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

Abstract

Cutaneous leishmaniasis is a neglected parasitic disease that manifests in infected individuals under different phenotypes, with a range of factors contributing to its broad clinical spectrum. One factor, Leishmania RNA Virus 1 (LRV1), has been described as an endosymbiont present in different species of Leishmania. LRV1 significantly worsens the lesion, exacerbating the immune response in both experimentally infected animals and infected individuals. Little is known about the composition and genetic diversity of these viruses. Here, we investigated the relationship between the genetic composition of LRV1 detected in strains of Leishmania (Viannia) braziliensis and L. (V.) guyanensis and the interaction between the endosymbiont and the parasitic species, analyzing an approximately 850 base pair region of the viral genome. We also included one LRV1 sequence detected in L. (V.) shawi, representing the first report of LRV1 in a species other than L. braziliensis and L. guyanensis. The results illustrate the genetic diversity of the LRV1 strains analyzed here, with smaller divergences detected among viral sequences from the same parasite species. Phylogenetic analyses showed that the LRV1 sequences are grouped according to the parasite species and possibly according to the population of the parasite in which the virus was detected, corroborating the hypothesis of joint evolution of the viruses with the speciation of Leishmania parasites.

Fig 1. Partial map of South America indicating the geographic distribution of Leishmania strains carrying LRV1 sequences included in the study.

Partial map of Brazil (white), divided by states. Neighboring countries are colored gray, with Bolivia, Suriname and French Guiana in dark gray. The groups are the same as those reported by Tirera et. al., 2017. Numbers indicate the sequences analyzed from each geographic region, following the ID numbers presented in Table 1. The map was constructed using Quantum GIS version 2.18.13 (http://download.qgis.org), the base layers were downloaded from Carlos Efrain Porto Tapiquen, Orogenesis Soluciones Geograficas, Porlamar, Venezuela, 2015, based on shapes from Environmental Systems Research Institute (ESRI) with free distribution (http://tapiquen-sig.jimdo.com). The points corresponding to cities and countries were obtained from Google Earth (http://earth.google.com).

Fig 2. Maximum likelihood tree of Leishmania RNA Virus 1 detected in Leishmania (Viannia) species from South American countries.

The analysis involved 43 nucleotide sequences. There was a total of 687 positions in the final dataset (Dataset I). Boxes indicate the clustering of M5313, 1398, 3542, and 2169 after analysis involving 47 nucleotide sequences, with a total of 351 positions. Groups A-F were defined as previously reported [23]. The tree was inferred based on the Tamura 92 model with a Gamma distribution and invariable sites (I). Bootstrap values (after 10,000 replicates) above 70% are shown. Sites containing gaps and missing data were excluded from the analysis. L.b. = L. braziliensis; L.g. = L. guyanensis; L.s. = L. shawi. For details of samples see Table 1.

Fig 3. NeighborNet presenting the relationship among LRV1 sequences from different Leishmania (Viannia) species.

The network was computed using SplitsTree software. EqualAngle was employed for splits transformation. Text colors refer to groups from Fig 4: red = cluster I, blue = cluster II, and green = cluster III. For sample details see Table 1.

Fig 4. Minimum spanning network displaying the connections among LRV1 sequences from different Leishmania (Viannia) species.

I = LRV1 sequences from L. guyanensis groups A, B, C and E, and L. shawi; II = LRV1 sequences from L. braziliensis group; III = LRV1 sequences from L. guyanensis group D. For sample details, see Fig 1 and Table 1.