Direct Nasal Swab for Rapid Test and Saliva as an Alternative Biological Sample for RT-PCR in COVID-19 Diagnosis

Sazed, Saiful Arefeen; Kibria, Mohammad Golam; Zamil, Md Fahad; Hossain, Mohammad Sharif; Khan, Jeba Zaman; Juthi, Rifat Tasnim; Hossain, Mohammad Enayet; Ahmed, Dilruba; Noor, Zannatun; Haque, Rashidul; Alam, Mohammad Shafiul

doi:10.1128/spectrum.01998-22

Cited by 6 publications

(5 citation statements)

References 33 publications

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“…For these reasons, in addition to examining nasopharyngeal samples, saliva, and urine samples were also used in this study. In the present study, the sensitivity of SARS-CoV-2 detection in saliva and nasopharynx samples was reported as 88.2% and 92.9%, respectively, the results were consistent with the results of Sazed et al [ 40 ]. Based on the obtained results in the current study, the RT-LAMP method can identify the virus carriers, if the RT-qPCR method proves otherwise.…”

Section: Discussionsupporting

confidence: 93%

“…However, RT-qPCR may fail to detect the virus and produce false-negative results, particularly if the viral load is very low in the patient’s sample. This can occur in patients who have recently been infected, or in patients who are in the early stages of the disease [ 22 , 40 ]. As in the current study, in the investigation of 55 asymptomatic people suspected of SARS-CoV-2 infection, all 55 cases were negative in the repeat RT-qPCR test after 48 h. However, in the repeat RT-LAMP test, 6 out of 55 people tested positive and still had no symptoms.…”

Section: Discussionmentioning

confidence: 99%

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Evaluation and comparison of one-step real-time PCR and one-step RT-LAMP methods for detection of SARS-CoV-2

Hanifehpour,

Ashrafi,

Siasi

et al. 2024

BMC Infect Dis

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Background There is an increasing disease trend for SARS-COV-2, so need a quick and affordable diagnostic method. It should be highly accurate and save costs compared to other methods. The purpose of this research is to achieve these goals. Methods This study analyzed 342 samples using TaqMan One-Step RT-qPCR and fast One-Step RT-LAMP (Reverse Transcriptase Loop-Mediated Isothermal Amplification). The One-Step LAMP assay was conducted to assess the sensitivity and specificity. Results The research reported positive samples using two different methods. In the RT-LAMP method, saliva had 92 positive samples (26.9%) and 250 negative samples (73.09%) and nasopharynx had 94 positive samples (27.4%) and 248 negative samples (72.51%). In the RT-qPCR method, saliva had 86 positive samples (25.1%) and 256 negative samples (74.8%) and nasopharynx had 93 positive samples (27.1%) and 249 negative samples (72.8%). The agreement between the two tests in saliva and nasopharynx samples was 93% and 94% respectively, based on Cohen’s kappa coefficient (κ) (P < 0.001). The rate of sensitivity in this technique was reported at a dilution of 1 × 101 and 100% specificity. Conclusions Based on the results of the study the One-Step LAMP assay has multiple advantages. These include simplicity, cost-effectiveness, high sensitivity, and specificity. The One-Step LAMP assay shows promise as a diagnostic tool. It can help manage disease outbreaks, ensure prompt treatment, and safeguard public health by providing rapid, easy-to-use testing.

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Section: Discussionsupporting

confidence: 93%

Section: Discussionmentioning

confidence: 99%

Evaluation and comparison of one-step real-time PCR and one-step RT-LAMP methods for detection of SARS-CoV-2

Hanifehpour,

Ashrafi,

Siasi

et al. 2024

BMC Infect Dis

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“…A notable advantage of the detection of COVID-19 through RT-PCR of saliva is that it reduces the chances of spreading SARS-CoV-2. A study evaluated saliva and NP samples, and the sensitivity was found to be 85.2% for saliva and 94.5% for NP [ 42 ]. Another study has reported the presence of SARS-CoV-2 in the nasal vestibule and the sensitivity of testing this particular specimen for diagnosis of SARS-CoV-2 infection.…”

Section: Discussionmentioning

confidence: 99%

Rapid, sensitive, and specific detection of SARS-CoV-2 in nasopharyngeal swab samples of suspected patients using a novel one-step loop-mediated isothermal amplification (one-step LAMP) technique

Khanizadeh

Malekshahi

Hanifehpour³

et al. 2023

BMC Microbiol

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Background In the absence of effective antiviral drugs or vaccines, early and accurate detection of SARS-CoV-2 infection is essential to the COVID-19 pandemic. This study developed and evaluated a novel rapid One-Step LAMP assay to directly detect the SARS-CoV-2 RNA from nasopharyngeal (NP) swab samples of patients with suspected SARS-CoV-2 infection living in deprived areas in comparison to One-Step Real-time PCR. Methods Two hundred fifty-four NP swab samples from patients suspected of COVID-19 infection living in deprived western areas of Iran were tested by TaqMan One-Step RT-qPCR and fast One-Step LAMP assays. Tenfold serial dilutions of SARS-CoV-2 RNA standard strain where the viral copy number in each dilution was previously determined using the qPCR and various templates were used to investigate the analytical sensitivity and specificity of the One-Step LAMP assay in triplicate. Also, the efficacy and reliability of the method compared to TaqMan One-Step RT-qPCR were evaluated using SARS-CoV-2 positive and negative clinical samples. Results The results of the One-Step RT-qPCR and One-Step LAMP tests were positive in 131 (51.6%) and 127 (50%) participants, respectively. Based on Cohen’s kappa coefficient (κ), the agreement between the two tests was 97%, which was statistically significant (P < 0.001). The detection limit for the One-Step LAMP assay was 1 × 101 copies of standard SARS-CoV-2 RNA per reaction in less than an hour in triplicates. Negative results in all samples with non-SARS-CoV-2 templates represent 100% specificity. Conclusions The results showed that the One-Step LAMP assay is an efficient consistent technique for detecting SARS-CoV-2 among suspected individuals due to its simplicity, speed, low cost, sensitivity, and specificity. Therefore, it has great potential as a useful diagnostic tool for disease epidemic control, timely treatment, and public health protection, especially in poor and underdeveloped countries.

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“…Meanwhile, the specificity was as high as ≥95%. Additionally, the CareStart TM COVID-19 Antigen Home Test was reported to be able to detect patients with different variants of SARS-CoV-2 [ 52 ].…”

Section: Antigen Tests Amid the Battle Against Sars-cov-2 In Koreamentioning

confidence: 99%

Rapid Antigen Tests during the COVID-19 Era in Korea and Their Implementation as a Detection Tool for Other Infectious Diseases

Widyasari

Kim

2023

Bioengineering

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Rapid antigen tests (RATs) are diagnostic tools developed to specifically detect a certain protein of infectious agents (viruses, bacteria, or parasites). RATs are easily accessible due to their rapidity and simplicity. During the COVID-19 pandemic, RATs have been widely used in detecting the presence of the specific SARS-CoV-2 antigen in respiratory samples from suspected individuals. Here, the authors review the application of RATs as detection tools for COVID-19, particularly in Korea, as well as for several other infectious diseases. To address these issues, we present general knowledge on the design of RATs that adopt the lateral flow immunoassay for the detection of the analyte (antigen). The authors then discuss the clinical utilization of the authorized RATs amidst the battle against the COVID-19 pandemic in Korea and their role in comparison with other detection methods. We also discuss the implementation of RATs for other, non-COVID-19 infectious diseases, the challenges that may arise during the application, the limitations of RATs as clinical detection tools, as well as the possible problem solving for those challenges to maximize the performance of RATs and avoiding any misinterpretation of the test result.

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Direct Nasal Swab for Rapid Test and Saliva as an Alternative Biological Sample for RT-PCR in COVID-19 Diagnosis

Cited by 6 publications

References 33 publications

Evaluation and comparison of one-step real-time PCR and one-step RT-LAMP methods for detection of SARS-CoV-2

Evaluation and comparison of one-step real-time PCR and one-step RT-LAMP methods for detection of SARS-CoV-2

Rapid, sensitive, and specific detection of SARS-CoV-2 in nasopharyngeal swab samples of suspected patients using a novel one-step loop-mediated isothermal amplification (one-step LAMP) technique

Rapid Antigen Tests during the COVID-19 Era in Korea and Their Implementation as a Detection Tool for Other Infectious Diseases

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