Biology subjects

Monne, I.

Publications and source records attributed to Monne, I..

7 recordsLinked to original sources

bioRxiv2026

Modelling assessment of the different paths of between-farm transmission of avian influenza HPAI in Northern Italy in 2021--2022

We propose a stochastic epidemic model to describe the spread of avian influenza in a network of poultry farms. We consider three main paths of infection transmission between poultry farms: from nearby farms, mainly through airborne diffusion; from farms belonging to the same company, through shared veterinarians, forage providers and similar; from undetected small farms or wildlife. From the parameter estimation, based on a modified Expectation-Maximization algorithm, we infer that approximately 63% of the farms were infected from nearby ones, with an infection force declining with distance; of these, more than one third belonged to the same company of the estimated infector. About 20% were infected from premises belonging to the same company but farther away than the distance threshold of 2 km; the remaining ones from wildlife or unidentified sources. These estimates have been validated by a comparison with genetic data, available for a subset of the farms: the genetic distance between two farms identified, with high probability, as an infector-infectee pair is much lower than between random pairs. These results may help in the implementation of tailored prevention and control measures for future outbreaks.

genetics↗

bioRxiv2026

Shamonda virus EU1 in Northern Italy, August 2026.

Background Following the emergence of a novel Shamonda-like virus (SHAV) in Europe, suspected clinical cases in dairy cattle were reported in Northeastern Italy. Investigation was required in dairy cattle in Northeastern Italy. Methods Samples were collected from 28 farms displaying fever and reduced milk yield and were screened using molecular methods (PanSimbu real-time RT-PCR followed by Sanger sequencing and differential PCRs for SBV/BTV). Positive samples were subsequently confirmed by Sanger sequencing and selected samples underwent whole-genome sequencing using a metagenomic approach. Results Twenty-four among sera and blood samples from 12 farms tested positive for SHAV. WGS confirmed that Italian strains share maximum identity with the European SHAV-EU1 clade. Limitations This study concerns the results of clinical investigations on suspected cases in the two autonomous provinces of Trento and Bolzano. At present, it is not possible to infer on the circulation of the virus in other Italian provinces. Conclusions This study documents the first detection and genetic characterization of SHAV-EU1 in Italian cattle, indicating active circulation of this virus across Europe. Its identification in two north-eastern Italian provinces does not rule out wider, undetected circulation. In this regard, assessing its geographical extent requires careful evaluation, just as much remains to be discovered about its host range and the severity of symptoms.

microbiology↗

bioRxiv2026

Two epidemics, one genotype, different outcomes: evolutionary changes of Avian Influenza H5N1, genotype EA-2024-DI

Since 2020, high pathogenicity avian influenza H5Nx viruses of clade 2.3.4.4b have become enzootic in Europe, causing recurrent epidemic waves characterized by extensive reassortment events. Here, we describe the emergence of a single high-fitness genotype (EA-2024-DI) that has driven two consecutive waves, evolving into distinct sub-lineages. While its circulation is ongoing, during the 2025-2026 wave it caused an unprecedented number of cases in wild birds. Using phylodynamic analyses of a large dataset of genomic sequences, we compared the spatial diffusion and host transmission pattern of the EA-2024-DI sub-lineages across the three most recent epidemic waves (2023-2024, 2024-2025 and 2025-2026). We show that the genotype has persisted over time and has spread primarily through wild Anseriformes, but with a marked change in the transmission patterns between the different waves and a shift in the epicenter from Eastern to Central Europe, the latter having emerged as an important hub for virus diffusion throughout Europe. Our results reveal a recent increase in the frequency of viruses from wild and domestic mammals carrying mutations enhancing virus replication in mammalian hosts, highlighting the importance of proactive monitoring of this group of hosts to better understand its role in the virus ecology and evolution.

evolutionary biology↗

bioRxiv2025

Validation and multi-site deployment of a lyophilized qRT-PCR reagent for the molecular diagnosis of avian influenza and rabies in Sub-Saharan African regions

Molecular methods are widely accepted as gold standard techniques for the laboratory diagnosis of most human and animal pathogens. However, most molecular protocols rely on reagents that need to be transported and stored at a freezing temperature, a requirement that might affect their reliability in areas where the cold chain cannot be guaranteed. Over the years, several lyophilized molecular products have been marketed to circumvent this issue. We therefore evaluated the feasibility of replacing liquid reagents with freeze-dried formulations for the molecular diagnosis of avian influenza (AIV) and rabies (RABV) viruses, two priority zoonotic pathogens widely spread in Sub-Saharan Africa. Among the available kits, we selected the Qscript lyo 1-step kit (Quantabio) due to its easy-to-use features, single-reaction format, and preliminary performance assessment. Through a more in-depth evaluation, we determined its analytical and diagnostic performance and formulation stability, and obtained results comparable to those of standard liquid master mixes. Notably, for the detection of divergent lyssaviruses, the lyophilized reagents sensitivity was affected by suboptimal complementarity between the oligonucleotides and the target sequences. Finally, a multi-site evaluation in four veterinary diagnostic laboratories located in Sub-Saharan Africa demonstrated the successful deployment of AIV and RABV assays utilizing freeze-dried reagents, which can interchangeably replace liquid master mixes. Altogether our results indicate that the Qscript lyo 1-step kit (Quantabio) represents a valid alternative to wet reagents for the molecular diagnosis of avian influenza and rabies, and has the potential for broader applications to other relevant infectious diseases upon proper validation. Author summaryMolecular diagnostic protocols rely on reagents that need to be transported and stored at freezing temperatures. Meeting this requirement can be challenging in areas where the maintenance of the cold chain is not guaranteed, such as in sub-Saharan Africa. Our study aimed to assess the feasibility of using lyophilized reagents as a replacement for liquid reagents in the molecular diagnosis of two widespread zoonotic pathogens in Sub-Saharan Africa, namely avian influenza and rabies. To accomplish this, we selected a commercially available lyophilized reagent based on its format and performance characteristics. We conducted a laboratory validation to assess the use of the lyophilized reagent throughout the entire diagnostic process. We also conducted a reproducibility test involving African laboratories as potential end-users. Our findings confirm that the lyophilized reagent can replace traditional liquid reagents to diagnose rabies and avian influenza and suggest its possible use for a wider range of infectious diseases after undergoing appropriate validation.

microbiology↗

bioRxiv2024

Immunological findings of West Caucasian bat virus in an accidental host

The Lyssavirus genus includes seventeen neurotropic viral species which are able to cause rabies, an acute and almost invariably fatal encephalomyelitis of mammals. Rabies virus (RABV), the genus prototype, is a multi-host pathogen that undergoes multiple events of host-switching, thus occupying several geographical and ecological niches. In contrast, non-RABV lyssaviruses are mainly confined within a single natural host with rare spillover events never followed by adaptation to new accidental host species. In this scenario, unveiling the mechanisms underlying the host immune response against a virus is crucial to understand the dynamics of infection but also to predict the probability of colonization and adaptation to a new target species. Presently, the host response to lyssaviruses has only been partially explored, with the majority of data inferred from RABV infection, under the assumption that all members of the genus exhibit a similar behavior. Through our study we have investigated the immune response determined by the West Caucasian bat virus (WCBV). Indeed, WCBV has been recently associated with a spillover event to a domestic cat, raising concern about the risks for public health due to the circulation of the virus in its natural host. We selected the Syrian hamster as an animal model representative for an accidental host, and chose the intramuscular route in order to mimic the natural route of infection. In hamsters, WCBV was highly pathogenic, determining 100% lethality and mild encephalitis. In comparison with Duvenhage virus (DUVV) and RABV, we found that WCBV displayed an intermediate ability to promote cellular antiviral response, produce pro-inflammatory cytokines, recruit and activate lymphocytes in the hamsters central nervous system. Author SummaryViruses belonging to the genus Lyssavirus cause rabies, a zoonotic and almost invariably fatal encephalomyelitis. However, not all lyssaviruses behave in the same way, with Rabies virus (RABV) being a multi-host pathogen and non-RABV ones remaining mostly confined to their natural hosts. Host-pathogen interaction might help to elucidate the mechanisms behind the differences observed among lyssaviruses in terms of disease dynamics and ability to cross the species barrier, adapting to novel hosts. In our study, we have investigated the host immune response triggered by the WCBV strain spilled-over from its host (the bent-winged bat) to a domestic cat in 2020. Our study offers a key to understand and generalize the mechanisms underlying lyssavirus spillover and pathogenicity in accidental hosts. More generally, our work confirms and marshals previous, fragmentary evidence indicating a strong and inverse relationship between lyssavirus pathogenicity and immune response induction.

microbiology↗

bioRxiv2022

In-depth characterization of the Syrian hamster as translational model for COVID-19 in humans

The emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has highlighted the importance of having proper tools and models to study the pathophysiology of emerging infectious diseases to test therapeutic protocols, assess changes in viral phenotype and evaluate the effect of viral evolution. This study provides a comprehensive characterization of the Syrian hamster (Mesocricetus auratus) as an animal model for SARS-CoV-2 infection, using different approaches (description of clinical signs, viral load, receptor profiling and host immune response) and targeting four different organs (lungs, intestine, brain and PBMCs). Our data showed that both male and female hamsters are susceptible to the infection and develop a disease similar to the one observed in patients with COVID-19, including moderate to severe pulmonary lesions, inflammation and recruitment of the immune system in lungs and at systemic level. However, all animals recovered within 14 days without developing the severe pathology seen in humans, and none of them died. We found faint evidence for intestinal and neurological tropism associated with the absence of lesions and a minimal host response in intestines and brains, highlighting another crucial difference with the multi-organ impairment of severe COVID-19. When comparing male and female hamsters, it was observed that males sustained higher viral RNA shedding and replication in the lungs, suffered from more severe symptoms and histopathological lesions and triggered higher pulmonary inflammation. Overall, these data confirm the Syrian hamster as a suitable model for mildmoderate COVID-19 and reflect sex-related differences in the response against the virus observed in humans.

immunology↗

bioRxiv2022

Zoonotic avian influenza viruses evade human BTN3A3 restriction

Cross-species transmission of avian influenza A viruses (IAVs) into humans could represent the first step of a future pandemic1. Multiple factors limiting the spillover and adaptation of avian IAVs in humans have been identified, but they are not sufficient to explain which virus lineages are more likely to cross the species barrier1,2. Here, we identified human BTN3A33 (butyrophilin subfamily 3 member A3) as a potent inhibitor of avian but not human IAVs. We determined that BTN3A3 is constitutively expressed in human airways and its antiviral activity evolved in primates. We show that BTN3A3 restriction acts at the early stages of virus replication by inhibiting avian IAV vRNA transcription. We identified residue 313 in the viral nucleoprotein (NP) as the genetic determinant of BTN3A3 sensitivity (313F, or rarely 313L in avian viruses) or evasion (313Y or 313V in human viruses). However, several serotypes of avian IAVs that spilled over into humans in recent decades evade BTN3A3 restriction. In these cases, BTN3A3 evasion is due to substitutions (N, H or Q) in NP residue 52 that is adjacent to residue 313 in the NP structure4. Importantly, we identified more than 150 avian IAV lineages with a BTN3A3-resistant genotype. In conclusion, sensitivity or resistance to BTN3A3 is another factor to consider in the risk assessment of the zoonotic potential of avian influenza viruses.

microbiology↗