ABSTRACTRationalePneumonia is a respiratory condition with complex aetiology. Host genetic variation is thought to contribute to individual differences in susceptibility and symptom manifestation.MethodsWe analysed pneumonia data from the UK Biobank (14,780 cases and 439,096 controls) and FinnGen (9,980 cases and 86,519 controls). We perform genome-wide association study (GWAS) meta-analysis, gene-based test, colocalisation, genetic correlation, latent causal variable and polygenic prediction in an independent Australian sample (N=5,595) to draw insights into the genetic aetiology of pneumonia risk.ResultsWe identify two independent loci on chromosome 15 (lead SNPs rs2009746 and rs76474922) to be associated with pneumonia(p<5e-8). Gene-based tests revealed eighteen genes in chromosomes 15,16 and 9, including IL127, PBX3, APOBR and smoking related genes CHRNA3/5, associated with pneumonia. Evidence of HYKK and PBX3 involvement in pneumonia risk was supported by eQTL colocalisation analysis. We observed genetic correlations between pneumonia and cardiorespiratory, psychiatric and inflammatory related traits. Latent causal variable analysis suggests a strong genetic causal relationship cardiovascular health phenotypes and pneumonia risk. Polygenic risk scores (PRS) for pneumonia significantly predicted self-reported pneumonia history in an independent Australian sample, albeit with a small effect size (OR=1.11 95%CI=[1.04-1.19], p<0.05). Sensitivity analyses suggested the associations in chromosome 15 are mediated by smoking history, but the association of genes in chromosome 16 and 9, and polygenic prediction were robust to adjustment for smoking.ConclusionsAltogether, our results highlight common genetic variants, genes and potential pathways that contribute to individual differences in susceptibility to pneumonia, and advance our understanding of the genetic factors underlying heterogeneity in respiratory medical outcomes.