Aine Niamh O’Toole

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

This paper introduces squirrel, a tool for analyzing MPXV genomes to detect outbreaks and classify APOBEC3 mutations, aiding public health responses.

ARTIC RSV amplicon sequencing reveals global RSV genotype dynamics.

This study introduces two novel amplicon sequencing schemes for RSV A and B, demonstrating their effectiveness in generating high-quality genomes globally and revealing minimal geographic clustering of RSV sequences.

PrimalScheme: open-source community resources for low-cost viral genome sequencing

PrimalScheme provides open-source tools for designing low-cost viral genome sequencing primers, generating over 67,000 schemes and enabling large-scale genomic surveillance.

Epigenetic age estimation of wild mice using faecal samples

This paper develops an epigenetic clock using faecal DNA from lab mice to estimate age in wild mice, finding higher methylation and epigenetic age in wild mice compared to lab mice.

SARS-CoV-2 lineage assignments using phylogenetic placement/UShER are superior to pangoLEARN machine learning method

This study compares pangoLEARN and pUShER for SARS-CoV-2 lineage assignment, finding pUShER more stable and accurate across pangolin versions.

Automated detection and classification of polioviruses from nanopore sequencing reads using piranha

The paper introduces piranha, a tool for automated detection and classification of polioviruses from nanopore sequencing reads, enabling efficient intratypic differentiation and identification of wild-type and vaccine-derived polioviruses.

SARS-CoV-2 genomic surveillance in Rwanda: Introductions and local transmission of the B.1.617.2 (Delta) variant of concern

This study reports genomic surveillance in Rwanda from June to September 2021, showing the rapid spread and dominance of the Delta variant over other lineages, with implications for cross-border transmission.

Making Genomic Surveillance Deliver: A Lineage Classification and Nomenclature System to Inform Rabies Virus Elimination

This paper introduces a lineage classification system for rabies virus based on SARS-CoV-2 nomenclature, enabling high-resolution tracking of viral spread and improving disease control.

Pango lineage designation and assignment using SARS-CoV-2 spike gene nucleotide sequences

The paper investigates how much Pango lineage information can be inferred from SARS-CoV-2 spike gene sequences and introduces the concept of lineage sets for classification.

Genomic Sequencing of SARS-COV-2 in Rwanda: evolution and regional dynamics

This study analyzes SARS-CoV-2 genomic sequences from Rwanda to track variant evolution and regional spread, identifying emerging sub-lineages and VOCs introduced through travel.

Methylation-Based Age Estimation in a Wild Mouse

This paper develops an epigenetic clock for wild wood mice using DNA methylation data to estimate age and study ageing rates in the wild.

Rapid SARS-CoV-2 whole genome sequencing for informed public health decision making in the Netherlands

The paper describes the early response to the SARS-CoV-2 outbreak in the Netherlands, focusing on whole genome sequencing and its role in public health decision making.