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Motivation: The acquisition of somatic mutations in hematopoietic stem and progenitor stem cells with resultant clonal expansion, termed clonal hematopoiesis (CH), is associated with increased risk of hematologic malignancies and other adverse outcomes. CH is generally present at low allelic fractions, but clonal expansion and acquisition of additional mutations leads to hematologic cancers in a small proportion of individuals. With high depth and high sensitivity sequencing, CH can be detected in most adults and its clonal trajectory mapped over time. However, accurate CH variant calling is challenging due to the difficulty in distinguishing low frequency CH mutations from sequencing artifacts. The lack of well-validated bioinformatic pipelines for CH calling may contribute to lack of reproducibility in studies of CH., Results: Here, we developed ArCH, an Artifact filtering Clonal Hematopoiesis variant calling pipeline for detecting single nucleotide variants and short insertions/deletions by combining the output of four variant calling tools and filtering based on variant characteristics and sequencing error rate estimation. ArCH is an end-to-end cloud-based pipeline optimized to accept a variety of inputs with customizable parameters adaptable to multiple sequencing technologies, research questions, and datasets. Using deep targeted sequencing data generated from six acute myeloid leukemia patient tumor: normal dilutions, 31 blood samples with orthogonal validation, and 26 blood samples with technical replicates, we show that ArCH improves the sensitivity and positive predictive value of CH variant detection at low allele frequencies compared to standard application of commonly used variant calling approaches., Availability and Implementation: The code for this workflow is available at: https://github.com/kbolton-lab/ArCH., (© The Author(s) 2024. Published by Oxford University Press.)

Recent results of high-altitude windborne mosquito migration raised questions about the viability of these mosquitoes despite ample evidence that many insect species, including other dipterans, have been known to migrate regularly over tens or hundreds of kilometers on high-altitude winds and retain their viability. To address these concerns, we subjected wild Anopheles gambiae s.l. Giles mosquitoes to a high-altitude survival assay, followed by oviposition (egg laying) and blood feeding assays. Despite carrying out the survival assay under exceptionally harsh conditions that probably provide the lowest survival potential following high altitude flight, a high proportion of the mosquitoes survived for 6- and even 11-h assay durations at 120- to 250-m altitudes. Minimal differences in egg laying success were noted between mosquitoes exposed to high altitude survival assay and those kept near the ground. Similarly, minimal differences were found in the female's ability to take an additional bloodmeal after oviposition between these groups. We conclude that similar to other high-altitude migrating insects, mosquitoes are able to withstand extended high-altitude flight and subsequently reproduce and transmit pathogens by blood feeding on new hosts., (Published by Oxford University Press on behalf of Entomological Society of America 2020.)

Currently, there exists a deficit of safe, active trapping methods for the collection of host-seeking Anopheles and other disease-causing arthropod vectors. The gold-standard approach for mosquito collection is that of human landing catch (HLC), in which an individual exposes bare skin to possibly infected vectors. Here, we present the development of a new method for mosquito collection, the Infoscitex tent, which uses modern tent materials coupled with a novel trap design. This provides an efficacious, a non-labor-intensive, and a safe method for vector collection. In these initial studies, we found it collected an average of 27.7 Anopheles gambiae s.l. per trap per night in rural villages in southeastern Senegal, and 43.8 Culex group Vper trap per night in the semiurban town of Kedougou, Senegal. In direct comparisons with HLC, the tent was not statistically different for collection of Culex quinquefasciatus in crepuscular sampling, but was significantly less efficacious at trapping the highly motile dusk-biter Aedes aegypti. These studies suggest that the Infoscitex tent is a viable and safe alternative to HLC for Anopheles and Culex sampling in areas of high vector-borne disease infection risk.

Tick-borne relapsing fever is caused by spirochetes within the genus Borrelia. The hallmark of this disease is recurrent febrile episodes and high spirochete densities in mammalian blood resulting from immune evasion. Between episodes of spirochetemia when bacterial densities are low, it is unknown whether ticks can acquire the spirochetes, become colonized by the bacteria, and subsequently transmit the bacteria once they feed again. We addressed these questions by feeding ticks, Omnithodoros hermsi Wheeler (Acari: Argasidae),daily on an infected mouse during low andhigh levels of spirochete infections. This study demonstrates that spirochete acquisition by the tick vector can occur during low levels of mammalian infection and that once a spirochetemic threshold is attained within the blood, nearly 100% of ticks become colonized by Borrelia hermsii.