Detection of live attenuated measles virus in the respiratory tract following subcutaneous MMR Vaccination.

The live attenuated measles vaccine is extremely effective in preventing measles and induces mucosal immunity in the respiratory tract, however the mechanism is not known. We show that live attenuated measles virus (LAMV) RNA is frequently detected in the respiratory tract 7-21 days after subcutaneous measles-mumps-rubella (MMR) vaccination in healthy children (n = 5/20) and macaques (n = 6/8). Replicating LAMV was isolated from the lungs of 2 macaques, with no evidence of transmission to unvaccinated individuals.

High burden of viruses and bacterial pathobionts drives heightened nasal innate immunity in children.

Studies during the COVID-19 pandemic showed that children had heightened nasal innate immune responses compared with adults. To evaluate the role of nasal viruses and bacteria in driving these responses, we performed cytokine profiling and comprehensive, symptom-agnostic testing for respiratory viruses and bacterial pathobionts in nasopharyngeal samples from children tested for SARS-CoV-2 in 2021-22 (n = 467). Respiratory viruses and/or pathobionts were highly prevalent (82% of symptomatic and 30% asymptomatic children; 90 and 49% for children <5 years).

Considerations for viral co-infection studies in human populations.

When respiratory viruses co-circulate in a population, individuals may be infected with multiple pathogens and experience possible virus-virus interactions, where concurrent or recent prior infection with one virus affects the infection process of another virus. While experimental studies have provided convincing evidence for within-host mechanisms of virus-virus interactions, evaluating evidence for viral interference or potentiation using population-level data has proven more difficult. Recent studies have quantified the prevalence of co-detections using populations drawn from clinical settings.

Double-take: SARS-CoV-2 has evolved to evade human innate immunity, twice.

Sequential replacement of the dominant SARS-CoV-2 virus by new variants has been a striking feature of the COVID-19 pandemic. In two recent articles, Bouhaddou et al. and Kehrer et al.

Causal identification of single-cell experimental perturbation effects with CINEMA-OT.

Recent advancements in single-cell technologies allow characterization of experimental perturbations at single-cell resolution. While methods have been developed to analyze such experiments, the application of a strict causal framework has not yet been explored for the inference of treatment effects at the single-cell level. Here we present a causal-inference-based approach to single-cell perturbation analysis, termed CINEMA-OT (causal independent effect module attribution + optimal transport).