Descriptive Epidemiology of Pathogens Associated with Acute Respiratory Infection in a Community-Based Study of K-12 School Children (2015-2023)

Abstract

School-based outbreaks often precede increased incidence of acute respiratory infections in the greater community. We conducted acute respiratory infection surveillance among children to elucidate commonly detected pathogens in school settings and their unique characteristics and epidemiological patterns. The ORegon CHild Absenteeism due to Respiratory Disease Study (ORCHARDS) is a longitudinal, laboratory-supported, school-based, acute respiratory illness (ARI) surveillance study designed to evaluate the utility of cause-specific student absenteeism monitoring for early detection of increased activity of influenza and other respiratory viruses in schools from kindergarten through 12th grade. Eligible participants with ARIs provided demographic, epidemiologic, and symptom data, along with a nasal swab or oropharyngeal specimen. Multipathogen testing using reverse-transcription polymerase chain reaction (RT-PCR) was performed on all specimens for 18 respiratory viruses and 2 atypical bacterial pathogens (Chlamydia pneumoniae and Mycoplasma pneumoniae). Between 5 January 2015 and 9 June 2023, 3498 children participated. Pathogens were detected in 2455 of 3498 (70%) specimens. Rhinovirus/enteroviruses (36%) and influenza viruses A/B (35%) were most commonly identified in positive specimens. Rhinovirus/enteroviruses and parainfluenza viruses occurred early in the academic year, followed by seasonal coronaviruses, RSV, influenza viruses A/B, and human metapneumovirus. Since its emergence in 2020, SARS-CoV-2 was detected year-round and had a higher median age than the other pathogens. A better understanding of the etiologies, presentations, and patterns of pediatric acute respiratory infections can help inform medical and public health system responses.

Keywords: acute respiratory infection; public health; respiratory illness; respiratory viruses; school-based surveillance; surveillance.

Figure 1

(a) Number of children—aged 4–18 years—recruited into the ORegon CHild Absenteeism due to Respiratory Disease Study (ORCHARDS) each month over the period from 5 January 2015 to 9 June 2023. Total participants = 3498. Box shows period from 2020 through 9 June 2023. (b) Detail showing number of children—aged 4–18 years—recruited into ORCHARDS each week from 2020 through 9 June 2023. Total participants in this time period = 1602. Boxes demonstrate periods when school was in session along with countermeasures employed due to the COVID-19 pandemic. Arrows depict school closure (March 2020) and end of mask requirement in schools (March 2022).

Figure 2

Number of enrollment inquiry calls and enrollments into the ORegon CHild Absenteeism due to Respiratory Disease Study (ORCHARDS) by month over the period from 5 January 2015 to 9 June 2023.

Figure 3

Number of pathogen detections in students from kindergarten through 12th grade in ORCHARDS over period from 5 January 2015 to 9 June 2023. Detections for virus subtypes are depicted by stippled bars. * The first detection of SARS-CoV-2 in ORCHARDS occurred on 17 March 2020; all archived specimens, starting on 1 September 2019, were tested for SARS-CoV-2.

Figure 4

Number of respiratory pathogens detected by a commercial multiplex RT-PCR test per week across nine academic years occurring between 5 January 2015 and 9 June 2023, in students from kindergarten through 12th grade with acute respiratory infections in the Oregon School District, Dane County, Wisconsin (n = 3498). The bacteria included in the multiplex RT-PCR and detected in the samples were M. pneumoniae and C. pneumoniae.

Figure 5

Number of respiratory pathogen detections by month from 5 January 2015 through 9 June 2023. * SARS-CoV-2 was not detected until March 2020. All strains of influenza A viruses, influenza B viruses, parainfluenza viruses, RSV, and seasonal coronaviruses are grouped together into a single category. Bacteria comprise M. pneumoniae and C. pneumoniae. (a) Violin plot of children’s ages for the detected respiratory pathogens. All strains of influenza A viruses, influenza B viruses, parainfluenza viruses, RSV, and seasonal coronaviruses are grouped together into a single category. Data are also shown for the bacterial pathogens M. pneumoniae and C. pneumoniae, grouped together as bacteria. (b) Box plot of participant age distributions for the detected respiratory pathogens, demonstrating the medians, lower quartiles, and upper quartiles of the participants’ ages associated with the detected pathogens.

Figure 5

Number of respiratory pathogen detections by month from 5 January 2015 through 9 June 2023. * SARS-CoV-2 was not detected until March 2020. All strains of influenza A viruses, influenza B viruses, parainfluenza viruses, RSV, and seasonal coronaviruses are grouped together into a single category. Bacteria comprise M. pneumoniae and C. pneumoniae. (a) Violin plot of children’s ages for the detected respiratory pathogens. All strains of influenza A viruses, influenza B viruses, parainfluenza viruses, RSV, and seasonal coronaviruses are grouped together into a single category. Data are also shown for the bacterial pathogens M. pneumoniae and C. pneumoniae, grouped together as bacteria. (b) Box plot of participant age distributions for the detected respiratory pathogens, demonstrating the medians, lower quartiles, and upper quartiles of the participants’ ages associated with the detected pathogens.