ABSTRACT: Despite long-standing vaccination programs, pertussis incidence has increased in numerous countries; transmission by asymptomatic individuals is a suspected driver of this resurgence. However, unequivocal evidence documenting asymptomatic infections in adults and children is lacking due, in part, to the cross-sectional nature of most pertussis surveillance studies. In addition, modern pertussis surveillance relies on quantitative PCR (qPCR) using fixed diagnostic thresholds to identify cases. To address this gap, we present a longitudinal analysis of 17,442 nasopharyngeal samples collected from a cohort of 1,320 Zambian mother/infant pairs. Using full-range cycle threshold (CT) values from IS481 qPCR assays, we document widespread asymptomatic infections among mothers and also, surprisingly, among young infants. From an initial group of eight symptomatic infants who tested positive by qPCR, we identify frequent contemporaneous subclinical infections in mothers. Within the full cohort, we observe strong temporal correlation between low- and high-intensity qPCR signals. We compute a single time-averaged score for each individual summarizing the evidence for pertussis infection (EFI), and show that EFI strongly clusters within mother/infant pairs, and is strongly associated with clinical symptomatology and antibiotic use. Overall, the burden of pertussis here is substantially underestimated when restricting diagnostic criteria to IS481 CT≤35. Rather, we find that full-range CT values provide valuable insights into pertussis epidemiology in this population, and illuminate the infection arc within individuals. These findings have significant implications for quantifying asymptomatic pertussis prevalence and its contribution to overall transmission. Our results also expose limitations of threshold-based interpretations of qPCR assays in infectious disease surveillance.Importance statement
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.
