Biology subjects

Ebel, G. D.

Publications and source records attributed to Ebel, G. D..

At least 19 recordsLinked to original sources

bioRxiv2025

Evaluation of the safety and insecticidal efficacy of ivermectin-treated bird feed formulations in different avian species

BackgroundWest Nile virus (WNV) is maintained in an enzootic cycle between reservoir host birds and Culex (Cx.) spp. mosquitoes. This relationship presents a potential target for vector control strategies. Ivermectin (IVM), an endectocidal drug that selectively affects invertebrates while remaining safe at high concentrations in mammals and birds, can be delivered to Cx. tarsalis via blood meals from birds fed IVM-treated bird feed. In this study we evaluated the safety, efficacy, and utility of IVM-treated bird feed as a novel vector control strategy by assessing its impact on multiple bird species and mosquitoes. MethodsMosquitoes were collected during peak WNV transmission season in Northern Colorado and DNA extracted from blood meals to determine host species. Chickens, pigeons, zebra finches, and house sparrows were fed different formulations of IVM-treated bird feed and observed for clinical signs, and their sera were fed to Cx. tarsalis mosquitoes to evaluate mosquitocidal efficacy. Feeding rates and IVM serum concentrations in birds were analyzed by unpaired t-test and one-way ANOVA, and mosquito survivorship was analyzed by Kaplan-Meier curves and compared using paired log-rank tests. IVM serum concentration and mosquito survivorship were compared using Spearman correlation. ResultsSpeciation analyses conducted on blood meals from Cx. tarsalis collected during peak WNV transmission season in Northern Colorado determined that they feed primarily on songbird species that commonly visit bird feeders, with house sparrows representing the most frequent blood meal host. In laboratory experiments using multiple formulations and doses of IVM, chickens, pigeons, zebra finches, and house sparrows ate comparable amounts of IVM-treated bird feed compared to untreated feed, had similar weight gain, and exhibited no clinical signs of toxicity. Both colony-reared and locally captured Cx. tarsalis showed significant mortality after feeding on sera from IVM-treated birds compared to controls. ConclusionsThese results suggest that targeting songbirds with IVM-treated bird feed should be safe for wildlife and may elicit high rates of IVM-induced mortality by reaching a large proportion of WNV vector mosquitoes via their proclivity for feeding on passerine birds.

microbiology↗

bioRxiv2025

Investigation of Powassan virus lineage II pathogenesis and neurotropism in mice

Powassan virus (POWV) is an emerging tick-borne flavivirus that causes disease in humans. POWV has considerable genetic and phenotypic diversity, including highly variable replication in vitro and pathogenesis in mice. This study sought to define the extent of variability in pathogenesis within POWV lineage II in mice and investigate possible viral determinants. Relative to other strains, two New York-derived isolates, NY.19.12 and NY.19.32, caused earlier clinical signs and earlier detection of viral RNA (vRNA) in the spleen and brain compared to mice infected with virus derived from a lineage II infectious clone (WI.97.ic). Sequencing revealed these strains share three amino acid substitutions in envelope, NS1, and NS5 compared to other lineage II strains, which were engineered into a mutant infectious clone. At early time points post-infection, clinical signs, vRNA detection in the cerebellum, and viral distribution in the brain were similar between NY.19.12 and the mutant clone, suggesting these mutations may play a role in disease progression and early neuroinvasion. However, NY.19.12 vRNA was detected in the spleen at significantly higher rates compared to both WI.97.ic and the mutant clone, indicating factors other than these mutations are responsible for increased spleen infection. Importantly, this study highlights the complexity of POWV pathogenesis and suggests that POWV lineage II strains have varying disease phenotypes likely driven by multiple genetic differences. ImportanceTick-borne flaviviruses exhibit considerable genetic and phenotypic diversity in nature, influencing their transmission and pathogenesis. Defining the mechanisms of pathogenesis requires understanding how inter-strain variation translates to phenotypic differences in viral dissemination and neuroinvasion. This study demonstrates that even closely related Powassan virus (POWV) lineage II strains display distinct disease phenotypes that are only partially attributable to nonsynonymous consensus mutations within the viral coding sequence. By highlighting the complexity of POWV infection dynamics in mice, these findings provide valuable insights into how POWV lineage II diversity may shape disease progression and severity in humans.

microbiology↗

bioRxiv2025

West Nile virus dissemination among individual wild mosquito vectors in Northern Colorado, 2023

West Nile virus (WNV) transmission risk is typically estimated from pooled whole-mosquito infection data, which may overestimate the proportion of mosquitoes capable of transmission. To assess natural viral dissemination in field-collected Culex tarsalis, we tested infection rates in tissues of 1,793 individual mosquitoes collected from Northern Colorado in August 2023. Abdomens were screened for WNV RNA, and corresponding thorax and head tissues from positive mosquitoes were tested. Fifteen mosquitoes had detectable abdominal infections, but WNV RNA was detected in only 53% (8/15) of both the thorax and head tissues, while another 27% (4/15) had WNV RNA detected in either the thorax or the head alone. Logistic regression suggests an inconsistent relationship between abdominal viral ribonucleic acid (RNA) load and virus dissemination, whereas receiver operating characteristic analysis identifies a threshold of [~]59,000 RNA copies in the abdomen predictive of dissemination (AUC 0.80, 95% CI: 0.545, 1). These results suggest whole-body RNA detection may overestimate transmission potential from field-captured mosquitoes, and that incorporating infection data could refine surveillance-based risk indices for WNV.

ecology↗

bioRxiv2025

Generation of broad-spectrum vaccine platforms against tick-borne flaviviruses using ancestral sequence reconstruction

Tick-Borne Flaviviruses (TBFs) pose a significant global health threat, but few vaccines exist against these viral pathogens. Currently approved vaccines against TBFs are only protective against specific virus species, leaving the population at risk for infection by many existing and emerging TBFs. The development of vaccines that provide broad protection against a range of related TBFs has the potential of reducing disease burden against known and unknown viral pathogens. In this study we utilized ancestral sequence reconstruction (ASR) to design recombinant antigens of extinct ancestral viruses to serve as vaccines against multiple modern day TBFs. We reconstructed a common ancestral envelope (E) antigen that possesses high sequence and structural identity to several modern-day TBF pathogens and engineered this ancestral E antigen sequence into an attenuated Sindbis virus vaccine platform. We observed that this Sindbis virus was replication competent and generated sustained antigen expression in vitro. Immunizing mice with this vaccine candidate resulted in the production of significant neutralizing antibody active against virulent Powassan (POWV) and Langat (LGTV) viruses. Antibody neutralization correlated well with decreased clinical signs and increased survival from virulent POWV challenge. These data indicate that a common ancestral antigen from TBFs can provide protection against multiple modern day TBFs, and that the ASR approach may provide a valuable new pathway to safe and effective pan-TBF vaccines.

microbiology↗

bioRxiv2025

Development of ENTV reverse genetics system and phenotypic evaluation of rescued virus reveals host-specific replication patterns in mosquitoes

Entebbe bat virus (ENTV) is a bat-associated flavivirus with no known vector. Research into the biology of this virus, including assessment of the possibility that it may be vector-transmitted, is hindered by a lack of molecular tools and robust genetic systems. Therefore, we sequenced the complete 3 untranslated region, which was not previously available, and developed an infectious clone of ENTV to facilitate further investigation of the virus. Virus derived from the clone replicated similarly to the parental virus isolate in various vertebrate cells. Surprisingly, ENTV replicated to high titers in Aedes aegypti and Aedes albopictus mosquito cell lines, but there was no replication or infection in Culex tarsalis cells. In addition, phylogenetic and bioinformatics analyses strongly suggested that ENTV may be associated with a mosquito host. Given the bioinformatics support and efficient growth in Aedes cells, we orally exposed Ae. aegypti and Ae. albopictus to ENTV to evaluate infection. The ENTV blood-fed mosquitoes were all negative for infection; however, when ENTV was intrathoracically inoculated, bypassing the initial midgut infection and escape barriers, it replicated to high levels in the body, without dissemination of infectious virus into the saliva. These findings suggest that, despite demonstrating high molecular compatibility at the cellular level in Aedes mosquitoes, Ae. aegypti and Ae. albopictus are unlikely to serve as competent vectors for ENTV transmission due to strong midgut infection barriers. The clone presented in this manuscript should help to clarify the mechanisms for transmission and maintenance of ENTV, which remain poorly understood.

microbiology↗

bioRxiv2024

A single-cell atlas of the Culex tarsalis midgut during West Nile virus infection

The mosquito midgut functions as a key interface between pathogen and vector. However, studies of midgut physiology and virus infection dynamics are scarce, and in Culex tarsalis - an extremely efficient vector of West Nile virus (WNV) - nonexistent. We performed single-cell RNA sequencing on Cx. tarsalis midguts, defined multiple cell types, and determined whether specific cell types are more permissive to WNV infection. We identified 20 cell states comprising 8 distinct cell types, consistent with existing descriptions of Drosophila and Aedes aegypti midgut physiology. Most midgut cell populations were permissive to WNV infection. However, there were higher levels of WNV RNA (vRNA) in enteroendocrine cells, suggesting enhanced replication in this population. In contrast, proliferating intestinal stem cells (ISC) had the lowest levels of vRNA, a finding consistent with studies suggesting ISC proliferation in the midgut is involved in infection control. ISCs were also found to have a strong transcriptional response to WNV infection; genes involved in ribosome structure and biogenesis, and translation were significantly downregulated in WNV-infected ISC populations. Notably, we did not detect significant WNV-infection induced upregulation of canonical mosquito antiviral immune genes (e.g., AGO2, R2D2, etc.) at the whole-midgut level. Rather, we observed a significant positive correlation between immune gene expression levels and vRNA load in individual cells, suggesting that within midgut cells, high levels of vRNA may trigger antiviral responses. Our findings establish a Cx. tarsalis midgut cell atlas, and provide insight into midgut infection dynamics of WNV by characterizing cell-type specific enhancement/restriction of, and immune response to, infection at the single-cell level. Author SummaryWest Nile virus is the leading cause of mosquito-borne disease in N. America. Cx. tarsalis is a highly competent vector of WNV that plays a central role in the transmission and maintenance of WNV in nature. It is hypothesized that the permissibility of mosquito midgut cells contributes to the midgut infection barrier and thus impacts the ability of pathogens to establish infection in a mosquito. Additionally, it is postulated that the midgut is the most important organ with respect to determining vector competence. The recent publication of the full Cx. tarsalis genome, in conjunction with the growing body of work demonstrating the successful application of single-cell RNA sequencing methodologies in insect models made it possible for us to examine the cellular composition of the Cx. tarsalis midgut, and WNV infection dynamics therein, at single-cell resolution. We found cell-type-specific differences in viral RNA levels suggesting variability in WNV replication efficiency in specific cell types, identified patterns of differential expression associated with WNV infection in specific cell populations, and characterized aspects of the innate immune response to WNV infection at the tissue and cellular level.

microbiology↗

bioRxiv2023

North American Powassan virus encompasses diverse in vitro phenotypes.

Powassan virus (POWV) is a tick-borne flavivirus which has resulted in increasing human cases over the past two decades. Despite high prevalence in ticks and evidence of broad distribution in North America, fewer than 50 human cases are detected annually with evidence of undetected asymptomatic infections. Experimental studies of the relationships between POWV genetic diversity and disease potential are currently lacking. In the present study, sixteen isolates originating from 13 locations in the United States and Canada were used to assess in vitro phenotypic diversity in human neuronal cells. Broad differences in replication and cytopathic ability were observed between isolates, even amongst those in the same sublineage. In vitro phenotype was not associated with geographic or temporal location and could not be associated with specific genotypes. These results support the observation that the North American POWV population may be highly genetically and phenotypically diverse. The degree to which in vitro phenotype reflects transmission and pathogenesis remains to be determined.

microbiology↗

bioRxiv2023

Phagocyte-expressed glycosaminoglycans promote capture of alphaviruses from the blood circulation in a host species-specific manner.

The magnitude and duration of vertebrate viremia are critical determinants of arbovirus transmission, geographic spread, and disease severity--yet, mechanisms determining arbovirus viremia levels are poorly defined. Previous studies have drawn associations between in vitro virion-glycosaminoglycan (GAG) interactions and in vivo clearance kinetics of virions from blood circulation. From these observations, it is commonly hypothesized that GAG-binding virions are rapidly removed from circulation due to ubiquitous expression of GAGs by vascular endothelial cells, thereby limiting viremia. Using an in vivo model for viremia, we compared the vascular clearance of low and enhanced GAG-binding viral variants of chikungunya (CHIKV), eastern-(EEEV), and Venezuelan-(VEEV) equine encephalitis viruses. We find GAG-binding virions are more quickly removed from circulation than their non-GAG-binding variant; however individual clearance kinetics vary between GAG-binding viruses, from swift (VEEV) to slow removal from circulation (EEEV). Remarkably, we find phagocytes are required for efficient vascular clearance of some enhanced GAG-binding virions. Moreover, transient depletion of vascular heparan sulfate (HS) impedes vascular clearance of only some GAG-binding viral variants and in a phagocyte-dependent manner, implying phagocytes can mediate vascular GAG-virion interactions. Finally, in direct contrast to mice, we find enhanced GAG-binding EEEV is resistant to vascular clearance in avian hosts, suggesting the existence of species-specificity in virion-GAG interactions. In summary, these data support a role for GAG-mediated clearance of some viral particles from the blood circulation, illuminate the potential of blood-contacting phagocytes as a site for GAG-virion binding, and suggest a role for species-specific GAG structures in arbovirus ecology. Significance StatementPreviously, evidence of arbovirus-GAG interactions in vivo has been limited to associations between viral residues shown to promote enhanced GAG-binding phenotypes in vitro and in vivo phenotypes of viral dissemination and pathogenesis. By directly manipulating host GAG expression, we identified virion-GAG interactions in vivo and discovered a role for phagocyte-expressed GAGs in viral vascular clearance. Moreover, we observe species-specific differences in viral vascular clearance of enhanced GAG-binding virions between murine and avian hosts. These data suggest species-specific variation in GAG structure is a mechanism to distinguish amplifying from dead-end hosts for arbovirus transmission.

microbiology↗

bioRxiv2023

Strain-dependent assessment of Powassan virus transmission to deer ticks.

1.Powassan virus (POWV) is an emergent tick-borne encephalitis virus of Lyme disease endemic sites in North America. Due to range expansion and local intensification of deer tick vector (Ixodes scapularis) populations in the northeastern and upper midwestern U.S., encephalitis cases are increasingly being reported. A better understanding of the transmission cycle of POWV may allow for predicting the eventual public health burden. Recent phylogeographic analyses of POWV have identified geographical structuring, with well-defined northeastern and midwestern clades of the deer tick virus subtype (lineage II); sublineages exist within each clade. It may be that the local sublineages differ in their capacity to be transmitted by the deer tick vector. Accordingly, we determined whether there are strain-dependent differences in transmission. Five recent, low passage POWV isolates were used to measure aspects of vector competence, using viremic and artificial infection methods. Infection rates in experimental ticks remained consistent between all five isolates tested, resulting in 12-20% infection rate and no clear differences in viral load. We conclude that there is a genotype independent ability of POWV to infect deer ticks, and that differences in transmission efficiency are not likely to serve as the basis for regional differences in apparent public health burden.

microbiology↗

bioRxiv2022

Semi-field and surveillance data define the natural diapause timeline for Culex pipiens across the United States

Culex pipiens is a globally-distributed mosquito of medical and veterinary importance, serving as a primary vector of West Nile virus (WNV). To survive winter, female Cx. pipiens mosquitoes undergo adult reproductive diapause initiated by photoperiod and temperature cues. While well-studied under laboratory conditions, the environmental signals that promote Cx. pipiens diapause induction in natural settings are less understood. Here, we evaluate Cx. pipiens in laboratory and semi-field studies to examine diapause induction, defining an approximate timeline beginning in late-August where mosquitoes become receptive to diapause. Using gravid (reproductive) mosquito surveillance data as a proxy for adult diapause incidence for locations across the United States (California, Colorado, Connecticut, Illinois, Iowa, Minnesota, Pennsylvania, and Virginia), we demonstrate consistent population declines coinciding with periods of diapause receptivity except in hybridization zones where Cx. quinquefasciatus is present, suggesting that Culex population genetics can significantly impact end-season population trends. Together, this study defines a window for diapause induction across the United States, shaped by temperature, latitude, elevation, and mosquito population genetics. Coinciding with the cessation of WNV activity, these data can have important implications for mosquito control, where targeted efforts prior to diapause induction can decrease mosquito populations and WNV overwintering to reduce mosquito-borne disease incidence the following season.

ecology↗

bioRxiv2022

Impact of prior infection on SARS-CoV-2 antibody responses in vaccinated long-term care facility staff

SARS-CoV-2 emerged in 2019 and has resulted in millions of deaths worldwide. Certain populations are at higher risk for infection, especially staff and residents at long term care facilities (LTCF), due to the congregant living setting, and residents with many comorbidities. Prior to vaccine availability, these populations represented a large fraction of total COVID-19 cases and deaths in the U.S. Due to the high-risk setting and outbreak potential, staff and residents were among the first groups to be vaccinated. To define the impact of prior infection on response to vaccination, we measured antibody responses in a cohort of staff members at a LTCF, many of whom were previously infected by SARS-CoV-2. We found that neutralizing, receptor-binding-domain (RBD) and nucleoprotein (NP) binding antibody levels were significantly higher post-full vaccination course in individuals that were previously infected, and NP antibody levels could discriminate individuals with prior infection from vaccinated individuals. While an anticipated antibody titer increase was observed after vaccine booster dose in naive individuals, boost response was not observed in individuals with previous COVID-19 infection. We observed a strong relationship between neutralizing antibodies and RBD-binding antibodies post-vaccination across all groups, suggesting RBD-binding antibodies may be used as a correlate of neutralization. One individual with high levels of neutralizing and binding antibodies experienced a breakthrough infection (prior to the introduction of Omicron), demonstrating that the presence of antibodies is not always sufficient for complete protection against infection. These results highlight that history of COVID-19 exposure significantly increases SARS-CoV-2 antibody responses following vaccination. ImportanceLong-term care facilities (LTCFs) have been disproportionately impacted by COVID-19, due to their communal nature, high-risk profile of residents and vulnerability to respiratory pathogens. In this study, we analyzed the role of prior natural immunity to SARS-CoV-2 on post-vaccination antibody responses. The LTCF in our cohort experienced a large outbreak with almost 40% of staff becoming infected. We found that individuals that were infected prior to vaccination, had higher levels of neutralizing and binding antibodies post-vaccination. Importantly, the second vaccine dose significantly boosted antibody levels in those that were immunologically naive prior to vaccination, but not those that had prior immunity. Regardless of pre-vaccination immune status, levels of binding and neutralizing antibodies were highly correlated. The presence of NP-binding antibodies can be used to identify individuals that were previously infected when pre-vaccination immune status is not known. Our results reveal that vaccination antibody responses differ depending on prior natural immunity.

immunology↗

bioRxiv2022

Genomic and phenotypic analyses suggest moderate fitness differences among Zika virus lineages

RNA viruses have short generation times and high mutation rates, allowing them to undergo rapid molecular evolution during epidemics. However, the extent of RNA virus phenotypic evolution within epidemics and the resulting effects on fitness and virulence remain mostly unknown. Here, we screened the 2015-2016 Zika epidemic in the Americas for lineage-specific fitness differences. We engineered a library of recombinant viruses representing twelve major Zika virus lineages and used them to measure replicative fitness within disease-relevant human primary cells and live mosquitoes. We found that two of these lineages conferred significant in vitro replicative fitness changes among human primary cells, but we did not find fitness changes in Aedes aegypti mosquitoes. Additionally, we found evidence for elevated levels of positive selection among five amino acid sites that define major Zika virus lineages. While our work suggests that Zika virus may have acquired several phenotypic changes during a short time scale, these changes were relatively moderate and do not appear to have enhanced virulence or transmission during the epidemic.

evolutionary biology↗

bioRxiv2021

Identification of microRNAs in the West Nile virus vector Culex tarsalis

BackgroundmicroRNAs (miRNAs) represent a group of small non-coding RNAs that are crucial gene regulators of important biological functions including development and pathogen defense in most living organisms. Presently, there is a lack of availability of information regarding the miRNAs in the mosquito Culex tarsalis, which is one of the most important vectors of West Nile virus (WNV) in the United States. We used small RNA sequencing data and in vitro and in vivo experiments to identify and validate the presence of a repertoire of miRNAs in Cx. tarsalis mosquitoes. ResultsUsing bioinformatic approaches we analyzed small RNA sequencing data from the Cx. tarsalis CT embryonic cell line to discover 86 miRNAs. Consistent with other mosquitoes such as Aedes albopictus and Cx. quinquefasciatus, mi-184 was found to be the most abundant miRNA in Cx tarsalis. We also identified an additional 20 novel miRNAs from the recently sequenced Cx. tarsalis genome, for a total of 106 miRNAs identified in this study. The presence of selected miRNAs was biologically validated in both cell line and adult Cx. tarsalis mosquitoes using RT-qPCR and sequencing. ConclusionsCx. tarsalis is an important vector of many medically important pathogens including WNV and Western Equine encephalitis. Here we report a detailed insight into the miRNA population in Cx. tarsalis mosquitoes. These results will open new avenues of research deciphering the role of miRNAs in different Cx. tarsalis biological events such as development, metabolism, immunity and pathogen infection.

genomics↗

bioRxiv2021

Durable antibody responses in staff at two long-term care facilities, during and post SARS-CoV-2 outbreaks

SARS-CoV-2 has had a disproportionate impact on non-hospital healthcare settings such as long-term care facilities (LTCFs). The communal nature of these facilities, paired with the high-risk profile of residents, has resulted in thousands of infections and deaths and a high case fatality rate. To detect pre-symptomatic infections and identify infected workers, we performed weekly surveillance testing of staff at two LTCFs which revealed a large outbreak at one of the sites. We collected serum from staff members throughout the study and evaluated it for binding and neutralization to measure seroprevalence, seroconversion, and type and functionality of antibodies. At the site with very few incident infections, we detected that over 40% of the staff had preexisting SARS-CoV-2 neutralizing antibodies, suggesting prior exposure. At the outbreak site, we saw rapid seroconversion following infection. Neutralizing antibody levels were stable for many weeks following infection, suggesting a durable, long-lived response. Receptor-binding domain antibodies and neutralizing antibodies were strongly correlated. The site with high seroprevalence among staff had two unique introductions of SARS-CoV-2 into the facility through seronegative infected staff during the period of study but these did not result in workplace spread or outbreaks. Together our results reveal that high seroprevalence rate among staff can contribute to herd immunity within a workplace and protect against subsequent infection and spread within a facility.

immunology↗

bioRxiv2020

Rapid evolution of enhanced Zika virus virulence during direct vertebrate transmission chains

Zika virus (ZIKV) has the unusual capacity to circumvent natural alternating mosquito-human transmission and be directly transmitted human-to-human via sexual and vertical routes. The impact of direct transmission on ZIKV evolution and adaptation to vertebrate hosts is unknown. Here we show that molecularly barcoded ZIKV rapidly adapted to a mammalian host during direct transmission chains in mice, coincident with the emergence of an amino acid substitution previously shown to enhance virulence. In contrast, little to no adaptation of ZIKV to mice was observed following chains of direct transmission in mosquitoes or alternating host transmission. Detailed genetic analyses revealed that ZIKV evolution in mice was generally more convergent and subjected to more relaxed purifying selection than in mosquitoes or alternate passages. These findings suggest that prevention of direct human transmission chains may be paramount to resist gains in ZIKV virulence.

microbiology↗

bioRxiv2020

SARS-CoV-2 infection, neuropathogenesis and transmission among deer mice: Implications for reverse zoonosis to New World rodents

Coronavirus disease-19 (COVID-19) emerged in November, 2019 in China and rapidly became pandemic. As with other coronaviruses, a preponderance of evidence suggests the virus originated in horseshoe bats (Rhinolophus spp.) and likely underwent a recombination event in an intermediate host prior to entry into human populations. A significant concern is that SARS-CoV-2 could become established in secondary reservoir hosts outside of Asia. To assess this potential, we challenged deer mice (Peromyscus maniculatus) with SARS-CoV-2 and found robust virus replication in the upper respiratory tract, lungs and intestines, with detectable viral RNA for up to 21 days in oral swabs and 14 days in lungs. Virus entry into the brain also occurred, likely via gustatory-olfactory-trigeminal pathway with eventual compromise to the blood brain barrier. Despite this, no conspicuous signs of disease were observed and no deer mice succumbed to infection. Expression of several innate immune response genes were elevated in the lungs, notably IFN, Cxcl10, Oas2, Tbk1 and Pycard. Elevated CD4 and CD8{beta} expression in the lungs was concomitant with Tbx21, IFN{gamma} and IL-21 expression, suggesting a type I inflammatory immune response. Contact transmission occurred from infected to naive deer mice through two passages, showing sustained natural transmission. In the second deer mouse passage, an insertion of 4 amino acids occurred to fixation in the N-terminal domain of the spike protein that is predicted to form a solvent-accessible loop. Subsequent examination of the source virus from BEI Resources indicated the mutation was present at very low levels, demonstrating potent purifying selection for the insert during in vivo passage. Collectively, this work has determined that deer mice are a suitable animal model for the study of SARS-CoV-2 pathogenesis, and that they have the potential to serve as secondary reservoir hosts that could lead to periodic outbreaks of COVID-19 in North America.

microbiology↗

bioRxiv2020

A Hyperactive Kunjin Virus NS3 Helicase Mutant Demonstrates Increased Dissemination and Mortality in Mosquitoes

The unwinding of double-stranded RNA intermediates is critical for replication and packaging of flavivirus RNA genomes. This unwinding activity is achieved by the ATP-dependent nonstructural protein 3 (NS3) helicase. In previous studies, we investigated the mechanism of energy transduction between the ATP and RNA binding pockets using molecular dynamics simulations and enzymatic characterization. Our data corroborated the hypothesis that Motif V is a communication hub for this energy transduction. More specifically, mutations T407A and S411A in Motif V exhibit a hyperactive helicase phenotype leading to the regulation of translocation and unwinding during replication. However, the effect of these mutations on viral infection in cell culture and in vivo is not well understood. Here, we investigated the role of Motif V in viral replication using T407A and S411A West Nile virus (Kunjin subtype) mutants in cell culture and in vivo. We were able to recover S411A Kunjin but unable to recover T407A Kunjin. Our results indicated that S411A Kunjin decreased viral infection, and increased cytopathogenicity in cell culture as compared to WT Kunjin. Similarly, decreased infection rates in surviving S411A-infected Culex quinquefasciatus mosquitoes were observed, but S411A Kunjin infection resulted in increased mortality compared to WT Kunjin. Additionally, S411A Kunjin increased viral dissemination and saliva positivity rates in surviving mosquitoes compared to WT Kunjin. These data suggest that S411A Kunjin increases pathogenesis in mosquitoes. Overall, these data indicate that NS3 Motif V may play a role in the pathogenesis, dissemination, and transmission efficiency of Kunjin virus. IMPORTANCEKunjin and West Nile viruses belong to the arthropod-borne flaviviruses, which can result in severe symptoms including encephalitis, meningitis, and death. Flaviviruses have expanded into new populations and emerged as novel pathogens repeatedly in recent years demonstrating they remain a global threat. Currently, there are no approved anti-viral therapeutics against either Kunjin or West Nile viruses. Thus, there is a pressing need for understanding the pathogenesis of these viruses in humans. In this study, we investigate the role of the Kunjin virus helicase on infection in cell culture and in vivo. This work provides new insight into how flaviviruses control pathogenesis and mosquito transmission through the nonstructural protein 3 helicase.

microbiology↗

bioRxiv2018

A reverse-transcription/RNase H based protocol for depletion of mosquito ribosomal RNA facilitates viral intrahost evolution analysis, transcriptomics and pathogen discovery.

Studies aimed at identifying novel viral sequences or assessing intrahost viral variation require sufficient sequencing coverage to assemble contigs and make accurate variant calling at low frequencies. Many samples come from host tissues where ribosomal RNA represents more than 90% of total RNA preparations, making unbiased sequencing of viral samples inefficient and highly expensive, as many reads will be wasted on cellular RNAs. In the presence of this amount of ribosomal RNA, it is difficult to achieve sufficient sequencing depth to perform analyses such as variant calling, haplotype prediction, virus population analyses, virus discovery or transcriptomic profiling. Many methods for depleting unwanted RNA or enriching RNA of interest have been devised, including poly-A selection, RNase H based specific depletion, duplex-specific nuclease treatment and hybrid capture selection, among others. Although these methods can be efficient, they either cannot be used for some viruses (i.e. non-polyadenylated viruses), have been optimized for use in a single species, or have the potential to introduce bias. In this study, we describe a novel approach that uses an RNaseH possessing reverse transcriptase coupled with selective probes for ribosomal RNA designed to work broadly for three medically relevant mosquito genera; Aedes, Anopheles, and Culex. We demonstrate significant depletion of rRNA using multiple assessment techniques from a variety of sample types, including whole mosquitoes and mosquito midgut contents from FTA cards. To demonstrate the utility of our approach, we describe novel insect-specific virus genomes from numerous species of field collected mosquitoes that underwent rRNA depletion, thereby facilitating their detection. The protocol is straightforward, relatively low-cost and requires only common laboratory reagents and the design of several small oligonucleotides specific to the species of interest. This approach can be adapted for use with other organisms with relative ease, thus potentially aiding virus population genetics analyses, virus discovery and transcriptomic profiling in both laboratory and field samples.

microbiology↗