John Hackett

TL;DR: SURPI is described, a computational pipeline for pathogen identification from complex metagenomic NGS data generated from clinical samples, and use of the pipeline is demonstrated in the analysis of 237 clinical samples comprising more than 1.1 billion sequences.

TL;DR: Analysis of environmental metagenome libraries detected PHV sequences in coastal marine waters of North America, suggesting that a potential association between PHV and diatoms (algae) that generate the silica matrix used in the spin columns may have resulted in inadvertent viral contamination during manufacture.

TL;DR: Results indicate that a streamlined metagenomics detection strategy can potentially replace the multiple conventional diagnostic tests required to investigate an outbreak of a novel pathogen, and provide a blueprint for comprehensive diagnosis of unexplained acute illnesses or outbreaks in clinical and public health settings.

TL;DR: There is evidence that seroreactivity using SARS-CoV-2 anti-nucleocapsid protein IgG and anti-spike IgM assays are generally predictive of in vitro neutralizing capacity, and the importance of using highly accurate tests for surveillance studies in low-prevalence populations is emphasized.

TL;DR: This IA was found to be capable of detecting the majority (89%) of infections, including 80% of those considered acute infections based on the presence of HIV RNA and the lack of detectable antibody to HIV.