The COVID-19 pandemic is putting enormous pressure on clinical and public health laboratories. The COVID-19 pandemic may be caused by widespread transmission, viral detection is key to isolate positive patients and stop viral transmission(44–48). rRT-PCR is the most reliable and widely used technology to diagnose viruses including coronaviruses(44–48). However, rRT-PCR has some limitations, which can not meet the huge demand for the global pandemic of COVID-19. Recently, the US FDA has been authorized multiple rapid molecular tests to meet the huge diagnostic need. Different diagnostic methods have proposed different virus targets for detection of the virus, which would detect SARS-CoV-2 and other related beta coronaviruses such as SARS-CoV, including RNA-dependent RNA polymerase (RdRp), envelope (E), spike (S), Open Reading Frame (ORF) 1a and nucleocapsid (N)(21, 47, 51, 52). This article discusses some of the diagnostic methods include EUA-granted assays.
To date, this study was the first meta-analysis on systematically evaluating the diagnostic efficiency of different method for detecting COVID-19. In this study, we analyzed the pooled sensitivity, specificity, PLR, NLR, DOR, AUC and Q* on each methods (ePlex, Panther Fusion, Simplexa, Cobas®, Xpert Xpress and RT-LAMP), respectively. The results demonstrated that these above methods bear higher sensitivity and specificity, and might be efficient methods complement to the gold standard.
The ePlex assay targets the N gene of SARS-CoV-2, which is an in vitro diagnostic test. The ePlex has a relatively short turnaround time, simple operational flow, but a shortage of supply and inventory limits its full implementation.
The Panther Fusion SARS-CoV-2 assay targets two conserved regions of ORF1ab in the same fluorescence channel. This platform is automated, high-throughput systems that can process > 1,000 specimens in 24 hours, which is met the huge diagnostic need.
Simplexa COVID-19 Direct assay targeted two distinct regions of the SARS-COV-2 genome, the surface (S) gene and the open reading frame 1AB(ORF1ab), distinguish with FAM and JOE fluorescent probes. Compared with RT-PCR, which requires nucleic acid extraction from clinical samples, Simplexa COVID-19 Direct assay can be detected directly from clinical samples. This detection method is easy to operate and does not require additional equipment such as a centrifuge or extraction system, which indicated is promising for laboratory diagnosis of COVID-19 and field application.
Cobas® SARS-CoV-2 is a qualitative dual target assay, includes the ORF1/a nonstructural regional unique to SARS-CoV-2 and a region on the E gene, which is conserved across the sarbecovirus subgenus. Cobas® SARS-CoV-2 is based on fully automated sample preparation (nucleic acid extraction and purification) followed by PCR amplification and detection(53). Automated solutions for molecular diagnostics can help process large numbers of samples, save testing time, allow non - professional operators. The assay has passed clinical evaluation and received EUA from the U.S. FDA(54–56).
The Xpert Xpress SARS-CoV-2 assay targets two genes, the E-gene (Sarbeco specific) and N2-gene (SARS-CoV-2 specific), which received EUA status on March 20, 2020. The Xpert test platform integrates specimen processing, nucleic acid extraction, reverse transcriptase polymerase chain reaction amplification of SARS-CoV-2 RNA, and amplicon detection in a single cartridge, which improves actionability overall. This assay is simple to operate with the least technical interventions, and FDA has authorized trained non-laboratorians to test.
RT-LAMP methodology is regarded as a new generation diagnostics(57), which was developed by Notomi et al.in 2000(58). This method has high sensitivity, high specificity, simple method, low cost and time saving, which has been widely applied for the detection of influenza virus, MERS-CoV, West Nile virus, Ebola virus, Zika virus, yellow fever virus, and a variety of other pathogens(59–64). The detection results are based on colorimetric display is easy to understand and does not require any expensive equipment which is suitable for countries with limited laboratory capacity.
We also encountered some limitations: i) the sample size of each method for detecting COVID-19 was relatively small. ii) the heterogeneity of some studies was significant though we have divided this meta-analysis based on the different methods, which might affect the stability of results to some extent. Therefore, more well designed study involving the different methods with a large sample size is urgent to be conducted.