In vitro selection of remdesivir-resistant severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) revealed the emergence of a V166L substitution, located outside of the polymerase active site of the Nsp12 protein, after 9 passages of a single lineage. V166L remained the only Nsp12 substitution after 17 passages (10 μM remdesivir), conferring a 2.3-fold increase in 50% effective concentration (EC 50 ).

The first confirmed case of COVID-19 in Quebec, Canada, occurred at Verdun Hospital on February 25, 2020. A month later, a localized outbreak was observed at this hospital. We performed tiled amplicon whole genome nanopore sequencing on nasopharyngeal swabs from all SARS-CoV-2 positive samples from 31 March to 17 April 2020 in 2 local hospitals to assess viral diversity (unknown at the time in Quebec) and potential associations with clinical outcomes. We report 264 viral genomes from 242 individuals–both staff and patients–with associated clinical features and outcomes, as well as longitudinal samples and technical replicates. Viral lineage assessment identified multiple subclades in both hospitals, with a predominant subclade in the Verdun outbreak, indicative of hospital-acquired transmission. Dimensionality reduction identified two subclades with mutations of clinical interest, namely in the Spike protein, that evaded supervised lineage assignment methods–including Pangolin and NextClade supervised lineage assignment tools. We also report that certain symptoms (headache, myalgia and sore throat) are significantly associated with favorable patient outcomes. Our findings demonstrate the strength of unsupervised, data-driven analyses whilst suggesting that caution should be used when employing supervised genomic workflows, particularly during the early stages of a pandemic.

Gene expression profiling provides a detailed molecular snapshot of cellular phenotypes that can be used to compare different biological conditions. Nanopore sequencing technology can generate high-resolution transcriptomic data in real-time and at low cost, which heralds new opportunities for molecular medicine. In this study, we demonstrate the clinical utility of real-time transcriptomic profiling by processing RNA sequencing data from childhood acute lymphoblastic leukemia (ALL) patients on-the-fly with a trained neural network classifier. This strategy successfully distinguished 11/12 representative ALL molecular subtypes and one non-leukemia control in as little as 5 minutes of sequencing on a MinION sequencer or in less than 1 hour on disposable, low cost Flongle flow cells. Our findings suggest that real-time transcriptomics constitutes a drastically efficient solution for the molecular diagnosis of ALL and other diseases, where conventional clinical workflows require days if not weeks to achieve similar results.

BACKGROUND: COVID-19 is usually a time-limited disease. However, prolonged infections and reinfections can occur among immunocompromised patients. It can be difficult to distinguish a prolonged infection from a new one, especially when reinfection occurs early. METHODS: We report the case of a 57-year-old man infected with SARS-CoV-2 while undergoing chemotherapy for follicular lymphoma. He experienced prolonged symptomatic infection for 3 months despite a 5-day course of remdesivir and eventually deteriorated and died. RESULTS: Viral genome sequencing showed that his final deterioration was most likely due to reinfection. Serologic studies confirmed that the patient did not seroconvert. CONCLUSIONS: This case report highlights that reinfection can occur rapidly (62–67 d) among immunocompromised patients after a prolonged disease. We provide substantial proof of prolonged infection through repeated nucleic acid amplification tests and positive viral culture at day 56 of the disease course, and we put forward evidence of reinfection with viral genome sequencing.