Whole genome sequencing reveals genomic diversity and evidence of Hybridization in Moroccan Leishmania infantum strains
In Morocco, Leishmania infantum is an endemic species responsible for visceral leishmaniasis (VL, fatal if untreated) as well as cutaneous leishmaniasis (CL). The number of cases and the distribution range of both forms are increasing, spreading into new areas. However, despite its clinical significance, the genomic diversity of this species remains largely overlooked. We performed whole-genome sequencing for six L. infantum strains from patients infected with VL, CL, CL/HIV, as well as from dogs and conducted comparative genomic analyses. Read depth analysis both on chromosome and gene levels revealed isolate-specific variability in ploidy and identified gene copy number variations (CNVs) mostly in genes involved in parasite virulence and survival. Principal component analysis (PCA) and SNP-based clustering revealed a notable divergence between the two cutaneous isolates and the other strains. We further confirmed the diversity of the CL/HIV strain studied previously using MLST technique. The strong divergence of strain FA23 to all other isolates suggested a possible hybrid origin, which we confirmed using the Kraken2 package revealed important introgression with genome sequences from L. donovani (22.21%). These findings demonstrate that comparative genomics are instrumental in detecting hybridization signals, supporting genetic exchange as a significant evolutionary process contributing in the diversification of new CL cases caused by L. infantum.