Advances in nucleic acid amplification techniques (NAATs): COVID-19 point-of-care diagnostics as an example

Kang, Tongjia; Lu, Jingming; Tian, Yu; Long, Yi; Liu, Guozhen

doi:10.1016/j.bios.2022.114109

Cited by 122 publications

(65 citation statements)

References 96 publications

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“…5,6 POCT has been in high demand for COVID-19, and one significant reason is that it helps to address the SARS-CoV-2 testing backlog in clinical laboratories. 7,8 In the United States, the Cue's COVID-19 test (Cue Health Inc.) 11 Compared to the reference methods, Donato and colleagues reported a good overall concordance of 97.8%, 11 which was similar to our data (95.0%). In addition, their invalid rate seemed lower than ours (8.6% vs. 10.7%), and their false positive rate seemed higher than ours (1.7% vs. 0%), however, these discrepancies are minor.…”

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confidence: 83%

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Clinical evaluation of the Cue's COVID‑19 diagnostic test to detect SARS‐CoV‐2 in the upper respiratory tract

Phan

Cravener

McCullough

et al. 2022

Journal of Medical Virology

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Point-of-care testing (POCT) known as near-patient testing has a relatively lower cost and short turnaround time. It is obvious that a short turnaround time can potentially improve patient care and outcomes by providing quick access to test results, expediting medical diagnosis, and facilitating earlier and more rapid decisions on treatment. 1,2 Another benefit of POCT is that it can be performed by clinical staff without laboratory training. POCT can be done at a healthcare provider's office, outpatient clinic, emergency room, and healthcare nursing home. 3,4 More than 2 years into the COVID-19 | 3517 Donato and colleagues performed the prospective study in the outpatient setting, and the Ct value or viral load of the positive specimens was random. 11 Our positive specimens were carefully selected to verify the lower sensitivity, and a majority of them (61.1%, 11 of 18) had high Ct values (>30.0). In our evaluation, the clinical performance of the Cue's COVID-19 test started to decline as the Ct values increased reflecting decreasing viral loads. This phenomenon was also observed in other rapid NAAT POCTs such as the ID NOW COVID-19 test which has the lower performance for specimens displaying the Ct value higher than 30.0. 12 Given the persistence of the SARS-CoV-2 testing backlog, low availability of testing supply, and shortage of licensed personnel in clinical laboratories, we need to migrate more testing capacity to the outpatient setting and the Cue's COVID-19 test is a good option. AUTHOR CONTRIBUTIONS Tung Phan and Alan Wells designed the study and wrote the manuscript. Zachary Cravener, Melissa McCullough, Ashley Mays, and Jamie Gribschaw managed the testing.

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supporting

confidence: 83%

“… 5 , 6 POCT has been in high demand for COVID‐19, and one significant reason is that it helps to address the SARS‐CoV‐2 testing backlog in clinical laboratories. 7 , 8 …”

Section: The Studymentioning

confidence: 99%

Clinical evaluation of the Cue's COVID‑19 diagnostic test to detect SARS‐CoV‐2 in the upper respiratory tract

Phan

Cravener

McCullough

et al. 2022

Journal of Medical Virology

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“…The primer design of the LAMP approach is relatively complicated, and the amplification temperature of LAMP is 60–65 °C, which is far from the ideal temperature of the CRISPR-Cas detection system. Nevertheless, the RPA reaction has the advantages of being quick, having a high amplification sensitivity and being able to perform multiplex reactions [ 29 ].…”

Section: Discussionmentioning

confidence: 99%

Establishment and application of a CRISPR-Cas12a-based RPA-LFS and fluorescence for the detection of Trichomonas vaginalis

Wang

et al. 2022

Parasites Vectors

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Background Infection with Trichomonas vaginalis can lead to cervicitis, urethritis, pelvic inflammatory disease, prostatitis and perinatal complications and increased risk of HIV transmission. Here, we used an RPA-based CRISPR-Cas12a assay system in combination with a lateral flow strip (LFS) (referred to as RPA-CRISPR-Cas12a) to establish a highly sensitive and field-ready assay and evaluated its ability to detect clinical samples. Methods We developed a one-pot CRISPR-Cas12a combined with RPA-based field detection technology for T. vaginalis, chose actin as the target gene to design crRNA and designed RPA primers based on the crRNA binding site. The specificity of the method was demonstrated by detecting genomes from nine pathogens. To improve the usability and visualize the RPA-CRISPR-Cas12a assay results, both fluorescence detection and LFS readouts were devised. Results The RPA-CRISPR-Cas12a assay platform was completed within 60 min and had a maximum detection limit of 1 copy/µl and no cross-reactivity with Candida albicans, Mycoplasma hominis, Neisseria gonorrhoeae, Escherichia coli, Cryptosporidium parvum, G. duodenalis or Toxoplasma gondii after specificity validation. Thirty human vaginal secretions were tested by RPA-CRISPR-Cas12a assays, and the results were read by a fluorescent reporter and LFS biosensors and then compared to the results from nested PCR detection of these samples. Both RPA-CRISPR-Cas12a assays showed 26.7% (8/30) T. vaginalis-positive samples and a consistency of 100% (8/8). The RPA-CRISPR-Cas12a assays had a higher sensitivity than nested PCR (only seven T. vaginalis-positive samples were detected). Conclusions The T. vaginalis RPA-CRISPR-Cas12a assay platform in this study can be used for large-scale field testing and on-site tests without the need for trained technicians or costly ancillary equipment. Graphical abstract

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“…Specific target sequences are chosen and employed in the construction of nucleic acid detection techniques based on the genomic sequence of SARS-CoV-2. For clinics, quarantine, rehabilitation, and discharge, nucleic acid testing is a useful diagnostic tool [ 23 ]. Current nucleic acid detection methods for SARS-CoV-2 include real-time quantitative polymerase chain reaction (RT-qPCR) [ 24 ], loop-mediated isothermal amplification (LAMP) [ 25 , 26 ], and clustered regularly interspaced short palindromic repeats/Cas associated system (CRISPR/Cas) [ 27 ].…”

Section: Sars-cov-2 Infection Mechanism and Diagnostic Methodsmentioning

confidence: 99%

Visual Detection of COVID-19 from Materials Aspect

Wang

Meng

et al. 2022

Adv. Fiber Mater.

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In the recent COVID-19 pandemic, World Health Organization emphasized that early detection is an effective strategy to reduce the spread of SARS-CoV-2 viruses. Several diagnostic methods, such as reverse transcription-polymerase chain reaction (RT-PCR) and lateral flow immunoassay (LFIA), have been applied based on the mechanism of specific recognition and binding of the probes to viruses or viral antigens. Although the remarkable progress, these methods still suffer from inadequate cellular materials or errors in the detection and sampling procedure of nasopharyngeal/oropharyngeal swab collection. Therefore, developing accurate, ultrafast, and visualized detection calls for more advanced materials and technology urgently to fight against the epidemic. In this review, we first summarize the current methodologies for SARS-CoV-2 diagnosis. Then, recent representative examples are introduced based on various output signals (e.g., colorimetric, fluorometric, electronic, acoustic). Finally, we discuss the limitations of the methods and provide our perspectives on priorities for future test development. Graphical Abstract

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Advances in nucleic acid amplification techniques (NAATs): COVID-19 point-of-care diagnostics as an example

Cited by 122 publications

References 96 publications

Clinical evaluation of the Cue's COVID‑19 diagnostic test to detect SARS‐CoV‐2 in the upper respiratory tract

Clinical evaluation of the Cue's COVID‑19 diagnostic test to detect SARS‐CoV‐2 in the upper respiratory tract

Establishment and application of a CRISPR-Cas12a-based RPA-LFS and fluorescence for the detection of Trichomonas vaginalis

Visual Detection of COVID-19 from Materials Aspect

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