Analyses of Leishmania-LRV Co-Phylogenetic Patterns and Evolutionary Variability of Viral Proteins

Abstract

Leishmania spp. are important pathogens causing a vector-borne disease with a broad range of clinical manifestations from self-healing ulcers to the life-threatening visceral forms. Presence of Leishmania RNA virus (LRV) confers survival advantage to these parasites by suppressing anti-leishmanial immunity in the vertebrate host. The two viral species, LRV1 and LRV2 infect species of the subgenera Viannia and Leishmania, respectively. In this work we investigated co-phylogenetic patterns of leishmaniae and their viruses on a small scale (LRV2 in L. major) and demonstrated their predominant coevolution, occasionally broken by intraspecific host switches. Our analysis of the two viral genes, encoding the capsid and RNA-dependent RNA polymerase (RDRP), revealed them to be under the pressure of purifying selection, which was considerably stronger for the former gene across the whole tree. The selective pressure also differs between the LRV clades and correlates with the frequency of interspecific host switches. In addition, using experimental (capsid) and predicted (RDRP) models we demonstrated that the evolutionary variability across the structure is strikingly different in these two viral proteins.

Elimination of LRVs Elicits Different Responses in Leishmania spp.

“…We used two LRV-positive Leishmania spp. ( L. guyanensis M4147 and L. major T44g) and overexpressed capsids of their own viruses (LRV1-4 and LRV2, respectively) as well as those of phylogenetically distant LRV1s from L. guyanensis Lg 2014 and L. braziliensis LEM2700 ( 21 ). Successful integration and capsid expression were confirmed by RT-qPCR and Western blotting.…”

“…The first approach is based on the disruption of the ideal 120:2 ratio between the capsid and fused (capsid-RDRP) protein, which results in a decreasing proportion of correctly assembled virions and subsequent viral loss ( 31 , 41 ). We also tested two C-terminally truncated versions that preserved all functional capsid elements ( 21 , 42 ), because it was demonstrated virus loss can be observed even with an abridged capsid protein in the case of the related L-A virus of yeasts ( 35 ). The results in the L. guyanensis- LRV1 system led to complete viral elimination, regardless of the experimental construct used, suggesting the C-terminal part of the capsid protein is not necessary for the assembly.…”

“…The dsRNA of LRV1 facilitates chronic inflammation and spread of L. guyanensis to secondary sites ( 16 – 18 ). It is generally assumed Leishmania and LRV coevolve ( 14 , 19 , 20 ), although occasional horizontal viral transfer events have also been reported ( 21 ). The genome of LRVs contains four open reading frames (ORFs), two of which (ORF2 and 3) encode the capsid and RNA-dependent RNA-polymerase (RDRP), respectively ( 22 , 23 ).…”

Leishmania guyanensis suppressed inducible nitric oxide synthase provoked by its viral endosymbiont

“…LRV1 has been found in New World species such as Lgy (Tarr et al, 1988) and Lbr (Zangger et al, 2013), while another species of LRV, termed LRV2 has been found in Old World L. major (Scheffter et al, 1994), L. aethiopica (Zangger et al, 2014) and L. infantum (Hajjaran et al, 2016). The difference between LRV1 and LRV2 lies within the genetic organization and replication mechanisms (Lee et al, 1996;Se et al, 2005;Fujimura and Esteban, 2011;Kostygov et al, 2021).…”

The Present and Future of Virology in the Czech Republic—A New Phoenix Made of Ashes?

“…Other groups of RNA viruses infecting trypanosomatids are bunyaviruses and narnaviruses, along with some viruses of more restricted distribution [48]. The applied methodological approaches include whole-genome and whole-transcriptome sequencing followed by the phylogenomic analyses of viruses and their respective trypanosomatid hosts [49].…”