Post-mortem Nasopharyngeal Microbiome Analysis of Zambian Infants with and without Respiratory Syncytial Virus Disease: A Nested Case Control Study

Our study compares the nasopharyngeal microbiome of the deceased RSV+ and deceased RSV- infants from the Zambia Pertussis and RSV Infant Mortality Estimation (ZPRIME) study. Infants were between four days and six months old and enrolled in the ZPRIME study within 48 hours of death. We selected a subset of community deaths for our analysis who were RSV+ with a PCR Ct<35. We selected 50 RSV+ infants via random sampling from and matched those to 50 RSV- infants from the same study. Due to age- and seasonality-related variations in RSV impact, we matched infants by age at death (4-28 days (0+ months), 29-61 days (1+ month), 62-152 days (2+ months) and 152-182 days (4+ months)) and date of death (+/- 1.5 months). All decedents underwent one-time, post-mortem NP sampling. NP samples were tested for RSV by reverse transcriptase quantitative PCR following the testing protocol developed by the Centers for Disease Control and Surveillance. 16S ribosomal DNA was amplified using PCR with primers specific to the V3-V4 region.