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Meta-Analysis
. 2024 Oct 14;10(10):CD015618.
doi: 10.1002/14651858.CD015618.

Laboratory-based molecular test alternatives to RT-PCR for the diagnosis of SARS-CoV-2 infection

Ingrid Arevalo-Rodriguez  1   2 , Miriam Mateos-Haro  3   4 , Jacqueline Dinnes  5   6 , Agustín Ciapponi  7 , Clare Davenport  5   6 , Diana Buitrago-Garcia  8   9 , Tayeb Bennouna-Dalero  10 , Marta Roqué-Figuls  11 , Ann Van den Bruel  12 , Karin J von Eije  13 , Devy Emperador  14 , Lotty Hooft  15 , René Spijker  15 , Mariska Mg Leeflang  16 , Yemisi Takwoingi  5   6 , Jonathan J Deeks  5   6
Affiliations
Meta-Analysis

Laboratory-based molecular test alternatives to RT-PCR for the diagnosis of SARS-CoV-2 infection

Ingrid Arevalo-Rodriguez et al. Cochrane Database Syst Rev. .

Abstract

Background: Diagnosing people with a SARS-CoV-2 infection played a critical role in managing the COVID-19 pandemic and remains a priority for the transition to long-term management of COVID-19. Initial shortages of extraction and reverse transcription polymerase chain reaction (RT-PCR) reagents impaired the desired upscaling of testing in many countries, which led to the search for alternatives to RNA extraction/purification and RT-PCR testing. Reference standard methods for diagnosing the presence of SARS-CoV-2 infection rely primarily on real-time reverse transcription-polymerase chain reaction (RT-PCR). Alternatives to RT-PCR could, if sufficiently accurate, have a positive impact by expanding the range of diagnostic tools available for the timely identification of people infected by SARS-CoV-2, access to testing and the use of resources.

Objectives: To assess the diagnostic accuracy of alternative (to RT-PCR assays) laboratory-based molecular tests for diagnosing SARS-CoV-2 infection.

Search methods: We searched the COVID-19 Open Access Project living evidence database from the University of Bern until 30 September 2020 and the WHO COVID-19 Research Database until 31 October 2022. We did not apply language restrictions.

Selection criteria: We included studies of people with suspected or known SARS-CoV-2 infection, or where tests were used to screen for infection, and studies evaluating commercially developed laboratory-based molecular tests for the diagnosis of SARS-CoV-2 infection considered as alternatives to RT-PCR testing. We also included all reference standards to define the presence or absence of SARS-CoV-2, including RT-PCR tests and established clinical diagnostic criteria.

Data collection and analysis: Two authors independently screened studies and resolved disagreements by discussing them with a third author. Two authors independently extracted data and assessed the risk of bias and applicability of the studies using the QUADAS-2 tool. We presented sensitivity and specificity, with 95% confidence intervals (CIs), for each test using paired forest plots and summarised results using average sensitivity and specificity using a bivariate random-effects meta-analysis. We illustrated the findings per index test category and assay brand compared to the WHO's acceptable sensitivity and specificity threshold for diagnosing SARS-CoV-2 infection using nucleic acid tests.

Main results: We included data from 64 studies reporting 94 cohorts of participants and 105 index test evaluations, with 74,753 samples and 7517 confirmed SARS-CoV-2 cases. We did not identify any published or preprint reports of accuracy for a considerable number of commercially produced NAAT assays. Most cohorts were judged at unclear or high risk of bias in more than three QUADAS-2 domains. Around half of the cohorts were considered at high risk of selection bias because of recruitment based on COVID status. Three quarters of 94 cohorts were at high risk of bias in the reference standard domain because of reliance on a single RT-PCR result to determine the absence of SARS-CoV-2 infection or were at unclear risk of bias due to a lack of clarity about the time interval between the index test assessment and the reference standard, the number of missing results, or the absence of a participant flow diagram. For index tests categories with four or more evaluations and when summary estimations were possible, we found that: a) For RT-PCR assays designed to omit/adapt RNA extraction/purification, the average sensitivity was 95.1% (95% CI 91.1% to 97.3%), and the average specificity was 99.7% (95% CI 98.5% to 99.9%; based on 27 evaluations, 2834 samples and 1178 SARS-CoV-2 cases); b) For RT-LAMP assays, the average sensitivity was 88.4% (95% CI 83.1% to 92.2%), and the average specificity was 99.7% (95% CI 98.7% to 99.9%; 24 evaluations, 29,496 samples and 2255 SARS-CoV-2 cases); c) for TMA assays, the average sensitivity was 97.6% (95% CI 95.2% to 98.8%), and the average specificity was 99.4% (95% CI 94.9% to 99.9%; 14 evaluations, 2196 samples and 942 SARS-CoV-2 cases); d) for digital PCR assays, the average sensitivity was 98.5% (95% CI 95.2% to 99.5%), and the average specificity was 91.4% (95% CI 60.4% to 98.7%; five evaluations, 703 samples and 354 SARS-CoV-2 cases); e) for RT-LAMP assays omitting/adapting RNA extraction, the average sensitivity was 73.1% (95% CI 58.4% to 84%), and the average specificity was 100% (95% CI 98% to 100%; 24 evaluations, 14,342 samples and 1502 SARS-CoV-2 cases). Only two index test categories fulfil the WHO-acceptable sensitivity and specificity requirements for SARS-CoV-2 nucleic acid tests: RT-PCR assays designed to omit/adapt RNA extraction/purification and TMA assays. In addition, WHO-acceptable performance criteria were met for two assays out of 35 when tests were used according to manufacturer instructions. At 5% prevalence using a cohort of 1000 people suspected of SARS-CoV-2 infection, the positive predictive value of RT-PCR assays omitting/adapting RNA extraction/purification will be 94%, with three in 51 positive results being false positives, and around two missed cases. For TMA assays, the positive predictive value of RT-PCR assays will be 89%, with 6 in 55 positive results being false positives, and around one missed case.

Authors' conclusions: Alternative laboratory-based molecular tests aim to enhance testing capacity in different ways, such as reducing the time, steps and resources needed to obtain valid results. Several index test technologies with these potential advantages have not been evaluated or have been assessed by only a few studies of limited methodological quality, so the performance of these kits was undetermined. Only two index test categories with enough evaluations for meta-analysis fulfil the WHO set of acceptable accuracy standards for SARS-CoV-2 nucleic acid tests: RT-PCR assays designed to omit/adapt RNA extraction/purification and TMA assays. These assays might prove to be suitable alternatives to RT-PCR for identifying people infected by SARS-CoV-2, especially when the alternative would be not having access to testing. However, these findings need to be interpreted and used with caution because of several limitations in the evidence, including reliance on retrospective samples without information about the symptom status of participants and the timing of assessment. No extrapolation of found accuracy data for these two alternatives to any test brands using the same techniques can be made as, for both groups, one test brand with high accuracy was overrepresented with 21/26 and 12/14 included studies, respectively. Although we used a comprehensive search and had broad eligibility criteria to include a wide range of tests that could be alternatives to RT-PCR methods, further research is needed to assess the performance of alternative COVID-19 tests and their role in pandemic management.

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Conflict of interest statement

Ingrid Arevalo‐Rodriguez: IAR has been an employee of the Cochrane Central Executive Team (Cochrane Response/Evidence, Production & Methods Directorate) since 2021.

Miriam Mateos: none known.

Jacqueline Dinnes: none known.

Clare Davenport: none known.

Agustin Ciapponi: none known.

Diana Buitrago‐Garcia: none known.

Tayeb Bennouna Dalero: none known.

Marta Roque‐Figuls: none known.

Ann Van den Bruel: none known.

Karin Jasmijn von Eije: KVE worked as a staff member till mid‐January 2021 for WHO; in that capacity, she has been involved in guidance on SARS‐CoV‐2 diagnostics. After that, she worked as a clinical virologist at the UMCG in Groningen and, in that capacity, was not directly involved in activities of WHO regarding guidance on molecular diagnostics for SARS‐CoV‐2; her contracted work did include work focused on the WHO SARS‐CoV‐2 laboratory network until August 2023. Since September 2023, she has worked at the Erasmus MC, University Medical Center, as a clinical virologist and has continued to perform contracted work, but not on WHO guidance on clinical molecular diagnostics for SARS‐CoV‐2 or the WHO SARS‐CoV‐2 laboratory network.

Devy Emperador: DE is employed by FIND with funding from DFID and KFW. FIND is a global non‐for‐profit product development partnership and WHO Diagnostic Collaboration Centre. It is FIND's role to accelerate access to high‐quality diagnostic tools for low‐resource settings, and this is achieved by supporting both R&D and access activities for a wide range of diseases, including COVID‐19. FIND has several clinical research projects to evaluate multiple new diagnostic tests against published Target Product Profiles that have been defined through consensus processes. These studies are for diagnostic products developed by private sector companies who provide access to know‐how, equipment/reagents, and contribute through unrestricted donations as per FIND policy and external SAC review.

Lotty Hooft: none known.

Mariska MG Leeflang: none known.

René Spijker: the Dutch Cochrane Centre (DCC) has received grants for performing commissioned systematic reviews. The commissioner did not have any influence on the results of this work.

Yemisi Takwoingi: none known.

Jonathan J Deeks: JD has published or been quoted in opinion pieces in scientific publications, and in the mainstream and social media related to diagnostic testing. JD is a member of the Royal Statistical Society (RSS) COVID‐19 task force steering group and co‐chair of the RSS Diagnostic Test Advisory Group. He is a consultant adviser to the WHO Essential Diagnostic List. JD receives payment from the BMJ as their Chief Statistical advisor.

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References

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Fowler 2020 (b) {published data only}
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    1. Fowler VL, Armson B, Gonzales JL, Wise EL, Howson ELA, Vincent-Mistiaen Z, et al. A reverse-transcription loop-mediated isothermal amplification (RT-LAMP) assay for the rapid detection of SARS-CoV-2 within nasopharyngeal and oropharyngeal swabs at Hampshire Hospitals NHS Foundation Trust. medRxiv [Preprint] 2020;NA:1-30. [DOI: 10.1101/2020.06.30.20142935] - DOI
Fowler 2020 (c) {published data only}
    1. Fowler VL, Armson B, Gonzales JL, Wise EL, Howson ELA, Vincent-Mistiaen Z, et al. A highly effective reverse-transcription loop-mediated isothermal amplification (RT-LAMP) assay for the rapid detection of SARS-CoV-2 infection. Journal of Infection 2021;82(1):117-25. [DOI: 10.1016/j.jinf.2020.10.039] [PMID: ] - DOI - PMC - PubMed
    1. Fowler VL, Armson B, Gonzales JL, Wise EL, Howson ELA, Vincent-Mistiaen Z, et al. A reverse-transcription loop-mediated isothermal amplification (RT-LAMP) assay for the rapid detection of SARS-CoV-2 within nasopharyngeal and oropharyngeal swabs at Hampshire Hospitals NHS Foundation Trust. medRxiv [Preprint] 2020;NA:1-30. [DOI: 10.1101/2020.06.30.20142935] - DOI
Freedman 2022 {published data only}
    1. Freedman SB, Oberding LK, Kim K, Xie J, Berenger BM, Goulden R, et al. SARS-CoV-2 viral load quantification, clinical findings and outcomes in children seeking Emergency Department care: prospective cohort study. Pediatric Infectious Disease Journal 2022;41(7):566-9. [PMID: ] - PMC - PubMed
Freire‐Paspuel 2021 {published data only}
    1. Freire-Paspuel B, Garcia-Bereguiain MA. Low clinical performance of the Isopollo COVID-19 detection kit (M Monitor, South Korea) for RT-LAMP SARS-CoV-2 diagnosis: a call for action against low quality products for developing countries. International Journal of Infectious Diseases 2021;104:303-5. [PMID: ] - PMC - PubMed
Ghosh 2022 {published data only}
    1. Ghosh P, Chowdhury R, Hossain ME, Hossain F, Miah M, Rashid MU, et al. Evaluation of recombinase-based isothermal amplification assays for point-of-need detection of SARS-CoV-2 in resource-limited settings. International Journal of Infectious Diseases 2022;114:105-11. [PMID: ] - PMC - PubMed
Gorzalski 2020 {published data only}
    1. Gorzalski AJ, Tian H, Laverdure C, Morzunov S, Verma SC, VanHooser S, et al. High-throughput transcription-mediated amplification on the Hologic Panther is a highly sensitive method of detection for SARS-CoV-2. Journal of Clinical Virology 2020;129:104501. [PMID: ] - PMC - PubMed
Higashimoto 2020 {published data only}
    1. Higashimoto Y, Ihira M, Kawamura Y, Inaba M, Shirato K, Suzuki T, et al. Dry loop-mediated isothermal amplification assay for detection of SARS-CoV-2 from clinical specimens. Fujita Medical Journal 2023;9(2):84-9. [DOI: ] - PMC - PubMed
    1. Higashimoto Y, Masaru I, Yoshiki K, Masato I, Kazuya S, Tadaki S, et al. Dry loop mediated isothermal amplification assay for detection of SARS-CoV-2 from clinical specimens. medRxiv [Preprint] 2020;NA:1-26. [DOI: 10.1101/2020.09.29.20204297] - DOI - PMC - PubMed
Jerbi 2022 {published data only}
    1. Jerbi L, Azrad M, Peretz A. Evaluation of factors that affect the performance of COVID-19 molecular assays including presence of symptoms, number of detected genes and RNA extraction type. Molecular Diagnosis & Therapy 2022;26(2):229-38. [PMID: ] - PMC - PubMed
Kanwar 2021 {published data only}
    1. Kanwar N, Banerjee D, Sasidharan A, Abdulhamid A, Larson M, Lee B, et al. Comparison of diagnostic performance of five molecular assays for detection of SARS-CoV-2. Diagnostic Microbiology and Infectious Disease 2021;101(4):115518. [PMID: ] - PMC - PubMed
Kidd 2021 (a) {published data only}
    1. Kidd SP, Burns D, Armson B, Beggs AD, Howson ELA, Williams A, et al. Reverse-transcription loop-mediated isothermal amplification has high accuracy for detecting severe acute respiratory syndrome Coronavirus 2 in saliva and nasopharyngeal/oropharyngeal swabs from asymptomatic and symptomatic individuals. Journal of Molecular Diagnostics 2022;24(4):320-36. [PMID: ] - PMC - PubMed
Kidd 2021 (b) {published data only}
    1. Kidd SP, Burns D, Armson B, Beggs AD, Howson ELA, Williams A, et al. Reverse-transcription loop-mediated isothermal amplification has high accuracy for detecting severe acute respiratory syndrome Coronavirus 2 in saliva and nasopharyngeal/oropharyngeal swabs from asymptomatic and symptomatic individuals. Journal of Molecular Diagnostics 2022;24(4):320-36. [PMID: ] - PMC - PubMed
Kidd 2021 (c) {published data only}
    1. Kidd SP, Burns D, Armson B, Beggs AD, Howson ELA, Williams A, et al. Reverse-transcription loop-mediated isothermal amplification has high accuracy for detecting severe acute respiratory syndrome Coronavirus 2 in saliva and nasopharyngeal/oropharyngeal swabs from asymptomatic and symptomatic individuals. Journal of Molecular Diagnostics 2022;24(4):320-36. [PMID: ] - PMC - PubMed
Kidd 2021 (d) {published data only}
    1. Kidd SP, Burns D, Armson B, Beggs AD, Howson ELA, Williams A, et al. Reverse-transcription loop-mediated isothermal amplification has high accuracy for detecting severe acute respiratory syndrome Coronavirus 2 in saliva and nasopharyngeal/oropharyngeal swabs from asymptomatic and symptomatic individuals. Journal of Molecular Diagnostics 2022;24(4):320-36. [PMID: ] - PMC - PubMed
Kim 2021 {published data only}
    1. Kim KB, Choi H, Lee GD, Lee J, Lee S, Kim Y, et al. Analytical and clinical performance of Droplet Digital PCR in the detection and quantification of SARS-CoV-2. Molecular Diagnosis & Therapy 2021;25(5):617-28. [PMID: ] - PMC - PubMed
Kitagawa 2020 {published data only}
    1. Kitagawa Y, Orihara Y, Kawamura R, Imai K, Sakai J, Tarumoto N, et al. Evaluation of rapid diagnosis of novel coronavirus disease (COVID-19) using loop-mediated isothermal amplification. Journal of Clinical Virology 2020;58(9):e01438-20. [PMID: ] - PMC - PubMed
Kitajima 2021 (a) {published data only}
    1. Kitajima H, Tamura Y, Yoshida H, Kinoshita H, Katsuta H, Matsui C, et al. Clinical COVID-19 diagnostic methods: comparison of reverse transcription loop-mediated isothermal amplification (RT-LAMP) and quantitative RT-PCR (qRT-PCR). Journal of Clinical Virology 2021;139:104813. [PMID: ] - PMC - PubMed
Kitajima 2021 (b) {published data only}
    1. Kitajima H, Tamura Y, Yoshida H, Kinoshita H, Katsuta H, Matsui C, et al. Clinical COVID-19 diagnostic methods: comparison of reverse transcription loop-mediated isothermal amplification (RT-LAMP) and quantitative RT-PCR (qRT-PCR). Journal of Clinical Virology 2021;139:104813. [PMID: ] - PMC - PubMed
Kuo 2021 {published data only}
    1. Kuo P, Realegeno S, Pride DT. Comparison of two nucleic acid amplification tests (NAATs) and two antigen tests for detection of SARS-CoV-2 from upper respiratory specimens. Journal of Clinical Virology Plus 2021;1(1):100011. [PMID: ] - PMC - PubMed
Kušnierová 2021 {published data only}
    1. Kušnierová P, Stejskal D, Švagera Z, Slepčanová H, Malurová M, Špulerová Z, et al. Comparison of two analytical methods for SARS-CoV-2 determination, RT-PCR vs. reverse transcription and loop-mediated isothermal amplification (RT-LAMP). Klinicka Biochemie a Metabolismus 2021;29(3):151-5. [EMBASE: covidwho-1820639]
LeGoff 2021 (a) {published data only}
    1. LeGoff J, Kernéis S, Elie C, Mercier-Delarue S, Gastli N, Choupeaux L, et al. Evaluation of a saliva molecular point of care for the detection of SARS-CoV-2 in ambulatory care. Scientific Reports 2021;11(1):21126. [PMID: ] - PMC - PubMed
LeGoff 2021 (b) {published data only}
    1. LeGoff J, Kernéis S, Elie C, Mercier-Delarue S, Gastli N, Choupeaux L, et al. Evaluation of a saliva molecular point of care for the detection of SARS-CoV-2 in ambulatory care. Scientific Reports 2021;11(1):21126. [PMID: ] - PMC - PubMed
Lephart 2021 {published data only}
    1. Lephart PR, Bachman MA, LeBar W, McClellan S, Barron K, Schroeder L, et al. Comparative study of four SARS-CoV-2 Nucleic Acid Amplification Test (NAAT) platforms demonstrates that ID NOW performance is impaired substantially by patient and specimen type. Diagnostic Microbiology and Infectious Disease 2021;99(1):115200. [PMID: ] - PMC - PubMed
Li 2022 {published data only}
    1. Li Z, Bruce JL, Cohen B, Cunningham CV, Jack WE, Kunin K, et al. Development and implementation of a simple and rapid extraction-free saliva SARS-CoV-2 RT-LAMP workflow for workplace surveillance. PLoS One 2022;17(5):e0268692. [PMID: ] - PMC - PubMed
Lieberman 2020 {published data only}
    1. Lieberman JA, Pepper G, Naccache SN, Huang ML, Jerome KR, Greninger AL. Comparison of commercially available and laboratory-developed assays for in vitro detection of SARS-CoV-2 in clinical laboratories. Journal of Clinical Microbiology 2020;58(8):e00821-20. [PMID: ] - PMC - PubMed
Lima 2020 {published data only}
    1. Lima A, Healer V, Vendrone E, Silbert S. Validation and comparison of a modified CDC assay with two commercially available assays for the detection of SARS-CoV-2 in respiratory specimen. bioRxiv [Preprint] 2020;NA:1-24. [DOI: 10.1101/2020.06.29.179192] - DOI - PMC - PubMed
    1. Lima A, Healer V, Vendrone E, Silbert S. Validation of a modified CDC assay and performance comparison with the NeuMoDx™ and DiaSorin® automated assays for rapid detection of SARS-CoV-2 in respiratory specimens. Journal Clinical Virology 2020;133:104688. [PMID: ] - PMC - PubMed
Liotti 2020 {published data only}
    1. Liotti FM, Menchinelli G, Marchetti S, Morandotti GA, Sanguinetti M, Posteraro B, et al. Evaluation of three commercial assays for SARS-CoV-2 molecular detection in upper respiratory tract samples. European Journal of Clinical Microbiology and Infectious Diseases 2021;40(2):269-77. [PMID: ] - PMC - PubMed
Marino 2022 {published data only}
    1. Marino FE, Proffitt E, Joseph E, Manoharan A. A rapid, specific, extraction-less, and cost-effective RT-LAMP test for the detection of SARS-CoV-2 in clinical specimens. PLoS One 2022;17(4):e0266703. [PMID: ] - PMC - PubMed
Milosevic 2022 {published data only}
    1. Milosevic D, Moyer AM, Majumdar R, Kipp BR, Yao JD. A reverse-transcription droplet digital PCR assay to detect and quantify SARS-CoV-2 RNA in upper respiratory tract specimens. Journal of Clinical Virology 2022;153:105216. [PMID: ] - PMC - PubMed
Mizoguchi 2021 [A] {published data only}
    1. Mizoguchi M, Harada S, Okamoto K, Higurashi Y, Ikeda M, Moriya K. Comparative performance and cycle threshold values of 10 nucleic acid amplification tests for SARS-CoV-2 on clinical samples. PLoS One 2021;16(6):e0252757. [PMID: ] - PMC - PubMed
Mizoguchi 2021 [B] {published data only}
    1. Mizoguchi M, Harada S, Okamoto K, Higurashi Y, Ikeda M, Moriya K. Comparative performance and cycle threshold values of 10 nucleic acid amplification tests for SARS-CoV-2 on clinical samples. PLoS One 2021;16:e0252757. [PMID: ] - PMC - PubMed
Mizoguchi 2021 [C] {published data only}
    1. Mizoguchi M, Harada S, Okamoto K, Higurashi Y, Ikeda M, Moriya K. Comparative performance and cycle threshold values of 10 nucleic acid amplification tests for SARS-CoV-2 on clinical samples. PLoS One 2021;16(6):e0252757. [PMID: ] - PMC - PubMed
Mizoguchi 2021 [D] {published data only}
    1. Mizoguchi M, Harada S, Okamoto K, Higurashi Y, Ikeda M, Moriya K. Comparative performance and cycle threshold values of 10 nucleic acid amplification tests for SARS-CoV-2 on clinical samples. PLoS One 2021;16(6):e0252757. [PMID: ] - PMC - PubMed
Ogawa 2023 {published data only}
    1. Ogawa M, Sato M, Yamakami A, Hayasaka Y, Saya Y, Une K, et al. Diagnostic test property of transcription-reverse transcription concerted reaction reagent TRCReady® SARS-CoV-2 i using nasopharyngeal swab samples. Journal of Infection and Chemotherapy 2023;29(1):115-7. [PMID: ] - PMC - PubMed
Österdahl 2020 {published data only}
    1. Österdahl MF, Lee KA, Lochlainn MN, Wilson S, Douthwaite S, Horsfall R, et al. Detecting SARS-CoV-2 at point of care: preliminary data comparing loop-mediated isothermal amplification (LAMP) to polymerase chain reaction (PCR). BMC Infectious Diseases 2020;20(1):783. [PMID: ] - PMC - PubMed
    1. Österdahl MF, Lee KA, Ni Lochlainn M, Wilson S, Douthwaite S, Horsfall R, et al. Detecting SARS-CoV-2 at point of care: preliminary data comparing Loop-mediated isothermal amplification (LAMP) to PCR. medRxiv 2020;NA:1-9. [DOI: 10.1101/2020.04.01.20047357] - DOI - PMC - PubMed
Peto 2020 {published data only}
    1. Peto L, Rodger G, Carter DP, Osman KL, Yavuz M, Johnson K, et al. Diagnosis of SARS-CoV-2 infection with LamPORE, a high-throughput platform combining loop-mediated isothermal amplification and nanopore sequencing. Journal of Clinical Microbiology 2021;59(6):e03271-20. [PMID: ] - PMC - PubMed
    1. Peto L, Rodger G, Carter DP, Osman KL, Yavuz M, Johnson K, et al. Diagnosis of SARS-CoV-2 infection with LamPORE, a high-throughput platform combining loop-mediated isothermal amplification and nanopore sequencing. medRxiv 2020;NA:1-23. [DOI: 10.1101/2020.09.18.20195370] - DOI - PMC - PubMed
Pham 2020 {published data only}
    1. Pham J, Meyer S, Nguyen C, Williams A, Hunsicker M, McHardy I, et al. Performance characteristics of a high-throughput automated transcription-mediated amplification test for SARS-CoV-2 detection. Journal Clinical Microbiology 2020;58(10):e01669-20. [PMID: ] - PMC - PubMed
Potter 2022 [A] {published data only}
    1. Potter RF, Ransom EM, Wallace MA, Johnson C, Kwon JH, Babcock HM, et al. Multiplatform assessment of saliva for SARS-CoV-2 molecular detection in symptomatic healthcare personnel and patients presenting to the Emergency Department. Journal of Applied Laboratory Medicine 2022;7(3):727-36. [PMID: ] - PMC - PubMed
Potter 2022 [B] {published data only}
    1. Potter RF, Ransom EM, Wallace MA, Johnson C, Kwon JH, Babcock HM, et al. Multiplatform assessment of saliva for SARS-CoV-2 molecular detection in symptomatic healthcare personnel and patients presenting to the Emergency Department. Journal of Applied Laboratory Medicine 2022;7(3):727-36. [PMID: ] - PMC - PubMed
Procop 2021 {published data only}
    1. Procop GW, Brock JE, Reineks EZ, Shrestha NK, Demkowicz R, Cook E, et al. A comparison of five SARS-CoV-2 molecular assays with clinical correlations. American Journal of Clinical Pathology 2021;155(1):69-78. [PMID: ] - PMC - PubMed
Promlek 2022 {published data only}
    1. Promlek T, Thanunchai M, Phumisantiphong U, Hansirisathit T, Phuttanu C, Dongphooyao S, et al. Performance of colorimetric reverse transcription loop-mediated isothermal amplification as a diagnostic tool for SARS-CoV-2 infection during the fourth wave of COVID-19 in Thailand. International Journal of Infectious Diseases 2022;116:133-7. [PMID: ] - PMC - PubMed
Ptasinska 2021 (a) {published data only}
    1. Ptasinska A, Whalley C, Bosworth A, Poxon C, Bryer C, Machin N, et al. Diagnostic accuracy of loop-mediated isothermal amplification coupled to nanopore sequencing (LamPORE) for the detection of SARS-CoV-2 infection at scale in symptomatic and asymptomatic populations. Clinical Microbiology and Infection 2021;27(9):1348.e1-1348.e7. [PMID: ] - PMC - PubMed
Ptasinska 2021 (b) {published data only}
    1. Ptasinska A, Whalley C, Bosworth A, Poxon C, Bryer C, Machin N, et al. Diagnostic accuracy of loop-mediated isothermal amplification coupled to nanopore sequencing (LamPORE) for the detection of SARS-CoV-2 infection at scale in symptomatic and asymptomatic populations. Clinical Microbiology and Infection 2021;27(9):1348.e1-1348.e7. [PMID: ] - PMC - PubMed
Ptasinska 2021 (c) {published data only}
    1. Ptasinska A, Whalley C, Bosworth A, Poxon C, Bryer C, Machin N, et al. Diagnostic accuracy of loop-mediated isothermal amplification coupled to nanopore sequencing (LamPORE) for the detection of SARS-CoV-2 infection at scale in symptomatic and asymptomatic populations. Clinical Microbiology and Infection 2021;27(9):1348.e1-1348.e7. [PMID: ] - PMC - PubMed
Raju 2021 {published data only}
    1. Raju S, Anderson NW, Robinson E, Squires C, Wallace MA, Zhang R, et al. Comparison of 6 SARS-CoV-2 molecular methods and correlation with the cycle threshold distribution in clinical specimens. Journal of Applied Laboratory Medicine 2021;6(6):1452-62. [PMID: ] - PMC - PubMed
Rodel 2020 (a) {published data only}
    1. Rodel J, Egerer R, Suleyman A, Sommer-Schmid B, Baier M, Henke A, et al. Use of the variplex SARS-CoV-2 RT-LAMP as a rapid molecular assay to complement RT-PCR for COVID-19 diagnosis. Journal of Clinical Virology 2020;132:104616. [PMID: ] - PMC - PubMed
Rodel 2020 (b) {published data only}
    1. Rodel J, Egerer R, Suleyman A, Sommer-Schmid B, Baier M, Henke A, et al. Use of the variplex SARS-CoV-2 RT-LAMP as a rapid molecular assay to complement RT-PCR for COVID-19 diagnosis. Journal of Clinical Virology 2020;132:104616. [PMID: ] - PMC - PubMed
Rosenstierne 2021 (a) {published data only}
    1. Rosenstierne MW, Joshi S, Danielsen ET, Webb H, Luong DM, Bjerring J, et al. SARS-CoV-2 detection using reverse transcription strand invasion based amplification and a portable compact size instrument. Scientific Reports 2021;11(1):22214. [PMID: ] - PMC - PubMed
Rosenstierne 2021 (b) {published data only}
    1. Rosenstierne MW, Joshi S, Danielsen ET, Webb H, Luong DM, Bjerring J, et al. SARS-CoV-2 detection using reverse transcription strand invasion based amplification and a portable compact size instrument. Scientific Reports 2021;11(1):22214. [PMID: ] - PMC - PubMed
Rosenstierne 2021 (c) {published data only}
    1. Rosenstierne MW, Joshi S, Danielsen ET, Webb H, Luong DM, Bjerring J, et al. SARS-CoV-2 detection using reverse transcription strand invasion based amplification and a portable compact size instrument. Scientific Reports 2021;11(1):22214. [PMID: ] - PMC - PubMed
Sauleda 2022 {published data only}
    1. Sauleda S, Palacios L, Brès V, Piñana M, Alonso-Hernandez L, Bes M, et al. Clinical evaluation of the Procleix SARS-CoV-2 assay, a sensitive, high-throughput test that runs on an automated system. Diagnostic Microbiology and Infectious Disease 2022;102(1):115560. [PMID: ] - PMC - PubMed
Schneider 2022 (a) {published data only}
    1. Schneider FS, Molina L, Picot MC, L'Helgoualch N, Espeut J, Champigneux P, et al. Performances of rapid and connected salivary RT-LAMP diagnostic test for SARS-CoV-2 infection in ambulatory screening. Scientific Reports 2022;12(1):2843. [PMID: ] - PMC - PubMed
Schneider 2022 (b) {published data only}
    1. Schneider FS, Molina L, Picot MC, L'Helgoualch N, Espeut J, Champigneux P, et al. Performances of rapid and connected salivary RT-LAMP diagnostic test for SARS-CoV-2 infection in ambulatory screening. Scientific Reports 2022;12(1):2843. [PMID: ] - PMC - PubMed
Shin 2022 {published data only}
    1. Shin W, Lee CJ, Lee YM, Choi YB, Mun S, Han K. Rapid identification of SARS-CoV-2 in the point-of-care using digital PCR-based Dr. PCR™ Di20K COVID-19 Detection Kit without viral RNA extraction. Genes & Genomics 2022;44(5):617-28. [PMID: ] - PMC - PubMed
Tanimoto 2022 {published data only}
    1. Tanimoto Y, Mori A, Miyamoto S, Ito E, Arikawa K, Iwamoto T. Comparison of RT-PCR, RT-LAMP, and antigen quantification assays for the detection of SARS-CoV-2. Japanese Journal of Infectious Diseases 2022;75(3):249-53. [PMID: ] - PubMed
Tibbetts 2020 (a) {published data only}
    1. Tibbetts R, Callahan K, Rofoo K, Zarbo RJ, Samuel L. Comparison of the NeuMoDX, Diasorin Simplexa, Cepheid and Roche CDC SARS-CoV 2 EUA assays using nasopharyngeal/nasal swabs in universal transport media (UTM) and sputum and tracheal aspirates. bioRxiv [Preprint] 2020;NA:1-16. [DOI: 10.1101/2020.05.26.118190] - DOI
Tibbetts 2020 (b) {published data only}
    1. Tibbetts R, Callahan K, Rofoo K, Zarbo RJ, Samuel L. Comparison of the NeuMoDX, Diasorin Simplexa, Cepheid and Roche CDC SARS-CoV 2 EUA assays using nasopharyngeal/nasal swabs in universal transport media (UTM) and sputum and tracheal aspirates. bioRxiv [Preprint] 2020;NA:1-16. [DOI: 10.1101/2020.05.26.118190] - DOI
Trémeaux 2020 (a) {published data only}
    1. Trémeaux P, Lhomme S, Abravanel F, Raymond S, Mengelle C, Mansuy JM, et al. Evaluation of the Aptima™ transcription-mediated amplification assay (Hologic®) for detecting SARS-CoV-2 in clinical specimens. Journal of Clinical Virology 2020;129:104541. [PMID: ] - PMC - PubMed
Trémeaux 2020 (b) {published data only}
    1. Trémeaux P, Lhomme S, Abravanel F, Raymond S, Mengelle C, Mansuy JM. Evaluation of the Aptima™ transcription-mediated amplification assay (Hologic®) for detecting SARS-CoV-2 in clinical specimens. Journal of Clinical Virology 2020;129:104541. [PMID: ] - PMC - PubMed
Wanney 2022 {published data only}
    1. Wanney J, Lüsebrink J, Spölgen G, Demuth S, Schildgen V, Schildgen O. Direct comparison of Altona-SARS-CoV-2 dual target RT-qPCR assay with commercial LAMP assay using throat washes in health care staff testing. Journal of Clinical Virology Plus 2022;2(3):100088. [PMID: ] - PMC - PubMed
Watanabe 2022 {published data only}
    1. Watanabe N, Watari T, Otsuka Y. Quality control of loop-mediated isothermal amplification (LAMP) using external control: detection of SARS-CoV-2 using nasopharyngeal specimens. Access Microbiology [Preprint] 2022;NA:1-21. [DOI: 10.1099/acmi.0.000477.v1] - DOI
Xu 2021 {published data only}
    1. Xu J, Kirtek T, Xu Y, Zheng H, Yao H, Ostman E, et al. Digital droplet PCR for SARS-CoV-2 resolves borderline cases. American Journal of Clinical Pathology 2021;155(6):815-22. [PMID: ] - PMC - PubMed
Zhen 2020 {published data only}
    1. Zhen W, Manji R, Smith E, Berry GJ. Comparison of four molecular in vitro diagnostic assays for the detection of SARS-CoV-2 in nasopharyngeal specimens. Journal of Clinical Microbiology 2020;58(8):e00743-20. [PMID: ] - PMC - PubMed

References to studies excluded from this review

Abasiyanik 2021 {published data only}
    1. Abasiyanik MF, Flood B, Lin J, Ozcan S, Rouhani SJ, Pyzer A, et al. Sensitive detection and quantification of SARS-CoV-2 in saliva. Scientific Reports 2021;11(1):12425. [PMID: ] - PMC - PubMed
Akimkin 2022 {published data only}
    1. Akimkin VG, Petrov VV, Krasovitov KV, Borisova NI, Kotov IA, Rodionova EN, et al. Molecular methods for diagnosing novel coronavirus infection: comparison of loop-mediated isothermal amplification and polymerase chain reaction. Voprosy Virusologii 2022;66(6):417-24. [PMID: ] - PubMed
Alekseenko 2021 {published data only}
    1. Alekseenko A, Barrett D, Pareja-Sanchez Y, Howard R, Strandback E, Ampah-Korsah H, et al. Detection of SARS-CoV-2 using non-commercial RT-LAMP regents and raw samples. Scientific Reports 2021;11(1):1820. [PMID: ] - PMC - PubMed
Ali 2020 {published data only}
    1. Ali Z, Aman R, Mahas A, Gundra S, Tehseen M, Marsic T, et al. ISCAN: an RT-LAMP-coupled CRISPR-Cas12 module for rapid, sensitive detection of SARS-CoV-2. Virus Research 2020;288:198129. [PMID: ] - PMC - PubMed
Anahtar 2020 {published data only}
    1. Anahtar MN, McGrath GEG, Rabe BA, Tanner NA, White BA, Lennerz JKM, et al. Clinical assessment and validation of a rapid and sensitive SARS-CoV-2 test using reverse-transcription loop-mediated isothermal amplification. Open Forum Infectious Diseases 2020;8(2):1-9. [PMID: ] - PMC - PubMed
Artik 2022 {published data only}
    1. Artik Y, Coşğun AB, Cesur NP, Hızel N, Uyar Y, Sur H, et al. Comparison of COVID-19 laboratory diagnosis by commercial kits: effectivity of RT-PCR to the RT-LAMP. Journal of Medical Virology 2022;94(5):1998-2007. [PMID: ] - PMC - PubMed
Assennato 2020 {published data only}
    1. Assennato SM, Ritchie AV, Nadala C, Goel N, Tie C, Nadala LM, et al. Performance evaluation of the SAMBA II SARS-CoV-2 test for point-of-care detection of SARS-CoV-2. Journal of Clinical Microbiology 2020;59(1):e01262-20. [PMID: ] - PMC - PubMed
Avetyan 2020 {published data only}
    1. Avetyan D, Chavushyan A, Ghazaryan H, Melkonyan A, Stepanyan A, Zakharyan R, et al. SARS-CoV-2 detection by extraction-free qRT-PCR for massive and rapid COVID-19 diagnosis during a pandemic. medRxiv 2020;NA:1-25. [DOI: 10.1101/2020.09.10.20191189] - DOI - PMC - PubMed
Baba 2021 {published data only}
    1. Baba MM, Bitew M, Fokam J, Lelo EA, Ahidjo A, Asmamaw K, et al. Diagnostic performance of a colorimetric RT -LAMP for the identification of SARS-CoV-2: a multicenter prospective clinical evaluation in sub-Saharan Africa. EClinicalMedicine 2021;40:101101. [PMID: ] - PMC - PubMed
Baek 2020 {published data only}
    1. Baek YH, Um J, Antigua KJC, Park JH, Kim Y, Oh S, et al. Development of a reverse transcription-loop-mediated isothermal amplification as a rapid early-detection method for novel SARS-CoV-2. Emerging Microbes & Infections 2020;9(1):998-1007. [PMID: ] - PMC - PubMed
Behrmann 2020 {published data only}
    1. Behrmann O, Bachmann I, Spiegel M, Schramm M, Abd El Wahed A, Dobler G, et al. Rapid detection of SARS-CoV-2 by low volume real-time single tube reverse transcription recombinase polymerase amplification using an Exo Probe with an internally linked quencher (Exo-IQ). Clinical Chemistry 2020;66(8):1047-54. [PMID: ] - PMC - PubMed
Ben‐Assa 2020 {published data only}
    1. Ben-Assa N, Naddaf R, Gefen T, Capucha T, Hajjo H, Mandelbaum N, et al. Direct on-the-spot detection of SARS-CoV-2 in patients. Experimental Biology and Medicine 2020;245(14):1187-93. [PMID: ] - PMC - PubMed
Bhoyar 2021 {published data only}
    1. Bhoyar RC, Jain A, Sehgal P, Divakar MK, Sharma D, Imran M, et al. High throughput detection and genetic epidemiology of SARS-CoV-2 using COVIDSeq next generation sequencing. PLoS One 2021;16(2):e0247115. [PMID: ] - PMC - PubMed
Bloom 2020 {published data only}
    1. Bloom JS, Jones EM, Gasperini M, Lubock NB, Sathe L, Munugala C, et al. Swab-Seq: a high-throughput platform for massively scaled up SARS-CoV-2 testing. medRxiv 2020;NA:1-58. [DOI: 10.1101/2020.08.04.20167874] - DOI
Buck 2020 {published data only}
    1. Buck MD, Poirier EZ, Cardoso A, Frederico B, Canton J, Barrell S, et al. Standard operating procedures for SARS-CoV-2 detection by a clinical diagnostic RT-LAMP assay. medRxiv 2020;NA:1-28. [PMID: 10.1101/2020.06.29.20142430v1] - DOI - PMC - PubMed
Butler 2020 {published data only}
    1. Butler DJ, Mozsary C, Meydan C, Danko D, Foox J, Rosiene J, et al. Shotgun transcriptome and isothermal profiling of SARS-CoV-2 infection reveals unique host responses, viral diversification, and drug interactions. bioRxiv 2020;NA:1-50. [DOI: 10.1101/2020.04.20.048066] - DOI - PMC - PubMed
Butt 2020 {published data only}
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Cassinari 2021 {published data only}
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Chow 2020 {published data only}
    1. Chow FW, Chan TT, Tam AR, Zhao S, Yao W, Fung J, et al. A rapid, simple, inexpensive, and mobile colorimetric assay COVID-19-LAMP for mass on-site screening of COVID-19. International Journal of Molecular Sciences 2020;21(15):5380. [PMID: ] - PMC - PubMed
Collier 2020 {published data only}
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Dao 2020 {published data only}
    1. Dao Thi VL, Herbst K, Boerner K, Meurer M, Kremer LPM, Kirrmaier D, et al. Screening for SARS-CoV-2 infections with colorimetric RT-LAMP and LAMP sequencing. medRxiv 2020;NA:1-28. [DOI: 10.1101/2020.05.05.20092288] - DOI
Davda 2020 {published data only}
    1. Davda JN, Frank K, Prakash S, Purohit G, Vijayashankar DP, Vedagiri D, et al. An inexpensive RT-PCR endpoint diagnostic assay for SARS-CoV-2 using nested PCR: direct assessment of detection efficiency of RT-qPCR tests and suitability for surveillance. bioRxiv 2020;NA:1-21. [DOI: 10.1101/2020.06.08.139477] - DOI
Deiana 2020 {published data only}
    1. Deiana M, Mori A, Piubelli C, Scarso S, Favarato M, Pomari E. Assessment of the direct quantitation of SARS-CoV-2 by droplet digital PCR. Scientific Reports 2020;10(1):18764. [PMID: ] - PMC - PubMed
De Puig 2021 {published data only}
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Desai 2021 {published data only}
    1. Desai KT, Alfaro K, Mendoza L, Faron M, Mesich B, Maza M, et al. Multisite clinical validation of isothermal amplification-based SARS-CoV-2 detection assays using different sampling strategies. Microbiology Spectrum 2021;9(2):e0084621. [PMID: ] - PMC - PubMed
Dewhurst 2022 {published data only}
    1. Dewhurst RE, Heinrich T, Watt P, Ostergaard P, Marimon JM, Moreira M, et al. Validation of a rapid, saliva-based, and ultra-sensitive SARS-CoV-2 screening system for pandemic-scale infection surveillance. Scientific Reports 2022;12(1):5936. [PMID: ] - PMC - PubMed
Dierks 2021 {published data only}
    1. Dierks S, Bader O, Schwanbeck J, Groß U, Weig MS, Mese K, et al. Diagnosing SARS-CoV-2 with antigen testing, transcription-mediated amplification and real-time PCR. Journal of Clinical Medicine 2021;10(11):2404. [PMID: ] - PMC - PubMed
Dimke 2021 {published data only}
    1. Dimke H, Larsen SL, Skov MN, Larsen H, Hartmeyer GN, Moeller JB. Phenol-chloroform-based RNA purification for detection of SARS-CoV-2 by RT-qPCR: comparison with automated systems. PLoS One 2021;16(2):e0247524. [PMID: ] - PMC - PubMed
Ding 2020 {published data only}
    1. Ding X, Yin K, Li Z, Lalla RV, Ballesteros E, Sfeir MM, et al. Ultrasensitive and visual detection of SARS-CoV-2 using all-in-one dual CRISPR-Cas12a assay. Nature Communications 2020;11(1):4711. [PMID: ] - PMC - PubMed
Donato 2021 {published data only}
    1. Donato LJ, Trivedi VA, Stransky AM, Misra A, Pritt BS, Binnicker MJ, et al. Evaluation of the Cue Health point-of-care COVID-19 (SARS-CoV-2 nucleic acid amplification) test at a community drive through collection center. Diagnostic Microbiology and Infectious Disease 2021;100(1):115307. [PMID: ] - PMC - PubMed
Fasching 2022 {published data only}
    1. Fasching CL, Servellita V, McKay B, Nagesh V, Broughton JP, Sotomayor-Gonzalez A, et al. COVID-19 variant detection with a high-fidelity CRISPR-Cas12 enzyme. Journal of Clinical Microbiology 2022;60(7):e0026122. [PMID: ] - PMC - PubMed
Fernández‐Pittol 2020 {published data only}
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Figueiredo 2022 {published data only}
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Guan 2021 {published data only}
    1. Guan B, Frank KM, Maldonado JO, Beach M, Pelayo E, Warner BM, et al. Sensitive extraction-free SARS-CoV-2 RNA virus detection using a novel RNA preparation method. medRxiv 2021;NA:1-34. [DOI: 10.1101/2021.01.29.21250790] - DOI - PMC - PubMed
Guruceaga 2020 {published data only}
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Haq 2020 {published data only}
    1. Haq F, Sharif S, Khurshid A, Shabbir I, Salman M, Badar N, et al. Development optimization and validation of RT-LAMP based COVID-19 facility in Pakistan. bioRxiv 2020;NA:1-14. [PMID: 10.1101/2020.05.29.124123] - DOI
Hou 2020 {published data only}
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Huang W 2020 {published data only}
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Huang WE 2020 {published data only}
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Huang Z 2020 {published data only}
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Iqbal 2022 {published data only}
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Israeli 2020 {published data only}
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Jacobson 2022 {published data only}
    1. Jacobson M, Hart C, Huen W, Suarez Guardado G, Villanueva A, Whitman J, et al. A rapid nucleic-acid-amplification-test-based, conditional-release-to-work policy for health care personnel with symptoms consistent with COVID-19. Journal of Occupational and Environmental Medicine 2022;65(2):125-7. [PMID: ] - PMC - PubMed
Joung 2020 {published data only}
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Karino 2021 {published data only}
    1. Karino M, Harada M, Yamada C, Fukuoka K, Sugo M, Hanada H, et al. Evaluation of the efficacy of LAMP-based SARS-CoV-2 detection with simple RNA extraction from nasopharyngeal swabs: a prospective observational study. PLoS One 2021;16(12):e0260732. [PMID: ] - PMC - PubMed
Kiran 2020 {published data only}
    1. Kiran U, Gokulan CG, Kuncha SK, Vedagiri D, Tallapaka KB, Mishra RK, et al. Improved and simplified diagnosis of Covid-19 using TE extraction from dry swabs. bioRxiv 2020;NA:1-13. [DOI: 10.1101/2020.05.31.126342] - DOI
Klein 2020 {published data only}
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Kuiper 2020 {published data only}
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Lamb 2020 {published data only}
    1. Lamb LE, Bartolone SN, Ward E, Chancellor MB. Rapid detection of novel coronavirus/Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) by reverse transcription-loop-mediated isothermal amplification. PLoS One 2020;15(6):e0234682. [PMID: ] - PMC - PubMed
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Lee 2020 {published data only}
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Li J 2022 {published data only}
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Liu 2020 {published data only}
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Liu X 2020 {published data only}
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Lu 2020 {published data only}
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Lu 2022 {published data only}
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Malta 2021 {published data only}
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Mancini 2020 {published data only}
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Marchio 2021 {published data only}
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Méndez 2021 {published data only}
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Meza‐Robles 2020 {published data only}
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Michel 2020 {published data only}
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Misra 2022 {published data only}
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Mohon 2020 {published data only}
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Mokhtar 2020 {published data only}
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Moses 2020 {published data only}
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Motohashi 2022 {published data only}
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Naranbat 2022 {published data only}
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Nassir 2020 {published data only}
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Patchsung 2020 {published data only}
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Pierri 2022 {published data only}
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Qian 2020 {published data only}
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Ratcliff 2020 {published data only}
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Rauch 2020 {published data only}
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Rauch 2021 {published data only}
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Rebbapragada 2022 {published data only}
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Rodriguez‐Manzano 2021 {published data only}
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Sahajpal 2020 {published data only}
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Saluzzo 2021 {published data only}
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Schellenberg 2020 {published data only}
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Smyrlaki 2020 {published data only}
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Suo 2020 {published data only}
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Tan 2022 {published data only}
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Van Nguyen 2022 {published data only}
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Van Poelvoorde 2021 {published data only}
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Wang 2020 {published data only}
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Wang J 2020a {published data only}
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Wang J 2020b {published data only}
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Wang M 2020 {published data only}
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Wang X 2020 {published data only}
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Wei F 2020 {published data only}
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Wei S 2021 {published data only}
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Woo 2020 {published data only}
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Wozniak 2020 {published data only}
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References to ongoing studies

ChiCTR2000029810 {unpublished data only}
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CTRI/2021/02/030950 {unpublished data only}
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NCT04510454 {unpublished data only}
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NCT04625257 {unpublished data only}
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