Chapter 3.3.1 : Pathogenic Viruses and Protozoa Transmitted by Soil

Abstract:

Soil is a reservoir for a diversity of transient human pathogenic viruses and protozoa that include some species with truly edaphic lifestyles. The ability to detect these pathogens in soil has increased in tandem with concerns about the impact of human activity on soil quality. Separation from the sample matrix and concentration in solution free of interfering contaminants are key preliminary steps to the detection and/or identification of specific species, which is increasingly performed with sensitive molecular methods. The present chapter describes procedures applied in the separation of viruses from soil by desorption from soil particles, their concentration and detection/quantification in laboratory-grown mammalian cell cultures using Quantal methods or plaque assays. Methods for extraction of nucleic acids to permit detection of viruses that are presently difficult or impossible due grow in vitro due to a lack of suitable cell lines (noroviruses, astroviruses, sapoviruses, rotaviruses, hepatitis A and E viruses) by polymerase chain reaction (PCR), conventional reverse-transcription PCR (RT-PCR) or real-time PCR and RT-PCR are also presented. The detection of protozoa against the large background microflora and extraneous components in soil requires a series of variable preliminary elution, concentration and purification steps that are determined by the properties of both sample and target protozoa. Classical methods that rely on microscopic examination for detection/identification of Acanthamoeba spp, Entamoeba histolytica, Naegleria fowleri, Giardia spp., Balantidium coli, Toxoplasma gondii, Cyclospora cayetanensis and Cryptosporidium parvum are presented along with alternative molecular approaches based on the recognition of specific antigens or DNA sequences.