Evento: SPPC 2021

Poster Número: 003

Autores e Afiliações:

José Pereira, Daniela Fonseca e Silva, Inês Baldaque

Departamento de Virologia, Instituto Português de Oncologia do Porto Francisco Gentil, EPE


COVID-19 is a disease caused by SARS-CoV-2 virus and is currently a major public health concern worldwide. The gold standard for diagnosis is real time reverse transcription polymerase chain reaction (RT-PCR). In our laboratory, the default method for diagnosis is the AllplexTM Kit from Seegene® that runs in the Microlab STARlet IVD® Hamilton. Recently we implemented a new method to detect SARS-CoV-2, the Cobas® SARS-CoV-2 kit, ran in the Cobas® Liat® System, because of its shorter run time. The aim of this study was to compare the results from these two methods.

Materials and Methods

We included a total of 269 samples tested by both methods. The main difference between these two is their running time and the genes they are able to detect. Both use real time RT-PCR, but the AllplexTM kit takes up to 3 hours to provide results while the Cobas® SARS-CoV-2 Kit only takes 20 minutes. The results for each gene are given in amplification cycle thresholds (CT). 

All procedures followed manufacturers’ information sheets. Data analysis was performed in Microsoft Office Excel 2016.


Of the 267 samples tested, we obtained 1 invalid and 16 inconclusive results. These were excluded from the database. 

In our laboratory we consider the results provided by the AllplexTM Kit as the most precise and accurate, according to the manufacturer’s information sheet. For this reason, we used the results obtained with this kit to determine if the patient was positive or negative for SARS-CoV-2 infection. When comparing the results from the two methods, we obtained 19 true positive, 227 true negative, 1 false negative and 3 false positive results.

Conclusion and Discussion

The Cobas® SARS-CoV-2 Kit manufacturer’s results claimed a sensibility and specificity of 100% with 56 true positives and 229 true negatives, on a total of 285 samples. In our database of 250 samples we achieved a good specificity as well (98.70%) but we determined a lower sensitivity (95.00%).

The 19 true positives had all three genes amplified by the AllplexTM kit with variable CTs and with CTs < 31 in the Cobas® SARS-CoV-2 Kit.

The 3 samples that only amplified in Cobas® SARS-CoV-2 Kit (false positives) had CTs above 35. For this reason, the authors suggest that the samples that have CTs > 35 in Cobas® SARS-CoV-2 Kit should be retested using another kit to confirm the results.

All sixteen samples with inconclusive results belonged to patients that had COVID-19 in the past. Using the AllplexTM kit these samples amplified only one or two genes with CTs between 35 and 40. They were negative when tested with the Cobas® SARS-CoV-2 Kit. This difference may be explained by the fact that in patients previously infected with SARS-CoV-2, residual RNA may be present at the collection site of nasopharyngeal swabs and can still amplify specific genes in RT-PCR but at higher CT values.

Being a faster method, we intend to use the Cobas® SARS-CoV-2 Kit in patients requiring emergency care. The comparison of the methods’ performance was acceptable but full agreement between both methods was not found. The results we obtained with this study can be used to validate the method so it can be used in our laboratory to detect SARS-CoV-2.

The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper.