Biology subjects

de Vries, R. D.

Publications and source records attributed to de Vries, R. D..

13 recordsLinked to original sources

bioRxiv2026

Andes virus from the MV Hondius outbreak is highly pathogenic in hamsters and airborne shed

In May 2026, an outbreak of hantavirus pulmonary syndrome (HPS) caused by Andes virus (ANDV) was detected aboard the cruise ship MV Hondius, sparking public health measures in multiple countries. ANDV infections in humans are mostly sporadic, most often linked to exposure to infected rodents in South America, although small clusters of human cases, like the 2026 outbreak on the MV Hondius occur as well. It is not known whether virological factors may contribute to this distinct epidemiology, and no phenotypic characterisation of the newly emerged ANDV (ANDV2026) has been carried out to date. Here, using an ANDV isolate from a presymptomatic patient from the MV Hondius, we studied pathogenesis, identified sites of viral replication, characterized innate and adaptive immune responses, and quantified shedding in golden Syrian hamsters. ANDV2026 proved to be highly pathogenic in hamsters, causing severe pulmonary disease reminiscent of HPS. ANDV2026 triggered a delayed type-I IFN response and inflammatory response in the lungs consistent with the key pathological features of HPS, and we detected viral replication in both respiratory and extra-respiratory tissues, including the brain. Infected animals mounted neutralising antibodies and T cell responses, the latter directed predominantly against the L and N proteins. Importantly, ANDV2026-infected animals shed virus through multiple routes, and we detected infectious virus in air samplers connected to cages housing ANDV2026-infected hamsters. In contrast, control hamsters infected with a rodent-derived ANDV isolate (ANDV9717869) shed little virus and air samples were consistently negative. These findings consolidate established features of ANDV pathogenesis, while revealing properties not previously described. Phenotypic characterisation of patient-derived ANDV isolates in animal models can strengthen outbreak preparedness, identify markers of disease severity, and support the development of medical countermeasures.

microbiology↗

bioRxiv2026

Systematic Evaluation of Nasal Immune Cell Sampling and Antigen-specific T cell Detection using Cryopreserved Nasal Swabs

The upper respiratory tract is a key entry point for pathogens, yet local tissue-resident memory T cells (Trm) remain underexplored compared to peripheral blood. We systematically compared nasal curettes and 8 different swab types for immune cell collection, assessing yield, operator variability, and T cell phenotypes across the three turbinates and nasopharynx. The use of flocked swabs yielded higher immune cell numbers while being similarly tolerated, especially with reduced sampling duration. Nasal Trm subsets were consistent across the turbinates, whereas nasopharyngeal Trm displayed a more recently recruited phenotype. Multiple cryopreservation media were evaluated and all demonstrated high viability after thawing. Antigen-specificity was assessed using the activation induced marker (AIM) assay, peptideHLA tetramers and bulk TCR-sequencing following expansion. Notably, influenza-specific T cell frequencies were reliably detected by AIM and correlated between fresh and cryopreserved nasal samples. Downregulation of the CD3/TCR complex was observed in nasal samples. These findings establish a robust approach for nasal Trm profiling, demonstrating that cryopreservation preserves functional antigen-specific T cells. This work enables centralized, minimally invasive nasal T cell analysis for multicenter studies, including mucosal vaccination trials and controlled human infection models.

immunology↗

bioRxiv2024

A 2022 avian H5N1 influenza A virus from clade 2.3.4.4b attaches to and replicates better in human respiratory epithelium than a 2005 H5N1 virus from clade 2.3.2.1

BackgroundHighly pathogenic avian influenza (HPAI) H5 viruses of the A/Goose/Guangdong/1/1996 (GsGd) lineage pose significant global risks to wildlife, domestic animals, and humans. Recent cross-species transmission events to mammals, including humans, highlight this risk. Critical determinants for cross-species and intra-species transmission include the ability to attach to and replicate in respiratory epithelial cells. Although these factors have been studied for HPAI H5N1 viruses in the past, limited studies are available for currently circulating strains. MethodsWe compared level of adaptation to human respiratory tract of a HPAI H5N1 clade 2.3.4.4b (H5N12022) virus with those of well characterized HPAI H5N1 clade 2.1.3.2 (H5N12005) and seasonal H3N22003 viruses by three methods. First, we compared pattern of virus attachment by virus histochemistry. Second, we compared efficiency of infection and replication, as well as innate immune responses in human respiratory epithelium in vitro. Lastly, we compared polymerase complex activity in a minigenome assay. FindingsThe H5N12022 virus attached more abundantly to and replicated more efficiently in cells of the human respiratory tract compared to H5N12005 and H3N2 viruses. This increased replication was not associated with an increased polymerase activity of H5N12022 virus compared to H3N22003 virus. The efficient replication of H5N12022 virus infection induced a robust innate immune response almost comparable to H3N22003. InterpretationThe pattern of virus attachment and replication efficiency of a HPAI H5N12022 virus resembled that of H3N22003 virus more closely than a HPAI H5N12005. This could contribute to an increased risk for both human infection and virus adaptations to humans. FundingThe Netherlands Organization for Health Research and Development Research in contextO_ST_ABSEvidence before this studyC_ST_ABSHighly pathogenic avian influenza (HPAI) H5 viruses of the A/Goose/Guangdong/1/1996 (GsGd) lineage (clade 2.3.4.4b) have the ability to spread to a wide range of domesticated and wild mammalian species, including humans. Cross species transmission and transmission among humans requires-- among other factors--efficient infection of epithelial cells in the respiratory epithelium of the upper respiratory tract. Added value of this studyIn our study we show that a recent clade 2.3.4.4b HPAI H5N1 virus attached to and replicated more efficiently in respiratory epithelium than a clade 2.1.3.2 H5N1 virus that circulated in 2005. Implications of all the available dataThese data suggest that there might be an increased risk of human infections with the currently circulating 2.3.4.4b HPAI H5N1 viruses, which might facilitate opportunities for human adaptation.

microbiology↗

bioRxiv2024

Neuroinvasive and neurovirulent potential of SARS-CoV-2 in the acute and post-acute phase of intranasally inoculated ferrets

Severe acute respiratory syndrome corona virus 2 (SARS-CoV-2) can cause systemic disease, including neurological complications, even after mild respiratory disease. Previous studies have shown that SARS-CoV-2 infection can induce neurovirulence through microglial activation in the brains of patients and experimentally inoculated animals, which are models representative for moderate to severe respiratory disease. Here, we aimed to investigate the neuroinvasive and neurovirulent potential of SARS-CoV-2 in intranasally inoculated ferrets, a model for subclinical to mild respiratory disease. The presence of viral RNA, histological lesions, virus-infected cells, and the number and surface area of microglia and astrocytes were investigated. Viral RNA was detected in various respiratory tissue samples by qPCR at 7 days post inoculation (dpi). Virus antigen was detected in the nasal turbinates of ferrets sacrificed at 7 dpi and was associated with inflammation. Viral RNA was detected in the brains of ferrets sacrificed 7 dpi, but in situ hybridization nor immunohistochemistry did not verify evidence of infection. Histopathological analysis of the brains showed no evidence for an influx of inflammatory cells. Despite this, we observed an increased number of Alzheimer type II astrocytes in the hindbrains of SARS-CoV-2 inoculated ferrets. Additionally, we detected an increased microglial activation in the olfactory bulb and hippocampus, and a decrease in the astrocytic activation status in the white matter and hippocampus of SARS-CoV-2 inoculated ferrets. In conclusion, although showed that SARS-CoV-2 has limited neuroinvasive potential in this model for subclinical to mild respiratory disease, there is evidence for neurovirulent potential. This study highlights the value of this ferret model to study the neuropathogenecity of SARS-CoV-2 and reveals that a mild SARS-CoV-2 infection can affect both microglia and astrocytes in different parts of the brain.

microbiology↗

bioRxiv2024

Targets of influenza Human T cell response are mostly conserved in H5N1

Frequent recent spillovers of subtype H5N1 clade 2.3.4.4b highly pathogenic avian influenza (HPAI) virus into poultry and mammals, especially dairy cattle, including several human cases, increased concerns over a possible future pandemic. Here, we performed an analysis of epitope data curated in the Immune Epitope Database (IEDB). We found that the patterns of immunodominance of seasonal influenza viruses circulating in humans and H5N1 are similar. We further conclude that a significant fraction of the T cell epitopes is conserved at a level associated with cross-reactivity between avian and seasonal sequences, and we further experimentally demonstrate extensive cross-reactivity in the most dominant T cell epitopes curated in the IEDB. Based on these observations, and the overall similarity of the neuraminidase (NA) N1 subtype encoded in both HPAI and seasonal H1N1 influenza virus as well as cross-reactive group 1 HA stalk-reactive antibodies, we expect that a degree of pre-existing immunity is present in the general human population that could blunt the severity of human H5N1 infections.

immunology↗

bioRxiv2024

Bivalent COVID-19 vaccines boost the capacity of pre-existing SARS-CoV-2-specific memory B cells to cross-recognize Omicron subvariants

Bivalent COVID-19 vaccines comprising ancestral Wuhan-Hu-1 (WH1) and the Omicron BA.1 or BA.5 subvariant elicit enhanced serum antibody responses to emerging Omicron subvariants. We characterized the memory B-cell (Bmem) response following a fourth dose with a BA.1 or BA.5 bivalent vaccine, and compared the immunogenicity with a WH1 monovalent fourth dose. Healthcare workers previously immunized with mRNA or adenoviral vector monovalent vaccines were sampled before and one-month after a monovalent, BA.1 or BA.5 bivalent fourth dose COVID-19 vaccine. RBD-specific Bmem were quantified with an in-depth spectral flow cytometry panel including recombinant RBD proteins of the WH1, BA.1, BA.5, BQ.1.1, and XBB.1.5 variants. All recipients had slightly increased WH1 RBD-specific Bmem numbers. Recognition of Omicron subvariants was not enhanced following monovalent vaccination, while both bivalent vaccines significantly increased WH1 RBD-specific Bmem cross-recognition of all Omicron subvariants tested by flow cytometry. Thus, Omicron-based bivalent vaccines can improve recognition of descendent Omicron subvariants by pre-existing, WH1-specific Bmem, beyond that of a conventional, monovalent vaccine. This provides new insights into the capacity of variant-based mRNA booster vaccines to improve immune memory against emerging SARS-CoV-2 variants.

immunology↗

bioRxiv2022

The pro-inflammatory response to influenza A virus infection is fueled by endothelial cells

Morbidity and mortality from influenza are associated with high levels of systemic inflammation. Endothelial cells have been shown to play a key role in this systemic inflammatory response during severe influenza A virus (IAV) infections, despite the fact that these are rarely infected in humans. However, how endothelial cells contribute to these systemic inflammatory responses is unclear. To investigate this, we developed a transwell-system in which airway organoid-derived differentiated human lung epithelial cells at the apical side were co-cultured with primary human lung microvascular endothelial cells (LMEC) at the basolateral side. We compared the susceptibility of endothelial cells to pandemic H1N1 virus isolated in 2009 and seasonal H1N1 and H3N2 virus isolated in 2019, and assessed the associated immune responses. Despite the detection of IAV nucleoprotein in LMEC monocultures, there was no evidence for productive infection. In epithelial-endothelial co-cultures, abundant IAV infection of epithelial cells resulted in the breakdown of the epithelial barrier, but infection of LMECs was rarely detected. Furthermore, we observed a significantly higher secretion of pro-inflammatory cytokines in LMECs when co-cultured with IAV-infected epithelial cells, compared to LMEC monocultures exposed to IAV. Taken together, our data show that endothelial cells are abortively infected by IAV, but can fuel the inflammatory response. As endothelial cells are a prominent cell type in the lung, it is possible that they play an important role in the systemic inflammatory response during IAV infections.

microbiology↗

bioRxiv2022

Pulmonary lesions following inoculation with the SARS-CoV-2 Omicron BA.1 (B.1.1.529) variant in Syrian golden hamsters

The Omicron BA.1 (B.1.1.529) SARS-CoV-2 variant is characterized by a high number of mutations in the viral genome, associated with immune-escape and increased viral spread. It remains unclear whether milder COVID-19 disease progression observed after infection with Omicron BA.1 in humans is due to reduced pathogenicity of the virus or due to pre-existing immunity from vaccination or previous infection. Here, we inoculated hamsters with Omicron BA.1 to evaluate pathogenicity and kinetics of viral shedding, compared to Delta (B.1.617.2) and to animals re-challenged with Omicron BA.1 after previous SARS-CoV-2 614G infection. Omicron BA.1 infected animals showed reduced clinical signs, pathological changes, and viral shedding, compared to Delta-infected animals, but still showed gross- and histopathological evidence of pneumonia. Pre-existing immunity reduced viral shedding and protected against pneumonia. Our data indicate that the observed decrease of disease severity is in part due to intrinsic properties of the Omicron BA.1 variant.

microbiology↗

bioRxiv2022

Omicron BA.1 and BA.2 are antigenically distinct SARS-CoV-2 variants

The emergence and rapid spread of SARS-CoV-2 variants may impact vaccine efficacy significantly1. The Omicron variant termed BA.2, which differs genetically substantially from BA.1, is currently replacing BA.1 in several countries, but its antigenic characteristics have not yet been assessed2,3. Here, we used antigenic cartography to quantify and visualize antigenic differences between SARS-CoV-2 variants using hamster sera obtained after primary infection. Whereas early variants are antigenically similar, clustering relatively close to each other in antigenic space, Omicron BA.1 and BA.2 have evolved as two distinct antigenic outliers. Our data show that BA.1 and BA.2 both escape (vaccine-induced) antibody responses as a result of different antigenic characteristics. Close monitoring of the antigenic changes of SARS-CoV-2 using antigenic cartography can be helpful in the selection of future vaccine strains.

microbiology↗

bioRxiv2021

Sustained replication of synthetic canine distemper virus defective genomes in vitro and in vivo

Defective interfering (DI) genomes restrict viral replication and induce type-I interferon. Since DI genomes have been proposed as vaccine adjuvants or therapeutic antiviral agents, it is important to understand their generation, delineate their mechanism of action, develop robust production capacities, assess their safety and in vivo longevity and determine their long-term effects. To address this, we generated a recombinant (r) canine distemper virus (CDV) from an entirely synthetic molecular clone designed using the genomic sequence from a clinical isolate obtained from a free-ranging raccoon with distemper. rCDV was serially passaged in vitro to identify DI genomes that naturally arise during rCDV replication. Defective genomes were identified by Sanger and next-generation sequencing techniques and predominant genomes were synthetically generated and cloned into T7-driven plasmids. Fully encapsidated DI particles (DIPs) were then generated using a rationally attenuated rCDV as a producer virus to drive DI genome replication. We demonstrate these DIPs interfere with rCDV replication in a dose-dependent manner in vitro. Finally, we show sustained replication of a fluorescent DIP in experimentally infected ferrets over a period of 14 days. Most importantly, DIPs were isolated from the lymphoid tissues which are a major site of CDV replication. Our established pipeline for detection, generation and assaying DIPs is transferable to highly pathogenic paramyxoviruses and will allow qualitative and quantitative assessment of the therapeutic effects of DIP administration on disease outcome. ImportanceDefective interfering (DI) genomes have long been considered inconvenient artifacts that suppressed viral replication in vitro. However, advances in sequencing technologies have led to DI genomes being identified in clinical samples, implicating them in disease progression and outcome. It has been suggested that DI genomes could be harnessed therapeutically. Negative strand RNA virus research has provided a rich pool of natural DI genomes over many years and they are probably the best understood in vitro. Here, we demonstrate identification, synthesis, production and experimental inoculation of novel CDV DI genomes in highly susceptible ferrets. These results provide important evidence that rationally designed and packaged DI genomes can survive the course of a wild-type virus infection.

microbiology↗

bioRxiv2020

Intranasal fusion inhibitory lipopeptide prevents direct contact SARS-CoV-2 transmission in ferrets

Containment of the COVID-19 pandemic requires reducing viral transmission. SARS-CoV-2 infection is initiated by membrane fusion between the viral and host cell membranes, mediated by the viral spike protein. We have designed a dimeric lipopeptide fusion inhibitor that blocks this critical first step of infection for emerging coronaviruses and document that it completely prevents SARS-CoV-2 infection in ferrets. Daily intranasal administration to ferrets completely prevented SARS-CoV-2 direct-contact transmission during 24-hour co-housing with infected animals, under stringent conditions that resulted in infection of 100% of untreated animals. These lipopeptides are highly stable and non-toxic and thus readily translate into a safe and effective intranasal prophylactic approach to reduce transmission of SARS-CoV-2. One-sentence summaryA dimeric form of a SARS-CoV-2-derived lipopeptide is a potent inhibitor of fusion and infection in vitro and transmission in vivo.

microbiology↗

bioRxiv2020

Identification and characterization of CD4+ T cell epitopes after Shingrix vaccination.

Infections with varicella zoster virus (VZV), a member of the Herpesviridae family, are associated with a range of clinical manifestations. Primary infection with VZV causes chicken pox, and due to the viruss capacity to remain latent in neurons, it can reactivate later in life causing herpes zoster (HZ), also known as shingles. Two different vaccines have been developed to prevent HZ, one based on a live attenuated VZV strain (Zostavax) and the other on adjuvanted gE recombinant protein (Shingrix). While Zostavax efficacy wanes with age, Shingrix protection retains its efficacy in elderly subjects (80 years of age and beyond). In this context, it is of much interest to understand if there is a role for T cell immunity in differential clinical outcome, and if there is a correlate of protection between T cell immunity and Shingrix efficacy. In this study, we characterized Shingrix specific ex vivo CD4 T cell responses in the context of natural exposure and HZ vaccination using pools of predicted epitopes. We show that T cell reactivity following natural infection and Zostavax vaccination dominantly targets non-structural proteins (NS), while Shingrix vaccination redirects dominant reactivity to target gE. We mapped the gE-specific responses following Shingrix vaccination to 89 different gE epitopes, 34 of which accounted for 80% of the response. Using antigen presentation assays and single HLA molecule transfected lines, we experimentally determined HLA restrictions for 94 different donor/peptide combinations. Finally, we used our results as a training set to assess strategies to predict restrictions based on measured or predicted HLA binding and the corresponding HLA types of responding subjects. ImportanceUnderstanding the T cell profile associated with the protection observed in elderly vaccinees following Shingrix vaccination is relevant to the general definition of correlates of vaccine efficacy. Our study enables these future studies by clarifying patterns of immunodominance associated with Shingrix vaccination, as opposed to natural infection or Zostavax vaccination. Identification of epitopes recognized by Shingrix-induced CD4 T cells and their associated HLA restrictions enables the generation of tetrameric staining reagents and, more broadly, the capability to characterize specificity, magnitude and phenotype of VZV specific T cells.

immunology↗

bioRxiv2019

Measles skin rash: infection of lymphoid and myeloid cells in the dermis precedes viral dissemination to keratinocytes in the epidermis

Measles is characterised by fever and a maculopapular skin rash, which is associated with immune clearance of measles virus (MV)-infected cells. Histopathological analyses of skin biopsies from humans and non-human primates (NHPs) with measles rash have identified MV-infected keratinocytes and mononuclear cells in the epidermis, around hair follicles and near sebaceous glands. Here, we address the pathogenesis of measles skin rash by combining data from experimentally infected NHPs, ex vivo infection of human skin sheets and in vitro infection of primary human keratinocytes. Longitudinal analysis of the skin of experimentally MV-infected NHPs demonstrated that infection in the skin precedes onset of rash by several days. MV infection was initiated in lymphoid and myeloid cells in the dermis before dissemination to the epidermal keratinocytes. These data were in good concordance with ex vivo MV infections of human skin sheets, in which dermal cells were more targeted than the epidermal ones. To address viral dissemination to the epidermis and to determine whether the dissemination is receptor-dependent, we performed experimental infections of primary keratinocytes collected from healthy or nectin-4-deficient donors. These experiments demonstrated that MV infection of keratinocytes is nectin-4-dependent, and nectin-4 expression was higher in differentiated than in proliferating keratinocytes. Based on these data, we hypothesise that measles skin rash is initiated by migrating MV-infected lymphocytes that infect dermal skin-resident CD150+ immune cells. The infection is subsequently disseminated from the dermal papillae to nectin-4+ keratinocytes in the basal epidermis. Lateral spread of MV infection is observed in the superficial epidermis, most likely due to the higher level of nectin-4 expression on differentiated keratinocytes. Finally, MV-infected cells are cleared by infiltrating immune cells, causing hyperaemia and oedema, which give the appearance of morbilliform skin rash. Author SummarySeveral viral infections are associated with skin rash, including parvovirus B19, human herpesvirus type 6, dengue virus and rubella virus. However, the archetype virus infection that leads to skin rash is measles. Although all of these viral exanthemata often appear similar, their pathogenesis is different. In the case of measles, the appearance of skin rash is a sign that the immune system is clearing MV-infected cells from the skin. How the virus reaches the skin and is locally disseminated remains unknown. Here we combine observations and expertise from pathologists, dermatologists, virologists and immunologists to delineate the pathogenesis of measles skin rash. We show that MV infection of dermal myeloid and lymphoid cells precedes viral dissemination to the epidermal keratinocytes. We speculate that immune-mediated clearance of these infected cells results in hyperaemia and oedema, explaining the redness of the skin and the slightly elevated spots of the morbilliform rash.

microbiology↗