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

Published online by Cambridge University Press:  16 July 2001

T. L. GOLDBERG ,
R. M. WEIGEL ,
E. C. HAHN  and
G. SCHERBA
T. L. GOLDBERG
Affiliation:
University of Illinois, Department of Veterinary Pathobiology, 2001 South Lincoln Avenue, Urbana IL 61820, USA
R. M. WEIGEL
Affiliation:
University of Illinois, Department of Veterinary Pathobiology, 2001 South Lincoln Avenue, Urbana IL 61820, USA
E. C. HAHN
Affiliation:
University of Illinois, Department of Veterinary Pathobiology, 2001 South Lincoln Avenue, Urbana IL 61820, USA
G. SCHERBA
Affiliation:
University of Illinois, Department of Veterinary Pathobiology, 2001 South Lincoln Avenue, Urbana IL 61820, USA
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Abstract

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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).

Type
Research Article
Information
Epidemiology & Infection , Volume 126 , Issue 3 , June 2001 , pp. 415 - 424
Copyright
© 2001 Cambridge University Press