Asymptomatic Bordetella pertussis infections in young African infants and their mothers identified within a longitudinal cohort.

Current pertussis epidemiology rests largely on cross-sectional surveys that use diagnostic thresholds to interpret qPCR results as positive or negative, and thus fail to capture arcs of infection within individuals or populations. By longitudinally monitoring a cohort of African mother/infant pairs and using full-range qPCR results, we quantify the otherwise-hidden evidence for pertussis infection (EFI) in individuals. We demonstrate strong clustering of EFI within mother/infant pairs and quantify the association between EFI and both pertussis symptoms and antibiotic use. Critically, we find strong evidence that asymptomatic pertussis is common in both infants and mothers, indicating that the burden of pertussis has been significantly underestimated in this population. Our results also inform qPCR-based monitoring of other pathogens, such as SARS-CoV-2.