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Sironen, T.

Publications and source records attributed to Sironen, T..

At least 19 recordsLinked to original sources

Detection and characterisation of alpha- and betacoronaviruses in rodents and bats from Germany, France, Belgium and Ireland

Recent zoonotic coronavirus outbreaks have sparked an interest in understanding coronaviruses circulating in animal reservoirs. While bats are recognised as major reservoirs for these viruses, coronaviruses have also been detected in a wide range of terrestrial small mammals, particularly rodents. However, coronavirus diversity in these mammals, specifically in Europe, is still poorly characterised. In this study, we detected and characterised coronaviruses in terrestrial small mammals and bats from Belgium, France, Germany, and Ireland. We screened tissue samples from rodents and shrews and environmental bat guano using pan-coronavirus real-time and conventional PCRs, with positive results confirmed by sanger sequencing. Among 2667 bat and 1152 terrestrial mammal samples, we detected 59 positive samples, 36 from bats and 23 from rodents, from which we recovered 60 coronavirus sequences, spanning both Alphacoronavirus and Betacoronavirus lineages. Through next generation sequencing we identified one Pipistrellus pygmaeus bat guano sample carrying two distinct alphacoronaviruses, representing Nyctacovirus and Pedacovirus subgenera. Among rodents, most coronavirus-positive samples originated from a zoo in Belgium, where several CoV lineages co-circulated. The identified rodent coronaviruses clustered among previously described rodent-associated lineages, some of which also include human and other mammal-derived coronavirus sequences. Consistent with previous studies, we found sarbecoviruses in horseshoe bats (particularly Rhinolophus ferrumequinum and R. hipposideros) and merbecoviruses in Plecotus auritus bats, and these viruses are distantly related to the human coronaviruses of the respective families. Similar to bat coronaviruses, some rodent coronaviruses strains seemed to be association with specific rodent species. In conclusion, our study enhances the understanding of coronaviruses in rodents and bats, revealing potential hotspots for these viruses and their implication for human and animal health. These findings underscore the necessity for continued surveillance of coronaviruses in wildlife reservoirs to mitigate future zoonotic spillover risks.

microbiology↗

A rational design strategy and validation for protease-resistant fusion-inhibitor antiviral peptides

Peptide-based fusion inhibitors are promising pharmaceuticals in the fight against enveloped viruses relying on membrane fusion for host infection. However, peptide therapeutic applications have long been hindered by their poor stability in vivo. Here, we discovered that peptide inhibitors with the wildtype sequence of the heptad repeat 2 (HR2) domain of the SARS-CoV-2 spike protein are efficiently cleaved by Transmembrane Protease, Serine 2 (TMPRSS2), a key protease involved in the SARS-CoV-2 virus-cell fusion pathway. We then identified the corresponding cleavage sites and designed three protease-resistant peptides using ranking based on deep mutational scanning and natural occurrence. The three candidates all exhibit inhibitory activity in a cell-cell fusion assay. A high-resolution cryo-EM structure of the top candidate, HR2-NHN, bound to its HR1 target reveals the molecular basis for its potent activity. The top candidate of the cell-based screening assay significantly improved efficacy relative to the wildtype peptide when administered 12 h before infection in both an authentic virus-cell infection assay and a mouse assay. More broadly, our results suggest that the design strategies for protease-resistant peptides could be applied to a broad spectrum of other enveloped viruses and pave the way for the development of safe, prophylactic antivirals that can be administered before exposure.

microbiology↗

Co-circulating TBEV lineages and evidence for vertical transmission in wild bank voles from Poland

Tick-borne encephalitis virus (TBEV) is a zoonotic flavivirus maintained in complex enzootic cycles involving ticks and vertebrate hosts. While vector-mediated transmission has been extensively studied, host-associated mechanisms, including vertical transmission and prolonged viral carriage in natural reservoir populations, remain poorly understood. Here, we investigated TBEV circulation, genetic diversity, and evidence for vertical transmission in bank voles (Clethrionomys glareolus) from a highly endemic region of North-eastern Poland. A total of 258 wild rodents were screened using molecular and serological approaches. TBEV RNA was detected in 14.3% of individuals, whereas seroprevalence was substantially lower (6.6%), revealing limited concordance between viral presence and humoral response under natural conditions. Near-complete genome sequences were obtained from 10 TBEV-positive individuals, representing the first near-complete TBEV genomes generated from wild rodents in Poland. All isolates belonged to the European subtype (TBEV-Eu), and phylogenetic analysis revealed two genetically distinct viral clades co-circulating within a narrow spatiotemporal window. Importantly, TBEV RNA and/or envelope protein were detected in embryos from naturally infected females, providing evidence consistent with vertical transmission in a wild reservoir host. Together, these findings suggest that vertical transmission and complex host infection dynamics may be underappreciated components of TBEV maintenance in natural reservoir populations. Our results highlight the need to integrate vertebrate host dynamics into models of TBEV ecology and support expanded wildlife-based surveillance to better understand and predict zoonotic risk.

microbiology↗

Egyptian rousette bat humoral immunity to H9 influenza hemagglutinin

In mammals, antibodies are central to antiviral defense, but they can also impose selective pressure that drives viral evolution. The interplay between viral antigenic variation and host antibody diversification constitutes a molecular arms race that influences pathogenicity, transmission, and spillover risk. Bats are reservoirs for zoonotic viruses with pandemic potential yet they appear to tolerate infection without overt disease. Although distinctive features of bat innate immunity have been described, the role of adaptive immunity--particularly antibody-mediated responses--remains largely undefined. Moreover, how antibody evolutionary pressure operates in bats is unknown, in part because tools to interrogate bat B cell responses at the monoclonal level are limited. Here, we developed a yeast surface display library of bat antibodies derived from splenic RNA of wild-caught Egyptian rousette bats to interrogate humoral responses to the bat-derived H9 influenza hemagglutinin. We isolated monoclonal antibodies recognizing the hemagglutinin (HA) antigen and defined their gene usage, somatic hypermutation frequency, binding affinities, and breadth. We then used cryo-EM to structurally characterize three bat antibodies in complex with HA engaging distinct antigenic sites. Together, these data enable direct comparison with human anti-influenza antibodies highlighting similarities in humoral immunity across mammals and provides a tool to examine bat antibody responses to other potential zoonotic viruses.

immunology↗

Bartonella and hemotropic Mycoplasma species in synanthropic bats in Kenya

Identifying and characterizing zoonotic pathogens in wildlife is essential for understanding disease risk to humans. In Sub-Saharan Africa, many people live with bats in their houses and are exposed to their pathogens, yet little is known about the bacterial pathogens in Afrotropical bat species. Globally, Bartonella spp. (bartonellae) and hemotropic Mycoplasma spp. (hemoplasmas) are common bacterial pathogens in bats, and some lineages are known to spill over and cause infections in humans. To evaluate this disease risk, we screened three common synanthropic bat species in Kenya, and their ectoparasites, for hemoplasmas and bartonellae and assessed their relatedness to known human pathogens. Of 767 bats across 21 sites, 17.9% of bats were Bartonella spp. positive and 19.3% were hemoplasma positive. Bat ectoparasites had similar Bartonella prevalence (13.5-25.0%) and, for most bat species, ectoparasite loads were not associated with increased likelihood of Bartonella infection. We found that Bartonella lineages displayed phylogenetic overlap between different bat species and ectoparasites, suggesting pathogen sharing between species, while hemoplasma lineages corresponded strictly to host taxonomy. Finally, we found that 16S rRNA sequences from one heart-nosed bat (Cardioderma cor) were 97.85% similar to a human-associated hemoplasma found previously in Schreibers bats (Miniopterus schreibersii) in Spain. We show that synanthropic bats host bacteria of potential public health concern, highlighting the need to investigate the emerging impacts of these pathogens on human health in Kenya and elsewhere in Sub-Saharan Africa.

ecology↗

Rat hepatitis E virus and novel paramyxoviruses in synanthropic rodents and shrews in Kenya

The majority of emerging infectious diseases are zoonotic, having their origin in wildlife before spilling over into the human population. While small mammals are recognized as critical reservoirs for these viruses, their viral diversity remains largely uncharacterized across many African countries. We conducted molecular surveillance of synanthropic rodents and shrews in the Kibera informal settlement in Nairobi and the rural Taita Hills region of Kenya to detect and characterize potential zoonotic viruses. Tissue samples from 228 rodents and shrews were screened for six viral families using PCR assays. Rat hepatitis E virus (HEV) (Rocahepevirus ratti), a rodent-associated virus with potential for human spillover, was identified in Mus musculus and Rattus norvegicus from Kibera. NGS was conducted for the HEV positive samples, and we obtained two near-complete HEV genomes from Rattus norvegicus, which clustered within rodent-associated HEV genotypes in the phylogenetic analysis. The two sequences from the Rattus norvegicus cluster together, indicating a close genetic relationship. Paramyxoviruses belonging to the genera Jeilongvirus and Parahenipavirus were detected both from Taita and Kibera in nine different samples from Rattus norvegicus, Mus minutoides, Crocidura sp and Acomys ignitus. One paramyxovirus positive sample (Acomys ignitus) from Taita was selected for further sequencing with NGS, and a complete genome of a new jeilongvirus was assembled. Phylogenetic analysis of the detected viruses confirmed the close relation to previously known rodent-borne jeilongviruses but also revealed potentially novel jeilong- and parahenipavirus species. Our findings highlight the circulation of potentially zoonotic viruses in both urban and rural small mammals in Kenya. It emphasizes the necessity of continued genomic surveillance of zoonotic viruses to mitigate risks of their spillover into human populations. HighlightsO_LISurveillance reveals diverse rodent-borne viruses circulating in Kenya. C_LIO_LIRat-HEV was detected in Rattus norvegicus and Mus musculus from an urban low-income area. C_LIO_LIParamyxoviruses were detected across multiple rodent and shrew species, including novel Acomys ignitus jeilongvirus. C_LI Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=139 SRC="FIGDIR/small/719784v1_ufig1.gif" ALT="Figure 1"> View larger version (66K): org.highwire.dtl.DTLVardef@86c94aorg.highwire.dtl.DTLVardef@10946adorg.highwire.dtl.DTLVardef@1ff45eforg.highwire.dtl.DTLVardef@4876f1_HPS_FORMAT_FIGEXP M_FIG C_FIG

microbiology↗

Age-dependent effects of infection on survival of a wild rodent reservoir host

Due to long co-evolutionary histories, many zoonotic pathogens are thought to exert little or no negative effects on their wildlife reservoir hosts. However, there remains a lack of rigorous investigations in natural settings. We conducted a 3-year factorial field experiment to investigate how survival of the Puumala hantavirus (PUUV) reservoir, the bank vole, is impacted by PUUV infection, nematode infections, and food availability. We hypothesized that PUUV would not impact survival, but that coinfection with nematodes would negatively impact survival, and that increased food availability would mitigate the negative effects of coinfection. Surprisingly, we demonstrated that PUUV infected voles had substantially reduced survival when compared to uninfected voles, and this strong negative effect manifested in young voles. Nematode removal increased survival of young voles and food supplementation interacted with movement rather than survival. Our results provide empirical evidence in a natural system for infection reducing survival of its reservoir host.

ecology↗

American mink as an animal model to study SARS-CoV-2 and vaccine response

Selecting a suitable animal model is crucial in understanding infectious diseases and developing vaccines. Here, we developed a receptor-binding domain -based SARS-CoV-2 vaccine with mouse Fc an immunopotentiator in a mink model. Four different variations of the vaccine were tested in groups of 30-31 American mink and followed for IgG and neutralizing antibodies (nAb) up to 27 weeks. Subcutaneous version induced a strong IgG and nAb response within two weeks and was still detectable at 27 weeks. Intranasal version also caused a detectable, although weaker, immune response. A simultaneously given subcutaneous vaccine against virus enteritis, botulism and hemorrhagic pneumonia potentially caused a lower SARS-CoV-2 antibody response, highlighting the need for further studies on co-effects of vaccines. In virus challenge with Alpha variant (B.1.1.7), vaccinated mink had a stronger antibody response than unvaccinated mink. Despite not preventing the infection, vaccinated mink had milder clinical signs and less virus in saliva. Another challenge of unvaccinated mink with Omicron variant showed similar results to alpha (BA.1) variant. Virus RNA was detected in the brain of unvaccinated mink but not vaccinated mink by in situ hybridization, indicating a suitability of mink to study neurological effects of SARS-CoV-2 and potentially long COVID as well. Author summaryFinding a good animal model is very important in studying infectious diseases and their treatment. The recent SARS-CoV2 pandemic highlighted this dilemma. We have developed an animal model based on mink due to their close match to humans in the symptomology of this disease. Such model will enable the study of relative susceptibility, transmission, tissue tropism, complex pathogenesis and long COVID, as well as prophylaxis and vaccines. This model will also help reduce the use of primates in this research. We have further developed a new vaccine for SARS-CoV2 based on the receptor binding domain of the S-protein with an inbuilt immune-enhancer. This vaccine underwent extensive testing in mink to determine response, long term protection, and safety. The vaccine was found to provide excellent titers of neutralizing antibodies with wide range in target variants. It also reduced the severity and duration of visible symptoms in the animals significantly. We propose this vaccine candidate for further study and future commercialization.

microbiology↗

Drivers of host-pathogen community assemblies in European forests and urban green spaces

Major advances in the understanding of infectious diseases have been achieved in the last decades. However, the persistence and re-emergence of pathogens continue to raise public and veterinary health concerns, of which the recent COVID-19 pandemic may be one of the most dramatic examples. Understanding the impact of habitat alterations and concomitant biodiversity loss on pathogen transmission and emergence from wildlife remains challenging. Here, we aim to elucidate the interlinkages between biodiversity and rodent-borne diseases at local and European scales. We present recently collected host-pathogen data from 21 temperate forest sites and eight urban green spaces throughout five European countries, environments where rodents are abundant and human/domestic animals - wildlife interactions are likely to occur. 3766 specimens were analyzed during the period from 2020 to 2022 comprising 15 different small mammal species. Different organ tissues of each specimen were screened for bacteria by either 16S rRNA amplicon sequencing or specific PCR. The presence of antibodies to different families of viruses was screened using immunofluorescent assays. A multitude of pathogens of zoonotic potential from several genera including Bartonella, Borrelia, Mycoplasma, Anaplasma, Neoehrlichia, Leptospira, Orthohantavirus and Orthopoxvirus were detected at non-negligible prevalence in 11 different terrestrial mammal species. A shift in host community composition was observed along the anthropization gradient with more urban adapters in more anthropized sites. Pathogen richness increased with an increase in host species diversity, following the "host-diversity begets parasite-diversity" hypothesis. The absence of some vector-transmitted parasites in urban areas suggests a shift in pathogen community along the anthropization gradient. Host species and host intrinsic factors were dominant explanatory variables for endoparasitic Mycoplasma species and Sarcocystidae, while extrinsic environmental and climatic factors where influential in explaining variations in occurrences of several vector-transmitted pathogens. Apodemus sylvaticus and Clethrionomys glareolus were important connector host species in respectively urban green spaces and temperate forests. Increased host diversity, but not anthropization, correlated with a richer pathogen community. These results ultimately lead to an increased understanding of the complex host-pathogen system at the local landscape that can aid future management decisions and support the public health sector.

ecology↗

Ecological factors alter how spatial overlap predicts viral infection dynamics in wild rodent populations

Spatial overlap between animals in wildlife populations can have important implications for pathogen transmission. Ecological factors and animal demographic traits can influence animal space use and spatial overlap, but it is unclear how these interactions drive pathogen transmission. We experimentally manipulated wild bank vole populations via resource supplementation and anthelmintic treatment. Using network analysis, we investigated the relationship between spatial overlap and infection likelihood of an endemic zoonotic hantavirus, including how vole sex and reproductive status interact with spatial behaviour to affect infection likelihood. Spatial overlap in a previous month drove the likelihood of current hantavirus infection, and food supplementation and anthelmintic treatment altered the effects of spatial overlap on infection likelihood. Vole sex and reproductive status were important factors determining whether spatial overlap increased or decreased the likelihood of hantavirus infection and interacted with resource supplementation and anthelmintic treatment, generating different infection dynamics in each treatment. Our research provides rare empirical evidence linking previous spatial overlap to current infection status in wildlife populations, with implications for understanding disease dynamics and persistence as well as developing effective management efforts. We further highlight the importance of incorporating variation in ecological factors and host demography when studying pathogen transmission in wildlife systems.

ecology↗

Equine dermatitis outbreak associated with parapoxvirus

Parapoxviruses (PPV) cause skin and mucous membrane lesions in several animal species, and of the five recognized PPVs, at least three are zoonotic. Equine PPV (EqPPV) is the sixth one initially described in humans in the United States and later in a severely sick horse in Finland in 2013-2015. In 2021-2022, a large-scale pustulo-vesicular pastern dermatitis outbreak occurred in horses all over Finland. This study aimed at analysing the outbreak, identifying and describing the causative agent, describing clinical signs, and searching for risk factors. EqPPV was identified as a probable causative agent and co-infections with several potentially pathogenic and zoonotic bacteria were observed. Histopathologically, suppurative and ulcerative dermatitis was diagnosed. Due to the lack of specific tests for this virus, we developed a novel diagnostic EqPPV-PCR with sensitivity of 10 copies/reaction. Based on a large proportion of the genome sequenced directly from clinical samples, very little variation was detected between the sequences of the case from 2013 and the cases from 2021-2022. Based on an epidemiological survey, the main risk factor for pastern dermatitis was having racehorses. Approximately one third of the horses at each affected stable got clinical dermatitis, manifesting as severe skin lesions. Skin lesions were also occasionally reported in humans, indicating potential zoonotic transmission. Case stables commonly reported attendance in race events before acquiring the disease. Survey also identified differences in practises between case and control stables. Taken together, these results enable a better preparedness, diagnostics, and guidelines for future outbreaks.

microbiology↗

Complete Protection from SARS-CoV-2 Lung Infection in Mice Through Combined Intranasal Delivery of PIKfyve Kinase and TMPRSS2 Protease Inhibitors

Emerging variants of concern of SARS-CoV-2 can significantly reduce the prophylactic and therapeutic efficacy of vaccines and neutralizing antibodies due to mutations in the viral genome. Targeting cell host factors required for infection provides a complementary strategy to overcome this problem since the host genome is less susceptible to variation during the life span of infection. The enzymatic activities of the endosomal PIKfyve phosphoinositide kinase and the serine protease TMPRSS2 are essential to meditate infection in two complementary viral entry pathways. Simultaneous inhibition in cultured cells of their enzymatic activities with the small molecule inhibitors apilimod dimesylate and nafamostat mesylate synergistically prevent viral entry and infection of native SARS-CoV-2 and vesicular stomatitis virus (VSV)-SARS-CoV-2 chimeras expressing the SARS-CoV-2 surface spike (S) protein and of variants of concern. We now report prophylactic prevention of lung infection in mice intranasally infected with SARS-CoV-2 beta by combined intranasal delivery of very low doses of apilimod dimesylate and nafamostat mesylate, in a formulation that is stable for over 3 months at room temperature. Administration of these drugs up to 6 hours post infection did not inhibit infection of the lungs but substantially reduced death of infected airway epithelial cells. The efficiency and simplicity of formulation of the drug combination suggests its suitability as prophylactic or therapeutic treatment against SARS-CoV-2 infection in households, point of care facilities, and under conditions where refrigeration would not be readily available.

microbiology↗

Evolution and Genetic Characterization of Seoul Virus in Wild Rats Rattus Norvegicus from an urban park in Lyon, France 2020-2022

Seoul virus (SEOV) is an orthohantavirus primarily carried by rats that can cause hemorrhagic fever with renal syndrome (HFRS) in humans. Nowaday s, its incidence is likely underestimated. We developed a comprehensive serological and molecular characterization of SEOV in Rattus norvegicus population from a popular urban park within a large city ( Park of La Tete dOr, Lyon, France) between 2020 and 2022. We confirmed the circulation of SEOV in rats from the park (seroprevalence 17.2%). The SEOV strains detected showed high genetic similar ity with the strain previously described in 2013 in this area. We found low structuring of wild rat populations within Lyon city. This study confirms the circulation of SEOV in Lyon city, in a park where opportunities for SEOV transmission to humans are numerous. Given the high gene flow between rat populations in the park and the rest of the city, we recommend conducting city-wide SEOV surveillance.

microbiology↗

The infectivity of SARS-CoV-2 progeny virions requires the activity of host cell N-myristoyltransferases and it is severely compromised by their inhibition

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which caused the coronavirus disease 2019 (COVID-19) pandemic, remains a global health concern despite vaccines, neutralizing antibodies, and antiviral drugs. Emerging mutations can reduce the effectiveness of these treatments, suggesting that targeting host cell factors may be a valuable alternative. N-myristoyltransferases (NMT) are essential enzymes for protein N-myristoylation, affecting stability, interaction, localization, and function of numerous proteins. We demonstrate that selective inhibition of host cell NMT decreases SARS-CoV-2 infection by 90% in human lung and primary nasal epithelial cells, and choroid plexus-cortical neuron organoids. NMT inhibition does not affect viral entry, replication or release, but impairs the maturation and incorporation of viral envelope proteins into newly assembled virions, leading to compromised infectivity of released virions. The inhibition of host NMT triggers a Golgi-bypassing pathway for SARS-CoV-2 progeny virion egress, which occurs through endoplasmic reticulum and lysosomal intermediates.

microbiology↗

Enhanced Viral Metagenomics with Lazypipe 2

Viruses are the main agents causing emerging and re-emerging infectious diseases. It is therefore important to screen for and detect them and uncover the evolutionary processes that support their ability to jump species boundaries and establish themselves in new hosts. Metagenomic next-generation sequencing (mNGS) is a high-throughput, impartial technology that has enabled virologists to detect either known or novel, divergent viruses from clinical, animal, wildlife and environmental samples, with little a priori assumptions. mNGS is heavily dependent on bioinformatic analysis, with an emerging demand for integrated bioinformatic workflows. Here, we present Lazypipe2, an updated mNGS pipeline with, as compared to Lazypipe1, significant improvements in code stability, transparency, with added functionality and support for new software components. We also present extensive benchmarking results, including evaluation on a novel canine simulated metagenome, and precision and recall of virus detection at varying sequencing depth and low to extremely low proportion of viral genetic material. Additionally we report accuracy of virus detection with two strategies: homology searches using nucleotide or amino acid sequences. We show that Lazypipe2 with nucleotide-based annotation approaches near perfect detection of eukaryotic viruses and, in terms of accuracy, outperforms the compared pipelines. We also discuss the importance of homology searches with amino acid sequences for the detection of highly divergent novel viruses.

bioinformatics↗

Wild red deer (Cervus elaphus) do not play a role as vectors or reservoirs of SARS-CoV-2 in north-eastern Poland.

Several studies reported a high prevalence of SARS-CoV-2 among white-tailed deer in North America. Monitoring cervids in all regions to better understand SARS-CoV-2 infection and circulation in other deer populations has been urged. To evaluate deer exposure to SARS-CoV-2 in Poland, we sampled 90 reed deer individuals shot by hunters in five hunting districts in northeastern Poland. Serum and nasopharyngeal swabs were collected, and then the Immunofluorescent Assay (IFA) to detect anti-SARS-CoV-2 antibodies was performed as well as real-time PCR with reverse transcription for direct virus detection. No positive samples were detected. There is no evidence of spillover of SARS-CoV-2 from the human to deer population in Poland.

microbiology↗

Nanobody engineering for SARS-CoV-2 neutralization and detection

In response to the ongoing SARS-CoV-2 pandemic, the quest for coronavirus inhibitors has inspired research on a variety of small proteins beyond conventional antibodies, including robust single-domain antibody fragments, nanobodies. Here, we explore the potential of nanobody engineering in the development of antivirals and diagnostic tools. Through fusion of nanobody domains that target distinct binding sites, we engineered multimodular nanobody constructs that neutralize wild-type SARS-CoV-2 and the Alpha and Delta variants with high potency, with IC50 values up to 50 pM. However, we observed a limitation in the efficacy of multimodular nanobodies against the Beta (B.1.351) and Omicron variants (B.1.1.529), underlining the importance of accounting for viral evolution in the design of biologics. To further explore the applications of nanobody engineering in outbreak management, we present a novel detection assay, based on fusions of nanobodies with fragments of NanoLuc luciferase that can detect sub-nanomolar quantities of the SARS-CoV-2 spike protein in a single step. Our work showcases the potential of nanobody engineering to combat emerging infectious disease.

microbiology↗