MOLECULAR DETECTION PROTOCOL OF SARS-COV-2 THROUGH SELF-COLLECTED SALIVA SPECIMENS VERSUS NASOPHARYNGEAL SWABS

Authors

  • Abderrezak GHIDOUCHE 1Faculté des Sciences de la Nature et de la Vie, Université de Bejaia, Bejaia, Algérie. 2Laboratoire de Génie Biologique des Cancers, Université de Bejaia, Bejaia, Algérie.
  • Sarah HALLOUCHE 2Laboratoire de Génie Biologique des Cancers, Université de Bejaia, Bejaia, Algérie. 3Faculté de Médecine, Université de Bejaia, Bejaia, Algérie.
  • Djida AIT-ALI 1Faculté des Sciences de la Nature et de la Vie, Université de Bejaia, Bejaia, Algérie. 2Laboratoire de Génie Biologique des Cancers, Université de Bejaia, Bejaia, Algérie.
  • Lila BOUDRAHEM-HANNOU 3Faculté de Médecine, Université de Bejaia, Bejaia, Algérie. 4Service des maladies infectieuses, CHU de Bejaia, Algérie.
  • Hamid NOURI Laboratoire de Microbiologie Appliquée, Université de Bejaia, Bejaia, Algérie. Faculté des Sciences de la Nature et de la Vie, Université de Bejaia, Bejaia, Algérie.
  • Souhil TLIBA Laboratoire de Génie Biologique des Cancers, Université de Bejaia, Bejaia, Algérie. Service de Neurochirurgie, CHU de Blida, Algérie
  • Idir BITAM Ecole Supérieure en Sciences de l'Aliment et des Industries Agroalimentaires (ESSAIA), El Harrach, Alger, Algérie. Aix Marseille Univ, IRD, VITROME, IHU Méditerranée Infection, Marseille, France.
  • Adel AMIROUCHE Uiversity of BEJAIA

DOI:

https://doi.org/10.21010/Ajidv18i2.1

Keywords:

SARS-CoV-2, Diagnostic, Nasopharyngeal swab, Saliva, RT-PCR.

Abstract

Background : Various detection methods, based on specific nucleotide sequences of SARS-CoV-2, were rapidly developed and used as emergency laboratory applications. The most common diagnostic method for detecting SARS-CoV-2 infection is real-time quantitative reverse transcriptase-polymerase chain reaction (RT-qPCR).

Aims: Here, we carried out to assess the sensitivity and specificity of using saliva self-collected from adult and pediatric patients, as a biological sample for RT-PCR diagnosis.

Methods: We compared the sensitivity and specificity of RT-qPCR from 85 samples of adult and pediatric patient, including nasopharyngeal swabs (NPS) and saliva.

Results: Our RT-qPCR results provide that saliva samples showed the highest sensitivity followed by a nasopharyngeal swab for symptomatic as well as for asymptomatic adult patients. On the other hand, samples from symptomatic patients showed a higher sensitivity as compared to asymptomatic patients, while a cycle threshold (Ct) value exhibited a higher sensitivity as compared to higher Ct value. Together, including symptomatic and asymptomatic subjects, the overall agreement between the saliva sample and the nasopharyngeal is about 84%.

Conclusion: The sensitivity of saliva samples remains acceptable; it may still be a viable option in locations where laboratory facilities are lacking for diagnostic purposes in the early phase of the disease.

References

Amirouche, A., D. Ait-Ali, H. Nouri, L. Boudrahme-Hannou, S. Tliba, A. Ghidouche and I. Bitam. 2021. TRIzol-Based RNA Extraction for Detection Protocol for SARS-CoV-2 of Coronavirus Disease 2019. New Microbes and New Infections 41 (mai): 100874. https://doi.org/10.1016/j.nmni.2021.100874.

Báez-Santos, Yahira M., Sarah E. St. John and Andrew D. Mesecar. 2015. The SARS-Coronavirus Papain-like Protease: Structure, Function and Inhibition by Designed Antiviral Compounds. Antiviral Research 115 (mars): 21‑38. https://doi.org/10.1016/j.antiviral.2014.12.015.

Beyerstedt, Stephany, Expedito Barbosa Casaro and Érika Bevilaqua Rangel. 2021. COVID-19: Angiotensin-Converting Enzyme 2 (ACE2) Expression and Tissue Susceptibility to SARS-CoV-2 Infection. European Journal of Clinical Microbiology & Infectious Diseases 40 (5): 905‑19. https://doi.org/10.1007/s10096-020-04138-6.

Butler-Laporte, Guillaume, Alexander Lawandi, Ian Schiller, Mandy Yao, Nandini Dendukuri, Emily G. McDonald and Todd C. Lee. 2021. Comparison of Saliva and Nasopharyngeal Swab Nucleic Acid Amplification Testing for Detection of SARS-CoV-2: A Systematic Review and Meta-Analysis. JAMA Internal Medicine 181 (3): 353. https://doi.org/10.1001/jamainternmed.2020.8876.

Fan, Guang, Xuan Qin, Daniel N. Streblow, Cristina Magallanes Hoyos and Donna E. Hansel. 2021. Comparison of SARS-CoV-2 PCR-Based Detection Using Saliva or Nasopharyngeal Swab Specimens in Asymptomatic Populations. Microbiology Spectrum 9 (1): e00062-21. https://doi.org/10.1128/Spectrum.00062-21.

Hoffmann M, Kleine-Weber H, Schroeder S, Krüger N, Herrler T, Erichsen S, Schiergens TS, Herrler G, Wu NH, Nitsche A, Müller MA, Drosten C and Pöhlmann S. 2020. SARS-CoV-2 Cell Entry Depends on ACE2 and TMPRSS2 and Is Blocked by a Clinically Proven Protease Inhibitor. Cell 181 (2): 271-280.e8. https://doi.org/10.1016/j.cell.2020.02.052.

Jamal AJ, Mozafarihashjin M, Coomes E, Powis J, Li AX, Paterson A, Anceva-Sami S, Barati S, Crowl G, Faheem A, Farooqi L, Khan S, Prost K, Poutanen S, Taylor M, Yip L, Zhong XZ, McGeer AJ, Mubareka S; Toronto Invasive Bacterial Diseases Network COVID-19 Investigators. 2021. Sensitivity of Nasopharyngeal Swabs and Saliva for the Detection of Severe Acute Respiratory Syndrome Coronavirus 2. Clinical Infectious Diseases 72 (6): 1064‑66. https://doi.org/10.1093/cid/ciaa848.

Karim, Salim S Abdool and Quarraisha Abdool Karim. 2021. Omicron SARS-CoV-2 Variant: A New Chapter in the COVID-19 Pandemic. The Lancet 398 (10317): 2126‑28. https://doi.org/10.1016/S0140-6736(21)02758-6.

Laiton-Donato K, Franco-Muñoz C, Álvarez-Díaz DA, Ruiz-Moreno HA, Usme-Ciro JA, Prada DA, Reales-González J, Corchuelo S, Herrera-Sepúlveda MT, Naizaque J, Santamaría G, Rivera J, Rojas P, Ortiz JH, Cardona A, Malo D, Prieto-Alvarado F, Gómez FR, Wiesner M, Martínez MLO and Mercado-Reyes M. 2021. Characterization of the Emerging B.1.621 Variant of Interest of SARS-CoV-2. Infection, Genetics and Evolution 95 (Nov): 105038. https://doi.org/10.1016/j.meegid.2021.105038.

Mestdagh P, Gillard M, Dhillon SK, Pirnay JP, Poels J, Hellemans J, Hutse V, Vermeiren C, Boutier M, De Wever V, Soentjens P, Djebara S, Malonne H, André E, Arbyn M, Smeraglia J and Vandesompele J. 2021. Evaluating Diagnostic Accuracy of Saliva Sampling Methods for Severe Acute Respiratory Syndrome Coronavirus 2 Reveals Differential Sensitivity and Association with Viral Load. The Journal of Molecular Diagnostics 23 (10): 1249‑58. https://doi.org/10.1016/j.jmoldx.2021.07.017.

Mohammadi, Mehrdad, Mohammad Shayestehpour and Hamed Mirzaei. 2021. The Impact of Spike Mutated Variants of SARS-CoV2 [Alpha, Beta, Gamma, Delta, and Lambda] on the Efficacy of Subunit Recombinant Vaccines. The Brazilian Journal of Infectious Diseases 25 (4): 101606. https://doi.org/10.1016/j.bjid.2021.101606.

Mousavizadeh, Leila and Sorayya Ghasemi. 2021. Genotype and Phenotype of COVID-19: Their Roles in Pathogenesis. Journal of Microbiology, Immunology and Infection 54 (2): 159‑63. https://doi.org/10.1016/j.jmii.2020.03.022.

Nasiri, Kaveh and Aleksandra Dimitrova. 2021. Comparing Saliva and Nasopharyngeal Swab Specimens in the Detection of COVID-19: A Systematic Review and Meta-Analysis. Journal of Dental Sciences 16 (3): 799‑805. https://doi.org/10.1016/j.jds.2021.01.010.

Raman, Renuka, Krishna J. Patel and Kishu Ranjan. 2021. « COVID-19: Unmasking Emerging SARS-CoV-2 Variants, Vaccines and Therapeutic Strategies ». Biomolecules 11 (7): 993. https://doi.org/10.3390/biom11070993.

Sakanashi D, Asai N, Nakamura A, Miyazaki N, Kawamoto Y, Ohno T, Yamada A, Koita I, Suematsu H, Hagihara M, Shiota A, Kurumiya A, Sakata M, Kato S, Muramatsu Y, Koizumi Y, Kishino T, Ohashi W, Yamagishi Y and Mikamo H. 2021. Comparative Evaluation of Nasopharyngeal Swab and Saliva Specimens for the Molecular Detection of SARS-CoV-2 RNA in Japanese Patients with COVID-19. Journal of Infection and Chemotherapy 27 (1): 126‑29. https://doi.org/10.1016/j.jiac.2020.09.027.

Scott L, Hsiao NY, Moyo S, Singh L, Tegally H, Dor G, Maes P, Pybus OG, Kraemer MUG, Semenova E, Bhatt S, Flaxman S, Faria NR and de Oliveira T. 2021. Track Omicron’s Spread with Molecular Data. Science 374 (6574): 1454‑55. https://doi.org/10.1126/science.abn4543.

Tan, Steph H, Orchid Allicock, Mari Armstrong-Hough and Anne L Wyllie. 2021. Saliva as a Gold-Standard Sample for SARS-CoV-2 Detection . The Lancet Respiratory Medicine 9 (6): 562‑64. https://doi.org/10.1016/S2213-2600(21)00178-8.

To KK, Tsang OT, Yip CC, Chan KH, Wu TC, Chan JM, Leung WS, Chik TS, Choi CY, Kandamby DH, Lung DC, Tam AR, Poon RW, Fung AY, Hung IF, Cheng VC, Chan JF and Yuen KY. 2020. Consistent Detection of 2019 Novel Coronavirus in Saliva. Clinical Infectious Diseases 71 (15): 841‑43. https://doi.org/10.1093/cid/ciaa149.

To KK, Lu L, Yip CC, Poon RW, Fung AM, Cheng A, Lui DH, Ho DT, Hung IF, Chan KH and Yuen KY. 2017. Additional Molecular Testing of Saliva Specimens Improves the Detection of Respiratory Viruses. Emerging Microbes & Infections 6 (1): 1‑7. https://doi.org/10.1038/emi.2017.35.

Tsang, Nicole Ngai Yung, Hau Chi So, Ka Yan Ng, Benjamin J Cowling, Gabriel M Leung and Dennis Kai Ming Ip. 2021. Diagnostic Performance of Different Sampling Approaches for SARS-CoV-2 RT-PCR Testing: A Systematic Review and Meta-Analysis. The Lancet Infectious Diseases 21 (9): 1233‑45. https://doi.org/10.1016/S1473-3099(21)00146-8.

Van Boheemen S, de Graaf M, Lauber C, Bestebroer TM, Raj VS, Zaki AM, Osterhaus AD, Haagmans BL, Gorbalenya AE, Snijder EJ and Fouchier RA. 2012. Genomic Characterization of a Newly Discovered Coronavirus Associated with Acute Respiratory Distress Syndrome in Humans. Édité par Michael J. Buchmeier. MBio 3 (6): e00473-12. https://doi.org/10.1128/mBio.00473-12.

Wyllie AL, Fournier J, Casanovas-Massana A, Campbell M, Tokuyama M, Vijayakumar P, Warren JL, Geng B, Muenker MC, Moore AJ, Vogels CBF, Petrone ME, Ott IM, Lu P, Venkataraman A, Lu-Culligan A, Klein J, Earnest R, Simonov M, Datta R, Handoko R, Naushad N, Sewanan LR, Valdez J, White EB, Lapidus S, Kalinich CC, Jiang X, Kim DJ, Kudo E, Linehan M, Mao T, Moriyama M, Oh JE, Park A, Silva J, Song E, Takahashi T, Taura M, Weizman OE, Wong P, Yang Y, Bermejo S, Odio CD, Omer SB, Dela Cruz CS, Farhadian S, Martinello RA, Iwasaki A, Grubaugh ND and Ko AI. 2020. Saliva or Nasopharyngeal Swab Specimens for Detection of SARS-CoV-2. New England Journal of Medicine 383 (13): 1283‑86. https://doi.org/10.1056/NEJMc2016359.

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Published

2024-03-08

How to Cite

GHIDOUCHE, A., HALLOUCHE, S., AIT-ALI, D., BOUDRAHEM-HANNOU, L., NOURI, H., TLIBA, S., BITAM, I., & AMIROUCHE, A. (2024). MOLECULAR DETECTION PROTOCOL OF SARS-COV-2 THROUGH SELF-COLLECTED SALIVA SPECIMENS VERSUS NASOPHARYNGEAL SWABS. African Journal of Infectious Diseases (AJID), 18(2), 1–7. https://doi.org/10.21010/Ajidv18i2.1

Issue

Vol. 18 No. 2 (2024)

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Articles

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