Biology subjects

Duggan, A. T.

Publications and source records attributed to Duggan, A. T..

7 recordsLinked to original sources

bioRxiv2026

Evaluation of MeaSeq: comprehensive analysis and reporting of measles virus whole genome sequences.

Although vaccine-preventable, measles virus (MeV) continues to pose a significant public health challenge, with a substantial resurgence of cases worldwide. As whole-genome sequencing (WGS) becomes increasingly affordable and routinely adopted in public health laboratories, reliable and accessible analysis of next-generation sequencing (NGS) data is critical for outbreak investigation and molecular surveillance. Here, we present MeaSeq, a fast, user-friendly, open-source bioinformatics pipeline for MeV analysis using Illumina or Oxford Nanopore Technologies (ONT) NGS data. MeaSeq performs quality control assessments, consensus genome assembly and variant detection, optional genotype-specific reference selection, Distinct Sequence Identifier (DSId) assignment via user-provided databases or hashing, sub-consensus variant visualization, genome quality assessment, and standardized HTML reporting. We compared the performance of MeaSeq on NGS data generated from multiple sequencing platforms and targeted enrichment strategies against gold-standard Sanger data, reference genomes, and publicly available comparative data. This validation demonstrates that MeaSeq provides an accurate, reproducible, and accessible solution for routine MeV WGS analysis, supporting genomic surveillance and outbreak response workflows in public health and research settings. Impact StatementThe recent surge in measles cases worldwide, causing several countries to lose their measles elimination status, underscores the urgent need for effective and accessible genomic surveillance. Our manuscript introduces MeaSeq, a comprehensive and open-source bioinformatics pipeline specifically designed for analyzing MeV NGS data. MeaSeq includes MeV specific analyses such as genotype prediction from sequencing reads with optional genotype-specific reference selection; DSId assignment; quality control checks such as genome rule-of-six divisibility and gene CDS validation; subconsensus nucleotide analysis with mixed-site highlighting; and genomic plotting. By leveraging NGS technology, our pipeline can facilitate the identification of transmission chains and may provide critical insights into the dynamics of MeV outbreaks. This information is essential for public health officials and researchers to implement targeted interventions and optimize vaccine strategies. Additionally, the open-source nature of MeaSeq fosters collaboration and innovation within the scientific measles community along with providing access to a wider range of researchers. Data SummaryThe MeaSeq pipeline code is available on GitHub (https://github.com/phac-nml/measeq). Comparative datasets of publicly available WGS data were accessed through the NCBI Sequence Read Archive under the following BioProjects: PRJNA869081 (https://www.ncbi.nlm.nih.gov/bioproject/PRJNA869081) PRJNA480551 (https://www.ncbi.nlm.nih.gov/bioproject/PRJNA480551) PRJNA1017431 (https://www.ncbi.nlm.nih.gov/bioproject/PRJNA1017431) PRJNA1241325 (https://www.ncbi.nlm.nih.gov/bioproject/PRJNA1241325) PRJNA1174053 (https://www.ncbi.nlm.nih.gov/bioproject/PRJNA1174053) PRJNA1293457 (https://www.ncbi.nlm.nih.gov/bioproject/PRJNA1293457) PRJNA843031 (https://www.ncbi.nlm.nih.gov/bioproject/PRJNA843031) Whole-genome sequences were included in the validation analysis if they consisted of paired-end data (Illumina) and achieved [≥]95% genome completeness following trimming of the 5' and 3' untranslated regions (UTRs). This criterion ensured sufficient genome coverage for robust validation while allowing for limited missing data arising from regions of low sequencing depth or amplicon dropout. A complete list of sequences included in the validation, along with their accession numbers, is provided in Supplementary Table 1.

bioinformatics↗

bioRxiv2025

Human outbreak detection and best practice MPXV analysis and interpretation with squirrel

High numbers of reported mpox cases and recent identification of multiple sustained human outbreaks of MPXV have highlighted the need for robust, best-practice genomic surveillance tools. In light of the SARS-CoV-2 pandemic, many labs across the globe developed the capacity to do virus genome sequencing, however MPXV presents additional analytical challenges due to its large genome size, tracts of low-complexity or repeat regions, genetically distinct clades, and the need to perform bespoke APOBEC3-mutation reconstruction. We present squirrel (Some Quick Reconstruction to Resolve Evolutionary Links), an open source bioinformatic tool that can perform clade-aware alignment, mutation quality assessment, phylogenetic inference and automated APOBEC3-mutation classification on branches of the phylogeny. Squirrel can be run on the command line or launched through the EPI2ME GUI through the squirrel-nf workflow, enabling robust analysis without need for the command line. With the interactive output report produced and publication-ready APOBEC3-reconstruction visualisation, squirrel enables researchers to distinguish between zoonotic and sustained human outbreaks and help accurately inform public health responses.

evolutionary biology↗

bioRxiv2023

In silico analyses identify sequence contamination thresholds for Nanopore-generated SARS-CoV-2 sequences

The SARS-CoV-2 pandemic has brought molecular biology and genomic sequencing into the public consciousness and lexicon. With an emphasis on rapid turnaround, genomic data has been used to inform both diagnostic and surveillance decisions for the current pa ndemic at a previously unheard-of scale. The surge in the submission of genomic data to publicly-available databases has proved essential as comparing different genome sequences offers a wealth of knowledge, including phylogenetic links, modes of transmission, rates of evolution, and the impact of mutations on infection and disease severity. However, the scale of the pandemic has meant that once sequencing runs are performed, they are rarely repeated due to limited sample material and/or the availability of sequencing resources, resulting in some imperfect runs being uploaded to public repositories. As a result, it is crucial to investigate the data obtained from these imperfect runs to determine whether the results are reliable. Numerous studies have identified a variety of sources of contamination in public next-generation sequencing (NGS) data as the number of NGS studies increases along with the diversity of sequencing technologies and procedures [1-3]. For this study, we conducted an in silico experiment with known SARS-CoV-2 sequences produced from Oxford Nanopore Technologies sequencing to investigate the effect of contamination on lineage calls and single nucleotide variations (SNVs). Through a series of analyses, we identified a contamination threshold below which runs are expected to generate accurate lineage calls and maintain genomic sequence integrity. Together, these findings provide a benchmark below which imperfect runs may be considered robust for reporting results to both stakeholders and public repositories and reduce the need for repeat or wasted runs. Author SummaryLarge-scale genomic comparisons provide a wealth of knowledge, including modes of transmission, rates of evolution, and the impact of mutations on infection, disease severity, and treatment effectiveness. As a result, the public release of genomic data has proven to be crucial. However, studies continue to show that some of the genomic data in public repositories are contaminated due to a variety of reasons. For instance, in the case of SARS-CoV-2 sequences, the pandemic prevented many sequencing runs from being repeated, resulting in some imperfect runs being uploaded to public repositories. It is of note that when genomic data is contaminated, both scientific decisions/studies and public health measures may be compromised. To identify genome contamination threshold(s) for SARS-CoV-2 sequences generated by Nanopore sequencing, computational biology techniques were utilized to generate artificially subsampled contaminated genomes. This is the first study of its kind and so our hope is that the results obtained provide a starting point for the investigation of reporting contamination of NGS data.

genomics↗

bioRxiv2022

Genomic data suggest parallel dental vestigialization within the xenarthran radiation

AO_SCPLOWBSTRACTC_SCPLOWThe recent influx of genomic data has provided greater insights into the molecular basis for regressive evolution, or vestigialization, through gene loss and pseudogenization. As such, the analysis of gene degradation patterns has the potential to provide insights into the evolutionary history of regressed anatomical traits. We specifically applied these principles to the xenarthran radiation (anteaters, sloths, armadillos), which is characterized by taxa with a gradation in regressed dental phenotypes. Whether the pattern among extant xenarthrans is due to an ancient and gradual decay of dental morphology or occurred repeatedly in parallel is unknown. We tested these competing hypotheses by examining 11 core dental genes in most living species of Xenarthra, characterizing shared inactivating mutations and patterns of relaxed selection during their radiation. Here we report evidence of independent and distinct events of dental gene loss in the major xenarthran subclades. First, we found strong evidence of complete enamel loss in the common ancestor of sloths and anteaters, suggested by the inactivation of five enamel-associated genes (AMELX, AMTN, MMP20, ENAM, ACP4). Next, whereas dental regression appears to have halted in sloths, presumably a critical event that ultimately permitted adaptation to an herbivorous lifestyle, anteaters continued losing genes on the path towards complete tooth loss. Echoes of this event are recorded in the genomes of all living anteaters, being marked by a 2-bp deletion in a gene critical for dentinogenesis (DSPP) and a putative shared 1-bp insertion in a gene linked to tooth retention (ODAPH). By contrast, in the two major armadillo clades, genes pertaining to the dento-gingival junction and amelogenesis appear to have been independently inactivated prior to losing all or some enamel. These genomic data provide evidence for multiple pathways and rates of anatomical regression, and underscore the utility of using pseudogenes to reconstruct evolutionary history when fossils are sparse.

evolutionary biology↗

bioRxiv2022

Ancient Clostridium DNA and variants of tetanus neurotoxins associated with human archaeological remains

The analysis of microbial genomes from human archaeological samples offers a historic snapshot of ancient pathogens and provides insights into the origins of modern infectious diseases. Here, through a large-scale metagenomic analysis of archeological samples, we discovered bacterial species related to modern-day Clostridium tetani, which produces the tetanus neurotoxin (TeNT) and causes the disease tetanus. We assembled draft genomes from 38 distinct human archeological samples spanning five continents and dating to as early as ~4000 BCE. These genomes had varying levels of completeness and a subset of them displayed hallmarks of ancient DNA damage. While 24 fall into known C. tetani clades, phylogenetic analysis revealed novel C. tetani lineages, as well as two novel Clostridium species ("Clostridium sp. X and Y") closely related to C. tetani. Within these genomes, we found 13 TeNT variants with unique substitution profiles, including a subgroup of TeNT variants found exclusively in ancient samples from South America. We experimentally tested a TeNT variant selected from a ~6000-year-old Chilean mummy sample and found that it induced tetanus muscle paralysis in mice with potency comparable to modern TeNT. Our work identifies neurotoxigenic C. tetani in ancient DNA, new Clostridium species unique to ancient human samples, and a novel variant of TeNT that can cause disease in mammals.

genomics↗

bioRxiv2020

North American deer mice are susceptible to SARS-CoV-2

The zoonotic spillover of the pandemic SARS-coronavirus 2 (SARS-CoV-2) from an animal reservoir, currently presumed to be the Chinese horseshoe bat, into a naive human population has rapidly resulted in a significant global public health emergency. Worldwide circulation of SARS-CoV-2 in humans raises the theoretical risk of reverse zoonosis events with wildlife, reintroductions of SARS-CoV-2 into permissive non-domesticated animals, potentially seeding new host reservoir species and geographic regions in which bat SARS-like coronaviruses have not historically been endemic. Here we report that North American deer mice (Peromyscus maniculatus) and some closely related members of the Cricetidae family of rodents possess key amino acid residues within the angiotensin-converting enzyme 2 (ACE2) receptor known to confer SARS-CoV-2 spike protein binding. Peromyscus rodent species are widely distributed across North America and are the primary host reservoirs of several emerging pathogens that repeatedly spill over into humans including Borrelia burgdorferi, the causative agent of Lyme disease, deer tick virus, and Sin Nombre orthohantavirus, the causative agent of hantavirus pulmonary syndrome (HPS). We demonstrate that adult deer mice are susceptible to SARS-CoV-2 infection following intranasal exposure to a human isolate, resulting in viral replication in the upper and lower respiratory tract with little or no signs of disease. Further, shed infectious virus is detectable in nasal washes, oropharyngeal and rectal swabs, and viral RNA is detectable in feces and occasionally urine. We further show that deer mice are capable of transmitting SARS-CoV-2 to naive deer mice through direct contact. The extent to which these observations may translate to wild deer mouse populations remains unclear, and the risk of reverse zoonosis and/or the potential for the establishment of Peromyscus rodents as a North American reservoir for SARS-CoV-2 is unknown. Nevertheless, efforts to monitor wild, peri-domestic Peromyscus rodent populations are likely warranted as the SARS-CoV-2 pandemic progresses.

microbiology↗

bioRxiv2017

The gateway into Remote Oceania: new insights from genome-wide data

A widely accepted two-wave scenario of human settlement of Oceania involves the first out-of-Africa migration ca 50,000 ya, and one of the most geographically-widespread dispersals of people, known as the Austronesian expansion, which reached the Bismarck Archipelago by about 3,450 ya. While earlier genetic studies provided evidence for extensive sex-biased admixture between the incoming and the indigenous populations, some archaeological, linguistic and genetic evidence indicates a more complicated picture of settlement. To study regional variation in Oceania in more detail, we have compiled a genome-wide dataset of 823 individuals from 72 populations (including 50 populations from Oceania) and over 620,000 autosomal SNPs. We show that the initial dispersal of people from the Bismarck Archipelago into Remote Oceania occurred in a \"leapfrog\" fashion, completely by-passing the main chain of the Solomon Islands, and that the colonization of the Solomon Islands proceeded in a bi-directional manner. Our results also support a divergence between western and eastern Solomons, in agreement with the sharp linguistic divide known as the Tryon-Hackman line. We also report substantial post-Austronesian gene flow across the Solomons. In particular, Santa Cruz (in Remote Oceania) exhibits extraordinarily high levels of Papuan ancestry that cannot be explained by a simple bottleneck/founder event scenario. Finally, we use simulations to show that discrepancies between different methods for dating admixture likely reflect different sensitivities of the methods to multiple admixture events from the same (or similar) sources. Overall, this study points to the importance of fine-scale sampling to understand the complexities of human population history.

evolutionary biology↗