Extensive recombination challenges the utility of Sugarcane mosaic virus phylogeny and strain typing

Abstract

Sugarcane mosaic virus (SCMV) is distributed worldwide and infects three major crops: sugarcane, maize, and sorghum. The impact of SCMV is increased by its interaction with Maize chlorotic mottle virus which causes the synergistic maize disease maize lethal necrosis. Here, we characterised maize lethal necrosis-infected maize from multiple sites in East Africa, and found that SCMV was present in all thirty samples. This distribution pattern indicates that SCMV is a major partner virus in the East African maize lethal necrosis outbreak. Consistent with previous studies, our SCMV isolates were highly variable with several statistically supported recombination hot- and cold-spots across the SCMV genome. The recombination events generate conflicting phylogenetic signals from different fragments of the SCMV genome, so it is not appropriate to group SCMV genomes by simple similarity.

Molecular Characterization of Potato Virus Y (PVY) Using High-Throughput Sequencing: Constraints on Full Genome Reconstructions Imposed by Mixed Infection Involving Recombinant PVY Strains

“…However, the growing evidence of "divergent" PVY isolates escaping accurate identification using such tests, which were developed with a limited pool of isolates [42], pinpoints the usefulness of complete genome analyses to characterize PVY strain variability [16]. Indeed, the challenges of viral strain identification due to extensive recombination were recently addressed for the sugarcane mosaic virus (SCMV), another member of genus potyvirus, where it was advised to use whole genome phylogenetic analysis for viral strain identification [43].…”

Complete Genome Sequence of a Novel Potyvirus Infecting Miscanthus Sinensis (Silver Grass)

“…Potyviruses represent the largest and most economically damaging group of known plant RNA viruses [4]. Potyviruses are aphid-borne, infecting both monocotyledonous and eudicotyledonous angiosperms [7].…”

Post-COVID-19 Action: Guarding Africa’s Crops against Viral Epidemics Requires Research Capacity Building That Unifies a Trio of Transdisciplinary Interventions

“…From the genome information, RT-PCR diagnostics were developed [58]. Whole-genome information revealed that getting reliable tests for SCMV would be tricky due to high genetic diversity and virus recombination [41]. Therefore, the most reliable tests for MLN are anchored on detection of MCMV, which is risky.…”