Laser microdissection pinpoints candidate viruses behind broiler stunting disease

A new spatially informed viromic study has brought researchers closer to resolving one of the most persistent puzzles in poultry health: which viruses are actually responsible for broiler stunting diseases. Published in the journal Microbiome, the research by Shen-Yuan Hsieh, Christopher J. Creevey, Victoria J. Smyth, Ilias Kyriazakis and colleagues at Queen’s University Belfast, the Agri-Food and Biosciences Institute and the Animal and Plant Health Agency used laser-capture microdissection to slice out microscopic lesion regions from archived poultry tissues and then sequenced the viral genetic material contained within them. By anchoring virome analysis directly to the sites of tissue damage, the team identified three enteric viruses consistently enriched within the gastrointestinal lesions of birds affected by runting-stunting syndrome, a condition that inflicts substantial economic losses on the global broiler industry through poor growth, uneven flocks and elevated mortality.

Broiler stunting diseases have long frustrated veterinary virologists. Runting-stunting syndrome, often abbreviated as RSS, is associated with malabsorption and typically presents in young chicks as stunted growth, poor feathering and abnormal droppings. A related but distinct condition, transmissible viral proventriculitis or TVP, involves maldigestion linked to inflammation of the proventriculus, the glandular stomach of the bird. Viral infections have repeatedly been proposed as contributors to both syndromes, and numerous candidate agents have been put forward over the decades. Yet the aetiological roles of specific viruses remain obscure. Conventional virome studies, which typically sequence viral genetic material from homogenised whole tissues or faecal samples, lack spatial resolution. They cannot determine which viruses are physically localised to lesion sites and which are merely passing through the gut lumen, a limitation that severely constrains inference about direct viral involvement in pathogenesis.

The team’s methodological innovation was to couple laser-capture microdissection of formalin-fixed paraffin-embedded tissues with metatranscriptomic sequencing. Formalin-fixed paraffin-embedded, or FFPE, tissues are the standard material of diagnostic histopathology, preserving cellular architecture so that pathologists can score lesions and identify affected regions. Using a laser microdissection system, the researchers excised histologically defined lesion areas from four regions of the gastrointestinal tract, the duodenum, jejunum, proventriculus and gizzard, alongside matching unaffected non-lesion regions from the same tissue sections. This design meant that viral communities within lesions could be compared directly with those in adjacent healthy tissue within the same birds and the same flocks, effectively using each animal as its own experimental control and filtering out background viral noise from feed, environment and commensal carriage.

The sequencing generated a rich catalogue of viral operational taxonomic units across the sampled tissues. In the RSS-derived laser-microdissected samples, which totalled 71 distinct lesion and non-lesion preparations, three enteric viruses emerged as consistently enriched within gastrointestinal lesion tissues relative to non-lesion tissues. The first was Gallivirus spp., detected as multiple strains, a genus of small RNA viruses that has circulated in poultry for years without a clearly defined disease role. The second was Avastrovirus galli, an avian astrovirus species known to infect the intestinal tract. The third was Rotavirus deltagastroenteritidis, a member of the rotavirus species that infects the gastrointestinal systems of birds. All three belong to virus groups long suspected of involvement in enteric disease, but this study provided the spatial evidence that conventional approaches could not deliver: their genetic material concentrates precisely where the tissue damage is.

Importantly, these candidate viruses were not confined to a single outbreak. The researchers detected them across multiple affected farms, and in individual lesion samples the viruses co-occurred, suggesting that co-infections may contribute to the development or severity of stunting disease. This pattern of co-occurrence raises questions familiar from other enteric disease systems, where combinations of viruses, rather than any single agent, may overwhelm the gut’s absorptive capacity or immune defences. The consistency of enrichment across farms strengthens the case that these three viruses are meaningfully associated with RSS pathology rather than being incidental findings, although the authors are careful to frame them as candidate agents whose causal roles still require further investigation.

A particularly revealing component of the study came from the comparative analysis with transmissible viral proventriculitis. The team analysed 49 laser-microdissected samples derived from TVP cases and found that the enteric virome compositions of the two syndromes were clearly distinct. Differential enrichment of vaccine-like strains was observed in the TVP samples, indicating that live attenuated vaccine viruses may occupy a different ecological or pathological niche in this maldigestion-associated condition. The contrast between the RSS and TVP viral signatures confirmed that the spatially informed approach can discriminate disease-specific viral profiles, a proof of principle that extends beyond this single question. Where two clinically related but pathologically distinct syndromes could previously be interrogated only with blunt whole-tissue sequencing, the lesion-anchored method now separates their viromes with histological precision.

Suspicions raised by sequencing were then tested against independent material. All three RSS candidate viruses were confirmed in matched fresh-frozen tissue homogenates from the same birds using reverse transcription PCR, quantitative RT-PCR and amplicon sequencing, verifying that the microdissection findings were not artefacts of FFPE processing or sequencing bias. The researchers went a step further and attempted virus isolation, successfully recovering chicken astrovirus in cell culture. This chain of evidence, from histological lesion to spatially resolved viral sequence to independent molecular confirmation in frozen tissue to live virus in culture, represents a rigorous workflow for implicating candidate pathogens in a disease complex that has resisted definitive attribution for decades.

The technical achievement rests on careful handling of a notoriously difficult sample type. FFPE tissue is chemically preserved and fragmented, which complicates RNA extraction and library preparation, and laser-capture microdissection demands expert histological guidance to distinguish lesion from non-lesion tissue reliably. The authors acknowledge the histological laboratory of the Agri-Food and Biosciences Institute at Stormont for preparing tissue samples, and Professor Imre Lengyel and Dr Jamie Mitchell of Queen’s University Belfast’s Wellcome Wolfson Institute for Experimental Medicine for training and laboratory support in the microdissection experiments. The work was funded by the UK Biotechnology and Biological Sciences Research Council under grant number BB/X01732X/1, with additional collaboration from the Animal and Plant Health Agency and St. David’s poultry team in clinical diagnosis, post-mortem investigation and tissue sample preparation.

The significance of the framework extends beyond the broiler house. Spatially informed viromics, as the authors describe it, moves beyond conventional virome surveys by linking viral abundance patterns to histopathological context, converting a list of detected viruses into a map of where each virus resides relative to tissue injury. The same logic applies to any disease in which a virome has been catalogued but causation remains contested, from respiratory infections in livestock to chronic inflammatory conditions in humans where archived biopsy material is abundant. By demonstrating that lesion-anchored analysis can separate disease-specific viral signatures between two syndromes in the same host species, the study establishes a template for turning diagnostic pathology archives into high-resolution virological evidence.

For the poultry industry, the immediate value lies in the candidate agents themselves. Gallivirus, avian astrovirus and the avian rotavirus now have concrete spatial and molecular evidence tying them to RSS lesions across multiple farms, giving researchers specific targets for experimental infection studies, vaccine development and diagnostic assay design. The open question the authors highlight is whether these viruses function as primary pathogens or as co-factors that act alongside other infectious or husbandry-related stresses to produce stunting disease. Answering that question will require controlled challenge experiments and longitudinal field work, but for the first time those experiments can be aimed at a shortlist of candidates selected not merely by abundance in a sequencing library but by their physical presence within the lesions where the damage is done.

Subject of Research: Spatial viromics of broiler stunting disease lesions to identify candidate viral pathogens

Article Title: Lesion-anchored viromics identifies candidate viral agents of broiler stunting diseases

Article References: Lesion-anchored viromics identifies candidate viral agents of broiler stunting diseases. (n.d.). https://doi.org/10.1186/s40168-026-02556-w

Image Credits: AI Generated

DOI: 10.1186/s40168-026-02556-w

Keywords: broiler, runting-stunting syndrome, transmissible viral proventriculitis, viromics, metatranscriptomics, laser-capture microdissection, astrovirus, rotavirus, gallivirus, poultry health, viral enteritis, histopathology