Clinical usefulness of extraction-free PCR assay to detect SARS-CoV-2

Due to the coronavirus disease 2019 pandemic, the demand for an easily accessible high-throughput screening test is increasing. We aimed to evaluate the usefulness of the extrac-tion-free polymerase chain reaction (PCR) as a screening test to detect severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2). Real-time reverse transcription PCR was performed in 300 samples (260 SARS-CoV-2 positives and 40 negatives), using both the conventional nucleic acid extraction method (standard method) and the direct method without nucleic acid extraction (direct method). The overall agreement between the standard and direct methods was 86.8 % (kappa 0.60), and the sensitivity of the direct method compared to the standard method was 85.4 %. When the cycle threshold (Ct) value was less than 35, the sensitivity was approximately 90 %-98 %, and when Ct exceeded 35, it decreased to approximately 60 %-65 %. The extraction-free PCR could be useful as a screening test that processes many samples in a short time.

Rapid point-of-care detection of SARS-CoV-2 using reverse transcription loop-mediated isothermal amplification (RT-LAMP)

Background

Fast, reliable and easy to handle methods are required to facilitate urgently needed point-of-care testing (POCT) in the current coronavirus pandemic. Life-threatening severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has rapidly spread all over the world, infecting more than 33,500,000 people and killing over 1 million of them as of October 2020. Infected individuals without any symptoms might still transfer the virus to others underlining the extraordinary transmissibility of this new coronavirus. In order to identify early infections effectively, treat patients on time and control disease spreading, rapid, accurate and onsite testing methods are urgently required.

Results

Here we report the development of a loop-mediated isothermal amplification (LAMP) based method to detect SARS-CoV-2 genes ORF8 and N directly from pharyngeal swab samples. The established reverse transcription LAMP (RT-LAMP) assay detects SARS-CoV-2 directly from pharyngeal swab samples without previous time-consuming and laborious RNA extraction. The assay is sensitive and highly specific for SARS-CoV-2 detection, showing no cross reactivity when tested on 20 other respiratory pathogens. The assay is 12 times faster and 10 times cheaper than routine reverse transcription real-time polymerase chain reaction, depending on the assay used.

Conclusion

The fast and easy to handle RT-LAMP assay amplifying specifically the genomic regions ORF8 and N of SARS-CoV-2 is ideally suited for POCT at e.g. railway stations, airports or hospitals. Given the current pandemic situation, rapid, cost efficient and onsite methods like the here presented RT-LAMP assay are urgently needed to contain the viral spread.

Extraction-free SARS-CoV-2 detection by rapid RT-qPCR universal for all primary respiratory materials

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Rapid SARS-CoV-2 detection without RNA extraction.

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Universal direct RT-qPCR protocol suitable for all respiratory materials.

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Significant correlation of Ct values between direct and RNA RT-qPCR.

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High SARS-CoV-2 detection rate by direct RT-qPCR of 95.8 % for Ct values <35.

Background

Fast and reliable detection of SARS-CoV-2 is crucial for efficient control of the COVID-19 pandemic. Due to the high demand for SARS-CoV-2 testing there is a worldwide shortage of RNA extraction reagents. Therefore, extraction-free RT-qPCR protocols are urgently needed.

Objectives

To establish a rapid RT-qPCR protocol for the detection of SARS-CoV-2 without the need of RNA extraction suitable for all respiratory materials.

Material and methods

Different SARS-CoV-2 positive respiratory materials from our routine laboratory were used as crude material after heat inactivation in direct RT-qPCR with the PrimeDirect™ Probe RT-qPCR Mix (TaKaRa). SARS-CoV-2 was detected using novel primers targeted to the E-gene.

Results

The protocol for the detection of SARS-CoV-2 in crude material used a prepared frozen-PCR mix with optimized primers and 5 μl of fresh, undiluted and pre-analytically heat inactivated respiratory material. For validation, 91 respiratory samples were analyzed in direct comparison to classical RNA-based RT-qPCR. Overall 81.3 % of the samples were detected in both assays with a strong correlation between both Ct values (r = 0.8492, p < 0.0001). The SARS-CoV-2 detection rate by direct RT-qPCR was 95.8 % for Ct values <35. All negative samples were characterized by low viral loads (Ct >35) and/or long storage times before sample processing.

Conclusion

Direct RT-qPCR is a suitable alternative to classical RNA RT-qPCR, provided that only fresh samples (storage <1 week) are used. RNA extraction should be considered if samples have longer storage times or if PCR inhibition is observed. In summary, this protocol is fast, inexpensive and suitable for all respiratory materials.