Biology subjects

Foret-Lucas, C.

Publications and source records attributed to Foret-Lucas, C..

5 recordsLinked to original sources

bioRxiv2026

Mechanism-based prediction of insertion-driven high pathogenicity avian influenza virus emergence

High pathogenicity avian influenza viruses (HPAIVs) emerge from H5 and H7 low-pathogenicity avian influenza virus progenitors through mutations that introduce a multibasic cleavage site in haemagglutinin. Although nucleotide insertions recurrently generate this motif, the molecular determinants of insertion and whether particular HA sequences are genetically predisposed to evolve toward HPAIV remain unknown. Combining experimental virology and thermodynamic modelling, we show that insertions arise through polymerase slippage controlled by local product-template duplex thermodynamics within the viral polymerase catalytic site. Predicted RNA secondary structures outside the polymerase are not required for high-frequency insertions and only modestly modulate insertion rates. We formalize this mechanism in HPAIVpredict, which predicts insertion profiles, recapitulates intermediates associated with documented HPAIV emergence events and identifies H5 and H7 sequence backgrounds predisposed to acquire functional multibasic cleavage sites.

microbiology↗

bioRxiv2026

RNA length and receptor usage define innate immune recognition across species.

Recognition of viral double-stranded RNA (dsRNA) is a central trigger of innate antiviral immunity, yet the role of RNA length in shaping immune sensing across species remains poorly defined. Here, we identify RNA length as a key determinant of innate immune activation and demonstrate that this parameter is differentially tuned across vertebrate hosts. Using defined dsRNA molecules, we compared immune responses in human, duck, and chicken cells. Short 5-triphosphorylated dsRNAs, including influenza-derived mini viral RNAs, robustly activated antiviral responses in human and duck cells but failed to do so in chicken cells. In contrast, longer dsRNAs induced immune activation across all species, revealing a species-specific threshold for dsRNA recognition. Mechanistically, this threshold is defined by differential engagement of RNA sensors. In human cells, sensing of short and intermediate dsRNA is strictly dependent on RIG-I, whereas in chicken cells, which lack RIG-I, MDA5 mediates dsRNA recognition and imposes a higher length requirement for activation. Consistent with this, duck cells, which retain RIG-I, respond to short dsRNA similarly to human cells. These differences in dsRNA sensing are accompanied by differential activation of downstream antiviral pathways, including PKR-dependent translational control and OAS/RNase L activation. Together, our findings identify RNA length as a fundamental parameter governing innate immune recognition and reveal that species-specific usage of RNA sensors constrains antiviral sensing, with implications for host susceptibility and virus-host interactions. Significance StatementRecognition of viral RNA is central to antiviral immunity, yet the rules governing which viral RNAs are sensed across species remain poorly understood. Here, we show that RNA length defines a species-specific threshold for innate immune recognition. Human and duck cells efficiently detect short viral double-stranded RNAs generated during influenza infection, whereas chicken cells respond only to substantially longer RNA duplexes. Mechanistically, this difference reflects the usage of distinct antiviral RNA sensors: RIG-I enables sensing of short viral RNAs, while MDA5 imposes a higher length requirement for activation. Our findings reveal that host species differ in the spectrum of viral RNA ligands accessible to immune detection, providing a framework for understanding species-specific antiviral responses and host susceptibility.

microbiology↗

bioRxiv2023

The Feather Epithelium Contributes to the Dissemination and Ecology of clade 2.3.4.4b H5 High Pathogenicity Avian Influenza Virus in Ducks

Immature feathers are known replication sites for high pathogenicity avian influenza viruses (HPAIVs) in poultry. However, it is unclear whether feathers play an active role in viral transmission. This study aims to investigate the contribution of the feather epithelium to the dissemination of clade 2.3.4.4b goose/Guangdong/1996 lineage H5 HPAIVs in the environment, based on natural and experimental infections of domestic ducks. During the 2016-22 outbreaks, H5 HPAIVs exhibited persistent and marked feather epitheliotropism in naturally infected commercial ducks. Infection of feathers resulted in epithelial necrosis, disruption, and the production and release of infectious virions. Viral and feather antigens colocalized in dust samples obtained from poultry barns housing naturally infected birds. In summary, the feather epithelium contributes to viral replication, and it is a likely source of environmental infectious material. This underestimated excretion route could greatly impact the ecology of HPAIVs, facilitating airborne and preening-related infections within a flock, and promoting prolonged viral infectivity and long-distance viral transmission between poultry farms. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=112 SRC="FIGDIR/small/550633v1_ufig1.gif" ALT="Figure 1"> View larger version (54K): org.highwire.dtl.DTLVardef@16f6b24org.highwire.dtl.DTLVardef@1e33c82org.highwire.dtl.DTLVardef@199b745org.highwire.dtl.DTLVardef@cf2024_HPS_FORMAT_FIGEXP M_FIG C_FIG

microbiology↗

bioRxiv2021

The strength of the innate immune response drives the within-host competition between highly and low pathogenic avian influenza viruses

Highly pathogenic avian influenza viruses (HPAIV) emerge from low pathogenic avian influenza viruses (LPAIV) through the introduction of basic amino acids at the hemagglutinin (HA) cleavage site. Following viral evolution, the newly formed HPAIV likely represents a minority variant within the index host, predominantly infected with the LPAIV precursor. Using reverse-genetics engineered H5N8 viruses differing solely at the HA cleavage, we tested the hypothesis that the interaction between the minority HPAIV and the majority LPAIV could modulate the risk of HPAIV emergence and that the nature of the interaction could depend on the host species. In chickens, we observed that the H5N8LP increased H5N8HP replication and pathogenesis. By contrast, the H5N8LP antagonized H5N8HP replication and pathogenesis in ducks. Ducks mounted a more potent antiviral innate immune response than chickens against the H5N8LP, which correlated with H5N8HP inhibition. These data provide experimental evidence that HPAIV may be more likely to emerge in chickens than in ducks and underscore the importance of within-host viral variants interactions in viral evolution.

microbiology↗

bioRxiv2021

Intranasal type I interferon treatment is beneficial only when administered before clinical signs onset in the SARS-CoV-2 hamster model

Impaired type I interferons (IFNs) production or signaling have been associated with severe COVID-19, further promoting the evaluation of recombinant type I IFNs as therapeutics against SARS-CoV-2 infection. In the Syrian hamster model, we show that intranasal administration of IFN- starting one day pre-infection or one day post-infection limited weight loss and decreased viral lung titers. By contrast, intranasal administration of IFN- starting at the onset of symptoms three days post-infection had no impact on the clinical course of SARS-CoV-2 infection. Our results provide evidence that early type I IFN treatments are beneficial, while late interventions are ineffective, although not associated with signs of enhanced disease. One Sentence SummaryThe timing of type I interferon treatment is a critical determinant of its efficacy against SARS-CoV-2 infection.

microbiology↗