Dissecting respiratory virus ecology and immunity in a community cohort in West Africa

Thushan de Silva (University of Sheffield, UK)

12:25 - 13:00 Thursday 16 April Morning

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Abstract

Respiratory viruses are a leading cause of illness in low- and middle-income countries (LMICs), yet their true incidence, transmission dynamics and immune determinants of susceptibility remain inadequately characterised. The talk will describe data from a prospective household cohort in The Gambia, following 349 individuals across 52 households with weekly PCR testing regardless of symptoms and serial serum and mucosal sampling over one year. This intensive design captured SARS-CoV-2 Delta and Omicron BA.1 waves alongside a full seasonal cycle of other respiratory viruses including RSV, rhinovirus, parainfluenza and seasonal coronaviruses. The study reveals substantial heterogeneity in respiratory virus ecology. Most infections were asymptomatic, although SARS-CoV-2, RSV and influenza were associated with higher symptom rates. Age strongly shaped risk across viruses, with young children experiencing markedly higher incidence for several pathogens. We also quantified virus-specific shedding kinetics and household secondary attack rates, identifying key differences in transmissibility. To dissect immune protection, we integrated PCR outcomes with multiplex serology and mucosal antibody data using a unified modelling framework. For SARS-CoV-2, we show that prior infection and serum neutralising antibodies reduce risk for Delta, but protection is substantially diminished for Omicron BA.1. For RSV, combining PCR and serology increased inferred attack rates, and mucosal pre-fusion F IgA emerged as the strongest correlate of reduced infection risk, with additive effects from serum pre-fusion IgG. These findings provide rare high-resolution insights into respiratory virus transmission and immunity in an LMIC community and demonstrate a generalisable modelling framework for defining correlates of protection from natural infection data.

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