Comparative utility of restriction fragment length polymorphism analysis and gene sequencing to the molecular epidemiological investigation of a viral outbreak

Restriction fragment length polymorphism (RFLP) analysis and partial-genome DNA sequencing are commonly used to infer genetic relationships among path ogens. This study compares the application of both techniques to the analys is of 16 pseudorabies virus isolates collected during a 1989 outbreak. Gene tic distances derived from RFLP and DNA sequence data were not significantl y correlated with geographic distances between farms from which isolates we re collected. RFLP-based genetic distance was, however, strongly correlated with temporal distance between isolates (days separating time of isolation ). Sequence-based genetic distance was significantly correlated with tempor al distance only when synonymous changes (nucleotide changes not leading to amino acid changes) were considered separately. Conversely, non-synonymous changes were correlated with the host species of origin of the viral isola te. These results indicate that selectively-neutral genetic changes most ac curately reflect historical relationships, but that non-neutral changes mos t accurately reflect the biological environment of the viral isolate (e.g. host immune system).