Validation of the GeneXpert Xpress SARS-CoV-2 PCR assay using saliva as biological specimen

Abstract

In the pandemic, rapid and accurate detection of SARS-CoV-2 is crucial in controlling the outbreak. Recent studies have shown a high detection rate using saliva/oral fluids as specimens for laboratory detection of the virus. We intended to evaluate the test performance of the Xpert Xpress SARS-CoV-2 cartridge assay in comparison to a conventional qRT-PCR testing, using saliva as biological specimen. Forty saliva samples from symptomatic participants were collected. Conventional qRT-PCR was performed for amplification of E and RdRp genes and the Xpert Xpress SARS-CoV-2 assay amplified E and N2 genes. In the conventional assay, the median cycle threshold value of the E gene was 34.9, and of the RdRp gene was 38.3. In the Xpert Xpress assay, the median cycle threshold value of the E gene was 29.7, and of the N2 gene was 31.6. These results can allow a broaden use of molecular tests for management of COVID-19 pandemic, especially in resources-limited settings.

Evaluation of SARS-CoV-2 in the Vaginal Secretions of Women with COVID-19: A Prospective Study

“…Positive results for both methods were determined according to known values [ 22 , 23 ]. Specifically, a positive result for genes E and N2 was determined with values of Ct < 45 [ 23 ]. The method used for each sample was chosen for convenience .…”

“…A positive result for the genes E and N2 is determined with values of Ct < 45 [ 22 ]. Positive results for both methods were determined according to known values [ 22 , 23 ]. Cycle threshold (Ct) levels are inversely proportional to the amount of mRNA of the targeted antigen.…”

ESCMID COVID-19 guidelines: diagnostic testing for SARS-CoV-2

“… In patients with signs and symptoms compatible with severe or critical COVID-19 for the diagnosis of COVID-19 infection, we suggest the use of NAAT in nasopharyngeal swab samples versus NAAT in saliva samples for diagnosis of COVID-19. Weak against Very low [ 13 , 92 , [98] , [99] , [100] , [101] , [102] , [103] , [104] , [105] , [106] , [107] , [108] , [109] , [110] , [111] , [112] , [113] , [114] , [115] , [116] ] 22 In patients with signs and symptoms compatible with COVID-19 of equal or less than 7 days onset , should saliva sampling be used, compared with nasopharyngeal swab sampling for diagnosis of COVID-19 with NAAT? In patients with signs and symptoms compatible with COVID-19 of equal or less than 7 days-onset, we suggest the use of NAAT in saliva samples versus NAAT in nasopharyngeal swab samples for diagnosis of COVID-19.…”

“… In patients with signs and symptoms compatible with COVID-19 of equal or less than 7 days-onset, we suggest the use of NAAT in saliva samples versus NAAT in nasopharyngeal swab samples for diagnosis of COVID-19. Weak for Very low [ 90 , 95 , 104 , 108 , 109 , 113 , 114 ] 23 In patients with signs and symptoms compatible with COVID-19 of more than 7 days onset , should saliva sampling be used, compared with nasopharyngeal swab for diagnosis of COVID-19 with NAAT? In patients with signs and symptoms compatible with COVID-19 of more than 7 days-onset, we suggest the use of NAAT in nasopharyngeal swab samples versus NAAT in saliva samples for diagnosis of COVID-19.…”

“… In patients with signs and symptoms compatible with COVID-19 at risk for severe illness, we suggest the use of NAAT in nasopharyngeal swab samples versus NAAT in saliva samples for diagnosis of COVID-19. Weak against Very low [ 13 , [90] , [91] , [92] , [93] , [94] , [95] , [96] , [97] , [98] , [99] , [100] , [101] , [102] , [103] , [104] , [105] , [106] , [107] , [108] , [109] , [110] , [111] , [112] , [113] , [114] , [115] , [116] , [117] , [118] ] a Strength of recommendation (strong against, weak against, in research only, weak for, strong for). b Overall certainty of the evidence (high, moderate, low, very low).…”