RT-PCR is used as you know to test for suspected infection of the new coronavirus (SARS-CoV-2). Sensitivity and specificity are very important in testing, but there are some doubts as to how high the generally implemented RT-PCR could detect SARS-CoV-2 without cross-reactivity to other coronaviruses including influenza viruses. Therefore, the following groups have reported a novel methodology for improving the specificity of SARS-CoV-2 detection without sacrificing sensitivity.
https://www.mdpi.com/2075-4418/10/10/775
As the methodology, they adopted the followings, (1) in the domain of structural protein of SRAS-CoV-2, design dual-target PCR primers targeting on coding region of the accessory and envelope proteins (ORF3ab-E primers) and that of the capsid protein (N primers), and (2) use a peptide nucleic acid (PAN) designed to target on the N region as a blocker of PCR reaction.
Peptide nucleic acids are artificial compounds in which the deoxyribose phosphate backbone is replaced by a pseudo-peptide polymer to which the nucleobases are linked, and the binding affinity for target DNA and RNA is remarkably increased by nearly 1000 times, and therefore, it does not act as a primer but act as an inhibitor of PCR.
As a result, cross-reactivity to other coronaviruses and influenza viruses disappeared completely, and the detection rate of SARS-CoV-2 was 100% for ORF3ab-E and 82.6% for PNA-N.