Surveillance of respiratory viruses among children attending a primary school in rural coastal Kenya

Abstract

Background: Respiratory viruses are primary agents of respiratory tract diseases. Knowledge on the types and frequency of respiratory viruses affecting school-children is important in determining the role of schools in transmission in the community and identifying targets for interventions. Methods: We conducted a one-year (term-time) surveillance of respiratory viruses in a rural primary school in Kilifi County, coastal Kenya between May 2017 and April 2018. A sample of 60 students with symptoms of ARI were targeted for nasopharyngeal swab (NPS) collection weekly. Swabs were screened for 15 respiratory virus targets using real time PCR diagnostics. Data from respiratory virus surveillance at the local primary healthcare facility was used for comparison. Results: Overall, 469 students aged 2-19 years were followed up for 220 days. A total of 1726 samples were collected from 325 symptomatic students; median age of 7 years (IQR 5-11). At least one virus target was detected in 384 (22%) of the samples with a frequency of 288 (16.7%) for rhinovirus, 47 (2.7%) parainfluenza virus, 35 (2.0%) coronavirus, 15 (0.9%) adenovirus, 11 (0.6%) respiratory syncytial virus (RSV) and 5 (0.3%) influenza virus. The proportion of virus positive samples was higher among lower grades compared to upper grades (25.9% vs 17.5% respectively; χ ² = 17.2, P -value <0.001). Individual virus target frequencies did not differ by age, sex, grade, school term or class size. Rhinovirus was predominant in both the school and outpatient setting. Conclusion: Multiple respiratory viruses circulated in this rural school population. Rhinovirus was dominant in both the school and outpatient setting and RSV was of notably low frequency in the school. The role of school children in transmitting viruses to the household setting is still unclear and further studies linking molecular data to contact patterns between the school children and their households are required.

Keywords: Respiratory viruses; acute respiratory infections; coastal Kenya; nasopharyngeal samples; real-time PCR; school children; school surveillance.

Figure 1.. The distribution of six virus types detected in all samples collected in the entire school over the study duration.

(RSV- respiratory Syncytial Virus; FLU- Influenza virus A, B, C; PIV -Parainfluenza virus 1-4; Corona- Human coronavirus NL63, E229, OC43; Rhinovirus-Human rhinovirus).

Figure 2.. Distributions of the six different virus groups detected in samples collected from school children over a one school year stratified by age.

Proportions (%) are the number positive out of the number of samples collected, by age group., (RSV- respiratory Syncytial Virus; FLU- Influenza virus A, B, C; PIV -Parainfluenza virus 1–4; Corona- Human coronavirus NL63,E229,OC43; Rhinovirus-Human rhinovirus).

Figure 3.. Proportions of virus positive samples in each of the grades in lower primary.

Each panel shows the distribution of the six different virus groups per grade. (RSV- respiratory Syncytial Virus; FLU- Influenza virus A, B, C; PIV -Parainfluenza virus 1–4; Corona- Human coronavirus NL63, E229, OC43; Rhinovirus-Human rhinovirus).

Figure 4.. Proportions of virus positive samples in each of the grades in upper primary.

Each panel shows the distribution of the six different virus groups per grade. (RSV- respiratory Syncytial Virus; FLU- Influenza virus A, B, C; PIV -Parainfluenza virus 1–4; Corona- Human coronavirus NL63, E229, OC43; Rhinovirus-Human rhinovirus).

Figure 5.. Temporal distribution of the proportion of virus-positive nasopharyngeal swab samples over the period May 2017 to April 2018 (with school breaks indicated) for the six virus groups obtained during the surveillance of ARI in the primary school.

(RSV- respiratory Syncytial Virus; FLU- Influenza virus A, B, C; PIV -Parainfluenza virus 1-4; Corona- Human coronavirus NL63, E229, OC43; Rhinovirus-Human rhinovirus)

Figure 6.. Comparison of virus surveillance between the school setting and the local outpatient facility for children aged between 3–9 years and 10–20 years.

The left and right panels shows a comparison of the proportion of positive nasopharyngeal samples positive for each of the six virus groups in the school and outpatient facility among children aged 3–9 years and 10–20 years, respectively . (RSV- respiratory Syncytial Virus; FLU- Influenza virus A, B, C; PIV -Parainfluenza virus 1-4; Corona- Human coronavirus NL63, E229, OC43; Rhinovirus-Human rhinovirus).

Figure 7.. Comparison of virus surveillance between the school setting, the local outpatient facility and inpatient hospital for children below five years.