Biology subjects

Pfaff, F.

Publications and source records attributed to Pfaff, F..

10 recordsLinked to original sources

bioRxiv2026

Two incursions, two viruses: Emergence of a second novel Shamonda virus clade in Central Europe, 2026

Following the emergence of Shamonda virus (SHAV) in Europe in 2026, we identified a second, genetically distinct SHAV clade in cattle in Germany. Consistent differences across all three genome segments together with divergent regional distribution patterns indicate independent introductions. We have designated the two clades as SHAV Europe 1 (SHAV-EU1) and SHAV Europe 2 (SHAV-EU2). The unexpected co-circulation of these two clades has important implications for diagnostics, surveillance, host range assessment, risk evaluation, and control measures.

microbiology↗

bioRxiv2026

It happened again - emergence of a Shamonda-like orthobunyavirus in Central Europe, 2026

Since mid-June 2026, an acute, non-fatal syndrome with high herd morbidity, reduced milk yield, diarrhea, fever and lethargy affected dairy cattle in southern Germany and Switzerland. Major viral pathogens were excluded. Pan-Simbuvirus PCR first detected an orthobunyavirus, subsequently confirmed by metagenomic sequencing, which enabled recovery of a complete "Shamonda-like" genome. One sentence summary lineMore than a decade after the emergence of Schmallenberg virus in 2011, a novel "Shamonda-like" orthobunyavirus of the Simbu serogroup has now emerged in Central Europe.

microbiology↗

bioRxiv2026

Buffaloed in Brandenburg: Germany's first Brush with Foot-and-Mouth Disease after four Decades of Freedom

Foot-and-mouth disease (FMD) virus is one of the most feared and most consequential pathogens of livestock worldwide. It can be spread rapidly by the transboundary movement of animals, animal products and byproducts. In January 2025, Germany detected its first FMD outbreak since 1988 in extensively reared water buffalo on a small farm in the state of Brandenburg, directly outside Berlin, the federal capital. Immediate control measures including a standstill for movements of susceptible animals and pre-emptive culling were implemented by the veterinary authorities. Whole-genome sequencing identified the virus as serotype O, topotype ME-SA, lineage SA-2018 and revealed extensive recombination, but cross-neutralization assays suggested good heterologous protection by an O/PanAsia-2 vaccine strain. Epidemiological back-calculation placed the time of virus introduction in late December 2024. Although the entry route remains unresolved, human-associated introduction is most likely. Network analysis revealed minimal farm connectivity, and simulations predicted low potential for onward transmission, which is consistent with the outbreak being ultimately restricted to a single herd. This event underscores the constant and unpredictable risk of introduction of the virus. Early detection through increased awareness and comprehensive differential diagnostics as well as the international collaboration of veterinary services, laboratories and experts are essential in the face of the global presence of FMD.

microbiology↗

bioRxiv2026

A novel genetically distinct Amdoparvovirus in Sorex araneus in the United Kingdom highlights an unexplored ancestral link

Amdoparvoviruses have historically been documented almost exclusively in carnivores, with recent detections in bats. However, endogenous viral elements in rodent genomes suggest a more ancient and taxonomically broader evolutionary history. Despite this, small mammals have never been systematically surveyed for extant amdoparvovirus infections. In this study, we used whole genome sequencing to screen four different shrew species and wild American mink in the UK, which may act as a reservoir host for amdoparvoviruses. We identified a highly divergent amdoparvovirus in native common shrews (Sorex araneus) from northern England, tentatively named Shrew parvovirus 1(SP 1). Classical amdoparvovirus sequences were also detected in wild American mink (Neogale vison), confirming the presence of known amdoparvovirus strains in UK mustelids. Phylogenetic analysis revealed that the shrew virus, SP 1, forms a distinct clade, suggesting ancient divergence or long-term cryptic circulation in small mammal reservoirs. These findings fundamentally challenge the hypothesis that amdoparvoviruses are carnivore-restricted pathogens and underscore the importance of systematic wildlife surveillance for understanding viral host range evolution and assessing spillover risks.

evolutionary biology↗

bioRxiv2025

Wuhan sharpbelly bornavirus (genus Cultervirus) can infect a wide range of host cells and establishes persistent infection in diverse cypriniform cells

Our recent study using in silico data mining identified novel culterviruses (family: Bornaviridae) in fish, including a variant of W[u]han sharpbelly bornavirus (WhSBV) in grass carp kidney and liver cell lines. Here, metagenomic sequencing of different fish cell lines revealed WhSBV in two cell lines from grass carp (Ctenopharyngodon idella; order: Cypriniformes). Using these cell lines, we investigated the ability of WhSBV to infect and establish persistent infection in other cell lines from bony fish (Cypriniformes, Chichliformes, Salmoniformes, Centrarchiformes and Spariformes), reptiles (Testudines and Squamata), birds (Galliformes) and mammals (Primates and Rodentia). WhSBV showed efficient replication and a time-dependent increase in viral RNA levels in cypriniform cells, whereas replication was limited, confined to single cells, and lacked a clear time-dependent increase in cells from other bony fish and reptiles. No replication was detected in avian and mammalian cells. In situ hybridisation and electron microscopy confirmed the presence of viral RNA and particles in infected cypriniform cells. Transcriptomic sequencing revealed minimal innate immune activation during early stages of infection and antiviral response only at later stages, suggesting that WhSBV establishes persistence by evading early immune recognition. In addition, we identified polycistronic viral mRNAs regulated by specific transcriptional start and termination sites and RNA splicing. Viral proteins were detected, confirming previous in silico predictions. These findings provide insights into the potential infectivity, persistence mechanisms and transcriptional strategies of WhSBV. This study validates previous findings from in silico data mining, further reinforcing its effectiveness as a powerful tool for discovering hidden viruses. IMPORTANCEUnderstanding the diversity and host range of viruses is crucial for assessing their ecological role, associated diseases and zoonotic potential. However, many newly discovered viruses are characterised using sequence data alone because isolates are often difficult to obtain. Using cell culture models, this study characterises W[u]han sharpbelly bornavirus (WhSBV), a member of the genus Cultervirus. Here we demonstrate its ability to establish persistent infection in cypriniform fish cell lines, while exhibiting restricted replication in certain non-cypriniform fish. The identification of polycistronic transcription, splicing events and immune evasion mechanisms advances our understanding of the molecular biology of WhSBV and culterviruses in general. By validating in silico predictions, this study highlights the power of computational approaches in uncovering viral diversity. As cypriniform fish include economically important species such as carp, understanding the dynamics of WhSBV host range and infection biology may be crucial for future aquaculture health management.

molecular biology↗

bioRxiv2023

Small in size but huge as reservoir -- insights into the virome of European white-toothed shrews

While the virome and immune system of bats and rodents have been extensively studied, comprehensive data are lacking for insectivores. Anthropogenic land use and outdoor recreational activities may lead to an expansion of the human-shrew interface with the risk of zoonotic infections, as reported for Borna disease virus 1. We investigated the virosphere of four white-toothed shrew species from Central Europe, addressing the One Health concept of spillover prevention. A high diversity of viruses was identified, including several co-infections. Whole genomes were generated for novel species of paramyxoviruses (n=3), nairoviruses (n=2) and hepevirus. Phylogenetically, they are closely related to WHO priority diseases, such as henipaviruses. High viral loads of orthoparamyxoviruses were detected in kidneys, in well-perfused organs for orthonairoviruses, and an association with liver and intestine was identified for orthohepevirus. Our study highlights the virus diversity present in shrews, not only in biodiversity hotspots but also in industrialised countries.

evolutionary biology↗

bioRxiv2023

Diving Deep into Fish Bornaviruses: Uncovering Hidden Diversity and Transcriptional Strategies through Comprehensive Data Mining

Recently, we discovered two novel orthobornaviruses in colubrid and viperid snakes using an in silico data mining approach. Here, we present the results of a screening of more than 100,000 nucleic acid sequence datasets of fish samples from the Sequence Read Archive (SRA) for potential bornaviral sequences. We discovered the potentially complete genomes of seven bornaviruses in datasets from osteichthyans and chondrichthyans. Four of these are likely to represent novel species within the genus Cultervirus, and we propose that one genome represents a novel genus within the family of Bornaviridae. Specifically, we identified sequences of W[u]han sharpbelly bornavirus (WhSBV) in sequence data from the widely used grass carp liver and kidney cell lines L8824 and CIK, respectively. A complete genome of Murray-Darling carp bornavirus (MDCBV) was identified in sequence data from a goldfish (Carassius auratus). The newly discovered little skate bornavirus (LSBV), identified in the little skate (Leucoraja erinacea) dataset, contained a novel and unusual genomic architecture (N-Vp1-Vp2-X-P-G-M-L), as compared to other bornaviruses. Its genome is thought to encode two additional open reading frames (tentatively named Vp1 and Vp2), which appear to represent ancient duplications of the gene encoding for the viral glycoprotein (G). The datasets also provided insights into the possible transcriptional gradients of these bornaviruses and revealed previously unknown splicing mechanisms.

evolutionary biology↗

bioRxiv2022

Mystery of fatal "Staggering disease" unravelled: Novel rustrela virus causes severe encephalomyelitis in domestic cats

Staggering disease is a neurological disorder considered a threat to European domestic cats (Felis catus) for almost five decades. However, its aetiology has remained obscure. Rustrela virus (RusV), a relative of rubella virus, has recently been shown to be associated with encephalitis in a broad range of mammalian hosts. Here, we report the detection of RusV RNA and antigen by metagenomic sequencing, RT-qPCR, in-situ hybridization and immunohistochemistry in brain tissues of 28 out of 29 cats with non-suppurative meningoencephalomyelitis and staggering disease-like neurological disorder from Sweden, Austria, and Germany, but not in non-affected control cats. Screening of possible reservoir hosts in Sweden revealed RusV infection in wood mice (Apodemus sylvaticus). Our work strongly indicates RusV as the long-sought cause of feline staggering disease. Given its broad host spectrum and considerable geographic range, RusV may be the aetiological agent of neuropathologies in further mammals, possibly even including humans.

microbiology↗

bioRxiv2021

Revisiting rustrela virus - new cases of encephalitis and a solution to the capsid enigma

Rustrela virus (RusV, species Rubivirus strelense) is a recently discovered relative of rubella virus (RuV) that has been detected in cases of encephalitis across a wide spectrum of mammals, including placental and marsupial animals. Here we diagnosed two additional cases of fatal RusV-associated meningoencephalitis in a South American coati (Nasua nasua) and a Eurasian otter (Lutra lutra) that were detected in a zoological garden with history of prior RusV infections. Both animals showed abnormal movement or unusual behaviour and their brains tested positive for RusV using specific RT-qPCR and RNA in situ hybridization. As previous sequencing of RusV proved to be very challenging, we employed a sophisticated target-specific capture enrichment with specifically designed RNA baits to generate complete RusV genome sequences from both detected encephalitic animals and apparently healthy wild yellow-necked field mice (Apodemus flavicollis). Furthermore, the technique was used to revise three previously published RusV genomes from two encephalitic animals and a wild yellow-necked field mouse. Virus-to-host sequence ratio and thereby sequence coverage improved markedly using the enrichment method as compared to standard procedures. When comparing the newly generated RusV sequences to the previously published RusV genomes, we identified a previously undetected stretch of 309 nucleotides predicted to represent the intergenic region and the sequence encoding the N-terminus of the capsid protein. This indicated that the original RusV sequence was likely incomplete due to misassembly of the genome at a region with an exceptionally high G+C content of >80 mol%, which could not be resolved even by enormous sequencing efforts with standard methods. The updated capsid protein amino acid sequence now resembles those of RuV and ruhugu virus in size and harbours a predicted RNA binding domain that was not encoded in the original RusV genome version. The new sequence data indicate that RusV has the largest overall genome (9,631 nucleotides), intergenic region (290 nucleotides) and capsid protein-encoding sequence (331 codons) within the genus Rubivirus.

microbiology↗

bioRxiv2021

Adherent and suspension baby hamster kidney cells have a different cytoskeleton and surface receptor repertoire

Animal cell culture, with single cells growing in suspension, ideally in a chemically defined environment, is a mainstay of biopharmaceutical production. The synthetic environment lacks exogenous growth factors and usually requires a time-consuming adaptation process to select cell clones that proliferate in suspension to high cell numbers. The molecular mechanisms that facilitate the adaptation and that take place inside the cell are largely unknown. Especially for cell lines that are used for virus antigen production such as baby hamster kidney (BHK) cells, the restriction of virus growth through the evolution of undesired cell characteristics is highly unwanted. The comparison between adherently growing BHK cells and suspension cells with different susceptibility to foot-and-mouth disease virus revealed differences in the expression of cellular receptors such as integrins and heparan sulfates, and in the organization of the actin cytoskeleton. Transcriptome analyses and growth kinetics demonstrated the diversity of BHK cell clones and confirmed the importance of well-characterized parental cell clones and mindful screening to make sure that essential cellular features do not get lost during adaptation.

cell biology↗