Evaluation of different respiratory samples and saliva for the detection of SARS-CoV-2 RNA

Year 2021, Volume: 34 Issue: 1, 51 - 56, 29.01.2021

Rabia Can Sarınoglu Deniz Guneser Buket Erturk Sengel Volkan Korten Aysegul Karahasan Yagcı

https://doi.org/10.5472/marumj.866658

Cited By: 2

Abstract

Objective: We aimed to analyse the positivity rate and cycle threshold values indicating viral loads for SARS CoV-2 among different
respiratory specimens. Additionally, we evaluated the diagnostic efficacy of saliva samples.
Patients and Methods: We included combined oropharyngeal and nasopharyngeal swab (cONS), sputum, and tracheal aspirate
(TA) specimens of patients. Unpreserved saliva samples were collected prospectively from hospitalized patients within 72 hours of
admission. SARS CoV-2 RNA was extracted by using Bio-Speedy viral nucleic acid buffer than RT-PCR was performed with Bio-
Speedy COVID-19 qPCR detection kit.
Results: Retrospective evaluation revealed SARS CoV-2 RNA in 19.66% of cONS (n: 5819), 30.77% of sputum (n: 39), 29.41% of TA
samples (n: 34) from 4812 patients. In the majority (86.72%) of the samples, the first cONS sample was positive. Consecutive cONS
and sputum/TA samples were investigated in 52 patients of whom 11 were positive with either of these samples. Saliva positivity was
detected in 60% of cONS positive (n: 20) and 30% of cONS negative (n: 12) patients.
Conclusion: Although, cONS samples show the greatest diagnostic guidance, repeated sampling from multiple sites of the respiratory
tract increases the possibility of COVID-19 diagnosis. Saliva samples might be considered as an alternative specimen.

Keywords

SARS CoV-2, OVID-19, RT-PCR, Upper respiratory samples, Saliva, Cycle threshold

References

• 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. doi:10.1056/NEJMoa2001017.
• World Health Organization. Diagnostic testing for SARSCoV- 2, interim guidance. https://www.who.int/publications/i/ item/diagnostic-testing-for-sars-cov-2 (accessed 20 September 2020).
• World Health Organization. COVID 19 Weekly Epidemiological Update, file:///C:/Users/HP/Downloads/20201201_Weekly_ Epi_Update_16.pdf, (accessed 3 December 2020).
• Turkish Ministry of Health, https://covid19.saglik.gov.tr/, (accessed 3 December 2020).
• See A, Toh ST. Respiratory sampling for severe acute respiratory syndrome coronavirus 2: An Overview. Head Neck 2020;42:1652-6. doi:10.1002/hed.26232.
• Zou L, Ruan F, Huang M, et al. SARS-CoV-2 Viral load in upper respiratory specimens of infected patients. N Engl J Med 2020;382:1177-9. doi: 10.1056/NEJMc2001737.
• Xie C, Jiang L, Huang G, et al. Comparison of different samples for 2019 novel coronavirus detection by nucleic acid amplification tests. Int J Infect Dis 2020;93:264-7. doi: 10.1016/j.ijid.2020.02.050.
• Centers for Disease Control and Prevention. Interim Guidelines for Collecting. Handling, and Testing Clinical Specimens from Persons for Coronavirus Disease 2019 (COVID-19). https://www.cdc.gov/coronavirus/2019-ncov/ lab/guidelines-clinical-specimens.html, (accessed September 19, 2020).
• The Republic of Turkey, Ministry of Health, Directorate General of Public Health, COVID 19 (SARS-CoV-2 Infection) Guide, Study of Scientific Board, General Information, Epidemiology and Diagnosis, 30 May 2020, https://hsgm. saglik.gov.tr/depo/birimler/goc_sagligi/covid19/rehber/ COVID-19_Rehberi20200414_eng_v4_002_14.05.2020.pdf, (accessed 1 November 2020).
• Pan Y, Zhang D, Yang P, Poon LLM, Wang Q. Viral load of SARS-CoV-2 in clinical samples. Lancet Infect Dis 2020;20:411-2. doi:10.1016/S1473-3099(20)30113-4.
• Huang Y, Chen S, Yang Z, et al. SARS-CoV-2 viral load in clinical samples from critically ill patients. Am J Respir Crit Care Med 2020;201:1435-8. doi:10.1164/rccm.202.003.0572LE.
• Patel R, Babady E, Theel ES, et al. Report from the American Society for Microbiology COVID-19 International Summit, 23 March 2020: Value of diagnostic testing for SARS-CoV-2/ COVID-19. mBio 2020;11:e00722-20. doi: 10.1128/mBio.
• Williams E, Bond K, Zhang B, Putland M, Williamson DA. Saliva as a noninvasive specimen for detection of SARSCoV- 2. J Clin Microbiol 2020;58:e00776-20. doi: 10.1128/ JCM.00776-20.
• To KK, Tsang OT, 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;20:575-84. doi:https://doi.org/10.1016/S1473-3099(19)30626-7.
• Guidance on regulations for the transport of infectious substances 2019–2020. Geneva: World Health Organization: https://www.who.int/ihr/publications /WHO – WHECPI- 2019.20/en/. (accessed 10 September 2020).
• Yang J, Zheng Y, Gou X, et al. Prevalence of comorbidities and its effects in patients infected with SARS-CoV-2: a systematic review and meta-analysis. Int J Infect Dis 2020;94:91-5. doi: 10.1016/j.ijid.2020.03.017.
• Lauer SA, Grantz KH, Bi Q, et al. The incubation period of coronavirus disease 2019 (COVID-19) from publicly reported confirmed cases: Estimation and application. Ann Intern Med 2020;172:577-82. doi: 10.7326/M20-0504.
• Pascarella G, Strumia A, Piliego C, et al. COVID-19 diagnosis and management: a comprehensive review. J Intern Med 2020;288:192-206. doi: 10.1111/joim.13091.
• Wang W, Xu Y, Gao R, et al. Detection of SARS-CoV-2 in different types of clinical specimens. JAMA 2020;323:1843-4. doi:10.1001/jama.2020.3786.
• Liu R, Han H, Liu F, et al. Positive rate of RT-PCR detection of SARS-CoV-2 infection in 4880 cases from one hospital in Wuhan, China, from Jan to Feb 2020. Clin Chim Acta 2020;505:172-5. doi:10.1016/j.cca.2020.03.009.
• Zheng S, Fan J, Yu F, et al. Viral load dynamics and disease severity in patients infected with SARS-CoV-2 in Zhejiang province, China, January-March 2020: retrospective cohort study. BMJ 2020;369:m1443. doi: 10.1136/bmj.m1443.
• Li Y, Yao L, Li J, et al. Stability issues of RT-PCR testing of SARS-CoV-2 for hospitalized patients clinically diagnosed with COVID-19. J Med Virol 2020;92:903-908. doi: 10.1002/ jmv.25786.
• Yu F, Yan L, Wang N et al. Quantitative Detection and Viral Load Analysis of SARS-CoV-2 in Infected Patients. Clin Infect Dis. 2020;71:793-798. doi: 10.1093/cid/ciaa345. PMID: 32221523; PMCID: PMC7184442.
• McCormick-Baw C, Morgan K, Gaffney D, et al. Saliva as an alternate specimen source for detection of SARS-CoV-2 in symptomatic patients using Cepheid Xpert Xpress SARSCoV- 2. J Clin Microbiol 2020;58:e01109-20. doi: 10.1128/ JCM.01109-20.
• Azzi L, Carcano G, Gianfagna F, et al. Saliva is a reliable tool to detect SARS-CoV-2. J Infect 2020;81:e45-e50. doi:10.1016/j. jinf.2020.04.005.
• 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 :S1198-743X(20)30278-0. doi:10.1016/j.cmi.2020.05.001.