Abstract
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.
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Claims 3
Claim · model-written summary
The sequencing method reconstructed two closely related RYMV genomes in artificial mixes up to a 99/1 ratio.
- Taxon
- rice
Oryza sativae1 - Interactor
- rice yellow mottle virusRice yellow mottle viruse1pathogen
- Outcome
- successful reconstruction of two viral genomese0
- Value
- 99/1e0
- Qualifier
- less than a hundred nucleotides aparte0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“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”
e1“rice yellow mottle virus (RYMV)”
Claim · model-written summary
A single rice sample from Burkina Faso contained up to three RYMV isolates.
- Taxon
- riceOryza sativae0
- Interactor
- RYMVe0pathogen
- Outcome
- RYMV isolatese0
- Value
- up to threee0
- Setting
- Burkina Fasoe0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“revealing up to three RYMV isolates within one single rice plant sample from Burkina Faso”
Claim · model-written summary
The method obtained complete viral genome sequences in most cases.
- Taxon
- riceOryza sativae1
- Interactor
- rice yellow mottle virusRice yellow mottle viruse1pathogen
- Outcome
- complete genome sequences were obtainede0
- Qualifier
- In most casese0
Not reportedComparatorValue
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“In most cases, the complete genome sequences were obtained”
e1“rice yellow mottle virus (RYMV)”