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. 2023 Sep 14:46:21.
doi: 10.11604/pamj.2023.46.21.39483. eCollection 2023.

Comparative analysis of SARS-CoV-2 detection methods using stool, blood, and nasopharyngeal swab samples

Marceline Adhiambo Oloo  1 , Shehu Shagari Awandu  2 , Benson Onyango  1 , Richard Odongo Magwanga  1 , Alfred Ochieng Oluoch  1 , Shirley Lidechi  3 , Erick Mbata Muok  3 , Stephen Munga  3 , Benson Estambale  2
Affiliations

Comparative analysis of SARS-CoV-2 detection methods using stool, blood, and nasopharyngeal swab samples

Marceline Adhiambo Oloo et al. Pan Afr Med J. .

Abstract

Introduction: as a public health policy, the ongoing global coronavirus disease 2019 vaccination drives require continuous tracking, tracing, and testing of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Diagnostic testing is important in virus detection and understanding its spread for timely intervention. This is especially important for low-income settings where the majority of the population remains untested. This is well supported by the fact that of about 9% of the Kenyan population had been tested for the virus.

Methods: this was a cross-sectional study conducted at the Kisumu and Siaya Referral Hospitals in Kenya. Here we report on the sensitivity and specificity of the rapid antigen detection test (Ag-RDT) of SARS-CoV-2 compared with the quantitative reverse transcriptase polymerase chain reaction (RT-qPCR) using stool and nasopharyngeal swab samples. Further, the mean Immunoglobulin M (IgM) and Immunoglobulin G (IgG) antibody levels among symptomatic and asymptomatic individuals in western Kenya were evaluated.

Results: the sensitivity and specificity of Ag-RDT were 76.3% (95% CI, 59.8-88.6%) and 96.3% (95% CI, 87.3-99.5%) with a negative and positive predictive value of 85% (95% CI, 73.8%-93.0%) and 93% (95% CI, 78.6%-99.2%) respectively. There was substantial agreement of 88% (Kappa value of 0.75, 95% CI, 0.74-0.77) between Ag-RDT and nasopharyngeal swab RT-qPCR, and between stool and nasopharyngeal swab RT-qPCR results (83.7% agreement, Kapa value 0.62, 95% CI 0.45-0.80). The mean IgM and IgG antibody response to SARS-CoV-2 were not different in asymptomatic individuals, 1.11 (95% CI, 0.78-1.44) and 0.88 (95% CI, 0.65-1.11) compared to symptomatic individuals 4.30 (95% CI 3.30-5.31) and 4.16 (95% CI 3.32 -5.00).

Conclusion: the choice of an appropriate SARS-CoV-2 diagnostic, screening, and surveillance test should be guided by the specific study needs and a rational approach for optimal results.

Keywords: Severe acute respiratory syndrome corona virus 2; enzyme-linked immunosorbent assay; immunoglobulin G; immunoglobulin M; polymerase chain reaction; rapid antigen detection test.

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Conflict of interest statement

The authors declare no competing interests.

Figures

Figure 1
Figure 1
map of the study sites in Kisumu and Siaya counties in western Kenya showing the sampling locations of Kisumu County Referral Hospital (KCRH) and the Siaya County Referral Hospital (SCRH)
Figure 2
Figure 2
prototypical STARD diagram to report flow of participants through the study
Figure 3
Figure 3
comparison between cycle thresholds for the targeted genes, the open reading frame 1ab (ORF1ab) and the nucleocapsid (N) in nasopharyngeal swab and stool samples
Figure 4
Figure 4
mean IgM and IgG antibody levels in COVID-19 asymptomatic and symptomatic patients
See this image and copyright information in PMC

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