@article{fdi:010092644,
  title = {{D}eciphering mixed infections by plant {RNA} virus and reconstructing complete genomes simultaneously present within-host},
  author = {{B}angratz, {M}artine and {C}omte, {A}urore and {B}illard, {E}stelle and {G}uigma, {A}. {K}. and {G}andolfi, {G}. and {K}assankogno, {A}. {I}. and {S}{\'e}r{\'e}m{\'e}, {D}. and {P}oulicard, {N}ils and {T}ollenaere, {C}harlotte},
  editor = {},
  language = {{ENG}},
  abstract = {{L}ocal co-circulation of multiple phylogenetic lineages is particularly likely for rapidly evolving pathogens in the current context of globalisation. {W}hen 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. {T}his is the case in {B}urkina {F}aso for the rice yellow mottle virus ({RYMV}), which is endemic to {A}frica and a major constraint on rice production. {W}e aimed to decipher the distinct {RYMV} isolates that simultaneously infect a single rice plant and to sequence their genomes. {T}o this end, we tested different sequencing strategies, and we finally combined direct c{DNA} {ONT} ({O}xford {N}anopore {T}echnology) sequencing with the bioinformatics tool {RV}haplo. {T}his 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. {W}e 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 {B}urkina {F}aso. {I}n 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. {T}he 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. {I}t is efficient, cost-effective, as well as portable, so that it could further be implemented where {RYMV} is endemic. {P}rospects include unravelling mixed infections with other {RNA} viruses that threaten crop production worldwide.},
  keywords = {},
  booktitle = {},
  journal = {{PL}o{S} {O}ne},
  volume = {20},
  numero = {1},
  pages = {e0311555 [16 ]},
  ISSN = {1932-6203},
  year = {2025},
  DOI = {10.1371/journal.pone.0311555},
  URL = {https://www.documentation.ird.fr/hor/fdi:010092644},
}