There are numerous techniques available for detecting and quantifying viruses (de Miranda, 2008; see also the BEEBOOK paper on molecular methods (Evans et al., 2013). Most of these detect only a small portion of the viral genome or the capsid proteins, and almost all require some sort of amplification, either of the target (most of the nucleic acid-based detection technologies) or the detection signal (most of the protein-based detection technologies). Both are important considerations to bear in mind when interpreting virus diagnostic data. Here we will only cover the most commonly used methods.
Secondly, despite the popular classification of molecular assays as either ‘qualitative’ (presence/absence) or ‘quantitative’ (concentration), ultimately all assays are quantitative: qualitative assays are simply quantitative assays with a detection threshold (a visible colour; a band on a gel; a fluorescence level; a Cq value; a statistical index). This is an important consideration, since there are many factors besides the initial virus amount that can influence whether or not an assay reaches a detection threshold, such as degradation of the sample, changes to storage-extraction procedures, assay deterioration etc.. Furthermore, the molecular and mathematical rules underpinning any assay are the same whether this assay is ‘qualitative’ or ‘quantitative’. The only difference is that in ‘quantitative’ assays these rules are specifically acknowledged and accounted for, whereas in ‘qualitative’ assays they are often ignored. It is therefore advisable to approach any experiment or assay from a quantitative perspective first, and include the appropriate controls for threshold-conversion to ‘qualitative’ data, if this is desired.