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Available online 20 July 2021
Discordant results of SARS-CoV-2 PCR-based tests in the early phase of pandemic in Indonesia: Infection control consequences
Discordancia de los resultados de las pruebas PCR para SARS-CoV-2 en la fase temprana de la pandemia en Indonesia: consecuencias para el control de la infección
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A. Pranataa,b,c,d, B. Zulkiflid,e,f, S.F. Santosad,g, A. Oktiviyaria,b,d, Z. Zulfitrid,e, Z. Hayatia,b,d,h, M. Mudatsira,b,d,h, I. Ichsana,b,d,h, H. Harapana,b,d,h,
Corresponding author
harapan@unsyiah.ac.id

Corresponding author.
a Medical Research Unit, School of Medicine, Universitas Syiah Kuala, Banda Aceh 23111, Indonesia
b Tropical Disease Centre, School of Medicine, Universitas Syiah Kuala, Banda Aceh 23111, Indonesia
c Department of Parasitology, School of Medicine, Universitas Syiah Kuala, Banda Aceh 23111, Indonesia
d Infectious Disease Laboratory, Universitas Syiah Kuala, Banda Aceh 23111, Indonesia
e Department of Biology, School of Medicine, Universitas Syiah Kuala, Banda Aceh 23111, Indonesia
f Center for Tropical Veterinary Studies, Universitas Syiah Kuala, Banda Aceh 23111, Indonesia
g Laboratory of Research, Faculty of Veterinary Medicine, Syiah Kuala University, Banda Aceh 23111, Indonesia
h Department of Microbiology, School of Medicine, Universitas Syiah Kuala, Banda Aceh 23111, Indonesia
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Table 1. Discordant results between LiliF COVID-19 Real-Time RT-PCR and Live Rifer Novel Coronavirus COVID-19 (2019-nCoV) Real Time Multiplex RT-PCR Kit (n=33).
Abstract
Introduction

Growing evidence suggest that cycle threshold (CT)-value of reverse transcription polymerase chain reaction (RT-PCR) is correlated with transmission of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and some kits set different CT-value cut-off. This report presents the discordant results of two widely used RT-PCR kits in Indonesia due to different CT-value cut-offs and highlights its potential consequence in SARS-CoV-2 containment.

Methods

Nasopharyngeal swab samples with SARS-CoV-2 negative with a RT-PCR kit (manufacture pre-set CT-value cut-off was 35 amplification cycles) were retested with another RT-PCR kit with a higher pre-set CT-value of 40 amplification cycles. All procedures were performed according to the manufacturer protocols.

Results

In total, 30 samples with SARS-CoV-2 negative for the first kit were retested. We found that 25 out of 33 samples (75.5%) were positive using the second RT-PCR kit that had a higher manufacture pre-set CT-value cut-off. In addition, among 500 RT-PCR tests using the first RT-PCR kit, 103 of them (20.6%) were categorized as inconclusive results based on the second manufacturer’ guideline.

Discussion and conclusion

Our data suggest the possibility of discordant results of SARS-CoV-2 detection due to different pre-set cut-offs by the companies. As consequence, this could leave a fraction of individuals who were misclassified that could act as source of virus transmission within community.

Keywords:
COVID-19
RT-PCR
Sensitivity
Specificity
Diagnostic
Resumen
Introducción

La evidencia creciente sugiere que el valor del ciclo umbral (CT) de la RT-PCR (reacción en cadena de la polimerasa por transcripción inversa) guarda relación con la transmisión del síndrome respiratorio agudo severo por coronavirus 2 (SARS-CoV-2), y algunos kits establecen diferentes puntos de corte para dicho valor. El presente informe presenta la discordancia de los resultados de dos kits RT-PCR de amplio uso en Indonesia debido a los diferentes puntos de corte del valor CT, y subraya su consecuencia potencial para la contención del SARS-CoV-2.

Métodos

Se reanalizaron las muestras de los hisopos nasofaríngeos negativos para SARS-CoV-2 con un kit RT-PCR (el punto de corte del valor CT preestablecido de fábrica fue de 35 ciclos de ampliación) con otro kit para RT-PCR con un valor CT establecido superior, de 40 ciclos de ampliación. Todos los procedimientos fueron realizados con arreglo a los protocolos de fabricación.

Resultados

En total se reanalizaron 30 muestras con SARS-CoV-2 negativas para el primer kit. Encontramos que 25 de entre 33 muestras (75,5%) eran positivas utilizando el segundo kit para RT-PCR, que tenía un punto de corte del valor CT preestablecido superior. Además, entre las 500 pruebas RT-PCR que utilizaron el primer kit para RT-PCR, 103 de ellas (el 20,6%) fueron categorizadas como resultados no concluyentes sobre la base de la guía del segundo fabricante.

Discusión y conclusión

Nuestros datos sugieren la posibilidad de discordancia en los resultados de detección del SARS-CoV-2 debido a los diferentes puntos de corte preestablecidos por los fabricantes. Por tanto, esto podría suponer que la mala clasificación de una parte de los individuos fuera la causa de la transmisión del virus dentro de la comunidad.

Palabras clave:
COVID-19
RT-PCR
Sensibilidad
Especificidad
Diagnóstico

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