To be or not to be a virus: A novel chimeric circular Rep-encoding single stranded DNA virus with interfamilial gene exchange illustrates the considerable evolutionary capacity of ssDNA viruses

Abstract

Viruses in the family Geminiviridae cause significant economic losses in numerous crops worldwide. Some geminiviruses are often associated with satellite DNA molecules, such as alphasatellites (familly Alphasatellitidae), that require the assistance of a helper virus for their transmission. Here, we report the discovery of a chimeric virus, tentatively named Cenchrus purpureus associated virus (CPAV), in Cenchrus purpureus plants in La Réunion. The genome of CPAV consists of a single component that is primarily geminivirus-like. It contains a rep gene phylogenetically most closely related alphasatellites. This rep gene is positioned upstream of, and in the same orientation as, the movement and capsid protein genes. Both of these genes are phylogenetically most related to members of the genus Mastrevirus (family Geminiviridae). We found that CPAV is associated in the field with Cenchrus purpureus mild streak virus (CPMSV). Using agroinfectious clones and insect transmission assays, we demonstrated that CPAV is able to initiate infections in C. purpureus but its ability to establish long-term infection and be insect transmitted is apparently facilitated by CPMSV. This raises the question of whether CPAV qualifies as an autonomous virus or rather a satellite-like element with partial autonomy. The chimeric nature of CPAV illustrates the interfamily gene exchange between circular ssDNA viruses and satellites and how such recombination events can blur the boundaries between viruses and subviral agents. These findings highlight the evolutionary plasticity of circular ssDNA viruses and suggest that chimerism may be a key mechanism driving the emergence of novel viral forms with modified pathogenicity and host range.

Fig 1. Leaves of Cenchrus purpureus plants from La Réunion showing (A) discontinuous chlorotic streaks and (B) continuous parallel chlorotic streaks, naturally infected by Cenchrus purpureus mild streak virus (CPMSV), and coinfected by CPMSV and Cenchrus purpureus associated virus (CPAV), respectively.

Fig 2. Schematic genome organizations of (A) Cenchrus purpureus associated virus (CPAV) and (B) Cenchrus mild streak virus (CPMSV).

Open reading frames are shown with colored arrows and intergenic regions with thin colored lines. The stem-loop and nonanucleotide motif sequence are also shown. (C) Gene cluster comparison of CPAV with the nearest sequences of viruses for each ORFs.

Fig 3. (A) Unrooted maximum likelihood tree inferred from aligned replication associated protein (Rep) amino acid sequences of viruses in family Alphasatellitidae. (B) On the left, unrooted maximum likelihood tree inferred from aligned capsid protein (CP) and on the right, unrooted neighbor-joining tree inferred from the aligned movement protein (MP) amino acid sequences of representative mastreviruses. CPAV is shown in bold font. Open and closed circles on nodes indicate bootstrap support for the branches to their left of 70-89% and ≥90% respectively.