Biology subjects

Lambrechts, L.

Publications and source records attributed to Lambrechts, L..

At least 19 recordsLinked to original sources

bioRxiv2026

Interpersonal Synchronization of Brain and Body Tracks Attention and Listening Engagement

Purpose: Speech perception is a fundamental part of everyday communication that relies on more than simple identification of words and sentences. Attention and listening engagement both contribute to speech perception, while representing distinct aspects of the listening experience. Attention is typically associated with cognitive focus, whereas listening engagement additionally involves cognitive and affective immersion in sound. Despite their importance, these states remain difficult to disentangle, behaviorally and physiologically. Both have been linked to interpersonal synchronization (the synchronization of biobehavioral signals across individuals), raising questions about what this synchronization actually reflects. Method: In this study, we disentangled attention and listening engagement by independently manipulating both factors within a single experiment. Thirty participants listened to two simultaneously presented streams of meaningful speech and were instructed to focus on only one. Both attended and unattended stimuli were designed to be either engaging or non-engaging. Neural activity was recorded using EEG, while physiological responses were measured using heart rate and electrodermal activity. Results: Interpersonal synchronization was computed from neural and bodily signals, alongside a self-report measure of listening engagement and auditory attention decoding (AAD), a neural measure of selective attention. Interpersonal synchronization of all three modalities significantly predicted listening engagement, whereas neural interpersonal synchronization was the only measure that significantly predicted attention. These findings suggest that attention is primarily driven by cognitive processes represented in the brain, while listening engagement additionally involves affective processes that are more strongly reflected in bodily responses. Conclusions: Overall, this study demonstrates that different forms of interpersonal synchronization reflect distinct dimensions of the listening experience and supports interpersonal synchronization as a potential objective marker of listening engagement.

neuroscience↗

bioRxiv2026

Non-retroviral Endogenous Viral Element Acts as a Stable Antiviral Regulator Across Mosquito Life Stages and Generations

Endogenous viral elements (EVEs) from non-retroviral RNA viruses are widespread in host genomes, yet their functional significance in vivo remains poorly understood. In mosquitoes, EVEs have been shown to suppress cognate viral replication through the PIWI-interacting RNA (piRNA) pathway. However, how this antiviral activity shapes virus-host dynamics beyond reducing viral replication remains unclear. Here, we established Aedes aegypti mosquito lines naturally infected with cell-fusing agent virus (CFAV) that differ in the presence or absence of a CFAV-derived EVE (CFAV-EVE1). Using this natural virus-host system, we showed that CFAV-EVE1 suppressed viral replication across sexes, tissues, developmental stages, and generations. This antiviral effect is initiated by EVE-derived primary piRNAs, as demonstrated in ovaries and heads. Despite reducing viral load, CFAV-EVE1 conferred no measurable benefits on mosquito survival or reproduction, nor did it eliminate CFAV from the naturally infected population under standard laboratory conditions. However, vertical transmission rates were reduced in EVE-containing mosquitoes and prolonged egg storage further reduced viral prevalence, suggesting that environmental stress may reveal EVE-mediated viral suppression. Together, these findings demonstrate that EVEs function as stable, heritable regulators of persistent virus-host interactions and highlight that ecological context may be critical for fully appreciating their functional significance.

microbiology↗

bioRxiv2026

Dengue virus infection in Aedes aegypti mosquito brains elicits minimal transcriptional response

Billions of people each year are at risk from infection by dengue, Zika, yellow fever, and chikungunya viruses, which are transmitted by female Aedes aegypti mosquitoes. Mosquitoes themselves are infected by these arboviruses, but how the mosquito nervous system responds to arboviral infection is unknown. We combined whole-mount immunofluorescence with single-head bulk RNA-sequencing to characterize dengue virus (DENV) infection in the brain of Aedes aegypti. DENV productively infects brain cells in a bimodal pattern: individual brains showed either sparse or widespread infection, with no intermediate phenotypes. An infectious blood meal altered thousands of genes, including 64 immunity genes, at 7 days post-feeding (DPF), yet active viral replication in the head did not increase the transcriptional response. Heads with and without detectable DENV showed minimal transcriptional differences, with no induction of canonical immune effectors. Despite productive infection, the mosquito brain tolerates DENV replication with minimal transcriptional response.

microbiology↗

bioRxiv2026

LRSomatic: a highly scalable and robust pipeline for somatic variant calling in long-read sequencing data

MotivationLong-read sequencing is increasingly used in cancer research and clinical genomics due to its ability to resolve complex genomic variation and previously inaccessible regions of the genome. However, dedidated workflows for comprehensive somatic variant analysis from long-read whole-genome data remain scarce, limiting uptake in cancer genomics. ResultsWe present LRSomatic, a Nextflow-based, nf-core-compliant pipeline supporting somatic SNV, indel, structural variant, and copy number calling from PacBio HiFi and ONT data. LRSomatic supports paired tumor-normal and tumor-only designs, as well as integration of epigenetic integration via Fiber-seq. Benchmarked on COLO829 and HG008 reference cell lines, LRSomatic achieves state-of-the-art performance across both platforms and variant types. Applied to a case of clear cell sarcoma, it recovers all identified driver alterations, including the pathognomonic EWSR1::ATF1 fusion, and resolves haplotype-specific chromatin accessibility via Fiber-seq. Availability and ImplementationFreely available at https://github.com/intgenomicslab/lrsomatic, implemented in Nextflow DSL2, supported via Docker and Singularity.

bioinformatics↗

bioRxiv2025

Natural salivary gland barrier curtails Zika virus transmission in Thai Aedes aegypti

BackgroundVector competence is a critical determinant of arbovirus transmission dynamics, yet most studies in Thailand have primarily examined Aedes aegypti susceptibility to infection and systemic viral dissemination rather than the mosquitos potential to transmit infectious virions. Given that transmission potential varies among mosquito populations, identifying population-specific transmission barriers is crucial for optimizing vector control strategies especially under budget and resource constrains. Methodology/Principal FindingsThis study assessed the Zika virus (ZIKV) transmission potential of three Ae. aegypti populations from Thailand: two field-derived populations from Chiang Mai (CSP) and Nakhon Sawan (NAK) and a long-established laboratory strain (DMSC). Following oral exposure to a locally circulating ZIKV strain, viral transmission potential was evaluated. CSP mosquitoes demonstrated the earliest and highest ZIKV prevalence in salivary glands at 7 days post-infectious blood meal (dpibm), with DMSC and NAK populations reaching comparable infection levels at later time points. Despite this, NAK mosquitoes exhibited a strong barrier, resulting in significantly lower transmission potential. Genetic crosses revealed that this phenotype is inherited as an autosomal dominant trait and is similarly effective against dengue virus serotype 2 (DENV2), underscoring the broad-spectrum potential of NAK Ae. aegypti for transmission suppression. Furthermore, male NAK mosquitoes exhibited superior mating competitiveness, reinforcing their viability as a tool for vector control by population replacement. Conclusions/SignificanceOur findings highlight significant variability in ZIKV vector competence among Thai Ae. aegypti populations, emphasizing the importance of direct transmission assessments in vector competence studies. The discovery of a naturally occurring, heritable salivary gland escape barrier presents an opportunity for vector control strategies through NAK-based population replacement approaches. With their strong mating capability and broad arbovirus-blocking ability, NAK mosquitoes provide a natural alternative to Wolbachia-based and genetically modified mosquito interventions. Author summaryAedes aegypti is the primary vector of arboviruses such as Zika virus (ZIKV) and dengue virus (DENV), but not all mosquitoes that become infected successfully transmit the virus. While most research in Thailand has focused on mosquito infection and virus dissemination, fewer studies have examined the ability of mosquitoes to transmit infectious virus through their saliva. We discovered a mosquito population from Nakhon Sawan (NAK) that exhibits a natural barrier to virus release from the salivary glands, leading to significant blocking of virus transmission in ZIKV-infected mosquitoes. This salivary gland escape barrier of NAK is a heritable autosomal dominant characteristic that also restricts DENV transmission. Given their high mating competitiveness, NAK mosquitoes present a promising candidate for population replacement strategies aimed at reducing arbovirus transmission. Our findings emphasize the importance of assessing transmission rates rather than relying solely on infection and dissemination rates. Furthermore, the discovery of a naturally occurring mosquito population with reduced transmission potential offers a practical and sustainable vector control approach. The implementation of NAK-based population replacement strategies could serve as an alternative to traditional control methods, such as insecticide application or genetically modified mosquito releases. Future research should focus on field trials to validate the efficacy of this approach in real-world settings and assess its long-term impact on virus transmission dynamics.

microbiology↗

bioRxiv2025

Interpersonal synchronization as an objective measure of listening engagement

Listening engagement plays a crucial role in effective communication and knowledge transfer, reflecting a state of deep absorption in an auditory stimulus. The available behavioral assessments of listening engagement are limited in capturing its multidimensional nature. Measuring listening engagement objectively using brain and body signals is a compelling alternative. In particular, interpersonal synchronization--observed through synchronized neural and physiological responses among listeners--may offer a promising objective measure. In this study, we examined synchronization of brain activity, heart rate, and electrodermal activity between participants while they listened to engaging and non-engaging stories. Subjective engagement ratings were collected as a ground truth reference. Results showed higher interpersonal synchronization across all modalities when participants listened to engaging stories compared to non-engaging ones, with significant correlations between synchronization measures and ratings of subjective engagement. These results confirm that synchronization may be a reliable, objective marker of listening engagement. We anticipate that these results will provide a powerful framework for future research in relevant domains, including auditory neuroscience, education, and communication science, and enable impactful real-world applications, such as automatically tracking audience engagement in education, entertainment, and broader societal contexts.

neuroscience↗

bioRxiv2025

Dengue virus susceptibility in Aedes aegypti linked to natural cytochrome P450 variants

The mosquito Aedes aegypti is the primary vector for dengue virus (DENV), which infects millions of people annually. Variability in DENV susceptibility among wild Ae. aegypti populations is governed by genetic factors, but specific causal variants are unknown. Here, we identify a cytochrome P450-encoding gene (CYP4G15) whose variants drive differences in DENV susceptibility in a natural Ae. aegypti population. CYP4G15 is transiently upregulated in DENV-resistant midguts, while knockdown increases susceptibility, and transgenic overexpression enhances resistance. A naturally occurring 18-base-pair promoter deletion reduces CYP4G15 expression and confers higher DENV susceptibility. The unexpected role of a cytochrome P450 in DENV susceptibility challenges the long-standing focus on canonical immune pathways and opens new avenues for understanding antiviral defense and DENV transmission in mosquitoes.

microbiology↗

bioRxiv2025

BuzzWatch: uncovering multi-scale temporal patterns in mosquito behavior through continuous long-term monitoring

Understanding the temporal dynamics of mosquito behavior is essential for developing effective interventions against pathogen transmission. However, limited knowledge exists about the environmental, physiological, and genetic factors influencing mosquito activity patterns. This knowledge gap is partly due to a lack of tools to accurately quantify the behavior of free-flying mosquitoes over extended periods. Here, we introduce BuzzWatch, an open-source, low-cost platform designed to continuously monitor mosquito flight behavior over several weeks with high temporal resolution. BuzzWatch records videos of mosquitoes freely flying in a transparent cage and automates the extraction, analysis, and visualization of behavioral data, including flight trajectories and population-level flight and sugar-feeding statistics. Using BuzzWatch, we quantified the daily rhythms of 10 Aedes aegypti populations from various geographic origins. Globally invasive Ae. aegypti showed increased sugar feeding and flight activity during midday compared to native African populations. Our platform further revealed subtle, long-lasting effects of blood feeding on activity patterns and a complex response to extended daylight periods. By integrating a host-seeking module in BuzzWatch to deliver CO2 and heat pulses, we observed a twofold increase in Ae. aegyptis response to host-associated cues during the daytime compared to nighttime. Combined, these results demonstrate BuzzWatchs potential to investigate responses to host cues over seconds, natural variability in daily rhythms over hours, and phenotypic plasticity over days. BuzzWatch offers a novel perspective on mosquito behavior over multiple timescales, paving the way for advanced ecological and epidemiological studies that can inform targeted and effective vector control strategies. Short SummaryThis study introduces a new experimental platform to monitor multiple features of mosquito behavior (flight activity, sugar feeding, short-range host-seeking) with high temporal resolution over several weeks. HighlightsO_LIContinuous month-long tracking of mosquito flight activity in a laboratory setting. C_LIO_LIMultiscale analysis of flight behavior, from seconds to weeks. C_LIO_LIMapping of natural variation in daily rhythm of Aedes aegypti populations. C_LIO_LIQuantifying the long-lasting effect of physiological (blood-meal digestion) and environmental (photoperiod increase) perturbations. C_LIO_LIAutomatically monitoring response to short-range host-seeking cues at specific times of the day. C_LI

animal behavior and cognition↗

bioRxiv2025

Polygenic viral factors enable efficient mosquito-borne transmission of African Zika virus

Zika virus (ZIKV) is a mosquito-borne flavivirus primarily transmitted among humans by Aedes aegypti. Over the past two decades, it has caused significant outbreaks associated with birth defects and neurological disorders. Phylogenetically, ZIKV consists of two main genotypes referred to as the African and Asian lineages, each exhibiting distinct biological properties. African lineage strains are transmitted more efficiently by mosquitoes, but pinpointing the genetic basis of this difference has remained challenging. Here, we address this question by comparing recent African and Asian strains using chimeric viruses, in which segments of the parental genomes are swapped. Our results show that the structural genes from the African strain enhance viral internalization, while the non-structural genes improve genome replication and infectious particle production in mosquito cells. In vivo mosquito transmission is most significantly influenced by the structural genes, although no single viral gene alone determines this effect. Additionally, we develop a stochastic model of in vivo viral dynamics in mosquitoes that mirrors the observed patterns, suggesting that the primary difference between the African and Asian strains lies in their ability to traverse the mosquito salivary glands. Overall, our findings suggest that the polygenic nature of ZIKV transmissibility has prevented Asian lineage strains from achieving the same epidemic potential as African lineage strains, underscoring the importance of lineage-specific adaptive landscapes in shaping ZIKV evolution and emergence.

microbiology↗

bioRxiv2024

Limited impact of the siRNA pathway on transposable element expression in Aedes aegypti

Transposable elements (TEs) are DNA sequences that can change their position within a genome. In the germline of arthropods, post-transcriptional regulation of TE expression is mainly mediated by the Piwi-interacting RNA (piRNA) pathway. piRNAs are small RNAs of 24-30 nucleotides (nt) in length produced from genomic precursor transcripts as well as through a ping-pong amplification cycle. In somatic tissues, certain insects, such as Drosophila, instead rely on the small interfering RNA (siRNA) pathway as a key regulator of TE expression. siRNAs are 21nt small RNAs produced from double-stranded RNA by the endonuclease Dicer2, which guides an RNA-induced silencing complex to degrade a complementary RNA. However, whether the siRNA pathway also regulates TE expression in the mosquito Aedes aegypti, a medically significant vector species with abundant somatic piRNAs, is unknown. To address this question, we investigated the expression of TEs and small RNAs in both somatic and gonadal tissues of a Dicer2 mutant line of Ae. aegypti and its wild-type counterpart. Our results show a modified pattern of TE expression and a decrease in TE-derived 21nt small RNAs in the Dicer2 mutant, but no major shift of TE transcript abundance. The lack of a functional siRNA pathway also causes perturbations in piRNA ping-pong signatures and the expression of certain piRNA-associated genes, but without clear evidence for compensation by increased piRNA pathway activity. We conclude that the mosquito Ae. aegypti produces siRNAs targeting TEs but these lack a critical role in the regulation of TE expression both in somatic and in gonadal tissues.

genomics↗

bioRxiv2024

Global genomics of Aedes aegypti unveils widespread and novel persistent infectious viruses capable of triggering a small RNA response

The mosquito Aedes aegypti is a prominent vector for arboviruses, but the breadth of mosquito viruses that infects this specie is not fully understood. In the broadest global survey to date of over 200 Ae. aegypti small RNA samples, we detected viral small interfering RNAs (siRNAs) and Piwi interacting RNAs (piRNAs) arising from mosquito viruses. We confirmed that most academic laboratory colonies of Ae. aegypti lack persisting viruses, yet two commercial strains were infected by a novel tombus-like virus. Ae. aegypti from North to South American locations were also teeming with multiple insect viruses, with Anphevirus and a bunyavirus displaying geographical boundaries from the viral small RNA patterns. Asian Ae. aegypti small RNA patterns indicate infections by similar mosquito viruses from the Americas and reveal the first wild example of dengue virus infection generating viral small RNAs. African Ae. aegypti also contained various viral small RNAs including novel viruses only found in these African substrains. Intriguingly, viral long RNA patterns can differ from small RNA patterns, indicative of viral transcripts evading the mosquitoes RNA interference (RNAi) machinery. To determine whether the viruses we discovered via small RNA sequencing were replicating and transmissible, we infected C6/36 and Aag2 cells with Ae. aegypti homogenates. Through blind passaging, we generated cell lines stably infected by these mosquito viruses which then generated abundant viral siRNAs and piRNAs that resemble the native mosquito viral small RNA patterns. This mosquito small RNA genomics approach augments surveillance approaches for emerging infectious diseases.

genomics↗

bioRxiv2023

Extensive variation and strain-specificity in dengue virus susceptibility among African Aedes aegypti populations

African populations of the mosquito Aedes aegypti are usually considered less susceptible to infection by human-pathogenic flaviviruses than globally invasive populations found outside Africa. Although this contrast has been well documented for Zika virus (ZIKV), it is unclear to what extent it is true for dengue virus (DENV), the most prevalent flavivirus of humans. Addressing this question is complicated by substantial genetic diversity among DENV strains, most notably in the form of four genetic types (DENV1 to DENV4), that can lead to genetically specific interactions with mosquito populations. Here, we carried out a continent-wide survey of DENV susceptibility using a panel of field-derived Ae. aegypti colonies from across the African range of the species and a colony from Guadeloupe, French West Indies as non-African reference. We found considerable variation in the ability of African Ae. aegypti populations to acquire and replicate a panel of six DENV strains spanning the four DENV types. Although African Ae. aegypti populations were generally less susceptible than the reference non-African population from Guadeloupe, in several instances some African populations were equally or more susceptible than the Guadeloupe population. Moreover, the relative level of susceptibility between African mosquito populations depended on the DENV strain, indicating genetically specific interactions. We conclude that unlike ZIKV susceptibility, there is no clear-cut dichotomy in DENV susceptibility between African and non-African Ae. aegypti. DENV susceptibility of African Ae. aegypti populations is highly heterogeneous and largely governed by the specific pairing of mosquito population and DENV strain. Author summaryAfrican populations of the mosquito Aedes aegypti are usually thought to be less likely to get infected by flaviviruses compared to Ae. aegypti mosquitoes found outside Africa. While this has been well-demonstrated for Zika virus, it is not clear if the same is true for dengue virus, which is the most common flavivirus in humans. Studying this is complicated by the strain diversity of dengue virus, including four main genetic types, potentially causing different interactions. In this study, we compared several mosquito populations and found that, in general, African mosquitoes were less likely to get infected by dengue virus compared to mosquitoes from outside Africa. However, in some cases, African mosquitoes were just as or even more likely to get infected. The specific strain of dengue virus also influenced how likely African mosquitoes were to get infected, showing that the relationship between African mosquitoes and dengue virus is complex.

microbiology↗

bioRxiv2023

Differential intra-host infection kinetics in Aedes aegypti underlie superior transmissibility of African relative to Asian Zika virus

Despite numerous studies highlighting the higher transmissibility of the African Zika virus (ZIKV) lineage compared to the Asian lineage in mosquito vectors, little is known about how the viruses interact with different tissues during the early steps of mosquito infection. To address this gap, we aimed to characterize intra-host infection barriers by combining a tissue-level monitoring of infection using plaque assays and a novel quantitative analysis of single-cell level infection kinetics by in situ immunofluorescent staining. Our results revealed that, in Aedes aegypti, an African ZIKV strain exhibited a higher replication rate across various tissues than an Asian ZIKV strain. This difference was potentially due to a higher virus production in individual cells, faster spread within tissues, or a combination of both factors. Furthermore, we observed that higher bloodmeal titers resulted in a faster viral spread to neighboring cells suggesting that intra-host infection dynamics depend on inoculum size. We also identified a significant bottleneck during midgut infection establishment for both ZIKV lineages, with only a small percentage of the virus population successfully initiating infection. Finally, the in situ immunofluorescent staining technique enabled the examination of virus infection characteristics in different cell types and revealed heterogeneity in viral replication. Together, these findings demonstrate that differences in intra-host infection kinetics underlie differential transmissibility between African and Asian ZIKV lineages. This information could serve as a starting point to further investigate the underlying mechanisms and ultimately inform the development of alternative control strategies. ImportanceThe recent Zika virus (ZIKV) epidemic in the Americas highlights its potential public health threat. While the Asian ZIKV lineage has been identified as the main cause of the epidemic, the African lineage, which has been primarily confined to Africa, has shown evidence of higher transmissibility in Aedes mosquitoes. To gain a deeper understanding of this differential transmissibility, our study employed a combination of tissue-level infection kinetics and single-cell level infection kinetics using in situ immunofluorescent staining. We discovered that the African ZIKV lineage propagates more rapidly and spreads more efficiently within mosquito cells and tissues than its Asian counterpart. This information lays the groundwork for future exploration of the viral and host determinants driving these variations in propagation efficiency.

microbiology↗

bioRxiv2023

Molecular signature of domestication in the arboviral vector Aedes aegypti

BackgroundDomestication is a complex, multi-stage and species-specific process that results in organisms living close to humans. In the arboviral vector Aedes aegypti adaptation to living in proximity with anthropogenic environments has been recognized as a major evolutionary shift, separating a generalist form, Aedes aegypti formosus (Aaf), from the domestic form Aedes aegypti aegypti (Aaa), which tends to deposit eggs artificial containers and bite humans for a blood meal. These behaviors enhance the mosquito vectorial capacity. The extent to which domestication has impacted the Ae. aegypti genome has not been thoroughly investigated yet. ResultsTaking advantage of two forms distinct and historically documented geographic distributions, we analyzed the genomes of 634 worldwide Ae. aegypti mosquitoes. Using more than 300 million high-confidence SNPs, we found a unique origin for all out-of-Africa Ae. aegypti mosquitoes, with no evidence of admixture events in Africa, apart from Kenya. A group of genes were under positive selection only in out-of-Africa mosquitoes and 236 genes had nonsynonymous mutations, occurring at statistically different frequencies in Aaa and Aaf mosquitoes. ConclusionWe identified a clear signal of genetic differentiation between Aaa and Aaf, circumscribed to a catalogue of candidate genes. These "Aaa molecular signature" genes extend beyond chemosensory genes to genes linked to neuronal and hormonal functions. This suggests that the behavioral shift to domestication may rely on the fine regulation of metabolic and neuronal functions, more than the role of a few significant genes. Our results also provide the foundation to investigate new targets for the control of Ae. aegypti populations.

evolutionary biology↗

bioRxiv2023

HIV-PULSE: A long-read sequencing assay for high-throughput near full-length HIV-1 proviral genome characterization

A deep understanding of the composition of the HIV-1 reservoir is necessary for the development of targeted therapies and the evaluation of curative efforts. However, current near full-length (NFL) HIV-1 proviral genome sequencing assays are based on labor-intensive and costly principles of repeated PCRs at limiting dilution, restricting their scalability. To address this, we developed a high-throughput, long-read sequencing assay called HIV-PULSE (HIV Proviral UMI-mediated Long-read Sequencing). This assay uses unique molecular identifiers (UMIs) to tag individual HIV-1 genomes, allowing for the omission of the limiting dilution step and enabling long-range PCR amplification of many NFL genomes in a single PCR reaction, while simultaneously overcoming poor single-read accuracy. We optimized the assay using HIV-infected cell lines and then applied it to blood samples from 18 individuals living with HIV on antiretroviral therapy, yielding a total of 1,308 distinct HIV-1 genomes. Benchmarking against the widely applied Full-Length Individual Proviral Sequencing assay revealed similar sensitivity (11% vs 18%) and overall good concordance, though at a significantly higher throughput. In conclusion, HIV-PULSE is a cost-efficient and scalable assay that allows for the characterization of the HIV-1 proviral landscape, making it an attractive method to study the HIV-1 reservoir composition and dynamics.

molecular biology↗

bioRxiv2022

Multifaceted contributions of Dicer2 to arbovirus transmission by Aedes aegypti

Arthropod-borne viruses (arboviruses) transmitted by Aedes aegypti mosquitoes are an increasing threat to global health. The small interfering RNA (siRNA) pathway is considered the main antiviral immune pathway of insects, and thus represents a potential key target in the development of novel transmission-blocking strategies against arboviruses. Although the antiviral function of the siRNA pathway in Ae. aegypti is well established, its effective impact on arbovirus transmission is surprisingly poorly understood. Here, we used CRISPR/Cas9-mediated gene editing to create a line of Ae. aegypti in which we mutated Dicer2, a gene encoding the RNA sensor and key component of the siRNA pathway. Our Dicer2 null mutant line is viable and fertile, and only displays minor fitness defects despite being unable to produce siRNAs. The loss of Dicer2 affects early viral replication and systemic viral dissemination of four medically significant arboviruses (chikungunya, Mayaro, dengue, and Zika viruses) representing two viral families. However, measures of virus transmission potential indicate that Dicer2 null mutants and wild-type mosquitoes display an overall similar level of vector competence. Additionally, Dicer2 null mutants undergo significant virus-induced mortality during infection with chikungunya virus, but not dengue virus. Together, our results define a multifaceted role for Dicer2 in the transmission of arboviruses by Ae. aegypti mosquitoes and pave the way for further mechanistic investigations.

microbiology↗

bioRxiv2021

In-depth single-cell analysis of translation-competent HIV-1 reservoirs identifies cellular sources of plasma viremia

Clonal expansion of HIV-infected cells contributes to the long-term persistence of the HIV reservoir in ART-suppressed individuals. However, the contribution to plasma viremia from cell clones that harbor inducible proviruses is poorly understood. Here, we describe a single-cell approach to simultaneously sequence the TCR, integration sites and proviral genomes from translation-competent reservoir cells, called STIP-Seq. By applying this approach to blood samples from eight participants, we showed that the translation-competent reservoir mainly consists of proviruses with short deletions at the 5-end of the genome, often involving the major splice donor site. TCR and integration site sequencing revealed that antigen-responsive cells can harbor inducible proviruses integrated into cancer-related genes. Furthermore, we found several matches between proviruses retrieved with STIP-Seq and plasma viruses obtained during ART and upon treatment interruption, showing that STIP-Seq can capture clones that are responsible for low-level viremia or viral rebound.

microbiology↗

bioRxiv2021

In-depth characterization of HIV-1 reservoirs reveals links to viral rebound during treatment interruption

The HIV-1 reservoir is composed of cells harboring latent proviruses that are capable of contributing to viremia upon antiretroviral treatment (ART) interruption. Although this reservoir is known to be maintained by clonal expansion, the contribution of large, infected cell clones to residual viremia and viral rebound remains underexplored. Here, we conducted an extensive analysis on four ART-treated individuals who underwent an analytical treatment interruption (ATI). We performed subgenomic (V1-V3 env), near full-length proviral and integration site sequencing, and used multiple displacement amplification to sequence both the integration site and provirus from single HIV-infected cells. We found eight proviruses that could phylogenetically be linked to plasma virus obtained before or during the ATI. This study highlights a role for HIV-infected cell clones in the maintenance of the replication-competent reservoir and suggests that infected cell clones can directly contribute to rebound viremia upon ATI.

microbiology↗