Biology subjects

Trebbien, R.

Publications and source records attributed to Trebbien, R..

6 recordsLinked to original sources

bioRxiv2026

Mapping Tissue-Specific Protease Dynamics in the Pig Respiratory Tract During Influenza A Virus Infection

Influenza A virus (IAV) is a zoonotic pathogen capable of infecting diverse avian and mammalian hosts, causing seasonal epidemics and occasional global pandemics in humans. Viral entry requires proteolytic activation of hemagglutinin (HA). While serine proteases such as TMPRSS2, and HAT are known HA activators, the respiratory tract harbours additional proteases whose contributions to infection remain unclear. Dysregulation of these proteases can enhance viral replication, tissue damage, and inflammation, highlighting the need for a systems-level view of the proteolytic landscape. Here, we use high-throughput, proteome-wide proteomics and N-terminomics to identify 112 host proteases across the nasal mucosa, trachea, and lung. We monitor and validate 28 proteases with targeted proteomics and microfluidic qPCR, representing a comprehensive degradome analysis in the respiratory tract of the highly translational pig model of influenza infection. We show that protease abundance and activity were highly tissue-specific: while the nasal mucosa showed selective activation of broad- and narrow-specificity proteases alongside robust antiviral responses, the trachea exhibited modest modulation with subtle shifts in protease-inhibitor balance, and the lung maintained predominantly active proteases despite lower viral loads but severe tissue damage, indicative of immune-mediated pathology. Sequence motif analysis revealed distinct cleavage preferences across tissues, indicating differential protease processing across the studied respiratory tissues in antiviral pathways, antigen processing, and tissue remodelling. Several identified proteases, including ST14, KLKB1, PRSS8, and LGMN, were increased and functionally active upon infection, suggesting roles in viral processing and host immune regulation. Collectively, our results define a spatially organised proteolytic network that shapes tissue-specific antiviral host responses and contributes to H1N1 influenza pathogenesis.

immunology↗

bioRxiv2024

Rapid Surge of Reassortant A(H1N1) Influenza Viruses in Danish Swine and their Zoonotic Potential

In 2018, a single detection of a novel reassortant swine influenza A virus (swIAV) was made in Denmark. The hemagglutinin (HA) of the virus was from the H1N1 pandemic 2009 (H1N1pdm09) lineage and the neuraminidase (NA) from the H1N1 Eurasian avian-like swine lineage (H1N1av). By 2022, the novel reassortant virus (H1pdm09N1av) constituted 27 % of swIAVs identified through the Danish passive swIAV surveillance program. Sequencing detected two H1pdm09N1av genotypes; Genotype 1 contained an internal gene cassette of H1N1pdm09 origin, Genotype 2 differed by carrying an NS gene segment of H1N1av origin. The internal gene cassette of Genotype 2 became increasingly dominant, not only in the H1pdm09N1av population, but also in other Danish enzootic swIAV subtypes. Phylogenetic analysis of the HA genes from H1pdm09N1av viruses revealed a monophyletic source, a higher substitution rate compared to other H1N1pdm09 viruses and genetic differences with human seasonal and other swine adapted H1N1pdm09 viruses. Correspondingly, H1pdm09N1av viruses were antigenically distinct from human H1N1pdm09 vaccine viruses. Both H1pdm09N1av genotypes transmitted between ferrets by direct contact, but only Genotype 1 was capable of efficient aerosol transmission. The rapid spread of H1pdm09N1av viruses in Danish swine herds is concerning for swine and human health. Their zoonotic threat is highlighted by the limited pre-existing immunity observed in the human population, aerosol transmission in ferrets and the finding that the internal gene cassette of Genotype 2 was present in the first two zoonotic infections ever detected in Denmark.

genomics↗

bioRxiv2024

Exploring genetic signatures of zoonotic influenza A virus at the swine-human interface with phylogenetic and ancestral sequence reconstruction

Influenza A viruses (IAVs) in swine have zoonotic potential and pose a continuous threat of causing human pandemics, as demonstrated by the H1N1 pandemic in 2009. Despite increased genomic surveillance, we have limited knowledge of the IAV evolutionary dynamics leading to such zoonotic events and no clear understanding of genetic markers associated with interspecies transmission of IAV between humans and swine. To explore this, we analyzed a comprehensive publicly available whole genome dataset of human and swine IAV sequences. We conducted phylogenetic analyses and inference of ancestral host and sequence states for each IAV segment and mapped inferred mutations that were associated with transmission within and between swine and human hosts. We developed a custom python library to combine information from host and ancestral sequence annotated trees and applied statistical models to identify genetic markers associated with intra- or interspecies transmissions between swine and humans. This included analyzing mutation rates and the selective pressures acting on the viral proteins following intra- and interspecies transmissions and using a scalable, gradient-boosted decision tree machine learning approach to predict key amino acid positions critical for different transmission types. Our analyses indicated complex mutational patterns within and across viral proteins, but also suggested that specific protein regions and amino acid positions of especially several of the internal gene segments were more important for interspecies transmission. Our findings identify potential genetic signatures across the IAV proteins associated with host adaptation and zoonotic potential, offering valuable markers for early-warning genomic surveillance systems to enhance animal health and minimize the potential for zoonotic transmission of IAV.

bioinformatics↗

bioRxiv2024

The avian and human influenza A virus receptors sialic acid (SA)-α2,3 and SA-α2,6 are widely expressed in the bovine mammary gland

An outbreak of H5N1 highly pathogenic influenza A virus (HPIAV) has been detected in dairy cows in the United States. Influenza A virus (IAV) is a negative-sense, single-stranded, RNA virus that has not previously been associated with widespread infection in cattle. As such, cattle are an extremely under-studied domestic IAV host species. IAV receptors on host cells are sialic acids (SAs) that are bound to galactose in either an 2,3 or 2,6 linkage. Human IAVs preferentially bind SA-2,6 (human receptor), whereas avian IAVs have a preference for 2,3 (avian receptor). The avian receptor can further be divided into two receptors: IAVs isolated from chickens generally bind more tightly to SA-2,3-Gal-{beta}1,4 (chicken receptor), whereas IAVs isolated from duck to SA-2,3-Gal-{beta}1,3 (duck receptor). We found all receptors were expressed, to a different degree, in the mammary gland, respiratory tract, and cerebrum of beef and/or dairy cattle. The duck and human IAV receptors were widely expressed in the bovine mammary gland, whereas the chicken receptor dominated the respiratory tract. In general, only a low expression of IAV receptors was observed in the neurons of the cerebrum. These results provide a mechanistic rationale for the high levels of H5N1 virus reported in infected bovine milk and show cattle have the potential to act as a mixing vessel for novel IAV generation. Graphical abstractCreated with Biorender.com O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=60 SRC="FIGDIR/small/592326v1_ufig1.gif" ALT="Figure 1"> View larger version (24K): org.highwire.dtl.DTLVardef@1d6493org.highwire.dtl.DTLVardef@1b60585org.highwire.dtl.DTLVardef@1247e69org.highwire.dtl.DTLVardef@e75da1_HPS_FORMAT_FIGEXP M_FIG C_FIG

microbiology↗

bioRxiv2021

A novel Pan-viral prophylaxis strategy using vaccine adjuvant CAF09b protects against influenza virus infection

The SARS-CoV-2 pandemic caused a massive health and societal crisis, although the fast development of effective vaccines reduced some of the impact. To prepare for future pandemics, a pan-viral prophylaxis could be used to control the initial virus outbreak in the period prior to vaccine approval. The liposomal vaccine adjuvant CAF(R)09b contains the TLR3 agonist polyinosinic:polycytidylic acid, which induces a type I interferon (IFN-I) response and an antiviral state in the affected tissues. When testing CAF09b as a potential pan-viral prophylaxis, we observed that intranasal administration of CAF09b to mice resulted in an influx of innate immune cells into the nose and lungs and upregulation of IFN-I related gene expression. When CAF09b was administered prior to challenge with mouse-adapted influenza A/Puerto Rico/8/1934 virus, it protected from severe disease, although virus was still detectable in the lungs. However, when CAF09b was administered after influenza challenge, the mice had a similar disease course to controls. In conclusion, CAF09b may be a suitable candidate as a pan-viral prophylactic treatment for epidemic viruses, but must be administered prior to virus exposure to be effective.

immunology↗

bioRxiv2020

Co-circulation of multiple influenza A variants in swine harboring genes from seasonal human and swine influenza viruses

Since the influenza pandemic in 2009, there has been an increased focus on swine influenza A virus (swIAV) surveillance. This paper describes the results of the surveillance of swIAV in Danish swine from 2011 to 2018. In total, 3800 submissions were received with a steady increase in swIAV positive submissions, reaching 56% in 2018. Ten different swIAV subtypes were detected. Full genome sequences were obtained from 129 swIAV positive samples. Altogether, 17 different circulating genotypes were identified including novel reassortants and subtypes harboring human seasonal IAV gene segments. The phylogenetic analysis revealed substantial genetic drift and also evidence of positive selection occurring mainly in antigenic sites of the hemagglutinin protein and confirmed the presence of a swine divergent cluster among the H1pdm09Nx viruses. The results provide essential data for the control of swIAV in pigs and for early detection of novel swIAV strains with zoonotic potential.

microbiology↗