Evaluation and comparison of the sensitivity of three commercial RT-qPCR kits used for the detection of SARS-CoV-2 in Santiago, Chile

Abstract

IntroductionThe COVID-19 pandemic is still in force, causing global public health challenges and threats. Although vaccination and herd immunity have proven to be the most efficient way to control the pandemic, massive and early testing of patients using the RT-qPCR technique is crucial for constant genomic surveillance. The appearance of variants of SARS-CoV-2 with new mutations can reduce the efficiency of diagnostic detection. In this sense, several commercial RT-qPCR kits have been the target of extensive analysis because low assay performance could lead to false-negative diagnoses.MethodsIn this study, we evaluated the performance of three commercial RT-qPCR kits; Thermo Fisher (TaqMan 2019-nCoV Assay Kit v1), BGI and Roche (LightCycler® Multiplex RNA Virus Master) used for the diagnosis of COVID-19 throughout the pandemic in Santiago de Chile.ResultsUnder our best assay conditions, we found significant differences in Cq amplification values for control and viral probes, against the same nasopharyngeal swab samples (NPSs). In addition, in some cases, the sensitivity of the RT-qPCR kits decreased against viral variants.ConclusionOur study suggests evaluating the RT-qPCR kits used to detect SARS-CoV-2 because variants such as Omicron, which has several mutations, can compromise their detection and underestimate viral circulation.

A retrospective study suggests 55 days of persistence of SARS-CoV-2 during the first wave of the pandemic in Santiago de Chile

“…1 A), with a Cq for ORF1ab = 33.79 (viral load 6 × 10 1 ) and RNase P was Cq = 16.58 ( Table 1 ). These Cq for ORF1ab indicate both positive results for SARS-CoV-2 according to the previously reported limit of detection [ 18 ]. The full sequence of 1405–124 and 0807–052 aligned against the SARS-CoV-2 reference sequence.…”

“…The viral detection of SARS-CoV-2 was carried out using the ORF1ab gene probe (TaqMan™ 2019 nCoV Assay Kit v1 (Thermo Fisher Scientific, Reference code. A47532) as previously reported [ 18 ].…”

An ecological study on reinfection rates using a large dataset of RT-qPCR tests for SARS-CoV-2 in Santiago of Chile

“…The cycle threshold (Ct) value during the diagnosis of COVID-19 is closely related to the viral load of the infected patient ( 35 ), the risk of mortality during infection ( 36 ), and a greater capacity for the transmission and generation of contagion outbreaks ( 37 ). We evaluated the relationship between the Ct values of the second diagnosis (Ct2) against the initial infection (Ct1) to determine whether this reinfection was associated with a lower or higher viral load.…”