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

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Dr Mohan Z Mani

"Thank you very much for having published my article in record time.I would like to compliment you and your entire staff for your promptness, courtesy, and willingness to be customer friendly, which is quite unusual.I was given your reference by a colleague in pathology,and was able to directly phone your editorial office for clarifications.I would particularly like to thank the publication managers and the Assistant Editor who were following up my article. I would also like to thank you for adjusting the money I paid initially into payment for my modified article,and refunding the balance.
I wish all success to your journal and look forward to sending you any suitable similar article in future"

Dr Mohan Z Mani,
Professor & Head,
Department of Dermatolgy,
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
Head, Department of Pediatrics, Pramukhswami Medical College, Karamsad
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."

Dr Kalyani R
Professor and Head
Department of Pathology
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.
As an experienced dentist and an academician, I proudly recommend this journal to the dental fraternity as a good quality open access platform for rapid communication of their cutting-edge research progress and discovery.
I wish JCDR a great success and I hope that journal will soar higher with the passing time."

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
Department of Pharmacology
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,
Associate Professor of Anatomy,
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 : DC20 - DC23 Full Version

Comparison of Cepheid Xpert Xpress SARS-CoV-2 Assay with Standard RT-PCR Test for Detection of COVID-19 Infection: A Retrospective Cohort Study

Published: February 1, 2023 | DOI:
Nitika Dhuria, Nitin Nagpal, Vishal Sharma, Arun Kumar

1. Assistant Professor, Department of Microbiology, GGSMCH, Faridkot, Punjab, India. 2. Professor, Department of General Surgery, GGSMCH, Faridkot, Punjab, India. 3. Associate Professor, Department of Microbiology, GGSMCH, Faridkot, Punjab, India. 4. Research Scientist, Department of Microbiology, GGSMCH, Faridkot, Punjab, India.

Correspondence Address :
Dr. Nitika Dhuria,
Assistant Professor, Department of Microbiology, GGSMCH, Faridkot, Punjab, India.


Introduction: Real time Reverse Transcription-Polymerase Chain Reaction (RT-PCR) test, the gold standard test for Severe Acute Respiratory Syndrome-Coronavirus-2 (SARS-CoV-2) detection, is a tedious process and requires proficient workforce. Accurate and fast test results may permit more efficient use of protective and isolation resources and allow rapid therapeutic interventions.

Aim: To evaluate the analytical performance characteristics of the Cepheid Xpert Xpress SARS-CoV-2 test, a rapid, automated molecular test for SARS-CoV-2 with gold standard RT-PCR test.

Materials and Methods: This retrospective cohort study was conducted in Virus Research and Diagnostic Laboratory (VRDL) in Department of Microbiology at GGS Medical College, Faridkot, Punjab, India, from January to June 2021. A total of 100 nasopharyngeal samples, collected from clinically suspected Coronavirus Diseae-2019 (COVID-19) cases admitted at GGSMC during 1st January-30th June 2021 were tested both by Xpert assay and RT-PCR test simultaneously, taking RT-PCR as the gold standard test. The data was analysed by MedCalc® statistical software version 19.6.4., and sensitivity, specificity, predictive values, likelihood ratios and the agreement between the two tests were calculated.

Results: The mean age of the study participants was 46 years. Of these, 55 were males and 45 were females. The overall sample sensitivity and specificity of the Xpert assay were both 100% and there was perfect agreement across specimens, if authors, set a cut-off Cycle threshold value (Ct value) at 40 cycles for Xpert. Of 100 samples, 32 were positive for SARS-CoV-2 by either of the tests and 68 were negative. Xpert assay could detect 100% positive cases and RT-PCR test could detect 84.37% positive cases. Out of the 32 samples which were positive by Xpert assay, 5 (15.62%) samples had a Ct value greater than 40.

Conclusion: The Xpert assay found to be useful as a point-of-care test in acute scenario, where rapid and authentic diagnosis is essential, but do not have expertise and infrastructure to perform RT-PCR.


Coronavirus disease-2019, Point-of-care, Reverse transcriptase-polymerase chain reaction, Severe acute respiratory syndrome-coronavirus-2

A cluster of cases of pneumonia of unknown cause emerged in Wuhan in December 2019. The International Committee of Taxonomy of Viruses (ICTV) identified novel beta coronavirus and named as Severe Acute Respiratory Syndrome-Coronavirus-2 (SARS-CoV-2) and the disease been named COVID-19, by World Health Organisation (WHO). The WHO declared it a public health emergency of international concern on January 30, 2020 and further declared it as a global pandemic on March 11, 2020 (1). Latest updates by WHO, suggest a total of 45,84,79,635 confirmed cases of COVID-19, including 60,47,653 deaths (2).

This pandemic has created an urgent need for rapid diagnostic tests in controlling the outbreak, and includes serological and molecular assays (3). The preferred testing method for SARS-CoV-2 virus is the real-time RT-PCR test targeting different genes- N, E, S, Ribonucleic Acid (RNA) dependent RNA polymerase (RdRp) and Observer Research Foundation (ORF) with different recommendations of which target to use (4),(5),(6),(7). Despite being the gold standard test for diagnosis of SARS-CoV-2 infection, the process involves a turnaround time of approximately 12-24 hours and requires trained manpower. Thereby, a high quality rapid point-of-care diagnostic test is needed for early detection of SARS-CoV-2 (8).

Among these, Cepheid Xpert Xpress SARS-CoV-2 (Xpert) assay one of those that received authorisation for emergency use from the US Food and Drug Administration and Indian Council of Medical Research (ICMR) in year 2020 (9),(10). The Xpert assay is an automated in-vitro diagnostic test for qualitative detection of nucleic acid from SARS-CoV-2. The targets are E gene and N2 gene in Xpert with a limit of detection of 250 copies/mL (11). The study was carried out at a tertiary care hospital with gain in bringing down turnaround time, for diagnosis of SARS-CoV-2 infection, with the objective of assessing the performance of Xpert assay, considering RT-PCR test as the gold standard test.

Material and Methods

The retrospective cohort study was conducted at VRDL in Department of Microbiology at GGSMCH, Faridkot, Punjab, India, from 1st January to 30th June 2021. Analysis of data was done in February 2022. Institutional Ethical Committee (IEC) approval was not taken as study was conducted in a reference laboratory, all samples tested with Xpert assay were also subjected to RT-PCR considering it as gold standard, but for study purpose only 100 samples were taken, for whom Ct values of all genes were available and data was collected retrospectively from year 2021.

Inclusion criteria: Patients admitted in GGSMCH with acute respiratory infection (influenza-like illness) with fever of ≥38°C, cough, and onset within the last 10 days, were included in the study.

Exclusion criteria: Samples not sent in proper storage conditions or leaked, were excluded from the study.

Study Procedure

A total of 617 nasopharyngeal samples were collected for testing with Xpert assay between given time period. The collected nasopharyngeal swabs were transported immediately to the molecular laboratory in HiViralTM Transport Medium (HiMedia Laboratories Pvt. Ltd., Mumbai, India) at 2° to 8°C. Of these 617 samples, 100 non random convenient samples were included in the study. Though, all samples tested with Xpert assay were also subjected to RT-PCR considering it as gold standard, but for study purpose only 100 samples were taken, for whom Ct values for all genes were available and data was collected retrospectively from year 2021.

GeneXpert assay: The Xpert Xpress SARS-CoV-2 test is an automated in-vitro diagnostic test for qualitative detection of nucleic acid from SARS-CoV-2 on GeneXpert instrument system which performs automated specimen processing, Ribonucleic Acid (RNA) extraction, RT-PCR of SARS-CoV-2 RNA, and amplicon detection in a single run. Results were analysed using E gene, N2 gene and Sample Processing Control (SPC) and the detection of both genes or N2 gene alone is considered positive, and the detection of E gene alone is considered presumptive positive (Ct value <45) (9).

RT-PCR test: Using MagMaxTM viral/pathogen nucleic acid isolation kit, viral RNA from nasopharyngeal sample was extracted following manufacturer’s instructions. RT-PCR assay was performed using applied biosystems TM 7500 fast Dx real-time PCR instrument. Extracted RNA samples were amplified using Genes2Me Viral Detect-|| Multiplex RT-PCR kit for COVID-19 targeting Envelope (E), Nucleocapsid (N) and RdRp genes. RNAse P gene was used as an amplification control. The assay was run for 40 cycles and amplification data was interpreted based on cut-off cycle threshold (Ct) values i.e., samples with Ct value ≤37 were considered positive and those with >37 negative for SARS-CoV-2 infection. The percent positivity for SARS-CoV-2 with Xpert assay was 20.74% (Table/Fig 1).

Statistical Analysis

Data was analysed using Microsoft excel. Using MedCalc® Statistical Software version 19.6.4 (MedCalc Software Ltd., Ostend, Belgium), sensitivity, specificity, Negative Predictive Values (NPV) and Positive Predictive Values (PPV), Positive Likelihood Ratio (PLR) and Negative Likelihood Ratios (NLR) were calculated. Agreement between the two tests was assessed by Cohen’s Kappa coefficient (κ). The association was explored through correlation coefficients and scatter plots using IBM ® Statistical Package for the Social Sciences (SPSS) version 20.0.


A total of 100 non random convenient samples were included in the study from all age groups with a mean age of 46 years. Of these, 55 were males and 45 were females. Total 100 non random convenient samples were tested with both Xpert assay and RT-PCR by taking RT-PCR as a gold standard. Comparison between the sensitivity, specificity, PPV, NPV, PLR and NLR among Xpert assay and RT-PCR at different cut-off Ct values is shown in (Table/Fig 2). Of 100 samples, 32 were positive for SARS-CoV-2 by either of the tests and 68 were negative. Xpert assay could detect 100% positive cases and RT-PCR test could detect 84.37% positive cases. Out of the 32 samples which were positive by Xpert assay, 5 (15.62%) samples had a Ct value greater than 40.

Considering 40 as the cut-off Ct value for both the assays, there were 27 samples positive for SARS-CoV-2 by either of the tests.

A perfect agreement was seen between the two tests considering cut-off Ct value of 40 (κ=1) for Xpert assay (Table/Fig 3),(Table/Fig 4).

The association of Ct values of genes of Xpert assay and GENES2 ME Viral Detect-|| Multiplex RT-PCR Kit (27 were positive by both assays) were explored using Pearson’s correlation coefficient which depicted a statistically strong significant association between Ct value among different genes of both assay and were as follows:

Xpert E gene Ct vs Genes2Me Viral Detect-|| Multiplex Real Time PCR kit E gene Ct, r=0.992, p<0.001,
Xpert N gene Ct vs Genes2Me N gene Ct, r=0.0.973, p<0.001,
Xpert E gene Ct vs Xpert N gene Ct, r=0.0.998, p<0.001,
Genes2Me E gene Ct vs Genes2Me N gene Ct gene Ct, r=0.0.975, p<0.001,
Genes2Me E gene Ct vs Genes2Me RdRp gene Ct, r=0.0.961, p<0.001,
Genes2Me N gene Ct vs Genes2Me RdRp gene Ct, r=0.987, p<0.001


Early diagnosis of COVID-19 is often deterimental in not only decision making for quarantine/isolation but also can help in early initiation of therapy in acute severe disease. RT-PCR is recognised as benchmark for COVID-19 testing, but this test requires well equipped laboratory facilities, highly skilled technologists and multiple reagents. Emergency approval was given both by WHO and United States Food and Drug Administration (US FDA) for use of Xpert assay platform for COVID-19 testing which is a closed nature platform, requires minimum sample handling, pose minimum biosafety hazard and has less turnaround time. This has been dependably used for diagnosis of Tuberculosis (TB) under Revised National TB Control Programme (RNTCP) and the facilities were already available across India (12).

As per manufacturer’s recommendation in Xpert assay, sample with no amplification for E gene but Ct value upto 45 for N2 gene is considered positive. This suggests that automatic interpretation of the results by Xpert assay software may lead to high number of false positives thus affecting its specificity, as in the present study we ended up getting 32 positives by Xpert assay and 27 positive by RT-PCR. Due to low copy numbers of target sequence to primer, the gene failed to amplify in RT-PCR test, resulting in five discordant samples.

But, when authors took a Ct value of 40 as cut-off the results became comparable with RT-PCR and hence, improved specificity by decreasing the false positives. This was further supported by statistical analysis and both the assays showed perfect agreement at a cut-off value of 40. Similar observations were purported by Rakotosamimanana N et al., in their study, in which of 40 nasopharyngeal specimens that were previously confirmed as positive (n=20) or negative (n=20) using Da An Gene RT-PCR test were tested on the GeneXpert platform using the Xpert Xpress SARS-CoV-2 assay and found sensitivity and specificity of the Xpert Xpress SARS-CoV-2 assay to be 100% (20 of 20) and 80% (16 of 20), respectively, due to different limits-of-detection of the two assays but positive specimens showed similar Ct values individually, which favours similar analytical sensitivity. By using an arbitrary cut-off at 40 cycles, improves the specificity and does not affect the sensitivity of the test or increase the risk of getting a false negative result (13). However, different authors from various geographical regions have reported agreement at different Ct value. Das R et al.,suggested a substantial agreement at a cut-off Ct value of 35 with sensitivity and specificity of Xpert assay to be 65.52% and 93.15%, respectively (14).

Various authors suggested a good agreement among different assays even at a Ct value of 45. The overall sample sensitivity and specificity were both 100% between Xpert assay and Roche Cobas 6800 assay and observed very high coefficients of determination of the different viral gene targets (15). The test performance of the GeneXpert assay compared to the Liferiver RT-PCR showed that, sensitivity and specificity were both 100% (16). Singh K et al., also considered cut-off value more than 40 as insignificant (17). A Ct value more than 40 in positive samples may carry few copies of viral RNA which may be insignificant in disease transmission and overall reduce the patient burden in already exhausted healthcare facilities during the peak of COVID-19 second wave. Moreover, the extended turnaround time associated with reference laboratory testing can be avoided as this technology has utilitarian in acute care hospitals in high-prevalence settings, where testing can be done on demand and rapid triage decisions can be made regarding patient disposition and isolation and the targeted use of personal protective equipment for healthcare workers and potentially lifesaving treatment.


As different studies suggest different cut-off for Ct values, a larger sample size with prospective double blinding is desirable to establish a cut-off value of 40 as standard. Also, comparison of viral load with Ct value was not done. Another limitation was thought to be that samples were processed, when second deadly wave was at their peak and microbiology staff was overburdened with handling, processing and reporting of COVID-19 samples and after requiescence for some time, sample load again was on rise impending third wave, leads to delay in compilation of data.


Despite the advantages of being a rapid and easy to perform test, the available system can only process limited samples in a day. Also, the cost per test is relatively higher, hence, the authors recommend its routine use in patients presenting with acute severe illness, where it can be detrimental in early initiation of therapy and thus, can be helpful in reducing morbidity and mortality. In the future, further advanced Xpert assay testing system, with a high throughput, can further widen its application.


Priyadarshi K, Nag VL, Kombade SP, Gadepalli RS, Misra S, Singh K. Molecular diagnosis of COVID-19: An update and review. Ann Natl Acad Med Sci. 2020;3:126-37. [crossref]
Data at WHO-WHO | World Health Organization. Available at: https://www.who. int › data (Accesed on 15th March).
Center of Disease Control and Prevention. Interim Guidelines for Collecting, Handling, and Testing Clinical Specimens for COVID-19. Available at: https:// (Accesed on: 30th January).
Chu DKW, Pan Y, Cheng SMS, Hui KPY, Krishnan P, Liu Y, et al. Molecular diagnosis of a novel coronavirus (2019-nCoV) causing an outbreak of pneumonia. Clin Chem. 2020;66(4):549-55. [crossref] [PubMed]
Corman VM, Landt O, Kaiser M, Molenkamp R, Meijer A, Chu DKW, et al. Detection of 2019 novel coronavirus (2019-nCoV) by real-time RTPCR. Euro Surveill. 2020;25(3):2000045. [crossref] [PubMed]
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DOI and Others

DOI: 10.7860/JCDR/2023/59191.17541

Date of Submission: Jul 20, 2022
Date of Peer Review: Sep 08, 2022
Date of Acceptance: Nov 04, 2022
Date of Publishing: Feb 01, 2023

• Financial or Other Competing Interests: None
• Was Ethics Committee Approval obtained for this study? No
• 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

• Plagiarism X-checker: Jul 21, 2022
• Manual Googling: Oct 18, 2022
• iThenticate Software: Nov 02, 2022 (14%)

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