摘要：SummaryLeishmaniasis is a neglected tropical disease endemic in over 90 countries. The disease has two main pathologies; cutaneous leishmaniasis (CL) that generally self-heals, and visceral leishmaniasis (VL) that is fatal if untreated. The majority of VL cases, concentrated on the Indian subcontinent (ISC) and East Africa, are caused byLeishmania donovani. However, recent foci of CL on the ISC have been attributed as an atypical phenotype ofL.donovaniincluding a recent outbreak in Himachal Pradesh, India. Whole genome sequencing and phylogenetic analysis was undertaken to investigate the origins and genetic factors leading to this pathology atypical ofL.donovani. Here we demonstrate the isolate from Himachal Pradesh is derived from a genetic hybridization between two independentL.donovaniparents from the ‘Yeti’ ISC1 divergent clade of parasites, identified in the Nepalese highlands. This reveals that intraspeciesL.donovanihybrids can give rise to a novel strain associated with CL.Graphical abstractDisplay OmittedHighlights•A novel focus of cutaneous Leishmaniasis is emerging in Himachal Pradesh•The normally visceral Leishmania donovani parasite is responsible for the focus•The isolated parasite is an intraspecies genetic hybrid•Extensive genomic hybridization could explain this atypical phenotypeBiological sciences; Genetics; Genomics; Microbial genomics; Microbiology parasite
