A Novel Cryptic Virus Isolated from Galphimia spp. in Mexico

Abstract

Galphimia spp. is a plant employed in traditional medicine in Mexico because of its anxiolytic and sedative effects. Viruses have been associated with different alterations in plants, although asymptomatic agents (i.e., cryptic viruses) are also known. High-throughput sequencing (HTS) allows for the detection of pathogenic and non-pathogenic viral agents in plants, including potential novel viruses. The aim of this study was to investigate the presence of viral agents in two populations of Galphimia spp. by HTS. Sequencing was conducted on an Illumina NextSeq 550 platform, and a putative novel virus was identified. Two contigs showed homology to partitiviruses, and these encoded the RNA-dependent RNA polymerase and coat protein. These proteins showed the highest identities with orthologs in the recently discovered Vitis cryptic virus. A phylogenetic analysis of both RNAs showed that the new virus clusters into the monophyletic genus Deltapartitivirus along with other plant-infecting viruses. The result of the HTS analysis was validated by conventional RT-PCR and Sanger sequencing. A novel virus was discovered in a symptomless Galphimia spp. plant and tentatively named the Galphimia cryptic virus (GCV). This is the first virus discovered in medicinal plants in Mexico.

Keywords: Mexico; cryptic virus; high-throughput sequencing; medicinal plant.

Figure 1

Asymptomatic leaves in Galphimia spp. plants. (a), Guanajuato population; (b), Morelos population.

Figure 2

Proposed near-complete genome organization of Galphimia cryptic virus (GCV). (a), RNA molecules and corresponding genes are presented as gray boxes. (b), fold coverage of aligned reads for the two RNA sequences. Numbers represent nucleotide position in the virus genome.

Figure 3

Phylogenetic trees showing the relationship of Galphimia cryptic virus with other members of the Partitiviridae family. The evolutionary history was inferred using amino acid sequence of the (a), RNA-dependent RNA polymerase and (b), coat protein. The human picobirna virus was included as outgroup. GenBank accession numbers are provided.