Testing for SARS-CoV-2 can be for individual or public health, and it can be performed in specialised laboratories, at the point of care, or in the community. Also, samples can be collected from symptomatic patients or asymptomatic individuals, as well as from wastewater.
Considering sensitivity, specificity, and frequency of testing, which SARS-CoV-2 tests are more suitable for i) diagnosis, ii) screening, and iii) surveillance?
You will find an excellent summary here:
https://www.nytimes.com/2020/12/09/well/live/covid-coronavirus-testing.html
Given its high sensitivity and specificity, real time RT-PCR remains the diagnostic method of choice.
Although it has seen some improvements since the pandemic started, real time RT-PCR is too expensive and elaborate to be used for screening. In my opinion, the best method for screening is a rapid antigen test. The sensibility of such tests is lower than that of PCR-based techniques, but high enough to be useful. Also, for screening, clinical signs and symptoms may be used. Other methods such as detection of the virus in saliva, are yet to fully prove themselves.
1. For diagnosis, RT-qPCR, with all its flaws, remains to be the best choice as testing platform. However, to reduce the risk of false negatives, standardization of sampling collection (such as nasopharyngeal-oropharyngeal [NP-OP] swab) and consideration of more than one sample source (beyond NP-OP swab, such as saliva. sputum and stool) should be implemented. Detection is one thing, however, and another issue altogether is determine the degree of infectiousness which cannot be explained by a mere positive result. One way to go in assessing infectiousness, theoretically, is to consider the CT value, but this depends strongly on a lot of factors (including sampling quality and the specific RT-qPCR kit/machine) which must be assessed by formal research investigations.
2. While there is increasing acceptance of rapid antibody/antigen tests for screening, I still find the performance estimates of these kits questionable considering the negative public health implications of false positive and false negative results. Although it may not exactly fit the conventional picture of a screening test, pooled sample testing through RT-qPCR may be an alternative to this purpose. However, the limitations of RT-qPCR still apply, and with increasing disease prevalence, the cost-effectiveness of this strategy sharply declines.
3. Serologic tests such as ELISA may be helpful for surveillance purposes as in the case of other infections. However, as our knowledge of the virus increases, particularly with regards to its structure and antigenicity, these tools be continuously optimized at a faster rate, I think, than RT-qPCR platforms.
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