Comparison of COVID‐19 laboratory diagnosis by commercial kits: Effectivity of RT‐PCR to the RT‐LAMP

Abstract

Coronavirus disease 2019 or COVID-19 caused by novel coronavirus/severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2 or 2019-nCoV) is an ongoing pandemic that has emerging global effects and requires rapid and reliable diagnostic testing. Quantitative reverse transcription-polymerase chain reaction (q-RT-PCR) is the gold standard method for SARS-CoV-2 detections. On the other hand, new approaches remedy the diagnosis difficulties gradually. Reverse transcription loopmediated isothermal amplification (RT-LAMP) as one of these novel approaches may also contribute to faster and cheaper field-based testing. The present study was designed to evaluate this rapid screening diagnostic test that can give results in 30-45 min and to compare the effectiveness of LAMP to the q-RT-PCR. The 30 randomly chosen patient samples were generated by nasopharyngeal swabs with a portion of the SARS-CoV-2 nucleic sequence. The sample of quantification cycle (Cq) values was tested using RT-LAMP as well as by conventional q-RT-PCR. The patient samples were tested with four different kits (SENSObiz COVID-19 [SARS-CoV-2] LAMP Assay, the QIAseq DIRECT SARS-CoV-2 kit, Biospeedy SARS-CoV-2 Variant Plus kit, and CoVirion-CV19-2 SARS-CoV-2 OneStep RT-PCR kit) and two different PCR devices (GDS Rotor-Gene Q Thermocycler and Inovia TechnologiesGenX series). Based on 30 patient samples, the positive/negative ratio (P/N) was 30/0 as Biospeedy and Covirion (positivity 100%), 28/2 as Qiagen kit (positivity 93.3%) for the samples studied on the Inovia device while the same samples on the Rotor-Gene device were 30/0 as Biospeedy and Covirion (positivity 100%), 29/1 as Qiagen kit at the first day (96.7%). On the fifth day, the samples were studied in the Inovia device and the respective results were obtained: 27/3 as Biospeedy (positivity 90%), 16/14 as Qiagen (positivity 53.3%), 28/2 as Covirion kit (positivity 93.3%). When these samples were studied in the Rotor-Gene device, it was 29/1 in Biospeedy and Covirion (positivity 96.7%), 19/11 in the Qiagen kit (positivity 63.3%).When these samples were compared with the LAMP method it was found to be 19/11 (positivity 63.3%) on the first day and 18/12 (positivity 60%) on the fifth day. SARS-CoV-2 test studies will contribute to a proactive approach to the development of rapid diagnosis systems. The LAMP approach presents promising results to monitor exposed individuals and also improves screening efforts in potential ports of entry.

Spike protein of SARS-CoV-2 variants: a brief review and practical implications

“…A nasopharyngeal or oropharyngeal swab followed by quantitative real-time reverse transcriptase-polymerase chain reaction (qRT–PCR) is the standard procedure for diagnosis [ 36 – 40 ]. Some immunochromatography assays and other technologies, such as reverse transcription loop-mediated isothermal amplification (RT-LAMP) [ 41 – 43 ], can be used as complements.…”

Progression of LAMP as a Result of the COVID-19 Pandemic: Is PCR Finally Rivaled?

“…In October of 2020, Österdahl et al’s investigation of RT-LAMP compared to RT-PCR resulted in a PPV (positive predictive value) of 73% and NPV (negative predictive value) of 80%, meaning both clinical sensitivity and specificity were lower than that of PCR, though the test is especially prone to false positives [ 111 ]. Artik et al also reported high false positives in their LAMP reactions (with a 63% positivity) [ 112 ]. Two groups, Usherwood et al and Pu et al, reported LAMP tests that yielded lower clinical sensitivities, resulting in higher false-negative rates [ 113 , 114 ].…”

Clinic Evaluation of The Destrovir Spray Effectiveness in SARS-CoV-2 Disease

“…Moreover, the C-terminal of the S1 subunit (S1 CTD) consists of the receptor-binding domain (RBD) which takes the critical role in recognizing and binding the host receptor as shown in Figue 1. Moreover, S protein also takes an important role in recognizing host range and tissue tropism, alongside being responsible for inducing many of the host immune responses [4,5]. On the other hand, ACE2 receptor plays a crucial role in regulating oxygen/carbon dioxide transfer, commonly found within the respiratory epithelia.…”