Integrating epidemiological and genetic data with different sampling intensities into a dynamic model of respiratory syncytial virus transmission

Journal article

Respiratory syncytial virus (RSV) is responsible for a significant burden of severe acute lower respiratory tract illness in children under 5 years old; particularly infants. Prior to rolling out any vaccination program, identification of the source of infant infections could further guide vaccination strategies. We extended a dynamic model calibrated at the individual host level initially fit to social-temporal data on shedding patterns to include whole genome sequencing data available at a lower sampling intensity. The study population was 493 individuals (55 aged < 1 year) distributed across 47 households, observed through one RSV season in coastal Kenya. We found that 58/97 (60%) of RSV-A and 65/125 (52%) of RSV-B cases arose from infection probably occurring within the household. Nineteen (45%) infant infections appeared to be the result of infection by other household members, of which 13 (68%) were a result of transmission from a household co-occupant aged between 2 and 13 years. The applicability of genomic data in studies of transmission dynamics is highly context specific; influenced by the question, data collection protocols and pathogen under investigation. The results further highlight the importance of pre-school and school-aged children in RSV transmission, particularly the role they play in directly infecting the household infant. These age groups are a potential RSV vaccination target group

Authors: Kombe, IK; Agoti, CN; Munywoki, PK; Baguelin, M; Nokes, DJ

• Publication status: Published
• Peer review status: Peer reviewed
• Publisher: Nature Research
• Journal: Scientific Reports
• Volume: 11
• Issue: 1
• Pages: 1463-1463
• Article number: 1463
• Publication date: 2021-01-14
• DOI: 10.1038/s41598-021-81078-x
• EISSN: 2045-2322
• ISSN: 2045-2322
• Language: English
• Keywords: Sampling (signal processing); Epidemiology; Internal medicine; Transmission (telecommunications); Computer science; Pathology; Medicine; Respiratory system; Virology; Biology; Virus; Telecommunications