Comparative analysis of primer-probe sets for the laboratory confirmation of SARS-CoV-2

Abstract

Coronavirus disease 2019 (COVID-19) is newly emerging human infectious diseases, which is caused by Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2, also previously known as 2019-nCoV). Within two months of the outbreak, more than 80,000 cases of COVID-19 have been confirmed worldwide. Since the human to human transmission occurred easily and the human infection is rapidly increasing, the sensitive and early diagnosis is essential to prevent the global outbreak. Recently, World Health Organization (WHO) announced various primer and probe sets for SARS-CoV-2 previously developed in China, Germany, Hong Kong, Japan, Thailand, and USA. In this study, we compared the ability to detect SARS-CoV-2 RNA among the seven primer-probe sets for N gene and the three primer-probe sets for Orf1 gene. The result of the comparative analysis represented that the ‘2019-nCoV_N2, N3’ of USA and the ‘ORF1ab’ of China are the most sensitive primer-probe sets for N and Orf1 genes, respectively. Therefore, the appropriate combination from ORF1ab (China), 2019-nCoV_N2, N3 (USA), and NIID_2019-nCOV_N (Japan) sets should be selected for the sensitive and reliable laboratory confirmation of SARS-CoV-2.

Presence and vitality of SARS-CoV-2 virus in wastewaters and rivers

“…CC-BY-NC-ND 4.0 International license It is made available under a is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. (which was not certified by peer review) targeted genes proved different sensitivity thresholds (Jung et al, 2020), so that estimates of viral concentration should be weighted by the sensitivity of the employed marker. In this respect, ORF1ab gene showed the highest frequency of positivity, and resulted amplified in all positive samples, while both the other two genes (N and E) failed to be amplified in two out of five positive cases.…”

Development of Reverse Transcription Loop-mediated Isothermal Amplification (RT-LAMP) Assays Targeting SARS-CoV-2

“…SARS-CoV-2 viral RNA was prepared as previously described [20]. hCoV-229E and hCoV-OC43 viral RNA were isolated from culture media of infected MRC-5 cells (ATCC ® CCL-171 ™ ).…”

Analytical Validation of a COVID-19 qRT-PCR Detection Assay Using a 384-well Format and Three Extraction Methods

“…The ability of high-complexity, College of American Pathologist/CLIA88 compliant laboratories to rapidly and reliably adapt locally developed and validated testing procedures will play a key role in the United States' ability to confront this clinical need. Other groups have recently provided important data on the relative performance of different primer/probe sets for SARS-CoV2 [4,7]. Intriguingly, Bruce et al [8] provide data indicating that qRT-PCR detection of SARS-CoV2 could be successful on nasopharyngeal swab samples without any prior RNA extraction, at least as a screening mechanism.…”

“…The preferred method for diagnosis of coronavirus infections is by one-step quantitative reverse transcriptase PCR (qRT-PCR) [1][2][3][4]. For the majority of qRT-PCR procedures, RNA must be extracted from patient samples [1,3].…”