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