Variation in surface protein expression leads to heterogeneous Trypanosoma cruzi populations during host cell infection

Trypanosoma cruzi possesses hundreds of genes associated with 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, we assembled T. cruzi Sylvio X10 strain chromosomes from telomere-to-telomere. The genome provides accurate organization of multigene family genes, confirming their distribution in expanded clusters or scattered throughout the chromosomes. Quantitative proteomics shows stage-specific proteins and numerous trans-sialidases upregulated in trypomastigotes. The expression of virulence gene families varied in trypomastigotes after each round of cell infection, resulting in heterogeneous parasite populations with variable cell invasion capacity. A T. cruzi genome-wide yeast surface display screen against Chagas disease patients’ antibodies reveals genes expressed during human infections. However, limited conservation in their antibody-binding sites suggests their sequence diversity and variation might help parasites avert antibody recognition. The data point to a role for some multigene families in infection persistence.