Biology subjects

Breban, M. I.

Publications and source records attributed to Breban, M. I..

7 recordsLinked to original sources

bioRxiv2026

Evolutionary history of Jamestown Canyon virus disentangles complex multi-vector ecology

Jamestown Canyon virus (JCV) is a re-emerging mosquito-borne virus of increasing concern in North America. It has been historically understudied, leading to significant gaps in our understanding of its evolutionary history, ecological maintenance, and transmission dynamics. Here, we generated 658 whole-genome JCV sequences from the Northeast United States, including 84% (500/597) of all JCV-positive mosquitoes detected in Connecticut from 1997-2022. Then we applied phylodynamic methods to demonstrate how mosquito phenology and host interaction structure the persistence and spread of JCV. Our phylogenetic analyses estimate that JCV was introduced in the Northeast by at least the early 1700s and the primary introductions of lineages A and B into Connecticut occurred during the mid-1800s to mid-1900s. Further, we estimate that JCV evolves at a rate of [~]3 x 10-5 s/s/y, making it one of the slowest evolving known RNA viruses, because the virus spends [~]10 months per year in evolutionary stasis while over-wintering in mosquito eggs. To investigate ecological drivers of JCV spread in Connecticut, we paired discrete trait and continuous phylogeographic reconstructions with mosquito surveillance data. We estimate that JCV has a low diffusion rate of [~]30-60 km2/year, which is more similar to slow-moving tick-borne viruses than other mosquito-borne viruses. We found that univoltine Aedes mosquitoes were likely to maintain the virus across years through overwintering in eggs, accounting for its slow evolution and dispersal, while multivoltine mosquitoes contribute to periodic bursts of spatial diffusion and amplification within seasons. By characterizing seasonal dynamics of JCV, we demonstrate the utility of dense sequencing and phylodynamics to disentangle complex transmission cycles, offering a framework to rapidly advance our evolutionary and ecological knowledge of understudied viruses.

ecology↗

bioRxiv2025

A targeted amplicon sequencing panel for cost-effective high-throughput genotyping of Aedes aegypti

The mosquito Aedes aegypti is the primary vector for several medically significant arboviruses, including dengue, Zika, chikungunya, and yellow fever. Studying the genetic diversity of Ae. aegypti is crucial for understanding its evolutionary history, population dynamics, and the effectiveness of vector control methods. Due to the large genome size of Ae. aegypti, whole-genome sequencing (WGS) is often cost-prohibitive for large-scale studies. Recent advances in reduced-representation methods, aiming to reduce costs by sequencing only a small portion of the genome, provide cost-effective alternatives. However, a standardized set of genome-wide markers specifically designed for population genetic studies of Ae. aegypti remains unavailable. Here, we present a targeted amplicon sequencing panel designed for cost-effective, high-throughput genotyping across 291 loci distributed throughout the Ae. aegypti genome. Our in silico analyses indicate that this amplicon panel effectively replicates population structure analyses typically derived from WGS data. We demonstrate that the amplicon panel accurately discriminates between diverse laboratory colonies of Ae. aegypti and consistently measures individual genetic admixture to a degree comparable with WGS. By enabling high-throughput genotyping at a reduced cost, we anticipate that our targeted amplicon sequencing panel will facilitate large-scale genotyping studies of Ae. aegypti for vector surveillance and population structure analyses, especially in resource-limited settings.

genomics↗

bioRxiv2025

Heterogeneity in inhibition of genetically diverse dengue virus strains by Wolbachia

The release of Aedes aegypti mosquitoes transinfected with the virus-inhibiting Wolbachia bacterium has the potential to reduce the burden caused by dengue virus (DENV). However, the robustness of this control strategy across the wide genetic diversity of DENV remains unknown. Here, we systematically tested two commonly used Wolbachia strains (wAlbB and wMelM) for their ability to inhibit 60 genetically diverse DENV isolates spanning all four serotypes. We found stronger inhibition by wMelM (median relative dissemination: 0.04) than wAlbB (median relative dissemination: 0.19). Furthermore, while we found substantial heterogeneity in inhibition across DENV isolates, we found that more DENV-3 isolates were weakly inhibited (median relative dissemination: 0.47 for wAlbB and 0.39 for wMelM) compared to the other serotypes (median relative disseminations: 0.10-0.18 for wAlbB and 0-0.11 for wMelM). Using transmission dynamic models, we further showed that differential Wolbachia inhibition results in increased probability of reemergence, particularly in high transmission intensity settings, with strong selection for DENV strains that have higher relative dissemination in mosquitoes. Our work highlights the importance of considering DENV genetic diversity, including the long-term risk of selection, in Wolbachia-based control interventions.

microbiology↗

bioRxiv2025

Implications of successive blood feeding on Wolbachia-mediated dengue virus inhibition in Aedes aegypti mosquitoes

Dengue virus (DENV) is a mosquito-borne virus that poses a continued and increasing threat to public health. A promising strategy to mitigate the burden of DENV is introgression of the virus-inhibiting Wolbachia pipientis bacterium into Aedes aegypti populations in the field. While previous studies on Wolbachia-mediated virus inhibition have typically assessed viral replication following a single bloodmeal, the main vector of DENV, Ae. aegypti, feeds frequently, often biting multiple hosts per gonotrophic cycle and promptly attempting to refeed following egg laying. Previously, we demonstrated that successive blood feeding reduces the extrinsic incubation period (EIP) and shortens the time it takes for a mosquito to be able to transmit viruses to a new host. With this in mind, we investigated the impact of successive blood meals on DENV serotype 2 (DENV-2) in Ae. aegypti in the presence or absence of Wolbachia (wAlbB and wMelM). We found that both WT and Wolbachia transinfected had increased DENV-2 dissemination 7 days post-infection as well as higher body titers of DENV-2 in the double-fed groups. Using these empirical data in a binomial regression model, we estimated that successive feeding increased the probability of WT and Wolbachia transinfected mosquitoes surviving the EIP. When we estimated the odds of surviving the EIP for mosquitoes with Wolbachia relative to WT mosquitoes, successive feeding increased the chances of WT mosquitoes surviving the EIP more than in mosquitoes with Wolbachia, indicating a strong inhibitory effect of Wolbachia even in the context of natural frequent blood feeding behavior. Our work shows that mosquito feeding behavior should be considered when assessing the inhibitory effects of Wolbachia on DENV.

microbiology↗

bioRxiv2024

Tiled Amplicon Sequencing Enables Culture-free Whole-Genome Sequencing of Pathogenic Bacteria From Clinical Specimens

Pathogen sequencing is an important tool for disease surveillance and demonstrated its high value during the COVID-19 pandemic. Viral sequencing during the pandemic allowed us to track disease spread, quickly identify new variants, and guide the development of vaccines. Tiled amplicon sequencing, in which a panel of primers is used for multiplex amplification of fragments across an entire genome, was the cornerstone of SARS-CoV-2 sequencing. The speed, reliability, and cost-effectiveness of this method led to its implementation in academic and public health laboratories across the world and adaptation to a broad range of viral pathogens. However, similar methods are not available for larger bacterial genomes, for which whole-genome sequencing typically requires in vitro culture. This increases costs, error rates and turnaround times. The need to culture poses particular problems for medically important bacteria such as Mycobacterium tuberculosis, which are slow to grow and challenging to culture. As a proof of concept, we developed two novel whole-genome amplicon panels for M. tuberculosis and Streptococcus pneumoniae. Applying our amplicon panels to clinical samples, we show the ability to classify pathogen subgroups and to reliably identify markers of drug resistance without culturing. Development of this work in clinical settings has the potential to dramatically reduce the time of diagnosis of drug resistance for multiple drugs in parallel, enabling earlier intervention for high priority pathogens.

genomics↗

bioRxiv2023

Survey of white-footed mice in Connecticut, USA reveals low SARS-CoV-2 seroprevalence and infection with divergent betacoronaviruses

Diverse mammalian species display susceptibility to and infection with SARS-CoV-2. Potential SARS-CoV-2 spillback into rodents is understudied despite their host role for numerous zoonoses and human proximity. We assessed exposure and infection among white-footed mice (Peromyscus leucopus) in Connecticut, USA. We observed 1% (6/540) wild-type neutralizing antibody seroprevalence among 2020-2022 residential mice with no cross-neutralization of variants. We detected no SARS-CoV-2 infections via RT-qPCR, but identified non-SARS-CoV-2 betacoronavirus infections via pan-coronavirus PCR among 1% (5/468) of residential mice. Sequencing revealed two divergent betacoronaviruses, preliminarily named Peromyscus coronavirus-1 and -2. Both belong to the Betacoronavirus 1 species and are [~]90% identical to the closest known relative, Porcine hemagglutinating encephalomyelitis virus. Low SARS-CoV-2 seroprevalence suggests white-footed mice may not be sufficiently susceptible or exposed to SARS-CoV-2 to present a long-term human health risk. However, the discovery of divergent, non-SARS-CoV-2 betacoronaviruses expands the diversity of known rodent coronaviruses and further investigation is required to understand their transmission extent.

ecology↗

bioRxiv2021

A stem-loop RNA RIG-I agonist confers prophylactic and therapeutic protection against acute and chronic SARS-CoV-2 infection in mice

As SARS-CoV-2 continues to cause morbidity and mortality around the world, there is an urgent need for the development of effective medical countermeasures. Here, we assessed the antiviral capacity of a minimal RIG-I agonist, stem-loop RNA 14 (SLR14), in viral control, disease prevention, post-infection therapy, and cross-variant protection in mouse models of SARS-CoV-2 infection. A single dose of SLR14 prevented viral replication in the lower respiratory tract and development of severe disease in a type I interferon (IFN-I) dependent manner. SLR14 demonstrated remarkable protective capacity against lethal SARS-CoV-2 infection when used prophylactically and retained considerable efficacy as a therapeutic agent. In immunodeficient mice carrying chronic SARS-CoV-2 infection, SLR14 elicited near-sterilizing innate immunity by inducing IFN-I responses in the absence of the adaptive immune system. In the context of infection with variants of concern (VOC), SLR14 conferred broad protection and uncovered an IFN-I resistance gradient across emerging VOC. These findings demonstrate the therapeutic potential of SLR14 as a host-directed, broad-spectrum antiviral for early post-exposure treatment and for treatment of chronically infected immunosuppressed patients.

immunology↗