|Year : 2020 | Volume
| Issue : 4 | Page : 346-348
Saliva as an alternate specimen source for the diagnosis of coronavirus disease 2019 in symptomatic patients using cepheid xpert xpress SARS-CoV-2
Maya Habous1, Rania Medhat Seliem1, Laila AlDabal2, Firas Al-Najjar3, Maimona Elimam1, Meera Jainmboo1, Bayan Abdalla1, Zahra Abdullahi1, Ayesha Nasser1
1 Department of Pathology, Rashid Hospital, Dubai, United Arab Emirates
2 Department of Medical Affairs, Infectious Diseases Unit, Rashid Hospital, Dubai, United Arab Emirates
3 Department of Emergency, Rashid Hospital, Dubai, United Arab Emirates
|Date of Submission||10-Sep-2020|
|Date of Acceptance||26-Sep-2020|
|Date of Web Publication||30-Dec-2020|
Dr. Maya Habous
Microbiology & Infection Control Unit, Pathology and Genetics Department, Rashid Hospital, Dubai
United Arab Emirates
Source of Support: None, Conflict of Interest: None
Background: Rapid and accurate SARS-CoV-2 diagnostic testing is essential for controlling the ongoing coronavirus disease 2019 (COVID-19) pandemic. The current gold standard for COVID-19 diagnosis is real-time reverse transcription-polymerase chain reaction (RT-PCR) detection of SARS-CoV-2 from nasopharyngeal swab (NPS) specimens. The objective of this study is to assess saliva specimens for the diagnosis of COVID-19 using the GeneXpert® Xpress SARS-CoV-2 assay. Materials and Methods: In June 2020, we prospectively simultaneously collected saliva samples and a standard NPS from 60 patients meeting case definition of COVID-19 in the Emergency Department and from inpatients in Rashid Hospital at Dubai Health Authority during the outbreak of COVID-19. Real-time RT-PCR using the Cepheid Xpert Xpress SARS-CoV-2 was performed, and the results of the two specimens were compared. Results: A total of 60 paired NPS and saliva specimens were tested. An analysis of the agreement between the two specimens demonstrated a 97% observed agreement. 30/28 samples were positive in saliva when compared to the NPS, resulting in a positive percent agreement of 93%. 30/32 samples had a negative saliva and NPS. Two samples demonstrated detectable levels of SARS-CoV-2 nucleic acid in the saliva, but the NPS was negative, resulting in a negative percent agreement of 94%. Conclusion: Our data showed that saliva is an acceptable sensitive and specific alternative source for detecting SARS-CoV-2 nucleic acid and the use of saliva samples is safer and more convenient for the patient. NPS sampling inconsistency may be one of the potential issues for false-negative results.
Keywords: Coronavirus disease 2019, saliva, SARS-CoV-2
|How to cite this article:|
Habous M, Seliem RM, AlDabal L, Al-Najjar F, Elimam M, Jainmboo M, Abdalla B, Abdullahi Z, Nasser A. Saliva as an alternate specimen source for the diagnosis of coronavirus disease 2019 in symptomatic patients using cepheid xpert xpress SARS-CoV-2. Biomed Biotechnol Res J 2020;4:346-8
|How to cite this URL:|
Habous M, Seliem RM, AlDabal L, Al-Najjar F, Elimam M, Jainmboo M, Abdalla B, Abdullahi Z, Nasser A. Saliva as an alternate specimen source for the diagnosis of coronavirus disease 2019 in symptomatic patients using cepheid xpert xpress SARS-CoV-2. Biomed Biotechnol Res J [serial online] 2020 [cited 2022 Jan 27];4:346-8. Available from: https://www.bmbtrj.org/text.asp?2020/4/4/346/305638
| Introduction|| |
SARS-CoV-2 is one of the epidemic human coronaviruses which include SARS-CoV and MERS-CoV. Other human pathogenic coronaviruses include HCoV-229E, HCoV-NL63, HCoV-OC43, and HCoV-HKU1 that are endemic.
One of the most important steps in containing emerging highly infectious viral epidemics is getting access to accurate and rapid diagnostic tools.
In the United Arab Emirates (UAE), as in many other countries, the diagnosis of SARS-CoV-2 relied on real-time polymerase chain reaction (PCR) tests using different platforms. Early in the course of the local epidemic, both oropharyngeal and nasopharyngeal swabs (NPSs) were used to confirm the diagnosis of coronavirus disease 2019 (COVID-19) infection. However, later on, managing physicians relied on nasopharyngeal collected samples only. This was always done by trained medical professionals, usually physicians in most diagnosis and admission facilities.
The collection of these specimen types is a relatively invasive method and requires close contact between health-care workers and patients, which may pose a risk of transmission of the virus to the health-care workers. Furthermore, the collection of nasopharyngeal or oropharyngeal specimens causes discomfort and may cause bleeding, especially in patients with thrombocytopenia.
With the increasing need for alternative sources, our hospital sought to validate saliva specimens for the diagnosis of COVID-19 using the Cepheid Xpert Xpress SARS-CoV-2 (Sunnyvale, CA) PCR test. Saliva specimens can be provided easily by asking patients to spit into a sterile bottle. Since no invasive procedures are required and nonaerosol generating, the collection of saliva can greatly minimize the chance of exposing health-care workers to 2019-nCoV. A previous study demonstrated that saliva has a high concordance rate of >90% with nasopharyngeal specimens in the detection of respiratory viruses, including coronaviruses., In some patients, coronavirus was detected only in saliva but not in nasopharyngeal aspirate, as NPS sampling inconsistency may be one of the potential issues for false negative, monitoring an internal control for proper sample collection, may provide an alternative evaluation technique. Saliva has also been used in screening respiratory viruses among hospitalized patients without fever or respiratory symptoms. SARS-CoV-2 can be detected in saliva at high titers.
The Xpert® Xpress SARS-CoV-2 assay is a sample to answer real-time reverse transcription (RT)-PCR test with a run time of approximately 45 min. The Xpert test (Cepheid, Sunnyvale, California, U. S. A) received EUA status on March 20, 2020. It is a platform to integrate specimen processing, nucleic acid extraction, RT-PCR amplification of SARS-CoV-2 RNA, and amplicon detection in a single cartridge. Specimens can be tested as soon as they are received as the testing instrument provides random access to individual cartridges. The test detects the nucleocapsid gene (N2) and the envelope gene (E). There are two targets, E and N2, where detection of both targets or N2 alone is considered positive and detection of E alone is considered presumptive positive.
Our hospital started using Cepheid Xpert Xpress SARS-CoV-2. With this rapid technology, the length of stay and time in isolation in the emergency department (ED) were decreased. Moreover, rapid triage decisions were made regarding patient disposition and isolation.
Our aim of this study was to evaluate saliva as an acceptable alternative source for detecting SARS-CoV-2 nucleic acid.
| Materials and Methods|| |
Study type and population
This is a prospective study conducted on June 2020 in the Pathology Department at Rashid Hospital, Dubai Health Authority, UAE. A total of 60 patients were selected for this study and included symptomatic patients of all adults above the age of 18 years presenting to the hospital with features compatible with COVID-19 infection.
We compared NPS using 3 mL viral transport media with unpreserved saliva samples which were collected in the ED and from inpatients in a COVID-positive hospital unit in the early stage of infection. The specimens were collected prospectively in the ED, when a patient with suspected COVID-19 is being investigated.
Educational materials were distributed to the ED nursing staff and the nurses on the COVID unit to encourage proper saliva collection. Furthermore, it was highly recommended that patients not have any food, drink, tobacco, or gum for 30 min before collection. Saliva was collected in a sterile, leak-proof container. Five milliliters of saliva was requested; however, specimens were considered acceptable if approximately 1 mL saliva was submitted.
Cepheid Xpert Xpress SARS-CoV-2 test
The GeneXpert® 106 Dx System (Cepheid, Sunnyvale, CA) is an integrated diagnostic device that performs automated specimen processing and real-time RT PCR analysis. The Xpert test consists of two main components: the Xpert plastic cartridge, which contains liquid sample processing and PCR buffers and lyophilized real-time RT-PCR reagents, and the GeneXpert instrument, which controls intra-cartridge fluidics and performs real-time RT-PCR analysis.
The physicians have collected pairs of specimens, one NPS and one saliva from patients meeting case definition with the diagnosis of COVID19, and tested by GeneXpert assay.
The liquid, nonviscous components of each specimen were drawn into the disposable pipettes (300 μl) issued with Xpert SARS-CoV-2 cartridges and directly will be transferred to the sample chamber of the assay cartridge. The lid is then closed and the cartridge is loaded onto the GeneXpert platform, which performs automated sample processing and real-time RT-PCR for viral RNA detection. The NPS was collected in the standard fashion, and similarly, testing was performed according to the manufacturer's instructions. The median day of sample collection for confirmed patients was 10 days from symptom onset.
This study was approved by the Dubai Scientific Research Ethics Committee of Dubai Health Authority (Ref: DSREC-07/2020_01) and was performed in accordance with all national regulations.
| Results|| |
A total of 60 paired NPS and saliva specimens were tested. The overall positivity was 30/60 (50%).
58/60 (97%) samples were in overall agreement. 30/28 samples were positive in saliva when compared to the NPS, resulting in a positive percent agreement of 93%. 30/32 samples had a negative saliva and NPS. Two samples demonstrated detectable levels of SARS-CoV-2 nucleic acid in the saliva, but the NPS was negative, resulting in a negative percent agreement of 94%.
The average cycle threshold values are summarized and compared in [Table 1].
|Table 1: Average cycle threshold values for targets envelope gene and nucleocapsid gene in nasopharyngeal and saliva specimens (n=30) from Xpert Xpress SARS-CoV-2 polymerase chain reaction assay|
Click here to view
| Discussion|| |
This is the first study in the UAE for the diagnosis of COVID-19 using GeneXpert® Xpress SARS-CoV-2 assay from saliva specimens; it has generated valuable information regarding the reliability tool of saliva to detect SARS-CoV-2.
In our study, we have demonstrated that COVID-19 could be detected in the saliva specimens of 30 of the 60 patients studied.
Our results showed that an important preanalytical variable for SARS-CoV-2 testing is a proper nasopharyngeal collection which may have been a contributing factor for the discrepant saliva-positive/NPS-negative sample.
We found that using saliva as a diagnostic tool of choice instead of nasopharyngeal or oropharyngeal samples has several advantages; First, saliva specimens can be provided by the patient him/herself easily without any invasive procedures and without the need of a health-care provider collecting the samples. Therefore, the use of saliva specimens could reduce the risk of health-care exposure to infectious particles which can be attributed to the cases of COVID-19 infection among health-care workers which have been found in our hospital. In addition, it is known that patients with viral pneumonias tend to have dry cough and less purulent sputum, which makes lower respiratory tract samples not easily obtainableand higher infectious risks are associated with sputum induction or bronchoalveolar lavage techniques. Second, saliva samples can be collected from children, adolescents, and geriatrics or those with nasofacial anomalies without discomfort. Since our hospital is a major trauma center and there is a high turnover of polytrauma cases including patients with maxillofacial injuries making nasopharyngeal or oropharyngeal sample collection not practical or even contraindicated.
Third, the use of saliva will allow specimen collection outside the hospitals where airborne infection isolation rooms are not available, such as in outpatient clinics or in the community. In the setting where a large number of individuals require screening, saliva would represent a practical noninvasive specimen type. Forth, since health-care workers are not required to collect saliva specimens, the use of saliva specimens will eliminate the waiting time for specimen collection, and hence, the results would be available much sooner. This is especially important in busy clinical settings where the number of available staff is limited. Finally, a more cost-effective approach is to test saliva instead of NPS. Since the collection of saliva is a relatively low cost, it could reduce the cost of special kit needed for the NSP and decrease personal protective equipment usage.
| Conclusion|| |
Our data showed that saliva is an acceptable sensitive and specific alternative source for detecting SARS-CoV-2 nucleic acid and the use of saliva samples is safer and more convenient for the patient. NPS sampling inconsistency may be one of the potential issues for false-negative results.
Saliva is a reliable tool to detect SARS-CoV-2, and the role of saliva in COVID-19 diagnosis could not be limited to a qualitative detection of the virus, but it may also provide information about the clinical evolution of the disease. Salivary diagnostics may play a pivotal role in detection of COVID-19 and can offer mass screening of the population. Further studies are needed to assess virus clearance using saliva testing, and to evaluate the potential diagnostic of COVID-19 in saliva and its impact on transmission of this virus, which is pivotal to develop rapid diagnostic tests and effective strategies for prevention.
Financial support and sponsorship
Conflicts of interest
There are no conflicts of interest.
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