CMV Detection and Pneumocystis Infection in the PERCH Cohort

The Pneumonia Etiology Research for Child Health (PERCH) study identified pneumonia due to the fungus Pneumocystis jirovecii as the most common fungal cause of pneumonia in infants. Whether Pneumocystis jirovecii pneumonia (PJP) is complicated by other pathogens remains unclear. To address this, we performed targeted next-generation sequencing on archived PERCH samples and found that human cytomegalovirus (CMV) was the most common virus detected, particularly in Africa. Here, CMV status was defined as detection of CMV nucleic acid in the nasopharyngeal specimen by targeted sequencing, not CMV seropositivity. Despite CMV detection being common, analyses of clinical metadata did not show any impact on clinical parameters such as oxygen requirement or hospital stay. Because sequence detection reflects the presence of CMV at the upper respiratory tract, these findings should not be interpreted as evidence of a causal role in pneumonia. However, future studies should consider assessing CMV co-infection to determine if CMV affects post-pneumonia sequelae in children.