Biology subjects

Harder, T.

Publications and source records attributed to Harder, T..

11 recordsLinked to original sources

bioRxiv2026

Experimental reproduction numbers disentangle vaccine effects on susceptibility and infectiousness during H5N1 transmission in geese

Vaccination against high pathogenicity avian influenza virus (HPAIV) is increasingly used to protect poultry, but vaccine performance is commonly inferred from clinical protection and virus shedding rather than measured transmission. We asked whether reproduction numbers from controlled transmission experiments can quantify how vaccination changes susceptibility and infectiousness. Domestic geese were prime-boost vaccinated with an H5 clade 2.3.4.4b RNA-replicon vaccine and challenged with homologous HPAIV H5N1. Replicated seeder-sentinel groups represented transmission among unvaccinated animals, to vaccinated contacts, and from vaccinated breakthrough-infected animals. Vaccinated directly challenged geese remained clinically protected although all became RT-qPCR-positive. Estimated reproduction numbers were R0=4.7 (95% CI, 2.8-8.0) among unvaccinated geese, Rs=2.6 (1.6-4.5) for transmission to vaccinated contacts, Ri=3.7 (2.0-6.8) for transmission from vaccinated infected geese, and Rvacc=2.0 (0.8-4.9) for a fully vaccinated population. Vaccination reduced transmission but did not reduce the point estimate for Rvacc below one under these intensive exposure conditions. Vaccinated infected geese also shed substantially less viral RNA, whereas the estimated reduction in infectiousness was more modest, indicating that RNA shedding alone may not reliably predict transmission reduction. Experimental reproduction numbers therefore provide a direct population-level complement to conventional vaccine endpoints and separate effects on susceptibility from effects on onward transmission.

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

High pathogenicity avian influenza virus H5N1 (clade 2.3.4.4b) drives mass mortality in Eurasian crane (Grus grus) populations in Germany, 2025

In autumn 2025, an unprecedented mass mortality event was observed among the western migrating subpopulation of Eurasian cranes (Grus grus) in Germany. Systemic infection with highly pathogenic avian influenza virus H5N1, clade 2.3.4.4b, genotype DI.2.1, was identified as the cause of acute death. The gregarious behaviour of cranes at feeding and resting sites likely has contributed to the rapid and massive dissemination of viruses within the crane population.

ecology↗

bioRxiv2025

Outbreak dynamics of high pathogenicity avian influenza virus H5N1, clade 2.3.4.4b euBB, in black-headed gulls and common terns in Germany in 2023

Since winter 2022/23, high pathogenicity avian influenza virus (HPAIV) H5N1 clade 2.3.4.4b, genotype euBB, has caused extensive mortality among wild birds. This genotype emerged in France in spring 2022 through reassortment between a gull-adapted low-pathogenicity virus and HPAIV H5N1. Phylogeographic and spatiotemporal analyses show that transmission into German breeding colonies of black-headed gulls (Chroicocephalus ridibundus) and common terns (Sterna hirundo) involved multiple independent incursions, likely via black-headed gulls returning from wintering grounds in the Netherlands, Belgium, and France. It spilled over into common terns, which breed in shared colonies with black-headed gulls, and led to high adult mortality in both species in 2023 (at least 8,137 black-headed gulls and 614 common terns; >3% of the breeding population), followed by significant breeding pair declines in 2024 (-15.9% in black-headed gulls, -5.8% in common terns). Increased immunity, at least in common terns, may have contributed to the apparent fade-out of genotype euBB. These findings highlight how integrating ornithological, epidemiological, and virological data can aid our understanding of viral transmission routes and population-level impacts, while also stressing that HPAIV should be added to the growing list of pressures on seabirds, a group that was already the most threatened among all bird taxa globally. Research Highlights- HPAIV H5N1 euBB caused mass mortality in gulls and terns in Germany in 2023 - Multiple independent viral incursions occurred into different parts of Germany - Serology showed survival and rising H5-seroprevalence in common terns - Outbreaks reduced the black-headed gull breeding populations by up to 24%

ecology↗

bioRxiv2025

Experimental inoculation of pigs with porcine respirovirus type 1 revealed pathological manifestations in the upper respiratory tract

Several pathogens are known to affect the respiratory tract of pigs resulting in decreased health and welfare. Virological investigations and the use of metagenomic sequencing of samples allowed the identification of new viruses in pigs, such as porcine respirovirus type 1 (PRV1) and swine orthopneumovirus (SOV). The pathogenicity of PRV1 has been investigated experimentally by one research group, whereas SOV is yet to be studied. In this experimental trial, groups of weaners were inoculated with a European isolate of PRV1 (n = 8), a pool of SOV RNA-positive clinical nasal swab material (n = 8) or culture medium serving as controls (n = 4). Four days post inoculation (DPI), two controls and four pigs from each of the PRV1 and SOV groups were euthanized and necropsied. All SOV inoculated pigs tested negative for SOV at DPI 4 and therefore four of these pigs were transferred to the stable with the PRV1- infected pigs to assess direct-contact transmission. Nasal swab samples were collected at regular intervals after challenge and blood samples were collected at DPI 0, 4, and 14. At 14 DPI, the remaining pigs (n = 10) were euthanized and necropsied. Nasal swab samples and tissues from the respiratory tract were examined for PRV1 RNA by reverse transcriptase real- time PCR and blood samples were investigated for PRV1 antibodies by ELISA. Respiratory tissues were also evaluated macro- and microscopically and selected tissues were investigated for in situ detection of PRV1 mRNA by RNAscope. No clinical signs, except for nasal discharge, were observed in any of the pigs. PRV1-shedding was observed from DPI 2 to 11 with peaks between DPI 4 and 7, and PRV1 was transmitted horizontally to all direct-contact pigs. The highest viral load was detected in the upper respiratory tract, i.e. nose, upper and lower trachea compared to the lower respiratory tract, i.e., bronchioles, and alveoli. Generally, a chronic tracheitis at 4 DPI, developing into chronic, erosive tracheitis at 14 DPI was observed in the PRV1 groups and was supported by in situ detection of PRV1 by RNAscope. Three pigs also developed mild, bronchointerstitial pneumonia at 14 DPI. In conclusion, these results showed that PRV1 is a primary porcine respiratory pathogen. Author summaryRespiratory diseases in pigs impair porcine health and welfare and are often caused by a complex interaction between pathogens. We investigated the pathogenesis of two recently discovered viruses: porcine respirovirus type 1 (PRV1) and swine orthopneumovirus (SOV). An experimental model in weaner pigs showed that PRV1 is capable of efficient replication, horizontal transmission and caused pathological manifestations mainly in the upper respiratory tract. The lesions consisted of chronic, erosive tracheitis in all PRV1 infected pigs, resulting in a breakage of the tracheal epithelial barrier, and a few pigs developed bronchointerstitial pneumonia. These findings confirm that PRV1 should be considered a primary porcine respiratory pathogen, but in contrast, SOV did not result in a successful infection, and the reasons why remain to be elucidated. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=100 SRC="FIGDIR/small/666573v1_ufig1.gif" ALT="Figure 1"> View larger version (41K): org.highwire.dtl.DTLVardef@d93a11org.highwire.dtl.DTLVardef@17341e9org.highwire.dtl.DTLVardef@1ec4ca4org.highwire.dtl.DTLVardef@9bd42f_HPS_FORMAT_FIGEXP M_FIG C_FIG Graphical abstract created with Biorender.com

microbiology↗

bioRxiv2024

A CRISPR-Cas9 assisted analysis of single-cell microbiomes for identifying rare bacterial taxa in phycospheres of diatoms

Primary production in aquatic systems is governed by interactions between microalgae and their associated bacteria. Most of our knowledge about algal microbiomes stems from natural mixed communities or isolated algal monocultures, which therefore does neither address the role of genotypic diversity among the algal host cells nor do they reveal how this host diversity impacts the assembly process of associated bacteria. To overcome this knowledge gap, we developed a single-cell 16S sequencing approach in combination with CRISPR-Cas9 guided depletion of host 16S contaminations from the chloroplast. The validity of this novel method was tested by comparing bacterial communities of 144 single-cells across three genotypes of the Arctic marine diatom Thalassiosira gravida grown under different environmental conditions. From these, 62 single-cells were additionally sequenced after CRISPR-Cas9 treatment. Due to the improved sequencing depth, bacterial richness associated with individual diatom cells was increased by up to 56%. By applying this CRISPR-Cas9 treatment we not only revealed intraspecific host-genotype associations but also rare bacterial taxa that were not detected by standard 16S rRNA gene metabarcoding. Thus, the CRISPR-Cas9 assisted single-cell approach developed in this study advances our understanding on how the intraspecific diversity among algal hosts impacts the assembly process of their associated bacteria. This knowledge is essential to understand the co-evolution and adaptation of species in algal microbiomes.

microbiology↗

bioRxiv2024

Utilization and degradation of laminarin-based substrates by marine yeasts suggests their niche-specific role in microbial loop dynamics.

In the oceans, the diversity of phytoplankton primary products supports a wide range of microbial heterotrophs, including bacteria and fungi. The organic substrate dynamics within pelagic microbial communities are strongly controlled by microorganismal interactions, resulting in a dense interactome. While the role of bacteria in the microbial loop is well documented, the degradation capacity and substrate specificity of marine fungi, as well as their role and function in metabolic guilds with bacteria, is comparatively less understood. We chose the polysaccharide laminarin, a major product of marine primary production, as well as oligomeric laminarin subunits and monomeric glucose, to study the degradation capacity of eleven marine yeast isolates from the pelagic microbial community of Helgoland Roads. Our aim was to measure yeast growth and correlate degradation yields and putative intermediate degradation products with the size of laminarin-based organic precursor substrates. We developed a reproducible, temporally resolved, high-throughput growth protocol to measure resource-specific yeast growth. Measurement of temporally fine-scaled growth kinetic models of isolates were accompanied with qualitative and quantitative chemical analyses of substrates and degradation intermediates. Our data showed that yeast growth was negatively correlated with oligomer length. Fluorophore-assisted carbohydrate electrophoresis suggested the lack of enzymatic endo-activity for laminarin in yeasts under investigation, suggesting they may occupy a niche in the microbial loop, benefitting from extracellular hydrolysis of carbohydrates by other microorganisms. In terrestrial environments, namely forest soil ecosystems, yeasts have been assigned a similar niche, supporting a prominent role of yeasts in microbial interactomes.

microbiology↗

bioRxiv2024

Red knots in Europe - a dead end host species or a new niche for highly pathogenic avian influenza?

The 2020/2021 epidemic in Europe of highly pathogenic avian influenza virus (HPAIV) of subtype H5 surpassed all previously recorded European outbreaks in size, genotype constellations and reassortment frequency and continued into 2022 and 2023. The causative 2.3.4.4b viral lineage proved to be highly proficient with respect to reassortment with cocirculating low pathogenic AIV and seems to establish an endemic status in northern Europe. A specific HPAIV reassortant of the subtype H5N3 was detected almost exclusively in red knots (Calidris canutus islandica) in December 2020. It caused systemic and rapidly fatal disease leading to a singular and self-limiting mass mortality affecting about 3.500 birds in the German Wadden Sea, roughly 1% of the entire flyway population of islandica red knots. Phylogenetic analyses revealed that the H5N3 reassortant very likely had formed in red knots and remained confined to this species. While mechanisms of virus circulation in potential reservoir species, dynamics of spill-over and reassortment events and the roles of environmental virus sources remain to be identified, the year-round infection pressure poses severe threats to endangered avian species, and prompts adaptation of habitat and species conservation practices. One-Sentence SummaryHigh red knot mortality in Europe (December 2020) was associated with infection of a unique genotype of HPAIV H5N3 clade 2.3.4.4b.

ecology↗

bioRxiv2023

Pathogen-prey-predator relations of avian raptors during epizootics of highly pathogenic avian influenza virus HPAIV H5N1 (clade 2.3.4.4b) in Germany

Transition of highly pathogenic clade 2.3.4.4b H5 avian influenza virus (HPAIV) from epizootic to enzootic status in Northern European countries was associated with severe losses and even mass mortalities among various wild bird species. Both avian and mammalian raptors hunting infected debilitated birds or scavenging on virus-contaminated avian carcasses contracted HPAIV infection. This precarious pathogen-prey-predator relation further worsened when in 2021 and 2022 outbreaks in Germany overlapped with the hatching season of avian raptor species. Retro- and prospective surveillance revealed avian raptors as important indicators of HPAIV and its genetic diversity on the one hand. On the other hand, their role as victims of HPAIV is stipulated. The first case of an HPAIV H5N1-related death of a white-tailed sea eagle (Haliaeetus albicilla; WTSE) hatch in Germany, 2021, followed by several such cases in 2022, and a low overall seropositivity rate of 5.0-7.9% among WTSE nestlings, raised fears of a serious negative impact on reproduction rates of WTSEs and other birds of prey when HPAIV becomes enzootic in an ecosystem. However, comparably stable breeding success of WTSE in the study area in 2022 and a potentially evolving natural immunity raises hope for a less severe long-term impact. Article impact statementAdapted surveillance measures were developed to assess risks for the conservation of avian raptors due to the panzootic spread of HPAIV.

microbiology↗

bioRxiv2023

Highly pathogenic avian influenza A virus (HPAIV) H5N1 infection in two European grey seals (Halichoerus grypus) with encephalitis.

Recent reports documenting sporadic infections in carnivorous mammals worldwide with highly pathogenic avian influenza virus (HPAIV) H5N1 clade 2.3.4.4b have raised concerns about the potential risk of adaptation to sustained transmission in mammals, including humans. We report H5N1 clade 2.3.4.4b infection of two grey seals (Halichoerus grypus) from coastal waters of The Netherlands and Germany in December 2022 and February 2023, respectively. Histological and immunohistochemical investigations showed in both animals a non-suppurative and necrotizing encephalitis with viral antigen restricted to the neuroparenchyma. Whole genome sequencing showed the presence of HPAIV H5N1 clade 2.3.4.4b strains in brain tissue, which were closely related to sympatric avian influenza viruses. Viral RNA was also detected in the lung of the seal from Germany by real-time quantitative PCR. No other organs tested positive. The mammalian adaptation PB2-E627K mutation was identified in approximately 40% of the virus population present in the brain tissue of the German seal. Retrospective screening for nucleoprotein specific antibodies, of sera collected from 251 seals sampled in this region from 2020 to 2023, did not show evidence of influenza A virus specific antibodies. Similarly, screening by reverse transcription PCR of lung and brain tissue of 101 seals that had died along the Dutch coast in the period 2020-2021, did not show evidence of influenza virus infection. Collectively, these results indicate that individual seals are sporadically infected with HPAIV-H5N1 clade 2.3.4.4b, resulting in an encephalitis in the absence of a systemic infection, and with no evidence thus far of onward spread between seals.

ecology↗

bioRxiv2022

Cold-passaged isolates and bat-swine influenza A chimeric viruses as modified live-attenuated vaccines against influenza A viruses in pigs

Swine influenza A virus (swIAV) infections in pig populations cause considerable morbidity and economic losses. Frequent reverse zoonotic incursions of human IAV boost reassortment opportunities with authentic porcine and avian-like IAV in swine herds potentially enhancing zoonotic and even pre-pandemic potential. Vaccination using adjuvanted inactivated full virus vaccines is frequently used in attempting control of swIAV infections. Accelerated antigenic drift of swIAV in large swine holdings and interference of maternal antibodies with vaccine in piglets can compromise these efforts. Potentially more efficacious modified live-attenuated vaccines (MLVs) bear the risk of reversion of MLV to virulence. Here we evaluated new MLV candidates based on cold-passaged swIAV or on reassortment-incompetent bat-IAV-swIAV chimeric viruses. Serial cold-passaging of various swIAV subtypes did not yield unambiguously temperature-sensitive mutants although safety studies in mice and pigs suggested some degree of attenuation. Chimeric bat-swIAV expressing the hemagglutinin and neuraminidase of an avian-like H1N1, in contrast, proved to be safe in mice and pigs, and a single nasal inoculation induced protective immunity against homologous challenge in pigs. Reassortant-incompetent chimeric bat-swIAV vaccines could aid in reducing the amount of swIAV circulating in pig populations, thereby increasing animal welfare, limiting economic losses and lowering the risk of zoonotic swIAV transmission.

microbiology↗