Spit or Swab? The Diagnostic Accuracy of Saliva-Based Testing as a Sars-Cov-2 Surveillance Tool
DOI:
https://doi.org/10.21141/PJP.2022.14Keywords:
qRT-PCR, rapid antigen test, pooling, SARS-CoV-2, COVID-19Abstract
Background. Nasopharyngeal swab/oropharyngeal swab (NPS/OPS) qRT-PCR is the gold standard for detecting SARS-CoV-2. However, it has its own limitations including cost and invasiveness. As an alternative, individual qRT-PCR testing of saliva samples was validated and shown to be comparable in sensitivity and specificity with NP-OP qRT-PCR. To further maximize its utility, the researchers wish to explore antigen and pooled testing methods.
Objective. The study aimed to evaluate the diagnostic accuracy of detecting SARS-CoV-2 infection using saliva-based pooled qRT-PCR and rapid antigen test compared with individual saliva qRT-PCR.
Methodology. In this retrospective cross-sectional study, saliva specimen from individuals aged 18 years old and above from the outpatient specimen collection station at the Philippine Children’s Medical Center were tested individually using qRT-PCR (Mag-bind RNA Extraction Kit/MACURA, Allsheng Extraction Machine, Sansure PCR kit, and MA-600 Sansure Biotech). Non-probability convenience sampling was utilized. Based on the individual results, pools of five (5) individual specimens, which includes one (1) positive sample were tested with qRT-PCR for sensitivity. DNK-2150-1S Dynamiker SARS-CoV-2 Ag Rapid Test (Dynamiker Biotechnology Co., Ltd., Tianjin, China) was also used to test individual saliva specimens.
. Out of 196 individual saliva specimens, 73 were detected to have SARS-COV-2 by qRT-PCR, while the remaining 123 were negative. Compared with the individual saliva qRT-PCR, rapid antigen tests done showed sensitivity of 46.58% (95% CI 35.13%, 58.02%), specificity of 86.18% (95% CI 80.08%, 92.28%), positive and negative predictive value of 66.67% (95% CI 53.71%, 79.60%) and 73.10% (95% CI 65.89%, 80.32%) respectively. Based on the results of individual saliva-based qRT-PCR, 62 pools were tested and showed sensitivity of 98.39% (95% CI 91.34%, 99.96%).
Conclusion and Recommendation. Pooled saliva-based testing for SARS-CoV-2 is comparable with individual saliva-based rapid antigen testing. The use of rapid antigen testing is less sensitive and less specific compared with qRT-PCR consistent with prior reports. Additional studies are recommended to determine optimal conditions for testing.
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2. Lo R, Barrientos A, Espiritu B, Santiago FK, et al. An Evaluation of pooling strategies for RT-qPCR testing for SARS-CoV-2 infection: a pragmatic multi-site parallel operational study. Philipp J Pathol. 2020;5(2):12–33. https://doi.org/10.21141/PJP.2020.12.
3. Cerutti F, Burdino E, Milia MG, et al. Urgent need of rapid tests for SARS CoV-2 antigen detection: evaluation of the SD-Biosensor antigen test for SARS-CoV-2. J Clin Virol. 2020;132:104654. https://pubmed.ncbi.nlm.nih.gov/3305349. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7522649. https://doi.org/10.1016/j.jcv.2020.104654.
4. Duque FT. Interim guidelines for the conduct of saliva-based RT-PCR testing for the detection of SARS CoV-2; 2021. Department of Health. https://doh.gov.ph/sites/default/files/health-update/dm2021-0161.pdf. Accessed February 14, 2021.
5. Fogarty A, Joseph A, Shaw D. Pooled saliva samples for COVID-19 surveillance programme. Lancet Respir Med. 2020;8(11):1078–80. https://pubmed.ncbi.nlm.nih.gov/32976755. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7508511. https://doi.org/10.1016/S2213-2600(20)30444-6.
6. Mina MJ, Parker R, Larremore DB. Rethinking Covid-19 test sensitivity - a strategy for containment. N Engl J Med. 2020;383(22):e120. https://pubmed.ncbi.nlm.nih.gov/32997903. https://doi.org/10.1056/NEJMp2025631.
7. Ranoa DRE, Holland RL, Alnaji FG, et al. Saliva-based molecular testing for SARS-CoV-2 that Bypasses RNA extraction. bioRxiv. https://doi.org/10.1101/2020.06.18.159434.
8. To KK-W, Tsang OT-Y, Leung WS, et al. Temporal profiles of viral load in posterior oropharyngeal saliva samples and serum antibody responses during infection by SARS-CoV-2: an observational cohort study. Lancet Infect Dis. 2020;20(5):565–74. https://pubmed.ncbi.nlm.nih.gov/32213337. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7158907. https://doi.org/10.1016/S1473-3099(20)30196-1.
9. Wyllie AL, Fournier J, Casanovas-Massana A, et al. Saliva or nasopharyngeal swab specimens for detection of SARS-CoV-2. N Engl J Med. 2020;383(13):1283–6. https://pubmed.ncbi.nlm.nih.gov/32857487. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7484747. https://doi.org/10.1056/NEJMc2016359.
10. Watkins AE, Fenichel EP, Weinberger DM, et al. Increased SARAS-CoV-2 testing capacity with pooled saliva samples. Emerg Infect Dis. 2021;27(4):1184-7. https://pubmed.ncbi.nlm.nih.gov/33755009. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8007323. https://doi.org/10.3201/eid2704.204200.
11. Nagura-Ikeda M, Imai K, Tabata S, et al. Clinical evaluation of self-collected saliva by quantitative reverse transcription-PCR (RT-qPCR), direct RT-qPCR, reverse transcription–loop-mediated isothermal amplification, and a rapid antigen test to diagnose COVID-19. J Clin Microbiol. 2020;58(9) :e01438-20. https://pubmed.ncbi.nlm.nih.gov/32636214. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7448663. https://doi.org/10.1128/JCM.01438-20.
12. Barat B, Das S, De Giorgi V, et al. Pooled saliva specimens for SARS-CoV-2 testing. J Clin Microbiol. 2021;59(3): e02486-20. https://pubmed.ncbi.nlm.nih.gov/33262219. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8106731. https://doi.org/10.1128/JCM.02486-20.
13. Rainey A, Pierce A, Deng X, et al. Validation and deployment of a direct saliva real-time RT-PCR test on pooled samples for COVID-19 surveillance testing. PLoS One. 2021;16(12):e0261956. https://pubmed.ncbi.nlm.nih.gov/34969053. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8718011. https://doi.org/10.1371/journal.pone.0261956.
14. Dynamiker Biotechnology (Tianjin) Co. L. DNK-2105-1S Dynamiker SARS-CoV-2. http://en.dynamiker.com/index/index/pro_info/aid/640.html. Accessed October 20, 2021.
15. Dynamiker SARS-CoV-2 AG rapid test (saliva). FIND Diagnosis for all. https://www.finddx.org/test-directory/?subpage=variants-panel. Accessed October 20, 2021.
16. Diao B, Wen K, Chen J, et al. Diagnosis of acute respiratory syndrome coronavirus 2 infection by detection of nucleocapsid protein. medRxiv. https://doi.org/10.1101/2020.03.07.20032524. Accessed January 1, 2020.
17. De Marinis Y, Pesola A-K, Söderlund Strand A, Norman A, Pernow G, Aldén M, et al. Detection of SARS-CoV-2 by rapid antigen tests on saliva in hospitalized patients with COVID-19. Infect Ecol Epidemiol. 2021;11(1):1993535. https://pubmed.ncbi.nlm.nih.gov/34745449. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8567870. https://doi.org/10.1080/20008686.2021.1993535.
18. Hajian-Tilaki K. Sample size estimation in diagnostic test studies of biomedical informatics. J Biomed Inform. 2014;48:193–204. https://pubmed.ncbi.nlm.nih.gov/24582925. https://doi.org/10.1016/j.jbi.2014.02.013.
19. Department of Health Philippines. Department of Health - nCOV tracker; 2020. https://ncovtracker.doh.gov.ph/. Accessed September 18, 2020.
20. Oguri S, Fujisawa S, Kamada K, et al. Effect of varying storage conditions on diagnostic test outcomes of SARS-CoV-2. J Infect. 2021;83(1):119–45. https://pubmed.ncbi.nlm.nih.gov/33823203. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8018904. https://doi.org/10.1016/j.jinf.2021.03.026.
21. Buban JMA, Villanueva PN, Gregorio GE. Should RT-PCR of saliva samples be used for diagnosis of COVID19? Philippine COVID-19 Living Clinical Practice Guidelines Inst Clin Epidemiol Natl Institutes Heal UP Manila; 2021. Available from https://www.psmid.org/wp-content/uploads/2021/05/SALIVA-RT-PCR-CPG-FINAL_031521_MMA.pdf.
22. Butler-Laporte G, Lawandi A, Schiller I, et al. Comparison of saliva and nasopharyngeal swab nucleic acid amplification testing for Detection of SARS-CoV-2: a systematic review and meta-analysis. JAMA Intern Med. 2021;181(3):353-60. https://pubmed.ncbi.nlm.nih.gov/33449069. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7811189. https://doi.org/10.1001/jamainternmed.2020.8876.
23. The Health Technology Assessment Council (HTAC). HTAC recommendation on the use of saliva as an alternative specimen for RT-PCR testing; 2021. Available from https://hta.doh.gov.ph/wp-content/uploads/2021/05/Evidence_Summary_RT-PCR_Testing_for_COVID-19-Recommendation.pdf.
24. Product evaluation status antigen test kits. Research Institute for Tropical Medicine. https://ritm.gov.ph/covid-19-kit-evaluation/ongoing-evaluations/product-evaluation-status-antigen-test-kits/. Accessed January 29, 2022.
25. Seitz T, Schindler S, Winkelmeyer P, et al. Evaluation of rapid antigen tests based on saliva for the detection of SARS‐CoV‐2. J Med Virol. 2021;93(7):4161–2. https://pubmed.ncbi.nlm.nih.gov/33788280. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8251355. https://doi.org.10.1002/jmv.26983.
26. Potential for false positive results with antigen tests for rapid detection of SARS-CoV-2 - letter to clinical laboratory staff and health care providers. USFDA. https://www.fda.gov/medical-devices/letters-health-care-providers/potential-false-positive-results-antigen-tests-rapid-detection-sars-cov-2-letter-clinical-laboratory. Accessed January 29, 2022.
27. Gonong DA, Misiona G, Sionzon M, Santiago FK, Lira AJ, Lo R. Analysis of SARS-CoV-2 RT-PCR testing and pooling strategies for screening of asymptomatic individuals - the Philippine Children’s Medical Center experience. Philipp J Pathol. 2021;6(1):18–25. https://doi.org/10.21141/PJP.2021.03.
28. Sahajpal NS, Mondal AK, Ananth S, et al. SalivaSTAT: direct-PCR and pooling of saliva samples collected in healthcare and community setting for SARS-CoV-2 mass surveillance. Diagnostics (Basel). 2021;11(5):904. https://pubmed.ncbi.nlm.nih.gov/34069462. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8159081. https://doi.org/10.3390/diagnostics11050904.
29. Esteves E, Mendes AK, Barros M, et al. Population wide testing pooling strategy for SARS-CoV-2 detection using saliva. PLoS One. 2022;17(1):e0263033. https://pubmed.ncbi.nlm.nih.gov/35089942. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8797214. https://doi.org/10.1371/journal.pone.0263033.
30. Padua Jr. R. Diagnostic testing strategies to manage COVID-19 pandemic: proposed by the Philippine Society of Pathologists, Inc. Philipp J Pathol. 2020;5(1):5–8. https://doi.org/10.21141/PJP.2020.08.
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