Original Research

Evaluation of the concordance between nasopharyngeal and oropharyngeal swabs in the detection of COVID-19

Michel C. Tommo Tchouaket, Joseph Fokam, Ezéchiel N. Semengue, Yagai Bouba, Collins A. Chenwi, Alex D. Nka, Mirice Mbazo'o, Désiré Takou, Samuel M. Sosso, Grace A. Beloumou, Aude C. Ka’e, Aurelie M. Ngueko, Nadine Fainguem, Laeticia Y. Heunko, Sandrine C. Ndjeyep, Willy L. Pabo, Davy-Hyacinthe G. Anguechia, Naomi-Karell Etame, Evariste Molimbou, Rachel A. Mundo, Aissatou Abba, Gregory-Edie Halle-Ekane, Anne-Cecile Z.K. Bissek, Vittorio Colizzi, Carlo-Federico Perno, Alexis Ndjolo
Journal of Public Health in Africa | Vol 17, No 1 | a1236 | DOI: https://doi.org/10.4102/jphia.v17i1.1236 | © 2026 Michel C. Tommo Tchouaket, Joseph Fokam, Ezéchiel N. Semengue, Yagai Bouba, Collins A. Chenwi, Alex D. Nka, Mirice Mbazo’o, Désiré Takou, Samuel M. Sosso, Grâce A. Beloumou, Aude C. Ka’e, Aurelie M. Ngueko, Nadine Fainguem, Laeticia Y. Heunko, Sandrine C. | This work is licensed under CC Attribution 4.0
Submitted: 19 December 2024 | Published: 26 February 2026

About the author(s)

Michel C. Tommo Tchouaket, Chantal Biya International Reference Centre for Research on HIV/AIDS Prevention and Management (CIRCB), Yaoundé School of Health Sciences, Catholic University of Central Africa, Yaoundé, Cameroon
Joseph Fokam, Chantal Biya International Reference Centre for Research on HIV/AIDS Prevention and Management (CIRCB), Yaoundé School of Health Sciences, Catholic University of Central Africa, Yaoundé Faculty of Health Sciences, University of Buea, Buea, Cameroon
Ezéchiel N. Semengue, Chantal Biya International Reference Centre for Research on HIV/AIDS Prevention and Management (CIRCB), Yaoundé, Cameroon Faculty of Science and Technology, Evangelical University of Cameroon, Bandjoun, Cameroon University of Rome ‘Tor Vergata’, Rome, Italy
Yagai Bouba, Chantal Biya International Reference Centre for Research on HIV/AIDS Prevention and Management (CIRCB), Yaoundé, Cameroon University of Rome ‘Tor Vergata’, Rome, Italy
Collins A. Chenwi, Chantal Biya International Reference Centre for Research on HIV/AIDS Prevention and Management (CIRCB), Yaoundé, Cameroon University of Rome ‘Tor Vergata’, Rome, Italy
Alex D. Nka, Chantal Biya International Reference Centre for Research on HIV/AIDS Prevention and Management (CIRCB), Yaoundé, Cameroon Faculty of Science and Technology, Evangelical University of Cameroon, Bandjoun, Cameroon University of Rome ‘Tor Vergata’, Rome, Italy
Mirice Mbazo'o, Faculty of Medicine and Biomedical Sciences, University of Yaoundé I, Yaoundé, Cameroon
Désiré Takou, Chantal Biya International Reference Centre for Research on HIV/AIDS Prevention and Management (CIRCB), Yaoundé, Cameroon
Samuel M. Sosso, Chantal Biya International Reference Centre for Research on HIV/AIDS Prevention and Management (CIRCB), Yaoundé, Cameroon
Grace A. Beloumou, Chantal Biya International Reference Centre for Research on HIV/AIDS Prevention and Management (CIRCB), Yaoundé, Cameroon
Aude C. Ka’e, Chantal Biya International Reference Centre for Research on HIV/AIDS Prevention and Management (CIRCB), Yaoundé, Cameroon University of Rome ‘Tor Vergata’, Rome, Italy
Aurelie M. Ngueko, Chantal Biya International Reference Centre for Research on HIV/AIDS Prevention and Management (CIRCB), Yaoundé, Cameroon University of Rome ‘Tor Vergata’, Rome, Italy
Nadine Fainguem, Chantal Biya International Reference Centre for Research on HIV/AIDS Prevention and Management (CIRCB), Yaoundé, Cameroon University of Rome ‘Tor Vergata’, Rome, Italy
Laeticia Y. Heunko, Chantal Biya International Reference Centre for Research on HIV/AIDS Prevention and Management (CIRCB), Yaoundé, Cameroon
Sandrine C. Ndjeyep, Chantal Biya International Reference Centre for Research on HIV/AIDS Prevention and Management (CIRCB), Yaoundé, Cameroon
Willy L. Pabo, Chantal Biya International Reference Centre for Research on HIV/AIDS Prevention and Management (CIRCB), Yaoundé, Cameroon
Davy-Hyacinthe G. Anguechia, Chantal Biya International Reference Centre for Research on HIV/AIDS Prevention and Management (CIRCB), Yaoundé Faculty of Medicine and Biomedical Sciences, University of Yaoundé I, Yaoundé, Cameroon
Naomi-Karell Etame, Chantal Biya International Reference Centre for Research on HIV/AIDS Prevention and Management (CIRCB), Yaoundé Faculty of Medicine and Biomedical Sciences, University of Yaoundé I, Yaoundé, Cameroon
Evariste Molimbou, Chantal Biya International Reference Centre for Research on HIV/AIDS Prevention and Management (CIRCB), Yaoundé Faculty of Science and Technology, University of Yaoundé I, Yaoundé, Cameroon
Rachel A. Mundo, Chantal Biya International Reference Centre for Research on HIV/AIDS Prevention and Management (CIRCB), Yaoundé, Cameroon
Aissatou Abba, Chantal Biya International Reference Centre for Research on HIV/AIDS Prevention and Management (CIRCB), Yaoundé, Cameroon
Gregory-Edie Halle-Ekane, School of Health Sciences, Catholic University of Central Africa, Yaoundé, Cameroon
Anne-Cecile Z.K. Bissek, Faculty of Medicine and Biomedical Sciences, University of Yaoundé I, Yaoundé Division of Health Operational Research, Ministry of Public Health, Yaoundé, Cameroon
Vittorio Colizzi, Chantal Biya International Reference Centre for Research on HIV/AIDS Prevention and Management (CIRCB), Yaoundé, Cameroon Faculty of Science and Technology, Evangelical University of Cameroon, Bandjoun, Cameroon University of Rome ‘Tor Vergata’, Rome, Italy
Carlo-Federico Perno, Chantal Biya International Reference Centre for Research on HIV/AIDS Prevention and Management (CIRCB), Yaoundé, Cameroon Bambino Gesu Pediatric Hospital, Rome, Italy
Alexis Ndjolo, Chantal Biya International Reference Centre for Research on HIV/AIDS Prevention and Management (CIRCB), Yaoundé Faculty of Medicine and Biomedical Sciences, University of Yaoundé I, Yaoundé, Cameroon

Abstract

Background: Nasopharyngeal swabs (NASO) cause discomfort for patients, which can discourage them from getting tested for COVID-19 and limit case detection. It is therefore necessary to consider an alternative, more comfortable swab.
Aim: Evaluated the concordance between nasopharyngeal and oropharyngeal sampling for COVID-19 diagnosis in the Cameroonian context.
Setting: This study was carried out at “Chantal Biya” International Reference Centre for Research on HIV/AIDS Prevention and Management (CIRCB) in Yaoundé, Cameroon.
Methods: A comparative study was conducted in April 2021 among consenting participants tested for COVID-19 at “Chantal Biya” International Reference Centre for Research on HIV/AIDS Prevention and Management (CIRCB) in Yaoundé, Cameroon. Sampling began with nasopharyngeal swabs, followed by oropharyngeal swabs, all taken by the same technician, and analysis was carried out using polymerase chain reaction (PCR) tests on the Abbott platform. Statistical analyses were performed using GraphPad version 6.0; p < 0.05 was considered statistically significant.
Results: A total of 154 participants were enrolled (59.7% male, median age 38 years, interquartile range [IQR]: 30–49). Following PCR testing, the overall COVID-19 positivity rate was 36.36% (56/154), with 34.41% (n = 53/154) in nasopharyngeal versus 16.23% (n = 25/154) in oropharyngeal samples, p < 0.0002. The overall concordance rate was 78% (n = 120/154), with 39.28% positive concordance and 74.24% negative concordance (kappa = 0.441 [0.289–0.513]). According to severe acute respiratory syndrome coronavirus 2 viral load, the positive concordance was improved with high viral load (cycle threshold [CT]: ≤ 25): 61% (n = 11/18) versus 31% (n = 11/35) with low viral load (CT > 25), p = 0.037; odds ratio (OR) = 3.43. According to gender, the positive concordance was higher in men, 55% (n = 16/29), versus 25% (n = 6/24) in women, p = 0.021; OR = 0.27. Using nasopharyngeal swab as the gold standard, oropharyngeal swab had a sensitivity of 41.50% (n = 22/53), specificity 97.02% (n = 98/101), positive predictive value (PPV) 88% (n = 22/25) and negative predictive value (NPV) 76% (n = 98/129).
Conclusion: Our evidence suggests a superiority effect of nasopharyngeal in detecting cases of COVID-19. However, the overall high PPV of oropharyngeal swab, and its improved performance with high viral load.
Contribution: Therefore, in case of counter-indication to nasopharyngeal swabbing, oropharyngeal can be an acceptable alternative.


Keywords

concordance; COVID-19; nasopharyngeal swabs; oropharyngeal swabs; detection

Sustainable Development Goal

Goal 3: Good health and well-being

Metrics

Total abstract views: 275
Total article views: 364


Crossref Citations

No related citations found.