Extraction and Purification of Viral Nucleic Acids from Environmental Samples

Abstract

Molecular biological techniques (i.e., polymerase chain reaction [PCR], nucleotide sequencing, etc.) have been widely utilized in the field of clinical, food, and environmental virology, because they enable rapid detection and/or characterization of viral genomes in a given sample or specimen. However, the results of molecular detection are often limited because of the presence of inhibitory substances (such as humic and fulvic acids, RNases and DNases), co-extracted from the sample matrix, that can produce false-negative results-this is one of the major challenges to overcome especially when attempting to identify viral genomes in complex sample matrices that contain a large amount of inhibitors. Therefore, viral nucleic acid preparation (i.e., extraction and purification) is a critical step in the molecular detection procedure. This chapter provides a background on the intricacies of nucleic acid preparation for reliable detection of virus genomes in various matrices, by an overview of the sample matrix, inhibitory substances, viral nucleic acid extraction/purification, and quality control and quality assurance steps necessary for effective viral nucleic acid extraction and purification.