Exploring the significant genetic diversity of Iranian isolates of Leishmania RNA virus 2 using whole genome sequence analysis

Abstract

Background: Our work presents the whole genome sequence and phylogenetic analysis of five Leishmania RNA virus 2 (LRV2) isolates obtained from patients with cutaneous leishmaniasis (CL) in Iran.

Methods: The whole genome sequencing of LRV2 was performed using a primer walking approach. The resulting sequences were analyzed for genetic and haplotype diversity, highlighting their independent evolution and significant genetic divergence.

Results: The whole genome sequence of the current LRV2 showed high genetic and haplotype diversity. The study also revealed the existence of three distinct clades of LRV2, with the LRV2 sequences infecting L. major, L. aethiopica, and sauroleishmania belonging to separate lineages. These lineages have seemingly evolved independently, as the geographic distribution of their flagellate hosts does not overlap with the Leishmania species. The divergence between these three clades is attributed to considerable antiquity, leading to genetic modifications within the viruses residing in them and resulting in structural differences in their genome.

Conclusions: These findings contribute to our understanding of the genetic diversity and evolution of LRVs, providing valuable insights into their role in Leishmania infections. Further investigations are needed to understand the significance of these polymorphic sites and their potential impact on viral characteristics and disease outcomes.

Keywords: Cutaneous leishmaniasis; Genetic diversity; Leishmania RNA virus 2; Primer walking; Whole genome sequence.

Fig. 1

Gel electrophoresis of amplified products using primer-walking technique. M: 100 bp ladder, Lane 1-10: Current samples, Line M: Marker 100 bp

Fig. 2

Phylogenetic tree of whole genome sequences of Leishmania RNA virus in the present study and other LRVs from the New World Leishmaniasis and Old World Leishmaniasis sequences obtained from GenBank. Maximum likelihood tree of LRVs built on completed sequence alignment using Tamura 3-parameter models

Fig. 3

Split tree phylogenetic network of whole genome of LRV2 isolates. Group 1, LRV2-L.major (A), group 2, LRV2-sauroleishmania (B) and groups 3, LRV2-L.ethiopica (C). The sequences of this research are marked with a red circle

Fig. 4

Phylogenetic network analysis of whole genome of LRVs. Two distinct haplogroups: LRV1 (51 sequences), and LRV2 (19 sequences). In LRV2 group, small red circles corresponding to current samples, small yellow circles: LRV2-L.major, small green circles: LRV2-L.ethiopica, and LRV2-sauroleishmania are also represented by small blue circles

Fig. 5

Singleton variable and parsimony informative sites in the capsid and RdRp regions of current sequences

Fig. 6

Presenting the frequency of nucleotides in the capsid polymorphic positions of the current sequences of this study

Fig. 7

Presenting the frequency of nucleotides in the RdRp polymorphic positions of the current sequences of this study