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Guerin, J.-L.

Publications and source records attributed to Guerin, J.-L..

9 recordsLinked to original sources
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↗
bioRxiv2024

Latest RNA and DNA nanopore sequencing allows for rapid avian influenza profiling

Avian influenza virus (AIV) currently causes a panzootic with extensive mortality in wild birds, poultry, and wild mammals, thus posing a major threat to global health and underscoring the need for efficient monitoring of its distribution and evolution. Here, we utilized a well-defined AIV strain to systematically investigate AIV characterization through rapid, portable nanopore sequencing by (i) benchmarking the performance of fully portable RNA extraction and viral detection; (ii) comparing the latest DNA and RNA nanopore sequencing approaches for in-depth AIV profiling; and (iii) evaluating the performance of various computational pipelines for viral consensus sequence creation and phylogenetic analysis. Our results show that the latest RNA-specific nanopores can accurately genomically profile AIV from native RNA while additionally detecting RNA epigenetic modifications. We further identified an optimal laboratory and bioinformatic pipeline for reconstructing viral consensus genomes from nanopore sequencing data at various rarefaction thresholds, which we validated by application to real-world environmental samples for AIV monitoring in livestock. Author SummaryWe tested portable, rapid, and easy-to-use technology to obtain more information about the potentially zoonotic RNA virus avian influenza virus, or AIV. AIV has spread globally via the migratory paths of wild birds, and endangers domestic birds, mammals, and human populations given past evidence of infections of different animal species. We here used novel genomic technology that is based on nanopores to explore the genomes of the virus; we established optimized ways of creating the viral genome by comparing different laboratory and computational approaches and the performance of nanopores that either sequence the viral RNA directly or the converted DNA. We then applied the optimized protocol to dust samples which were collected from a duck farm in France during an AIV outbreak. We showed that we were able to use the resulting data to reconstruct the relationship between the virus responsible for the outbreak and previously detected AIV. Altogether, we showed how novel easy-to-use genomic technology can support the surveillance of potentially zoonotic pathogens by accurately recreating the viral genomes to better understand evolution and transmission of these pathogens.

genomics↗
bioRxiv2023

High pathogenicity avian influenza A (H5N1) clade 2.3.4.4b virus infection in a captive Tibetan black bear (Ursus thibetanus): investigations based on paraffin-embedded tissues, France, 2022

High pathogenicity avian influenza viruses H5Nx (HPAIVs) of clade 2.3.4.4b have been circulating increasingly in both wild and domestic birds in recent years. In turn, this has led to an increase in the number of spillovers events affecting mammals. In November 2022, a HPAIV H5N1 caused an outbreak in a zoological park in the south of France, resulting in the death of a Tibetan black bear (Ursus thibetanus) and several captive and wild bird species. We detected the virus in various tissues of the bear and a wild black-headed gull found dead in its enclosure using histopathology, two different in-situ detection techniques and next generation sequencing, all performed on formalin fixed paraffin embedded tissues. Phylogenetic analysis performed on HA gene segment showed that bear and gull strains shared 99.998% genetic identity, making the bird strain the closest related one. We detected the PB2 E627K mutation in minute quantities in the gull, whereas it predominated in the bear, which suggests that this mammalian adaptation marker was selected during the bear infection. Our results provide the first molecular and histopathological characterization of an H5N1 virus infection in this bear species.

microbiology↗
bioRxiv2023

A real-time colorimetric reverse transcription loop-mediated isothermal amplification (RT-LAMP) assay for the rapid detection of highly pathogenic H5 clade 2.3.4.4b avian influenza viruses

Highly pathogenic avian influenza viruses (HPAIV) are a major threat to the global poultry industry and public health due to their zoonotic potential. Since 2016, Europe and France have faced major epizootics caused by clade 2.3.4.4b H5 HPAIV. To reduce sample-to-result times, point-of-care testing is urgently needed to help prevent further outbreaks and the propagation of the virus. This study presents the design of a novel real-time colorimetric reverse transcription loop-mediated isothermal amplification (RT-LAMP) assay for the detection of clade 2.3.4.4b H5 HPAIV. A clinical validation of this RT-LAMP assay was performed on 198 pools of clinical swabs sampled in 52 poultry flocks during the H5 HPAI 2020-2022 epizootics in France. This RT-LAMP assay allowed the specific detection of HPAIV H5Nx clade 2.3.4.4b within 30 minutes with a sensitivity of 86.11%. This rapid, easy-to-perform, inexpensive, molecular detection assay could be included in the HPAIV surveillance toolbox.

microbiology↗
bioRxiv2022

Two major epidemics of highly pathogenic avian influenza virus H5N8 and H5N1 in domestic poultry in France, 2020-2022

The spread of highly pathogenic avian influenza (HPAI) viruses worldwide has serious consequences for animal health and a major economic impact on the poultry production sector. Since 2014, Europe has been severely hit by several HPAI epidemics, with France being the most affected country. Most recently, France was again affected by two devastating highly pathogenic avian influenza epidemics in 2020-21 and 2021-22. We conducted a descriptive analysis of the 2020-21 and 2021-22 epidemics, in a first step towards identifying the poultry sectors remaining vulnerabilities regarding HPAI viruses in France. We examined the spatio-temporal distribution of outbreaks that occurred in France in 2020-21 and 2021-22, and we assessed the outbreaks spatial distribution in relation to two High-Risk Zones recently incorporated into French legislation to strengthen HPAI prevention and control. There were 468 reported outbreaks during the 2020-21 epidemic, and 1,223 outbreaks during the 2021-22 epidemic. In both epidemics, most outbreaks (80.6% and 74.0%) were located into the two High-Risk Zones. The southwestern High-Risk Zone was affected in both epidemics, while the western High-Risk Zone was affected for the first time in 2021-22, explaining the extremely high number of outbreaks reported. We showed that the spatial distribution model used to create the two High-Risk Zones was able to predict the location of outbreaks for the 2020-21 and 2021-22 epidemics. These zones were characterized by high poultry farm densities; future efforts should therefore focus on reducing the density of susceptible poultry in highly dense areas.

ecology↗
bioRxiv2021

Phylodynamic assessment of control measures for highly pathogenic avian influenza epidemics in France

Phylodynamic methods have successfully been used to describe viral spread history but their applications for assessing specific control measures are rare. In 2016-17, France experienced a devastating epidemic of a highly pathogenic avian influenza virus (H5N8 clade 2.3.4.4b). Using 196 viral genomes, we conducted a phylodynamic analysis combined with generalised linear model and showed that the large-scale preventive culling of ducks significantly reduced the viral spread between departements (French administrative division). We also found that the virus likely spread more frequently between departements that shared borders, but the spread was not linked to duck transport between departements. Duck transport within departements increased the within-departement transmission intensity, although the association was weak. Together, these results indicated that the virus spread in short-distances, either between adjacent departements or within departements. Results also suggested that the restrictions on duck transport within departements might not have stopped the viral spread completely. Overall, by testing specific hypothesis related to different control measures, we demonstrated that phylodynamics methods are capable of investigating the impacts of control measures on viral spread.

evolutionary biology↗
bioRxiv2021

Detection of a novel enterotropic Mycoplasma gallisepticum-like in European Starling (Sturnus vulgaris) around poultry farms in France

Recent outbreaks of highly pathogenic avian influenza in southwest France have raised questions regarding the role of commensal wild birds in the introduction and dissemination of pathogens between poultry farms. To assess possible infectious contacts at the wild-domestic bird interface, the presence of Mycoplasma gallisepticum (MG) was studied in the two sympatric compartments in southwest France. Among various peridomestic wild birds (n=385), standard PCR primers targeting the 16S rRNA of MG showed a high apparent prevalence (up to 45%) in cloacal swabs of European starlings (Sturnus vulgaris, n=108), while the MG-specific mgc2 gene was not detected. No tracheal swab of these birds tested positive, and no clinical sign was observed in positive birds, suggesting commensalism in the digestive tract of starlings. A mycoplasma strain was then isolated from a starling swab and its whole genome was sequenced using both Illumina and Nanopore technologies. Phylogenetic analysis showed that it was closely related to MG and M. tullyi, although it was a distinct species. A pair of specific PCR primers targeting the mgc2-like gene of this MG-like strain was designed and used to screen again the same avian populations and a wintering urban population of starlings (n=50). Previous PCR results obtained in starlings were confirmed to be mostly due to this strain (20/22 positive pools). In contrast, the strain was not detected in fresh faeces of urban starlings. Furthermore, it was detected in one tracheal pool of cattle egrets and one cloacal pool of white wagtails, suggesting infectious transmissions between synanthropic birds with similar feeding behaviour. As the new starling mycoplasma was not detected in free-range ducks (n=80) in close contact with positive starlings, nor in backyard (n=320) and free-range commercial (n=720) chickens of the area, it might not infect poultry. However, it could be involved in mycoplasma gene transfer in such multi-species contexts.

microbiology↗
bioRxiv2020

Inferring within-flock transmission dynamics of highly pathogenic avian influenza (H5N8) in France, 2020

Following the emergence of highly pathogenic avian influenza (H5N8) in France in early December 2020, we used duck mortality data of the index case to investigate within-flock transmission dynamics. A stochastic epidemic model was adjusted to the daily mortality data and model parameters were estimated using an approximate Bayesian computation sequential Monte Carlo (ABC-SMC) algorithm. Results suggested that the virus was introduced 4 days (95% credible interval: 3 - 5) prior to the day suspicion was reported and that the transmission rate was 3.7 day-1 (95%CI: 2.6 - 5.3). On average, ducks started being infectious 3.1 hours (95%CI: 0.4 - 8.0) after infection and remained infectious for 4.4 days (95%CI: 3.1 - 5.6). Model outputs also suggested that the number of infectious ducks was already 3239 (95%CI: 26 - 3706) the day before suspicion, emphasising the substantial latent threat this virus could pose to other poultry farms and to neighbouring wildlife. These estimations can be applied to upcoming outbreaks and made available to veterinary services within few hours. This study illustrates how mechanistic models can provide rapid relevant insights to contribute to the management of infectious disease outbreaks of farmed animals.

ecology↗