Journal Article

Deciphering mixed infections by plant RNA virus and reconstructing complete genomes simultaneously present within-host

Institut de l'Environnement et Recherches Agricoles [Ouagadougou] (INERA) ; Centre national de la recherche scientifique et technologique [Ouagadougou] (CNRST), Bangratz, Martine, Plant Health Institute of Montpellier (UMR PHIM) ; Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro Montpellier ; Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Université de Montpellier (UM), Gandolfi, Guillaume, Tollenaere, Charlotte, Kassankogno, Abalo Itolou, Sérémé, Drissa, Guigma, Abdoul Kader, Billard, Estelle, Poulicard, Nils, Comte, Aurore, ANR-20-CE35-0004,EVCOPAR,Evolution des pathogènes co-infectant le riz

2025

Overview

Local co-circulation of multiple phylogenetic lineages is particularly likely for rapidly evolving pathogens in the current context of globalisation. When different phylogenetic lineages co-occur in the same fields, they may be simultaneously present in the same host plant (i.e. mixed infection), with potentially important consequences for disease outcome. This is the case in Burkina Faso for the rice yellow mottle virus (RYMV), which is endemic to Africa and a major constraint on rice production. We aimed to decipher the distinct RYMV isolates that simultaneously infect a single rice plant and to sequence their genomes. To this end, we tested different sequencing strategies, and we finally combined direct cDNA ONT (Oxford Nanopore Technology) sequencing with the bioinformatics tool RVhaplo. This method was validated by the successful reconstruction of two viral genomes that were less than a hundred nucleotides apart (out of a genome of 4450nt length, i.e. 2–3%), and present in artificial mixes at a ratio of up to a 99/1. We then used this method to subsequently analyze mixed infections from field samples, revealing up to three RYMV isolates within one single rice plant sample from Burkina Faso. In most cases, the complete genome sequences were obtained, which is particularly important for a better estimation of viral diversity and the detection of recombination events. The method described thus allows to identify various haplotypes of RYMV simultaneously infecting a single rice plant, obtaining their full-length sequences, as well as a rough estimate of relative frequencies within the sample. It is efficient, cost-effective, as well as portable, so that it could further be implemented where RYMV is endemic. Prospects include unravelling mixed infections with other RNA viruses that threaten crop production worldwide.

• Publisher: CCSD,Public Library of Science,Public Library of Science (PLoS)
• Subject: Bioinformatics / Biology and Life Sciences / Burkina Faso / Capital costs / Control / Crop production / Datasets / Diseases and pests / Epidemics / France / Gene sequencing / Genetic aspects / Genome, Viral / Genomes / Globalization / Growth / Haplotypes / High-throughput screening (Biochemical assaying) / Host plants / Identification and classification / Infections / Life Sciences / Methods / Microbiology and Parasitology / Mixed infection / Nucleotide sequence / Nucleotides / Oryza - virology / Performance evaluation / Phylogeny / Plant Diseases - virology / Plant virus diseases / Plant viruses / Plant Viruses - genetics / Research and Analysis Methods / Rice / RNA viruses / RNA Viruses - genetics / Viral infections / Virology / Viruses / Whole genome sequencing
• ISBN: 0013973178000