Biology subjects

Rasmussen, T. B.

Publications and source records attributed to Rasmussen, T. B..

9 recordsLinked to original sources

bioRxiv2026

Detection of merbecoviruses in Danish bats using a novel broad-range RT-qPCR assay

Bat-associated merbecoviruses comprise a genetically diverse group of coronaviruses with variable receptor usage and host range, highlighting the need for efficient tools for their surveillance. Here, we developed and optimized a broad-range reverse transcription quantitative PCR (RT-qPCR) assay for the detection of bat-associated merbecoviruses, including the lineage previously identified in brown long-eared bats (Plecotus auritus) in Denmark. In silico analysis predicted detection of 898 of 941 (95.4%) merbecovirus sequences, and the assay detected all bat-associated merbecoviruses included in the experimental panel. The assay was applied to 33 bats sampled through the Danish national bat surveillance program in 2025. Merbecovirus RNA was detected in two samples, one from a P. auritus and one from a Nathusius' pipistrelle (Pipistrellus nathusii), representing the first detection of a merbecovirus in P. nathusii in Denmark. Metagenomic next-generation sequencing recovered a complete merbecovirus genome from the P. nathusii sample. Phylogenetic analysis assigned the virus to the MOW clade and showed that it was closely related to the Russian MOW15-22 virus, sharing 98.67% nucleotide identity across the complete genome and 99.85% amino acid identity in the spike protein. Limited sequence data obtained from the P. auritus sample was consistent with the merbecovirus lineage previously identified in this species in Denmark. Together, these findings demonstrate the utility of broad-range RT-qPCR combined with metagenomic sequencing for surveillance and genomic characterization of bat-associated merbecoviruses.

microbiology↗

bioRxiv2026

Efficient primer design for broad-range virus detection: A semi-automated workflow using sequence clustering and varVAMP

Broad-range RT-qPCR assays are essential for detecting highly diverse viruses within virus families, but designing suitable primers remains challenging because of extensive sequence diversity and biases in public sequence databases. Here, we present a semi-automated workflow that combines sequence clustering and varVAMP to streamline pan-RT-qPCR primer design. The workflow reduces sequence redundancy, improves the representation of viral diversity, and facilitates the identification of broadly reactive primer candidates. We demonstrate the workflow using the arboviral genera Orthoflavivirus and Alphavirus as proof-of-concept datasets, showing its applicability to large and genetically diverse viral sequence collections. The workflow provides a practical, scalable, and reproducible framework for developing broad-range primer candidates and may support surveillance, diagnostics, and preparedness for emerging or divergent viruses.

microbiology↗

bioRxiv2026

Targeted metagenomic recovery of coronaviruses from wildlife samples

Coronaviruses (CoVs) are diverse RNA viruses infecting a wide range of hosts, with significant implications for public health, animal production and welfare. Bats are key reservoirs of mammalian CoVs and have contributed to the emergence and circulation of several zoonotic viruses in a wildlife context, while mustelids represent important hosts at the human-animal interface, as highlighted by SARS-CoV-2 outbreaks in farmed mink. Using metagenomic next-generation sequencing, we screened bats and wild mustelids and recovered and characterized full-length CoV genomes. Building on previous findings in Danish wildlife, including alpha-CoVs and a MERS-related beta-CoV in bats, this study expands current knowledge of coronavirus diversity and evolution in wildlife, emphasizing their relevance for zoonotic emergence.

microbiology↗

bioRxiv2024

Geothermal ecosystems on Mt. Erebus, Antarctica, support diverse and taxonomically novel biota

Mt. Erebus, Antarctica, is the southernmost active volcano in the world and harbors a diverse and geochemically unique array of geothermal ecosystems including Subglacial and Exposed features, surrounded by a vast desert of ice and snow. Previous studies, although limited in scope, have highlighted the unique and potentially endemic biota present on Mt. Erebus. In this study, we provide a systematic biodiversity study across all domains of life and all types of geothermal features present on Mt. Erebus. We present physicochemical and biological data from 39 Exposed samples and 9 Subglacial samples from Mt. Erebus. The taxonomic novelty of prokaryotes and fungi found supports past hypotheses of high endemism among the biota of Mt. Erebus; in particular, the large number of taxonomically divergent fungal sequences was surprising. We found that different site types had unique physicochemistry and biota; in particular, Exposed sites were significantly warmer than Subglacial sites (median: 40 vs 10 for Exposed and Subglacial, respectively) and tended to have greater abundances of photosynthetic organisms (Cyanobacteria and Chlorophyta). Subglacial sites were characterized by a greater abundance of prokaryotes from the phylum Actinobacteriota, correlated with the greater concentrations of Ca, Mg, and Sr present. Additionally, we found that Tramway Ridge differed from other Exposed sites as well as all Subglacial sites in physicochemistry (significantly greater conductivity, water content, total carbon, and total nitrogen levels) and biota (greater relative abundances of order Nitrososphaeria and phylum Bacteroidota). In this study, we provide a blueprint for future work aimed at better understanding the novel biota of Mt. Erebus.

microbiology↗

bioRxiv2024

Emergence and spread of SARS-CoV-2 variants from farmed mink to humans and back during the epidemic in Denmark, June-November 2020.

The severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) not only caused the COVID-19 pandemic but also had a major impact on farmed mink production in several European countries. In Denmark, the entire population of farmed mink (over 15 million animals) was culled in late 2020. During the period of June to November 2020, mink on 290 farms (out of about 1100 in the country) were shown to be infected with SARS-CoV-2. Genome sequencing identified changes in the virus within the mink and it is estimated that about 4000 people in Denmark became infected with these mink virus variants. However, the routes of transmission of the virus to, and from, the mink have been unclear. Phylogenetic analysis revealed the generation of multiple clusters of the virus within the mink. Detailed analysis of changes in the virus during replication in mink and, in parallel, in the human population in Denmark, during the same time period, has been performed here. The majority of cases in mink involved variants with the Y435F substitution and the H69/V70 deletion within the Spike (S) protein; these changes emerged early in the outbreak. However, further introductions of the virus, by variants lacking these changes, from the human population into mink also occurred. Based on phylogenetic analysis of viral genome data, we estimate, using a conservative approach, that about 17 separate examples of mink to human transmission occurred in Denmark but up to 59 such events (90% credible interval: (39-77)) were identified using parsimony to count cross-species jumps on transmission trees inferred using Bayesian methods. Using the latter approach, 136 jumps (90% credible interval: (117-164)) from humans to mink were found, which may underlie the farm-to-farm spread. Thus, transmission of SARS-CoV-2 from humans to mink, mink to mink, from mink to humans and between humans were all observed. (298 words) Author summaryIn addition to causing a pandemic in the human population, SARS-CoV-2 also infected farmed mink. In Denmark, after the first identification of infection in mink during June 2020, a decision was made in November 2020 to cull all the farmed mink. Within this outbreak, mink on 290 farms (out of about 1100 in the country) were found to have been infected. We showed, by analysis of the viruses from the mink, that the viruses on the farms were mainly of three different, but closely related, types (termed Clusters 2, 3 and 4) that shared certain distinctive features. Thus, we found that many outbreaks in mink resulted from transmission of the virus between mink farms. However, we identified that new introductions of other virus variants, presumably from infected humans, also occurred. Furthermore, we showed that spread of the virus from infected mink to humans also happened on multiple occasions. Thus, transmission of these viruses from humans to mink, mink to mink, from mink to humans and between humans were all observed. (172 words)

microbiology↗

bioRxiv2023

Release of fragmented host, cell-free, genomic DNA into the circulation of pigs during infection by virulent African swine fever virus

African swine fever virus (ASFV) causes a severe hemorrhagic disease in domestic pigs resulting in high case fatality rates. The virus replicates in circulating cells of the monocyte-macrophage lineage and within lymphoid tissues, e.g. tonsils, spleen and lymph nodes. The infection results in high fever and a variety of clinical signs from about 3 days post infection. In this study, it was observed that one of many changes resulting from ASFV- infection within pigs was a large (>1000-fold) increase in the level of circulating cell-free DNA (cfDNA), including the beta-actin gene, derived from the nuclei of host cells, in the serum. This change occurred in parallel with the increase in circulating ASFV DNA. In addition, elevated levels (about 30-fold higher) of host mitochondrial DNA (mtDNA) were detected in serum from ASFV-infected pigs, but with a much higher baseline level of mtDNA in sera from uninfected pigs. The host derived cfDNA is derived from dead cells which may, or may not, have been infected. For comparison, the release of the cellular enzyme, lactate dehydrogenase (LDH), a commonly used marker of cellular damage, was also found to be elevated during the infection. The cfDNA is readily detected in serum and is a more sensitive host marker of ASFV infection than the release of mtDNA or LDH. In addition, sera from pigs infected by classical swine fever virus (CSFV), which causes a clinically similar disease as ASFV, were also tested but this infection did not result in the release of cfDNA, mtDNA or LDH. Author summaryAfrican swine fever virus causes a severe hemorrhagic disease in domestic pigs and wild boar, which often leads to death within a week. The infection results in a spectrum of different clinical signs and other changes within infected animals. In this study, we have shown, for the first time, that one consequence of infection by a highly virulent strain of this virus is the release into the blood of host genomic DNA, in a highly fragmented form. We found an increase of >1000-fold in the level of this cell-free DNA within the serum of infected animals. Furthermore, we also showed that the level of the small circular DNA from the cell mitochondria is also elevated in serum from infected animals as is the cellular enzyme lactate dehydrogenase but these changes were less marked and occurred later. The increase in the level of the cell-free host DNA is coincident with the increase in level of the viral DNA within blood and may act as a marker for infection by a highly virulent form of the virus. Remarkably, pigs infected by classical swine fever virus, which produces similar clinical signs, did not have elevated levels of these markers in their serum.

microbiology↗

bioRxiv2023

Unlocking Predictive Power: A Machine Learning Tool Derived from In-Depth Analysis to Forecast the Impact of Missense Variants in Human Filamin C

Cardiomyopathies, diseases of the heart muscle, are a leading cause of heart failure. An increasing proportion of cardiomyopathies have been associated with specific genetic changes, such as mutations in FLNC, the gene that codes for filamin C. Altogether, more than 300 variants of FLNC have been identified in patients, including a number of single point mutations. However, the role of a significant number of these mutations remains unknown. Here, we conducted a comprehensive analysis, starting from clinical data that led to identification of new pathogenic and non-pathogenic FLNC variants. We selected some of these variants for further characterization that included studies of in vivo effects on the morphology of neonatal cardiomyocytes to establish links to phenotype, and the in vitro thermal stability and structure determination to understand biophysical factors impacting function. We used these findings to compile vast datasets of pathogenic and non-pathogenic variant structures and developed a machine-learning-based neural network (AMIVA-F) to predict the impact of single point mutations. AMIVA-F outperformed most commonly used predictors both in disease related as well as neutral variants, approaching [~]80% accuracy. Taken together, our study documents additional FLNC variants, their biophysical and structural properties, and their link to the disease phenotype. Furthermore, we developed a state-of-the-art web-based server AMIVA-F that can be used for accurate predictions regarding the effect of single point mutations in human filamin C, with broad implications for basic and clinical research.

biophysics↗

bioRxiv2021

Infection, recovery and re-infection of farmed mink with SARS-CoV-2

Mink, on a farm with about 15,000 animals, became infected with SARS-CoV-2. Over 75% of tested animals were positive for SARS-CoV-2 RNA in throat swabs and 100% of tested animals were seropositive. The virus responsible had a deletion of nucleotides encoding residues H69 and V70 within the spike protein gene. The infected mink recovered and after free-testing of the mink, the animals remained seropositive. During follow-up studies, after a period of more than 2 months without virus detection, over 75% of tested animals scored positive again for SARS-CoV-2 RNA. Whole genome sequencing showed that the virus circulating during this re-infection was most closely related to the virus identified in the first outbreak on this farm but additional sequence changes had occurred. Animals had much higher levels of anti-SARS-CoV-2 antibodies after re-infection than at free-testing. Thus, following recovery from an initial infection, seropositive mink rapidly became susceptible to re-infection by SARS-CoV-2. Article Summary LineFollowing widespread infection with SARS-CoV-2 of mink on a farm, all tested animals had seroconverted and the farm was then tested free of infection; however, less than 3 months later, a further round of infection affected more than 75% of tested animals.

microbiology↗

bioRxiv2020

Conserved cysteines in titin sustain the mechanical function of cardiomyocytes

The protein titin determines cardiomyocyte contraction and truncating variants in the titin gene (TTN) are the most common cause of dilated cardiomyopathy (DCM). Different to truncations, missense variants in TTN are currently classified as variants of uncertain significance due to their high frequency in the population and the absence of functional annotation. Here, we report the regulatory role of conserved, mechanically active titin cysteines, which, contrary to current views, we uncover to be reversibly oxidized in basal conditions leading to isoform- and force-dependent modulation of titin stiffness and dynamics. Building on our functional studies, we demonstrate that missense mutations targeting a conserved titin cysteine alter myocyte contractile function and cause DCM in humans. Our findings have a direct impact on genetic counselling in clinical practice. One sentence summaryMutations targeting cysteines key to the mechanoredox control of titin cause human dilated cardiomyopathy

physiology↗