Genetic variability of blainvillea yellow spot virus (Begomovirus blainvilleae) reveals recombinant variants and a distinct nonanucleotide motif

Abstract

Viruses from wild plants may emerge as new economically important agricultural pathogens through spillover events. Blainvillea yellow spot virus ( Begomovirus blainvilleae , BlYSV) is a bipartite geminivirus which is ubiquitous in the non-cultivated plant Blainvillea rhomboidea . To better understand the ecological and evolutionary aspects of this virus, we sampled B. rhomboidea in three Brazilian states between 2020 and 2023. Following rolling-circle amplification, cloning and Sanger sequencing, a dataset was assembled with 23 complete DNA-A sequences plus an additional set of 30 BlYSV sequences retrieved from GenBank. Four variants (named A to D) were identified based on sequence comparisons, one of which (variant A) was classified as a different strain. A recombination event in variant B isolates, followed by positive selection in their AC4 gene, may have increased the fitness of these isolates, which replaced variant C isolates in Viçosa and Coimbra between 2014 and 2022. Four sequences in variant A exhibited a nucleotide substitution (A2667G) within the geminivirus conserved nonanucleotide motif (from TAATATTAC to TAATGTTAC). Our results confirm the high genetic variability of this virus which was hinted at in previous studies. Future studies will be directed at understanding the impact of the observed mutations in viral fitness, and whether this could facilitate spillover of BlYSV to other hosts, including cultivated plants.

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