Biology subjects

Downey, N.

Publications and source records attributed to Downey, N..

3 recordsLinked to original sources

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↗

bioRxiv2020

Efficient Sequencing, Assembly, and Annotation of Human KIR Haplotypes

The homology, recombination, variation, and repetitive elements in the natural killer-cell immunoglobulin-like receptor (KIR) region has made full haplotype DNA interpretation impossible without physical separation of chromosomes. Here, we present a new approach using long-read sequencing to efficiently capture, sequence, and assemble diploid human KIR haplotypes. Sequences for capture probe design were derived from public full-length gene and haplotype sequences. IDT xGen(R) Lockdown probes were used to capture 2-8 kb of sheared DNA fragments followed by sequencing on a PacBio Sequel. The sequences were error corrected, binned, and then assembled using the Canu assembler. The assembly was evaluated on 16 individuals (8 African American and 8 Europeans) from whom ground truth was known via long-range sequencing on fosmid-isolated chromosomes. Using only 18 capture probes, the results show that the assemblies cover 97% of the GenBank reference, are 99.97% concordant, and it takes only 1.8 contigs to cover 75% of the reference. We also report the first assembly of diploid KIR haplotypes from long-read WGS, including the first sequencing of cB05[~]tB01, which pairs a KIR2DS2/KIR2DS3 fusion with the tB01 region. Our targeted hybridization probe capture and sequencing approach is the first of its kind to fully sequence and phase all diploid human KIR haplotypes, and it is efficient enough for population-scale studies and clinical use.

bioinformatics↗

bioRxiv2020

Functional and genetic markers of niche partitioning among enigmatic members of the human oral microbiome

Microbial residents of the human oral cavity have long been a major focus of microbiology due to their influence on host health and their intriguing patterns of site specificity amidst the lack of dispersal limitation. Yet, the determinants of niche partitioning in this habitat are yet to be fully understood, especially among the taxa that belong to recently discovered branches of microbial life. Here we assembled metagenomes from daily tongue and dental plaque samples from multiple individuals and reconstructed 790 non-redundant genomes, 43 of which resolved to TM7 that formed six monophyletic clades distinctly associated either with plaque or with tongue. Both pangenomic and phylogenomic analyses grouped tongue-specific TM7 clades with other host-associated TM7 genomes. In contrast, plaque-specific TM7 grouped together with environmental TM7 genomes. Besides offering deeper insights into the ecology, evolution, and the mobilome of the cryptic members of the oral microbiome, our study reveals an intriguing resemblance between dental plaque and non-host environments indicated by the TM7 evolution, suggesting that plaque may have served as a stepping stone for environmental microbes to adapt to host environments for some clades of human associated microbes. Additionally, we report that prophages are widespread amongst oral-associated TM7, while absent from environmental TM7, suggesting that prophages may have played a role in adaptation of TM7 to the host environment.

microbiology↗