Stochastic variation in surface protein expression diversifies Trypanosoma cruzi infection

Trypanosoma cruzi possesses hundreds of genes associated with its pathogenesis. The extent and organization of this diverse gene repertoire, expression, and role in infection remain unclear. Using accurate long-read sequencing and chromatin conformation capture, T. cruzi chromosomes were assembled from telomere-to-telomere. The genome revealed multigene families of virulence genes accounting for [~]70% of some chromosomes, organized in clusters or scattered through housekeeping genes. Quantitative proteomics identified stage-specific proteins and numerous trans-sialidases upregulated in trypomastigotes. Notably, the expression of virulence gene families changed stochastically in trypomastigotes, conferring T. cruzi fitness to cardiomyocyte infection while diversifying the invasion to multiple tissues. A T. cruzi genome-wide yeast surface display screen against Chagas disease patients antibodies revealed virulence genes expressed during human infections. However, limited conservation in their antibody-binding sites suggests their sequence diversity and variation help parasites avert antibody recognition. The data point to a role for virulence multigene families in infection persistence.