Evaluation of RT-qPCR and Loop-Mediated Isothermal Amplification (LAMP) Assays for the Detection of SARS-CoV-2 in Argentina

被引：6

作者：

Dolores Feltner, Maria ^{[1
]}

Bonaventura, Romina ^{[2
]}

Basiletti, Jorge ^{[1
]}

Avaro, Martin ^{[3
]}

Benedetti, Estefania ^{[3
]}

Campos, Ana ^{[3
]}

Elena Dattero, Maria ^{[3
]}

Russo, Mara ^{[3
]}

Vladmirsky, Sara ^{[4
]}

Molina, Viviana ^{[5
]}

Irazu, Lucia ^{[6
]}

Rodriguez, Marcelo A. ^{[6
]}

Pontoriero, Andrea ^{[3
]}

Cisterna, Daniel M. ^{[2
]}

Baumeister, Elsa G. ^{[3
]}

机构：

[1] Inst Nacl Enfermedades Infecciosas ANLIS Dr Carlo, Dept Virol, Serv Virus Oncogen, 1282AFF, Buenos Aires, DF, Argentina

[2] Inst Nacl Enfermedades Infecciosas ANLIS Dr Carlo, Dept Virol, Serv Neurovirosis, 1282AFF, Buenos Aires, DF, Argentina

[3] Inst Nacl Enfermedades Infecciosas ANLIS Dr Carlo, Dept Virol, Serv Virosis Resp, 1282AFF, Buenos Aires, DF, Argentina

[4] Inst Nacl Enfermedades Infecciosas ANLIS Dr Carlo, Dept Virol, Serv Hepatitis Virales, 1282AFF, Buenos Aires, DF, Argentina

[5] Inst Nacl Enfermedades Infecciosas ANLIS Dr Carlo, 1282AFF, Buenos Aires, DF, Argentina

[6] Inst Nacl Enfermedades Infecciosas ANLIS Dr Carlo, Unidad Evaluac Metodos Diagnost & Estadist Aplica, 1282AFF, Buenos Aires, DF, Argentina

来源：

GENES | 2021年 / 12卷 / 05期

关键词：

SARS-CoV-2; RT-qPCR; RT-LAMP;

D O I：

10.3390/genes12050659

中图分类号：

Q3 [遗传学];

学科分类号：

071007 ; 090102 ;

摘要：

Our aim was to evaluate the analytical and clinical performance of the SARS-CoV-2 molecular detection kits used in Argentina. Nine real-time reverse-transcription polymerase chain reaction (RT-qPCR) and three reverse-transcription loop-mediated isothermal amplification (RT-LAMP) assays were evaluated using the World Health Organization (WHO) recommended test as reference method. A secondary standard calibrated for the E, N and RdRp genes against the Pan American Health Organization-World Health Organization-International Standard was used to calculate the limit of detection (LoD). A panel of artificial clinical samples, 32 positive and 30 negative for SARS-CoV-2, were analyzed to estimate the kappa concordance (kappa) and the diagnostic performance. Differences among the LoD values for the target genes amplified by each kit were >1 log copies/reaction. The kappa for the RT-qPCR kits was greater than 0.9, whereas that for the RT-LAMP assays ranged from 0.75 to 0.93. The clinical performance of RT-qPCR kits showed 100% specificity and high sensitivity, although with variations according to the gene analyzed. The E and N genes provided greater clinical sensitivity, whereas the RdRp gene increased the clinical specificity. The RT-LAMP assays revealed a variable diagnostic performance. The information provided can be useful to choose the most appropriate diagnostic test and may contribute to the establishment of a consensus in the diagnosis of SARS-CoV-2 in Argentina and the region.

引用

页数：14

共 37 条

[1] Direct detection of SARS-CoV-2 using non-commercial RT-LAMP reagents on heat-inactivated samples [J].

Alekseenko, Alisa ;

Barrett, Donal ;

Pareja-Sanchez, Yerma ;

Howard, Rebecca J. ;

Strandback, Emilia ;

Ampah-Korsah, Henry ;

Rovsnik, Urska ;

Zuniga-Veliz, Silvia ;

Klenov, Alexander ;

Malloo, Jayshna ;

Ye, Shenglong ;

Liu, Xiyang ;

Reinius, Bjorn ;

Elsasser, Simon J. ;

Nyman, Tomas ;

Sandh, Gustaf ;

Yin, Xiushan ;

Pelechano, Vicent .

SCIENTIFIC REPORTS, 2021, 11 (01)

[2] Molecular analysis of several in-house rRT-PCR protocols for SARS-CoV-2 detection in the context of genetic variability of the virus in Colombia [J].

Alvarez-Diaz, Diego A. ;

Franco-Munoz, Carlos ;

Laiton-Donato, Katherine ;

Usme-Ciro, Jose A. ;

Franco-Sierra, Nicolas D. ;

Florez-Sanchez, Astrid C. ;

Gomez-Rangel, Sergio ;

Rodriguez-Calderon, Luz D. ;

Barbosa-Ramirez, Juliana ;

Ospitia-Baez, Erika ;

Walteros, Diana M. ;

Ospina-Martinez, Martha L. ;

Mercado-Reyes, Marcela .

INFECTION GENETICS AND EVOLUTION, 2020, 84

[3] A Recurrent Mutation at Position 26340 of SARS-CoV-2 Is Associated with Failure of the E Gene Quantitative Reverse Transcription-PCR Utilized in a Commercial Dual-Target Diagnostic Assay [J].

Artesi, Maria ;

Bontems, Sebastien ;

Gobbels, Paul ;

Franckh, Marc ;

Maes, Piet ;

Boreux, Raphael ;

Meex, Cecile ;

Melin, Pierrette ;

Hayette, Marie-Pierre ;

Bours, Vincent ;

Durkin, Keith .

JOURNAL OF CLINICAL MICROBIOLOGY, 2020, 58 (10)

[4] Development of a reverse transcription-loop-mediated isothermal amplification as a rapid early-detection method for novel SARS-CoV-2 [J].

Baek, Yun Hee ;

Um, Jihye ;

Antigua, Khristine Joy C. ;

Park, Ji-Hyun ;

Kim, Yeonjae ;

Oh, Sol ;

Kim, Young-il ;

Choi, Won-Suk ;

Kim, Seong Gyu ;

Jeong, Ju Hwan ;

Chin, Bum Sik ;

Nicolas, Halcyon Dawn G. ;

Ahn, Ji-Young ;

Shin, Kyeong Seob ;

Choi, Young Ki ;

Park, Jun-Sun ;

Song, Min-Suk .

EMERGING MICROBES & INFECTIONS, 2020, 9 (01) :998-1007

[5] Two-step strategy for the identification of SARS-CoV-2 variant of concern 202012/01 and other variants with spike deletion H69-V70, France, August to December 2020 [J].

Bal, Antonin ;

Destras, Gregory ;

Gaymard, Alexandre ;

Stefic, Karl ;

Marlet, Julien ;

Eymieux, Sebastien ;

Regue, Hadrien ;

Semanas, Quentin ;

d'Aubarede, Constance ;

Billaud, Genevieve ;

Laurent, Frederic ;

Gonzalez, Claudia ;

Mekki, Yahia ;

Valette, Martine ;

Bouscambert, Maude ;

Gaudy-Graffin, Catherine ;

Lina, Bruno ;

Morfin, Florence ;

Josset, Laurence .

EUROSURVEILLANCE, 2021, 26 (03)

[6] A familial cluster of pneumonia associated with the 2019 novel coronavirus indicating person-to-person transmission: a study of a family cluster [J].

Chan, Jasper Fuk-Woo ;

Yuan, Shuofeng ;

Kok, Kin-Hang ;

To, Kelvin Kai-Wang ;

Chu, Hin ;

Yang, Jin ;

Xing, Fanfan ;

Liu, Jieling ;

Yip, Cyril Chik-Yan ;

Poon, Rosana Wing-Shan ;

Tsoi, Hoi-Wah ;

Lo, Simon Kam-Fai ;

Chan, Kwok-Hung ;

Poon, Vincent Kwok-Man ;

Chan, Wan-Mui ;

Ip, Jonathan Daniel ;

Cai, Jian-Piao ;

Cheng, Vincent Chi-Chung ;

Chen, Honglin ;

Hui, Christopher Kim-Ming ;

Yuen, Kwok-Yung .

LANCET, 2020, 395 (10223) :514-523

[7] Loop-mediated isothermal amplification (LAMP): An effective molecular point-of-care technique for the rapid diagnosis of coronavirus SARS-CoV-2 [J].

Chaouch, Melek .

REVIEWS IN MEDICAL VIROLOGY, 2021, 31 (06)

[8] Molecular Diagnosis of a Novel Coronavirus (2019-nCoV) Causing an Outbreak of Pneumonia [J].

Chu, Daniel K. W. ;

Pan, Yang ;

Cheng, Samuel M. S. ;

Hui, Kenrie P. Y. ;

Krishnan, Pavithra ;

Liu, Yingzhi ;

Ng, Daisy Y. M. ;

Wan, Carrie K. C. ;

Yang, Peng ;

Wang, Quanyi ;

Peiris, Malik ;

Poon, Leo L. M. .

CLINICAL CHEMISTRY, 2020, 66 (04) :549-555

[9] Detection of 2019 novel coronavirus (2019-nCoV) by real-time RT-PCR (Publication with Expression of Concern) [J].

Corman, Victor M. ;

Landt, Olfert ;

Kaiser, Marco ;

Molenkamp, Richard ;

Meijer, Adam ;

Chu, Daniel K. W. ;

Bleicker, Tobias ;

Bruenink, Sebastian ;

Schneider, Julia ;

Schmidt, Marie Luisa ;

Mulders, Daphne G. J. C. ;

Haagmans, Bart L. ;

van der Veer, Bas ;

van den Brink, Sharon ;

Wijsman, Lisa ;

Goderski, Gabriel ;

Romette, Jean-Louis ;

Ellis, Joanna ;

Zambon, Maria ;

Peiris, Malik ;

Goossens, Herman ;

Reusken, Chantal ;

Koopmans, Marion P. G. ;

Drosten, Christian .

EUROSURVEILLANCE, 2020, 25 (03) :23-30

[10] Optimizing direct RT-LAMP to detect transmissible SARS-CoV-2 from primary nasopharyngeal swab samples [J].

Dudley, Dawn M. ;

Newman, Christina M. ;

Weiler, Andrea M. ;

Ramuta, Mitchell D. ;

Shortreed, Cecilia G. ;

Heffron, Anna S. ;

Accola, Molly A. ;

Rehrauer, William M. ;

Friedrich, Thomas C. ;

O'Connor, David H. .

PLOS ONE, 2020, 15 (12)

← 1 2 3 4 →