Biology subjects

SOUBIES, S. M.

Publications and source records attributed to SOUBIES, S. M..

3 recordsLinked to original sources

bioRxiv2026

A novel coronavirus associated with enteritis in broiler chickens, France, 2025

Coronaviruses of the genus Gammacoronavirus cause major poultry diseases, including infectious bronchitis in chickens and enteritis in turkeys and guinea fowl. Until now, no enteric coronavirus distinct from infectious bronchitis virus had been reported in chickens. Between late 2024 and 2025, severe enteritis outbreaks affected broiler farms in southwestern France, causing increased mortality, wet litter, cyanosis, lethargy, ruffled feathers, and high slaughter condemnation rates. Necropsy and histopathology revealed diffuse enteritis and dehydration. Metagenomic sequencing identified abundant coronavirus reads as the only pathogenic viral signal. Whole-genome phylogeny showed a novel gammacoronavirus lineage closely related to guinea fowl coronavirus but distinct from infectious bronchitis virus and turkey coronavirus. Viral RNA was detected in enterocytes by RNAscope in situ hybridization, and electron microscopy revealed coronavirus-like particles. These findings describe a novel enteritis-associated coronavirus in broiler chickens (ChECoV), although the drivers of its host-range expansion into chickens remain to be elucidated.

microbiology↗

bioRxiv2025

Detection and isolation of H5N1 clade 2.3.4.4b high pathogenicity avian influenza virus from ticks (Ornithodoros maritimus) recovered from a naturally infected slender-billed gull (Chroicocephalus genei)

Laridae birds, such as gulls, are known reservoirs of H13 and H16 low pathogenicity avian influenza virus (LPAIV) subtypes. However, during the recent outbreaks linked to the reemergence of high pathogenicity avian influenza virus (HPAIV) H5N1 clade 2.3.4.4b of the Goose/Guangdong lineage, European populations of Laridae birds suffered significant losses. HPAI cases were reported not only along the coastlines but also inland areas, particularly in France and Central Europe. During a diagnostic investigation of a group of Laridae birds, part of a HPAIV outbreak reported in the South of France in 2023, larval stages of Ornithodoros maritimus, a nidicolous soft tick parasitizing seabirds, were recovered from a slender-billed gull (Chroicocephalus genei). Affected birds exhibited gross and histopathological lesions consistent with systemic HPAIV infection. Immunohistochemistry revealed marked neurotropism, oculotropism and multicentric epitheliotropism. Viral isolation and sequencing analysis confirmed the presence of HPAIV H5N1 clade 2.3.4.4b in both the gull and ectoparasites, showing from 99.64% to 100% nucleotide identity across five of eight RNA segments. While additional research is needed to properly assess the vector competence of O. maritimus for HPAIV, ticks may represent an interesting non-invasive surveillance tool for these viruses. This is the first time a HPAIV has been successfully isolated from tick larvae. These findings represent a first step toward understanding the potential role played by ticks in the spread of avian influenza viruses within marine bird colonies and among other ecosystems, considering the occurrence of specific behavioral traits, such as kleptoparasitim and the position of gulls at the interface between wild and domestic species.

microbiology↗

bioRxiv2025

Duck Slurry as a Matrix for Avian Influenza Virus Surveillance and Genetic Characterization in Domestic Flocks

Avian influenza viruses (AIVs) circulate widely in domestic and wild birds and continue to pose major risks to animal and public health, in particular those of high pathogenicity (HP). Ducks play a key role in AIV ecology due to frequent subclinical infections and high viral shedding. Efficient environmental surveillance approaches are needed to complement costly individual testing, especially in the context of large-scale anti-H5 vaccination as implemented in France. We evaluated duck slurry, the wastewater produced in duck fattening units, as a matrix for AIV detection and optimized molecular protocols for sensitive molecular detection and genetic characterization. Slurry samples (n = 172) were collected from 37 duck farms in southwestern France between May 2024 and March 2025. Among several extraction strategies, RNA extraction from the solid fraction using TRIzol LS followed by magnetic bead purification yielded the highest sensitivity. Using this optimized protocol, 82% of samples tested positive for AIV RNA, with 30% of positives being H5-positive; no H7 viruses were detected. Whole-segment RT-PCR and sequencing were successful for shorter genomic segments, enabling subtype determination, although virus isolation consistently failed. These findings demonstrate that slurry is a promising matrix for AIV detection, providing valuable molecular data. Slurry-based surveillance may therefore serve as an effective complement to individual testing and improve early warning capacities for influenza surveillance in a One Health perspective. ImportanceIn France, current surveillance of high pathogenicity avian influenza in ducks relies mainly on individual swabs, which may miss subclinical or transient infections, particularly with low-pathogenicity strains. By targeting slurry, a wastewater generated in duck fattening units, we developed an affordable and practical approach for environmental surveillance. Slurry samples captured high levels of avian influenza RNA and allowed partial genomic characterization despite failed virus isolation. This strategy is directly relevant to monitoring avian influenza viruses dynamics under current anti-H5 vaccination and can be extended to other livestock systems. Duck slurry-based surveillance thus represents an efficient One Health tool to strengthen preparedness against avian influenza outbreaks.

microbiology↗