Unraveling the genetic diversity and phylogeny of Leishmania RNA virus 1 strains of infected Leishmania isolates circulating in French Guiana

Abstract

IntroductionLeishmania RNA virus type 1 (LRV1) is an endosymbiont of some Leishmania (Vianna) species in South America. Presence of LRV1 in parasites exacerbates disease severity in animal models and humans, related to a disproportioned innate immune response, and is correlated with drug treatment failures in humans. Although the virus was identified decades ago, its genomic diversity has been overlooked until now.Methodology/Principles findingsWe subjected LRV1 strains from 19 L. (V.) guyanensis and one L. (V.) braziliensis isolates obtained from cutaneous leishmaniasis samples identified throughout French Guiana with next-generation sequencing and de novo sequence assembly. We generated and analyzed 24 unique LRV1 sequences over their full-length coding regions. Multiple alignment of these new sequences revealed variability (0.5%–23.5%) across the entire sequence except for highly conserved motifs within the 5’ untranslated region. Phylogenetic analyses showed that viral genomes of L. (V.) guyanensis grouped into five distinct clusters. They further showed a species-dependent clustering between viral genomes of L. (V.) guyanensis and L. (V.) braziliensis, confirming a long-term co-evolutionary history. Noteworthy, we identified cases of multiple LRV1 infections in three of the 20 Leishmania isolates.Conclusions/SignificanceHere, we present the first-ever estimate of LRV1 genomic diversity that exists in Leishmania (V.) guyanensis parasites. Genetic characterization and phylogenetic analyses of these viruses has shed light on their evolutionary relationships. To our knowledge, this study is also the first to report cases of multiple LRV1 infections in some parasites. Finally, this work has made it possible to develop molecular tools for adequate identification and genotyping of LRV1 strains for diagnostic purposes. Given the suspected worsening role of LRV1 infection in the pathogenesis of human leishmaniasis, these data have a major impact from a clinical viewpoint and for the management of Leishmania-infected patients.

New insights into the genetic diversity of Leishmania RNA Virus 1 and its species-specific relationship with Leishmania parasites

“…braziliensis and L . guyanensis available in GenBank, corresponding to sequences reported from studies in French Guiana [ 23 ], Bolivia [ 5 , 27 ], and Brazil [ 5 , 27 ]. The LRV1 sequences obtained in the present study (n = 13) were from strains of L .…”

“… *IOC/L code related to strains deposited in the Leishmania Collection from the Oswaldo Cruz Foundation ** isolated in French Guiana, but the geographic location of infection was reported as in the region of Manaus, Amazonas state (AM), Brazil [ 23 ] 1 Total length of the sequence available in the Genbank or obtained in this study 2 Nucleotide position and sequence length defined after sequences alignment. MHOM = Mammalia, Homo sapiens ; MCEB = Mammalia, Cebus apella ; IWHI = Insecta , Lutzomyia whitmani ; L .…”

“…A recent study reported for the first time that level of genomic diversity among LRV1 in parasites of the L . guyanensis species is low and suggested evolutionary relationships between the viruses and the parasites [ 23 ].…”

Toward an objective diagnostic for detection of Leishmania RNA virus (LRV) in clinical samples from cutaneous leishmaniasis patients

“…Considering that different Leishmania strains can carry different LRV1 loads, an alternative detection method was used to determine whether a more conserved nucleotide sequence region could be used to improve detection sensitivity (10, 11, 13, 33). This detection was accomplished using a modified version of the RT-qPCR method described by Massayuki et al .…”

“…At the epidemiologic level, LRV1/2 has been found at frequencies ranging from 0 to 87% in clinical samples from patients with leishmaniasis (15, 17, 19–33); the strength of the association between viral presence and complication development varies according to the study (24, 28) and among different South-American Regions (30). The wide range in LRV1 frequency of detection in clinical samples may reflect diverse experimental approaches that do not account for differences in clinical specimens.…”