Rapid direct nucleic acid amplification test without RNA extraction for SARS-CoV-2 using a portable PCR thermocycler

Soon Keong Wee; Suppiah Paramalingam Sivalingam; Eric Peng Huat Yap

Reduction in amplification efficiency is a common concern in DIRECT-PCR from crude samples (e.g. respiratory samples, blood and serum). The presence of PCR inhibitors can decrease the sensitivity and accuracy of pathogen detection through interfering with polymerase activity, degradation of nucleic acids and efficient cell lysis (23) . A variety of methods have been developed to overcome such inhibition, including inhibitor tolerant polymerases, additives and buffer modification. In our study, we used one commercially available formulation that tolerated PCR inhibition in sputum and nasal exudates as well as blood/serum/urine (data not shown), and it is not unlikely that other formulations could be used as well in our study. While amplification directly from sputum and nasal exudate reduced the efficiency of PCR compared to water controls, there was no net effect on the threshold of detection.