Biology subjects

Carrillo, J.

Publications and source records attributed to Carrillo, J..

At least 19 recordsLinked to original sources

bioRxiv2025

Island invasions by the non-native vinegar fly Drosophila suzukii and its parasitoid wasps

Understanding how island characteristics influence the establishment and impact of invasive species and their natural enemies could inform both island biogeography and biological control theory. We studied the occurrence and relative abundances of the globally invasive fruit fly, Drosophila suzukii, and its recently introduced larval parasitoids, Leptopilina japonica and Ganaspis kimorum, across islands with varying sizes and levels of human-mediated transport in the Gulf and San Juan Islands of British Columbia (Canada) and Washington State (USA). Across two years and 58 sites, we collected D. suzukii and its parasitoids from wild blackberry, Rubus armeniacus, fruit. We predicted that parasitoids were more likely to be present on larger islands with higher levels of human activity and higher D. suzukii densities, and that the less specialized parasitoid species (L. japonica) would be more likely to establish on islands. We detected D. suzukii across all islands, indicating widespread establishment of this invasive pest. In contrast, we observed parasitoids on fewer than half of the islands. Leptopilina japonica was the only parasitoid of D. suzukii detected on islands. Parasitoid presence was marginally positively associated with island area and host density, but not average annual vehicle-ferry traffic (an indicator of human-mediated propagule pressure). Parasitism levels were low throughout the study region and we did not observe lower relative abundances of D. suzukii on islands where parasitoids were present - in fact, the relative abundance of D. suzukii tended to be higher on islands where the parasitoid L. japonica was detected. These findings suggest that island characteristics, host density, and a consumers host specificity may be associated with early establishment of introduced consumers on islands, but that a consumers presence may not inevitably result in host population suppression, at least over the short term.

ecology↗

bioRxiv2025

ALANizer: Design and validation of experimental lighting rig for studying artificial light at night in ecosystems

1Over the past few centuries, human activity has introduced astoundingly bright light to the environment at a rapidly accelerating pace. Artificial light at night (ALAN) has detrimental effects on a wide range of organisms, including arthropods. To minimise impact, we must understand how different organisms are affected and whether certain lights are less perturbing. We designed a novel tool for introducing and monitoring different types of ALAN, called ALANizer, composed of open-source software and inexpensive, widely-available hardware. We describe the design and assembly of ALANizer as well as a feasibility study where we installed 12 ALANizers in hedgerows and monitored arthropod activity using pitfall traps. Understanding ALANs impacts on ecosystems only grows more pressing as LED technology proliferates. As an effective, low-cost, and scalable tool for introducing and monitoring ALAN in ecosystems, ALANizer can help advance this key area of research.

ecology↗

bioRxiv2025

Pediatric Long COVID Is Characterized by Myeloid CCR6 Suppression and Immune Dysregulation

The biological mechanisms underlying long COVID in the pediatric population are poorly understood. Our study aimed to characterize the immune pathophysiology of long COVID in children and young people (CYP). We analyzed major immune cell compartments in PBMCs, as well as specific SARS-CoV-2 antibody response in CYP with (n=99) and without (n=18) long COVID at three months following acute infection. Our findings indicate that pediatric long COVID is associated with a dysregulated immune response characterized by altered innate immunity and overactivated T-, B- and NK-cell responses. Furthermore, CYP with long COVID had an impaired humoral response to SARS-CoV-2 marked by a dysregulated B-cell compartment and lower levels of anti-RBD IgG and IgA. This correlated with reduced neutralizing capacity against SARS-CoV-2. Random forest analysis identified CCR6 expression on myeloid cells as the most relevant biomarker that distinguishes long COVID from control individuals with 79% accuracy. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=154 SRC="FIGDIR/small/671713v1_ufig1.gif" ALT="Figure 1"> View larger version (32K): org.highwire.dtl.DTLVardef@1145480org.highwire.dtl.DTLVardef@1b7a635org.highwire.dtl.DTLVardef@fb13org.highwire.dtl.DTLVardef@63a49a_HPS_FORMAT_FIGEXP M_FIG C_FIG

immunology↗

bioRxiv2025

A General Method for Detection and Segmentation of Terrestrial Arthropods in Images

To better understand the status and trends of insects and other arthropods, emerging technologies like image recognition are developing rapidly. This is creating a strong demand for efficient and accurate algorithms for detection and localization of arthropods in images. Existing models have modest performance and do not generalise well to variation in scale, appearance and density of specimens, or imaging conditions. Consequently, each new application often requires manual labeling of training data and model training, which limits the uptake of image-based tools and technologies. Here, we introduce flatbug, which is a powerful and general model to count and outline insects and other terrestrial arthropods in images. The training dataset is large and diverse and represent 23 different lab- and field-based imaging systems. The best flatbug model achieves an average F 1 = 94.2% on our validation dataset. Crucially, we show that flatbug has great out-of-the-box performance and generalises well to novel contexts. When images from a given dataset are left out of model training, the performance of flatbug is only reduced by on average 7.1% for the dataset in question. By using truly stratified cross-validation, we set a precedent for robust evaluation of deep learning model performance and generalization. We also take steps towards scale- and size-agnostic arthropod detection, by developing an integrated tiling framework for inference and training. Additionally, flatbug s implementation of YOLOv8 for instance segmentation enables downstream background removal and body size estimation. The generaliseability of flatbug stems from the diversity of contexts represented in the flatbug dataset, including 113550 arthropods annotated across 6131 images. Alongside a fully documented Python package with tutorials for integration and analysis via https://github.com/darsa-group/flat-bug/, the flatbug dataset is available from https://www.doi.org/10.5281/zenodo.14761447. By providing performant models and the accompanying dataset, flatbug offers both a ready-to-use tool and a benchmark for the future. Overall, flatbug represents a significant methodological advance within arthropod image detection, with user-friendly integration for monitoring and research. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=134 SRC="FIGDIR/small/647223v1_ufig1.gif" ALT="Figure 1"> View larger version (80K): org.highwire.dtl.DTLVardef@2d25c0org.highwire.dtl.DTLVardef@9929borg.highwire.dtl.DTLVardef@77ff28org.highwire.dtl.DTLVardef@10bd2f_HPS_FORMAT_FIGEXP M_FIG C_FIG

ecology↗

bioRxiv2025

Predicting bacterial-mediated entomopathogenicity through comparative genomics and statistical modeling

Bacterial genomes encode for vast functional diversity and have both beneficial and detrimental effects on insect hosts. However, connecting bacterial genotype to a host-associated phenotype can be experimentally time-consuming, particularly if insecticidal mechanisms are highly host-specific. To streamline the identification of virulence genes on a new host, we tested if merging existing mechanistic knowledge with in vivo tests on a small number of bacterial isolates could predict bacterial genes associated with entomopathogenesis. We used a model consisting of Drosophila melanogaster interactions with pathogenic and commensal genome-sequenced strains of Pseudomonas bacteria. We compiled a database of previously described insecticidal and biocontrol genes within the Pseudomonas genus and used comparative genomics to probe the distribution of these genes across Pseudomonas strains. We found natural variation in the presence of known insecticidal genes across the genus. We tested the insect-killing capacity of 13 Pseudomonas spp. strains against D. melanogaster and found natural variation in insecticidal activity. To identify bacterial genes associated with fly mortality, we employed two statistical models to correlate bacterial virulence with the presence of previously described insecticidal activity. To validate our predictions, we used a P. aeruginosa PAO1 transposon mutant library and identified 8 operons that are necessary for killing D. melanogaster. We show that by combining existing literature with phenotyping a small number of strains, we can identify genes necessary for insecticidal activity in a previously untested insect model. More broadly these findings illustrate a discovery pipeline for bacterial virulence mechanisms, accelerating the discovery of insect pest biocontrol mechanisms.

microbiology↗

bioRxiv2024

A human-ACE2 knock-in mouse model for SARS-CoV-2 infection recapitulates respiratory disorders but avoids neurological disease associated with the transgenic K18-hACE2 model.

Animal models have been instrumental in elucidating the pathogenesis of SARS-CoV-2 infection and testing COVID-19 vaccines and therapeutics. Wild-type (WT) mice are not susceptible to many SARS-CoV-2 variants, therefore transgenic K18-hACE2 mice have emerged as a standard model system. However, this model is characterized by severe disease, particularly associated with neuroinfection, which leads to early humane endpoint euthanasia. Here, we established a novel knock-in (KI) mouse model by inserting the original K18-hACE2 transgene into the collagen COL1A1 locus using a recombinase mediated cassette exchange (RMCE) system. Once the Col1a1-K18-hACE2 mouse colony was established, animals were challenged with a B.1 SARS-CoV-2 (D614G) isolate and were monitored for up to 14 days. Col1a1-K18-hACE2 mice exhibited an initial weight loss similar to the K18-hACE2 transgenic model but did not develop evident neurologic clinical signs. The majority of Col1a1-K18-hACE2 mice did not reach the preestablished humane endpoint, showing progressive weight gain after 9 days post-infection (dpi). Importantly, despite this apparent milder pathogenicity of the virus in this mouse model compared to the K18-hACE2 transgenic model, high levels of viral RNA were detected in lungs, oropharyngeal swab, and nasal turbinate. Remaining lesions and inflammation in lungs were still observed after 14 dpi. In contrast, although low level viral RNA could be detected in a minority of Col1a1-K18- hACE2 animals, no brain lesions were observed at any timepoint. Overall, Col1a1-K18- hACE2 mice constitute a new model for investigating SARS-CoV-2 pathogenesis and treatments, with potential implications for studying long-term COVID-19 sequelae. ImportanceK18-hACE2 mice express high levels of the human protein ACE2, the receptor for SARS- CoV-2, and can therefore be infected by this virus. These animals have been crucial to understand viral pathogenesis and to test COVID-19 vaccines and antiviral drugs. However, K18-hACE2 often die after infection with initial SARS-CoV-2 variants likely due to a massive brain infection that does not occur in humans. Here, we used a technology known as knock-in that allows for the targeted insertion of a gene into a mouse and we have generated a new hACE2-mouse. We have characterized this new animal model demonstrating that the virus replicates in the respiratory tract, damaging lung tissue and causing inflammation. In contrast to K18-hACE2 mice, only limited or no brain infection could be detected, and most animals recovered from infection with remaining lung lesions. This new model could be instrumental for the study of specific disease aspects such as post-COVID condition, sequelae, and susceptibility to reinfection.

microbiology↗

bioRxiv2023

VLP-mediated delivery of structure-selected neoantigens demonstrates immunogenicity and antitumoral activity in mice

BackgroundNeoantigens are patient- and tumor-specific peptides that arise from somatic mutations. They stand as promising targets for personalized therapeutic cancer vaccines. The identification process for neoantigens has evolved with the use of next-generation sequencing technologies and bioinformatic tools in tumor genomics. However, in silico strategies for selecting immunogenic neoantigens still have very low accuracy rates, since they mainly focus on predicting peptide binding to Major Histocompatibility Complex (MHC) molecules, which is key but not the sole determinant for immunogenicity. MethodsWe developed a novel neoantigen selection pipeline based on existing software combined with a novel prediction method, the Neoantigen Optimization Algorithm (NOAH), which takes into account structural features of the peptide/MHC-I interaction in its prediction strategy. Moreover, to maximize neoantigens therapeutic potential, neoantigen-based vaccines should be manufactured in an optimal delivery platform that elicits robust de novo immune responses and bypasses central and peripheral tolerance. ResultsWe generated a highly immunogenic vaccine platform based on engineered HIV-1 Gag-based Virus-Like Particles (VLPs) expressing a high copy number of each in silico selected neoantigen. We tested different neoantigen-loaded VLPs (neoVLPs) in a B16-F10 melanoma mouse model to evaluate their capability to generate new immunogenic specificities. NeoVLPs were used in in vivo immunogenicity and tumor challenge experiments. ConclusionsNeoVLPs can promote the generation of de novo antitumor-specific immune responses, resulting in a delay in tumor growth. Vaccination with the neoVLP platform is a robust alternative to current therapeutic vaccine approaches and a promising candidate for future personalized immunotherapy. WHAT IS ALREADY KNOWN ON THIS TOPICIdentification of highly immunogenic neoantigens is still challenging, currently available pipelines base their prediction on MHC-I binding affinity. Moreover, neoantigen-based vaccine delivery needs to be improved to increase the potency of anti-tumor immune response. WHAT THIS STUDY ADDSNOAH is a novel pipeline for the identification and selection of neoantigens that combines binding affinity and structural features of the peptide/MHC-I interaction. Preclinical studies show highly immunogenic vaccine platform based on HIV-1 Gag based VLPs (neoVLPs) generates antitumor-specific immune responses, delaying tumor growth. HOW THIS STUDY MIGHT AFFECT RESEARCH, PRACTICE OR POLICYThe combination of NOAH and neoVLP platform represents an alternative to current therapeutic vaccine approaches and a promising candidate for future personalized immunotherapy.

immunology↗

bioRxiv2023

Atypical memory B cells form a pre-plasmacellular reservoir for steady-state IgD responses to common nasopharyngeal antigens

The human nasopharyngeal mucosa includes organized lymphoepithelial structures continually engaged in frontline immune responses to aerodigestive antigens. Advancing our understanding of these responses might lead to the development of new strategies for the prevention and treatment of common immune disorders such as allergies. Here we identified a hitherto elusive tonsillar subset of atypical IgD class-switched IgD+IgM- memory (IgD-ME) B cells that were clonally related to IgD+IgM- germinal center (IgD-GC) B cells and IgD-secreting IgD+IgM- plasma cells (IgD-PCs) but not anergic IgD+IgM- B cells. Consistent with their pre-plasmacellular properties, IgD-ME B cells served as preferential precursors of IgD-PCs over IgD-GC B cells. IgD antibodies from IgD+IgM- cells acquired reactivity to multiple oral, airborne and commensal antigens through a mutation-dependent pathway involving both innate and adaptive signals. Thus, IgD-ME B cells may form a ready-to-use pre-plasmacellular reservoir for steady-state IgD responses likely aimed at enhancing nasopharyngeal homeostasis. One Sentence SummaryTonsillar atypical memory B cells form a ready-to-use pre-plasmacellular repertoire for IgD responses to common aerodigestive antigens.

immunology↗

bioRxiv2023

Novel Spike-stabilized trimers with improved production protect K18-hACE2 mice and golden Syrian hamsters from the highly pathogenic SARS-CoV-2 Beta variant.

Most COVID-19 vaccines are based on the SARS-CoV-2 Spike glycoprotein (S) or their subunits. However, the S shows some structural instability that limits its immunogenicity and production, hampering the development of recombinant S-based vaccines. The introduction of the K986P and V987P (S-2P) mutations increases the production of the recombinant S trimer and, more importantly, its immunogenicity, suggesting that these two parameters are related. However, S-2P still shows some molecular instability and it is produced with low yield. Thus, S-2P production can be further optimized. Here we described a novel set of mutations identified by molecular modelling and located in the S2 region of the Spike that increase S-2P production up to five-fold. Besides their immunogenicity, the efficacy of two representative S-2P-based mutants, S-29 and S-21, protecting from a heterologous SARS-CoV-2 Beta variant challenge was assayed in K18-hACE2 mice (an animal model of severe SARS-CoV-2 disease) and golden Syrian hamsters (GSH) (a moderate disease model). S-21 induced higher level of WH1 and Delta variants neutralizing antibodies than S-2P in K18-hACE2 mice three days after challenge. Viral load in nasal turbinate and oropharyngeal samples were reduced in S-21 and S-29 vaccinated mice. Despite that, only the S-29 protein protected 100% of K18-hACE2 mice from severe disease. When GSH were analyzed, all immunized animals were protected from disease development irrespectively of the immunogen they received. Therefore, the higher yield of S-29, as well as its improved immunogenicity and efficacy protecting from the highly pathogenic SARS-CoV-2 Beta variant, pinpoint the S-29 spike mutant as an alternative to the S-2P protein for future SARS-CoV-2 vaccine development. Authors summaryThe rapid development of SARS-CoV-2 vaccines have been pivotal in the control of the COVID-19 pandemic worldwide. Most of these vaccines include the S glycoprotein as the main immunogen since this protein, and particularly its receptor binding domain (RBD), is the major target of neutralizing antibodies. SARS-CoV-2 have been evolving from the beginning of the pandemic and several variants with increased transmissibility, pathogenicity or resistance to infection- or vaccine-induced immunity have emerged. Different strategies have been adopted to improve vaccine protection including additional booster doses or the adaptation of the S immunogens to the novel SARS-CoV-2 variants. As a complementary strategy we have identified a combination of non-proline mutations that increase S production by 5-fold (S-29 protein). Despite the sequence of this novel S-29 immunogen is based on the ancestral SARS-CoV-2 WH1 variant, it effectively protects animal model from the highly pathogenic and neutralization resistant SARS-CoV-2 Beta variant. Thus, we describe a novel set of mutations that can increase the production and efficacy of S-based COVID-19 vaccines.

immunology↗

bioRxiv2022

Beta-Cyclodextrins as affordable antivirals to treat coronavirus infection

The SARS-CoV-2 pandemic made evident that we count with few coronavirus-fighting drugs. Here we aimed to identify a cost-effective antiviral with broad spectrum activity and high safety and tolerability profiles. We began elaborating a list of 116 drugs previously used to treat other pathologies or characterized in pre-clinical studies with potential to treat coronavirus infections. We next employed molecular modelling tools to rank the 44 most promising inhibitors and tested their efficacy as antivirals against a panel of and {beta} coronavirus, e.g., the HCoV-229E and SARS-CoV-2 viruses. Four drugs, OSW-1, U18666A, hydroxypropyl-{beta}-cyclodextrin (H{beta}CD) and phytol, showed antiviral activity against both HCoV-229E (in MRC5 cells) and SARS-CoV-2 (in Vero E6 cells). The mechanism of action of these compounds was studied by transmission electron microscopy (TEM) and by testing their capacity to inhibit the entry of SARS-CoV-2 pseudoviruses in ACE2-expressing HEK-293T cells. The entry was inhibited by H{beta}CD and U18666A, yet only H{beta}CD could inhibit SARS-CoV-2 replication in the pulmonary cells Calu-3. With these results and given that cyclodextrins are widely used for drug encapsulation and can be safely administered to humans, we further tested 6 native and modified cyclodextrins, which confirmed {beta}-cyclodextrins as the most potent inhibitors of SARS-CoV-2 replication in Calu-3 cells. All accumulated data points to {beta}-cyclodextrins as promising candidates to be used in the therapeutic treatments for SARS-CoV-2 and possibly other respiratory viruses.

microbiology↗

bioRxiv2021

Adventive larval parasitoids reconstruct their close association with spotted-wing drosophila in the invaded North American range

Two species of larval parasitoids of the globally invasive fruit pest, Drosophila suzukii (Diptera: Drosophilidae), Leptopilina japonica and Ganaspis brasiliensis (both Hymenoptera: Figitidae), were detected in British Columbia, Canada in 2019. Both are presumed to have been unintentionally introduced from Asia, however; the extent of their establishment across different habitats with diverse host plants used by D. suzukii was unclear. In addition, there was no knowledge of the temporal dynamics of parasitism of D. suzukii by these two parasitoids. We repeatedly sampled the fruits of known host plants of D. suzukii over the entire 2020 growing season in British Columbia. We documented the presence of L. japonica and G. brasiliensis and estimated the apparent percentage of D. suzukii parasitized. Across a large region of southwestern British Columbia, both L. japonica and G. brasiliensis were found to be very common across a variety of mostly unmanaged habitats over the entire course of the season (May-October) in the fruits of most host plants known to host D. suzukii larvae. The two parasitoids were responsible for more than 98% of D. suzukii larval parasitism and usually co-existed. Parasitism of D. suzukii was variable among hosts plants and sites (0-66% percent parasitism) and appeared to be time-structured. Our study demonstrates that the close association between the two larval parasitoids and D. suzukii that exists in Asia has evidently been reconstructed in North America, resulting in the highest parasitism levels of D. suzukii yet recorded outside of its area of origin.

ecology↗

bioRxiv2021

Intrinsic variation in the vertically transmitted insect-specific core virome of Aedes aegypti

Since 2009, local outbreaks of dengue (serotypes 1-3) mediated by Aedes aegypti mosquitoes have occurred in the United States, particularly in Florida (FL). In 2016 and 2017, dengue virus serotype 4 was found alongside several insect-specific viruses (ISVs) in pools of A. aegypti from sites in Manatee County, FL, in the absence of an index case. Although ISVs have been characterized in A. aegypti globally, the constitution of a core virome in natural populations remains unclear. Using mosquitoes sampled from the same area in 2018, we compared baseline ovary viromes of field (G0) and lab (Orlando) A. aegypti via metagenomic RNA sequencing. Across all samples, virome composition varied by sample type (field- or colony-derived). Four ISVs comprised >97% of virus sequences: a novel partiti-like virus (Partitiviridae), a previously described toti-like virus (Totiviridae), unclassified Riboviria, and four previously described orthomyxo-like viruses (Orthormyxoviridae). Whole or partial genomes for the toti-like virus, partiti-like virus, and one orthomyxo-like virus were assembled and analyzed phylogenetically. Multigenerational maintenance of these ISVs was confirmed orthogonally by RT-PCR in G0 and G7 mosquitoes, indicating vertical transmission as the mechanism for ISV sustentation. This study provides fundamental information regarding ISV ecology, persistence, and variation in A. aegypti in nature.

microbiology↗

bioRxiv2021

Sticky Pi, an AI-powered smart insect trap for community chronoecology

In the face of severe environmental crises that threaten insect biodiversity, new technologies are imperative to monitor both the identity and ecology of insect species. Traditionally, insect surveys rely on manual collection of traps, which provide abundance data but mask the large intra- and inter-day variations in insect activity, an important facet of their ecology. Although laboratory studies have shown that circadian processes are central to insects biological functions, from feeding to reproduction, we lack the high-frequency monitoring tools to study insect circadian biology in the field. To address these issues, we developed the Sticky Pi, a novel, autonomous, open-source, insect trap that acquires images of sticky cards every twenty minutes. Using custom deep-learning algorithms, we automatically and accurately scored where, when and which insects were captured. First, we validated our device in controlled laboratory conditions with a classic chronobiological model organism, Drosophila melanogaster. Then, we deployed an array of Sticky Pis to the field to characterise the daily activity of an agricultural pest, Drosophila suzukii, and its parasitoid wasps. Finally, we demonstrate the wide scope of our smart trap by describing the sympatric arrangement of insect temporal niches in a community, without targeting particular taxa a priori. Together, the automatic identification and high sampling rate of our tool provide biologists with unique data that impacts research far beyond chronobiology; with applications to biodiversity monitoring and pest control as well as fundamental implications for phenology, behavioural ecology, and ecophysiology. We released the Sticky Pi project as an open community resource on https://doc.sticky-pi.com.

ecology↗

bioRxiv2021

SARS-CoV-2 B.1.351 (beta) variant shows enhanced infectivity in K18-hACE2 transgenic mice and expanded tropism to wildtype mice compared to B.1 variant

SARS-CoV-2 variants display enhanced transmissibility and/or immune evasion and can be generated in humans or animals, like minks, thus generating new reservoirs. The continuous surveillance of animal susceptibility to new variants is necessary to predict pandemic evolution. In this study we demonstrate that, compared to the B.1 SARS-CoV-2 variant, K18-hACE2 transgenic mice challenged with the B.1.351 variant displayed a faster progression of infection. Furthermore, we also report that B.1.351 can establish infection in wildtype mice, while B.1 cannot. B.1.351-challenged wildtype mice showed a milder infection than transgenic mice, confirmed by detectable viral loads in oropharyngeal swabs and tissues, lung pathology, immunohistochemistry and serology. In silico models supported these findings by demonstrating that the Spike mutations in B.1.351 resulted in increased affinity for both human and murine ACE2 receptors. Overall, this study highlights the plasticity of SARS-CoV-2 animal susceptibility landscape, which may contribute to viral persistence and expansion.

microbiology↗

bioRxiv2021

Siglec-1 on dendritic cells mediates SARS-CoV-2 trans-infection of target cells while on macrophages triggers proinflammatory responses

COVID-19 pandemic is not yet under control by vaccination, and effective antivirals are critical for preparedness. Here we report that macrophages and dendritic cells, key antigen presenting myeloid cells (APCs), are largely resistant to SARS-CoV-2 infection. APCs effectively captured viruses within cellular compartments that lead to antigen degradation. Macrophages sense SARS-CoV-2 and released higher levels of cytokines, including those related to cytokine storm in severe COVID-19. The sialic acid-binding Ig-like lectin 1 (Siglec-1/CD169) present on APCs, which interacts with sialylated gangliosides on membranes of retroviruses or filoviruses, also binds SARS-CoV-2 via GM1. Blockage of Siglec-1 receptors by monoclonal antibodies reduces SARS-CoV-2 uptake and transfer to susceptible target cells. APCs expressing Siglec-1 and carrying SARS-CoV-2 are found in pulmonary tissues of non-human primates. Single cell analysis reveals the in vivo induction of cytokines in those macrophages. Targeting Siglec-1 could offer cross-protection against SARS-CoV-2 and other enveloped viruses that exploit APCs for viral dissemination, including those yet to come in future outbreaks.

microbiology↗

bioRxiv2021

Highly functional Cellular Immunity in SARS-CoV-2 Non-Seroconvertors is associated with immune protection

The role of T cells in the control of SARS-CoV-2 infection has been underestimated in favor of neutralizing antibodies. However, cellular immunity is essential for long-term viral control and protection from disease severity. To understand T-cell immunity in the absence of antibody generation we focused on a group of SARS-CoV-2 Non-Seroconvertors (NSC) recovered from infection. We performed an immune comparative analysis of SARS-CoV-2 infected individuals stratified by the absence or presence of seroconversion and disease severity. We report high levels of total naive and low effector CD8+ T cells in NSC. Moreover, polyfunctional Nucleocapsid (NP)-specific CD8+ T-cell responses, as well as reduced levels of T-cell activation monitored by PD-1 and activation-induced markers, were distinctive immunological traits in NSC. Longitudinal data support the stability of the NSC phenotype over three months. Our results implicate highly functional SARS-CoV-2 Spike and NP T-cell responses with low immune activation in protection from disease severity in the absence of seroconversion. SUMMARYTo understand SARS-CoV-2 specific T-cell immunity in the absence of seroconversion, we characterized immunological features of Non-Seroconvertors recovered from infection. Highly functional specific T-cell responses and low immune activation were determinants of immune protection from severe disease.

immunology↗

bioRxiv2021

Previous SARS-CoV-2 infection increases B.1.1.7 cross-neutralization by vaccinated individuals.

To assess the potential impact of predominant circulating SARS-CoV-2 variants on neutralizing activity of infected and/or vaccinated individuals, we analyzed neutralization of pseudoviruses expressing the spike of the original Wuhan strain, the D614G and B.1.1.7 variants. Our data show that parameters of natural infection (time from infection and infecting variant) determined cross-neutralization. Importantly, upon vaccination, previously infected individuals developed equivalent B.1.1.7 and Wuhan neutralizing responses. In contrast, uninfected vaccinees showed reduced neutralization against B.1.1.7. FundingThis study was funded by Grifols, the Departament de Salut of the Generalitat de Catalunya, the Spanish Health Institute Carlos III, CERCA Programme/Generalitat de Catalunya, and the crowdfunding initiatives #joemcorono, BonPreu/Esclat and Correos.

immunology↗

bioRxiv2021

Protection against reinfection with D614- or G614-SARS-CoV-2 isolates in hamsters

Reinfections with SARS-CoV-2 have already been documented in humans, although its real incidence is currently unknown. Besides having great impact on public health, this phenomenon raises the question if immunity generated by a single infection is sufficient to provide sterilizing/protective immunity to a subsequent SARS-CoV-2 re-exposure. The Golden Syrian hamster is a manageable animal model to explore immunological mechanisms able to counteract COVID-19, as it recapitulates pathological aspects of mild to moderately affected patients. Here, we report that SARS-CoV-2-inoculated hamsters resolve infection in the upper and lower respiratory tracts within seven days upon inoculation with the Cat01 (G614) SARS-CoV-2 isolate. Three weeks after primary challenge, and despite high titers of neutralizing antibodies, half of the animals were susceptible to reinfection by both identical (Cat01, G614) and variant (WA/1, D614) SARS-CoV-2 isolates. However, upon re-inoculation, only nasal tissues were transiently infected with much lower viral replication than those observed after the first inoculation. These data indicate that a primary SARS-CoV-2 infection is not sufficient to elicit a sterilizing immunity in hamster models but protects against lung disease.

pathology↗