This study investigated the evolutionary rate of citrus tristeza virus (CTV) using capsid protein gene sequences from 107 isolates collected worldwide between 1990 and 2010. Using Bayesian coalescent methods, researchers estimated CTV's evolutionary rate at 1.58×10⁻⁴ nucleotides per site per year. When examining synonymous substitution rates—a measure less affected by purifying selection—CTV ranked in the 10th percentile among 88 RNA viruses analyzed, placing it among the slowest-evolving RNA viruses alongside some animal RNA viruses. The study revealed that major CTV phylogenetic groups were already defined during citrus dissemination to Europe and the New World, explaining the absence of current geographical speciation. The low evolutionary rate likely results from multiple factors operating at viral and host levels, including linear replication mechanisms, restricted viral movement through phloem tissues, genetic bottlenecks during aphid transmission, and superinfection exclusion. These findings contradict earlier suggestions that CTV was exceptionally slowly evolving compared to other viruses.

Key findings

• CTV's evolutionary rate of 1.58×10⁻⁴ nucleotides per site per year ranks it among the slowest-evolving RNA viruses globally
• CTV's synonymous substitution rate places it in the 10th percentile among 88 RNA viruses studied, embedded among slow animal RNA viruses
• Major CTV phylogenetic groups were already established before citrus spread to Europe and the New World, preventing geographical speciation
• Multiple mechanisms—including linear replication, phloem restriction, transmission bottlenecks, and superinfection exclusion—collectively maintain CTV's slow evolutionary rate
• The large genome size (19.3 kb) of CTV, similar to coronaviruses, may contribute to its reduced evolutionary rate through unknown compensatory mechanisms