Source tracing of Leishmania donovani in recent outbreaks of visceral leishmaniasis in West Nepal

For decades, the Indian sub-continent (ISC) was the most endemic region for Visceral Leishmaniasis (VL) in the World. In 2005, a regional elimination program was launched in India, Nepal and Bangladesh, aiming to reduce VL anual incidence to less than one case per 10 000 at (sub-)district levels (1). Before the start of the elimination program, VL in Nepal was mainly confined to 12 VL endemic districts (out of a total of 77 districts), located in the lowlands in the east of the country. In more recent years, however, VL cases have spread from east to west in the country, as well as from lowlands to hilly and even mountainous districts, resulting in a total of 23 VL endemic districts at present, with many more districts reporting likely indigenous cases (1). There is clearly a need for a post-elimination surveillance system adapted to this new epidemiological profileHere, we demonstrate the proof-of-principle of SureSelect for genome surveillance of leishmaniasis, in the context of the reported expansion of VL to the West of Nepal. Blood samples were collected in 2019 and stored on DNA/RNA Shield (Appendix). Three samples with highest amounts of DNA, positive for Leishmania and originating from 3 different districts (Dolpa, Darchula and Bardiya) were sequenced, with a high genome coverage and compared to our database of L. donovani genome sequences in the ISC: the latter originated from 204 cultivated isolates (2002- 2011) from Nepal, India and Bangladesh (5), 52 clinical samples (2000-2015) from Nepal (4) and 3 isolates from Sri Lanka. Altogether, these earlier studies revealed 4 main genotypes: (i) a large core group (CG), genomically very homogeneous, in the lowlands of India, Nepal and Bangladesh, (ii) a small ISC1 population, genomically very different from CG, in hilly districts of Eastern Nepal, (iii) a single divergent Nepalese isolate, BPK512 and (iv) a Sri Lanka (SL) cluster. Our new phylogenomic analysis revealed that the three outbreak parasites from Western Nepal were clearly distinct from CG and SL: one sample branched close to ISC1, while the two others clustered together with BPK512.