Biology subjects

Johnson, W. L.

Publications and source records attributed to Johnson, W. L..

4 recordsLinked to original sources

bioRxiv2023

Choclo virus (CHOV) recovered from deep metatranscriptomics of archived museum tissues

BackgroundHantaviruses are negative-stranded RNA viruses that can sometimes cause severe disease in humans; however, they are maintained in mammalian populations without causing harm. In Panama, sigmodontine rodents serve as hosts to transmissible hantaviruses. Due to natural and anthropogenic forces, these rodent populations are having increased contact with humans. MethodsWe extracted RNA and performed Illumina deep metatranscriptomic sequencing on Orthohantavirus seropositive museum tissues from rodents. We acquired sequence reads mapping to Choclo virus (CHOV, Orthohantavirus chocloense) from the heart and kidney tissue of a two decade old sample from a Costa Rican pygmy rice rat (Oligoryzomys costaricensis) collected in Panama. Reads mapped to the CHOV reference were assembled and then validated by visualization of the mapped reads against the assembly. ResultsWe recovered a 91% complete consensus sequence from a reference-guided assembly to CHOV with an average of 16X coverage. The S and M segments used in our phylogenetic analyses were nearly complete (98% and 99%, respectively). There were 1,199 ambiguous base calls of which 93% were present in the L segment. Our assembled genome varied 1.3% from the CHOV reference sequence resulting in 11 nonsynonymous mutations. Further analysis of all publicly available partial S segment sequences support a clear relationship between CHOV clinical cases and O. costaricensis acquired strains. ConclusionsViruses occurring at extremely low abundances can be recovered from deep metatranscriptomics of archival tissues housed in museums or biorepositories. Our efforts resulted in the second CHOV genome publicly available. This genomic data is important for future surveillance and diagnostic tools as well as understanding the evolution and pathogenicity of CHOV. Author SummaryHantavirus cardiopulmonary syndrome (HCPS) in Panama, caused by Choclo virus (CHOV, Orthohantavirus chocloense), is intimately linked to the primary mammalian reservoir host, the Costa Rican pygmy rice rat (Oligoryzomys costaricensis). Although the prevalence of hantavirus disease is relatively low in Panama, over a quarter of the country has the agroecological conditions that favor this rodent. In addition, serologic evidence suggests infections are under-reported. Sequence data of the pathogen and host collected across temporal and spatial scales is necessary for diagnostics, surveillance, and forecasting; however, only one complete genome is available in NCBI GenBank. By leveraging deep metatranscriptomics of archived frozen mammal tissues, we generated a low-coverage genome using a reference-guided assembly approach. Sequence data can be used to develop pan-hantavirus diagnostic tools to facilitate acquisition of more detailed genetic data from archival samples to increase our understanding of the evolutionary and population dynamics of rare and neglected hantaviruses. Generating additional genomic sequence data will also be essential for developing a rigorous taxonomic framework to improve the understanding of hantavirus diversity and distribution.

genomics↗

bioRxiv2022

Genetic characterization of the zoonotic parasite Ancylostoma caninum in the central and eastern USA

Ancylostoma caninum is the most common nematode parasite of dogs in the United States. This study aimed to describe the molecular epidemiology of A. caninum isolates from the central and eastern states of the U.S. using the partial mitochondrial cox1 gene and to compare them with those reported globally. We isolated eggs from fecal samples of dogs and characterized each isolate based on cox1 sequences. A total of 60 samples originating from Kansas, Iowa, New York, Florida, and Massachusetts were included. 25 haplotypes were identified in the U.S. dataset with high haplotype diversity (0.904). Sequence data were compared to sequences from other world regions available in GenBank. Global haplotype analysis demonstrated 35 haplotypes with a haplotype diversity of 0.931. Phylogenetic and network analysis provide evidence for the existence of moderate geographical structuring of A. caninum haplotypes. Our results provide an updated summary of A. caninum haplotypes and data for neutral genetic markers with utility for tracking hookworm populations. Sequences have been deposited in GenBank (ON980650 - ON980674). Further studies of isolates from other regions are essential to understand the genetic diversity of this parasite.

microbiology↗

bioRxiv2019

Pan-genomic and Polymorphic Driven Prediction of Antibiotic Resistance in Elizabethkingia

The Elizabethkingia are a genetically diverse genus of emerging pathogens that exhibit multidrug resistance to a range of common antibiotics. Two representative species, Elizabethkingia bruuniana and Elizabethkingia meningoseptica, were phenotypically tested to determine minimum inhibitory concentrations for five antibiotics. Ultra-long read sequencing with Oxford Nanopore Technologies and subsequent de novo assembly produced complete, gapless circular genomes for each strain. Alignment based annotation with Prokka identified 5,480 features in E. bruuniana and 5,203 features in E. meningoseptica, where none of these identified genes or gene combinations corresponded to observed phenotypic resistance values. Pan-genomic analysis, performed with an additional 19 Elizabethkingia strains, identified a core-genome size of 2,658,537 bp, 32 uniquely identifiable intrinsic chromosomal antibiotic resistance core-genes and 77 antibiotic resistance pan-genes. Using core-SNPs and pan-genes in combination with six machine learning algorithms, binary classification of clindamycin and vancomycin resistance achieved f1 scores of 0.94 and 0.84 respectively. Performance on the more challenging multiclass problem for fusidic acid, rifampin and ciprofloxacin resulted in f1 scores of 0.70, 0.75 and 0.54 respectively.

bioinformatics↗

bioRxiv2017

Chromatin-associated RNA sequencing (ChAR-seq) maps genome-wide RNA-to-DNA contacts

RNA is a critical component of chromatin in eukaryotes, both as a product of transcription, and as an essential constituent of ribonucleoprotein complexes that regulate both local and global chromatin states. Here we present a proximity ligation and sequencing method called Chromatin-Associated RNA sequencing (ChAR-seq) that maps all RNA-to-DNA contacts across the genome. ChAR-seq provides unbiased, de novo identification of targets of chromatin-bound RNAs including nascent transcripts, chromosome-specific dosage compensation ncRNAs, and genome-wide trans-associated RNAs involved in co-transcriptional RNA processing.

genomics↗