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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)
E-mail: drrajendrak1@rediffmail.com
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.
E-mail: ravi.dr.shankar@gmail.com
On April 2011 Anuradha
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
E-mail: anuradha2nittur@gmail.com
On Jan 2020
Original article / research
Full Version
Usefulness of TrueNat: A Chip-based Real-time PCR Test for COVID-19
Correspondence Address :
Swarnim Swarn,
Tutor, Department of Biochemistry, Vardhman Institute of Medical Sciences,
Pawapuri, Nalanda-803115, Bihar, India.
E-mail: drswarnimswarnpatna@gmail.com
Introduction: For the containment of growing Coronavirus Disease (COVID-19) pandemic, rapid diagnostic facilities are need of today. Indigenously developed TrueNat assay is a point-of-care assay developed for early diagnosis of Severe Acute Respiratory Syndrome-Coronavirus-2 (SARS-CoV-2). It is a portable, fully automated, chip-based, real-time quantitative polymerase chain reaction system with a turnaround time of 1.5-2 hours.
Aim: To assess the practical utility and diagnostic accuracy of TrueNat testing for COVID-19 in a pandemic situation.
Materials and Methods: A cohort selection cross-sectional study was conducted from July to September 2020 at Department of Biochemistry, Vardhaman Institute of Medical Sciences, Pawapuri, Bihar, India, after obtaining Institutional Ethics Committee (IEC) approval. A total of 296 cases with symptoms of COVID-19 were selected for the study. Assuming real-time Reverse Transcription-Polymerase Chain Reaction (rRT-PCR) to be the gold standard, we collected oropharyngeal swabs from symptomatic COVID-19 suspected cases and tested by both TrueNat and standard RT-PCR. Agreement between both the assays were assessed by overall, Positive Percent Agreement (PPA) and Negative Percent Agreement (NPA) and Cohen’s kappa coefficient using Epitools (Ausvet 2020).
Results: Out of 296 oropharyngeal swabs taken from suspected COVID-19 patients, 19 were read as “invalid” and discarded; hence only 277 samples were tested by TrueNat and RT-PCR both. Assuming RT-PCR as standard, TrueNat assay demonstrated an overall percent agreement of 99.64%, PPA of 95.65%, NPA 99.81%. The kappa coefficient was 0.9546.
Conclusion: TrueNat assay offers a rapid, accurate and affordable technique for COVID-19. It may be deployed for mass screening and confirmation of COVID-19 cases in hospitals and remote areas.
Coronavirus Disease-19, Molecular diagnostic test, Polymerase chain reaction, Point-of-care assay, Rapid test
Coronavirus disease-2019 pandemic is the most devastating event for mankind in recent times. It has jeopardised human activity globally. On second December 2020, there were 63,144,362 confirmed cases of COVID-19 including 1,469,237 deaths in world and 9,499,413 confirmed cases of COVID-19 in India (1). World Health Organisation (WHO) declared a pandemic of COVID-19 in March 2020 (2).
Provision of the diagnostic test for rapid detection of SARS-CoV-2 is the mainstay for early diagnosis, prompt implementation of infection control measures and epidemiological tracking in both hospital setting and community. WHO recommends RT-PCR test for coronavirus detection and differentiation (3). Currently, real-time RT-PCR is accepted as the gold standard for detection of SARS-CoV-2 globally (4).
The RT-PCR testing requires centralised reference laboratories, skilled men power and elaborate infrastructure including recommended biosafety measures (3). It also requires significant financial investment and the results may take several hours to days. It may cause a delay in diagnosis and management of cases. To increase the testing capacity, Indian Council of Medical Research (ICMR) has set a network of Viral Research and Diagnostic Laboratories (VRDL) throughout India which are well-equipped labs for RT-PCR testing with at least Biosafety Level-2 (BSL-2). These VRDL work as State Nodal Centres for coordination of sample collection and shipment for rapid detection and reporting of SARS-CoV-2 cases (5).
To increase the further testing capacity and timely diagnosis and intervention, ICMR approved TrueNat testing for COVID-19 on April 14th 2020. TrueNat is a point of care testing facility which has strengthened the Indian testing capacity in urban as well as rural parts of India. TrueNat is a portable, microchip-based, battery-operated, optical detection, fully automated device developed by Molbio Diagnostics Private Limited, India. (Table/Fig 1). This device was originally developed for rapid detection of Mycobacterium tuberculosis and rifampicin resistance in pulmonary and extrapulmonary tuberculosis. TrueNat is a real-time quantitative micro-PCR testing for coronavirus Ribonucleic acid (RNA) in human oropharyngeal and nasopharyngeal swab specimen. The test detects Nucleocapsid Gene (N2) and Envelope Gene (E) and RNA-dependent RNA polymerase (RdRp) gene. The results are interpreted as positive, negative or invalid (6),(7),(8).
The TrueNat beta COV screens through E gene while TrueNat SARS-COV-2 RdRp gene for confirmation. A multiplex assay combining E-gene screening and Orf1a-gene confirmatory assay has been validated recently. It simultaneously amplifies and detects the target Deoxyribonucleic acid (DNA) during every cycle, thus the presence of target DNA and its quantity in each reaction is accurately detected without the need to analyse post PCR product separately. There is no need to prepare master mix and no need for clean hood. As a result, the peripheral laboratories with minimal infrastructure and minimally trained technician can easily perform these tests routinely in their facilities and report PCR results in less than an hour (6),(8),(9).
This cross-sectional study conducted at Department of Biochemistry, Vardhaman Institute of Medical Sciences, Pawapuri, Bihar, India, from July to September 2020. After receiving approval by the Institutional Ethics Committee (Vide no. 1015, dated 29.06.2020), 296 cases with symptoms of COVID-19 were selected for the study. Informed consent was obtained from every patient.
Inclusion criteria: Suspected cases of SARS-CoV-2 infection who meets the following clinical criteria: Acute onset of any three or more of the signs or symptoms- fever, cough, general weakness/fatigue, headache, myalgia, sore throat, coryza, dyspnoea, anorexia nausea/vomiting, diarrhoea, altered mental status and patients with severe acute respiratory illness recent onset of anosmia or ageusia in the absence of any other identified cause were included in the study. Epidemiological criteria like subjects residing or working in an area with high risk of transmission of virus, residing or travelled to an area with community transmission anytime within the fourteen days prior to symptom onset or subjects who were working in any health care setting were included in the study.
Exclusion criteria: Patients suffering from other respiratory infections such as history of chronic respiratory illness, known bacterial infections and pulmonary tuberculosis were excluded from the study.
Study Procedure
Oropharyngeal samples were taken using nylon flocked swab following standard protocols as per the instructions given by the manufacturer and transported to the laboratory in viral transport media within two hours. The extraction and amplification of the viral genome was done according to standard procedure.
The test was run on TrueNat machine as per the guidelines given in the brochure. The result was read as “detected” for positive results and “not detected” for negative results. Nineteen samples were read as invalid and hence discarded from the study. All the 277 patient samples were also tested by standard RT-PCR.
TrueNat SARS-CoV-2 works on the principle of real-time RT-PCR based on Taqman chemistry. First, the RNA is extracted from the patient sample using Trueprep AUTO/AUTO V2 universal cartridge-based sample prep device and sample prep kit. RNA obtained is then assayed using TrueNat beta COV test. If sample tests positive, then it is tested for SARS-CoV-2 in TrueNat lab (9).
Statistical Analysis
Statistical analysis was performed using Epitools (Ausvet 2020). The statistical guidance on reporting results from studies evaluating diagnostic tests issued by the US Department of Health and Human Services were followed (10). Proportion positive agreement, proportion negative agreement, Overall proportion agreement and Cohen’s kappa coefficient with 95% confidence intervals were determined (Table/Fig 2). Kappa value 0.81-1.00 was considered as almost perfect agreement.
Positive percent agreement=100%×a/(a+c)
Negative percent agreement=100%×d/(b+d)
Overall percent agreement=100%×(a+d)/(a+b+c+d)
Calculation of Cohen’s kappa may be performed according to the following formula:
κ=Pr(a)-Pr(e)/1-Pr(e)
Where Pr(a) represents the actual observed agreement, and Pr(e) represents chance agreement.
A total of 296 oropharyngeal swabs were taken from suspected COVID-19 patients. As 19 patients were read as invalid there were 277 sample size was considered for the study. Out of 277 patients, 202 were males and 75 were femles. The mean age for males, females and total sample was 35.6, 37.3 and 33.9 years respectively. The demographic data of total sample was presented in (Table/Fig 3).
Of the 277 cases, 12 were tested positive by TrueNat while RT-PCR gave only 11 positive results. A 265 samples were tested negative by TrueNat and RT-PCR gave 266 negative results (Table/Fig 4). PPA, NPA and overall percent agreement between the two methods were 95.65%, 99.81% and 99.64% respectively. The kappa coefficient was 0.9546 (Table/Fig 5).
Accurate and timely diagnosis of SARS-CoV-2 is crucial for policy-making, implementation of control measures, identification, isolation and contact tracing of patients and containment of people coming in contact with infected patient (8). RT-PCR is the gold standard for diagnosis of SARS-CoV-2. The TrueNat beta COV screens through E gene while TrueNat SARS-CoV-2 RdRp gene for confirmation. This is quicker as compared to rRT-PCR, which takes around 4-6 hour for the entire process. It has turn-around time 1.5-2 hours and run-time of only 45 minutes and is a very cost-effective procedure (6),(7),(9).
The present study was done to assess the practical utility and diagnostic accuracy of TrueNat testing for SARS-CoV-2 in a pandemic situation. Similar studies done in India has exhibited 100% sensitivity and specificity while this study showed PPA, NPA and overall percent agreement 95.65%, 99.81% and 99.64%, respectively (6),(8),(9). This study has further confirmed TrueNat to be highly accurate method for diagnosis of SARS-CoV-2 as a good alternative to RT-PCR. Other studies were done on confirmed cases of COVID-19 while the subjects in the present study and researchers both were blind. This difference in results may be due to sampling or procedural errors (6),(8),(9).
The samples were collected in viral lysis buffer and hence biosafety and biosecurity requirements for use of TrueNat are minimal. The study has shown TrueNat to be the simple, reliable and useful method for the case-to-case screening and confirmation of SARS-CoV-2. It is particularly helpful for small size sample testing especially for the hospital cases awaiting outpatient as well as inpatient surgical procedures and medical emergencies. Due to availability of TrueNat the burden of the testing centres doing RT-PCR will reduce (6),(8),(9). During the pandemic, a large number of samples require to be tested daily for screening and diagnostic purposes. While RT-PCR machines can test 96 samples at a run, TrueNat can test only four samples at a time. So, TrueNat can be used to test only small number samples in a day.
Limitation(s)
The sample size of the present study was small and the tests were performed only on the oropharyngeal swab. Studies with larger sample size performed in field settings are required to further validate the test. RNA degradation during storage or freeze thawing may occur leading to inability of TrueNat technique to successfully detect SAR-CoV-2 RNA but this problem can be solved with testing done at collection sites or nearby places.
Authors recommend this testing procedure for community testing centres and hospitals, especially during emergencies. Being a simple, accurate and affordable technique, it may be useful for COVID-19 pandemic across the globe. Inclusion of TrueNat at testing centres will increase the testing capacity, decrease the turnaround time and hence will hasten the process of early diagnosis, management and containment of COVID-19 Pandemic.
The authors would like to thank laboratory staffs of Microbiology laboratory, Vardhman Institute of Medical Sciences, Pawapuri, Bihar, India, for their extraordinary support in carrying out research work.
10.7860/JCDR/2021/48193.15348
Date of Submission: Dec 19, 2020
Date of Peer Review: Mar 10, 2021
Date of Acceptance: Jun 03, 2021
Date of Publishing: Sep 01, 2021
AUTHOR DECLARATION:
• 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. Yes
PLAGIARISM CHECKING METHODS:
• Plagiarism X-checker: Dec 21, 2020
• Manual Googling: Apr 10, 2021
• iThenticate Software: Jun 03, 2021 (22%)
ETYMOLOGY: Author Origin
- Emerging Sources Citation Index (Web of Science, thomsonreuters)
- Index Copernicus ICV 2017: 134.54
- Academic Search Complete Database
- Directory of Open Access Journals (DOAJ)
- Embase
- EBSCOhost
- Google Scholar
- HINARI Access to Research in Health Programme
- Indian Science Abstracts (ISA)
- Journal seek Database
- Popline (reproductive health literature)
- www.omnimedicalsearch.com