High sensitivity-low cost detection of SARS-CoV-2 by two steps end point RT-PCR with agarose gel electrophoresis visualization

More than one year since Coronavirus disease 2019 (COVID-19) pandemic outbreak, the gold standard technique for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) detection is still the RT-qPCR. This is a limitation to increase testing capacities, particularly at developing countries, as expensive reagents and equipment are required. We developed a two steps end point RT-PCR reaction with SARS-CoV-2 Nucleocapsid (N) gene and Ribonuclease P (RNase P) specific primers where viral amplicons were verified by agarose gel electrophoresis. We carried out a clinical performance and analytical sensitivity evaluation for this two-steps end point RT-PCR method with 242 nasopharyngeal samples using the CDC RT-qPCR protocol as a gold standard technique. With a specificity of 95.8%, a sensitivity of 95.1%, and a limit of detection of 20 viral RNA copies/uL, this two steps end point RT-PCR assay is an affordable and reliable method for SARS-CoV-2 detection. This protocol would allow to extend COVID-19 diagnosis to basic molecular biology laboratories with a potential positive impact in surveillance programs at developing countries.


RNA extraction.
All the samples were processed with AccuPrep Viral RNA extraction kit IVD (Bioneer, South Korea), following manufacturer's instructions. The same RNA aliquot was used for both investigated protocols (RT-qPCR and two step end point RT-PCR). The samples flow chart is presented in Fig. 1.

Two-step end point RT-PCR for SARS-CoV-2 detection.
Same concentrations for N1, N2 and RNase P primers than for the CDC RT-qPCR protocol were used. We carried out a two step RT-PCR protocol using High Capacity Superscript cDNA Reverse Transcription Kit (Applied Biosystems, USA) for retrotranscription (RT) and DreamTaq Green PCR Master Mix (Thermo Scientific, USA) for PCR. Both the RT and PCR were performed in a Mastercycler Pro (Eppendorf, USA) thermal cycler. Retrotranscription was performed with 5uL of RNA and 5uL of RT master mix using the following conditions: 25 °C 2 min, 37 °C 120 min, 85 °C 5 min. After RT reaction, 4uL of nuclease free water were added to the 10uL of cDNA in order to avoid possible PCR inhibitions. Then, PCR was performed in a final volume of 15ul using 3uL of the diluted cDNA as template. Analytical sensitivity. Limit of detection (LoD) was performed using the 2019-nCoV N positive control (IDT, USA) provided at 200.000 genome equivalents/uL for the SARS-CoV-2 CDC RT-qPCR protocol. As 40uL of elution buffer and 0.2 mL of sample are used in the RNA extraction protocol, a 200 conversion factor is applied to change LoD units from copies/uL of RNA extraction solution to copies/mL of nasopharyngeal sample.
Ethics statement. All samples have been submitted for routine patient care and diagnostics. Ethics approval was not sought because the study involves laboratory validation of test methods and the secondary use of anonymous pathological specimens that falls under the category 'exempted' by Comité de Etica para Investigación en Seres Humanos" from "Universidad de Las Américas".

Results
Clinical performance of the two steps end point RT-PCR method compared to the SARS-CoV-2 CDC RT-qPCR protocol. 242 samples were tested for SARS-CoV-2 following both protocols described in the methods. For the CDC RT-qPCR protocol, 122 samples were SARS-CoV-2 positive and 120 samples were Cohen's κ was run to determine the level of agreement between results obtained using two step end point RT-PCR and CDC RT-qPCR protocol for SARS-CoV-2 detection. There was almost perfect agreement between results obtained with both methodologies as indicated by a Cohen's κ = 0.909 (P < 0.001).

Analytical sensitivity for the two step end point RT-PCR method for SARS-CoV-2 detection.
The viral loads detailed in Supplementary Material 1 were calculated running a calibration curve with 2019-nCoV N positive control (IDT, USA). The LoD for the CDC RT-qPCR protocol was set at 1000 viral copies/mL of sample (or 5 viral copies/uL of RNA extraction solution) on previous studies 6, [10][11][12][13][14][15][16][17] . As it is detailed in Fig. 3, the LoD for the two step end point RT-PCR is estimated to be 20 viral copies/uL of RNA extraction (4000 viral copies/mL of sample), as the five replicates done at this concentration yielded a clear band on the agarose gel electrophoresis.

Discussion
Our results support that the detection of SARS-CoV-2 using the two step end point RT-PCR method described here, followed by agarose gel electrophoresis, is a reliable alternative to the gold standard RT-qPCR tecnique. With a specificity of 95.8%, a sensitivity of 95.1% and a LoD of 20 copies/uL, this affordable method has a similar clinical performance to most of the RT-qPCR commercial kits, usually more expensive [10][11][12][13][17][18][19][20][21] . Moreover, as it has also been recently reported that only patients with viral loads over 1 million copies/mL (5000 copies/ uL of RNA extraction on our experimental conditions) would be infectious, this two step end point RT-PCR method would virtually detect 100% of the infectious SARS-CoV-2 positive cases 22,23 . Table 1. Clinical performance of two step end point RT-PCR compared to the CDC RT-qPCR protocol for SARS-CoV-2 detection.   [24][25][26][27] , the present work was pioneer as it was already published as a preprint at MedRxiv in May 2020 27 . Actually, only one of those reports has already been published at a peer review journal, while the others are still at a preprint stage [24][25][26] . Moreover, with a sample size of 242, including 122 SARS-CoV-2 positive samples, this study is to our knowledge the most statistically significant, as the previous ones were done with substantially smaller samples size of 43 and 30 [24][25][26] . Also, this study is the only one using the primers set from the CDC-RT-qPCR protocol for SARS-CoV-2 detection and visualizing the results by agarose gel electrophoresis. Nevertheless, we found a sensitivity value for this two step end point RT-PCR method in the same range than those other studies, where sensitivity values of 94.2%, 96.9% and 100% were described [24][25][26][27] .
In summary, we herein describe a two step end point RT-PCR method as reliable for SARS-CoV-2 detection as most of the commercial kits for SARS-CoV-2 RT-qPCR. This two step end point RT-PCR protocol for SARS-CoV-2 detection would be helpful to reduce cost associated to SARS-CoV-2 surveillance and to improve diagnosis at locations lacking of Real Time PCR devices but with more basic molecular biology equipment, as it is usually the case for laboratories at middle and low income countries.  RT-PCR and agarose gel (3%) electrophoresis for "2019-nCoV N PC" positive control for N1 and N2 amplicons at the detailed concentrations were replicated 5 times. Values correspond to viral loads in copies/uL.