298-026-00240-2

Keywords: bacteriophage, phage Ptero, Klebsiella pneumoniae, antimicrobial resistance, phage therapy, baseplate, cryo-electron microscopy, viral genomics, host range, cell wall enzymes, environmental microbiology, Monash University

The stakes of this kind of work are hard to overstate. In the past two decades, three zoonotic coronaviruses—SARS-CoV-1, MERS-CoV, and SARS-CoV-2—have caused major outbreaks, and each emergence began with a virus crossing a species barrier. For sarbecoviruses, that barrier is defined largely by compatibility between the viral receptor-binding domain (RBD) on the spike protein and the host’s angiotensin-converting enzyme 2 (ACE2) receptor. If a virus’s RBD can engage a species’ ACE2 efficiently, that species becomes a plausible host; if it cannot, the chain of transmission breaks at the very first step. Understanding which receptors are vulnerable to which viruses is therefore central to anticipating where the next spillover might come from.

To build the atlas, the researchers first established an evolutionary framework. Phylogenetic analysis of the RBD sequences divided the 46 viruses—31 from bats, 10 from humans, three from civets, and two from pangolins—into three major clades, with clade 1 further splitting into subclades 1a and 1b. Clade 1a contains SARS-CoV-1 and related bat and civet strains; clade 1b contains SARS-CoV-2 and its closest relatives, including the bat virus RaTG13 and pangolin coronaviruses. Clade 2, which comprises most known sarbecoviruses, carries a distinctive double-segment deletion in the receptor-binding motif, while clade 3 viruses from African and European bats carry a single-segment deletion in the same region. These structural differences in the RBM, the loop that physically contacts ACE2, turned out to predict much of the functional variation the team later observed.

The functional screen itself relied on pseudotyped reporter viruses: vesicular stomatitis virus particles decorated with each sarbecovirus spike protein, whose entry into cells expressing a given ACE2 ortholog could be quantified by luminescence. The team confirmed comparable spike expression and incorporation across pseudovirus preparations by western blot and normalized viral input by quantitative RT-PCR, allowing a fair comparison across the roughly 3,000 possible virus-receptor pairings. The result is a heatmap of cross-species infectivity that functions as a kind of vulnerability index for each species’ receptor.

Clade 1 viruses emerged as the clear standouts in receptor breadth. Within clade 1b, the pangolin viruses PCoV-GD and PCoV-GX, which share 89.6 and 92.3 percent spike identity with SARS-CoV-2 respectively, showed broad ACE2 compatibility, with PCoV-GD efficiently infecting nearly all tested non-bat mammalian ACE2s and most bat ACE2s. Intriguingly, RaTG13—despite sharing 97.4 percent identity with SARS-CoV-2 across the full spike protein—displayed a more restricted host range, implying that subtle differences within the receptor-binding motif underlie the expanded tropism of SARS-CoV-2. Within clade 1a, human SARS-CoV-1 isolates used ACE2 orthologs from a wide range of bat families, whereas most bat- and civet-derived relatives showed narrower usage, with the bat virus WIV1 bridging human and bat lineages through its ability to engage ACE2 from multiple Rhinolophus and Myotis species.

Clade 2 and clade 3 viruses told very different stories. None of the clade 2 pseudoviruses, which represent the majority of known sarbecoviruses, mediated entry through any of the 66 ACE2 orthologs, consistent with their double RBM deletion and previously reported ACE2-independent entry mechanisms. Clade 3 viruses showed intermediate phenotypes: BtKY72 used ACE2 from only a few Rhinolophus species and did not engage human ACE2, while Khosta-2 showed broader tropism, infecting cells expressing rabbit ACE2 more than ten-fold more efficiently than those expressing the human receptor—a striking example of lineage-specific adaptation.

The study also delivered a decisive verdict on several proposed alternative receptors. Host factors including NRP1, CD147, AXL, and TMEM106B have each been suggested to facilitate SARS-CoV-2 entry in various experimental contexts. Yet across the entire 46-virus panel, none of these factors supported detectable infection when overexpressed in the assay cells, indicating that none functions as an independent entry receptor for any sarbecovirus tested. The authors are careful to note that context-dependent accessory roles in specific SARS-CoV-2 settings cannot be excluded, but the message is clear: ACE2 remains the only demonstrated primary entry receptor across this viral diversity.

Among the most consequential findings is the identification of two bat species whose receptors behave remarkably like the human version. Only the ACE2 orthologs of Rhinolophus affinis and Miniopterus schreibersii correlated strongly with human ACE2 usage across the viral panel, with correlation coefficients of 0.8314 and 0.8777 respectively. Surface plasmon resonance confirmed that M. schreibersii ACE2 binds the SARS-CoV-1 and SARS-CoV-2 RBDs with high affinity—dissociation constants of 8.14 × 10⁻⁸ M and 8.06 × 10⁻⁷ M, lower than human ACE2’s nanomolar binding but fully consistent with efficient entry. Because both species range across Southeast Asia, Europe, and North Africa in regions overlapping human habitats, the authors argue they should be priorities for ongoing surveillance. The data also flagged rabbits, cattle, sheep, raccoon dogs, badgers, Siberian chipmunks, and pigs as mammalian species whose ACE2 usage correlates strongly with human ACE2, marking them as candidate intermediate hosts worth investigating.

Perhaps the most mechanistically revealing part of the study concerns two closely related Miniopterus bats whose receptors sit at opposite ends of the permissiveness spectrum. M. schreibersii ACE2 supported entry by nearly all ACE2-dependent pseudoviruses, while the ACE2 of M. natalensis was entirely non-permissive—despite the two proteins differing by only seven amino acids. Three of those substitutions, at positions 27, 31, and 42, sit directly at the predicted RBD-binding interface. Molecular dynamics simulations using the molecular mechanics generalized Born surface area method showed that mutating M. schreibersii ACE2 residue I27 to lysine raised the binding free energy by roughly 5 kcal/mol, while the K42E substitution raised it by nearly 7 kcal/mol, disrupting a salt-bridge network involving residue D38 and the SARS-CoV-1 RBD residue Y442. Entry assays confirmed the simulations: the I27K mutation selectively impaired civet-derived SARS-CoV-1 entry, N31G had minimal impact, and K42E broadly abolished usage by nearly all pseudotypes. Reciprocally, introducing the corresponding M. schreibersii residues into M. natalensis ACE2 restored entry competence for multiple SARS-CoV-1 pseudotypes. Residues 27 and 42, in short, are the principal molecular switches governing Miniopterus receptor recognition.

The authors are candid about the limits of their approach. Pseudoviruses built from available sequences may not capture the full diversity of natural sarbecoviruses, and receptor compatibility is only one barrier to cross-species transmission; protease availability, replication competence, and immune evasion all matter for productive infection in a living animal. Efficient ACE2 engagement alone does not guarantee disease. Still, the atlas provides exactly the kind of mechanistic framework that field surveillance has lacked: a way to prioritize which of the world’s more than 1,400 bat species, and which of the hundreds of circulating sarbecovirus sequences, warrant the closest monitoring. As the authors put it, identifying species with ACE2 structures resembling the human receptor may help focus receptor-based risk assessment where it matters most—before, rather than after, the next spillover.

Subject of Research: Cross-species ACE2 receptor usage and host-range determinants of sarbecoviruses

Article Title: An atlas of sarbecovirus infectivity across diverse ACE2 orthologs

Article References: Sun, Y., Cheng, Z., Wu, X., Liu, K., Wang, L., Yang, D., Huang, W., & Nie, J. (2026). An atlas of sarbecovirus infectivity across diverse ACE2 orthologs. iScience, 29(10), Article 117769. https://doi.org/10.1016/j.isci.2026.117769

Image Credits: AI Generated

DOI: 10.1016/j.isci.2026.117769

Keywords: sarbecovirus, ACE2, SARS-CoV-2, SARS-CoV-1, bats, spillover, pseudovirus, receptor-binding domain, host range, surveillance, Miniopterus, Rhinolophus