Genomic characterization and phylogenetic placement of Matryoshka RNA virus 1 associated with Plasmodium vivax malaria in Africa

Abstract

Abstract Plasmodium vivax is a major cause of human malaria. It harbours Matryoshka RNA virus 1 (MaRNAV-1), a bi-segmented positive-sense RNA virus. MaRNAV-1 was first described in P. vivax and is now recognized as part of a wider group of Matryoshka viruses. These viruses also infect other haemosporidian parasites such as Leucocytozoon and Haemoproteus. The presence of MaRNAV-1 in African-origin human P. vivax, however, has not been clearly established. This study investigated whether MaRNAV-1 is present in public African-origin P. vivax transcriptomic datasets. Any viral sequences recovered were characterized using comparative genomic and phylogenetic analyses. A secondary in silico analysis targeted African-origin P. vivax RNA-seq runs from public repositories. Although the search covered Africa, only Ethiopian datasets could be confidently identified, retrieved and compiled at the time. After quality control and screening for MaRNAV-1 RNA-dependent RNA polymerase (RdRp) signals, three high-confidence runs were selected for further analysis. Reference-guided reconstruction, ORF prediction, blast-based validation and RdRp phylogenetic analysis were performed. MaRNAV-1 was identified in three Ethiopian P. vivax malaria transcriptomes. This was supported by strong segment-level mapping, near-complete coverage, high mean depth and minimal low-depth masking. The recovered genomes showed the expected bisegmented organization of MaRNAV-1. Segment I was highly conserved and encoded the canonical RdRp in all three consensus sequences. Segment II showed the conserved organization of two overlapping hypothetical ORFs in all three consensus sequences. Blast analyses confirmed close similarity to MaRNAV-1 reference sequences. Phylogenetic inference grouped the Ethiopian sequences within the broader P. vivax-associated MaRNAV-1 lineage, alongside other recognized MaRNAV lineages distinct from more divergent narna-like viruses. These findings provide genomic evidence for MaRNAV-1 in publicly available African-origin P. vivax transcriptomic datasets and add to the emerging evidence for the virus in the African malaria context.