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Could pooled samples method affect SARS-CoV-2 diagnosis accuracy using BGI and Sansure-Biotech RT-PCR kits used in Gabon, Central Africa?
- Source :
- PLoS ONE, PLoS ONE, Public Library of Science, 2022, 17 (1), pp.e0262733. ⟨10.1371/journal.pone.0262733⟩, PLoS ONE, Vol 17, Iss 1, p e0262733 (2022), PLoS ONE, Vol 17, Iss 1 (2022)
- Publication Year :
- 2022
- Publisher :
- HAL CCSD, 2022.
-
Abstract
- This study aims at establishing specimens pooling approach for the detection of SARS-CoV-2 using the RT-PCR BGI and Sansure-Biotech kits used in Gabon. To validate this approach, 14 positive samples, stored at -20°C for three to five weeks were analyzed individually (as gold standard) and in pools of five, eight and ten in the same plate. We created 14 pools of 5, 8 and 10 samples using 40 μL from each of the selected positive samples mixed with 4, 7 and 9 confirmed negative counterparts in a total volume of 200 μL, 320 μL and 400 μL for the pools of 5, 8 and 10 respectively. Both individual and pooled samples testing was conducted according to the BGI and Sansure-Biotech RT-PCR protocols used at the Professor Daniel Gahouma Laboratory (PDGL). Furthermore, the pooling method was also tested by comparing results of 470 unselected samples tested in 94 pools and individually. Results of our experiment showed that using a BGI single positive sample with cycle threshold (Ct) value of 28.42, confirmed by individual testing, detection occurred in all the pools. On the contrary samples with Ct >31 were not detected in pools of 10 and for these samples (Ct value as high as 37.17) their detection was possible in pool of 8. Regarding the Sansure-Biotech kit, positive samples were detected in all the pool sizes tested, irrespective of their Ct values. The specificity of the pooling method was 100% for the BGI and Sansure-Biotech RT-PCR assays. The present study found an increase in the Ct values with pool size for the BGI and Sansure-Biotech assays. This trend was statistically significant (Pearson’s r = 0.978; p = 0,022) using the BGI method where the mean Ct values were 24.04±1.1, 26.74±1.3, 27.91±1.1 and 28.32±1.1 for the individual, pool of 5, 8 and 10 respectively. The testing of the 470 samples showed that one of the 94 pools had a positive test similar to the individual test using the BGI and Sansure-Biotech kits. The saving of time and economizing test reagents by using the pooling method were demonstrated in this study. Ultimately, the pooling method could be used for the diagnosis of SARS-CoV-2 without modifying the accuracy of results in Gabon. We recommend a maximum pool size of 8 for the BGI kit. For the Sansure-Biotech kit, a maximum pool size of 10 can be used without affecting its accuracy compared to the individual testing.
- Subjects :
- RNA viruses
Viral Diseases
Coronaviruses
Artificial Gene Amplification and Extension
Polymerase Chain Reaction
Geographical Locations
Medical Conditions
Medicine and Health Sciences
Pathology and laboratory medicine
Virus Testing
Multidisciplinary
Gene Pool
Medical microbiology
Viral Load
Health Services
Infectious Diseases
COVID-19 Nucleic Acid Testing
Viruses
RNA, Viral
Medicine
SARS CoV 2
Pathogens
Research Article
SARS coronavirus
Science
Research and Analysis Methods
Microbiology
Sensitivity and Specificity
Specimen Handling
Diagnostic Medicine
Virology
Genetics
Humans
Gabon
Molecular Biology Techniques
Molecular Biology
Evolutionary Biology
Population Biology
SARS-CoV-2
Organisms
Viral pathogens
Biology and Life Sciences
COVID-19
Covid 19
Reverse Transcriptase-Polymerase Chain Reaction
Microbial pathogens
People and Places
Africa
[SDV.SPEE]Life Sciences [q-bio]/Santé publique et épidémiologie
Reagent Kits, Diagnostic
Population Genetics
Viral Transmission and Infection
Subjects
Details
- Language :
- English
- ISSN :
- 19326203
- Database :
- OpenAIRE
- Journal :
- PLoS ONE, PLoS ONE, Public Library of Science, 2022, 17 (1), pp.e0262733. ⟨10.1371/journal.pone.0262733⟩, PLoS ONE, Vol 17, Iss 1, p e0262733 (2022), PLoS ONE, Vol 17, Iss 1 (2022)
- Accession number :
- edsair.doi.dedup.....c33c9e687f365ddc599068e273644a74