María Dolores Fellner1, Romina Bonaventura2, Jorge Basiletti1, Martín Avaro3, Estefanía Benedetti3, Ana Campos3, María Elena Dattero3, Mara Russo3, Sara Vladmirsky4, Viviana Molina5, Lucía Irazu6, Marcelo A Rodriguez6, Andrea Pontoriero3, Daniel M Cisterna2, Elsa G Baumeister3. 1. Servicio de Virus Oncogénicos, Departamento de Virología, Instituto Nacional de Enfermedades Infecciosas-ANLIS Dr. Carlos G. Malbrán, Ciudad Autónoma de Buenos Aires 1282AFF, Argentina. 2. Servicio de Neurovirosis, Departamento de Virología, Instituto Nacional de Enfermedades Infecciosas-ANLIS Dr. Carlos G. Malbrán, Ciudad Autónoma de Buenos Aires 1282AFF, Argentina. 3. Servicio de Virosis Respiratorias, Departamento de Virología, Instituto Nacional de Enfermedades Infecciosas-ANLIS Dr. Carlos G. Malbrán, Ciudad Autónoma de Buenos Aires 1282AFF, Argentina. 4. Servicio de Hepatitis Virales, Departamento de Virología, Instituto Nacional de Enfermedades Infecciosas-ANLIS Dr. Carlos G. Malbrán, Ciudad Autónoma de Buenos Aires 1282AFF, Argentina. 5. Instituto Nacional de Enfermedades Infecciosas-ANLIS Dr. Carlos G. Malbrán, Ciudad Autónoma de Buenos Aires 1282AFF, Argentina. 6. Unidad de Evaluación de Métodos de Diagnóstico y Estadística Aplicada, Instituto Nacional de Enfermedades Infecciosas-ANLIS Dr. Carlos G. Malbrán, Ciudad Autónoma de Buenos Aires 1282AFF, Argentina.
Abstract
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 (κ) and the diagnostic performance. Differences among the LoD values for the target genes amplified by each kit were >1 log copies/reaction. The κ 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.
Our aim was to evaluate the analytical and clinical performance of the SARS-CoV-2 molecular detectioene">nn class="Gene">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 (κ) and the diagnostic performance. Differences among the LoD values for the target genes amplified by each kit were >1 log copies/reaction. The κ 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.
Authors: Bernhard Schermer; Francesca Fabretti; Maximilian Damagnez; Veronica Di Cristanziano; Eva Heger; Sita Arjune; Nathan A Tanner; Thomas Imhof; Manuel Koch; Alim Ladha; Julia Joung; Jonathan S Gootenberg; Omar O Abudayyeh; Volker Burst; Feng Zhang; Florian Klein; Thomas Benzing; Roman-Ulrich Müller Journal: PLoS One Date: 2020-11-02 Impact factor: 3.240
Authors: Arun K Nalla; Amanda M Casto; Meei-Li W Huang; Garrett A Perchetti; Reigran Sampoleo; Lasata Shrestha; Yulun Wei; Haiying Zhu; Keith R Jerome; Alexander L Greninger Journal: J Clin Microbiol Date: 2020-05-26 Impact factor: 5.948
Authors: J R Barnacle; H Houston; I Baltas; J Takata; K Kavallieros; N Vaughan; A K Amin; S A Aali; K Moore; P Milner; A Gupta Wright; L John Journal: J Hosp Infect Date: 2022-02-23 Impact factor: 8.944