Respiratory syncytial virus infection and reinfection patterns during a community outbreak in Kenya investigated by whole genome sequencing, 2023/2024

Abstract Background Respiratory syncytial virus (RSV) is a leading cause of severe acute respiratory infection in infants, young children and vulnerable adults. Despite implications for designing interventions, our understanding of RSV infection/reinfection patterns during community outbreaks is incomplete. Methods To characterize respiratory virus infections regardless of symptom status, we performed a prospective cohort surveillance in coastal Kenya from August 2023 to August 2024. Nasopharyngeal/oropharyngeal (NP/OP) swabs were collected 1-2 times weekly regardless of symptom status for quantitative PCR testing followed by genomic analysis. RSV reinfections were defined as two positive tests separated by ≥14 days and with intervening ≥1 negative tests. Results Of 672 individuals screened, 74 tested positive (93/22,000 swabs; 0.4%). The median age among infections was 4.2 years (interquartile range (IQR): 1.8-9.4), 58.1% being female versus a median age of 14.3 years (IQR: 4.8-29.6) and 64.4% female among uninfected individuals. Overall incidence rate was 19.8 infections/100 person-years, highest incidence among infants (174.0/100 person-years, 95% CI:103.0-274.0). Infection episodes fell into seven viral lineages: A.D (n=1), A.D.1 (n=2), A.D.1.11 (n=21), A.D.2.1 (n=19), A.D.3 (n=30), A.D.5.2 (n=1), and B.D.E.1 (n=2). Six individuals (8.1%; 13.7/100 person-years) experienced reinfections, three involving same viruses with 0-3 nucleotide differences across the entire RSV genome, while other three had 20,78 and 200 nucleotide differences. The (suspect) reinfected individuals were all under 2 years of age, included both males and females, and had no reported chronic illnesses. Conclusion RSV community infections predominantly occur in children regardless of clinical presentation. Reinfections within the same season are rare. Key points In a community cohort prospective study in coastal Kenya, RSV-A predominated the 2023/24 epidemic and seven lineages co-circulated. Overall incidence was 19.6 infections/100 person-years and highest in infants. Most reinfections (5/6) were asymptomatic and only half had amino acid changes.