J. Alvar, I. Velez, C. Bern, M. Herrero, P. Desjeux et al., Leishmaniasis worldwide and global estimates of its incidence):e35671. Pubmed Central PMCID: 3365071. https, PloS one, vol.7, issue.5, 2012.

C. David and N. Craft, Cutaneous and mucocutaneous leishmaniasis Dermatologic therapy, pp.491-502, 2009.

P. Tarr, R. Aline, . Jr, B. Smiley, J. Scholler et al., LR1: a candidate RNA virus of Leishmania., Proceedings of the National Academy of Sciences of the United States of America, pp.9572-9577, 1988.
DOI : 10.1073/pnas.85.24.9572

A. Wang and C. Wang, Discovery of a specific double-stranded RNA virus in Giardia lamblia. Molecular and biochemical parasitology, pp.269-76, 1986.

A. Wang and C. Wang, The double-stranded RNA in Trichomonas vaginalis may originate from virus-like particles., Proceedings of the National Academy of Sciences, vol.83, issue.20, pp.7956-60, 1986.
DOI : 10.1073/pnas.83.20.7956

S. Altschul, W. Gish, W. Miller, E. Myers, and D. Lipman, Basic local alignment search tool Journal of molecular biology, pp.403-413, 1990.
DOI : 10.1006/jmbi.1990.9999

H. Revets, D. Dekegel, W. Deleersnijder, D. Jonckheere, J. Peeters et al., Identification of virus-like particles in Eimeria stiedae. Molecular and biochemical parasitology, pp.209-224, 1989.

G. Widmer, A. Comeau, D. Furlong, D. Wirth, and J. Patterson, Characterization of a RNA virus from the parasite Leishmania., Proceedings of the National Academy of Sciences, vol.86, issue.15, pp.5979-82, 1989.
DOI : 10.1073/pnas.86.15.5979

A. Wang and C. Wang, Viruses of parasitic protozoa. Parasitology today, pp.76-80, 1991.

K. Stuart, R. Weeks, L. Guilbride, and P. Myler, Molecular organization of Leishmania RNA virus 1., Proceedings of the National Academy of Sciences, vol.89, issue.18, pp.8596-600, 1992.
DOI : 10.1073/pnas.89.18.8596

J. Maga, G. Widmer, and J. Lebowitz, Leishmania RNA virus 1-mediated cap-independent translation. Molecular and cellular biology, pp.4884-4893, 1995.
DOI : 10.1128/mcb.15.9.4884

URL : https://www.ncbi.nlm.nih.gov/pmc/articles/PMC230734/pdf

S. Scheffter, G. Widmer, and J. Patterson, Complete Sequence of Leishmania RNA Virus 1-4 and Identification of Conserved Sequences, Virology, vol.199, issue.2, pp.479-83, 1994.
DOI : 10.1006/viro.1994.1149

M. Ito, L. Catanhede, T. Katsuragawa, C. Da-silva-junior, L. Camargo et al., Correlation between presence of Leishmania RNA virus 1 and clinical characteristics of nasal mucosal leishmaniosis . Brazilian journal of otorhinolaryngology, pp.533-573, 2015.

S. Simon, M. Nacher, B. Carme, C. Basurko, A. Roger et al., Cutaneous leishmaniasis in French Guiana: revising epidemiology with PCR-RFLP, Tropical Medicine and Health, vol.10, issue.2, p.28265182, 2017.
DOI : 10.1186/1475-2875-10-100

URL : http://tropmedhealth.biomedcentral.com/track/pdf/10.1186/s41182-017-0045-x?site=tropmedhealth.biomedcentral.com

B. Rotureau, C. Ravel, M. Nacher, P. Couppie, I. Curtet et al., Molecular Epidemiology of Leishmania (Viannia) guyanensis in French Guiana, Journal of Clinical Microbiology, vol.44, issue.2, pp.468-73, 2006.
DOI : 10.1128/JCM.44.2.468-473.2006

B. Rotureau, C. Ravel, P. Couppie, F. Pratlong, M. Nacher et al., Use of PCR-Restriction Fragment Length Polymorphism Analysis To Identify the Main New World Leishmania Species and Analyze Their Taxonomic Properties and Polymorphism by Application of the Assay to Clinical Samples, Journal of Clinical Microbiology, vol.44, issue.2, pp.459-67, 2006.
DOI : 10.1128/JCM.44.2.459-467.2006

S. Simon, V. Veron, and B. Carme, Leishmania spp. identification by polymerase chain reaction-restriction fragment length polymorphism analysis and its applications in French Guiana. Diagnostic microbiology and infectious disease, Feb, vol.66, issue.2, pp.175-80, 2010.

E. Aronesty, Command-line tools for processing biological sequencing data Available from, 2011.

R. Schmieder and R. Edwards, Fast Identification and Removal of Sequence Contamination from Genomic and Metagenomic Datasets, PLoS ONE, vol.11, issue.3, p.21408061, 2011.
DOI : 10.1371/journal.pone.0017288.s002

A. Bankevich, S. Nurk, D. Antipov, A. Gurevich, M. Dvorkin et al., SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing Journal of computational biology: a journal of computational molecular cell biology, pp.455-77, 2012.

H. Li, Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM. arXiv:1303

K. Katoh and D. Standley, MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Molecular biology and evolution, pp.772-80, 2013.
DOI : 10.1093/molbev/mst010

URL : https://academic.oup.com/mbe/article-pdf/30/4/772/6420419/mst010.pdf

K. Tamura, D. Peterson, N. Peterson, G. Stecher, M. Nei et al., MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods Molecular biology and evolution, pp.2731-2740, 2011.
DOI : 10.1093/molbev/msr121

URL : https://academic.oup.com/mbe/article-pdf/28/10/2731/2954190/msr121.pdf

F. Ronquist, M. Teslenko, P. Van-der-mark, D. Ayres, A. Darling et al., MrBayes 3.2: Efficient Bayesian Phylogenetic Inference and Model Choice Across a Large Model Space, Systematic Biology, vol.61, issue.3, pp.539-581, 2012.
DOI : 10.1093/sysbio/sys029

D. Darriba, G. Taboada, R. Doallo, and D. Posada, ProtTest 3: fast selection of best-fit models of protein evolution, Bioinformatics, vol.27, issue.8, pp.1164-1169, 2011.
DOI : 10.1093/bioinformatics/btr088

M. Adams, E. Lefkowitz, A. King, and E. Carstens, Ratification vote on taxonomic proposals to the International Committee on Taxonomy of Viruses Archives of virology, pp.2831-2872, 2014.

M. Zamora, L. Guilbride, L. Sacks, and K. Stuart, Phylogenetic analysis of the 5' subterminal region of isolates of Leishmania RNA virus-1. Annals of tropical medicine and parasitology, pp.123-156, 2000.

D. Macedo, A. Menezes-neto, J. Rugani, A. Rocha, S. Silva et al., Low frequency of LRV1 in Leishmania braziliensis strains isolated from typical and atypical lesions in the State of Minas Gerais, Brazil. Molecular and biochemical parasitology, p.27546549, 2016.

L. Lye, K. Owens, H. Shi, S. Murta, A. Vieira et al., Retention and Loss of RNA Interference Pathways in Trypanosomatid Protozoans, PLoS Pathogens, vol.24, issue.Pt 16, 2010.
DOI : 10.1371/journal.ppat.1001161.s005

H. Zangger, C. Ronet, C. Desponds, F. Kuhlmann, J. Robinson et al., Detection of Leishmania RNA virus in Leishmania parasites):e2006. Pubmed Central PMCID: 3542153. https, PLoS neglected tropical diseases, vol.7, issue.1, 2013.