Detection of viral pathogens associated with acute lower respiratory infection in children in the Eastern Highlands Province of Papua New Guinea: a matched case-control study

Introduction In Papua New Guinea, acute lower respiratory infection (ALRI) is the most common reason for childhood hospitalisation and death. Recent changes in epidemiology, diagnostic approaches and vaccine policy warrant re-examination of the aetiology of ALRI. Methods A matched case-control study was performed using nasopharyngeal samples collected from a prospective study recruiting children < 5 years of age with moderate/severe pneumonia (cases) and community controls (2013–16). Respiratory viruses and Bordetella pertussis detection was undertaken using an in-house multiplex real-time reverse-transcriptase polymerase chain reaction (qRT-PCR) assay and the frequency of pathogen detection reported. Using multivariate logistic regression models, the population-attributable fraction was estimated. Results From the original sample cohort, 251 ALRI cases and 251 healthy matched controls were assessed. The median age was 12 months. One or more respiratory viruses were identified in 159 cases (63.3%) and 82 controls (32.7%). Rhinovirus was most frequently detected in both cases (23.1%) and controls (19.5%), followed by respiratory syncytial virus (HRSV; 21.8% and 2.0% respectively) and parainfluenza virus type 3 (HPIV3; 16.2% and 2.5% respectively). Co-infections were frequently detected. Significant differences in detection between cases and controls were observed for HRSV, influenza A, HPIV1, HPIV3, and seasonal human coronavirus types HCoV-NL63 and HCoV-229E. We estimated that respiratory viruses were responsible for at least 39.7% (95% CI: 28.2–49.4%) of ALRI. Discussion Respiratory viruses are a major contributor to ALRI in children < 5 years of age in this population, with HRSV representing a key pathogen. This underscores the need for targeted intervention strategies and ongoing surveillance of viral aetiology.