Kuvin Centre for the Study of Infectious and Tropical Diseases, IMRIC, Hebrew University-Hadassah, Medical School, Jerusalem, Israel
Henk Schallig
Amsterdam University Medical Centres – Academic Medical Centre at the University of Amsterdam, Department of Medical Microbiology – Experimental Parasitology, Amsterdam, Netherlands
Matthew Yeo
London School of Hygiene and Tropical Medicine, London, United Kingdom
Tapan Bhattacharyya
London School of Hygiene and Tropical Medicine, London, United Kingdom
Mohammad Z Alam
Department of Parasitology, Bangladesh Agricultural University, Mymensingh, Bangladesh
Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, United Kingdom
Thierry Wirth
Institut de Systématique, Evolution, Biodiversité, ISYEB, Muséum national d'Histoire naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, Paris, France; École Pratique des Hautes Études (EPHE), Paris Sciences & Lettres (PSL), Paris, France
Protozoan parasites of the Leishmania donovani complex – L. donovani and L. infantum – cause the fatal disease visceral leishmaniasis. We present the first comprehensive genome-wide global study, with 151 cultured field isolates representing most of the geographical distribution. L. donovani isolates separated into five groups that largely coincide with geographical origin but vary greatly in diversity. In contrast, the majority of L. infantum samples fell into one globally-distributed group with little diversity. This picture is complicated by several hybrid lineages. Identified genetic groups vary in heterozygosity and levels of linkage, suggesting different recombination histories. We characterise chromosome-specific patterns of aneuploidy and identified extensive structural variation, including known and suspected drug resistance loci. This study reveals greater genetic diversity than suggested by geographically-focused studies, provides a resource of genomic variation for future work and sets the scene for a new understanding of the evolution and genetics of the Leishmania donovani complex.