Differential Shape of Geminivirus Mutant Spectra Across Cultivated and Wild Hosts With Invariant Viral Consensus Sequences

Abstract

Geminiviruses (family Geminiviridae) possess single-stranded circular DNA genomes that are replicated by cellular polymerases in plant host cell nuclei. In their hosts, geminivirus populations behave as ensembles of mutant and recombinant genomes, known as viral quasispecies. This favors the emergence of new geminiviruses with altered host range, facilitating new or more severe diseases or overcoming resistance traits. In warm and temperate areas several whitefly-transmitted geminiviruses of the genus Begomovirus cause the tomato yellow leaf curl disease (TYLCD) with significant economic consequences. TYLCD is frequently controlled in commercial tomatoes by using the dominant Ty-1 resistance gene. Over a 45 day period we have studied the diversification of three begomoviruses causing TYLCD: tomato yellow leaf curl virus (TYLCV), tomato yellow leaf curl Sardinia virus (TYLCSV) and tomato yellow leaf curl Malaga virus (TYLCMaV, a natural recombinant between TYLCV and TYLCSV). Viral quasispecies resulting from inoculation of geminivirus infectious clones were examined in plants of susceptible tomato (ty-1/ty-1), heterozygous resistant tomato (Ty-1/ty-1), common bean, and the wild reservoir Solanum nigrum. Differences in virus fitness across hosts were observed while viral consensus sequences remained invariant. However, the complexity and heterogeneity of the quasispecies were high, especially in common bean and the wild host. Interestingly, the presence or absence of the Ty-1 allele in tomato did not lead to differences in begomovirus mutant spectra. However, the fitness decrease of TYLCSV and TYLCV in tomato at 45 dpi might be related to an increase in CP (Coat protein) mutation frequency. In Solanum nigrum the recombinant TYLCMaV, which showed lower fitness than TYLCSV, at 45 dpi actively explored Rep (Replication associated protein) ORF but not the overlapping C4. Our results underline the importance of begomovirus mutant spectra during infections. This is especially relevant in the wild reservoir of the viruses, which has the potential to maintain highly diverse mutant spectra without modifying their consensus sequences.

Lethal mutagenesis of Rift Valley fever virus induced by favipiravir

“…While the viral population that was passaged in absence of drug yielded 7 clones without mutations and 7 clones with only one mutation (24.1% in both cases), only 1 clone without mutations and 2 with one mutation were retrieved from the population that was passaged in the presence of favipiravir (1/29, 3.4%; 2/29, 6.9%, respectively). Finally, the consensus genomic nucleotide sequence (analyzed at passage 4) did not change as a result of replication in the presence of favipiravir, an observation already found during lethal mutagenesis of other RNA viruses (19, 27-30).…”

Natural Hosts and Genetic Diversity of the Emerging Tomato Leaf Curl New Delhi Virus in Spain

“…Begomoviruses have a high potential for increasing their genetic variability, as a result of high mutation and recombination rates, which are quite comparable to those reported for plant RNA viruses (Ge et al, 2007; Navas-Castillo et al, 2011; Lima et al, 2017). In particular, the presence of high intra-population diversity has been reported, which may allow for a rapid accumulation of variants during infection and generate diversity levels that allow for a rapid evolution and adaptation in response to new environments (Ge et al, 2007; Moriones and Navas-Castillo, 2008; Sánchez-Campos et al, 2018). For example, despite of invariant viral consensus sequences in TYLCV populations, the mutant swarm within-populations in cultivated tomato plants and wild hosts displayed a differential shape with greater complexity and heterogeneity in the alternative host, S. nigrum (Sánchez-Campos et al, 2018).…”

“…Within each mutant spectrum, mutations were counted against the consensus sequence. Mutational frequency (mut/nt) was calculated by scoring the number of different mutations divided by the total number of nucleotides sequenced (Sánchez-Campos et al, 2018), while mutational frequency for each gene (mut. freq/codon) was estimated as the addition of the mutation frequencies per codon of all codons in the gene divided by the total of codons.…”

“…freq/codon) was estimated as the addition of the mutation frequencies per codon of all codons in the gene divided by the total of codons. Mutant spectra heterogeneity was estimated by using the normalized Shannon entropy (Sánchez-Campos et al, 2018). Finally, the haplotype reconstruction, as the inference of the group of variants that was assembled in the full-length sequence, was performed with the software Haploclique (Topfer et al, 2014).…”

Plant Viruses Infecting Solanaceae Family Members in the Cultivated and Wild Environments: A Review

“…Examples of wild Solanaceae plants roles in virus life cycles can be observed in the case of begomoviruses causing TYLCD, which is known to act as bundles of genomes undergoing mutation and recombination, called quasispecies. When Sánchez-Campos et al [87] compared four plant hosts infected by three viruses causing TYLCD, the black nightshade wild reservoir plant had higher quasispecies heterogeneity than tomato, showing its potential to contribute to viral evolution by providing a larger supply of variants for the natural selection processes.…”