Comparing Nasopharyngeal Swab and Early Morning Saliva for the Identification of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2)

Mohan Rao, Fairuz A Rashid, Fashihah S A H Sabri, Nur Nadia Jamil, Rozainanee Zain, Rohaidah Hashim, Fairuz Amran, Huey Tean Kok, Md Anuar Abd Samad, Norazah Ahmad, Mohan Rao, Fairuz A Rashid, Fashihah S A H Sabri, Nur Nadia Jamil, Rozainanee Zain, Rohaidah Hashim, Fairuz Amran, Huey Tean Kok, Md Anuar Abd Samad, Norazah Ahmad

Abstract

Background: The ideal severe acute respiratory syndrome coronavirus 2 (SARs-CoV-2) testing method would be accurate and also be patient-performed to reduce exposure to healthcare workers. The aim of this study was to compare patient-performed testing based on a morning saliva sample with the current standard testing method, healthcare worker-collected sampling via a nasopharyngeal swab (NPS).

Methods: This was a prospective single center study which recruited 217 asymptomatic adult male participants in a coronavirus disease 2019 (COVID-19) quarantine center who had tested positive for SARS-CoV-2 8-10 days prior to isolation. Paired NPS and saliva specimens were collected and processed within 5 hours of sample collection. Real time reverse transcription polymerase chain reaction (RT-PCR) targeting Envelope (E) and RNA-dependent RNA polymerase (RdRp) genes was performed and the results were compared.

Results: Overall, 160 of the 217 (74%) participants tested positive for COVID-19 based on saliva, NPS, or both testing methods. The detection rate for SARS-CoV-2 was higher in saliva compared to NPS testing (93.1%, 149/160 vs 52.5%, 84/160, P < .001). The concordance between the 2 tests was 45.6% (virus was detected in both saliva and NPS in 73/160), whereas 47.5% were discordant (87/160 tested positive for 1 whereas negative for the other). The cycle threshold (Ct) values for E and RdRp genes were significantly lower in saliva specimens compared to NP swab specimens.

Conclusions: Our findings demonstrate that saliva is a better alternative specimen for detection of SARS-CoV-2. Taking into consideration, the simplicity of specimen collection, shortage of PPE and the transmissibility of the virus, saliva could enable self-collection for an accurate SARS-CoV-2 surveillance testing.

Keywords: COVID-19; SARS-CoV-2; nasopharyngeal swab; pandemic; saliva.

© The Author(s) 2020. Published by Oxford University Press for the Infectious Diseases Society of America.

Figures

Figure 1.
Figure 1.
Boxplots of SARS-CoV-2 Ct value (mean and interquartile range) of both E-gene and RdRp-gene of all the positive specimens. Ct values of both genes were lower in the saliva than nasopharyngeal swabs of studied asymptomatic individuals. Also included are Ct values of internal control (Human RnaseP-gene) of all the samples in both specimens. Abbreviations: Ct, cycle threshold; SARS-CoV-2, severe acute respiratory syndrome coronavirus 2.
Figure 2.
Figure 2.
Histogram represents distribution of Ct value of concordant (matched) specimens (n = 73) compared between specimen types and the targeted genes. Saliva has large distribution of Ct value of all the targeted genes in comparison to NPS. Meanwhile, nasopharyngeal swab shares most density of the histogram edging the upper limit. Abbreviation: Ct, cycle threshold.

References

    1. Phan T. Novel coronavirus: from discovery to clinical diagnostics. Infect Genet Evol 2020; 79:104211.
    1. Nishiura H, Linton NM, Akhmetzhanov AR, et al. . Initial cluster of novel coronavirus (2019-nCoV) infections in Wuhan, China, is consistent with substantial human-to-human transmission. J Clin Med 2020; 9:488.
    1. Tharanya Arumugam RK. 325 medical workers test positive for Covid-19. News Strait Times, NST [Internet]. 2020. [cited 2020 Jul 29]. Available at:
    1. Zhu N, Zhang D, Wang W, et al. ; China Novel Coronavirus Investigating and Research Team . A novel coronavirus from patients with pneumonia in China, 2019. N Engl J Med 2020; 382:727–33.
    1. Lin X, Gong Z, Xiao Z, Xiong J, Fan B, Liu J. Novel coronavirus pneumonia outbreak in 2019: computed tomographic findings in two cases. Korean J Radiol 2020; 21:365–8.
    1. To KK-WW, Tsang OT-YY, Yip CC-Y, et al. . Consistent detection of 2019 novel coronavirus in Saliva. Clin Infect Dis. 2020:4–6. Available at: .
    1. Bastola A, Sah R, Rodriguez-Morales AJ, et al. . The first 2019 novel coronavirus case in Nepal. Lancet Infect Dis 2020; 20:279–80.
    1. Zhang W, Du RH, Li B, et al. . Molecular and serological investigation of 2019 nCoV infected patients: implication of multiple shedding routes. Emerg Microbes Infect 2020; 9:386–9.
    1. To KKW, Yip CCY, Lai CYW, et al. . Saliva as a diagnostic specimen for testing respiratory virus by a point-of-care molecular assay: a diagnostic validity study. Clin Microbiol Infect 2019; 25:372–8.
    1. The jamovi project. jamovi - Stats. Open. Now. [Internet]. Version 1.2.2020. [cited 2020 Jun 22]. Available at: .
    1. World Health Organization. Guidelines for the collection of clinical specimens during field investigation of outbreaks WHO/CDS/CSR/EDC/2000.4. World Health Organization, 2000:1–51. Available at: . Accessed 22 June 2020.
    1. Wilson ML. General principles of specimen collection and transport. Clin Infect Dis 1996; 22:766–77.
    1. CDC. Interim guidelines for clinical specimens for COVID-19 | CDC. Centers for Disease Control and Prevention. 2020. [cited 2020 Jun 22]. Available at: .
    1. Landis JR, Koch GG. The measurement of observer agreement for categorical data. Biometrics 1977; 33:159.
    1. Pasomsub E, Watcharananan SP, Boonyawat K, et al. . Saliva sample as a non-invasive specimen for the diagnosis of coronavirus disease 2019: a cross-sectional study. Clin Microbiol Infect 2020.. doi:10.1016/j.cmi.2020.05.001. Available at: .
    1. Thompson WD, Walter SD. A reappraisal of the kappa coefficient. J Clin Epidemiol 1988; 41:949–58.
    1. Xu R, Cui B, Duan X, Zhang P, Zhou X, Yuan Q. Saliva: potential diagnostic value and transmission of 2019-nCoV. Int J Oral Sci 2020; 12:11.
    1. Azzi L, Carcano G, Gianfagna F, et al. . Saliva is a reliable tool to detect SARS-CoV-2. J Infect 2020; 1–6. doi:10.1016/j.jinf.2020.04.005.
    1. Wyllie AL, Fournier J, Casanovas-Massana A, et al. . Saliva is more sensitive for SARS-CoV-2 detection in COVID-19 patients than nasopharyngeal swabs. medRxiv. 2020. doi:10.11012020.04.16.20067835. Available at: .
    1. Williams E, Bond K, Zhang B, Putland M, Williamson DA. Saliva as a non-invasive specimen for detection of SARS-CoV-2. J Clin Microbiol 2020;50. Available at: .
    1. Becker D, Sandoval E, Amin A, et al. . Saliva is less sensitive than nasopharyngeal swabs for COVID-19 detection in the community setting. medRxiv. 2020. doi:10.1101/2020.05.11.20092338. Available at: .
    1. Chau NVV, Lam VT, Dung NT, et al. . The natural history and transmission potential of asymptomatic SARS-CoV-2 infection. medRxiv [Internet]. 2020. doi:10.1101/2020.04.27.20082347. Available at: .
    1. Jamal AJ, Mozafarihashjin M, Coomes E, et al. . Sensitivity of nasopharyngeal swabs and saliva for the detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Clin Infect Dis. 2020.
    1. Tiwari M. Science behind human saliva. J Natural Sci Biol Med 2; 2011:53–8.
    1. Iwasaki S, Fujisawa S, Nakakubo S, et al. . Comparison of SARS-CoV-2 detection in nasopharyngeal swab and saliva. J Infect 2020; 81:e145–7.
    1. Chen Y, Chen L, Deng Q, et al. . The presence of SARS-CoV-2 RNA in the feces of COVID-19 patients. J Med Virol 2020; 92:833–40.
    1. Wang W, Xu Y, Gao R, et al. . Detection of SARS-CoV-2 in different types of clinical specimens. JAMA 2020;323:2–3.
    1. Quilty BJ, Clifford S, Flasche S, Eggo RM. Effectiveness of airport screening at detecting travellers infected with novel coronavirus (2019-nCoV). Eurosurveillance 2020; 25:2000080.
    1. Chen Q, Zheng Z, Zhang C, et al. . Clinical characteristics of 145 patients with corona virus disease 2019 (COVID-19) in Taizhou, Zhejiang, China. Infection 2020;1:3.
    1. Ranney ML, Griffeth V, Jha AK. Critical supply shortages: the need for ventilators and personal protective equipment during the Covid-19 pandemic. N Engl J Med; 2020; 382:E41.
    1. To KKWW, Yip CCYY, Lai CYWW, et al. Saliva as a diagnostic specimen for testing respiratory virus by a point-of-care molecular assay: a diagnostic validity study. Clin Microbiol Infect; 2019; 25:372–8. Available at: .

Source: PubMed

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