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

Ivy K Kombe,Marc Baguelin,Graham F Medley,Charles N Agoti,Patrick K Munywoki,D James Nokes

doi:10.1038/s41598-021-81078-x

Abstract

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.

Highlights

Respiratory syncytial virus (RSV) is responsible for a significant burden of severe acute lower respiratory tract illness in children under 5 years old; infants
The data imputation process resulted in shedding episodes that ranged from 2 to 35 days for RSV A, and 3 to 45 days for RSV B
We compared the distributions of parameters estimated using RSV cases identified at the pathogen, group and cluster level in order to assess the impact of increased resolution in pathogen identification on estimated parameters

Summary

Introduction

Respiratory syncytial virus (RSV) is responsible for a significant burden of severe acute lower respiratory tract illness in children under 5 years old; infants. The results further highlight the importance of pre-school and school-aged children in RSV transmission, the role they play in directly infecting the household infant. These age groups are a potential RSV vaccination target group. In 2015 the estimated respiratory syncytial virus (RSV) acute lower respiratory illness (ALRI) burden in children less than 5 years old was 33.1 million cases resulting in 118,200 (94,600–149,400) deaths. In a modelling study using only the social-temporal data, it was found that about half of all cases occurred through within household transmission[27] These studies were unable to clearly determine who infected the infants with RSV and how infection spread once introduced in the household

Methods

Results

Conclusion