Biology subjects

Fauver, J. R.

Publications and source records attributed to Fauver, J. R..

11 recordsLinked to original sources

bioRxiv2026

Laboratory adaptation and complete genome assembly of a Beposo, Ghana strain of the human hookworm Necator americanus

Laboratory models are invaluable tools for studying parasite biology and pathogenesis, especially for helminth infections. However, the complex life cycles and frequently narrow host specificity of helminths present challenges to maintaining access to critical parasite material in a laboratory setting. This is especially true of Necator americanus, the most common species of hookworm that infects humans globally. Here we report the successful laboratory adaptation of an African strain of N. americanus, originally isolated from infected individuals in Beposo, Ghana. The Beposo strain has been successfully passaged across 9 generations in Golden Syrian hamsters maintained on oral dexamethasone. Differential susceptibility to mebendazole and albendazole was evaluated using an egg hatch assay, and DNA sequencing of the beta-tubulin isotype 1 gene did not identify known resistance-associated mutations in the endemic strain. Sequencing of the mitochondrial COX1 gene revealed that specimens of N. americanus from Ghana, along with reported sequences from Togo, are distinct from those from South America and Asia. Complementary microsatellite-based population analysis revealed substantial genetic variation in the founding parasite population. To further characterize the novel Beposo strain, a draft hybrid genome assembly was generated from genomic DNA extracted from a single adult male worm via an optimized Oxford Nanopore Technologies MinION library preparation approach tailored to low-input sample types. This high-quality assembly, including a complete mitogenome, is 202.8Mb in 950 contigs with an N50 >449 kb. It contains >95% of conserved nematode orthologs in complete single copy and is estimated by homology-based gene prediction to contain 12,804 genes. This study represents the first comprehensive characterization of a strain of N. americanus originating in Africa that has been successfully adapted to a laboratory animal model.

microbiology↗

bioRxiv2026

When clades collide: Genomic admixture in blacklegged ticks (Ixodes scapularis) from the Great Plains

Ixodes scapularis ticks transmit a number of pathogens important to human health, including Borrelia burgdorferi, the causative agent of Lyme disease. While I. scapularis is found across the Eastern United States, Lyme disease transmission is largely limited to the Northeast and Upper Midwest and is nearly absent in the South. This indicates that differences in northern versus southern clades of I. scapularis are associated with differences in Lyme disease transmission risk. I. scapularis is undergoing range expansion, including into the Great Plains region of the United States. Determining where I. scapularis populations in the Great Plains originated can inform future risk of Lyme disease transmission in this region. In this study, we use a population genomics framework to characterize diversity, structure, and B. burgdorferi infection rates of I. scapularis populations in the Great Plains region. We generated whole genome sequence data and single nucleotide polymorphism (SNP) datasets from I. scapularis ticks collected in Iowa, Kansas, Nebraska, and South Dakota to compare to publicly available data from across the species range. Our analysis of 200 I. scapularis SNP datasets indicated geographically well-defined populations that correspond to historical northern and southern ancestral clades of I. scapularis. Ticks from South Dakota, Iowa, and northeastern Nebraska are genetically similar populations from the Upper Midwest, while ticks from Kansas are more genetically similar to ticks from the Southeast. Ticks collected in the central eastern region of Nebraska, however, represent an evenly admixed population of both northern and southern genomic backgrounds. Analysis of B. burgdorferi reads from genomic datasets shows [~]50% infection rate in ticks from Iowa and northeastern Nebraska, whereas ticks from Kansas show no evidence of B. burgdorferi infection. Of note, evenly admixed ticks from the central eastern region of Nebraska also show no evidence of B. burgdorferi infection. These results provide further evidence that tick genomics may influence traits associated with B. burgdorferi infection status, and thus the potential for Lyme disease transmission. As the range of I. scapularis continues to expand, bringing historically isolated populations into contact, there is a clear need to understand the consequence of genomic admixture for B. burgdorferi transmission potential to inform future risk of Lyme disease in the United States.

genomics↗

bioRxiv2026

Hookworm genomic diversity and population structure from accessible sample types: A validated approach to generate genome-wide polymorphism datasets from individual third-stage larvae

Hookworm infection is a neglected tropical disease affecting hundreds of thousands of people annually in the tropics and sub-tropics. Population genomic approaches have the potential to improve our understanding of hookworm infection dynamics and control efficacy. Here, we validate an approach to generate genome-wide polymorphism datasets from accessible sample types in the zoonotic hookworm (Ancylostoma ceylanicum) then apply the validated approach in the human hookworm (Necator americanus) to compare laboratory- and field-derived samples. We first present an optimized method for purifying nucleic acid from individual third-stage hookworm larvae (L3s). We then measure the accuracy of variant call datasets generated through whole genome amplification (WGA) and next-generation sequencing (NGS). We demonstrate that WGA via multiple displacement amplification (MDA) introduces predictable biases that are exacerbated by low inputs and poor sample preservation but show that with sufficient input mass ([≥]0.1ng) we are still able to produce highly accurate variant call datasets from nucleic acid concentrations that reflect those of individual L3s. Using our validated approach, we infer laboratory- and field-collected samples of N. americanus as distinct populations, with higher levels of heterozygosity and nucleotide diversity identified in field-collected samples, suggesting signatures of inbreeding and/or drift are detectable in laboratory specimens within several years of initiation of infection. We also show that, despite expected reductions in heterozygosity, laboratory samples still possess numerous heterozygous sites, and we demonstrate that a reference genome generated from an adult worm from an early laboratory passage performs well for variant calling in both laboratory- and field-derived samples. Moving forward, our optimized method for nucleic acid purification can be broadly applied to generate input for any amplification-based approach where sequencing individual hookworm L3s, rather than a pool of specimens, is preferred. Our validated population genomics workflow can be used to characterize structure and connectivity of hookworm populations in endemic communities, with the goal of leveraging these insights to improve our approach to hookworm treatment and control. AUTHOR SUMMARYInfection with the human hookworm, Necator americanus, is a significant cause of morbidity in the global south. Population genomic techniques have the potential to improve our understanding of hookworm infection and control. However, third-stage larvae, or L3, which are the hookworm life-cycle stage we routinely have access to when screening infected people, are less than a millimeter long, and this small size makes generating genomic datasets from individual worms difficult. Here, we introduce an optimized approach for purifying DNA from individual L3s and validate its use with whole genome amplification (WGA) for population genomics. We found that WGA from L3s produces sequencing datasets that are biased in their breadth and depth of coverage across the hookworm genome. But by ensuring a minimum threshold for the mass of DNA input to WGA and setting strict criteria for variant filtration, these biases can be overcome to produce highly accurate variant calls genome-wide. We then use this approach to demonstrate reduced genetic diversity in a recently established laboratory hookworm strain as compared to field-collected samples. Our study outlines a specimen-through-analysis workflow that can be used with accessible sample types to measure population structure and diversity of hookworms in endemic communities.

genomics↗

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

Genomic Characterization of a Severe West Nile Virus Transmission Season using a Single Reaction Amplicon Sequencing Approach

West Nile virus (WNV) is an endemic arthropod-borne virus that has routinely caused seasonal outbreaks in the United States since it was first detected in 1999. While phylogenetic studies have shown how WNV has diversified and undergone genotype replacement since introduction, more geographically focused studies are needed to understand intricate transmission dynamics at local and regional scales. In this study, we validate the IDT xGen WNV panel, a novel single reaction amplicon-based Next-Generation Sequencing approach, to generate high-quality WNV genomes and compare it to the "Primal Scheme" assay for WNV, a common amplicon sequencing strategy. We show that the IDT xGen WNV panel generated complete and accurate WNV genomes and was more robust to amplicon drop out compared to the current sequencing approaches. Additionally, we used this approach to generate 100 complete WNV genomes from surveillance pools of mosquitoes collected in Nebraska during the 2023 outbreak. Our discrete phylogeographic analysis revealed substantial genetic diversity in WNV genomes from 2023 with minimal clustering across the state. This study demonstrated the utility of a single reaction amplicon-based sequencing approach to generate quality WNV genomes from routine surveillance samples and characterize WNV transmission dynamics in a high-incidence setting.

genomics↗

bioRxiv2025

Tracking West Nile virus dynamics using viral loads from trapped mosquitoes

Mosquito-borne virus transmission is increasing globally. Due to a lack of effective vaccines or targeted treatments, mitigation relies on reducing human exposure to infectious mosquitoes. Entomological surveillance provides estimates of human risk by quantifying the prevalence of arboviruses in mosquito populations. Testing of pooled mosquitoes via RT-qPCR is often used to infer infection prevalence, however these data are often binarised and ignore semi-quantitative cycle threshold (Ct values) that may provide valuable information on virus kinetics, mosquito infectiousness, and ultimately human risk. West Nile virus (WNV) is a globally distributed arbovirus and endemic to the United States. In this study, we analysed pooled Ct values from retrospective mosquito surveillance and found substantial variation that could not be explained by laboratory factors alone. To understand how underlying viral load and epidemiological dynamics might explain this variation, we developed a multi-scale model linking pooled Ct values to heterogeneous within-host viral kinetics in mosquitoes and birds and seasonal transmission dynamics. Our modelling suggests that Ct values from positive pools might reflect a mixture of potentially infectious and non-infectious mosquitoes, indicating that a substantial proportion of PCR-positive mosquitoes might not contribute to transmission. We then developed a method to estimate mosquito infection prevalence using only pooled Ct values that distinguishes infectious from non-infectious prevalence. Estimates of overall prevalence were comparable to standard methods using binarised data and remained accurate at higher prevalences where standard approaches fail. Overall, these findings demonstrate that entomological viral load data reflect biologically meaningful variation in mosquito infection status that is lost through binarisation. Accounting for heterogeneous mosquito viral kinetics can improve interpretation of surveillance data and estimates of transmission risk, with implications for arbovirus surveillance beyond WNV.

ecology↗

bioRxiv2022

Phylogeographic reconstruction of the emergence and spread of Powassan virus in the northeastern United States

Powassan virus is an emerging tick-borne virus of concern for public health, but very little is known about its transmission patterns and ecology. Here, we expanded the genomic dataset by sequencing 279 Powassan viruses isolated from Ixodes scapularis ticks from the northeastern United States. Our phylogeographic reconstructions revealed that Powassan virus lineage II was likely introduced or emerged from a relict population in the Northeast between 1940-1975. Sequences strongly clustered by sampling location, suggesting a highly focal geographical distribution. Our analyses further indicated that Powassan virus lineage II emerged in the northeastern U.S. mostly following a south to north pattern, with a weighted lineage dispersal velocity of ~3 km/year. Since the emergence in the Northeast, we found an overall increase in the effective population size of Powassan virus lineage II, but with growth stagnating during recent years. The cascading effect of population expansion of white-tailed deer and I. scapularis populations likely facilitated the emergence of Powassan virus in the northeastern U.S. Significance statementOur work provides important fundamental insights in the local transmission dynamics of an emerging tick-borne pathogen of public health concern. Without the availability of vaccines or specific treatments, prevention of Powassan virus infection is dependent on education and control. We identified that Powassan virus is maintained in highly localized transmission foci that have been maintained for several years, without introductions of new virus clades. This provides both opportunities for better education about high risk areas and effective targeted control in Powassan virus foci with a long lasting impact.

genomics↗

bioRxiv2021

Isolation and characterization of a novel Wolbachia bacteriophage from Allonemobius socius crickets in Missouri

Wolbachia are endosymbionts of numerous arthropod and some nematode species, are important for their development and if present can cause distinct phenotypes of their hosts. Prophage DNA has been frequently detected in Wolbachia, but particles of Wolbachia bacteriophages (phage WO) have been only occasionally isolated. Here, we report the characterization and isolation of a phage WO of the southern ground cricket, Allonemobius socius, and provided the first whole-genome sequence of phage WO from this arthropod family outside of Asia. We screened A. socius abdomen DNA extracts from a cricket population in eastern Missouri by quantitative PCR for Wolbachia surface protein and phage WO capsid protein and found a prevalence of 55% and 50%, respectively, with many crickets positive for both. Immunohistochemistry using antibodies against Wolbachia surface protein showed many Wolbachia clusters in the reproductive system of female crickets. Whole-genome sequencing using Oxford Nanopore MinION and Illumina technology allowed for the assembly of a high-quality, 55 kb phage genome containing 63 open reading frames (ORF) encoding for phage WO structural proteins and host lysis and transcriptional manipulation. Taxonomically important regions of the assembled phage genome were validated by Sanger sequencing of PCR amplicons. Analysis of the nucleotides sequences of the ORFs encoding the large terminase subunit (ORF2) and minor capsid (ORF7) frequently used for phage WO phylogenetics showed highest homology to phage WOKue of the Mediterranean flour moth Ephestia kuehniella (94.18% identity) and WOLig of the coronet moth, Craniophora ligustri (96.86% identity), respectively. Transmission electron microscopy examination of cricket ovaries showed a high density of phage particles within Wolbachia cells. Isolation of phage WO revealed particles characterized by 40-62 nm diameter heads and up to 190 nm long tails. This study provides the first detailed description and genomic characterization of phage WO from North America that is easily accessible in a widely distributed cricket species.

microbiology↗

bioRxiv2021

Title - Impact of extrinsic incubation temperature on natural selection during Zika virus infection of Aedes aegypti

Arthropod-borne viruses (arboviruses) require replication across a wide range of temperatures to perpetuate. While vertebrate hosts tend to maintain temperatures of approximately 37{degrees}C - 40{degrees}C, arthropods are subject to ambient temperatures which can have a daily fluctuation of > 10{degrees}C. Temperatures impact vector competence, extrinsic incubation period, and mosquito survival unimodally, with optimum occurring at some intermediate temperature. In addition, the mean and range of daily temperature fluctuations influence arbovirus perpetuation and vector competence. The impact of temperature on arbovirus genetic diversity during systemic mosquito infection, however, is poorly understood. Therefore, we determined how constant extrinsic incubation temperatures of 25{degrees}C, 28{degrees}C, 32{degrees}C, and 35{degrees}C control Zika virus (ZIKV) vector competence and population dynamics within Aedes aegypti and Aedes albopictus mosquitoes. We also examined diurnally fluctuating temperatures which more faithfully mimic field conditions in the tropics. We found that vector competence varied in a unimodal manner for constant temperatures peaking between 28{degrees}C and 32{degrees}C for both Aedes species. Transmission peaked at 10 days post-infection for Aedes aegypti and 14 days for Aedes albopictus. The effect of diurnal temperature was distinct and could not have been predicted from constant temperature-derived data. Using RNA-seq to characterize ZIKV population structure, we identified that temperature alters the selective environment in unexpected ways. During mosquito infection, constant temperatures more often elicited positive selection whereas diurnal temperatures led to strong purifying selection in both Aedes species. These findings demonstrate that temperature has multiple impacts on ZIKV biology within mosquitoes, including major effects on the selective environment within mosquitoes. Author SummaryArthropod-borne viruses (arboviruses) have emerged in recent decades due to complex factors that include increases in international travel and trade, the breakdown of public health infrastructure, land use changes, and many other factors. Climate change also has the potential to shift the geographical ranges of arthropod vectors, consequently increasing the global risk of arbovirus infection. Changing temperatures may also alter the virus-host interaction, ultimately resulting in the emergence of new viruses and virus genotypes in new areas. Therefore, we sought to characterize how temperature (both constant and fluctuating) alters the ability of Aedes aegypti and Aedes albopictus to transmit Zika virus, and how it influences virus populations within mosquitoes. We found that intermediate temperatures maximize virus transmission compared to more extreme and fluctuating temperatures. Constant temperatures increased positive selection on virus genomes, while fluctuating temperatures strengthened purifying selection. Our studies provide evidence that in addition to altering VC, temperature significantly influences the selective environment within mosquitoes.

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↗

bioRxiv2017

Multiple introductions of Zika virus into the United States revealed through genomic epidemiology

Zika virus (ZIKV) is causing an unprecedented epidemic linked to severe congenital syndromes1,2. In July 2016, mosquito-borne ZIKV transmission was first reported in the continental United States and since then, hundreds of locally-acquired infections have been reported in Florida3. To gain insights into the timing, source, and likely route(s) of introduction of ZIKV into the continental United States, we tracked the virus from its first detection in Miami, Florida by direct sequencing of ZIKV genomes from infected patients and Aedes aegypti mosquitoes. We show that at least four distinct ZIKV introductions contributed to the outbreak in Florida and that local transmission likely started in the spring of 2016 - several months before its initial detection. By analyzing surveillance and genetic data, we discovered that ZIKV moved among transmission zones in Miami. Our analyses show that most introductions are phylogenetically linked to the Caribbean, a finding corroborated by the high incidence rates and traffic volumes from the region into the Miami area. By comparing mosquito abundance and travel flows, we describe the areas of southern Florida that are especially vulnerable to ZIKV introductions. Our study provides a deeper understanding of how ZIKV initiates and sustains transmission in new regions.

epidemiology↗