Evaluation of simple nucleic acid extraction methods for the detection of SARS-CoV-2 in nasopharyngeal and saliva specimens during global shortage of extraction kits

Chu, Allen Wing-Ho; Chan, Wan-Mui; Ip, Jonathan Daniel; Yip, Cyril Chik-Yan; Chan, Jasper Fuk-Woo; Yuen, Kwok-Yung; To, Kelvin Kai-Wang

BACKGROUND: The severe shortage of nucleic acid extraction kits during the current COVID-19 pandemic represents a key limiting factor in testing capacity. OBJECTIVES: This study compared the results of SARS-CoV-2 RT-PCR using different simple nucleic acid extraction methods on nasopharyngeal and saliva specimens. STUDY DESIGN: Fifty nasopharyngeal swab and saliva specimens previously tested positive for SARS-CoV-2 were retrieved. Three different methods of nucleic acid extraction were compared. The first method involves incubating the specimen, with proteinase K, and then heat treatment at 98°C for 5 min (PHK); the second method involves heat treatment at 98°C fir 5 min without proteinase K pre-incubation (heat only); the third method involves no pre-processing steps (direct). The products from all 3 methods were tested by SARS-CoV-2 RT-PCR. RESULTS: PKH had significantly higher positive rate in SARS-CoV-2 RT-PCR (80%)than those of heat only (58%; P=0.001) or direct (56%; P=0.002). The median Ct value was significantly earlier for PKH (median Ct: 37.0, IQR 31.7-40) than that of heat only (median Ct: 40, IQR 36.2-41; P<0.0001) and direct (median Ct, 37.5; IQR 33.9-41.0; P=0.0049). Subgroup analysis showed that PKH had higher detection rate, lower limit of detection and earlier Ct values than the other two groups for both NPS and saliva specimens. CONCLUSIONS: PKH pre-processing resulted in the highest detection rate of SARS-CoV-2 by RT-PCR, and can serve as an alternative for nucleic acid extraction when commercial extraction kits are not available.