Fingerprinting viral assemblages by Pulsed Field Gel Electrophoresis (PFGE)

Abstract

Publisher Summary Viruses are the most abundant microorganisms in marine and freshwater environments, and perhaps the most genetically diverse. DNA-based fingerprinting approaches, which rely on amplification of rRNA gene fragments by polymerase chain reaction (PCR), have facilitated analyses of bacterial community composition. These approaches have a more restricted application when analyzing viral assemblages, because of the extreme genetic diversity among viruses. Unlike bacteria, there are no gene sequences conserved in all viruses, which can serve as universal primer sites for PCR amplification. The approach described here uses variation in genome size as the basis for obtaining a fingerprint of a viral assemblage. A whole genome fingerprinting approach is possible, because viral genomes can vary greatly in length (a few thousand to hundreds of thousands of base pairs) yet they fall within a range that is easily resolved using pulsed field gel electrophoresis (PFGE). The PFGE fingerprinting technique provides a quick and relatively simple means of visualizing differences in the composition of viral assemblages.