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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
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."



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Professor and Head
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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.
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Dr Saumya Navit
Professor and Head
Department of Pediatric Dentistry
Saraswati Dental College
Lucknow
On Sep 2018




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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,
Muzaffarnagar.
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,
Bengaluru.
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
Consultant
(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)
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

Important Notice

Original article / research
Year : 2022 | Month : November | Volume : 16 | Issue : 11 | Page : DC13 - DC15 Full Version

Efficacy of Nucleic Acid Extraction by Manual versus Automated Magnetic Bead-based Method to Detect SARS-CoV-2


Published: November 1, 2022 | DOI: https://doi.org/10.7860/JCDR/2022/58370.17136
Rakhi Bhargav, Nisha Chaudhary, Sugandh Rathore, Bitesh Kumar, Pradhumn Katara, Hariom Sharan

1. Research Scientist, Department of Microbiology, Autonomous State Medical College, Firozabad, Uttar Pradesh, India. 2. Assistant Professor, Department of Microbiology, Autonomous State Medical College, Firozabad, Uttar Pradesh, India. 3. Tutor, Department of Microbiology, Autonomous State Medical College, Firozabad, Uttar Pradesh, India. 4. Research Scientist, Department of Microbiology, Autonomous State Medical College, Firozabad, Uttar Pradesh, India. 5. Assistant Professor, Department of Community Medicine, Santosh Deemed to be University, Ghaziabad, Uttar Pradesh, India. 6. Professor and Head, Department of Microbiology, Autonomous State Medical College, Firozabad, Uttar Pradesh, India.

Correspondence Address :
Dr. Bitesh Kumar,
40/252, Bada Ukharra, Rajpur Chungi, Agra, Uttar Pradesh, India.
E-mail: biteshrajput@gmail.com

Abstract

Introduction: In December 2019, a rapid spread of highly infectious, Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2), was reported in Wuhan, China. The gold standard for diagnosis of SARS-CoV-2 infection is nucleic acid amplification technology by detecting its viral Ribonucleic Acid (RNA) from respiratory swabs (oropharyngeal and nasopharyngeal) by Reverse Transcription-Polymerase Chain Reaction (RT-PCR) whose specificity is approximately 95%. Magnetic bead RNA extraction was benchmarked against the commercial QIAcube extraction platform.

Aim: To compare the efficacy of nucleic acid extraction by manual method and automated magnetic bead-based method to detect SARS-CoV-2.

Materials and Methods: The present cross-sectional observational study was conducted in the Department of Microbiology, Autonomous State Medical College, Firozabad, Uttar Pradesh, India. Duration of the study was from February 2022 to March 2022. A total of 470 oropharyngeal and nasopharyngeal samples were included in the present study to observe the efficacy of nucleic acid extraction by manual extraction and automated extraction for SARS-CoV-2. Data were entered in Microsoft Excel software and analysed using Statistical Package for the Social Sciences (SPSS) version 26.0.

Results: During the present study period, a total of 470 individual samples were tested in 94 pools. Out of these 470 individuals, 331 were males (70.5%) and 139 were females (29.5%). All 94 pools were found negative by both automatic and manual extraction methods. Envelope (E) gene was found in one pool (1.06%) by the manual RNA extraction method. The E gene was absent in 93 pools (98.94%) by manual method. Internal control was found highest in 88 pools (93.62%) by the automated extraction method.

Conclusion: Automated workflows avoid human error from the sample processing pipeline and also ensure as well as enhance the meaningful output, diagnostic precision, and testing capacity. Automated instruments are in wide usage because of their capability of processing thousands of samples per day with the support of minimal staff.

Keywords

Coronavirus disease 2019, Diagnostic techniques and procedures, Diagnostic tests, Severe acute respiratory syndrome coronavirus-2

In December 2019, a rapid spread of highly infectious, SARS-CoV-2, was reported in Wuhan, China, which was declared a pandemic thereafter by the World Health Organisation (WHO) on 11th March 2020 (1). Currently, the standard test for diagnosis of SARS-CoV-2 infection is the detection of its viral RNA from respiratory swabs (oropharyngeal and nasopharyngeal) by RT-PCR. This method involves the reverse transcription of the genetic material of the virus (RNA) to complementary DNA (cDNA), followed by amplification of some regions of the cDNA. In this two-step testing procedure, several primers and probes set by several COVID-19 detection kits for targeting one or more of the SARS-CoV-2 genes-nucleocapsid (I#INI?I), an envelope protein (I#IEI?I), S glycoprotein (I#ISI?I), RNA-dependent RNA polymerase (RdRp) (2), or open reading frame 1ab (ORF1ab) region) is used in a single channel and utilises the detection of RNase P in a separate channel as the internal control (3). The sensitivity and specificity of RT-PCR is not 100%. It is estimated to be 70-98% sensitivity and specificity is approximately 95%. In addition, the genetic diversity of the SARS-CoV-2 plays an important role and may affect the results of the RT-PCR test (4),(5).

For measuring public health worldwide, the diagnosis of COVID-19 is implemented on a large scale. Various protocols are established for some preprocessing steps, like specimen lysis, along with the nucleic acid extraction of SARS-CoV-2 RNA, based on the magnetic bead-based nucleic acid extraction protocol (6). These preprocessing steps can be processed through manual protocols with individual instruments or can be processed through automated protocols via automated instruments. Manual protocols for magnetic nucleic acid extraction consist of many steps which are lengthy, time taking, and prone to impurities (7). These methods need heavy manpower, with a higher risk of cross-infections.

To overcome these drawbacks, automated protocols are convenient, simple, and companionable (8),(9) by performing in 96-well plates in combination with a magnet plate optimised for 96 deep-well plates using automated robotic pipetting, which minimises the pipetting and handling errors (2). Aim of the present study was to compare the process of manual and automated extraction of SARS-CoV-2 nucleic acid.

Material and Methods

The present cross-sectional observational study was conducted in the Department of Microbiology, Autonomous State Medical College (ASMC), Firozabad, Uttar Pradesh, India. An approval from the Head of Department, Department of Microbiology, In-charge, BSL-2 LAB, ASMC, Firozabad, Uttar Pradesh, India was obtained. Consent was not taken as no subject was involved, only a comparison of two different techniques done in the BSL-2 lab for the efficacy of better Coronavirus Disease 2019 (COVID-2019) results in the present study. Duration of this study from February 2022 to March 2022. A total of 470 oropharyngeal and nasopharyngeal samples were included in the present study. A total of 94 pools were made to cover these 470 samples. Each pool consisted of five samples.

Inclusion criteria: Samples of oropharyngeal and nasopharyngeal with proper identification and favourable temperature with triple-layer packing were included in the present study.

Exclusion criteria: Samples without proper marking, leakage and without maintaining temperature were excluded from the present study.

Study Procedure

In the present observational study, upper respiratory tract specimens (oropharyngeal and nasopharyngeal) of 470 individuals were collected. In the case of respiratory viral diseases, such as influenza or COVID-19, oropharyngeal and pharyngeal swabs were collected and tested for the presence of viral RNA. RNA isolation prior to detection is a pivotal step to ensure high specificity and sensitivity of detection in molecular assays (2). This established protocol for extracting SARS-CoV-2 viral RNA from respiratory swabs is a magnetic bead-based nucleic acid extraction protocol which is done via two different methods i.e. manual extraction and automated extraction method to compare within.

Manual RNA extraction: In the manual process, magnetic bead RNA extraction was performed individually in eppendorf vials in combination with a magnetic stand and transferred to various wash buffers like triple distilled water or 70% ethanol via manual pipetting instruments.

Automated RNA extraction: In many automated instruments, magnetic microbeads coated with silica are used to capture nucleic acids and are sequentially transferred into various wash solutions by a robotic pipetting instrument with a magnetic head in 96-well plates (10).

For optimising the result in a 96-well RT-PCR plate, RNA of 94 pools, comprised of five samples in each, covering 470 random samples, one negative control and one positive control were extracted via manual protocol and automated protocol (KingFisher™ Flex for 96) by using Q-Line Molecular Viral Extraction Kit Magnetic Bead Method as per the kit manufacturing instructions (Table/Fig 1)a,b. The extracted RNA from both manual and automated processes are amplified and evaluated by Thermocycler (BIORAD CFX-96) using RT-PCR kit (DiAGSure nCoV-19 Assay), which contains primers and probes that are specific for SARS-CoV-2 as per kit (Table/Fig 2). The process and results of the thermocycler obtained in the format of Ct value (cycle threshold) which were interpreted according to the kit manufacturing instructions (Table/Fig 3)a-c.

Statistical Analysis

Data were entered in Microsoft Excel software and analysed using SPSS version 26.0. Distribution and differentiation parameters were mentioned as a percentage. To determine the p-value, Z test calculator for two population proportions was used. The p-value <0.05 was considered as statistically significant.

Results

A total of 470 individual samples were tested. Out of these 470 individuals, 331 were males (70.5%) and 139 were females (29.5%). All Ct value obtained in RT-PCR/thermocycler shown in 96-well RT-PCR plate format by both manual and automatic RNA methods is shown in (Table/Fig 4), (Table/Fig 5).

The test was considered invalid when there was no amplification of the internal control. In the automated extraction method, internal control was found highest in 88/94 pools (93.62%), while in the manual extraction method, internal control was found 78/94 pools (82.98%). The test was considered as failure 6/94 pools (6.38%) in automatic extraction method while 16/94 pools (17.02%) in manual extraction method. The peroration of test failure was significantly higher (p-value=0.0238) in the manual extraction method in comparison with the automatic extraction method.

Discussion

Within the last decades, the frequency of emerging virus outbreaks has increased globally (2). Due to globalisation, many of the outbreaks have escalated the pandemic potential and produced a burden on society and health systems. The currently ongoing SARS-CoV-2 pandemic emphasises the urgency of appropriate response and preparedness. RT-PCR is adequately reliable and a fast technique for producing results in a few hours in a high output manner. The discovery of the RT-PCR method has paved the way for the detection of gene transcripts at trace levels, and the technique has been vastly utilised for contagious disease testing worldwide (11).

In the present observational study, the gold standard method for diagnosis of SARS-CoV-2 infection RT-PCR was used. The results of the thermocycler were interpreted according to the kit manufacturing instructions. The present study resulted in the peroration of test failure was significantly higher (p-value=0.0238) in the manual extraction method in comparison with the automatic extraction method.

Similarly, a review article based on automated SARS-COV-2 RNA extraction from patient nasopharyngeal samples using a modified DNA extraction kit found that automatic RNA extraction showed the efficient detection of RNA at low quantification cycle values (high nucleic acid/RNA extraction efficiency) (11). A report on the use of a DNA extraction kit, after modifications, to extract viral RNA found that the fully automated liquid handling robotic RNA extraction systems is very likely suitable for isolation and downstream detection assays for any kind of viral RNA isolated from the pharyngeal swabs (12).

A similar study on validation of automated SARS-CoV-2 clinical diagnostics also stated that, automated workflows are more preferable than manual protocols to achieve a meaningful output, diagnostic accuracy, and also avoid human error (13) also, automated nucleic acid extraction has takes less hands-on time (14) with maximum purity of extracted RNA (5).

Limitation(s)

The limitation of the present study was the small sample size.

Conclusion

A massive number of samples are being tested everyday, for which manual protocols are less preferable as the involvement of many lengthy steps which are time taking, and more prone to impurities. Manual methods also need heavy manpower, with a higher risk of cross-infection but do not affect the final costs of the test. Whereas, automated workflows avoid human error from the sample processing pipeline and also, ensure as well as enhance the meaningful output, diagnostic precision, and testing capacity. Automated instruments are in wide usage because of their capability of processing thousands of samples per day with the support of minimal staff. It also provides results in easy-to-use formats that are persuadable to point-of-care applications, without using complex instrumentation, but automatic protocols significantly increase the final costs, which hinders the massive testing in some areas, which is a drawback.

References

1.
World Health Organisation. Coronavirus disease 2019 (Covid-19) situation report 51. 2020. https://www.who.int/docs/default-source/coronaviruse/situation-reports/20200311-sitrep-51-covid-19.pdf. (Coronavirus disease 2019 (COVID-19) Situation Report - 51- Data as reported by national authorities by 10 AM CET 11 March 2020).
2.
Klein S, Müller TG, Khalid D, Sonntag-Buck V, Heuser AM, Glass B, et al. SARS-CoV-2 RNA extraction using magnetic beads for rapid large-scale testing by RT-qPCR and RT-LAMP. Viruses. 2020;12(8)863. [crossref] [PubMed]
3.
Bulterys PL, Garamani N, Stevens B, Sahoo MK, Huang CH, Hogan CA, et al. Comparison of a laboratory-developed test targeting the envelope gene with three nucleic acid amplification tests for detection of SARS-CoV-2. J Clin Virol. 2020;129:104427. [crossref] [PubMed]
4.
Goudouris ES. Laboratory diagnosis of COVID-19. Jornal de Pediatria, 2021;97(1):07-12. [crossref] [PubMed]
5.
Munne K, Bhanothu V, Bhor V, Patel V, Mahale SD, Pande S, et al. Detection of SARS-CoV-2 infection by RT-PCR test: Factors influencing the interpretation of results. Virus Disease. 2021;32(2):187-89. [crossref] [PubMed]
6.
He H, Li R, Chen Y, Pan P, Tong W, Dong X, et al. Integrated DNA and RNA extraction using magnetic beads from viral pathogens causing acute respiratory infections. Sci Rep. 2017;7(1):45199. [crossref] [PubMed]
7.
Wahlang L, Lakshmanan B, Thomas N, Bosewell A, Kollannur JJ, Chullipparambil S, et al. Comparative analysis of conventional and real time PCR for detection of haemoparasites in dogs. Indian J Biotech. 2019;18(1):09-15.
8.
Lee AH, Gessert SF, Chen Y, Sergeev NV, Haghiri B. Preparation of iron oxide silica particles for Zika viral RNA extraction. Heliyon. 2018;4(3):e00572. [crossref] [PubMed]
9.
Ali Z, Liang W, Jin L, Tang Y, Mou X, Shah MA, et al. Development of magnetic nanopar- ticles based nucleic acid extraction method and application in hepatitis c virus chemiluminescent detection. Sci Adv Mater. 2015;7(7):1233-40. [crossref]
10.
Safiabadi Tali SH, LeBlanc JJ, Sadiq Z, Oyewunmi OD, Camargo C, Nikpour B, et al. Tools and techniques for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)/COVID-19 detection. Clinical Microbiology Reviews. 2021;34(3):01-63. [crossref] [PubMed]
11.
Yüce M, Filiztekin E, Özkaya KG. COVID-19 diagnosis- A review of current methods. Biosensors and Bioelectronics. 2021;172:112752. [crossref] [PubMed]
12.
Al-Saud H, Al-Romaih K, Bakheet R, Mahmoud L, Al-Harbi N, Alshareef I, et al. Automated SARS-COV-2 RNA extraction from patient nasopharyngeal samples using a modified DNA extraction kit for high throughput testing. Ann Saudi Med. 2020;40(5):373-81. [crossref] [PubMed]
13.
Crone MA, Priestman M, Ciechonska M, Jensen K, Sharp DJ, Anand A, et al. A role for biofoundries in rapid development and validation of automated SARS-CoV-2 clinical diagnostics. Nat Commun. 2020;11(1):01-11. [crossref] [PubMed]
14.
Joseph N, Bahtiar N, Mahmud F, Hamid KA, Raman R, Yee H, et al. Comparison of automated and manual viral nucleic acid extraction kits for COVID-19 detection using qRT-PCR. Malaysian J Med Health Sci. 2022;18(1):14-19.

DOI and Others

DOI: 10.7860/JCDR/2022/58370.17136

Date of Submission: Jun 10, 2022
Date of Peer Review: Jul 11, 2022
Date of Acceptance: Sep 08, 2022
Date of Publishing: Nov 01, 2022

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? No
• For any images presented appropriate consent has been obtained from the subjects. NA

PLAGIARISM CHECKING METHODS:
• Plagiarism X-checker: Jun 21, 2022
• Manual Googling: Aug 06, 2022
• iThenticate Software: Aug 24, 2022 (22%)

ETYMOLOGY: Author Origin

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