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 pathogens. This study compares the application of both techniques to the analysis of 16 pseudorabies virus isolates collected during a 1989 outbreak. Genetic distances derived from RFLP and DNA sequence data were not significantly correlated with geographic distances between farms from which isolates were 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 temporal 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 isolate. These results indicate that selectively-neutral genetic changes most accurately reflect historical relationships, but that non-neutral changes most accurately reflect the biological environment of the viral isolate (e.g. host immune system).
Goldberg
T L
TL
University of Illinois, Department of Veterinary Pathobiology, Urbana 61820, USA.
Weigel
R M
RM
Hahn
E C
EC
Scherba
G
G
D000818:Animals; D001483:Base Sequence / Q000235:genetics*; D002417:Cattle; D002418:Cattle Diseases / Q000453:epidemiology* / Q000821:virology*; D016000:Cluster Analysis; D004279:DNA, Viral / Q000235:genetics*; D004196:Disease Outbreaks / Q000706:statistics & numerical data*; D004283:Dog Diseases / Q000453:epidemiology* / Q000821:virology*; D004285:Dogs; D014644:Genetic Variation / Q000235:genetics; D011558:Herpesvirus 1, Suid / Q000145:classification / Q000235:genetics*; D007087:Illinois / Q000453:epidemiology; D017720:Molecular Epidemiology / Q000379:methods* / Q000592:standards; D008969:Molecular Sequence Data; D010802:Phylogeny; D012150:Polymorphism, Restriction Fragment Length; D011557:Pseudorabies / Q000453:epidemiology* / Q000821:virology*; D011821:Raccoons; D012307:Risk Factors; D017422:Sequence Analysis, DNA / Q000379:methods* / Q000592:standards; D012689:Sequence Homology, Nucleic Acid; D012756:Sheep; D012757:Sheep Diseases / Q000453:epidemiology* / Q000821:virology*; D013552:Swine; D013553:Swine Diseases / Q000453:epidemiology* / Q000821:virology*; D013997:Time Factors
D004279:DNA, Viral