SARS-CoV-2 Coinfections and Severity in Hospitalized Children With Systematic Testing

Co-circulation of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) with other respiratory viruses raised concerns that coinfections may increase pediatric coronavirus disease 2019 (COVID-19) severity, but evidence is limited by variable testing practices. We assessed the epidemiology and outcomes of SARS-CoV-2 respiratory viral coinfections in hospitalized children.

We analyzed national surveillance data from the Canadian Immunization Monitoring Program, ACTive (IMPACT) COVID-19 study. Children aged <17 years hospitalized with confirmed COVID-19 during Delta and Omicron periods were included. Coinfection was defined as SARS-CoV-2 plus ≥1 additional respiratory virus. Primary analyses were restricted to centres with systematic multiplex polymerase chain reaction (PCR) testing of all admissions with acute respiratory illness (n = 5), while secondary analyses included all centres (n = 13). Associations with outcomes (respiratory support, ventilation, intensive care and severe COVID-19) were estimated using multivariable mixed-effects logistic regression and adjusted odds ratios (aORs).

Among 2831 hospitalized children, 938 were admitted at centers with systematic multiplex PCR testing, among whom 18.6% had ≥1 respiratory viral coinfection. Respiratory syncytial virus (39.7%) and enterovirus/rhinovirus (38.5%) coinfections were the most common. Coinfections were not associated with increased odds of severe COVID-19 in centers with systematic multiplex PCR testing (aOR 0.94; 95% confidence interval, 0.76-1.15). In secondary analyses including all centers irrespective of testing strategy, coinfections were associated with increased odds of severe COVID-19 (aOR 1.42; 95% confidence interval, 1.05-1.91).

In centers that systematically conducted multiplex PCR testing, SARS-CoV-2 respiratory viral coinfections were not associated with increased COVID-19 severity. Differences observed when including centers without systematic testing underscore the importance of considering testing strategies when evaluating the clinical impact of coinfections.