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Wu S, Shi X, Chen Q, Jiang Y, Zuo L, Wang L, Jiang M, Lin Y, Fang S, Peng B, Wu W, Liu H, Zhang R, Kwan PSL, Hu Q. Comparative evaluation of six nucleic acid amplification kits for SARS-CoV-2 RNA detection. Ann Clin Microbiol Antimicrob 2021; 20:38. [PMID: 34022903 PMCID: PMC8140580 DOI: 10.1186/s12941-021-00443-w] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Accepted: 05/11/2021] [Indexed: 01/19/2023] Open
Abstract
BACKGROUND SARS-CoV-2 is a newly emerged coronavirus, causing the coronavirus disease 2019 (COVID-19) outbreak in December, 2019. As drugs and vaccines of COVID-19 remain in development, accurate virus detection plays a crucial role in the current public health crisis. Quantitative real-time reverse transcriptase-polymerase chain reaction (RT-qPCR) kits have been reliably used for detection of SARS-CoV-2 RNA since the beginning of the COVID-19 outbreak, whereas isothermal nucleic acid amplification-based point-of-care automated kits have also been considered as a simpler and rapid alternative. However, as these kits have only been developed and applied clinically within a short timeframe, their clinical performance has not been adequately evaluated to date. We describe a comparative study between a newly developed cross-priming isothermal amplification (CPA) kit (Kit A) and five RT-qPCR kits (Kits B-F) to evaluate their sensitivity, specificity, predictive values and accuracy. METHODS Fifty-two clinical samples were used including throat swabs (n = 30), nasal swabs (n = 7), nasopharyngeal swabs (n = 7) and sputum specimens (n = 8), comprising confirmed (n = 26) and negative cases (n = 26). SARS-CoV-2 detection was simultaneously performed on each sample using six nucleic acid amplification kits. The sensitivity, specificity, positive/negative predictive values (PPV/NPV) and the accuracy for each kit were assessed using clinical manifestation and molecular diagnoses as the reference standard. Reproducibility for RT-qPCR kits was evaluated in triplicate by three different operators using a SARS-CoV-2 RNA-positive sample. On the basis of the six kits' evaluation results, CPA kit (Kit A) and two RT-qPCR Kits (Kit B and F) were applied to the SARS-CoV-2 detection in close-contacts of COVID-19 patients. RESULTS For Kit A, the sensitivity, specificity, PPV/NPV and accuracy were 100%. Among the five RT-qPCR kits, Kits B, C and F had good agreement with the clinical diagnostic reports (Kappa ≥ 0.75); Kits D and E were less congruent (0.4 ≤ Kappa < 0.75). Differences between all kits were statistically significant (P < 0.001). The reproducibility of RT-qPCR kits was determined using a coefficients of variation (CV) between 0.95% and 2.57%, indicating good reproducibility. CONCLUSIONS This is the first comparative study to evaluate CPA and RT-qPCR kits' specificity and sensitivity for SARS-CoV-2 detection, and could serve as a reference for clinical laboratories, thus informing testing protocols amid the rapidly progressing COVID-19 pandemic.
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Affiliation(s)
- Shuang Wu
- Shenzhen Center for Disease Control and Prevention, 8 Longyuan Road, Nanshan District, Shenzhen, 518055, China
| | - Xiaolu Shi
- Shenzhen Center for Disease Control and Prevention, 8 Longyuan Road, Nanshan District, Shenzhen, 518055, China
| | - Qiongcheng Chen
- Shenzhen Center for Disease Control and Prevention, 8 Longyuan Road, Nanshan District, Shenzhen, 518055, China
| | - Yixiang Jiang
- Shenzhen Center for Disease Control and Prevention, 8 Longyuan Road, Nanshan District, Shenzhen, 518055, China
| | - Le Zuo
- Shenzhen Center for Disease Control and Prevention, 8 Longyuan Road, Nanshan District, Shenzhen, 518055, China
| | - Lei Wang
- Shenzhen Center for Disease Control and Prevention, 8 Longyuan Road, Nanshan District, Shenzhen, 518055, China
| | - Min Jiang
- Shenzhen Center for Disease Control and Prevention, 8 Longyuan Road, Nanshan District, Shenzhen, 518055, China
| | - Yiman Lin
- Shenzhen Center for Disease Control and Prevention, 8 Longyuan Road, Nanshan District, Shenzhen, 518055, China
| | - Shisong Fang
- Shenzhen Center for Disease Control and Prevention, 8 Longyuan Road, Nanshan District, Shenzhen, 518055, China
| | - Bo Peng
- Shenzhen Center for Disease Control and Prevention, 8 Longyuan Road, Nanshan District, Shenzhen, 518055, China
| | - Weihua Wu
- Shenzhen Center for Disease Control and Prevention, 8 Longyuan Road, Nanshan District, Shenzhen, 518055, China
| | - Hui Liu
- Shenzhen Center for Disease Control and Prevention, 8 Longyuan Road, Nanshan District, Shenzhen, 518055, China
| | - Renli Zhang
- Shenzhen Center for Disease Control and Prevention, 8 Longyuan Road, Nanshan District, Shenzhen, 518055, China
| | - Patrick S L Kwan
- Shenzhen Center for Disease Control and Prevention, 8 Longyuan Road, Nanshan District, Shenzhen, 518055, China
| | - Qinghua Hu
- Shenzhen Center for Disease Control and Prevention, 8 Longyuan Road, Nanshan District, Shenzhen, 518055, China.
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Centoamore NHF, Chierato MER, Silveira VBV, Asano KM, Iamamoto K, Fahl WO, Scheffer KC, Achkar SM, Mesquita LP, Maiorka PC, Mori E. Comparison of five different laboratory techniques for the rabies diagnosis in clinically suspected cattle in Brazil. J Virol Methods 2020; 283:113918. [PMID: 32554044 DOI: 10.1016/j.jviromet.2020.113918] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Revised: 06/01/2020] [Accepted: 06/11/2020] [Indexed: 01/18/2023]
Abstract
The direct-fluorescent antibody test (dFAT) is considered the "gold standard" assay to diagnose rabies. However, it is crucial to develop molecular techniques, such as RT-PCR and RT-qPCR, since many laboratories lack the needed supplies for performing complementary methods (viral isolation, for example). For this purpose, diagnostic techniques must be specific and sensitive to guarantee accuracy. This present investigation aimed to detect rabies virus (RABV) in 126 clinically suspected cattle in Brazil using different diagnostic tests [dFAT, mouse inoculation test (MIT), immunohistochemistry (IHC), RT-PCR and RT-qPCR] and to compare those results obtained under routine laboratory conditions. The results of the present investigation demonstrate that the molecular techniques are more sensitive and may detect low viral load, even though the non-homogeneous viral distribution caused a false-negative result in dFAT. We also observed a usual alteration in antigens distribution among regions of the central nervous system (CNS). By both dFAT and IHC assays, the most reliable CNS structures were thalamus and midbrain. Although this investigation demonstrated diagnostic sensitivity and specificity close to 100 % in all laboratory techniques employed, a dFAT auxiliary test is required for bovine specimens, such as molecular techniques, when there are poor sampling conditions (low viral load combined with unavailability of brainstem structures).
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Affiliation(s)
- N H F Centoamore
- Department of Pathology, School of Veterinary Medicine and Animal Science, University of Sao Paulo, Sao Paulo, SP, Brazil
| | - M E R Chierato
- Department of Pathology, School of Veterinary Medicine and Animal Science, University of Sao Paulo, Sao Paulo, SP, Brazil
| | - V B V Silveira
- Instituto Pasteur de Sao Paulo, Avenida Paulista 393, Sao Paulo, SP 01311‑000, Brazil
| | - K M Asano
- Instituto Pasteur de Sao Paulo, Avenida Paulista 393, Sao Paulo, SP 01311‑000, Brazil
| | - K Iamamoto
- Instituto Pasteur de Sao Paulo, Avenida Paulista 393, Sao Paulo, SP 01311‑000, Brazil
| | - W O Fahl
- Instituto Pasteur de Sao Paulo, Avenida Paulista 393, Sao Paulo, SP 01311‑000, Brazil
| | - K C Scheffer
- Instituto Pasteur de Sao Paulo, Avenida Paulista 393, Sao Paulo, SP 01311‑000, Brazil
| | - S M Achkar
- Instituto Pasteur de Sao Paulo, Avenida Paulista 393, Sao Paulo, SP 01311‑000, Brazil
| | - L P Mesquita
- Department of Pathology, School of Veterinary Medicine and Animal Science, University of Sao Paulo, Sao Paulo, SP, Brazil
| | - P C Maiorka
- Department of Pathology, School of Veterinary Medicine and Animal Science, University of Sao Paulo, Sao Paulo, SP, Brazil
| | - E Mori
- Department of Pathology, School of Veterinary Medicine and Animal Science, University of Sao Paulo, Sao Paulo, SP, Brazil; Instituto Pasteur de Sao Paulo, Avenida Paulista 393, Sao Paulo, SP 01311‑000, Brazil.
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