Journal of Clinical and Diagnostic Research, ISSN - 0973 - 709X

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Dr Mohan Z Mani

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Believers Church Medical College,
Thiruvalla, Kerala
On Sep 2018

Prof. Somashekhar Nimbalkar

"Over the last few years, we have published our research regularly in Journal of Clinical and Diagnostic Research. Having published in more than 20 high impact journals over the last five years including several high impact ones and reviewing articles for even more journals across my fields of interest, we value our published work in JCDR for their high standards in publishing scientific articles. The ease of submission, the rapid reviews in under a month, the high quality of their reviewers and keen attention to the final process of proofs and publication, ensure that there are no mistakes in the final article. We have been asked clarifications on several occasions and have been happy to provide them and it exemplifies the commitment to quality of the team at JCDR."

Prof. Somashekhar Nimbalkar
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Chairman, Research Group, Charutar Arogya Mandal, Karamsad
National Joint Coordinator - Advanced IAP NNF NRP Program
Ex-Member, Governing Body, National Neonatology Forum, New Delhi
Ex-President - National Neonatology Forum Gujarat State Chapter
Department of Pediatrics, Pramukhswami Medical College, Karamsad, Anand, Gujarat.
On Sep 2018

Dr. Kalyani R

"Journal of Clinical and Diagnostic Research is at present a well-known Indian originated scientific journal which started with a humble beginning. I have been associated with this journal since many years. I appreciate the Editor, Dr. Hemant Jain, for his constant effort in bringing up this journal to the present status right from the scratch. The journal is multidisciplinary. It encourages in publishing the scientific articles from postgraduates and also the beginners who start their career. At the same time the journal also caters for the high quality articles from specialty and super-specialty researchers. Hence it provides a platform for the scientist and researchers to publish. The other aspect of it is, the readers get the information regarding the most recent developments in science which can be used for teaching, research, treating patients and to some extent take preventive measures against certain diseases. The journal is contributing immensely to the society at national and international level."

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Sri Devaraj Urs Medical College
Sri Devaraj Urs Academy of Higher Education and Research , Kolar, Karnataka
On Sep 2018

Dr. Saumya Navit

"As a peer-reviewed journal, the Journal of Clinical and Diagnostic Research provides an opportunity to researchers, scientists and budding professionals to explore the developments in the field of medicine and dentistry and their varied specialities, thus extending our view on biological diversities of living species in relation to medicine.
‘Knowledge is treasure of a wise man.’ The free access of this journal provides an immense scope of learning for the both the old and the young in field of medicine and dentistry as well. The multidisciplinary nature of the journal makes it a better platform to absorb all that is being researched and developed. The publication process is systematic and professional. Online submission, publication and peer reviewing makes it a user-friendly journal.
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Dr Saumya Navit
Professor and Head
Department of Pediatric Dentistry
Saraswati Dental College
On Sep 2018

Dr. Arunava Biswas

"My sincere attachment with JCDR as an author as well as reviewer is a learning experience . Their systematic approach in publication of article in various categories is really praiseworthy.
Their prompt and timely response to review's query and the manner in which they have set the reviewing process helps in extracting the best possible scientific writings for publication.
It's a honour and pride to be a part of the JCDR team. My very best wishes to JCDR and hope it will sparkle up above the sky as a high indexed journal in near future."

Dr. Arunava Biswas
MD, DM (Clinical Pharmacology)
Assistant Professor
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Calcutta National Medical College & Hospital , Kolkata

Dr. C.S. Ramesh Babu
" Journal of Clinical and Diagnostic Research (JCDR) is a multi-specialty medical and dental journal publishing high quality research articles in almost all branches of medicine. The quality of printing of figures and tables is excellent and comparable to any International journal. An added advantage is nominal publication charges and monthly issue of the journal and more chances of an article being accepted for publication. Moreover being a multi-specialty journal an article concerning a particular specialty has a wider reach of readers of other related specialties also. As an author and reviewer for several years I find this Journal most suitable and highly recommend this Journal."
Best regards,
C.S. Ramesh Babu,
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Muzaffarnagar Medical College,
On Aug 2018

Dr. Arundhathi. S
"Journal of Clinical and Diagnostic Research (JCDR) is a reputed peer reviewed journal and is constantly involved in publishing high quality research articles related to medicine. Its been a great pleasure to be associated with this esteemed journal as a reviewer and as an author for a couple of years. The editorial board consists of many dedicated and reputed experts as its members and they are doing an appreciable work in guiding budding researchers. JCDR is doing a commendable job in scientific research by promoting excellent quality research & review articles and case reports & series. The reviewers provide appropriate suggestions that improve the quality of articles. I strongly recommend my fraternity to encourage JCDR by contributing their valuable research work in this widely accepted, user friendly journal. I hope my collaboration with JCDR will continue for a long time".

Dr. Arundhathi. S
MBBS, MD (Pathology),
Sanjay Gandhi institute of trauma and orthopedics,
On Aug 2018

Dr. Mamta Gupta,
"It gives me great pleasure to be associated with JCDR, since last 2-3 years. Since then I have authored, co-authored and reviewed about 25 articles in JCDR. I thank JCDR for giving me an opportunity to improve my own skills as an author and a reviewer.
It 's a multispecialty journal, publishing high quality articles. It gives a platform to the authors to publish their research work which can be available for everyone across the globe to read. The best thing about JCDR is that the full articles of all medical specialties are available as pdf/html for reading free of cost or without institutional subscription, which is not there for other journals. For those who have problem in writing manuscript or do statistical work, JCDR comes for their rescue.
The journal has a monthly publication and the articles are published quite fast. In time compared to other journals. The on-line first publication is also a great advantage and facility to review one's own articles before going to print. The response to any query and permission if required, is quite fast; this is quite commendable. I have a very good experience about seeking quick permission for quoting a photograph (Fig.) from a JCDR article for my chapter authored in an E book. I never thought it would be so easy. No hassles.
Reviewing articles is no less a pain staking process and requires in depth perception, knowledge about the topic for review. It requires time and concentration, yet I enjoy doing it. The JCDR website especially for the reviewers is quite user friendly. My suggestions for improving the journal is, more strict review process, so that only high quality articles are published. I find a a good number of articles in Obst. Gynae, hence, a new journal for this specialty titled JCDR-OG can be started. May be a bimonthly or quarterly publication to begin with. Only selected articles should find a place in it.
An yearly reward for the best article authored can also incentivize the authors. Though the process of finding the best article will be not be very easy. I do not know how reviewing process can be improved. If an article is being reviewed by two reviewers, then opinion of one can be communicated to the other or the final opinion of the editor can be communicated to the reviewer if requested for. This will help one’s reviewing skills.
My best wishes to Dr. Hemant Jain and all the editorial staff of JCDR for their untiring efforts to bring out this journal. I strongly recommend medical fraternity to publish their valuable research work in this esteemed journal, JCDR".

Dr. Mamta Gupta
(Ex HOD Obs &Gynae, Hindu Rao Hospital and associated NDMC Medical College, Delhi)
Aug 2018

Dr. Rajendra Kumar Ghritlaharey

"I wish to thank Dr. Hemant Jain, Editor-in-Chief Journal of Clinical and Diagnostic Research (JCDR), for asking me to write up few words.
Writing is the representation of language in a textual medium i e; into the words and sentences on paper. Quality medical manuscript writing in particular, demands not only a high-quality research, but also requires accurate and concise communication of findings and conclusions, with adherence to particular journal guidelines. In medical field whether working in teaching, private, or in corporate institution, everyone wants to excel in his / her own field and get recognised by making manuscripts publication.

Authors are the souls of any journal, and deserve much respect. To publish a journal manuscripts are needed from authors. Authors have a great responsibility for producing facts of their work in terms of number and results truthfully and an individual honesty is expected from authors in this regards. Both ways its true "No authors-No manuscripts-No journals" and "No journals–No manuscripts–No authors". Reviewing a manuscript is also a very responsible and important task of any peer-reviewed journal and to be taken seriously. It needs knowledge on the subject, sincerity, honesty and determination. Although the process of reviewing a manuscript is a time consuming task butit is expected to give one's best remarks within the time frame of the journal.
Salient features of the JCDR: It is a biomedical, multidisciplinary (including all medical and dental specialities), e-journal, with wide scope and extensive author support. At the same time, a free text of manuscript is available in HTML and PDF format. There is fast growing authorship and readership with JCDR as this can be judged by the number of articles published in it i e; in Feb 2007 of its first issue, it contained 5 articles only, and now in its recent volume published in April 2011, it contained 67 manuscripts. This e-journal is fulfilling the commitments and objectives sincerely, (as stated by Editor-in-chief in his preface to first edition) i e; to encourage physicians through the internet, especially from the developing countries who witness a spectrum of disease and acquire a wealth of knowledge to publish their experiences to benefit the medical community in patients care. I also feel that many of us have work of substance, newer ideas, adequate clinical materials but poor in medical writing and hesitation to submit the work and need help. JCDR provides authors help in this regards.
Timely publication of journal: Publication of manuscripts and bringing out the issue in time is one of the positive aspects of JCDR and is possible with strong support team in terms of peer reviewers, proof reading, language check, computer operators, etc. This is one of the great reasons for authors to submit their work with JCDR. Another best part of JCDR is "Online first Publications" facilities available for the authors. This facility not only provides the prompt publications of the manuscripts but at the same time also early availability of the manuscripts for the readers.
Indexation and online availability: Indexation transforms the journal in some sense from its local ownership to the worldwide professional community and to the public.JCDR is indexed with Embase & EMbiology, Google Scholar, Index Copernicus, Chemical Abstracts Service, Journal seek Database, Indian Science Abstracts, to name few of them. Manuscriptspublished in JCDR are available on major search engines ie; google, yahoo, msn.
In the era of fast growing newer technologies, and in computer and internet friendly environment the manuscripts preparation, submission, review, revision, etc and all can be done and checked with a click from all corer of the world, at any time. Of course there is always a scope for improvement in every field and none is perfect. To progress, one needs to identify the areas of one's weakness and to strengthen them.
It is well said that "happy beginning is half done" and it fits perfectly with JCDR. It has grown considerably and I feel it has already grown up from its infancy to adolescence, achieving the status of standard online e-journal form Indian continent since its inception in Feb 2007. This had been made possible due to the efforts and the hard work put in it. The way the JCDR is improving with every new volume, with good quality original manuscripts, makes it a quality journal for readers. I must thank and congratulate Dr Hemant Jain, Editor-in-Chief JCDR and his team for their sincere efforts, dedication, and determination for making JCDR a fast growing journal.
Every one of us: authors, reviewers, editors, and publisher are responsible for enhancing the stature of the journal. I wish for a great success for JCDR."

Thanking you
With sincere regards
Dr. Rajendra Kumar Ghritlaharey, M.S., M. Ch., FAIS
Associate Professor,
Department of Paediatric Surgery, Gandhi Medical College & Associated
Kamla Nehru & Hamidia Hospitals Bhopal, Madhya Pradesh 462 001 (India)
On May 11,2011

Dr. Shankar P.R.

"On looking back through my Gmail archives after being requested by the journal to write a short editorial about my experiences of publishing with the Journal of Clinical and Diagnostic Research (JCDR), I came across an e-mail from Dr. Hemant Jain, Editor, in March 2007, which introduced the new electronic journal. The main features of the journal which were outlined in the e-mail were extensive author support, cash rewards, the peer review process, and other salient features of the journal.
Over a span of over four years, we (I and my colleagues) have published around 25 articles in the journal. In this editorial, I plan to briefly discuss my experiences of publishing with JCDR and the strengths of the journal and to finally address the areas for improvement.
My experiences of publishing with JCDR: Overall, my experiences of publishing withJCDR have been positive. The best point about the journal is that it responds to queries from the author. This may seem to be simple and not too much to ask for, but unfortunately, many journals in the subcontinent and from many developing countries do not respond or they respond with a long delay to the queries from the authors 1. The reasons could be many, including lack of optimal secretarial and other support. Another problem with many journals is the slowness of the review process. Editorial processing and peer review can take anywhere between a year to two years with some journals. Also, some journals do not keep the contributors informed about the progress of the review process. Due to the long review process, the articles can lose their relevance and topicality. A major benefit with JCDR is the timeliness and promptness of its response. In Dr Jain's e-mail which was sent to me in 2007, before the introduction of the Pre-publishing system, he had stated that he had received my submission and that he would get back to me within seven days and he did!
Most of the manuscripts are published within 3 to 4 months of their submission if they are found to be suitable after the review process. JCDR is published bimonthly and the accepted articles were usually published in the next issue. Recently, due to the increased volume of the submissions, the review process has become slower and it ?? Section can take from 4 to 6 months for the articles to be reviewed. The journal has an extensive author support system and it has recently introduced a paid expedited review process. The journal also mentions the average time for processing the manuscript under different submission systems - regular submission and expedited review.
Strengths of the journal: The journal has an online first facility in which the accepted manuscripts may be published on the website before being included in a regular issue of the journal. This cuts down the time between their acceptance and the publication. The journal is indexed in many databases, though not in PubMed. The editorial board should now take steps to index the journal in PubMed. The journal has a system of notifying readers through e-mail when a new issue is released. Also, the articles are available in both the HTML and the PDF formats. I especially like the new and colorful page format of the journal. Also, the access statistics of the articles are available. The prepublication and the manuscript tracking system are also helpful for the authors.
Areas for improvement: In certain cases, I felt that the peer review process of the manuscripts was not up to international standards and that it should be strengthened. Also, the number of manuscripts in an issue is high and it may be difficult for readers to go through all of them. The journal can consider tightening of the peer review process and increasing the quality standards for the acceptance of the manuscripts. I faced occasional problems with the online manuscript submission (Pre-publishing) system, which have to be addressed.
Overall, the publishing process with JCDR has been smooth, quick and relatively hassle free and I can recommend other authors to consider the journal as an outlet for their work."

Dr. P. Ravi Shankar
KIST Medical College, P.O. Box 14142, Kathmandu, Nepal.
On April 2011

Dear team JCDR, I would like to thank you for the very professional and polite service provided by everyone at JCDR. While i have been in the field of writing and editing for sometime, this has been my first attempt in publishing a scientific paper.Thank you for hand-holding me through the process.

Dr. Anuradha
On Jan 2020

Important Notice

Original article / research
Year : 2023 | Month : February | Volume : 17 | Issue : 2 | Page : DC11 - DC15 Full Version

Saliva as a Viable and Simple Alternative to Nasopharyngeal and Oropharyngeal Swabs for COVID-19 Real-Time Reverse Transcriptase Polymerase Chain Reaction

Published: February 1, 2023 | DOI:
Leimapokpam Sumitra Devi, Mukesh Sharma, Moumita Sardar

1. Tutor, Department of Microbiology, SGT Medical College Hospital and Research Institute, Gurugram, Haryana, India. 2. Associate Professor, Department of Microbiology, SGT Medical College Hospital and Research Institute, Gurugram, Haryana, India. 3. Associate Professor, Department of Microbiology, SGT Medical College Hospital and Research Institute, Gurugram, Haryana, India.

Correspondence Address :
Dr. Moumita Sardar,
CV Raman Hostel, SGT University Campus, Gurugram, Haryana, India.


Introduction: Attributable to the difficulties in specimen collection, discomfort and symptoms caused on by Nasopharyngeal Swab (NPS) and Oropharyngeal Swab (OPS) collection, and significant risk to Healthcare Workers (HCW), evaluation of an alternative specimen for the diagnosis of Coronavirus Disease-2019 (COVID-19) is required. Saliva specimen could be an alternative specimen with many advantages over NPS and OPS, however little is known about how well it performs this purpose.

Aim: To assess the efficacy of saliva as a viable and simple alternative specimen to NPS and OPS for COVID-19 Real-Time reverse transcriptase Polymerase Chain Reaction (rRT-PCR).

Materials and Methods: The present cross-sectional study was conducted in the Department of Microbiology, SGT Medical College Hospital and Research Institute, Haryana, India, from July to December 2020. A total of 60 symptomatic and 20 asymptomatic COVID-19 patients were recruited for the study and specimen viz., saliva, NPS and OPS were collected at four different sampling points i.e., on day one, five, seven and 14 after confirmation of COVID-19 rRT-PCR test positivity. Data obtained from the study was analysed and expressed as median, frequency, interquartile range and Chi-square test was done for comparison of categorical variables.

Results: Majority of the patients in symptomatic hospitalised COVID-19 patients were males 49 (81.7%) and remaining were females 11 (18.3%) and in asymptomatic group 8 (40%) were males and 12 (60%) were females. Saliva was the most sensitive specimen (74.2%), followed by NPS, Naso Oropharyngeal Swab (NOPS) with 70.8% each and OPS (65.8%) for detection of Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) in symptomatic patients at four different sampling points. Comparable findings were also observed in specimens obtained from asymptomatic individuals as well. In addition, the viral load was also highest in saliva sample, as measured by Cycle Threshold (Ct) value. Across all specimen types, high viral load (lower Ct values) was observed during the early period of infection. Majority of the study participants reported discomfort during NPS and OPS collection (90% and 85%, respectively), lacrimation, sneezing and gag reflex being the most commonly reported induced symptoms.

Conclusion: In the present study, saliva could be a viable and alternate specimen for COVID-19 diagnosis due to its ease in sample collection, specimen stability and reduced risk of transmission of infection due to droplets.


Coronavirus disease-2019, Cycle threshold value, Diagnostic specimen

In December 2019, Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) emerged in China’s Hubei Province, causing an outbreak of atypical viral pneumonia, Coronavirus Disease-2019 (COVID-19) [1,2]. Detection of SARS-CoV-2 in Nasopharyngeal Swab (NPS) and/or Oropharyngeal Swab (OPS) by Real-time reverse transcriptase Polymerase Chain Reaction (rRT-PCR) is still recommended for COVID-19 diagnosis by the World Health Organisation (WHO) (1),(3),(4). However, collection of NPS and/or OPS specimens a minimally invasive procedure involving close contact with patients, thus posing a risk of disease transmission to the Healthcare Workers (HCWs) because of aerosol droplets generated during the procedure. In addition, patients also experience discomfort and induce symptoms such as gag reflex, cough or sneezing, which can also result in bleeding of the NPS or oropharyngeal tissue, especially in thrombocytopenic individuals (5),(6),(7).

Salivary droplets are considered a prime source of human-to-human transmission of SARS-CoV-2 when social distancing (>2 m) is not maintained (8). Thus, saliva could be a promising alternative which is safe, non invasive and easy to collect specimen without requiring personal protective equipment for the diagnosis of COVID-19. Furthermore, saliva study can help explain the pathogenesis since epithelial oral cavity cells revealed abundant expression of the angiotensin-converting enzyme-2 receptor, which is essential for SARS-CoV-2 entry into cells (9). Various comparative studies have reported that in 84.6% to >90% of the patients who had positive rRT-PCR for SARS-CoV-2 in NPS, the virus was also detected in saliva (7),(10),(11),(12),(13). Despite the fact that saliva offers a number of advantages over NPS and OPS, there is little information on conclusive evidence about its diagnostic accuracy/performances. Thus, the present study aimed to evaluate saliva as an alternative specimen to NPS and/or OPS in COVID-19 diagnosis in a tertiary care hospital in north India. Additionally, the discomfort and the symptoms that were induced while collecting NPS or OPS specimens were evaluated.

Material and Methods

The cross-sectional study was conducted in the Department of Microbiology, SGT Medical College Hospital and Research Institute, Haryana, India, from July to December 2020. The study protocol was reviewed and approved by the Institutional Ethics Committee of SGT University (SGTU/FMHS/EC/2020/7). A total of 60 symptomatic hospitalised COVID-19 patients (group 1) and 20 asymptomatic COVID-19 patients (group 2) were recruited using convenience sampling.

Inclusion criteria: Symptomatic hospitalised COVID-19 patients aged >18 years, positive for SARS-CoV-2 by rRT-PCR by NPS and OPS specimens admitted to the COVID-19 care ward of SGT hospital during the study period were recruited in group 1 after obtaining written informed consent. Based on their severity of illness, they were further divided into mild, moderate, severe and critically ill patients (14). To compare if there is any difference in SARS-CoV-2 detection rate in various specimens from asymptomatic patients compared to symptomatic patients, asymptomatic HCWs from the SGT hospital sent on quarantine after one week of duty in COVID-19 specialised wards, as per our institutional protocol being followed then, and were thereafter COVID-19 positive by rRT-PCR test were included as group 2.

Exclusion criteria: Those participants whose follow-up specimens could be obtained or those who were not willing to participate in the study and refused to provide written informed consent were excluded from the study.

Study Procedure

After recruiting the study participants, a detailed proforma was filled out, which included information on demographics, clinical data including co-morbid conditions, level of discomfort and induced symptoms experienced by the study participants during NPS and/or OPS specimen collection. The levels of discomfort experienced by study participants were rated using an arbitrary rating scale (1-4), with 1 indicating no discomfort, 2-moderate (induced symptoms such as sneezing, gag reflex, lacrimation), 3-considerable (induced symptoms such as vomit, rhinorrhoea, headache) and 4-indicating extreme discomfort (bleeding/epistaxis) (15),(16).

Specimen collection and processing: Participants in the study were recruited after receiving the COVID-19 rRT-PCR test positive report released by the molecular laboratory of SGT hospital. Thus, within 12 hours following the test report, a saliva specimen was taken from each study participant, in addition to NPS and OPS (day one sample or first sampling point). After receiving the rRT-PCR COVID-19 positive report, follow-up samples were taken on days five (second sampling point), seven (third sampling point), and 14 (fourth sampling point).

Nasopharyngeal swab and OPS specimens were collected as per Indian Council of Medical Research (ICMR) guidelines by trained technicians using sterile nylon flocked swabs and placed immediately into a tube containing 3.5 mL of Viral Transport Medium (VTM) (17). For the collection of saliva specimen, patients were instructed to pool saliva in their mouth for a few minutes before collection and gently spit saliva into a sterile universal container. Neat saliva specimens were immediately transported to the laboratory in a cool box where an approximate 1:1 ratio of VTM was immediately added (7). The specimens were properly labelled and packed in triple layer packing and transported to the laboratory on ice in a cold box and later stored at -20°C for further processing.

The collected specimens, namely NPS, OPS, NPS with OPS and saliva specimens were vortexed properly and then 200 μL of each specimen was subjected to nucleic acid, Ribonucleic Acid (RNA) extraction using a viral nucleic acid extraction kit as per manufacturer’s instructions (TRUPCR Viral RNA Extraction Kit, 3B Blackbio Biotech India Ltd.,). After RNA extraction, rRT-PCR was performed by a multiplex rRT-PCR test using primers targeting Envelope gene (E-gene) and RNA dependent RNA Polymerase/Nucleocapsid genes (RdRp/N-genes) of SARS-CoV-2 (TRUPCR SARS-CoV-2 RT qPCR kit, 3B Blackbio Biotech India Ltd.,) in a 7500 fast real-time PCR system (Applied Biosystems). The test was performed in 25 μL reactions in a 0.1 mL PCR tube containing 10 μL master mix, 0.35 μL enzyme and 4.65 μL primer probe and 10 μL extracted RNA. The thermal cycling condition was: Complementary Deoxyribonucleic Acid (cDNA) synthesis at 50°C for 15 minutes, initial denaturation at 95°C for five minutes, followed by 38 cycles of amplification with denaturation at 95°C for five seconds, annealing at 60°C for 40 seconds, and extension at 72°C for 15 seconds. Positive and negative controls were included in each PCR run.

Statistical Analysis

Data on age and gender of the patients, number of days of sampling from the onset of symptoms, SARS-CoV-2 detection rate, Cycle Threshold (Ct) value and the level of discomfort and induced symptoms during collection of NPS and OPS were translated to a Microsoft (MS) excel spreadsheet, and manually assessed in terms of median, frequency and Interquartile range (IQR). For comparing categorical variables, Chi-square test was used, and a p-value <0.05 was considered as statistically significant.


Majority of the patients in group 1 i.e., symptomatic hospitalised COVID-19 patients were males 49 (81.7%) and remaining were females 11 (18.3%), with male:female ratio as 1:0.2, with a median age of 31 years (IQR: 27-41 years). Among them, 8 (13.3%) had serious illnesses requiring Intensive Care Unit (ICU) stay during hospital stay, while the rest of the study participants had mild to moderate illnesses (categories as described earlier) and were discharged within 14 days. None of the study participants’ conditions deteriorated throughout the study. Five individuals with serious illnesses requiring ICU care were over the age of sixty, with two of them suffering from diabetes and one from chronic obstructive pulmonary disease. The median number of days from symptom onset was two days at the time of the initial sampling (IQR 3-2 days) (Table/Fig 1).

Of the 20 asymptomatic HCWs i.e., group 2 patients, the male:female ratio was 0.7:1, with a median age of 30 years (IQR 26-32 years) and none of them had co-morbid conditions. During the period of the present study, no asymptomatic participant’s condition deteriorated (Table/Fig 1).

SARS-CoV-2 detection frequency and viral load: The present study evaluated matched NPS, OPS, Naso Oropharyngeal Swab (NOPS) and saliva specimens from all the study participants in both group 1 and group 2 at four distinct sampling points to compare SARS-CoV-19 detection by RT-PCR for each specimen type. The Ct values of RdRp gene for the rRT-PCR positive specimens were also analysed to determine the viral load.

In group 1 patients, SARS-CoV-2 was detected in all specimens obtained on first sampling point, with the lowest Ct value in saliva {IQR: 4.8 (24.1-19.4)}, reflecting a higher concentration of viral RNA, followed by NPS {IQR: 4.9 (25.5-20.7)}, NOPS {IQR: 5 (27.2-22.2)} and OPS {IQR: 4.6 (27.9-23.3)} [Table/Fig-2,3]. Analysis of specimens collected on second and third sampling points revealed the highest detection frequency in saliva specimen (100% and 86.7%, respectively) and lowest detection in OPS (91.7% and 71.7%, respectively). Comparable to first sampling point results, the Ct value of positive saliva specimens was lower than other specimens. The Ct value of each specimen type increased gradually on consecutive sampling points, SARS-CoV-2 rRT-PCR was positive at a low frequency even on sampling point 4 (day 14) specimens, i.e., 6.7% of NP and NOPS specimens and 10% of saliva specimens with high Ct values. Across all specimen types, lower Ct values were observed during the early period of infection. The frequency of detection of SARS-CoV-2 was significantly higher in saliva specimen with a higher viral load (low Ct value) compared to other specimens, viz., NPS, OPS and NOPS (p-value <0.05). Saliva was the most sensitive specimen (74.2%), followed by NPS, NOPS (70.8% each) and OPS (65.8%) for detection of SARS-CoV-2 in the present study. The overall percent agreement of rRT-PCR result of saliva to NPS and NOPS was 232/240 (96.7%) while to OPS was 220/240 (91.7%). Despite similar results between NPS and NOPS, the Ct value shows that NPS has a substantially higher viral load than NOPS.

In group 2, the pattern of detection of SARS-CoV-2 in different specimens indicated comparable findings as those of group 1. Saliva, NPS and NOPS showed comparable observations on first and second sampling points, i.e., 20/20 (100%) and 11/20 (55%) SARS-CoV-2 detection rates, respectively, for the three specimen 13types. SARS-CoV-2 detection rates in the third sampling point were found to be 6/20 (30%) and 5/20 (25%), respectively for NPS and saliva specimens. Only two NPS specimens were found to be positive for SARS-CoV-2 at the fourth sampling point, but none of the saliva specimens did. The OPS was found to be the least sensitive specimen with SARS-CoV-2 detection rates of 17/20 (85%), 8/20 (40%), 1/20 (5%) and 0/20 (0%) in the first, second, third and fourth sampling points, respectively. Despite the similarity in SARS-CoV-2 detection rates between NPS and NOPS, NOPS had a higher Ct value than NPS, indicating lower viral loads. It is worth noting that the positive specimens from asymptomatic HCWs had Ct values that were significantly higher than the Ct values of the positive specimens obtained from symptomatic patients, indicating that the viral load in the previous group was lower (p-value <0.05).

Assessment of discomfort levels and symptoms during NPS and OPS sampling: Approximately half of participants in both the groups reported a moderate degree of discomfort during the collection of NPS and OPS, while a few reported experiencing unbearable discomforts (Table/Fig 4). More individuals reported induced symptoms during NPS collection than during OPS collection. As revealed by the study participants, lacrimation (83.8%), sneezing (65%) and rhinorrhea (8.8%) were the most prevalently reported induced symptoms in the NPS collection whereas, gag reflex (62.5%), lacrimation (61.3%) and vomit (1.3%) were the most common ones in the OPS collection. Of the study participants, 65% of the individuals reported sneezing during NPS sampling while none reported sneezing during OPS sampling (Table/Fig 5). Saliva collection is therefore favourable because no discomforts or induced symptoms were noted.


The most common validated specimen for respiratory viruses, including SARS-CoV-2, has been identified to be NPS (4). The WHO and other regulatory authorities continue to recommend the identification of SARS-CoV-2 in respiratory specimens (i.e., NPS and/or OPS) using rRT-PCR as the gold standard method [1-4,18-20].

Studies on the new disease were not available at the outset of the pandemic because the aetiology was a novel respiratory virus, hence the previously widely accepted respiratory specimen i.e., NPS was used for diagnosis. However, collection of both NPS and OPS specimens faces several challenges as they are minimally invasive procedures causing discomfort and symptoms induced while collecting NPS or OPS specimens for the majority of individuals; for some, it is unbearably painful, which may reduce the willingness of individuals to undertake retesting when required (3). Therefore, to avoid discomfort for the patients, many researchers have assessed saliva specimens as a non invasive specimen, in quest of additional alternative specimens for detection of SARS-CoV-2.

The present study assessed matched NPS, OPS, NOPS and saliva specimens for SARS-CoV-2 detection by rRT-PCR in 60 COVID-19 symptomatic patients and 20 COVID-19 asymptomatic HCWs. Saliva was found to be the most sensitive specimen to detect SARS-CoV-2 among the various specimens obtained from symptomatic patients processed at four distinct sampling points i.e., day one, five, seven, and 14. Saliva was then followed by NPS, NOPS, and OPS, with a statistical difference between them. Thus, saliva may be used as an equally effective alternative specimen for up to 14 days, which corresponds to the period of infectiousness for general population infection (20). Similar to the present findings, other researchers have also reported that saliva could be an alternative specimen for COVID-19 screening and diagnosis [4,20,21]. A similar type of study conducted by Teo AKJ et al., on specimens collected from migrant workers with COVID-19 revealed that saliva was a sensitive and effective diagnostic specimen for the diagnosis of COVID-19. In addition, the study demonstrates that the probability of an rRT-PCR positive saliva test was higher than that of a NPS swab and self-administered nasal swab collected during the first and second weeks following the initial diagnosis, which is in accordance with the present study findings (21). Another study by Beyene GT et al., also revealed that saliva was more sensitive than NPS, with 92.1% vs 52.6%, 77.4% vs 20.3% and 100% vs 50% on paired saliva NPS specimens collected at the time of admission (five to seven days), week two and week three after initial detection of SARS-CoV-2 RNA by RT-PCR using NPS specimens (20). Bergevin MA et al., revealed that saliva and NOPS had comparable findings in a cohort of symptomatic patients presenting symptoms for <10 days, the sensitivity of NOPS was higher than that of saliva in patients with symptoms for more than 10 days (95.2% vs 71.4%) (22). Thus, due to the numerous reports on saliva from various countries as reliable specimen, in the recent guidelines by the Centers for Disease Control and Prevention (CDC) for collection of specimens for COVID-19 diagnosis, saliva has been included as one of the upper respiratory specimens one of the specimens suitable for RT-PCR [19,23]. Furthermore, the United States (US) Food and Drug Administration (FDA) had authorised diagnostic test using self-collected saliva specimens for COVID-19 diagnosis (24).

In the present study, NPS specimens obtained from asymptomatic HCWs at four different sampling points were found to be more sensitive for detection of SARS-CoV-2 by rRT-PCR, i.e., 39/80 (48.8%) compared to matched saliva specimens i.e., 36/80 (45%). A study by Melo Costa M et al., also demonstrated less sensitivity of saliva specimens (82.9%) than NPS for detecting SARS-CoV-2 from specimens mostly taken from asymptomatic individuals (25). Uddin MKM et al., also reported less sensitivity of saliva specimens (33%) compared with that of NPS to detect SARS-CoV-2 from asymptomatic patients (26). OPS were the least sensitive specimen in the present analysis compared to other specimen types obtained from both symptomatic and asymptomatic study participants. Similar results were found in a study by Wang H et al., with OPS being less sensitive than NPS for the detection of SARS-CoV-2 (15). Thus, saliva can be used as an effective alternate specimen for diagnosis of COVID-19 in early stage in both symptomatic as well as asymptomatic patients. To KK et al., also stated that the clinical management of patients with respiratory virus infections can be enhanced by additional saliva molecular testing, despite the fact that NPS continue to be the specimen of choice for the majority of patients due to their high viral contents (11). Furthermore, saliva has the advantage in terms of sample stability; atleast 20 days at 4°C without VTM (27).

Irrespective of the specimen types, authors observed that Ct values for SARS-CoV-2 rRT-PCR positive specimens were lower in those collected at the early period of infection, i.e., first sampling point, compared to specimens collected later in the period indicating higher viral load. Teo AKJ et al., also observed comparable results in saliva, NPS, and self-administered nasal swab specimens among migrant workers infected with COVID-19, whose onset of illness could be estimated (21). Although, there was no discernible difference between the Ct values of saliva and NPS in the present study, it was observed that the viral load, as determined by Ct value, was highest in saliva, followed by NPS, NOPS and OPS. In a study from Singapore, viral load in paired saliva NPS was compared on specimens obtained on the day of hospital admission and it was found that saliva had a significantly higher viral load than NPS (p-value <0.001) (21). Similar findings have been shown in a study by Wyllie AL et al., in which viral load in saliva was higher than NPS specimens (28). Rao M et al., also showed that the Ct values for E and RdRp genes were significantly lower in saliva (median IQR 30.6 (27.5-32.8) and 31.2 (27.3-33.6) than those for NPS (median IQR 33.2 (30.0-35.1) and 33.7 (30.0-36.0), indicating high viral loads in saliva specimens (29). Wang H et al., also reported a higher viral load in NPS than in OPS with significantly lower mean Ct values of NPS (37.8, 95% CI: 37.0-38.6) than those of OPS (39.4, 95% CI: 38.9-39.8) by 1.6 (95% CI 1.0-2.2, p-value <0.001), indicating that the SARS-CoV-2 load was significantly higher in NPS specimens (15). In contrast to the present study, Justo AFO et al., demonstrated higher Ct values in saliva compared to NPS, though their sensitivity for detection of SARS-CoV-2 was same i.e., 83.3% (30). These divergent outcomes among studies may be the result of various types of sampling/processing methods detection reagents used and the difference in study populations.

In the present study, authors assessed the patients’ discomfort levels during NPS and OPS sampling and found that approximately half of the study participants experienced a moderate degree of discomfort during NPS and OPS sampling and six out of 80 individuals reported unbearable discomfort. As reported in this study, other studies have also reported discomfort and induced symptoms during NPS collection (15),(20). A study from China by Wang H et al., reported 37.9% and 41.7% of individuals reporting moderate degrees of discomfort during NPS and OPS sampling (15). In contrast to the current study findings, Marra P et al., stated that the collection of NPS is largely a none to minimum discomfort inducing method and the variations in discomfort could be attributed to anatomical characteristics, highlighting the necessity for a patient specific and anatomy focused strategy (31). With further assessment of the symptoms, authors found that lacrimation and sneezing were the most common symptoms encountered by study participants during NPS collection, whereas gag reflex and lacrimation were the most common symptoms during OPS collection. The findings of a study by Wang H et al., were in accordance with the present study findings, though the individuals who experienced vomiting during OPS collection were fewer in this study (15). Although, NPS and OPS are recommended specimens for diagnosis of COVID-19, saliva may be used as an alternative specimen to avoid discomforts during specimen collection in certain scenarios, particularly in young children, individuals with nasal polyps or other anomalies, prior history of epistaxis or severe discomfort during specimen collection and in instances when selfcollection is requisite.


The primary limitations were the small sample size, from a single institute and disproportion between the two groups, which made it challenging for us to make appropriate inferences. Due to the small sample size, inferences about the effectiveness of saliva as a diagnostic specimen for COVID-19 in asymptomatic individuals may not be generalisable. In addition, follow-up sampling beyond 14 days after diagnosis of COVID-19 was not feasible as majority of the cases recovered and got discharged from the hospital.


The present study findings suggest that saliva may be used accurately for the diagnosis of SARS-CoV-2 early after the beginning of symptoms, since it has the advantages of ease of sample collection, reduced transmission of infection to HCWs owing to droplet, and sample stability. Being non intrusive and causing no discomfort, it would be preferable specimen for paediatric age group as well. Thus, saliva could be recommended for diagnosing COVID-19 and monitoring viral load among individuals and also for mass surveillance. Saliva collection and processing methods need to be standardised and further studies need to be done to assess its effectiveness as a validated diagnostic specimen.


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DOI and Others

DOI: 10.7860/JCDR/2023/59884.17502

Date of Submission: Aug 27, 2022
Date of Peer Review: Oct 01, 2022
Date of Acceptance: Nov 19, 2022
Date of Publishing: Feb 01, 2023

• Financial or Other Competing Interests: None
• Was Ethics Committee Approval obtained for this study? Yes
• Was informed consent obtained from the subjects involved in the study? Yes
• For any images presented appropriate consent has been obtained from the subjects. NA

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