2.2. Virus analyses
2.2.1. Concentration and nucleic acid extraction
The detection of viruses in the environment requires the concentration
of the viral particles into small volumes. This study was
conducted using optimised Standardised Operational Procedures
(SOPs) for virus concentration, nucleic acid extraction and quantitative
PCR (qPCR and RT-qPCR) detection. The SOPs incorporated
process controls and standard plasmid preparation. First, samples
with high levels of organic matter or sand were permitted to
sediment for 1 h to avoid any interference with the concentration
method. Then, clarified water was transferred to a new container
without disturbing the sediment. As established in ISO 5667-9:1992, seawater samples were collected from one meter below sea
level to avoid contamination with sand and suspended macro algae.