Skip to content
naulon

No retraction, correction or concern found when last checked on Oct 29, 2026.

An enhanced isothermal amplification assay for viral detection

Jason Qian, Sarah A. Boswell, Christopher Chidley and 8 more

Nature Communications · 2020 · CC BY

doi:10.1038/s41467-020-19258-y

Abstract

Rapid, inexpensive, robust diagnostics are essential to control the spread of infectious diseases. Current state of the art diagnostics are highly sensitive and specific, but slow, and require expensive equipment. Here we report the development of a molecular diagnostic test for SARS-CoV-2 based on an enhanced recombinase polymerase amplification (eRPA) reaction. eRPA has a detection limit on patient samples down to 5 viral copies, requires minimal instrumentation, and is highly scalable and inexpensive. eRPA does not cross-react with other common coronaviruses, does not require RNA purification, and takes ~45 min from sample collection to results. eRPA represents a first step toward at-home SARS-CoV-2 detection and can be adapted to future viruses within days of genomic sequence availability.

References 38

  1. 1.

    Dong E, Du H, Gardner L. An interactive web-based dashboard to track COVID-19 in real time. Lancet Infect. Dis. 2020;20:533-534.

    Not in our library10.1016/s1473-3099(20)30120-1

  2. 2.

    Park, A. Dr. Anthony Fauci “not overly confident” with U.S. COVID-19 testing capabilities. time.comanthony-fauci-covid–testing-capabilities. Accessed 24 May 2020.

    Not in our library

  3. 3.

    Temple, J. Why contact tracing may be a mess in America. Accessed 24 May 2020.

    Not in our library

  4. 4.

    Vogels, C. B. F. et al. SalivaDirect: A simplified and flexible platform to enhance SARS-CoV-2 testing capacity. medRxiv. 10.1101/2020.08.03.20167791 (2020).

    Not in our library10.1016/j.medj.2020.12.010

  5. 5.

    Srivatsan, S. et al. Preliminary support for a ‘dry swab, extraction free’ protocol for SARS-CoV-2 testing via RT-qPCR. bioRxiv10.1101/2020.04.22.056283 (2020).

    Not in our library

  6. 6.

    Beltrán-Pavez, C. et al. SARS-CoV-2 detection from nasopharyngeal swab samples without RNA extraction. bioRxiv10.1101/2020.03.28.013508 (2020).

    Not in our library

  7. 7.

    Wee, S. K., Sivalingam, S. P. & Yap, E. P. H. Rapid direct nucleic acid amplification test without RNA extraction for SARS-CoV-2 using a portable PCR thermocycler. bioRxiv10.1101/2020.04.17.042366 (2020).

    Not in our library10.3390/genes11060664

  8. 8.

    Yelin, I. et al. Evaluation of COVID-19 RT-qPCR test in multi-sample pools. medRxiv10.1101/2020.03.26.20039438 (2020).

    Not in our library10.1093/cid/ciaa531

  9. 9.

    Booeshaghi, A. S. et al. Fast and accurate diagnostics from highly multiplexed sequencing assays. medRxiv10.1101/2020.05.13.20100131 (2020).

    Not in our library10.1038/s41598-020-78942-7

  10. 10.

    Obande GA, Banga Singh KK. Current and future perspectives on isothermal nucleic acid amplification technologies for diagnosing infections. Infect. Drug Resist. 2020;13:455-483.

    Not in our library10.2147/idr.s217571

  11. 11.
  12. 12.
  13. 13.

    Notomi T, et al. Loop-mediated isothermal amplification of DNA. Nucleic Acids Res. 2000;28:63e-63e.

    Not in our library10.1093/nar/28.12.e63

  14. 14.
  15. 15.

    Zhang, Y. et al. Rapid molecular detection of SARS-CoV-2 (COVID-19) virus RNA using colorimetric LAMP. medRxiv10.1101/2020.02.26.20028373 (2020).

    Not in our library

  16. 16.

    Bhadra, S., Riedel, T. E., Lakhotia, S., Tran, N. D. & Ellington, A. D. High-surety isothermal amplification and detection of SARS-CoV-2, including with crude enzymes. bioRxiv10.1101/2020.04.13.039941 (2020).

    Not in our library10.1128/msphere.00911-20

  17. 17.

    Broughton JP, et al. CRISPR–Cas12-based detection of SARS-CoV-2. Nat. Biotechnol. 2020;38:870-874.

    Not in our library10.1038/s41587-020-0513-4

  18. 18.

    Joung, J. et al. Point-of-care testing for COVID-19 using SHERLOCK diagnostics. medRxiv10.1101/2020.05.04.20091231 (2020).

    Not in our library

  19. 19.

    Zhang, F., Abudayyeh, O. O. & Gootenberg, J. S. A protocol for detection of COVID-19 using CRISPR diagnostics. https://static1.squarespace.com/static/5b7c640be2ccd1703a3da4d3/t/5e7773f40df723159b16f262/1584886772519/COVID-19+detection+%28v.20200321%29.pdf (2020).

    Not in our library

  20. 20.

    Qian J, et al. Barcoded microbial system for high-resolution object provenance. Science. 2020;368:1135-1140.

    Not in our library10.1126/science.aba5584

  21. 21.

    Zucha D, Androvic P, Kubista M, Valihrach L. Performance comparison of reverse transcriptases for single-cell studies. Clin. Chem. 2019;66:217-228.

    Not in our library10.1373/clinchem.2019.307835

  22. 22.

    Koczula KM, Gallotta A. Lateral flow assays. Essays Biochem. 2016;60:111-120.

    Not in our library10.1042/ebc20150012

  23. 23.

    Ruano G, Pagliaro EM, Schwartz TR, Lamy K. Heat-soaked PCR: an efficient method for DNA amplification with applications to forensic analysis. Biotechniques. 1992;13:266-274.

    Not in our library

  24. 24.

    Myhrvold C, et al. Field-deployable viral diagnostics using CRISPR-Cas13. Science. 2018;360:444-448.

    Not in our library10.1126/science.aas8836

  25. 25.

    Chin, A. et al. Stability of SARS-CoV-2 in different environmental conditions. medRxiv10.1101/2020.03.15.20036673 (2020).

    Not in our library

  26. 26.

    Pasloske, B. L. & Wu, W. Method and reagents for inactivating ribonucleases RNase A, RNase I and RNase T1. Google Patents 6,777,210 (2004).

    Not in our library

  27. 27.

    He X, et al. Temporal dynamics in viral shedding and transmissibility of COVID-19. Nat. Med. 2020;26:672-675.

    Not in our library10.1038/s41591-020-0869-5

  28. 28.

    Zheng, S. et al. Viral load dynamics and disease severity in patients infected with SARS-CoV-2 in Zhejiang province, China, January–March 2020: retrospective cohort study. BMJ369, m1443 (2020).

    Not in our library10.1136/bmj.m1443

  29. 29.

    Pan Y, Zhang D, Yang P, Poon LLM, Wang Q. Viral load of SARS-CoV-2 in clinical samples. Lancet Infect. Dis. 2020;20:411-412.

    Not in our library10.1016/s1473-3099(20)30113-4

  30. 30.
  31. 31.

    Pasomsub, E. et al. Saliva sample as a non-invasive specimen for the diagnosis of coronavirus disease-2019 (COVID-19): a cross-sectional study. Clin. Microbiol. Infect.10.1016/j.cmi.2020.05.001 (2020).

    Not in our library10.1016/j.cmi.2020.05.001

  32. 32.

    Hasan, H. R. & Al-Issa, Y. A. A study of Rnase enzymes in saliva samples from women with breast tumors. Med. J. Islamic World Acad. Sci.19, 21–26 (2011).

    Not in our library

  33. 33.

    Acquier AB, et al. Comparison of salivary levels of mucin and amylase and their relation with clinical parameters obtained from patients with aggressive and chronic periodontal disease. J. Appl. Oral. Sci. 2015;23:288-294.

    Not in our library10.1590/1678-775720140458

  34. 34.

    Wyllie, A. L. et al. Saliva is more sensitive for SARS-CoV-2 detection in COVID-19 patients than nasopharyngeal swabs. medRxiv10.1101/2020.04.16.20067835 (2020).

    Not in our library

  35. 35.

    Seol J-H, et al. Different roles of histone H3 lysine 4 methylation in chromatin maintenance. Biochem. Biophys. Res. Commun. 2006;349:463-470.

    Not in our library10.1016/j.bbrc.2006.08.122

  36. 36.
  37. 37.
  38. 38.

    Wölfel R, et al. Virological assessment of hospitalized patients with COVID-2019. Nature. 2020;581:465-469.

    Not in our library10.1038/s41586-020-2196-x

Cited by papers we hold 3

Reads

Read by people on this page

None yet.

Checked or read by AI through naulon

None yet.

A person counts once a day per paper. We keep no cookie and no address: a reader is a hash that changes every day. Any month under five reads shows no number.

Are you an author?

Is this your paper?

Claim it to add your note and be paid when agents cite it. Free.